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Sample records for severe population bottleneck

  1. The effect of an extreme and prolonged population bottleneck on patterns of deleterious variation

    DEFF Research Database (Denmark)

    Pedersen, Casper-Emil Tingskov; Lohmueller, Kirk E.; Grarup, Niels

    2017-01-01

    The genetic consequences of population bottlenecks on patterns of deleterious genetic variation in human populations are of tremendous interest. Based on exome sequencing of 18 Greenlandic Inuit we show that the Inuit have undergone a severe ∼20,000-year-long bottleneck. This has led to a markedly...... more extreme distribution of allele frequencies than seen for any other human population tested to date, making the Inuit the perfect population for investigating the effect of a bottleneck on patterns of deleterious variation. When comparing proxies for genetic load that assume an additive effect...... of deleterious alleles, the Inuit show, at most, a slight increase in load compared to European, East Asian, and African populations. Specifically, we observe

  2. Reliability of genetic bottleneck tests for detecting recent population declines

    NARCIS (Netherlands)

    Peery, M. Zachariah; Kirby, Rebecca; Reid, Brendan N.; Stoelting, Ricka; Doucet-Beer, Elena; Robinson, Stacie; Vasquez-Carrillo, Catalina; Pauli, Jonathan N.; Palsboll, Per J.

    The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and

  3. An inbreeding model of associative overdominance during a population bottleneck.

    Science.gov (United States)

    Bierne, N; Tsitrone, A; David, P

    2000-08-01

    Associative overdominance, the fitness difference between heterozygotes and homozygotes at a neutral locus, is classically described using two categories of models: linkage disequilibrium in small populations or identity disequilibrium in infinite, partially selfing populations. In both cases, only equilibrium situations have been considered. In the present study, associative overdominance is related to the distribution of individual inbreeding levels (i.e., genomic autozygosity). Our model integrates the effects of physical linkage and variation in inbreeding history among individual pedigrees. Hence, linkage and identity disequilibrium, traditionally presented as alternatives, are summarized within a single framework. This allows studying nonequilibrium situations in which both occur simultaneously. The model is applied to the case of an infinite population undergoing a sustained population bottleneck. The effects of bottleneck size, mating system, marker gene diversity, deleterious genomic mutation parameters, and physical linkage are evaluated. Bottlenecks transiently generate much larger associative overdominance than observed in equilibrium finite populations and represent a plausible explanation of empirical results obtained, for instance, in marine species. Moreover, the main origin of associative overdominance is random variation in individual inbreeding whereas physical linkage has little effect.

  4. The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation: Insights from the Greenlandic Inuit.

    Science.gov (United States)

    Pedersen, Casper-Emil T; Lohmueller, Kirk E; Grarup, Niels; Bjerregaard, Peter; Hansen, Torben; Siegismund, Hans R; Moltke, Ida; Albrechtsen, Anders

    2017-02-01

    The genetic consequences of population bottlenecks on patterns of deleterious genetic variation in human populations are of tremendous interest. Based on exome sequencing of 18 Greenlandic Inuit we show that the Inuit have undergone a severe ∼20,000-year-long bottleneck. This has led to a markedly more extreme distribution of allele frequencies than seen for any other human population tested to date, making the Inuit the perfect population for investigating the effect of a bottleneck on patterns of deleterious variation. When comparing proxies for genetic load that assume an additive effect of deleterious alleles, the Inuit show, at most, a slight increase in load compared to European, East Asian, and African populations. Specifically, we observe Inuit. In contrast, proxies for genetic load under a recessive model suggest that the Inuit have a significantly higher load (20% increase or more) compared to other less bottlenecked human populations. Forward simulations under realistic models of demography support our empirical findings, showing up to a 6% increase in the genetic load for the Inuit population across all models of dominance. Further, the Inuit population carries fewer deleterious variants than other human populations, but those that are present tend to be at higher frequency than in other populations. Overall, our results show how recent demographic history has affected patterns of deleterious variants in human populations. Copyright © 2017 by the Genetics Society of America.

  5. Genomic inference accurately predicts the timing and severity of a recent bottleneck in a non-model insect population

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    McCoy, Rajiv C.; Garud, Nandita R.; Kelley, Joanna L.; Boggs, Carol L.; Petrov, Dmitri A.

    2015-01-01

    The analysis of molecular data from natural populations has allowed researchers to answer diverse ecological questions that were previously intractable. In particular, ecologists are often interested in the demographic history of populations, information that is rarely available from historical records. Methods have been developed to infer demographic parameters from genomic data, but it is not well understood how inferred parameters compare to true population history or depend on aspects of experimental design. Here we present and evaluate a method of SNP discovery using RNA-sequencing and demographic inference using the program δaδi, which uses a diffusion approximation to the allele frequency spectrum to fit demographic models. We test these methods in a population of the checkerspot butterfly Euphydryas gillettii. This population was intentionally introduced to Gothic, Colorado in 1977 and has since experienced extreme fluctuations including bottlenecks of fewer than 25 adults, as documented by nearly annual field surveys. Using RNA-sequencing of eight individuals from Colorado and eight individuals from a native population in Wyoming, we generate the first genomic resources for this system. While demographic inference is commonly used to examine ancient demography, our study demonstrates that our inexpensive, all-in-one approach to marker discovery and genotyping provides sufficient data to accurately infer the timing of a recent bottleneck. This demographic scenario is relevant for many species of conservation concern, few of which have sequenced genomes. Our results are remarkably insensitive to sample size or number of genomic markers, which has important implications for applying this method to other non-model systems. PMID:24237665

  6. Variation at innate immunity Toll-like receptor genes in a bottlenecked population of a New Zealand robin.

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    Catherine E Grueber

    Full Text Available Toll-like receptors (TLRs are an ancient family of genes encoding transmembrane proteins that bind pathogen-specific molecules and initiate both innate and adaptive aspects of the immune response. Our goal was to determine whether these genes show sufficient genetic diversity in a bottlenecked population to be a useful addition or alternative to the more commonly employed major histocompatibility complex (MHC genotyping in a conservation genetics context. We amplified all known avian TLR genes in a severely bottlenecked population of New Zealand's Stewart Island robin (Petroica australis rakiura, for which reduced microsatellite diversity was previously observed. We genotyped 17-24 birds from a reintroduced island population (including the 12 founders for nine genes, seven of which were polymorphic. We observed a total of 24 single-nucleotide polymorphisms overall, 15 of which were non-synonymous, representing up to five amino-acid variants at a locus. One locus (TLR1LB showed evidence of past directional selection. Results also confirmed a passerine duplication of TLR7. The levels of TLR diversity that we observe are sufficient to justify their further use in addressing conservation genetic questions, even in bottlenecked populations.

  7. Anatomy of a bottleneck: diagnosing factors limiting population growth in the Puerto Rican Parrot

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    S.R. Beissinger; Jr Wunderle; J.M. Meyers; B.E. Saether; S. Engen

    2008-01-01

    The relative importance of genetic, demographic, environmental, and catastrophic processes that maintain population bottlenecks has received little consideration. We evaluate the role of these factors in maintaining the Puerto Rican Parrot (Amazona vittata) in a prolonged bottleneck from 1973 through 2000 despite intensive conservation efforts. We first conduct a risk...

  8. Demographic and genetic factors in the recovery or demise of ex situ populations following a severe bottleneck in fifteen species of Hawaiian tree snails

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    Melissa R. Price

    2015-11-01

    Full Text Available Wild populations of endangered Hawaiian tree snails have declined precipitously over the last century due to introduced predators and other human impacts. Life history traits, such as very low fecundity (<5 offspring per year across taxa and maturity at approximately four years of age have made recovery difficult. Conservation efforts such as in situ predator-free enclosures may increase survival to maturity by protecting offspring from predation, but no long-term data existed prior to this study demonstrating the demographic and genetic parameters necessary to maintain populations within those enclosures. We evaluated over 20 years of evidence for the dynamics of survival and extinction in captive ex situ populations of Hawaiian tree snails established from wild-collected individuals. From 1991 to 2006, small numbers of snails (<15 from fifteen species were collected from the wild to initiate captive-reared populations as a hedge against extinction. This small number of founders resulted in a severe bottleneck in each of the captive-reared populations. We identified key demographic parameters that predicted population recovery from this bottleneck. Species with captive populations that produced between two and four offspring per adult per year and had 20–50% of those offspring survive to maturity recovered to numbers above 100 individuals, and maintained viable populations following a decline that occurred between 2009 and 2014. Those populations that had less than two offspring per adult per year and less than 20% survival to maturity did not reach 100 individuals in captivity, and many of these populations died out during the recent decline. We suggest that small reductions in fitness may contribute to extirpation in taxa with inherently low fecundity, by keeping populations below a threshold number essential to long-term recovery. Future ex situ populations should be founded with no less than 15 adults, and maintained in conditions closely

  9. Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps.

    Science.gov (United States)

    Zhang, Weihua; Collins, Andrew; Gibson, Jane; Tapper, William J; Hunt, Sarah; Deloukas, Panos; Bentley, David R; Morton, Newton E

    2004-12-28

    Genetic maps in linkage disequilibrium (LD) units play the same role for association mapping as maps in centimorgans provide at much lower resolution for linkage mapping. Association mapping of genes determining disease susceptibility and other phenotypes is based on the theory of LD, here applied to relations with three phenomena. To test the theory, markers at high density along a 10-Mb continuous segment of chromosome 20q were studied in African-American, Asian, and Caucasian samples. Population structure, whether created by pooling samples from divergent populations or by the mating pattern in a mixed population, is accurately bioassayed from genotype frequencies. The effective bottleneck time for Eurasians is substantially less than for migration out of Africa, reflecting later bottlenecks. The classical dependence of allele frequency on mutation age does not hold for the generally shorter time span of inbreeding and LD. Limitation of the classical theory to mutation age justifies the assumption of constant time in a LD map, except for alleles that were rare at the effective bottleneck time or have arisen since. This assumption is derived from the Malecot model and verified in all samples. Tested measures of relative efficiency, support intervals, and localization error determine the operating characteristics of LD maps that are applicable to every sexually reproducing species, with implications for association mapping, high-resolution linkage maps, evolutionary inference, and identification of recombinogenic sequences.

  10. Population bottlenecks, genetic diversity and breeding ability of the three-spined stickleback (Gasterosteus aculeatus) from three polluted English Rivers.

    Science.gov (United States)

    Santos, Eduarda M; Hamilton, Patrick B; Coe, Tobias S; Ball, Jonathan S; Cook, Alastair C; Katsiadaki, Ioanna; Tyler, Charles R

    2013-10-15

    Pollution is a significant environmental pressure on fish populations in both freshwater and marine environments. Populations subjected to chronic exposure to pollutants can experience impacts ranging from altered reproductive capacity to changes in population genetic structure. Few studies, however, have examined the reproductive vigor of individuals within populations inhabiting environments characterized by chronic pollution. In this study we undertook an analysis of populations of three-spined sticklebacks (Gasterosteus aculeatus) from polluted sites, to determine levels of genetic diversity, assess for evidence of historic population genetic bottlenecks and determine the reproductive competitiveness of males from these locations. The sites chosen included locations in the River Aire, the River Tees and the River Birket, English rivers that have been impacted by pollution from industrial and/or domestic effluents for over 100 years. Male reproductive competitiveness was determined via competitive breeding experiments with males and females derived from a clean water site, employing DNA microsatellites to determine parentage outcome. Populations of stickleback collected from the three historically polluted sites showed evidence of recent population bottlenecks, although only the River Aire population showed low genetic diversity. In contrast, fish collected from two relatively unpolluted sites within the River Gowy and Houghton Springs showed weak, or no evidence of such bottlenecks. Nevertheless, males derived from polluted sites were able to reproduce successfully in competition with males derived from clean water exposures, indicating that these bottlenecks have not resulted in any substantial loss of reproductive fitness in males. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus.

    Science.gov (United States)

    Sobel Leonard, Ashley; Weissman, Daniel B; Greenbaum, Benjamin; Ghedin, Elodie; Koelle, Katia

    2017-07-15

    The bottleneck governing infectious disease transmission describes the size of the pathogen population transferred from the donor to the recipient host. Accurate quantification of the bottleneck size is particularly important for rapidly evolving pathogens such as influenza virus, as narrow bottlenecks reduce the amount of transferred viral genetic diversity and, thus, may decrease the rate of viral adaptation. Previous studies have estimated bottleneck sizes governing viral transmission by using statistical analyses of variants identified in pathogen sequencing data. These analyses, however, did not account for variant calling thresholds and stochastic viral replication dynamics within recipient hosts. Because these factors can skew bottleneck size estimates, we introduce a new method for inferring bottleneck sizes that accounts for these factors. Through the use of a simulated data set, we first show that our method, based on beta-binomial sampling, accurately recovers transmission bottleneck sizes, whereas other methods fail to do so. We then apply our method to a data set of influenza A virus (IAV) infections for which viral deep-sequencing data from transmission pairs are available. We find that the IAV transmission bottleneck size estimates in this study are highly variable across transmission pairs, while the mean bottleneck size of 196 virions is consistent with a previous estimate for this data set. Furthermore, regression analysis shows a positive association between estimated bottleneck size and donor infection severity, as measured by temperature. These results support findings from experimental transmission studies showing that bottleneck sizes across transmission events can be variable and influenced in part by epidemiological factors. IMPORTANCE The transmission bottleneck size describes the size of the pathogen population transferred from the donor to the recipient host and may affect the rate of pathogen adaptation within host populations. Recent

  12. Ancient DNA reveals substantial genetic diversity in the California Condor (Gymnogyps californianus) prior to a population bottleneck

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    D'Elia, Jesse; Haig, Susan M.; Mullins, Thomas D.; Miller, Mark P.

    2016-01-01

    Critically endangered species that have undergone severe population bottlenecks often have little remaining genetic variation, making it difficult to reconstruct population histories to apply in reintroduction and recovery strategies. By using ancient DNA techniques, it is possible to combine genetic evidence from the historical population with contemporary samples to provide a more complete picture of a species' genetic variation across its historical range and through time. Applying this approach, we examined changes in the mitochondrial DNA (mtDNA) control region (526 base pairs) of the endangered California Condor (Gymnogyps californianus). Results showed a >80% reduction in unique haplotypes over the past 2 centuries. We found no spatial sorting of haplotypes in the historical population; the periphery of the range contained haplotypes that were common throughout the historical range. Direct examination of mtDNA from California Condor museum specimens provided a new window into historical population connectivity and genetic diversity showing: (1) a substantial loss of haplotypes, which is consistent with the hypothesis that condors were relatively abundant in the nineteenth century, but declined rapidly as a result of human-caused mortality; and (2) no evidence of historical population segregation, meaning that the available genetic data offer no cause to avoid releasing condors in unoccupied portions of their historical range.

  13. Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear.

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    Xenikoudakis, G; Ersmark, E; Tison, J-L; Waits, L; Kindberg, J; Swenson, J E; Dalén, L

    2015-07-01

    The Scandinavian brown bear went through a major decline in population size approximately 100 years ago, due to intense hunting. After being protected, the population subsequently recovered and today numbers in the thousands. The genetic diversity in the contemporary population has been investigated in considerable detail, and it has been shown that the population consists of several subpopulations that display relatively high levels of genetic variation. However, previous studies have been unable to resolve the degree to which the demographic bottleneck impacted the contemporary genetic structure and diversity. In this study, we used mitochondrial and microsatellite DNA markers from pre- and postbottleneck Scandinavian brown bear samples to investigate the effect of the bottleneck. Simulation and multivariate analysis suggested the same genetic structure for the historical and modern samples, which are clustered into three subpopulations in southern, central and northern Scandinavia. However, the southern subpopulation appears to have gone through a marked change in allele frequencies. When comparing the mitochondrial DNA diversity in the whole population, we found a major decline in haplotype numbers across the bottleneck. However, the loss of autosomal genetic diversity was less pronounced, although a significant decline in allelic richness was observed in the southern subpopulation. Approximate Bayesian computations provided clear support for a decline in effective population size during the bottleneck, in both the southern and northern subpopulations. These results have implications for the future management of the Scandinavian brown bear because they indicate a recent loss in genetic diversity and also that the current genetic structure may have been caused by historical ecological processes rather than recent anthropogenic persecution. © 2015 John Wiley & Sons Ltd.

  14. Population aging and migrant workers: bottlenecks in tuberculosis control in rural China.

    Science.gov (United States)

    Bele, Sumedh; Jiang, Wei; Lu, Hui; You, Hua; Fan, Hong; Huang, Lifang; Wang, Qungang; Shen, Hongbing; Wang, Jianming

    2014-01-01

    Tuberculosis is a serious global health problem. Its paradigms are shifting through time, especially in rapidly developing countries such as China. Health providers in China are at the forefront of the battle against tuberculosis; however, there are few empirical studies on health providers' perspectives on the challenges they face in tuberculosis control at the county level in China. This study was conducted among health providers to explore their experiences with tuberculosis control in order to identify bottlenecks and emerging challenges in controlling tuberculosis in rural China. A qualitative approach was used. Semi-structured, in-depth interviews were conducted with 17 health providers working in various positions within the health system of one rural county (ZJG) of China. Data were analyzed based on thematic content analysis using MAXQDA 10 qualitative data analysis software. Health providers reported several problems in tuberculosis control in ZJG county. Migrant workers and the elderly were repeatedly documented as the main obstacles in effective tuberculosis control in the county. At a personal level, doctors showed their frustration with the lack of new drugs for treating tuberculosis patients, and their opinions varied regarding incentives for referring patients. The results suggest that several problems still remain for controlling tuberculosis in rural China. Tuberculosis control efforts need to make reaching the most vulnerable populations a priority and encourage local health providers to adopt innovative practices in the local context based on national guidelines to achieve the best results. Considerable changes in China's National Tuberculosis Control Program are needed to tackle these emerging challenges faced by health workers at the county level.

  15. Population aging and migrant workers: bottlenecks in tuberculosis control in rural China.

    Directory of Open Access Journals (Sweden)

    Sumedh Bele

    Full Text Available BACKGROUND: Tuberculosis is a serious global health problem. Its paradigms are shifting through time, especially in rapidly developing countries such as China. Health providers in China are at the forefront of the battle against tuberculosis; however, there are few empirical studies on health providers' perspectives on the challenges they face in tuberculosis control at the county level in China. This study was conducted among health providers to explore their experiences with tuberculosis control in order to identify bottlenecks and emerging challenges in controlling tuberculosis in rural China. METHODS: A qualitative approach was used. Semi-structured, in-depth interviews were conducted with 17 health providers working in various positions within the health system of one rural county (ZJG of China. Data were analyzed based on thematic content analysis using MAXQDA 10 qualitative data analysis software. RESULTS: Health providers reported several problems in tuberculosis control in ZJG county. Migrant workers and the elderly were repeatedly documented as the main obstacles in effective tuberculosis control in the county. At a personal level, doctors showed their frustration with the lack of new drugs for treating tuberculosis patients, and their opinions varied regarding incentives for referring patients. CONCLUSION: The results suggest that several problems still remain for controlling tuberculosis in rural China. Tuberculosis control efforts need to make reaching the most vulnerable populations a priority and encourage local health providers to adopt innovative practices in the local context based on national guidelines to achieve the best results. Considerable changes in China's National Tuberculosis Control Program are needed to tackle these emerging challenges faced by health workers at the county level.

  16. High and distinct range-edge genetic diversity despite local bottlenecks.

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    Jorge Assis

    Full Text Available The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines.

  17. Resequencing data provide no evidence for a human bottleneck in Africa during the penultimate glacial period.

    Science.gov (United States)

    Sjödin, Per; E Sjöstrand, Agnès; Jakobsson, Mattias; Blum, Michael G B

    2012-07-01

    Based on the accumulation of genetic, climatic, and fossil evidence, a central theory in paleoanthropology stipulates that a demographic bottleneck coincided with the origin of our species Homo Sapiens. This theory proposes that anatomically modern humans--which were only present in Africa at the time--experienced a drastic bottleneck during the penultimate glacial age (130-190 kya) when a cold and dry climate prevailed. Two scenarios have been proposed to describe the bottleneck, which involve either a fragmentation of the range occupied by humans or the survival of one small group of humans. Here, we analyze DNA sequence data from 61 nuclear loci sequenced in three African populations using Approximate Bayesian Computation and numerical simulations. In contrast to the bottleneck theory, we show that a simple model without any bottleneck during the penultimate ice age has the greatest statistical support compared with bottleneck models. Although the proposed bottleneck is ancient, occurring at least 130 kya, we can discard the possibility that it did not leave detectable footprints in the DNA sequence data except if the bottleneck involves a less than a 3-fold reduction in population size. Finally, we confirm that a simple model without a bottleneck is able to reproduce the main features of the observed patterns of genetic variation. We conclude that models of Pleistocene refugium for modern human origins now require substantial revision.

  18. Comparison of historical bottleneck effects and genetic consequences of re-introduction in a critically endangered island passerine.

    Science.gov (United States)

    Bristol, Rachel M; Tucker, Rachel; Dawson, Deborah A; Horsburgh, Gavin; Prys-Jones, Robert P; Frantz, Alain C; Krupa, Andy; Shah, Nirmal J; Burke, Terry; Groombridge, Jim J

    2013-09-01

    Re-introduction is an important tool for recovering endangered species; however, the magnitude of genetic consequences for re-introduced populations remains largely unknown, in particular the relative impacts of historical population bottlenecks compared to those induced by conservation management. We characterize 14 microsatellite loci developed for the Seychelles paradise flycatcher and use them to quantify temporal and spatial measures of genetic variation across a 134-year time frame encompassing a historical bottleneck that reduced the species to ~28 individuals in the 1960s, through the initial stages of recovery and across a second contemporary conservation-introduction-induced bottleneck. We then evaluate the relative impacts of the two bottlenecks, and finally apply our findings to inform broader re-introduction strategy. We find a temporal trend of significant decrease in standard measures of genetic diversity across the historical bottleneck, but only a nonsignificant downward trend in number of alleles across the contemporary bottleneck. However, accounting for the different timescales of the two bottlenecks (~40 historical generations versus introduction. In some cases, the loss of genetic diversity per generation can, initially at least, be greater across re-introduction-induced bottlenecks. © 2013 John Wiley & Sons Ltd.

  19. Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long-lived tree endemic to Hainan Island, China.

    Science.gov (United States)

    Zheng, D-J; Xie, L-S; Zhu, J-H; Zhang, Z-L

    2012-09-01

    Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long-lived trees. Dracaena cambodiana is an endangered, long-lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat-private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  20. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA

    DEFF Research Database (Denmark)

    Rebolledo-Jaramillo, Boris; Su, Marcia Shu-Wei; Stoler, Nicholas

    2014-01-01

    The manifestation of mitochondrial DNA (mtDNA) diseases depends on the frequency of heteroplasmy (the presence of several alleles in an individual), yet its transmission across generations cannot be readily predicted owing to a lack of data on the size of the mtDNA bottleneck during oogenesis......, an order of magnitude higher than for nuclear DNA. Notably, we found a positive association between the number of heteroplasmies in a child and maternal age at fertilization, likely attributable to oocyte aging. This study also took advantage of droplet digital PCR (ddPCR) to validate heteroplasmies...... and confirm a de novo mutation. Our results can be used to predict the transmission of disease-causing mtDNA variants and illuminate evolutionary dynamics of the mitochondrial genome....

  1. Laboratory colonisation and genetic bottlenecks in the tsetse fly Glossina pallidipes.

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    Marc Ciosi

    2014-02-01

    Full Text Available The IAEA colony is the only one available for mass rearing of Glossina pallidipes, a vector of human and animal African trypanosomiasis in eastern Africa. This colony is the source for Sterile Insect Technique (SIT programs in East Africa. The source population of this colony is unclear and its genetic diversity has not previously been evaluated and compared to field populations.We examined the genetic variation within and between the IAEA colony and its potential source populations in north Zimbabwe and the Kenya/Uganda border at 9 microsatellites loci to retrace the demographic history of the IAEA colony. We performed classical population genetics analyses and also combined historical and genetic data in a quantitative analysis using Approximate Bayesian Computation (ABC. There is no evidence of introgression from the north Zimbabwean population into the IAEA colony. Moreover, the ABC analyses revealed that the foundation and establishment of the colony was associated with a genetic bottleneck that has resulted in a loss of 35.7% of alleles and 54% of expected heterozygosity compared to its source population. Also, we show that tsetse control carried out in the 1990's is likely reduced the effective population size of the Kenya/Uganda border population.All the analyses indicate that the area of origin of the IAEA colony is the Kenya/Uganda border and that a genetic bottleneck was associated with the foundation and establishment of the colony. Genetic diversity associated with traits that are important for SIT may potentially have been lost during this genetic bottleneck which could lead to a suboptimal competitiveness of the colony males in the field. The genetic diversity of the colony is lower than that of field populations and so, studies using colony flies should be interpreted with caution when drawing general conclusions about G. pallidipes biology.

  2. Traffic behavior at freeway bottlenecks.

    Science.gov (United States)

    2014-09-01

    This study examines traffic behavior in the vicinity of a freeway bottleneck, revisiting commonly held : assumptions and uncovering systematic biases that likely have distorted empirical studies of bottleneck : formation, capacity drop, and the funda...

  3. Logistics bottlenecks

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2010-09-15

    Many of the vulnerabilities to Energy Access, Energy Security, and Environmental Sustainability result from impediments to reaching a global demand-supply balance, as well as local balances, for various energy sources and carriers. Vulnerabilities result from multiple reasons: regional imbalances of energy production and consumption, the bulky character of the majority of energy fuels, the virtual necessity of electricity consumption following its production, among others. To detect and prioritize respective 'bottlenecks' across energy carriers, they have to be measured. In this report, production, consumption, exports, and imports were measured across all major energy carriers for seven key regions of the world for three time frames-2008, 2020, and 2050. Imbalances between production and consumption form bottlenecks in each region.

  4. A theory of traffic congestion at moving bottlenecks

    Energy Technology Data Exchange (ETDEWEB)

    Kerner, Boris S [Daimler AG, GR/PTF, HPC: G021, 71059 Sindelfingen (Germany); Klenov, Sergey L, E-mail: boris.kerner@daimler.co [Department of Physics, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region (Russian Federation)

    2010-10-22

    The physics of traffic congestion occurring at a moving bottleneck on a multi-lane road is revealed based on the numerical analyses of vehicular traffic with a discrete stochastic traffic flow model in the framework of three-phase traffic theory. We find that there is a critical speed of a moving bottleneck at which traffic breakdown, i.e. a first-order phase transition from free flow to synchronized flow, occurs spontaneously at the moving bottleneck, if the flow rate upstream of the bottleneck is great enough. The greater the flow rate, the higher the critical speed of the moving bottleneck. A diagram of congested traffic patterns at the moving bottleneck is found, which shows regions in the flow-rate-moving-bottleneck-speed plane in which congested patterns emerge spontaneously or can be induced through large enough disturbances in an initial free flow. A comparison of features of traffic breakdown and resulting congested patterns at the moving bottleneck with known ones at an on-ramp (and other motionless) bottleneck is made. Nonlinear features of complex interactions and transformations of congested traffic patterns occurring at on- and off-ramp bottlenecks due to the existence of the moving bottleneck are found. The physics of the phenomenon of traffic congestion due to 'elephant racing' on a multi-lane road is revealed.

  5. A theory of traffic congestion at moving bottlenecks

    International Nuclear Information System (INIS)

    Kerner, Boris S; Klenov, Sergey L

    2010-01-01

    The physics of traffic congestion occurring at a moving bottleneck on a multi-lane road is revealed based on the numerical analyses of vehicular traffic with a discrete stochastic traffic flow model in the framework of three-phase traffic theory. We find that there is a critical speed of a moving bottleneck at which traffic breakdown, i.e. a first-order phase transition from free flow to synchronized flow, occurs spontaneously at the moving bottleneck, if the flow rate upstream of the bottleneck is great enough. The greater the flow rate, the higher the critical speed of the moving bottleneck. A diagram of congested traffic patterns at the moving bottleneck is found, which shows regions in the flow-rate-moving-bottleneck-speed plane in which congested patterns emerge spontaneously or can be induced through large enough disturbances in an initial free flow. A comparison of features of traffic breakdown and resulting congested patterns at the moving bottleneck with known ones at an on-ramp (and other motionless) bottleneck is made. Nonlinear features of complex interactions and transformations of congested traffic patterns occurring at on- and off-ramp bottlenecks due to the existence of the moving bottleneck are found. The physics of the phenomenon of traffic congestion due to 'elephant racing' on a multi-lane road is revealed.

  6. Mitochondrial DNA sequence characteristics modulate the size of the genetic bottleneck.

    Science.gov (United States)

    Wilson, Ian J; Carling, Phillipa J; Alston, Charlotte L; Floros, Vasileios I; Pyle, Angela; Hudson, Gavin; Sallevelt, Suzanne C E H; Lamperti, Costanza; Carelli, Valerio; Bindoff, Laurence A; Samuels, David C; Wonnapinij, Passorn; Zeviani, Massimo; Taylor, Robert W; Smeets, Hubert J M; Horvath, Rita; Chinnery, Patrick F

    2016-03-01

    With a combined carrier frequency of 1:200, heteroplasmic mitochondrial DNA (mtDNA) mutations cause human disease in ∼1:5000 of the population. Rapid shifts in the level of heteroplasmy seen within a single generation contribute to the wide range in the severity of clinical phenotypes seen in families transmitting mtDNA disease, consistent with a genetic bottleneck during transmission. Although preliminary evidence from human pedigrees points towards a random drift process underlying the shifting heteroplasmy, some reports describe differences in segregation pattern between different mtDNA mutations. However, based on limited observations and with no direct comparisons, it is not clear whether these observations simply reflect pedigree ascertainment and publication bias. To address this issue, we studied 577 mother-child pairs transmitting the m.11778G>A, m.3460G>A, m.8344A>G, m.8993T>G/C and m.3243A>G mtDNA mutations. Our analysis controlled for inter-assay differences, inter-laboratory variation and ascertainment bias. We found no evidence of selection during transmission but show that different mtDNA mutations segregate at different rates in human pedigrees. m.8993T>G/C segregated significantly faster than m.11778G>A, m.8344A>G and m.3243A>G, consistent with a tighter mtDNA genetic bottleneck in m.8993T>G/C pedigrees. Our observations support the existence of different genetic bottlenecks primarily determined by the underlying mtDNA mutation, explaining the different inheritance patterns observed in human pedigrees transmitting pathogenic mtDNA mutations. © The Author 2016. Published by Oxford University Press.

  7. Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the kea (Nestor notabilis.

    Directory of Open Access Journals (Sweden)

    Nicolas Dussex

    Full Text Available The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis. Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000-5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410, historical (n = 15 and fossil samples (n = 4 showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 - 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines.

  8. Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the kea (Nestor notabilis).

    Science.gov (United States)

    Dussex, Nicolas; Rawlence, Nicolas J; Robertson, Bruce C

    2015-01-01

    The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis). Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000-5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410), historical (n = 15) and fossil samples (n = 4) showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial) but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 - 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines.

  9. Ancient and Contemporary DNA Reveal a Pre-Human Decline but No Population Bottleneck Associated with Recent Human Persecution in the Kea (Nestor notabilis)

    Science.gov (United States)

    Dussex, Nicolas; Rawlence, Nicolas J.; Robertson, Bruce C.

    2015-01-01

    The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis). Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000–5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410), historical (n = 15) and fossil samples (n = 4) showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial) but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 – 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines. PMID:25719752

  10. The strength and timing of the mitochondrial bottleneck in salmon suggests a conserved mechanism in vertebrates.

    Directory of Open Access Journals (Sweden)

    Jonci N Wolff

    Full Text Available In most species mitochondrial DNA (mtDNA is inherited maternally in an apparently clonal fashion, although how this is achieved remains uncertain. Population genetic studies show not only that individuals can harbor more than one type of mtDNA (heteroplasmy but that heteroplasmy is common and widespread across a diversity of taxa. Females harboring a mixture of mtDNAs may transmit varying proportions of each mtDNA type (haplotype to their offspring. However, mtDNA variants are also observed to segregate rapidly between generations despite the high mtDNA copy number in the oocyte, which suggests a genetic bottleneck acts during mtDNA transmission. Understanding the size and timing of this bottleneck is important for interpreting population genetic relationships and for predicting the inheritance of mtDNA based disease, but despite its importance the underlying mechanisms remain unclear. Empirical studies, restricted to mice, have shown that the mtDNA bottleneck could act either at embryogenesis, oogenesis or both. To investigate whether the size and timing of the mitochondrial bottleneck is conserved between distant vertebrates, we measured the genetic variance in mtDNA heteroplasmy at three developmental stages (female, ova and fry in chinook salmon and applied a new mathematical model to estimate the number of segregating units (N(e of the mitochondrial bottleneck between each stage. Using these data we estimate values for mtDNA Ne of 88.3 for oogenesis, and 80.3 for embryogenesis. Our results confirm the presence of a mitochondrial bottleneck in fish, and show that segregation of mtDNA variation is effectively complete by the end of oogenesis. Considering the extensive differences in reproductive physiology between fish and mammals, our results suggest the mechanism underlying the mtDNA bottleneck is conserved in these distant vertebrates both in terms of it magnitude and timing. This finding may lead to improvements in our understanding of

  11. The effect of isolation, fragmentation, and population bottlenecks on song structure of a Hawaiian honeycreeper

    Science.gov (United States)

    Pang-Ching, Joshua M.; Paxton, Kristina L.; Paxton, Eben H.; Pack, Adam A.; Hart, Patrick J.

    2018-01-01

    Little is known about how important social behaviors such as song vary within and among populations for any of the endemic Hawaiian honeycreepers. Habitat loss and non‐native diseases (e.g., avian malaria) have resulted in isolation and fragmentation of Hawaiian honeycreepers within primarily high elevation forests. In this study, we examined how isolation of Hawai'i ‘amakihi (Chlorodrepanis virens) populations within a fragmented landscape influences acoustic variability in song. In the last decade, small, isolated populations of disease tolerant ‘amakihi have been found within low elevation forests, allowing us to record ‘amakihi songs across a large elevational gradient (10–1800 m) that parallels disease susceptibility on Hawai'i island. To understand underlying differences among populations, we examined the role of geographic distance, elevation, and habitat structure on acoustic characteristics of ‘amakihi songs. We found that the acoustic characteristics of ‘amakihi songs and song‐type repertoires varied most strongly across an elevational gradient. Differences in ‘amakihi song types were primarily driven by less complex songs (e.g., fewer frequency changes, shorter songs) of individuals recorded at low elevation sites compared to mid and high elevation populations. The reduced complexity of ‘amakihi songs at low elevation sites is most likely shaped by the effects of habitat fragmentation and a disease‐driven population bottleneck associated with avian malaria, and maintained through isolation, localized song learning and sharing, and cultural drift. These results highlight how a non‐native disease through its influence on population demographics may have also indirectly played a role in shaping the acoustic characteristics of a species.

  12. Characterization of MHC class II B polymorphism in bottlenecked New Zealand saddlebacks reveals low levels of genetic diversity.

    Science.gov (United States)

    Sutton, Jolene T; Robertson, Bruce C; Grueber, Catherine E; Stanton, Jo-Ann L; Jamieson, Ian G

    2013-08-01

    The major histocompatibility complex (MHC) is integral to the vertebrate adaptive immune system. Characterizing diversity at functional MHC genes is invaluable for elucidating patterns of adaptive variation in wild populations, and is particularly interesting in species of conservation concern, which may suffer from reduced genetic diversity and compromised disease resilience. Here, we use next generation sequencing to investigate MHC class II B (MHCIIB) diversity in two sister taxa of New Zealand birds: South Island saddleback (SIS), Philesturnus carunculatus, and North Island saddleback (NIS), Philesturnus rufusater. These two species represent a passerine family outside the more extensively studied Passerida infraorder, and both have experienced historic bottlenecks. We examined exon 2 sequence data from populations that represent the majority of genetic diversity remaining in each species. A high level of locus co-amplification was detected, with from 1 to 4 and 3 to 12 putative alleles per individual for South and North Island birds, respectively. We found strong evidence for historic balancing selection in peptide-binding regions of putative alleles, and we identified a cluster combining non-classical loci and pseudogene sequences from both species, although no sequences were shared between the species. Fewer total alleles and fewer alleles per bird in SIS may be a consequence of their more severe bottleneck history; however, overall nucleotide diversity was similar between the species. Our characterization of MHCIIB diversity in two closely related species of New Zealand saddlebacks provides an important step in understanding the mechanisms shaping MHC diversity in wild, bottlenecked populations.

  13. Toll-like receptor variation in the bottlenecked population of the Seychelles warbler: computer simulations see the 'ghost of selection past' and quantify the 'drift debt'.

    Science.gov (United States)

    Gilroy, D L; Phillips, K P; Richardson, D S; van Oosterhout, C

    2017-07-01

    Balancing selection can maintain immunogenetic variation within host populations, but detecting its signal in a postbottlenecked population is challenging due to the potentially overriding effects of drift. Toll-like receptor genes (TLRs) play a fundamental role in vertebrate immune defence and are predicted to be under balancing selection. We previously characterized variation at TLR loci in the Seychelles warbler (Acrocephalus sechellensis), an endemic passerine that has undergone a historical bottleneck. Five of seven TLR loci were polymorphic, which is in sharp contrast to the low genomewide variation observed. However, standard population genetic statistical methods failed to detect a contemporary signature of selection at any TLR locus. We examined whether the observed TLR polymorphism could be explained by neutral evolution, simulating the population's demography in the software DIYABC. This showed that the posterior distributions of mutation rates had to be unrealistically high to explain the observed genetic variation. We then conducted simulations with an agent-based model using typical values for the mutation rate, which indicated that weak balancing selection has acted on the three TLR genes. The model was able to detect evidence of past selection elevating TLR polymorphism in the prebottleneck populations, but was unable to discern any effects of balancing selection in the contemporary population. Our results show drift is the overriding evolutionary force that has shaped TLR variation in the contemporary Seychelles warbler population, and the observed TLR polymorphisms might be merely the 'ghost of selection past'. Forecast models predict immunogenetic variation in this species will continue to be eroded in the absence of contemporary balancing selection. Such 'drift debt' occurs when a gene pool has not yet reached its new equilibrium level of polymorphism, and this loss could be an important threat to many recently bottlenecked populations. © 2017

  14. Population bottleneck triggering millennial-scale morphospace shifts in endemic thermal-spring melanopsids.

    Science.gov (United States)

    Neubauer, Thomas A; Harzhauser, Mathias; Georgopoulou, Elisavet; Wrozyna, Claudia

    2014-11-15

    For more than hundred years the thermal spring-fed Lake Pețea near Oradea, Romania, was studied for its highly endemic subfossil and recent fauna and flora. One point of focus was the species lineage of the melanopsid gastropod Microcolpia parreyssii , which exhibited a tremendous diversity of shapes during the earlier Holocene. As a consequence many new species, subspecies, and variety-names have been introduced over time, trying to categorize this overwhelming variability. In contrast to the varied subfossil assemblage, only a single phenotype is present today. We critically review the apparent "speciation event" implied by the taxonomy, based on the presently available information and new data from morphometric analyses of shell outlines and oxygen and carbon isotope data. This synthesis shows that one turning point in morphological evolution coincides with high accumulation of peaty deposits during a short time interval of maximally a few thousand years. The formation of a small, highly eutrophic swamp with increased input of organic matter marginalized the melanopsids and reduced population size. The presented data make natural selection as the dominating force unlikely but rather indicates genetic drift following a bottleneck effect induced by the environmental changes. This claim contrasts the "obvious trend" and shows that great morphological variability has to be carefully and objectively evaluated in order to allow sound interpretations of the underlying mechanisms.

  15. Kangaroo mother care: a multi-country analysis of health system bottlenecks and potential solutions.

    Science.gov (United States)

    Vesel, Linda; Bergh, Anne-Marie; Kerber, Kate J; Valsangkar, Bina; Mazia, Goldy; Moxon, Sarah G; Blencowe, Hannah; Darmstadt, Gary L; de Graft Johnson, Joseph; Dickson, Kim E; Ruiz Peláez, Juan; von Xylander, Severin; Lawn, Joy E

    2015-01-01

    Preterm birth is now the leading cause of under-five child deaths worldwide with one million direct deaths plus approximately another million where preterm is a risk factor for neonatal deaths due to other causes. There is strong evidence that kangaroo mother care (KMC) reduces mortality among babies with birth weight Asia as part of the Every Newborn Action Plan process. Country workshops involved technical experts to complete the survey tool, which is designed to synthesise and grade health system "bottlenecks", factors that hinder the scale-up, of maternal-newborn intervention packages. We used quantitative and qualitative methods to analyse the bottleneck data, combined with literature review, to present priority bottlenecks and actions relevant to different health system building blocks for KMC. Marked differences were found in the perceived severity of health system bottlenecks between Asian and African countries, with the former reporting more significant or very major bottlenecks for KMC with respect to all the health system building blocks. Community ownership and health financing bottlenecks were significant or very major bottlenecks for KMC in both low and high mortality contexts, particularly in South Asia. Significant bottlenecks were also reported for leadership and governance and health workforce building blocks. There are at least a dozen countries worldwide with national KMC programmes, and we identify three pathways to scale: (1) champion-led; (2) project-initiated; and (3) health systems designed. The combination of all three pathways may lead to more rapid scale-up. KMC has the potential to save lives, and change the face of facility-based newborn care, whilst empowering women to care for their preterm newborns.

  16. A theory of traffic congestion at heavy bottlenecks

    Energy Technology Data Exchange (ETDEWEB)

    Kerner, Boris S [Daimler AG, GR/ETI, HPC: G021, 71059 Sindelfingen (Germany)

    2008-05-30

    Spatiotemporal features and physics of vehicular traffic congestion occurring due to heavy highway bottlenecks caused for example by bad weather conditions or accidents are found based on simulations in the framework of three-phase traffic theory. A model of a heavy bottleneck is presented. Under a continuous non-limited increase in bottleneck strength, i.e., when the average flow rate within a congested pattern allowed by the heavy bottleneck decreases continuously up to zero, the evolution of the traffic phases in congested traffic, synchronized flow and wide moving jams, is studied. It is found that at a small enough flow rate within the congested pattern, the pattern exhibits a non-regular structure: a pinch region of synchronized flow within the pattern disappears and appears randomly over time; wide moving jams upstream of the pinch region exhibit a complex non-regular dynamics in which the jams appear and disappear randomly. At greater bottleneck strengths, wide moving jams merge onto a mega-wide moving jam (mega-jam) within which low-speed patterns with a complex non-regular spatiotemporal dynamics occur. We show that when the bottleneck strength is great enough, only the mega-jam survives and synchronized flow remains only within its downstream front separating free flow and congested traffic. Theoretical results presented can explain why no sequence of wide moving jams can often be distinguished in non-homogeneous traffic congestion measured at very heavy bottlenecks caused by bad weather conditions or accidents.

  17. A theory of traffic congestion at heavy bottlenecks

    International Nuclear Information System (INIS)

    Kerner, Boris S

    2008-01-01

    Spatiotemporal features and physics of vehicular traffic congestion occurring due to heavy highway bottlenecks caused for example by bad weather conditions or accidents are found based on simulations in the framework of three-phase traffic theory. A model of a heavy bottleneck is presented. Under a continuous non-limited increase in bottleneck strength, i.e., when the average flow rate within a congested pattern allowed by the heavy bottleneck decreases continuously up to zero, the evolution of the traffic phases in congested traffic, synchronized flow and wide moving jams, is studied. It is found that at a small enough flow rate within the congested pattern, the pattern exhibits a non-regular structure: a pinch region of synchronized flow within the pattern disappears and appears randomly over time; wide moving jams upstream of the pinch region exhibit a complex non-regular dynamics in which the jams appear and disappear randomly. At greater bottleneck strengths, wide moving jams merge onto a mega-wide moving jam (mega-jam) within which low-speed patterns with a complex non-regular spatiotemporal dynamics occur. We show that when the bottleneck strength is great enough, only the mega-jam survives and synchronized flow remains only within its downstream front separating free flow and congested traffic. Theoretical results presented can explain why no sequence of wide moving jams can often be distinguished in non-homogeneous traffic congestion measured at very heavy bottlenecks caused by bad weather conditions or accidents

  18. Bottleneck analysis at district level to illustrate gaps within the district health system in Uganda

    Science.gov (United States)

    Kiwanuka Henriksson, Dorcus; Fredriksson, Mio; Waiswa, Peter; Selling, Katarina; Swartling Peterson, Stefan

    2017-01-01

    ABSTRACT Background: Poor quality of care and access to effective and affordable interventions have been attributed to constraints and bottlenecks within and outside the health system. However, there is limited understanding of health system barriers to utilization and delivery of appropriate, high-impact, and cost-effective interventions at the point of service delivery in districts and sub-districts in low-income countries. In this study we illustrate the use of the bottleneck analysis approach, which could be used to identify bottlenecks in service delivery within the district health system. Methods: A modified Tanahashi model with six determinants for effective coverage was used to determine bottlenecks in service provision for maternal and newborn care. The following interventions provided during antenatal care were used as tracer interventions: use of iron and folic acid, intermittent presumptive treatment for malaria, HIV counseling and testing, and syphilis testing. Data from cross-sectional household and health facility surveys in Mayuge and Namayingo districts in Uganda were used in this study. Results: Effective coverage and human resource gaps were identified as the biggest bottlenecks in both districts, with coverage ranging from 0% to 66% for effective coverage and from 46% to 58% for availability of health facility staff. Our findings revealed a similar pattern in bottlenecks in both districts for particular interventions although the districts are functionally independent. Conclusion: The modified Tanahashi model is an analysis tool that can be used to identify bottlenecks to effective coverage within the district health system, for instance, the effective coverage for maternal and newborn care interventions. However, the analysis is highly dependent on the availability of data to populate all six determinants and could benefit from further validation analysis for the causes of bottlenecks identified. PMID:28581379

  19. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

    KAUST Repository

    Karmin, Monika; Saag, Lauri; Vicente, Má rio; Sayres, Melissa A. Wilson; Jä rve, Mari; Talas, Ulvi Gerst; Rootsi, Siiri; Ilumä e, Anne-Mai; Mä gi, Reedik; Mitt, Mario; Pagani, Luca; Puurand, Tarmo; Faltyskova, Zuzana; Clemente, Florian; Cardona, Alexia; Metspalu, Ene; Sahakyan, Hovhannes; Yunusbayev, Bayazit; Hudjashov, Georgi; DeGiorgio, Michael; Loogvä li, Eva-Liis; Eichstaedt, Christina; Eelmets, Mikk; Chaubey, Gyaneshwer; Tambets, Kristiina; Litvinov, Sergei; Mormina, Maru; Xue, Yali; Ayub, Qasim; Zoraqi, Grigor; Korneliussen, Thorfinn Sand; Akhatova, Farida; Lachance, Joseph; Tishkoff, Sarah; Momynaliev, Kuvat; Ricaut, Franç ois-Xavier; Kusuma, Pradiptajati; Razafindrazaka, Harilanto; Pierron, Denis; Cox, Murray P.; Sultana, Gazi Nurun Nahar; Willerslev, Rane; Muller, Craig; Westaway, Michael; Lambert, David; Skaro, Vedrana; Kovačevic´ , Lejla; Turdikulova, Shahlo; Dalimova, Dilbar; Khusainova, Rita; Trofimova, Natalya; Akhmetova, Vita; Khidiyatova, Irina; Lichman, Daria V.; Isakova, Jainagul; Pocheshkhova, Elvira; Sabitov, Zhaxylyk; Barashkov, Nikolay A.; Nymadawa, Pagbajabyn; Mihailov, Evelin; Seng, Joseph Wee Tien; Evseeva, Irina; Migliano, Andrea Bamberg; Abdullah, Syafiq; Andriadze, George; Primorac, Dragan; Atramentova, Lubov; Utevska, Olga; Yepiskoposyan, Levon; Marjanovic´ , Damir; Kushniarevich, Alena; Behar, Doron M.; Gilissen, Christian; Vissers, Lisenka; Veltman, Joris A.; Balanovska, Elena; Derenko, Miroslava; Malyarchuk, Boris; Metspalu, Andres; Fedorova, Sardana; Eriksson, Anders; Manica, Andrea; Mendez, Fernando L.; Karafet, Tatiana M.; Veeramah, Krishna R.; Bradman, Neil; Hammer, Michael F.; Osipova, Ludmila P.; Balanovsky, Oleg; Khusnutdinova, Elza K.; Johnsen, Knut; Remm, Maido; Thomas, Mark G.; Tyler-Smith, Chris; Underhill, Peter A.; Willerslev, Eske; Nielsen, Rasmus; Metspalu, Mait; Villems, Richard; Kivisild, Toomas

    2015-01-01

    It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

  20. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

    KAUST Repository

    Karmin, Monika

    2015-04-30

    It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

  1. Strong population bottleneck and repeated demographic expansions of Populus adenopoda (Salicaceae) in subtropical China.

    Science.gov (United States)

    Fan, Liqiang; Zheng, Honglei; Milne, Richard I; Zhang, Lei; Mao, Kangshan

    2018-03-14

    Glacial refugia and inter-/postglacial recolonization routes during the Quaternary of tree species in Europe and North America are well understood, but far less is known about those of tree species in subtropical eastern Asia. Thus, we have examined the phylogeographic history of Populus adenopoda (Salicaceae), one of the few poplars that naturally occur in this subtropical area. Genetic variations across the range of the species in subtropical China were surveyed using ten nuclear microsatellite loci and four chloroplast fragments (matK, trnG-psbK, psbK-psbI and ndhC-trnV). Coalescent-based analyses were used to test demographic and migration hypotheses. In addition, species distribution models (SDMs) were constructed to infer past, present and future potential distributions of the species. Thirteen chloroplast haplotypes were detected, and haplotype-rich populations were found in central and southern parts of the species' range. STRUCTURE analyses of nuclear microsatellite loci suggest obvious lineage admixture, especially in peripheral and northern populations. DIYABC analysis suggests that the species might have experienced two independent rounds of demographic expansions and a strong bottleneck in the late Quaternary. SDMs indicate that the species' range contracted during the Last Glacial Maximum (LGM), and contracted northward but expanded eastward during the Last Interglacial (LIG). Chloroplast data and SDMs suggest that P. adenopoda might have survived in multiple glacial refugia in central and southern parts of its range during the LGM. Populations of the Yunnan-Guizhou Plateau in the southern part have high chloroplast DNA diversity, but may have contributed little to the postglacial recolonization of northern and eastern parts. The three major demographic events inferred by DIYABC coincide with the initiation of the LIG, start of the LGM and end of the LGM, respectively. The species may have experienced multiple rounds of range contraction during

  2. Self-organized phenomena of pedestrian counterflow through a wide bottleneck in a channel

    Science.gov (United States)

    Dong, Li-Yun; Lan, Dong-Kai; Li, Xiang

    2016-09-01

    The pedestrian counterflow through a bottleneck in a channel shows a variety of flow patterns due to self-organization. In order to reveal the underlying mechanism, a cellular automaton model was proposed by incorporating the floor field and the view field which reflects the global information of the studied area and local interactions with others. The presented model can well reproduce typical collective behaviors, such as lane formation. Numerical simulations were performed in the case of a wide bottleneck and typical flow patterns at different density ranges were identified as rarefied flow, laminar flow, interrupted bidirectional flow, oscillatory flow, intermittent flow, and choked flow. The effects of several parameters, such as the size of view field and the width of opening, on the bottleneck flow are also analyzed in detail. The view field plays a vital role in reproducing self-organized phenomena of pedestrian. Numerical results showed that the presented model can capture key characteristics of bottleneck flows. Project supported by the National Basic Research Program of China (Grant No. 2012CB725404) and the National Natural Science Foundation of China (Grant Nos. 11172164 and 11572184).

  3. A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

    Science.gov (United States)

    Karmin, Monika; Saag, Lauri; Vicente, Mário; Wilson Sayres, Melissa A; Järve, Mari; Talas, Ulvi Gerst; Rootsi, Siiri; Ilumäe, Anne-Mai; Mägi, Reedik; Mitt, Mario; Pagani, Luca; Puurand, Tarmo; Faltyskova, Zuzana; Clemente, Florian; Cardona, Alexia; Metspalu, Ene; Sahakyan, Hovhannes; Yunusbayev, Bayazit; Hudjashov, Georgi; DeGiorgio, Michael; Loogväli, Eva-Liis; Eichstaedt, Christina; Eelmets, Mikk; Chaubey, Gyaneshwer; Tambets, Kristiina; Litvinov, Sergei; Mormina, Maru; Xue, Yali; Ayub, Qasim; Zoraqi, Grigor; Korneliussen, Thorfinn Sand; Akhatova, Farida; Lachance, Joseph; Tishkoff, Sarah; Momynaliev, Kuvat; Ricaut, François-Xavier; Kusuma, Pradiptajati; Razafindrazaka, Harilanto; Pierron, Denis; Cox, Murray P; Sultana, Gazi Nurun Nahar; Willerslev, Rane; Muller, Craig; Westaway, Michael; Lambert, David; Skaro, Vedrana; Kovačevic, Lejla; Turdikulova, Shahlo; Dalimova, Dilbar; Khusainova, Rita; Trofimova, Natalya; Akhmetova, Vita; Khidiyatova, Irina; Lichman, Daria V; Isakova, Jainagul; Pocheshkhova, Elvira; Sabitov, Zhaxylyk; Barashkov, Nikolay A; Nymadawa, Pagbajabyn; Mihailov, Evelin; Seng, Joseph Wee Tien; Evseeva, Irina; Migliano, Andrea Bamberg; Abdullah, Syafiq; Andriadze, George; Primorac, Dragan; Atramentova, Lubov; Utevska, Olga; Yepiskoposyan, Levon; Marjanovic, Damir; Kushniarevich, Alena; Behar, Doron M; Gilissen, Christian; Vissers, Lisenka; Veltman, Joris A; Balanovska, Elena; Derenko, Miroslava; Malyarchuk, Boris; Metspalu, Andres; Fedorova, Sardana; Eriksson, Anders; Manica, Andrea; Mendez, Fernando L; Karafet, Tatiana M; Veeramah, Krishna R; Bradman, Neil; Hammer, Michael F; Osipova, Ludmila P; Balanovsky, Oleg; Khusnutdinova, Elza K; Johnsen, Knut; Remm, Maido; Thomas, Mark G; Tyler-Smith, Chris; Underhill, Peter A; Willerslev, Eske; Nielsen, Rasmus; Metspalu, Mait; Villems, Richard; Kivisild, Toomas

    2015-04-01

    It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males. © 2015 Karmin et al.; Published by Cold Spring Harbor Laboratory Press.

  4. Bottleneck management in the German and European electricity supply

    International Nuclear Information System (INIS)

    Koenig, Carsten

    2013-01-01

    This publication describes how bottlenecks in the German and European electricity supply pose a danger to the realization of the European internal market in electricity, the transition to electricity production from renewable resources and to the safeguarding of grid availability and security of supply. Bottlenecks at cross-border interconnectors between member states of the European Union are hampering cross-border trade in electricity, posing an impediment to EU-wide competition among electricity production and electricity trading companies. Grid bottlenecks at cross-border interconnectors isolate national markets from one another, with the result that it is not always possible in the European Union to have the most competitive power plant produce electricity. This amounts to a loss of welfare compared with what it would be in the case of an electricity supply without bottlenecks. Furthermore, bottlenecks make it impossible for green electricity that would be eligible for promotion for reasons of climate and environmental protection to be transmitted unimpeded from the most suitable site to the consumer regions. Thus the transmission of electricity produced from wind power in Northern Germany to the industrial centres in Southern Germany is impeded by bottlenecks along the north-south lines of the national transmission network. Today some of the German electricity supply networks already have to be operated near the limits of their capacity, especially during high wind episodes. This poses a growing danger to network availability and security of supply. Since the installation, expansion and conversion of electricity supply networks in Germany and other member states of the European Union is no longer progressing at the required speed, growing importance attaches to the management of bottlenecks. The goal of bottleneck management is to resolve conflicts over network use such as can occur in overload situations with as little discrimination and as little

  5. Deep Complementary Bottleneck Features for Visual Speech Recognition

    NARCIS (Netherlands)

    Petridis, Stavros; Pantic, Maja

    Deep bottleneck features (DBNFs) have been used successfully in the past for acoustic speech recognition from audio. However, research on extracting DBNFs for visual speech recognition is very limited. In this work, we present an approach to extract deep bottleneck visual features based on deep

  6. Population genomics of the inbred Scandinavian wolf

    OpenAIRE

    Hagenblad, Jenny; Olsson, Maria; Parker, Heidi G.; Ostrander, Elaine A.; Ellegren, Hans

    2009-01-01

    The Scandinavian wolf population represents one of the genetically most well characterized examples of a severely bottlenecked natural population (with only two founders), and of how the addition of new genetic material (one immigrant) can at least temporarily provide a “genetic rescue”. However, inbreeding depression has been observed in this population and in the absence of additional immigrants, its long-term viability is questioned. To study the effects of inbreeding and selection on geno...

  7. Bottlenecks of motion processing during a visual glance: the leaky flask model.

    Directory of Open Access Journals (Sweden)

    Haluk Öğmen

    Full Text Available Where do the bottlenecks for information and attention lie when our visual system processes incoming stimuli? The human visual system encodes the incoming stimulus and transfers its contents into three major memory systems with increasing time scales, viz., sensory (or iconic memory, visual short-term memory (VSTM, and long-term memory (LTM. It is commonly believed that the major bottleneck of information processing resides in VSTM. In contrast to this view, we show major bottlenecks for motion processing prior to VSTM. In the first experiment, we examined bottlenecks at the stimulus encoding stage through a partial-report technique by delivering the cue immediately at the end of the stimulus presentation. In the second experiment, we varied the cue delay to investigate sensory memory and VSTM. Performance decayed exponentially as a function of cue delay and we used the time-constant of the exponential-decay to demarcate sensory memory from VSTM. We then decomposed performance in terms of quality and quantity measures to analyze bottlenecks along these dimensions. In terms of the quality of information, two thirds to three quarters of the motion-processing bottleneck occurs in stimulus encoding rather than memory stages. In terms of the quantity of information, the motion-processing bottleneck is distributed, with the stimulus-encoding stage accounting for one third of the bottleneck. The bottleneck for the stimulus-encoding stage is dominated by the selection compared to the filtering function of attention. We also found that the filtering function of attention is operating mainly at the sensory memory stage in a specific manner, i.e., influencing only quantity and sparing quality. These results provide a novel and more complete understanding of information processing and storage bottlenecks for motion processing.

  8. Bottlenecks of motion processing during a visual glance: the leaky flask model.

    Science.gov (United States)

    Öğmen, Haluk; Ekiz, Onur; Huynh, Duong; Bedell, Harold E; Tripathy, Srimant P

    2013-01-01

    Where do the bottlenecks for information and attention lie when our visual system processes incoming stimuli? The human visual system encodes the incoming stimulus and transfers its contents into three major memory systems with increasing time scales, viz., sensory (or iconic) memory, visual short-term memory (VSTM), and long-term memory (LTM). It is commonly believed that the major bottleneck of information processing resides in VSTM. In contrast to this view, we show major bottlenecks for motion processing prior to VSTM. In the first experiment, we examined bottlenecks at the stimulus encoding stage through a partial-report technique by delivering the cue immediately at the end of the stimulus presentation. In the second experiment, we varied the cue delay to investigate sensory memory and VSTM. Performance decayed exponentially as a function of cue delay and we used the time-constant of the exponential-decay to demarcate sensory memory from VSTM. We then decomposed performance in terms of quality and quantity measures to analyze bottlenecks along these dimensions. In terms of the quality of information, two thirds to three quarters of the motion-processing bottleneck occurs in stimulus encoding rather than memory stages. In terms of the quantity of information, the motion-processing bottleneck is distributed, with the stimulus-encoding stage accounting for one third of the bottleneck. The bottleneck for the stimulus-encoding stage is dominated by the selection compared to the filtering function of attention. We also found that the filtering function of attention is operating mainly at the sensory memory stage in a specific manner, i.e., influencing only quantity and sparing quality. These results provide a novel and more complete understanding of information processing and storage bottlenecks for motion processing.

  9. Central as well as peripheral attentional bottlenecks in dual-task performance activate lateral prefrontal cortices

    Directory of Open Access Journals (Sweden)

    Andre J Szameitat

    2016-03-01

    Full Text Available Human information processing suffers from severe limitations in parallel processing. In particular, when required to respond to two stimuli in rapid succession, processing bottlenecks may appear at central and peripheral stages of task processing. Importantly, it has been suggested that executive functions are needed to resolve the interference arising at such bottlenecks. The aims of the present study were to test whether central attentional limitations (i.e., bottleneck at the decisional response selection stage as well as peripheral limitations (i.e., bottleneck at response initiation both demand executive functions located in the lateral prefrontal cortex. For this, we re-analysed two previous studies, in which a total of 33 participants performed a dual-task according to the paradigm of the psychological refractory period (PRP during fMRI. In one study (N=17, the PRP task consisted of two two-choice response tasks known to suffer from a central bottleneck (CB group. In the other study (N=16, the PRP task consisted of two simple-response tasks known to suffer from a peripheral bottleneck (PB group. Both groups showed considerable dual-task costs in form of slowing of the second response in the dual-task (PRP effect. Imaging results are based on the subtraction of both single-tasks from the dual-task within each group. In the CB group, the bilateral middle frontal gyri and inferior frontal gyri were activated. Higher activation in these areas was associated with lower dual-task costs. In the PB group, the right middle frontal and inferior frontal gyrus were activated. Here, higher activation was associated with higher dual-task costs. In conclusion we suggest that central and peripheral bottlenecks both demand executive functions located in lateral prefrontal cortices. Differences between the CB and PB groups with respect to the exact prefrontal areas activated and the correlational patterns suggest that the executive functions resolving

  10. Advances and bottlenecks in microbial hydrogen production.

    Science.gov (United States)

    Stephen, Alan J; Archer, Sophie A; Orozco, Rafael L; Macaskie, Lynne E

    2017-09-01

    Biological production of hydrogen is poised to become a significant player in the future energy mix. This review highlights recent advances and bottlenecks in various approaches to biohydrogen processes, often in concert with management of organic wastes or waste CO 2 . Some key bottlenecks are highlighted in terms of the overall energy balance of the process and highlighting the need for economic and environmental life cycle analyses with regard also to socio-economic and geographical issues. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  11. Hybrid Bridge-Based Memetic Algorithms for Finding Bottlenecks in Complex Networks

    DEFF Research Database (Denmark)

    Chalupa, David; Hawick, Ken; Walker, James A

    2018-01-01

    We propose a memetic approach to find bottlenecks in complex networks based on searching for a graph partitioning with minimum conductance. Finding the optimum of this problem, also known in statistical mechanics as the Cheeger constant, is one of the most interesting NP-hard network optimisation...... as results for samples of social networks and protein–protein interaction networks. These indicate that both well-informed initial population generation and the use of a crossover seem beneficial in solving the problem in large-scale....

  12. Bottlenecks to coral recovery in the Seychelles

    Science.gov (United States)

    Chong-Seng, K. M.; Graham, N. A. J.; Pratchett, M. S.

    2014-06-01

    Processes that affect recovery of coral assemblages require investigation because coral reefs are experiencing a diverse array of more frequent disturbances. Potential bottlenecks to coral recovery include limited larval supply, low rates of settlement, and high mortality of new recruits or juvenile corals. We investigated spatial variation in local abundance of scleractinian corals in the Seychelles at three distinct life history stages (recruits, juveniles, and adults) on reefs with differing benthic conditions. Following widespread coral loss due to the 1998 bleaching event, some reefs are recovering (i.e., relatively high scleractinian coral cover: `coral-dominated'), some reefs have low cover of living macrobenthos and unconsolidated rubble substrates (`rubble-dominated'), and some reefs have high cover of macroalgae (`macroalgal-dominated'). Rates of coral recruitment to artificial settlement tiles were similar across all reef conditions, suggesting that larval supply does not explain differential coral recovery across the three reef types. However, acroporid recruits were absent on macroalgal-dominated reefs (0.0 ± 0.0 recruits tile-1) in comparison to coral-dominated reefs (5.2 ± 1.6 recruits tile-1). Juvenile coral colony density was significantly lower on macroalgal-dominated reefs (2.4 ± 1.1 colonies m-2), compared to coral-dominated reefs (16.8 ± 2.4 m-2) and rubble-dominated reefs (33.1 ± 7.3 m-2), suggesting that macroalgal-dominated reefs have either a bottleneck to successful settlement on the natural substrates or a high post-settlement mortality bottleneck. Rubble-dominated reefs had very low cover of adult corals (10.0 ± 1.7 %) compared to coral-dominated reefs (33.4 ± 3.6 %) despite no statistical difference in their juvenile coral densities. A bottleneck caused by low juvenile colony survivorship on unconsolidated rubble-dominated reefs is possible, or alternatively, recruitment to rubble-dominated reefs has only recently begun. This

  13. Flagella-Driven Flows Circumvent Diffusive Bottlenecks that Inhibit Metabolite Exchange

    Science.gov (United States)

    Short, Martin; Solari, Cristian; Ganguly, Sujoy; Kessler, John; Goldstein, Raymond; Powers, Thomas

    2006-03-01

    The evolution of single cells to large and multicellular organisms requires matching the organisms' needs to the rate of exchange of metabolites with the environment. This logistic problem can be a severe constraint on development. For organisms with a body plan that approximates a spherical shell, such as colonies of the volvocine green algae, the required current of metabolites grows quadratically with colony radius whereas the rate at which diffusion can exchange metabolites grows only linearly with radius. Hence, there is a bottleneck radius beyond which the diffusive current cannot keep up with metabolic demands. Using Volvox carteri as a model organism, we examine experimentally and theoretically the role that advection of fluid by surface-mounted flagella plays in enhancing nutrient uptake. We show that fluid flow driven by the coordinated beating of flagella produces a convective boundary layer in the concentration of a diffusing solute which in turn renders the metabolite exchange rate quadratic in the colony radius. This enhanced transport circumvents the diffusive bottleneck, allowing increase in size and thus evolutionary transitions to multicellularity in the Volvocales.

  14. The Case for a Gaian Bottleneck: The Biology of Habitability.

    Science.gov (United States)

    Chopra, Aditya; Lineweaver, Charles H

    2016-01-01

    The prerequisites and ingredients for life seem to be abundantly available in the Universe. However, the Universe does not seem to be teeming with life. The most common explanation for this is a low probability for the emergence of life (an emergence bottleneck), notionally due to the intricacies of the molecular recipe. Here, we present an alternative Gaian bottleneck explanation: If life emerges on a planet, it only rarely evolves quickly enough to regulate greenhouse gases and albedo, thereby maintaining surface temperatures compatible with liquid water and habitability. Such a Gaian bottleneck suggests that (i) extinction is the cosmic default for most life that has ever emerged on the surfaces of wet rocky planets in the Universe and (ii) rocky planets need to be inhabited to remain habitable. In the Gaian bottleneck model, the maintenance of planetary habitability is a property more associated with an unusually rapid evolution of biological regulation of surface volatiles than with the luminosity and distance to the host star.

  15. Managing Innovation Probabilities: Core-driven vs. Bottleneck-removing Innovations

    OpenAIRE

    Tsutomu Harada

    2015-01-01

    This paper provides a simplified framework of focusing devices that generate different patterns of innovation, i.e., core-driven and bottleneck-removing innovations, and discusses the managerial implications. We show that core-driven innovation should be undertaken when technology components are independent (independent technology system), while bottleneck-removing innovation should be pursued when they are interdependent (interdependent technology system). Different types of focusing device ...

  16. Narrower bottlenecks could be more efficient for concentrating choanoflagellates

    Science.gov (United States)

    Sparacino, J.; Miño, G.; Koehl, M. A. R.; King, N.; Stocker, R.; Banchio, A. J.; Marconi, V. I.

    2015-11-01

    In evolutionary biology choanoflagellates are broadly investigated as the closest living relatives of the animal ancestors. Under diverse environmental cues, choanoflagellate Salpingoeca rosetta can differentiate in two types of solitary swimming cells: slow and fast microswimmers. Here we present a first phenomenological 2D-model for the choanoflagellates dynamics confined into a flat device divided by a wall of asymmetric microconstrictions. The model allow us to optimize the geometry of the microchannels for directing and concentrating cell populations under strict control. We solve our set of dynamical equations using Langevin dynamics. Experimental parameters for the motility of the slow and fast cells were measured and used for our numerical estimations of the directed transport efficiency, otherwise we have no adjustable parameters. We find remarkable differences in the rectification results for slow and fast choanoflagellates, which give us a strategy to develop a suitable microfluidic sorting device. For a given population velocity, narrower bottlenecks, of similar size to the cell dimension, show to be more efficient as concentrator of populations. Experiments and simulations are in good agreement.

  17. Damage to white matter bottlenecks contributes to language impairments after left hemispheric stroke

    Directory of Open Access Journals (Sweden)

    Joseph C. Griffis

    2017-01-01

    Full Text Available Damage to the white matter underlying the left posterior temporal lobe leads to deficits in multiple language functions. The posterior temporal white matter may correspond to a bottleneck where both dorsal and ventral language pathways are vulnerable to simultaneous damage. Damage to a second putative white matter bottleneck in the left deep prefrontal white matter involving projections associated with ventral language pathways and thalamo-cortical projections has recently been proposed as a source of semantic deficits after stroke. Here, we first used white matter atlases to identify the previously described white matter bottlenecks in the posterior temporal and deep prefrontal white matter. We then assessed the effects of damage to each region on measures of verbal fluency, picture naming, and auditory semantic decision-making in 43 chronic left hemispheric stroke patients. Damage to the posterior temporal bottleneck predicted deficits on all tasks, while damage to the anterior bottleneck only significantly predicted deficits in verbal fluency. Importantly, the effects of damage to the bottleneck regions were not attributable to lesion volume, lesion loads on the tracts traversing the bottlenecks, or damage to nearby cortical language areas. Multivariate lesion-symptom mapping revealed additional lesion predictors of deficits. Post-hoc fiber tracking of the peak white matter lesion predictors using a publicly available tractography atlas revealed evidence consistent with the results of the bottleneck analyses. Together, our results provide support for the proposal that spatially specific white matter damage affecting bottleneck regions, particularly in the posterior temporal lobe, contributes to chronic language deficits after left hemispheric stroke. This may reflect the simultaneous disruption of signaling in dorsal and ventral language processing streams.

  18. Integrated Variable Speed Limits Control and Ramp Metering for Bottleneck Regions on Freeway

    Directory of Open Access Journals (Sweden)

    Ming-hui Ma

    2015-01-01

    Full Text Available To enhance the efficiency of the existing freeway system and therefore to mitigate traffic congestion and related problems on the freeway mainline lane-drop bottleneck region, the advanced strategy for bottleneck control is essential. This paper proposes a method that integrates variable speed limits and ramp metering for freeway bottleneck region control to relieve the chaos in bottleneck region. To this end, based on the analyses of spatial-temporal patterns of traffic flow, a macroscopic traffic flow model is extended to describe the traffic flow operating characteristic by considering the impacts of variable speed limits in mainstream bottleneck region. In addition, to achieve the goal of balancing the priority of the vehicles on mainline and on-ramp, increasing capacity, and reducing travel delay on bottleneck region, an improved control model, as well as an advanced control strategy that integrates variable speed limits and ramp metering, is developed. The proposed method is tested in simulation for a real freeway infrastructure feed and calibrates real traffic variables. The results demonstrate that the proposed method can substantially improve the traffic flow efficiency of mainline and on-ramp and enhance the quality of traffic flow at the investigated freeway mainline bottleneck.

  19. Anticipation Behavior Upstream of a Bottleneck

    NARCIS (Netherlands)

    Duives, D.C.; Daamen, W.; Hoogendoorn, S.P.

    2014-01-01

    Whether pedestrian movements do or do not follow similar patterns as vehicular traffic while experiencing congestion is not entirely understood. Using data gathered during bottleneck experiments under laboratory conditions, the phenomenon of anticipation before entering congestion is studied. This

  20. Density Estimation in Several Populations With Uncertain Population Membership

    KAUST Repository

    Ma, Yanyuan

    2011-09-01

    We devise methods to estimate probability density functions of several populations using observations with uncertain population membership, meaning from which population an observation comes is unknown. The probability of an observation being sampled from any given population can be calculated. We develop general estimation procedures and bandwidth selection methods for our setting. We establish large-sample properties and study finite-sample performance using simulation studies. We illustrate our methods with data from a nutrition study.

  1. Bottlenecks reduction using superconductors in high voltage transmission lines

    Directory of Open Access Journals (Sweden)

    Daloub Labib

    2016-01-01

    Full Text Available Energy flow bottlenecks in high voltage transmission lines known as congestions are one of the challenges facing power utilities in fast developing countries. Bottlenecks occur in selected power lines when transmission systems are operated at or beyond their transfer limits. In these cases, congestions result in preventing new power supply contracts, infeasibility in existing contracts, price spike and market power abuse. The “Superconductor Technology” in electric power transmission cables has been used as a solution to solve the problem of bottlenecks in energy transmission at high voltage underground cables and overhead lines. The increase in demand on power generation and transmission happening due to fast development and linked to the intensive usage of transmission network in certain points, which in turn, lead to often frequent congestion in getting the required power across to where it is needed. In this paper, a bottleneck in high voltage double overhead transmission line with Aluminum Conductor Steel Reinforced was modeled using conductor parameters and replaced by Gap-Type Superconductor to assess the benefit of upgrading to higher temperature superconductor and obtain higher current carrying capacity. This proved to reduce the high loading of traditional aluminum conductors and allow more power transfer over the line using superconductor within the same existing right-of-way, steel towers, insulators and fittings, thus reducing the upgrade cost of building new lines.

  2. Bottlenecks and Waiting Points in Nucleosynthesis in X-ray bursts and Novae

    Science.gov (United States)

    Smith, Michael S.; Sunayama, Tomomi; Hix, W. Raphael; Lingerfelt, Eric J.; Nesaraja, Caroline D.

    2010-08-01

    To better understand the energy generation and element synthesis occurring in novae and X-ray bursts, we give quantitative definitions to the concepts of ``bottlenecks'' and ``waiting points'' in the thermonuclear reaction flow. We use these criteria to search for bottlenecks and waiting points in post-processing element synthesis explosion simulations. We have incorporated these into the Computational Infrastructure for Nuclear Astrophysics, a suite of nuclear astrophysics codes available online at nucastrodata.org, so that anyone may perform custom searches for bottlenecks and waiting points.

  3. On the Inefficiency of Equilibria in Linear Bottleneck Congestion Games

    Science.gov (United States)

    de Keijzer, Bart; Schäfer, Guido; Telelis, Orestis A.

    We study the inefficiency of equilibrium outcomes in bottleneck congestion games. These games model situations in which strategic players compete for a limited number of facilities. Each player allocates his weight to a (feasible) subset of the facilities with the goal to minimize the maximum (weight-dependent) latency that he experiences on any of these facilities. We derive upper and (asymptotically) matching lower bounds on the (strong) price of anarchy of linear bottleneck congestion games for a natural load balancing social cost objective (i.e., minimize the maximum latency of a facility). We restrict our studies to linear latency functions. Linear bottleneck congestion games still constitute a rich class of games and generalize, for example, load balancing games with identical or uniformly related machines with or without restricted assignments.

  4. Cloud Technology May Widen Genomic Bottleneck - TCGA

    Science.gov (United States)

    Computational biologist Dr. Ilya Shmulevich suggests that renting cloud computing power might widen the bottleneck for analyzing genomic data. Learn more about his experience with the Cloud in this TCGA in Action Case Study.

  5. A methodology for determining and controlling the buffers before floating bottlenecks in heavy machinery production

    Directory of Open Access Journals (Sweden)

    R. Lenort

    2013-07-01

    Full Text Available Heavy machinery industry is characterized by a number of specific features that cause significant variations in the processing time of products in the individual workplaces and frequent occurrence of floating bottlenecks, which change their positions. Depending on the product range being processed, a given workplace is the bottleneck only for some period of time. When the bottleneck moves to another workplace, it leads to unnecessary loss of capacity of the floating bottleneck. To maximize the utilization, it is necessary to protect those bottlenecks by creating special buffers. The objective of this article is to design a methodology used for the determination and control of buffers that are going to protect the floating bottlenecks from operating capacity losses caused by transfer of the constrain to another workplace. These buffers are referred to as „power buffers“. The designed methodology has been verified in the process of forged pieces machining.

  6. About the Role of the Bottleneck/Cork Interface on Oxygen Transfer.

    Science.gov (United States)

    Lagorce-Tachon, Aurélie; Karbowiak, Thomas; Paulin, Christian; Simon, Jean-Marc; Gougeon, Régis D; Bellat, Jean-Pierre

    2016-09-07

    The transfer of oxygen through a corked bottleneck was investigated using a manometric technique. First, the effect of cork compression on oxygen transfer was evaluated without considering the glass/cork interface. No significant effect of cork compression (at 23% strain, corresponding to the compression level of cork in a bottleneck for still wines) was noticeable on the effective diffusion coefficient of oxygen. The mean value of the effective diffusion coefficient is equal to 10(-8) m(2) s(-1), with a statistical distribution ranging from 10(-10) to 10(-7) m(2) s(-1), which is of the same order of magnitude as for the non-compressed cork. Then, oxygen transfer through cork compressed in a glass bottleneck was determined to assess the effect of the glass/cork interface. In the particular case of a gradient-imposed diffusion of oxygen through our model corked bottleneck system (dry cork without surface treatment; 200 and ∼0 hPa of oxygen on both sides of the sample), the mean effective diffusion coefficient is of 5 × 10(-7) m(2) s(-1), thus revealing the possible importance of the role of the glass/stopper interface in the oxygen transfer.

  7. Genetic variability and bottleneck analyses of Kanni adu goat population using microsatellite markers [Indian Veterinary Journal, 2015, 92(3): 24-27

    International Nuclear Information System (INIS)

    Thiruvenkadan, R.; Jeyakumar, M.; Saravana, R.; Periasamy, K.

    2016-01-01

    Full text: The genetic characterization and bottleneck analysis in Kodi Adu goat was done using 25 FAO recommended microsatellite markers. The mean observed number of alleles and polymorphism information content (PIC) were estimated to be 11.52±-0.95 and 0.817±0.023 respectively. The mean observed and expected equilibrium hyterozygosities were 0.660±0.045 and 0.846±0.018 respectively. The mean expected equilibrium gene diversity across 21 microsatellite loci under TAM, SMM and TPM were 0.793±0.028, 0.854±0.023 and 0.827±0.026 respectively. All the three statistical tests revealed significant deviation of Kodi Adu goats from mutation-drift equilibrium under the IAM and TPM model. The mode shift analysis supported the results under SMM indicating the absence of genetic bottleneck in the recent past in Kodi Adu goats. (author)

  8. Fixation times in differentiation and evolution in the presence of bottlenecks, deserts, and oases.

    Science.gov (United States)

    Chou, Tom; Wang, Yu

    2015-05-07

    Cellular differentiation and evolution are stochastic processes that can involve multiple types (or states) of particles moving on a complex, high-dimensional state-space or "fitness" landscape. Cells of each specific type can thus be quantified by their population at a corresponding node within a network of states. Their dynamics across the state-space network involve genotypic or phenotypic transitions that can occur upon cell division, such as during symmetric or asymmetric cell differentiation, or upon spontaneous mutation. Here, we use a general multi-type branching processes to study first passage time statistics for a single cell to appear in a specific state. Our approach readily allows for nonexponentially distributed waiting times between transitions, reflecting, e.g., the cell cycle. For simplicity, we restrict most of our detailed analysis to exponentially distributed waiting times (Poisson processes). We present results for a sequential evolutionary process in which L successive transitions propel a population from a "wild-type" state to a given "terminally differentiated," "resistant," or "cancerous" state. Analytic and numeric results are also found for first passage times across an evolutionary chain containing a node with increased death or proliferation rate, representing a desert/bottleneck or an oasis. Processes involving cell proliferation are shown to be "nonlinear" (even though mean-field equations for the expected particle numbers are linear) resulting in first passage time statistics that depend on the position of the bottleneck or oasis. Our results highlight the sensitivity of stochastic measures to cell division fate and quantify the limitations of using certain approximations (such as the fixed-population and mean-field assumptions) in evaluating fixation times. Published by Elsevier Ltd.

  9. Four disruptive strategies for removing drug discovery bottlenecks.

    Science.gov (United States)

    Ekins, Sean; Waller, Chris L; Bradley, Mary P; Clark, Alex M; Williams, Antony J

    2013-03-01

    Drug discovery is shifting focus from industry to outside partners and, in the process, creating new bottlenecks. Technologies like high throughput screening (HTS) have moved to a larger number of academic and institutional laboratories in the USA, with little coordination or consideration of the outputs and creating a translational gap. Although there have been collaborative public-private partnerships in Europe to share pharmaceutical data, the USA has seemingly lagged behind and this may hold it back. Sharing precompetitive data and models may accelerate discovery across the board, while finding the best collaborators, mining social media and mobile approaches to open drug discovery should be evaluated in our efforts to remove drug discovery bottlenecks. We describe four strategies to rectify the current unsustainable situation. Copyright © 2012 Elsevier Ltd. All rights reserved.

  10. Low and Expensive Bandwidth Remains Key Bottleneck for ...

    African Journals Online (AJOL)

    PROF. O. E. OSUAGWU

    2013-06-01

    Jun 1, 2013 ... satellites in the orbit, aggressive deployment of broadband wireless technology, ... Key Words: ISPs, Quality of Service, Internet Diffusion, energy supply, bottlenecks, ..... then the transmission time for an IP packet of size LL3 ...

  11. Recolonization after habitat restoration leads to decreased genetic variation in populations of a terrestrial orchid.

    Science.gov (United States)

    Vandepitte, K; Gristina, A S; De Hert, K; Meekers, T; Roldán-Ruiz, I; Honnay, O

    2012-09-01

    Colonization is crucial to habitat restoration projects that rely on the spontaneous regeneration of the original vegetation. However, as a previously declining plant species spreads again, the likelihood of founder effects increases through recurrent population founding and associated serial bottlenecks. We related Amplified Fragment Length Polymorphism markers genetic variation and fitness to colonization history for all extant populations of the outcrossing terrestrial orchid Dactylorhiza incarnata in an isolated coastal dune complex. Around 1970, D. incarnata suffered a severe bottleneck yet ultimately persisted and gradually spread throughout the spatially segregated dune slacks, aided by the restoration of an open vegetation. Genetic assignment demonstrated dispersal to vacant sites from few nearby extant populations and very limited inflow from outside the spatially isolated reserve. Results further indicated that recurrent founding from few local sources resulted in the loss of genetic diversity and promoted genetic divergence (F(ST) = 0.35) among populations, but did not influence population fitness. The few source populations initially available and the limited inflow of genes from outside the study reserve, as a consequence of habitat degradation and spatial isolation, may have magnified the genetic effects of recurrent population founding. © 2012 Blackwell Publishing Ltd.

  12. How Strategic Is the Central Bottleneck: Can It Be Overcome by Trying Harder?

    Science.gov (United States)

    Ruthruff, Eric; Johnston, James C.; Remington, Roger W.

    2009-01-01

    Recent dual-task studies suggest that a bottleneck prevents central mental operations from working on more than one task at a time, especially at relatively low practice levels. It remains highly controversial, however, whether this bottleneck is structural (inherent to human cognitive architecture) or merely a strategic choice. If the strategic…

  13. The recent history and population structure of five Mandarina snail species from subtropical Ogasawara (Bonin Islands, Japan).

    Science.gov (United States)

    Davison, Angus; Chiba, Satoshi

    2006-09-01

    The effect of Pleistocene climate change on the organisms of tropical and subtropical regions is rather poorly understood. We therefore studied the land snail genus Mandarina (Bradybaenidae) of oceanic Ogasawara (Bonin Islands, Japan), with the aim of using population genetic data to understand their recent history. Our analysis of a mitochondrial 16S ribosomal RNA region from more than 600 snails in five ground-living species suggests that populations on the small islands of Mukoujima, Anejima, Imotojima and Meijima, as well as on the low-lying southern and central parts of Hahajima, have probably undergone recent bottlenecks followed by subsequent expansions. Except between the main island of Hahajima and Mukouijima, there is almost no evidence for gene flow among islands even though the islands were connected repeatedly by land bridges through the Pleistocene. Within islands the population structure is severe, suggestive of a long-term, low level of gene flow (F(ST) is frequently greater than 0.5 among geographically close populations). Finally, there is a marked genetic patchiness, meaning that genetically close populations are sometimes separated by genetically distant populations. These patterns could be a consequence of expansion from bottlenecks, low active dispersal and founder effects caused by rare long-distance migrants. Unfortunately, the exact nature of the refugia and bottlenecks remains unknown because the palaeoclimate of this region is poorly understood. Dating the population size changes is also challenging because the molecular clock is uncertain. We suggest, however, that arid conditions or deforestation induced by decreased atmospheric CO(2) may have been the main factor in determining population size.

  14. Understanding of empty container movement: A study on a bottleneck at an off-dock depot

    Science.gov (United States)

    Zain, Rosmaizura Mohd; Rahman, Mohd Nizam Ab; Nopiah, Zulkifli Mohd; Saibani, Nizaroyani

    2014-09-01

    Port not only function as connections between marine and land transportation but also as core business areas. In a port terminal, available space is limited, but the influx of container is growing. The off-dock depot is one of the key supply chain players that hold empty containers in the inventory. Therefore, this paper aims to identify the main factors of bottlenecks or congestion that hinder the rapid movement of empty containers from the off-dock depot to the customers. Thirty interviews were conducted with individuals who are key players in the container supply chain. The data were analyzed using Atlas.ti software and the analytic hierarchy process to rank the priority factors of bottlenecks. Findings show that several pertinent factors act as barriers to the key players in the container movement in the day-to-day operations. In future studies, strategies to overcome fragmentation in the container supply chain and logistics must be determined.

  15. Are all intertidal wetlands naturally created equal? Bottlenecks, thresholds and knowledge gaps to mangrove and saltmarsh ecosystems

    Science.gov (United States)

    Friess, Daniel A.; Krauss, Ken W.; Horstman, Erik M.; Balke, Thorsten; Bouma, Tjeerd J.; Galli, Demis; Webb, Edward L.

    2011-01-01

    Intertidal wetlands such as saltmarshes and mangroves provide numerous important ecological functions, though they are in rapid and global decline. To better conserve and restore these wetland ecosystems, we need an understanding of the fundamental natural bottlenecks and thresholds to their establishment and long-term ecological maintenance. Despite inhabiting similar intertidal positions, the biological traits of these systems differ markedly in structure, phenology, life history, phylogeny and dispersal, suggesting large differences in biophysical interactions. By providing the first systematic comparison between saltmarshes and mangroves, we unravel how the interplay between species-specific life-history traits, biophysical interactions and biogeomorphological feedback processes determine where, when and what wetland can establish, the thresholds to long-term ecosystem stability, and constraints to genetic connectivity between intertidal wetland populations at the landscape level. To understand these process interactions, research into the constraints to wetland development, and biological adaptations to overcome these critical bottlenecks and thresholds requires a truly interdisciplinary approach.

  16. Identification of environmental bottleneck using Bayesian Networks: a case study of an Indian pig iron manufacturing organization

    Directory of Open Access Journals (Sweden)

    Sen Parag

    2015-01-01

    Full Text Available Environmentally conscious manufacturing has become a global attention for the iron and steel manufacturers to prevent global warming and climate change while making money. Iron and steel sector is considered as one of the most polluting sectors in the world. It is also one of the most energy intensive industries. During pig iron manufacturing, there is a number of steps that affect the environment emitting different pollutants. While some step(s may be considered critical to damage the environment among all the steps, some pollutant(s may be considered critical to affect the environment among all the pollutants. This paper proposes environmental bottleneck to consider critical step and critical pollutant simultaneously. Unless environmental bottleneck is improved, environmental performance of the entire manufacturing process may not improve significantly even if other processes (i.e. other than environmental bottleneck are taken care of. Thus, environmental bottleneck must be taken care of properly by the manufacturing organization to enable environmentally conscious manufacturing. Hence, a method should be developed to identify environmental bottleneck. Current research work uses Bayesian Networks (BN to identify environmental bottleneck. The contribution of the paper is to identify the environmental bottleneck for an Indian pig iron manufacturing organization. Results suggest that carbon monoxide (CO emission from the blast furnace is the environmental bottleneck for the current pig iron manufacturing organization. Hence, proper precautions should be considered to control the CO emission from the blast furnace.

  17. Mitigating SDN controller performance bottlenecks

    DEFF Research Database (Denmark)

    Caba, Cosmin Marius; Soler, José

    2015-01-01

    The centralization of the control plane decision logic in Software Defined Networking (SDN) has raised concerns regarding the performance of the SDN Controller (SDNC) when the network scales up. A number of solutions have been proposed in the literature to address these concerns. This paper...... proposes a new approach for addressing the performance bottlenecks that arise from limited computational resources at the SDNC. The proposed approach is based on optimally configuring the operating parameters of the components residing inside the SDNC (network control functions such as monitoring, routing...

  18. Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in Salmonella typhimurium

    Energy Technology Data Exchange (ETDEWEB)

    McDermott, Jason E.; Taylor, Ronald C.; Yoon, Hyunjin; Heffron, Fred

    2009-02-01

    Recent advances in experimental methods have provided sufficient data to consider systems as large networks of interconnected components. High-throughput determination of protein-protein interaction networks has led to the observation that topological bottlenecks, that is proteins defined by high centrality in the network, are enriched in proteins with systems-level phenotypes such as essentiality. Global transcriptional profiling by microarray analysis has been used extensively to characterize systems, for example, cellular response to environmental conditions and genetic mutations. These transcriptomic datasets have been used to infer regulatory and functional relationship networks based on co-regulation. We use the context likelihood of relatedness (CLR) method to infer networks from two datasets gathered from the pathogen Salmonella typhimurium; one under a range of environmental culture conditions and the other from deletions of 15 regulators found to be essential in virulence. Bottleneck nodes were identified from these inferred networks and we show that these nodes are significantly more likely to be essential for virulence than their non-bottleneck counterparts. A network generated using Pearson correlation did not display this behavior. Overall this study demonstrates that topology of networks inferred from global transcriptional profiles provides information about the systems-level roles of bottleneck genes. Analysis of the differences between the two CLR-derived networks suggests that the bottleneck nodes are either mediators of transitions between system states or sentinels that reflect the dynamics of these transitions.

  19. Congestion in a city with a central bottleneck

    DEFF Research Database (Denmark)

    Fosgerau, Mogens; Palma, André de

    2010-01-01

    We consider dynamic congestion in an urban setting where trip origins are spatially distributed. All travelers must pass through a downtown bottleneck in order to reach their destination in the CBD. Each traveler chooses departure time to maximize general concave scheduling utility. At equilibriu...

  20. Congestion in a city with a central bottleneck

    DEFF Research Database (Denmark)

    Fosgerau, Mogens; Palma, André de

    2012-01-01

    We consider dynamic congestion in an urban setting where trip origins are spatially distributed. All travelers must pass through a downtown bottleneck in order to reach their destination in the CBD. Each traveler chooses departure time to maximize general concave scheduling utility. We find that,...

  1. Budget process bottlenecks for immunization financing in the Democratic Republic of the Congo (DRC).

    Science.gov (United States)

    Le Gargasson, Jean-Bernard; Mibulumukini, Benoît; Gessner, Bradford D; Colombini, Anaïs

    2014-02-19

    In Democratic Republic of the Congo (DRC), the availability of domestic resources for the immunization program is limited and relies mostly on external donor support. DRC has introduced a series of reforms to move the country toward performance-based management and program budgets. The objectives of the study were to: (i) describe the budget process norm, (ii) analyze the budget process in practice and associated bottlenecks at each of its phases, and (iii) collect suggestions made by the actors involved to improve the situation. Quantitative and qualitative data were collected through: a review of published and gray literature, and individual interviews. Bottlenecks in the budget process and disbursement of funds for immunization are one of the causes of limited domestic resources for the program. Critical bottlenecks include: excessive use of off-budget procedures; limited human resources and capacity; lack of motivation; interference from ministries with the standard budget process; dependency toward the development partner's disbursements schedule; and lack of budget implementation tracking. Results show that the health sector's mobilization rate was 59% in 2011. For the credit line specific to immunization program activities, the mobilization rate for the national Expanded Program for Immunization (EPI) was 26% in 2011 and 43% for vaccines (2010). The main bottleneck for the EPI budget line (2011) and vaccine budget line (2011) occurs at the authorization phase. Budget process bottlenecks identified in the analysis lead to a low mobilization rate for the immunization program. The bottlenecks identified show that a poor flow of funds causes an insufficient percentage of already allocated resources to reach various health system levels. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Mutational meltdown in laboratory yeast populations

    NARCIS (Netherlands)

    Zeyl, C.; Mizesko, M.; Visser, de J.A.G.M.

    2001-01-01

    In small or repeatedly bottlenecked populations, mutations are expected to accumulate by genetic drift, causing fitness declines. In mutational meltdown models, such fitness declines further reduce population size, thus accelerating additional mutation accumulation and leading to extinction. Because

  3. Managing bottlenecks in manual automobile assembly systems using discrete event simulation

    Directory of Open Access Journals (Sweden)

    Dewa, M.

    2013-08-01

    Full Text Available Batch model lines are quite handy when the demand for each product is moderate. However, they are characterised by high work-in-progress inventories, lost production time when changing over models, and reduced flexibility when it comes to altering production rates as product demand changes. On the other hand, mixed model lines can offer reduced work-in-progress inventory and increased flexibility. The object of this paper is to illustrate that a manual automobile assembling system can be optimised through managing bottlenecks by ensuring high workstation utilisation, reducing queue lengths before stations and reducing station downtime. A case study from the automobile industry is used for data collection. A model is developed through the use of simulation software. The model is then verified and validated before a detailed bottleneck analysis is conducted. An operational strategy is then proposed for optimal bottleneck management. Although the paper focuses on improving automobile assembly systems in batch mode, the methodology can also be applied in single model manual and automated production lines.

  4. Landscape genetics reveals inbreeding and genetic bottlenecks in the extremely rare short-globose cacti Mammillaria pectinifera (Cactaceae as a result of habitat fragmentation

    Directory of Open Access Journals (Sweden)

    Reyna Maya-García

    2017-02-01

    Full Text Available Mammillaria pectinifera is an endemic, short-globose cactus species, included in the IUCN list as a threatened species with only 18 remaining populations in the Tehuacán-Cuicatlán Valley in central Mexico. We evaluated the population genetic diversity and structure, connectivity, recent bottlenecks and population size, using nuclear microsatellites. M. pectinifera showed high genetic diversity but some evidence of heterozygote deficiency (FIS, recent bottlenecks in some populations and reductions in population size. Also, we found low population genetic differentiation and high values of connectivity for M. pectinifera, as the result of historical events of gene flow through pollen and seed dispersal. M. pectinifera occurs in sites with some degree of disturbance leading to the isolation of its populations and decreasing the levels of gene flow among them. Excessive deforestation also changes the original vegetation damaging the natural habitats. This species will become extinct if it is not properly preserved. Furthermore, this species has some ecological features that make them more vulnerable to disturbance such as a very low growth rates and long life cycles. We suggest in situ conservation to prevent the decrease of population sizes and loss of genetic diversity in the natural protected areas such as the Tehuacán-Cuicatlán Biosphere Reserve. In addition, a long-term ex situ conservation program is need to construct seed banks, and optimize seed germination and plant establishment protocols that restore disturbed habitats. Furthermore, creating a supply of living plants for trade is critical to avoid further extraction of plants from nature.

  5. Genetic differentiation in geographically close populations of the water rat Nectomys squamipes (Rodentia, Sigmodontinae from the Brazilian Atlantic Forest

    Directory of Open Access Journals (Sweden)

    Maroja L.S.

    2003-01-01

    Full Text Available We examined the genetic structure and the effects of a bottleneck in populations of the water rat Nectomys squamipes, a primary host of Schistosoma mansoni. Eight microsatellite loci were studied in 7 populations from the Sumidouro region of the Brazilian state of Rio de Janeiro. Our data, covering a four-year period during which a bottleneck occurred, revealed substantial variation (6-31 alleles per locus and high levels of both observed (0.718-0.789 and expected (0.748-0.832 heterozygosity. Most populations were in Hardy-Weinberg equilibrium without linkage disequilibrium between loci. Overall average genetic differentiation between populations (estimated with the F ST (q and R ST (r analogues was 0.037 for q and 0.060 for r. There was significant allelic and genotypic differentiation between populations, especially in pairwise comparisons that included the most geographically isolated population. Direct migration estimates showed a low rate of migration, indicating that infected N. squamipes populations had a limited ability to spread S. mansoni. When the pre- and post-bottleneck populations were compared there was no detectable reduction in heterozygosity or allele number, although a significant excess of heterozygosity was detected in the post-bottleneck population.

  6. Successful biological invasion despite a severe genetic load.

    Directory of Open Access Journals (Sweden)

    Amro Zayed

    2007-09-01

    Full Text Available Understanding the factors that influence the success of ecologically and economically damaging biological invasions is of prime importance. Recent studies have shown that invasive populations typically exhibit minimal, if any, reductions in genetic diversity, suggesting that large founding populations and/or multiple introductions are required for the success of biological invasions, consistent with predictions of the propagule pressure hypothesis. Through population genetic analysis of neutral microsatellite markers and a gene experiencing balancing selection, we demonstrate that the solitary bee Lasioglossum leucozonium experienced a single and severe bottleneck during its introduction from Europe. Paradoxically, the success of L. leucozonium in its introduced range occurred despite the severe genetic load caused by single-locus complementary sex-determination that still turns 30% of female-destined eggs into sterile diploid males, thereby substantially limiting the growth potential of the introduced population. Using stochastic modeling, we show that L. leucozonium invaded North America through the introduction of a very small number of propagules, most likely a singly-mated female. Our results suggest that chance events and ecological traits of invaders are more important than propagule pressure in determining invasion success, and that the vigilance required to prevent invasions may be considerably greater than has been previously considered.

  7. A decomposition heuristics based on multi-bottleneck machines for large-scale job shop scheduling problems

    Directory of Open Access Journals (Sweden)

    Yingni Zhai

    2014-10-01

    Full Text Available Purpose: A decomposition heuristics based on multi-bottleneck machines for large-scale job shop scheduling problems (JSP is proposed.Design/methodology/approach: In the algorithm, a number of sub-problems are constructed by iteratively decomposing the large-scale JSP according to the process route of each job. And then the solution of the large-scale JSP can be obtained by iteratively solving the sub-problems. In order to improve the sub-problems' solving efficiency and the solution quality, a detection method for multi-bottleneck machines based on critical path is proposed. Therewith the unscheduled operations can be decomposed into bottleneck operations and non-bottleneck operations. According to the principle of “Bottleneck leads the performance of the whole manufacturing system” in TOC (Theory Of Constraints, the bottleneck operations are scheduled by genetic algorithm for high solution quality, and the non-bottleneck operations are scheduled by dispatching rules for the improvement of the solving efficiency.Findings: In the process of the sub-problems' construction, partial operations in the previous scheduled sub-problem are divided into the successive sub-problem for re-optimization. This strategy can improve the solution quality of the algorithm. In the process of solving the sub-problems, the strategy that evaluating the chromosome's fitness by predicting the global scheduling objective value can improve the solution quality.Research limitations/implications: In this research, there are some assumptions which reduce the complexity of the large-scale scheduling problem. They are as follows: The processing route of each job is predetermined, and the processing time of each operation is fixed. There is no machine breakdown, and no preemption of the operations is allowed. The assumptions should be considered if the algorithm is used in the actual job shop.Originality/value: The research provides an efficient scheduling method for the

  8. Low and Expensive Bandwidth Remains Key Bottleneck for ...

    African Journals Online (AJOL)

    These bottlenecks have dwarfed the expectations of the citizens to fully participate in the new world economic order galvanized by e-commerce and world trade. It is estimated that M.I.T in Boston USA has bandwidth allocation that surpasses all the bandwidth allocated to Nigeria put together. Low bandwidth has been found ...

  9. Database architecture optimized for the new bottleneck: Memory access

    NARCIS (Netherlands)

    P.A. Boncz (Peter); S. Manegold (Stefan); M.L. Kersten (Martin)

    1999-01-01

    textabstractIn the past decade, advances in speed of commodity CPUs have far out-paced advances in memory latency. Main-memory access is therefore increasingly a performance bottleneck for many computer applications, including database systems. In this article, we use a simple scan test to show the

  10. Optimizing Database Architecture for the New Bottleneck: Memory Access

    NARCIS (Netherlands)

    S. Manegold (Stefan); P.A. Boncz (Peter); M.L. Kersten (Martin)

    2000-01-01

    textabstractIn the past decade, advances in speed of commodity CPUs have far out-paced advances in memory latency. Main-memory access is therefore increasingly a performance bottleneck for many computer applications, including database systems. In this article, we use a simple scan test to show the

  11. Highlight on Bottlenecks in Food Allergen Analysis: Detection and Quantification by Mass Spectrometry.

    Science.gov (United States)

    Planque, Mélanie; Arnould, Thierry; Renard, Patricia; Delahaut, Philippe; Dieu, Marc; Gillard, Nathlie

    2017-07-01

    Food laboratories have developed methods for testing allergens in foods. The efficiency of qualitative and quantitative methods is of prime importance in protecting allergic populations. Unfortunately, food laboratories encounter barriers to developing efficient methods. Bottlenecks include the lack of regulatory thresholds, delays in the emergence of reference materials and guidelines, and the need to detect processed allergens. In this study, ultra-HPLC coupled to tandem MS was used to illustrate difficulties encountered in determining method performances. We measured the major influences of both processing and matrix effects on the detection of egg, milk, soy, and peanut allergens in foodstuffs. The main goals of this work were to identify difficulties that food laboratories still encounter in detecting and quantifying allergens and to sensitize researchers to them.

  12. Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

    Directory of Open Access Journals (Sweden)

    Damien C Tully

    2016-05-01

    Full Text Available Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU, we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic "signatures" within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission.

  13. Phase space bottlenecks: A comparison of quantum and classical intramolecular dynamics for collinear OCS

    International Nuclear Information System (INIS)

    Gibson, L.L.; Schatz, G.C.; Ratner, M.A.; Davis, M.J.

    1987-01-01

    We compare quantum and classical mechanics for a collinear model of OCS at an energy (20 000 cm -1 ) where Davis [J. Chem. Phys. 83, 1016 (1985)] had previously found that phase space bottlenecks associated with golden mean tori inhibit classical flow between different chaotic regions in phase space. Accurate quantum eigenfunctions for this two mode system are found by diagonalizing a large basis of complex Gaussian functions, and these are then used to study the evolution of wave packets which have 20 000 cm -1 average energies. By examining phase space (Husimi) distributions associated with the wave functions, we conclude that these golden mean tori do indeed act as bottlenecks which constrain the wave packets to evolve within one (or a combination of) regions. The golden mean tori do not completely determine the boundaries between regions, however. Bottlenecks associated with resonance trapping and with separatrix formation are also involved. The analysis of the Husimi distributions also indicates that each exact eigenstate is nearly always associated with just one region, and because of this, superpositions of eigenstates that are localized within a region remain localized in that region at all times. This last result differs from the classical picture at this energy where flow across the bottlenecks occurs with a 2--4 ps lifetime. Since the classical phase space area through which flux must pass to cross the bottlenecks is small compared to h for OCS, the observed difference between quantum and classical dynamics is not surprising. Examination of the time development of normal mode energies indicates little or no energy flow quantum mechanically for wave packet initial conditions

  14. Two retrievals from a single cue: A bottleneck persists across episodic and semantic memory.

    Science.gov (United States)

    Orscheschek, Franziska; Strobach, Tilo; Schubert, Torsten; Rickard, Timothy

    2018-05-01

    There is evidence in the literature that two retrievals from long-term memory cannot occur in parallel. To date, however, that work has explored only the case of two retrievals from newly acquired episodic memory. These studies demonstrated a retrieval bottleneck even after dual-retrieval practice. That retrieval bottleneck may be a global property of long-term memory retrieval, or it may apply only to the case of two retrievals from episodic memory. In the current experiments, we explored whether that apparent dual-retrieval bottleneck applies to the case of one retrieval from episodic memory and one retrieval from highly overlearned semantic memory. Across three experiments, subjects learned to retrieve a left or right keypress response form a set of 14 unique word cues (e.g., black-right keypress). In addition, they learned a verbal response which involved retrieving the antonym of the presented cue (e.g., black-"white"). In the dual-retrieval condition, subjects had to retrieve both the keypress response and the antonym word. The results suggest that the retrieval bottleneck is superordinate to specific long-term memory systems and holds across different memory components. In addition, the results support the assumption of a cue-level response chunking account of learned retrieval parallelism.

  15. Give or take? Rewards versus charges for a congested bottleneck

    NARCIS (Netherlands)

    Rouwendal, J.; Verhoef, E.T.; Knockaert, J.

    2012-01-01

    This paper analyzes the possibilities to relieve traffic congestion using subsidies instead of Pigouvian taxes, as well as revenue-neutral combinations of rewards and taxes ('feebates'). The model considers a Vickrey-ADL model of bottleneck congestion with endogenous scheduling. With inelastic

  16. Population genetics of foxtail millet and its wild ancestor

    Directory of Open Access Journals (Sweden)

    Wang Yongfang

    2010-10-01

    Full Text Available Abstract Background Foxtail millet (Setaria italica (L. P. Beauv., one of the most ancient domesticated crops, is becoming a model system for studying biofuel crops and comparative genomics in the grasses. However, knowledge on the level of genetic diversity and linkage disequilibrium (LD is very limited in this crop and its wild ancestor, green foxtail (Setaria viridis (L. P. Beauv.. Such information would help us to understand the domestication process of cultivated species and will allow further research in these species, including association mapping and identification of agricultural significant genes involved in domestication. Results In this study, we surveyed DNA sequence for nine loci across 50 accessions of cultivated foxtail millet and 34 of its wild progenitor. We found a low level of genetic diversity in wild green foxtail (θ = 0.0059, θ means Watterson's estimator of θ. Despite of a 55% loss of its wild diversity, foxtail millet still harbored a considerable level of diversity (θ = 0.0027 when compared to rice and sorghum (θ = 0.0024 and 0.0034, respectively. The level of LD in the domesticated foxtail millet extends to 1 kb, while it decayed rapidly to a negligible level within 150 bp in wild green foxtail. Using coalescent simulation, we estimated the bottleneck severity at k = 0.6095 when ρ/θ = 1. These results indicated that the domestication bottleneck of foxtail millet was more severe than that of maize but slightly less pronounced than that of rice. Conclusions The results in this study establish a general framework for the domestication history of foxtail millet. The low level of genetic diversity and the increased level of LD in foxtail millet are mainly caused by a population bottleneck, although gene flow from foxtail millet to green foxtail is another factor that may have shaped the pattern of genetic diversity of these two related gene pools. The knowledge provided in this study will benefit future population

  17. Widening the Knowledge Acquisition Bottleneck for Constraint-Based Tutors

    Science.gov (United States)

    Suraweera, Pramuditha; Mitrovic, Antonija; Martin, Brent

    2010-01-01

    Intelligent Tutoring Systems (ITS) are effective tools for education. However, developing them is a labour-intensive and time-consuming process. A major share of the effort is devoted to acquiring the domain knowledge that underlies the system's intelligence. The goal of this research is to reduce this knowledge acquisition bottleneck and better…

  18. Genetic architecture and bottleneck analyses of Salem Black goat breed based on microsatellite markers

    Directory of Open Access Journals (Sweden)

    A. K. Thiruvenkadan

    2014-09-01

    Full Text Available Aim: The present study was undertaken in Salem Black goat population for genetic analysis at molecular level to exploit the breed for planning sustainable improvement, conservation and utilization, which subsequently can improve the livelihood of its stakeholders. Materials and Methods: Genomic DNA was isolated from blood samples of 50 unrelated Salem Black goats with typical phenotypic features in several villages in the breeding tract and the genetic characterization and bottleneck analysis in Salem Black goat was done using 25 microsatellite markers as recommended by the Food and Agricultural Organization, Rome, Italy. The basic measures of genetic variation were computed using bioinformatic software. To evaluate the Salem Black goats for mutation drift equilibrium, three tests were performed under three different mutation models, viz., infinite allele model (IAM, stepwise mutation model (SMM and two-phase model (TPM and the observed gene diversity (He and expected equilibrium gene diversity (Heq were estimated under different models of microsatellite evolution. Results: The study revealed that the observed number of alleles ranged from 4 (ETH10, ILSTS008 to 17 (BM64444 with a total of 213 alleles and mean of 10.14±0.83 alleles across loci. The overall observed heterozygosity, expected heterozygosity, inbreeding estimate and polymorphism information content values were 0.631±0.041, 0.820±0.024, 0.233±0.044 and 0.786±0.023 respectively indicating high genetic diversity. The average observed gene diversities (He pooled over different markers was 0.829±0.024 and the average expected gene diversities under IAM, TPM and SMM models were 0.769±0.026, 0.808±0.024 and 0.837±0.020 respectively. The number of loci found to exhibit gene diversity excess under IAM, TPM and SMM models were 18, 17 and 12 respectively. Conclusion: All the three statistical tests, viz., sign test, standardized differences test and Wilcoxon sign rank test, revealed

  19. Supply chain bottlenecks in the South African construction industry: Qualitative insights

    Directory of Open Access Journals (Sweden)

    Poobalan Pillay

    2017-07-01

    Full Text Available Background: The construction industry in South Africa has a lot of potential but its performance is still restricted by numerous internal and external challenges. Unless these challenges are identified and understood better, further growth of this industry is likely to be hindered, which has negative economic implications for the South African economy. Objectives: This study investigated supply chain bottlenecks faced by the construction industry in South Africa. It also discussed solutions for addressing the identified bottlenecks in order to facilitate the continued development of supply chain management in the construction industry. Method: The study used a qualitative approach in which in-depth interviews were held with purposively selected senior managers drawn from the construction industry in South Africa. Content analysis using ATLAS.ti software was employed to identify the themes from the collected data. Findings: The findings of the study showed that supply chain management in the construction industry in South Africa is constrained by five major bottlenecks: skills and qualifications, procurement practices and systems, supply chain integration, supply chain relationships and the structure of the construction industry. Recommendations for addressing each of these five challenges were put forward. Conclusion: The study concludes that both awareness and application of supply chain management in the construction industry in South Africa remains inhibited, which creates opportunities for further improvements in this area to realise the full potential of the industry.

  20. Statistical guidelines for detecting past population shifts using ancient DNA

    DEFF Research Database (Denmark)

    Mourier, Tobias; Ho, Simon Y. W.; Gilbert, Tom

    2012-01-01

    Populations carry a genetic signal of their demographic past, providing an opportunity for investigating the processes that shaped their evolution. Our ability to infer population histories can be enhanced by including ancient DNA data. Using serial-coalescent simulations and a range of both...... quantitative and temporal sampling schemes, we test the power of ancient mitochondrial sequences and nuclear single-nucleotide polymorphisms (SNPs) to detect past population bottlenecks. Within our simulated framework, mitochondrial sequences have only limited power to detect subtle bottlenecks and/or fast...... results provide useful guidelines for scaling sampling schemes and for optimizing our ability to infer past population dynamics. In addition, our results suggest that many ancient DNA studies may face power issues in detecting moderate demographic collapses and/or highly dynamic demographic shifts when...

  1. Practical solutions for bottlenecks in ecosystem services mapping

    OpenAIRE

    Palomo,Ignacio; Willemen,Louise; Drakou,Evangelia; Burkhard,Benjamin; Crossman,Neville; Bellamy,Chloe; Burkhard,Kremena; Campagne,C. Sylvie; Dangol,Anuja; Franke,Jonas; Kulczyk,Sylwia; Le Clec'h,Solen; Malak,Dania; Muñoz,Lorena; Narusevicius,Vytautas

    2018-01-01

    Backgroun Ecosystem services (ES) mapping is becoming mainstream in many sustainability assessments, but its impact on real world decision-making is still limited. Robustness, enduser relevance and transparency have been identified as key attributes needed for effective ES mapping. However, these requirements are not always met due to multiple challenges, referred to here as bottlenecks, that scientists, practitioners, policy makers and users from other public and private sectors encounter a...

  2. On the inefficiency of equilibria in linear bottleneck congestion games

    NARCIS (Netherlands)

    B. de Keijzer (Bart); G. Schäfer (Guido); O. Telelis (Orestis); S. Kontogiannis (Spyros); E. Koutsoupias (Elias); P.G. Spirakis (Paul)

    2010-01-01

    htmlabstractWe study the inefficiency of equilibrium outcomes in bottleneck congestion games. These games model situations in which strategic players compete for a limited number of facilities. Each player allocates his weight to a (feasible) subset of the facilities with the goal to minimize the

  3. Genetic variability and bottleneck analyses of Kanni adu goat population using microsatellite markers [Also published in The Indian Journal of Small Ruminants, 2015, 21(2): 216-22

    International Nuclear Information System (INIS)

    Jeyakumar, M.; Thiruvenkadan, R.; Saravana, R.; Periasamy, K.

    2016-01-01

    Full text: Microsatellite data on 25 loci were generated and utilized to evaluate the genetic architecture and mutation drift equilibrium of Kanni Adu goats of southern Tamil Nadu. The genetic diversity analysis of Kanni Adu goats displayed higher level of within breed variability in terms of mean number of alleles per locus (11.24±0.87) and heterozygosity values (Ho= 0.677±0.041, He=0.857±0.016). Within population inbreeding estimate (FIS=0.215±0.040) showed moderate level of inbreeding, which warrant adoption of appropriate breeding strategies under field conditions. The polymorphism information content (PIC) value ranged from 0.531 to 0.915 suggested higher polymorphism in this breed. In general, the sign, standardized differences and Wilcoxon rank tests indicated heterozygosity excess in Kanni Adu goat population in infinite alleles and two-phase model and non-significant in stepwise mutation model. Hence, the mode-shift indicator test was utilized and it indicated the absence of genetic bottleneck in the recent past in Kanni Adu goats. It suggests that any unique alleles present in this breed may not have been lost. The study indicated that Kanni adu goats exhibited substantial amount of genetic variation as reflected from the heterozygosity and number of alleles per locus. (author)

  4. Investigation of the performance of fermentation processes using a mathematical model including effects of metabolic bottleneck and toxic product on cells.

    Science.gov (United States)

    Sriyudthsak, Kansuporn; Shiraishi, Fumihide

    2010-11-01

    A number of recent research studies have focused on theoretical and experimental investigation of a bottleneck in a metabolic reaction network. However, there is no study on how the bottleneck affects the performance of a fermentation process when a product is highly toxic and remarkably influences the growth and death of cells. The present work therefore studies the effect of bottleneck on product concentrations under different product toxicity conditions. A generalized bottleneck model in a fed-batch fermentation is constructed including both the bottleneck and the product influences on cell growth and death. The simulation result reveals that when the toxic product strongly influences the cell growth and death, the final product concentration is hardly changed even if the bottleneck is removed, whereas it is markedly changed by the degree of product toxicity. The performance of an ethanol fermentation process is also discussed as a case example to validate this result. In conclusion, when the product is highly toxic, one cannot expect a significant increase in the final product concentration even if removing the bottleneck; rather, it may be more effective to somehow protect the cells so that they can continuously produce the product. Copyright © 2010 Elsevier Inc. All rights reserved.

  5. A bottleneck model of set-specific capture.

    Directory of Open Access Journals (Sweden)

    Katherine Sledge Moore

    Full Text Available Set-specific contingent attentional capture is a particularly strong form of capture that occurs when multiple attentional sets guide visual search (e.g., "search for green letters" and "search for orange letters". In this type of capture, a potential target that matches one attentional set (e.g. a green stimulus impairs the ability to identify a temporally proximal target that matches another attentional set (e.g. an orange stimulus. In the present study, we investigated whether set-specific capture stems from a bottleneck in working memory or from a depletion of limited resources that are distributed across multiple attentional sets. In each trial, participants searched a rapid serial visual presentation (RSVP stream for up to three target letters (T1-T3 that could appear in any of three target colors (orange, green, or lavender. The most revealing findings came from trials in which T1 and T2 matched different attentional sets and were both identified. In these trials, T3 accuracy was lower when it did not match T1's set than when it did match, but only when participants failed to identify T2. These findings support a bottleneck model of set-specific capture in which a limited-capacity mechanism in working memory enhances only one attentional set at a time, rather than a resource model in which processing capacity is simultaneously distributed across multiple attentional sets.

  6. Natural language processing and the Now-or-Never bottleneck.

    Science.gov (United States)

    Gómez-Rodríguez, Carlos

    2016-01-01

    Researchers, motivated by the need to improve the efficiency of natural language processing tools to handle web-scale data, have recently arrived at models that remarkably match the expected features of human language processing under the Now-or-Never bottleneck framework. This provides additional support for said framework and highlights the research potential in the interaction between applied computational linguistics and cognitive science.

  7. Genetic diversity and bottleneck studies in the Marwari horse breed

    Indian Academy of Sciences (India)

    Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (± s.e.) allelic diversity was 5.9 ...

  8. Genetic diversity and bottleneck studies in the Marwari horse breed

    Indian Academy of Sciences (India)

    Unknown

    [Gupta A. K., Chauhan M., Tandon S. N. and Sonia 2005 Genetic diversity and bottleneck studies in the Marwari horse breed. J. Genet. 84, 295–301] ... developed to carry out studies of genetic variation (Brad- ley et al. 1996; Canon et al. ..... 1996 Mitochondrial diversity and the origins of African and. European cattle. Proc.

  9. Eye shape and the nocturnal bottleneck of mammals.

    Science.gov (United States)

    Hall, Margaret I; Kamilar, Jason M; Kirk, E Christopher

    2012-12-22

    Most vertebrate groups exhibit eye shapes that vary predictably with activity pattern. Nocturnal vertebrates typically have large corneas relative to eye size as an adaptation for increased visual sensitivity. Conversely, diurnal vertebrates generally demonstrate smaller corneas relative to eye size as an adaptation for increased visual acuity. By contrast, several studies have concluded that many mammals exhibit typical nocturnal eye shapes, regardless of activity pattern. However, a recent study has argued that new statistical methods allow eye shape to accurately predict activity patterns of mammals, including cathemeral species (animals that are equally likely to be awake and active at any time of day or night). Here, we conduct a detailed analysis of eye shape and activity pattern in mammals, using a broad comparative sample of 266 species. We find that the eye shapes of cathemeral mammals completely overlap with nocturnal and diurnal species. Additionally, most diurnal and cathemeral mammals have eye shapes that are most similar to those of nocturnal birds and lizards. The only mammalian clade that diverges from this pattern is anthropoids, which have convergently evolved eye shapes similar to those of diurnal birds and lizards. Our results provide additional evidence for a nocturnal 'bottleneck' in the early evolution of crown mammals.

  10. Impact of memory bottleneck on the performance of graphics processing units

    Science.gov (United States)

    Son, Dong Oh; Choi, Hong Jun; Kim, Jong Myon; Kim, Cheol Hong

    2015-12-01

    Recent graphics processing units (GPUs) can process general-purpose applications as well as graphics applications with the help of various user-friendly application programming interfaces (APIs) supported by GPU vendors. Unfortunately, utilizing the hardware resource in the GPU efficiently is a challenging problem, since the GPU architecture is totally different to the traditional CPU architecture. To solve this problem, many studies have focused on the techniques for improving the system performance using GPUs. In this work, we analyze the GPU performance varying GPU parameters such as the number of cores and clock frequency. According to our simulations, the GPU performance can be improved by 125.8% and 16.2% on average as the number of cores and clock frequency increase, respectively. However, the performance is saturated when memory bottleneck problems incur due to huge data requests to the memory. The performance of GPUs can be improved as the memory bottleneck is reduced by changing GPU parameters dynamically.

  11. Pre-whaling genetic diversity and population ecology in eastern Pacific gray whales: insights from ancient DNA and stable isotopes.

    Directory of Open Access Journals (Sweden)

    S Elizabeth Alter

    Full Text Available Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ~5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size.

  12. Linguistics, cognitive psychology, and the Now-or-Never bottleneck.

    Science.gov (United States)

    Endress, Ansgar D; Katzir, Roni

    2016-01-01

    Christiansen & Chater (C&C)'s key premise is that "if linguistic information is not processed rapidly, that information is lost for good" (sect. 1, para. 1). From this "Now-or-Never bottleneck" (NNB), C&C derive "wide-reaching and fundamental implications for language processing, acquisition and change as well as for the structure of language itself" (sect. 2, para. 10). We question both the premise and the consequentiality of its purported implications.

  13. Probabilistic physical characteristics of phase transitions at highway bottlenecks: incommensurability of three-phase and two-phase traffic-flow theories.

    Science.gov (United States)

    Kerner, Boris S; Klenov, Sergey L; Schreckenberg, Michael

    2014-05-01

    Physical features of induced phase transitions in a metastable free flow at an on-ramp bottleneck in three-phase and two-phase cellular automaton (CA) traffic-flow models have been revealed. It turns out that at given flow rates at the bottleneck, to induce a moving jam (F → J transition) in the metastable free flow through the application of a time-limited on-ramp inflow impulse, in both two-phase and three-phase CA models the same critical amplitude of the impulse is required. If a smaller impulse than this critical one is applied, neither F → J transition nor other phase transitions can occur in the two-phase CA model. We have found that in contrast with the two-phase CA model, in the three-phase CA model, if the same smaller impulse is applied, then a phase transition from free flow to synchronized flow (F → S transition) can be induced at the bottleneck. This explains why rather than the F → J transition, in the three-phase theory traffic breakdown at a highway bottleneck is governed by an F → S transition, as observed in real measured traffic data. None of two-phase traffic-flow theories incorporates an F → S transition in a metastable free flow at the bottleneck that is the main feature of the three-phase theory. On the one hand, this shows the incommensurability of three-phase and two-phase traffic-flow theories. On the other hand, this clarifies why none of the two-phase traffic-flow theories can explain the set of fundamental empirical features of traffic breakdown at highway bottlenecks.

  14. A comparison of genetic map distance and linkage disequilibrium between 15 polymorphic dinucleotide repeat loci in two populations

    Energy Technology Data Exchange (ETDEWEB)

    Urbanek, M.; Goldman, D.; Long, J.C. [Lab. of Neurogenetics, Rockville, MD (United States)

    1994-09-01

    Linkage disequilibrium has recently been used to map the diastrophic dysplasia gene in a Finnish sample. One advantage of this method is that the large pedigrees required by some other methods are unnecessary. Another advantage is that linkage disequilibrium mapping capitalizes on the cumulative history of recombination events, rather than those occurring within the sampled individuals. A potential limitation of linkage disequilibrium mapping is that linkage equilibrium is likely to prevail in all but the most isolated populations, e.g., those which have recently experienced founder effects or severe population bottlenecks. In order to test the method`s generality, we examined patterns of linkage disequilibrium between pairs of loci within a known genetic map. Two populations were analyzed. The first population, Navajo Indians (N=45), is an isolate that experienced a severe bottleneck in the 1860`s. The second population, Maryland Caucasians (N=45), is cosmopolitan. We expected the Navajo sample to display more linkage disequilibrium than the Caucasian sample, and possibly that the Navajo disequilibrium pattern would reflect the genetic map. Linkage disequilibrium coefficients were estimated between pairs of alleles at different loci using maximum likelihood. The genetic isolate structure of Navajo Indians is confirmed by the DNA typings. Heterozygosity is lower than in the Caucasians, and fewer different alleles are observed. However, a relationship between genetic map distance and linkage disequilibrium could be discerned in neither the Navajo nor the Maryland samples. Slightly more linkage disequilibrium was observed in the Navajos, but both data sets were characterized by very low disequilibrium levels. We tentatively conclude that linkage disequilibrium mapping with dinucleotide repeats will only be useful with close linkage between markers and diseases, even in very isolated populations.

  15. The nocturnal bottleneck and the evolution of activity patterns in mammals

    Science.gov (United States)

    Gerkema, Menno P.; Davies, Wayne I. L.; Foster, Russell G.; Menaker, Michael; Hut, Roelof A.

    2013-01-01

    In 1942, Walls described the concept of a ‘nocturnal bottleneck’ in placental mammals, where these species could survive only by avoiding daytime activity during times in which dinosaurs were the dominant taxon. Walls based this concept of a longer episode of nocturnality in early eutherian mammals by comparing the visual systems of reptiles, birds and all three extant taxa of the mammalian lineage, namely the monotremes, marsupials (now included in the metatherians) and placentals (included in the eutherians). This review describes the status of what has become known as the nocturnal bottleneck hypothesis, giving an overview of the chronobiological patterns of activity. We review the ecological plausibility that the activity patterns of (early) eutherian mammals were restricted to the night, based on arguments relating to endothermia, energy balance, foraging and predation, taking into account recent palaeontological information. We also assess genes, relating to light detection (visual and non-visual systems) and the photolyase DNA protection system that were lost in the eutherian mammalian lineage. Our conclusion presently is that arguments in favour of the nocturnal bottleneck hypothesis in eutherians prevail. PMID:23825205

  16. BOTTLENECK ANALYSIS AND STRATEGIC PLANNING ON CHILDHOOD DIARRHEA MANAGEMENT IN 6 HIGH PRIORITY DISTRICTS OF GUJARAT

    Directory of Open Access Journals (Sweden)

    Rupani Mihir

    2015-01-01

    Full Text Available Introduction:Bottleneck Analysis and Strategic Planning exercise was carried out in 6 High Priority Districts (HPDs, under Call-to-Action for RMNCH+A strategy.Rationale: In spite of continued efforts, India is still lagging behind in its MDG goals.Objectives: To identify gaps in childhood diarrhea management and propose strategic options for the same.Materials and Methods: Bottleneck analysis exercisewas carried out based on the Tanahashi model, desk review and focused group discussions between district officials, front-line workers and UNICEF officials. These bottlenecks were pertaining to the availability, accessibility, utilization of services and quality of services being provided by the health department.Elaborating the Tanahashi model for the 6 HPDs, 94% of the front-line workers (FLWs had stock of Zinc-ORS; 88% FLWs were trained in diarrhea management; 98% villages had at least one FLW trained in diarrhea management; health care seeking for diarrhea cases was 17%; 5.1% diarrhea cases received Zinc-ORS from health worker and 2.4% care takers prepared Zinc-ORS in safe drinking water.Results: The major bottlenecks identified for Childhood Diarrhea management in the 6 High Priority Districts were poor demand generation, unsafe drinking water, poor access to improved sanitation facility and lack of equitable distribution of Zinc-ORS till the front-line worker level. The main strategic options that were suggested for relieving these bottlenecks were Zinc-ORS roll out in scale-up districts, develop IEC/BCC plan for childhood diarrhea management at state/district level, use of Drug Logistics Information Management System (DLIMS software for supply chain management of Zinc-ORS, strengthening of chlorination activity at household level, monitoring implementation of Nirmal Bharat Abhiyaan (NBA for constructing improved sanitation facilities at household level and to develop an IEC/BCC plan for hygiene promotion and usage of sanitary latrines

  17. BOTTLENECK ANALYSIS AND STRATEGIC PLANNING ON CHILDHOOD DIARRHEA MANAGEMENT IN 6 HIGH PRIORITY DISTRICTS OF GUJARAT

    Directory of Open Access Journals (Sweden)

    Rupani Mihir

    2015-12-01

    Full Text Available Introduction:Bottleneck Analysis and Strategic Planning exercise was carried out in 6 High Priority Districts (HPDs, under Call-to-Action for RMNCH+A strategy. Rationale: In spite of continued efforts, India is still lagging behind in its MDG goals. Objectives: To identify gaps in childhood diarrhea management and propose strategic options for the same. Materials and Methods: Bottleneck analysis exercisewas carried out based on the Tanahashi model, desk review and focused group discussions between district officials, front-line workers and UNICEF officials. These bottlenecks were pertaining to the availability, accessibility, utilization of services and quality of services being provided by the health department. Elaborating the Tanahashi model for the 6 HPDs, 94% of the front-line workers (FLWs had stock of Zinc-ORS; 88% FLWs were trained in diarrhea management; 98% villages had at least one FLW trained in diarrhea management; health care seeking for diarrhea cases was 17%; 5.1% diarrhea cases received Zinc-ORS from health worker and 2.4% care takers prepared Zinc-ORS in safe drinking water. Results: The major bottlenecks identified for Childhood Diarrhea management in the 6 High Priority Districts were poor demand generation, unsafe drinking water, poor access to improved sanitation facility and lack of equitable distribution of Zinc-ORS till the front-line worker level. The main strategic options that were suggested for relieving these bottlenecks were Zinc-ORS roll out in scale-up districts, develop IEC/BCC plan for childhood diarrhea management at state/district level, use of Drug Logistics Information Management System (DLIMS software for supply chain management of Zinc-ORS, strengthening of chlorination activity at household level, monitoring implementation of Nirmal Bharat Abhiyaan (NBA for constructing improved sanitation facilities at household level and to develop an IEC/BCC plan for hygiene promotion and usage of sanitary

  18. Process modeling and bottleneck mining in online peer-review systems.

    Science.gov (United States)

    Premchaiswadi, Wichian; Porouhan, Parham

    2015-01-01

    This paper is divided into three main parts. In the first part of the study, we captured, collected and formatted an event log describing the handling of reviews for proceedings of an international conference in Thailand. In the second part, we used several process mining techniques in order to discover process models, social, organizational, and hierarchical structures from the proceeding's event log. In the third part, we detected the deviations and bottlenecks of the peer review process by comparing the observed events (i.e., authentic dataset) with a pre-defined model (i.e., master map). Finally, we investigated the performance information as well as the total waiting time in order to improve the effectiveness and efficiency of the online submission and peer review system for the prospective conferences and seminars. Consequently, the main goals of the study were as follows: (1) to convert the collected event log into the appropriate format supported by process mining analysis tools, (2) to discover process models and to construct social networks based on the collected event log, and (3) to find deviations, discrepancies and bottlenecks between the collected event log and the master pre-defined model. The results showed that although each paper was initially sent to three different reviewers; it was not always possible to make a decision after the first round of reviewing; therefore, additional reviewers were invited. In total, all the accepted and rejected manuscripts were reviewed by an average of 3.9 and 3.2 expert reviewers, respectively. Moreover, obvious violations of the rules and regulations relating to careless or inappropriate peer review of a manuscript-committed by the editorial board and other staff-were identified. Nine blocks of activity in the authentic dataset were not completely compatible with the activities defined in the master model. Also, five of the activity traces were not correctly enabled, and seven activities were missed within the

  19. Ring-like size segregation in vibrated cylinder with a bottleneck

    International Nuclear Information System (INIS)

    Kong Xiangzhao; Hu Maobin; Wu Qingsong; Wu Yonghong

    2005-01-01

    In this Letter, a ring-like segregation pattern of bi-dispersed granular material in a vibrated bottleneck-cylinder is presented. The driving frequency can greatly affect the strength and structure of the convection roll and segregation pattern. The position and height of the ring (cluster of big beads) can be adjusted by altering the vibration frequency. And a heuristic theory is developed to interpret the ring's position dependence on driving frequency

  20. Note: Inhibiting bottleneck corrosion in electrical calcium tests for ultra-barrier measurements

    Energy Technology Data Exchange (ETDEWEB)

    Nehm, F., E-mail: frederik.nehm@iapp.de; Müller-Meskamp, L.; Klumbies, H.; Leo, K. [Institut für Angewandte Photophysik, Technische Universität Dresden, George-Bähr-Straße 1, 01069 Dresden (Germany)

    2015-12-15

    A major failure mechanism is identified in electrical calcium corrosion tests for quality assessment of high-end application moisture barriers. Accelerated calcium corrosion is found at the calcium/electrode junction, leading to an electrical bottleneck. This causes test failure not related to overall calcium loss. The likely cause is a difference in electrochemical potential between the aluminum electrodes and the calcium sensor, resulting in a corrosion element. As a solution, a thin, full-area copper layer is introduced below the calcium, shifting the corrosion element to the calcium/copper junction and inhibiting bottleneck degradation. Using the copper layer improves the level of sensitivity for the water vapor transmission rate (WVTR) by over one order of magnitude. Thin-film encapsulated samples with 20 nm of atomic layer deposited alumina barriers this way exhibit WVTRs of 6 × 10{sup −5} g(H{sub 2}O)/m{sup 2}/d at 38 °C, 90% relative humidity.

  1. A rangewide population genetic study of trumpeter swans

    Science.gov (United States)

    Oyler-McCance, S.J.; Ransler, F.A.; Berkman, L.K.; Quinn, T.W.

    2007-01-01

    For management purposes, the range of naturally occurring trumpeter swans (Cygnus buccinator) has been divided into two populations, the Pacific Coast Population (PP) and the Rocky Mountain Population (RMP). Little is known about the distribution of genetic variation across the species' range despite increasing pressure to make difficult management decisions regarding the two populations and flocks within them. To address this issue, we used rapidly evolving genetic markers (mitochondrial DNA sequence and 17 nuclear microsatellite loci) to elucidate the underlying genetic structure of the species. Data from both markers revealed a significant difference between the PP and RMP with the Yukon Territory as a likely area of overlap. Additionally, we found that the two populations have somewhat similar levels of genetic diversity (PP is slightly higher) suggesting that the PP underwent a population bottleneck similar to a well-documented one in the RMP. Both genetic structure and diversity results reveal that the Tri-State flock, a suspected unique, non-migratory flock, is not genetically different from the Canadian flock of the RMP and need not be treated as a unique population from a genetic standpoint. Finally, trumpeter swans appear to have much lower mitochondrial DNA variability than other waterfowl studied thus far which may suggest a previous, species-wide bottleneck. ?? 2007 Springer Science+Business Media, Inc.

  2. Decoupled systems on trial: Eliminating bottlenecks to improve aquaponic processes.

    Directory of Open Access Journals (Sweden)

    Hendrik Monsees

    Full Text Available In classical aquaponics (coupled aquaponic systems, 1-loop systems the production of fish in recirculating aquaculture systems (RAS and plants in hydroponics are combined in a single loop, entailing systemic compromises on the optimal production parameters (e.g. pH. Recently presented decoupled aquaponics (2-loop systems have been awarded for eliminating major bottlenecks. In a pilot study, production in an innovative decoupled aquaponic system was compared with a coupled system and, as a control, a conventional RAS, assessing growth parameters of fish (FCR, SGR and plants over an experimental period of 5 months. Soluble nutrients (NO3--N, NO2--N, NH4+-N, PO43-, K+, Ca2+, Mg2+, SO42-, Cl2- and Fe2+, elemental composition of plants, fish and sludge (N, P, K, Ca, Mg, Na, C, abiotic factors (temperature, pH, oxygen, and conductivity, fertilizer and water consumption were determined. Fruit yield was 36% higher in decoupled aquaponics and pH and fertilizer management was more effective, whereas fish production was comparable in both systems. The results of this pilot study clearly illustrate the main advantages of decoupled, two-loop aquaponics and demonstrate how bottlenecks commonly encountered in coupled aquaponics can be managed to promote application in aquaculture.

  3. Decoupled systems on trial: Eliminating bottlenecks to improve aquaponic processes.

    Science.gov (United States)

    Monsees, Hendrik; Kloas, Werner; Wuertz, Sven

    2017-01-01

    In classical aquaponics (coupled aquaponic systems, 1-loop systems) the production of fish in recirculating aquaculture systems (RAS) and plants in hydroponics are combined in a single loop, entailing systemic compromises on the optimal production parameters (e.g. pH). Recently presented decoupled aquaponics (2-loop systems) have been awarded for eliminating major bottlenecks. In a pilot study, production in an innovative decoupled aquaponic system was compared with a coupled system and, as a control, a conventional RAS, assessing growth parameters of fish (FCR, SGR) and plants over an experimental period of 5 months. Soluble nutrients (NO3--N, NO2--N, NH4+-N, PO43-, K+, Ca2+, Mg2+, SO42-, Cl2- and Fe2+), elemental composition of plants, fish and sludge (N, P, K, Ca, Mg, Na, C), abiotic factors (temperature, pH, oxygen, and conductivity), fertilizer and water consumption were determined. Fruit yield was 36% higher in decoupled aquaponics and pH and fertilizer management was more effective, whereas fish production was comparable in both systems. The results of this pilot study clearly illustrate the main advantages of decoupled, two-loop aquaponics and demonstrate how bottlenecks commonly encountered in coupled aquaponics can be managed to promote application in aquaculture.

  4. Identification of Bottlenecks in the Plant Life Cycle for Sustainable Conservation of Rare and Endangered Species

    Directory of Open Access Journals (Sweden)

    Giovanna Aronne

    2017-07-01

    Full Text Available Long term survival of a species relies on maintenance of genetic variability and natural selection by means of successful reproduction and generation turnover. Although, basic to monitor the conservation status of a plant species, life history data are rarely available even for threatened species due to the gap between the large amount of information required and the limits in terms of time and available economic resources to gather these data. Here, the focus on bottlenecks in life-cycle of rare endangered plant species is proposed as a resolving approach to address the challenges of feasible conservation actions. Basic considerations for this approach are: (a all biological and ecological studies on plant species can be scientifically important, but not all of them are equally relevant to conservation planning and management requirements; (b under a changing environment, long term survival of a species relies on generation turnover; (c for conservation purposes, priority should be given to studies aimed to focus on bottlenecks in the succession of generations because they prevent, or slow down natural selection processes. The proposed procedure, named Systematic Hazard Analysis of Rare-endangered Plants (SHARP, consists of a preliminary survey of the already available information on the species and two main components. The first component is the identification of the bottlenecks in the life cycle by means of field surveys. The second is the diagnosis of the causes of the bottleneck by appropriate experimental methods. The target is to provide researchers, managers and practitioners with substantiated indications for sustainable conservation measures.

  5. Bottlenecks and opportunities for quality improvement in fresh pineapple supply chains in Benin

    NARCIS (Netherlands)

    Fassinou Hotegni, V.N.; Lommen, W.J.M.; Vorst, van der J.G.A.J.; Agbossou, E.K.; Struik, P.C.

    2014-01-01

    This study mapped and diagnosed the fresh pineapple supply chains in Benin to identify bottlenecks in pineapple quality improvement for different markets. A research framework was defined that comprised all relevant aspects to be researched. After 54 semi-structured interviews with key informants,

  6. Bottlenecks, concerns and needs in malaria operational research: the perspectives of key stakeholders in Nigeria.

    Science.gov (United States)

    Onyiah, Pamela; Adamu, Al-Mukhtar Y; Afolabi, Rotimi F; Ajumobi, Olufemi; Ughasoro, Maduka D; Odeyinka, Oluwaseun; Nguku, Patrick; Ajayi, IkeOluwapo O

    2018-05-04

    We conducted a study to determine stakeholders' perspective of the bottlenecks, concerns and needs to malaria operational research (MOR) agenda setting in Nigeria. Eighty-five (37.9%) stakeholders identified lack of positive behavioural change as the major bottleneck to MOR across the malaria thematic areas comprising of malaria prevention 58.8% (50), case management 34.8% (39), advocacy communication and social mobilisation 4.7% (4) while procurement and supply chain management (PSM) and programme management experts had the least response of 1.2% (1) each. Other bottlenecks were inadequate capacity to implement (13.8%, n = 31), inadequate funds (11.6%, n = 26), poor supply management (9.4%, n = 21), administrative bureaucracy (5.8%, n = 13), inadequacy of experts (1.3%, n = 3) and poor policy implementation (4.9%, n = 11). Of the 31 stakeholders who opined lack of capacity to execute malaria operational research; 17 (54.8%), 10 (32.3%), 3 (9.7%) and 1 (3.2%) were experts in case management, malaria prevention, surveillance, monitoring and evaluation and PSM respectively. Improvement in community enlightenment and awareness strategies; and active involvement of health care workers public and private sectors were identified solutions to lack of positive behavioural change.

  7. Genomewide Linkage Disequilibrium Mapping of Severe Bipolar Disorder in a Population Isolate

    Science.gov (United States)

    Ophoff, Roel A.; Escamilla, Michael A.; Service, Susan K.; Spesny, Mitzi; Meshi, Dar B.; Poon, Wingman; Molina, Julio; Fournier, Eduardo; Gallegos, Alvaro; Mathews, Carol; Neylan, Thomas; Batki, Steven L.; Roche, Erin; Ramirez, Margarita; Silva, Sandra; De Mille, Melissa C.; Dong, Penny; Leon, Pedro E.; Reus, Victor I.; Sandkuijl, Lodewijk A.; Freimer, Nelson B.

    2002-01-01

    Genomewide association studies may offer the best promise for genetic mapping of complex traits. Such studies in outbred populations require very densely spaced single-nucleotide polymorphisms. In recently founded population isolates, however, extensive linkage disequilibrium (LD) may make these studies feasible with currently available sets of short tandem repeat markers, spaced at intervals as large as a few centimorgans. We report the results of a genomewide association study of severe bipolar disorder (BP-I), using patients from the isolated population of the central valley of Costa Rica. We observed LD with BP-I on several chromosomes; the most striking results were in proximal 8p, a region that has previously shown linkage to schizophrenia. This region could be important for severe psychiatric disorders, rather than for a specific phenotype. PMID:12119601

  8. Genetic impoverishment of the last black grouse (Tetrao tetrix) population in the Netherlands

    NARCIS (Netherlands)

    Larsson, J.K.; Jansman, H.A.H.; Niewold, F.J.J.; Segelbacher, G.; Höglund, J.; Koelewijn, H.P.

    2005-01-01

    We have studied a small isolated bottlenecked population of Black grouse (Tetrao tetrix) in the Netherlands to examine the impact of isolation and reduction in numbers on the genetic diversity. We compared the genetic diversity in the last present Dutch population with Dutch museum samples and three

  9. Severe Mental Illness in LGBT Populations: A Scoping Review.

    Science.gov (United States)

    Kidd, Sean A; Howison, Meg; Pilling, Merrick; Ross, Lori E; McKenzie, Kwame

    2016-07-01

    There is increasing attention to diversity in psychiatric services and widespread recognition of the mental health implications of stigma for individuals from sexual or gender minority groups. However, these areas remain markedly underdeveloped in the area of severe mental illness. The aim of this review was to map out the existing base of knowledge in these areas to help inform future research, practice, and policy directions. A review of the literature was conducted to answer the following question: What factors and strategies need to be considered when developing services for individuals from sexual or gender minority groups who are experiencing severe mental illness? A comprehensive search of MEDLINE, PsycINFO, and Google Scholar was completed by using Arksey and O'Malley's methodological framework for scoping reviews. A total of 27 publications were identified for review. Mental health services research indicated generally lower levels of service satisfaction among lesbian, gay, bisexual, transgender, and transsexual (LGBT) individuals and minimal evidence regarding specific interventions. Descriptive research suggested an increased risk of severe mental illness in LGBT populations, an association between this increased risk and discrimination, and the potential benefit of cultivating spaces where individuals can be "out" in all aspects of themselves. There is a pressing need for research into interventions for LGBT populations with severe mental illness as well as descriptive studies to inform efforts to reduce illness morbidity linked to discrimination.

  10. Saccadic Eye Movements Impose a Natural Bottleneck on Visual Short-Term Memory

    Science.gov (United States)

    Ohl, Sven; Rolfs, Martin

    2017-01-01

    Visual short-term memory (VSTM) is a crucial repository of information when events unfold rapidly before our eyes, yet it maintains only a fraction of the sensory information encoded by the visual system. Here, we tested the hypothesis that saccadic eye movements provide a natural bottleneck for the transition of fragile content in sensory memory…

  11. Identifying temporal bottlenecks for the conservation of large-bodied fishes: Lake Sturgeon (Acipenser fulvescens show highly restricted movement and habitat use over-winter

    Directory of Open Access Journals (Sweden)

    Donnette Thayer

    2017-04-01

    Full Text Available The relationship between species’ size and home range size has been well studied. In practice, home range may provide a good surrogate of broad spatial coverage needed for species conservation, however, many species can show restricted movement during critical life stages, such as breeding and over-wintering. This suggests the existence of either a behavioral or habitat mediated ‘temporal bottleneck,’ where restricted or sedentary movement can make populations more susceptible to harm during specific life stages. Here, we study over-winter movement and habitat use of Lake Sturgeon (Acipenser fulvescens, the largest freshwater fish in North America. We monitored over-winter movement of 86 fish using a hydro-acoustic receiver array in the South Saskatchewan River, Canada. Overall, 20 fish remained within our study system throughout the winter. Lake Sturgeon showed strong aggregation and sedentary movement over-winter, demonstrating a temporal bottleneck. Movement was highly restricted during ice-on periods (ranging from 0.9 km/day in November and April to 0.2 km/day in mid-November to mid-March, with Lake Sturgeon seeking deeper, slower pools. We also show that Lake Sturgeon have strong aggregation behavior, where distance to conspecifics decreased (from 575 to 313 m in preparation for and during ice-on periods. Although the Lake Sturgeon we studied had access to 1100 kilometers of unfragmented riverine habitat, we show that during the over-winter period Lake Sturgeon utilized a single, deep pool (<0.1% of available habitat. The temporal discrepancy between mobile and sedentary behaviors in Lake Sturgeon suggest adaptive management is needed with more localized focus during periods of temporal bottlenecks, even for large-bodied species.

  12. Earliest evidence for the structure of Homo sapiens populations in Africa

    Science.gov (United States)

    Scerri, Eleanor M. L.; Drake, Nick A.; Jennings, Richard; Groucutt, Huw S.

    2014-10-01

    Understanding the structure and variation of Homo sapiens populations in Africa is critical for interpreting multiproxy evidence of their subsequent dispersals into Eurasia. However, there is no consensus on early H. sapiens demographic structure, or its effects on intra-African dispersals. Here, we show how a patchwork of ecological corridors and bottlenecks triggered a successive budding of populations across the Sahara. Using a temporally and spatially explicit palaeoenvironmental model, we found that the Sahara was not uniformly ameliorated between ∼130 and 75 thousand years ago (ka), as has been stated. Model integration with multivariate analyses of corresponding stone tools then revealed several spatially defined technological clusters which correlated with distinct palaeobiomes. Similarities between technological clusters were such that they decreased with distance except where connected by palaeohydrological networks. These results indicate that populations at the Eurasian gateway were strongly structured, which has implications for refining the demographic parameters of dispersals out of Africa.

  13. Airlines' strategic interactions and airport pricing in a dynamic bottleneck model of congestion

    NARCIS (Netherlands)

    Silva Montalva, H.E.; Verhoef, E.T.; van den Berg, V.A.C.

    2014-01-01

    This paper analyzes efficient pricing at a congested airport dominated by a single firm. Unlike much of the previous literature, we combine a dynamic bottleneck model of congestion and a vertical structure model that explicitly considers the role of airlines and passengers. We show that a

  14. Memory bottlenecks and memory contention in multi-core Monte Carlo transport codes

    International Nuclear Information System (INIS)

    Tramm, J.R.; Siegel, A.R.

    2013-01-01

    The simulation of whole nuclear cores through the use of Monte Carlo codes requires an impracticably long time-to-solution. We have extracted a kernel that executes only the most computationally expensive steps of the Monte Carlo particle transport algorithm - the calculation of macroscopic cross sections - in an effort to expose bottlenecks within multi-core, shared memory architectures. (authors)

  15. Squeezing through the Now-or-Never bottleneck: Reconnecting language processing, acquisition, change, and structure.

    Science.gov (United States)

    Chater, Nick; Christiansen, Morten H

    2016-01-01

    If human language must be squeezed through a narrow cognitive bottleneck, what are the implications for language processing, acquisition, change, and structure? In our target article, we suggested that the implications are far-reaching and form the basis of an integrated account of many apparently unconnected aspects of language and language processing, as well as suggesting revision of many existing theoretical accounts. With some exceptions, commentators were generally supportive both of the existence of the bottleneck and its potential implications. Many commentators suggested additional theoretical and linguistic nuances and extensions, links with prior work, and relevant computational and neuroscientific considerations; some argued for related but distinct viewpoints; a few, though, felt traditional perspectives were being abandoned too readily. Our response attempts to build on the many suggestions raised by the commentators and to engage constructively with challenges to our approach.

  16. [Several problems concerning population investment].

    Science.gov (United States)

    Liu, Z

    1982-07-29

    Population investment is a major topic in the studies of population and economic relations. In this particular area, numerous theoretical and practical problems are still in need of solution. Concerning the problem of population concept, there are three different approaches: (1) to determine the definition of population investment from the relationship between the population growth and the capital from national income used for investment, including investment in the newly increased population and investment in the entire population; (2) to explain population investment from the economic viewpoint that people are producers; and (3) to explain population investment from the expense needed to change a simple labor force to a skillful labor force. The expenses include educational costs, maintanance spending, wages needed to compensate workers in labor, costs for workers to master and learn modern scientific techniques to be used for production, and the costs of keeping a young labor force in the next generation.

  17. Population genomics of the inbred Scandinavian wolf.

    Science.gov (United States)

    Hagenblad, Jenny; Olsson, Maria; Parker, Heidi G; Ostrander, Elaine A; Ellegren, Hans

    2009-04-01

    The Scandinavian wolf population represents one of the genetically most well-characterized examples of a severely bottlenecked natural population (with only two founders), and of how the addition of new genetic material (one immigrant) can at least temporarily provide a 'genetic rescue'. However, inbreeding depression has been observed in this population and in the absence of additional immigrants, its long-term viability is questioned. To study the effects of inbreeding and selection on genomic diversity, we performed a genomic scan with approximately 250 microsatellite markers distributed across all autosomes and the X chromosome. We found linkage disequilibrium (LD) that extended up to distances of 50 Mb, exceeding that of most outbreeding species studied thus far. LD was particularly pronounced on the X chromosome. Overall levels of observed genomic heterozygosity did not deviate significantly from simulations based on known population history, giving no support for a general selection for heterozygotes. However, we found evidence supporting balancing selection at a number of loci and also evidence suggesting directional selection at other loci. For markers on chromosome 23, the signal of selection was particularly strong, indicating that purifying selection against deleterious alleles may have occurred even in this very small population. These data suggest that population genomics allows the exploration of the effects of neutral and non-neutral evolution on a finer scale than what has previously been possible.

  18. Purine biosynthesis is the bottleneck in trimethoprim-treated Bacillus subtilis.

    Science.gov (United States)

    Stepanek, Jennifer Janina; Schäkermann, Sina; Wenzel, Michaela; Prochnow, Pascal; Bandow, Julia Elisabeth

    2016-10-01

    Trimethoprim is a folate biosynthesis inhibitor. Tetrahydrofolates are essential for the transfer of C 1 units in several biochemical pathways including purine, thymine, methionine, and glycine biosynthesis. This study addressed the effects of folate biosynthesis inhibition on bacterial physiology. Two complementary proteomic approaches were employed to analyze the response of Bacillus subtilis to trimethoprim. Acute changes in protein synthesis rates were monitored by radioactive pulse labeling of newly synthesized proteins and subsequent 2DE analysis. Changes in protein levels were detected using gel-free quantitative MS. Proteins involved in purine and histidine biosynthesis, the σ B -dependent general stress response, and sporulation were upregulated. Most prominently, the PurR-regulon required for de novo purine biosynthesis was derepressed indicating purine depletion. The general stress response was activated energy dependently and in a subpopulation of treated cultures an early onset of sporulation was observed, most likely triggered by low guanosine triphosphate levels. Supplementation of adenosine triphosphate, adenosine, and guanosine to the medium substantially decreased antibacterial activity, showing that purine depletion becomes the bottleneck in trimethoprim-treated B. subtilis. The frequently prescribed antibiotic trimethoprim causes purine depletion in B. subtilis, which can be complemented by supplementing purines to the medium. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Room-Temperature Coherent Optical Phonon in 2D Electronic Spectra of CH3NH3PbI3 Perovskite as a Possible Cooling Bottleneck

    Energy Technology Data Exchange (ETDEWEB)

    Monahan, Daniele M. [Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Kavli Energy NanoSciences Inst. at Berkeley, Berkeley, CA (United States); Guo, Liang [Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Kavli Energy NanoSciences Inst. at Berkeley, Berkeley, CA (United States); Lin, Jia [Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Kavli Energy NanoSciences Inst. at Berkeley, Berkeley, CA (United States); Dou, Letian [Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Kavli Energy NanoSciences Inst. at Berkeley, Berkeley, CA (United States); Yang, Peidong [Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Kavli Energy NanoSciences Inst. at Berkeley, Berkeley, CA (United States); Fleming, Graham R. [Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Kavli Energy NanoSciences Inst. at Berkeley, Berkeley, CA (United States)

    2017-06-29

    A hot phonon bottleneck may be responsible for slow hot carrier cooling in methylammonium lead iodide hybrid perovskite, creating the potential for more efficient hot carrier photovoltaics. In room-temperature 2D electronic spectra near the band edge, we observe in this paper amplitude oscillations due to a remarkably long lived 0.9 THz coherent phonon population at room temperature. This phonon (or set of phonons) is assigned to angular distortions of the Pb–I lattice, not coupled to cation rotations. The strong coupling between the electronic transition and the 0.9 THz mode(s), together with relative isolation from other phonon modes, makes it likely to cause a phonon bottleneck. Finally, the pump frequency resolution of the 2D spectra also enables independent observation of photoinduced absorptions and bleaches independently and confirms that features due to band gap renormalization are longer-lived than in transient absorption spectra.

  20. Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci: high variation but low differentiation

    DEFF Research Database (Denmark)

    Simonsen, Bo Thisted; Siegismund, H R; Arctander, P

    1998-01-01

    The African buffalo (Syncerus caffer) is widespread throughout sub-Saharan Africa and is found in most major vegetation types, wherever permanent sources of water are available, making it physically able to disperse through a wide range of habitats. Despite this, the buffalo has been assumed...... and analysis of variation at six microsatellite loci among 11 localities in eastern and southern Africa. High levels of genetic variability were found, suggesting that reported severe population bottlenecks due to outbreak of rinderpest during the last century did not strongly reduce the genetic variability...

  1. The Plasmodium bottleneck: malaria parasite losses in the mosquito vector

    Science.gov (United States)

    Smith, Ryan C; Vega-Rodríguez, Joel; Jacobs-Lorena, Marcelo

    2014-01-01

    Nearly one million people are killed every year by the malaria parasite Plasmodium. Although the disease-causing forms of the parasite exist only in the human blood, mosquitoes of the genus Anopheles are the obligate vector for transmission. Here, we review the parasite life cycle in the vector and highlight the human and mosquito contributions that limit malaria parasite development in the mosquito host. We address parasite killing in its mosquito host and bottlenecks in parasite numbers that might guide intervention strategies to prevent transmission. PMID:25185005

  2. Population genetic structure of the malaria vector Anopheles funestus, in a recently re-colonized area of the Senegal River basin and human-induced environmental changes.

    Science.gov (United States)

    Samb, Badara; Dia, Ibrahima; Konate, Lassana; Ayala, Diego; Fontenille, Didier; Cohuet, Anna

    2012-09-05

    Anopheles funestus is one of the major malaria vectors in tropical Africa. Because of several cycles of drought events that occurred during the 1970s, this species had disappeared from many parts of sahelian Africa, including the Senegal River basin. However, this zone has been re-colonized during the last decade by An. funestus, following the implementation of two dams on the Senegal River. Previous studies in that area revealed heterogeneity at the biological and chromosomal level among these recent populations. Here, we studied the genetic structure of the newly established mosquito populations using eleven microsatellite markers in four villages of the Senegal River basin and compared it to another An. funestus population located in the sudanian domain. Our results presume Hardy Weinberg equilibrium in each An. funestus population, suggesting a situation of panmixia. Moreover, no signal from bottleneck or population expansion was detected across populations. The tests of genetic differentiation between sites revealed a slight but significant division into three distinct genetic entities. Genetic distance between populations from the Senegal River basin and sudanian domain was correlated to geographical distance. In contrast, sub-division into the Senegal River basin was not correlated to geographic distance, rather to local adaptation. The high genetic diversity among populations from Senegal River basin coupled with no evidence of bottleneck and with a gene flow with southern population suggests that the re-colonization was likely carried out by a massive and repeated stepping-stone dispersion starting from the neighboring areas where An. funestus endured.

  3. Investigating the Genetic Diversity, Population Differentiation and Population Dynamics of Cycas segmentifida (Cycadaceae Endemic to Southwest China by Multiple Molecular Markers

    Directory of Open Access Journals (Sweden)

    Xiuyan Feng

    2017-05-01

    Full Text Available Climate change, species dispersal ability and habitat fragmentation are major factors influencing species distribution and genetic diversity, especially for the range-restricted and threatened taxa. Here, using four sequences of chloroplast DNAs (cpDNAs, three nuclear genes (nDNAs and 12 nuclear microsatellites (SSRs, we investigated the genetic diversity, genetic structure, divergence time and population dynamics of Cycas segmentifida D. Y. Wang and C. Y. Deng, a threatened cycad species endemic to Southwest China. High levels of genetic diversity and genetic differentiation were revealed in C. segmentifida. Haplotypes of networks showed two evolutionary units in C. segmentifida, with the exception of the nuclear gene GTP network. Meanwhile, the UPGMA tree, structure and PCoA analyses suggested that 14 populations of C. segmentifida were divided into two clades. There was significant effect of isolation by distance (IBD in this species. However, this species did not display a significant phylogeographic structure. The divergence time estimation suggested that its haplotypes diverged during the Middle Pleistocene. Additionally, the population dynamics inferred from different DNA sequences analyses were discordant. Bottleneck analysis showed that populations of C. segmentifida did not experience any recent bottleneck effect, but rather pointed to a contraction of its effective population size over time. Furthermore, our results suggested that the population BM which held an intact population structure and occupied undisturbed habitat was at the Hardy–Weinberg equilibrium, implying that this population is a free-mating system. These genetic features provide important information for the sustainable management of C. segmentifida.

  4. Dynamics of the central bottleneck: dual-task and task uncertainty.

    Directory of Open Access Journals (Sweden)

    Mariano Sigman

    2006-07-01

    Full Text Available Why is the human brain fundamentally limited when attempting to execute two tasks at the same time or in close succession? Two classical paradigms, psychological refractory period (PRP and task switching, have independently approached this issue, making significant advances in our understanding of the architecture of cognition. Yet, there is an apparent contradiction between the conclusions derived from these two paradigms. The PRP paradigm, on the one hand, suggests that the simultaneous execution of two tasks is limited solely by a passive structural bottleneck in which the tasks are executed on a first-come, first-served basis. The task-switching paradigm, on the other hand, argues that switching back and forth between task configurations must be actively controlled by a central executive system (the system controlling voluntary, planned, and flexible action. Here we have explicitly designed an experiment mixing the essential ingredients of both paradigms: task uncertainty and task simultaneity. In addition to a central bottleneck, we obtain evidence for active processes of task setting (planning of the appropriate sequence of actions and task disengaging (suppression of the plan set for the first task in order to proceed with the next one. Our results clarify the chronometric relations between these central components of dual-task processing, and in particular whether they operate serially or in parallel. On this basis, we propose a hierarchical model of cognitive architecture that provides a synthesis of task-switching and PRP paradigms.

  5. Molecular population genetics of the β-esterase gene cluster of ...

    Indian Academy of Sciences (India)

    We suggest that the demographic history (bottleneck and admixture of genetically differentiated populations) is the major factor shaping the pattern of nucleotide polymorphism in the -esterase gene cluster. However there are some 'footprints' of directional and balancing selection shaping specific distribution of nucleotide ...

  6. Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks.

    Directory of Open Access Journals (Sweden)

    Joseph Hughes

    2012-12-01

    Full Text Available The ability of influenza A viruses (IAVs to cross species barriers and evade host immunity is a major public health concern. Studies on the phylodynamics of IAVs across different scales - from the individual to the population - are essential for devising effective measures to predict, prevent or contain influenza emergence. Understanding how IAVs spread and evolve during outbreaks is critical for the management of epidemics. Reconstructing the transmission network during a single outbreak by sampling viral genetic data in time and space can generate insights about these processes. Here, we obtained intra-host viral sequence data from horses infected with equine influenza virus (EIV to reconstruct the spread of EIV during a large outbreak. To this end, we analyzed within-host viral populations from sequences covering 90% of the infected yards. By combining gene sequence analyses with epidemiological data, we inferred a plausible transmission network, in turn enabling the comparison of transmission patterns during the course of the outbreak and revealing important epidemiological features that were not apparent using either approach alone. The EIV populations displayed high levels of genetic diversity, and in many cases we observed distinct viral populations containing a dominant variant and a number of related minor variants that were transmitted between infectious horses. In addition, we found evidence of frequent mixed infections and loose transmission bottlenecks in these naturally occurring populations. These frequent mixed infections likely influence the size of epidemics.

  7. The Plasmodium bottleneck: malaria parasite losses in the mosquito vector

    Directory of Open Access Journals (Sweden)

    Ryan C Smith

    2014-08-01

    Full Text Available Nearly one million people are killed every year by the malaria parasite Plasmodium. Although the disease-causing forms of the parasite exist only in the human blood, mosquitoes of the genus Anopheles are the obligate vector for transmission. Here, we review the parasite life cycle in the vector and highlight the human and mosquito contributions that limit malaria parasite development in the mosquito host. We address parasite killing in its mosquito host and bottlenecks in parasite numbers that might guide intervention strategies to prevent transmission.

  8. Ethnicity of severe trauma patients: results of a population-based study, Auckland, New Zealand 2004.

    Science.gov (United States)

    Creamer, Gowan; Civil, Ian; Ng, Alex; Adams, David; Cacala, Shas; Koelmeyer, Timothy; Thompson, John

    2010-06-11

    To investigate the role of Māori and Pacific ethnicity within the severe trauma and population demographics of Auckland, New Zealand. A population-based study utilising prospectively gathered trauma databases and coronial autopsy information. Population data was derived from Statistics New Zealand resident population projections for the year 2004. The geographic boundaries of the Auckland district health boards (Waitemata DHB, Auckland DHB and Counties-Manukau DHB). Severe injury was defined as death or injury severity score more than 15. Combining data from coronial autopsy and four hospital trauma databases provided age, gender, ethnicity, mechanism, mortality and hospitalisation information for severely injured Aucklanders. Māori and Pacific had increased risk of severe injury and injury-related mortality. A major gender difference is apparent: Māori female at increased risk and Pacific female at decreased risk compared to the remaining female population; both Māori and Pacific male have high severe injury rate than the remaining population. The relative risk for severe injury (and mortality) for Māori RR=2.38 (RR=2.80) and Pacific RR=1.49 (RR=1.59) is higher than the remaining population, the highest risk (and more statistically significant) is seen in the 15-29 age group (Māori RR=2.87, Pacific RR=2.57). Road traffic crashes account for the greatest proportion of injuries in all groups. Māori have relatively higher rates of hanging and assault-related injury and death; Pacific have relatively higher rates of falls and assault. Ethnicity is a factor in severe injury and mortality rates in Auckland. Age is an important influence on these rates. Although mechanism of injury varies between ethnic groups, no particular mechanism of injury accounts for the overall differences between groups.

  9. The Addiction Severity Index: Reliability and validity in a Dutch alcoholic population

    NARCIS (Netherlands)

    Dejong, C.A.J.; Willems, J.C.E.W.; Schippers, G.M.; Hendriks, V.M.

    1995-01-01

    The Addiction Severity Index (ASI) was evaluated for its psychometric qualities in a Dutch alcoholic population admitted to an addiction treatment center in the Netherlands. Its factorial structure in this population was found to be consistent with the established six factor structure of the ASI.

  10. Omalizumab Treatment Response in a Population With Severe Allergic Asthma and Overlapping COPD.

    Science.gov (United States)

    Maltby, Steven; Gibson, Peter G; Powell, Heather; McDonald, Vanessa M

    2017-01-01

    Asthma and COPD are common airway diseases. Individuals with overlapping asthma and COPD experience increased health impairment and severe disease exacerbations. Efficacious treatment options are required for this population. Omalizumab (anti-IgE) therapy is effective in patients with severe persistent asthma, but limited data are available on efficacy in populations with overlapping asthma and COPD. Data from the Australian Xolair Registry were used to compare treatment responses in individuals with asthma-COPD overlap with responses in patients with severe asthma alone. Participants were assessed at baseline and after 6 months of omalizumab treatment. We used several different definitions of asthma-COPD overlap. First, we compared participants with a previous physician diagnosis of COPD to participants with no COPD diagnosis. We then made comparisons based on baseline lung function, comparing participants with an FEV 1 80% predicted after bronchodilator use. In the population with an FEV 1 Omalizumab treatment markedly improved asthma control and health-related quality of life in all populations assessed based on the Asthma Control Questionnaire and Asthma Quality of Life Questionnaire scores. Omalizumab treatment did not improve lung function (FEV 1 , FVC, or FEV 1 /FVC ratio) in populations that were enriched for asthma-COPD overlap (diagnosis of COPD or FEV 1  omalizumab improves asthma control and health-related quality of life in individuals with severe allergic asthma and overlapping COPD. These findings provide real-world efficacy data for this patient population and suggest that omalizumab is useful in the management of severe asthma with COPD overlap. Copyright © 2016 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.

  11. Turtle soup, Prohibition, and the population genetic structure of Diamondback Terrapins (Malaclemys terrapin).

    Science.gov (United States)

    Converse, Paul E; Kuchta, Shawn R; Hauswaldt, J Susanne; Roosenburg, Willem M

    2017-01-01

    Diamondback terrapins (Malaclemys terrapin) were a popular food item in early twentieth century America, and were consumed in soup with sherry. Intense market demand for terrapin meat resulted in population declines, notably along the Atlantic seaboard. Efforts to supply terrapins to markets resulted in translocation events, as individuals were moved about to stock terrapin farms. However, in 1920 the market for turtle soup buckled with the enactment of the eighteenth amendment to the United States' Constitution-which initiated the prohibition of alcoholic drinks-and many terrapin fisheries dumped their stocks into local waters. We used microsatellite data to show that patterns of genetic diversity along the terrapin's coastal range are consistent with historical accounts of translocation and cultivation activities. We identified possible instances of human-mediated dispersal by estimating gene flow over historical and contemporary timescales, Bayesian model testing, and bottleneck tests. We recovered six genotypic clusters along the Gulf and Atlantic coasts with varying degrees of admixture, including increased contemporary gene flow from Texas to South Carolina, from North Carolina to Maryland, and from North Carolina to New York. In addition, Bayesian models incorporating translocation events outperformed stepping-stone models. Finally, we were unable to detect population bottlenecks, possibly due to translocation reintroducing genetic diversity into bottlenecked populations. Our data suggest that current patterns of genetic diversity in the terrapin were altered by the demand for turtle soup followed by the enactment of alcohol prohibition. In addition, our study shows that population genetic tools can elucidate metapopulation dynamics in taxa with complex genetic histories impacted by anthropogenic activities.

  12. Design of a model to predict surge capacity bottlenecks for burn mass casualties at a large academic medical center.

    Science.gov (United States)

    Abir, Mahshid; Davis, Matthew M; Sankar, Pratap; Wong, Andrew C; Wang, Stewart C

    2013-02-01

    To design and test a model to predict surge capacity bottlenecks at a large academic medical center in response to a mass-casualty incident (MCI) involving multiple burn victims. Using the simulation software ProModel, a model of patient flow and anticipated resource use, according to principles of disaster management, was developed based upon historical data from the University Hospital of the University of Michigan Health System. Model inputs included: (a) age and weight distribution for casualties, and distribution of size and depth of burns; (b) rate of arrival of casualties to the hospital, and triage to ward or critical care settings; (c) eligibility for early discharge of non-MCI inpatients at time of MCI; (d) baseline occupancy of intensive care unit (ICU), surgical step-down, and ward; (e) staff availability-number of physicians, nurses, and respiratory therapists, and the expected ratio of each group to patients; (f) floor and operating room resources-anticipating the need for mechanical ventilators, burn care and surgical resources, blood products, and intravenous fluids; (g) average hospital length of stay and mortality rate for patients with inhalation injury and different size burns; and (h) average number of times that different size burns undergo surgery. Key model outputs include time to bottleneck for each limiting resource and average waiting time to hospital bed availability. Given base-case model assumptions (including 100 mass casualties with an inter-arrival rate to the hospital of one patient every three minutes), hospital utilization is constrained within the first 120 minutes to 21 casualties, due to the limited number of beds. The first bottleneck is attributable to exhausting critical care beds, followed by floor beds. Given this limitation in number of patients, the temporal order of the ensuing bottlenecks is as follows: Lactated Ringer's solution (4 h), silver sulfadiazine/Silvadene (6 h), albumin (48 h), thrombin topical (72 h), type

  13. To an optimal electricity supply system. Possible bottlenecks in the development to an optimal electricity supply system in northwest Europe

    International Nuclear Information System (INIS)

    Van Werven, M.J.N.; De Joode, J.; Scheepers, M.J.J.

    2006-02-01

    It is uncertain how the electricity system in Europe, and in particular northwest Europe and the Netherlands, will develop in the next fifteen years. The main objective of this report is to identify possible bottlenecks that may hamper the northwest European electricity system to develop into an optimal system in the long term (until 2020). Subsequently, based on the identified bottlenecks, the report attempts to indicate relevant market response and policy options. To be able to identify possible bottlenecks in the development to an optimal electricity system, an analytical framework has been set up with the aim to identify possible (future) problems in a structured way. The segments generation, network, demand, balancing, and policy and regulation are analysed, as well as the interactions between these segments. Each identified bottleneck is assessed on the criteria reliability, sustainability and affordability. Three bottlenecks are analysed in more detail: (1) The increasing penetration of distributed generation (DG) and its interaction with the electricity network. Dutch policy could be aimed at: (a) Gaining more insight in the costs and benefits that result from the increasing penetration of DG; (b) Creating possibilities for DSOs to experiment with innovative (network management) concepts; (c) Introducing locational signals; and (d) Further analyse the possibility of ownership unbundling; (2) The problem of intermittency and its implications for balancing the electricity system. Dutch policy could be aimed at: (a) Creating the environment in which the market is able to respond in an efficient way; (b) Monitoring market responses; (c) Market coupling; and (d) Discussing the timing of the gate closure; and (3) Interconnection and congestion issues in combination with generation. Dutch policy could be aimed at: (a) Using the existing interconnection capacity as efficient as possible; (b) Identifying the causes behind price differences; and (c) Harmonise market

  14. Identification, genealogical structure and population genetics of S-alleles in Malus sieversii, the wild ancestor of domesticated apple.

    Science.gov (United States)

    Ma, X; Cai, Z; Liu, W; Ge, S; Tang, L

    2017-09-01

    The self-incompatibility (SI) gene that is specifically expressed in pistils encodes the SI-associated ribonuclease (S-RNase), functioning as the female-specificity determinant of a gametophytic SI system. Despite extensive surveys in Malus domestica, the S-alleles have not been fully investigated for Malus sieversii, the primary wild ancestor of the domesticated apple. Here we screened the M. sieversii S-alleles via PCR amplification and sequencing, and identified 14 distinct alleles in this species. By contrast, nearly 40 are present in its close wild relative, Malus sylvestris. We further sequenced 8 nuclear genes to provide a neutral reference, and investigated the evolution of S-alleles via genealogical and population genetic analyses. Both shared ancestral polymorphism and an excess of non-synonymous substitution were detected in the S-RNases of the tribe Maleae in Rosaceae, indicating the action of long-term balancing selection. Approximate Bayesian Computations based on the reference neutral loci revealed a severe bottleneck in four of the six studied M. sieversii populations, suggesting that the low number of S-alleles found in this species is mainly the result of diversity loss due to a drastic population contraction. Such a bottleneck may lead to ambiguous footprints of ongoing balancing selection detected at the S-locus. This study not only elucidates the constituents and number of S-alleles in M. sieversii but also illustrates the potential utility of S-allele number shifts in demographic inference for self-incompatible plant species.

  15. An assessment of The Capacity Drops at The Bottleneck Segments: A review on the existing methodologies

    Directory of Open Access Journals (Sweden)

    Sugiarto Sugiarto

    2015-08-01

    Full Text Available The term of capacity is very useful to quantify the ability of transport facilities in terms of carrying traffic. The capacity of the road is an essential ingredient in the planning, design, and operation of roadways. It is desirable for traffic analyst to be able to predict the time and places where congestion will occur and the volumes to be expected. Most of urbanized areas have been experiencing of traffic congestion problems particularly at urban arterial systems. High traffic demand and limited supply of roadways are always the main factors produced traffic congestion. However, there are other sources of local and temporal congestion, such as uncontrolled access point, median opening and on-street parking activities, which are caused a reduction of roadway capacity during peak operations. Those locations could result in reduction of travel speed and road, as known as hidden bottlenecks. This is bottleneck which is without any changes in geometric of the segments. The Indonesian Highway Capacity Manual (IHCM, 1997 is used to assess urban arterial systems till current days. IHCM provides a static method for examining the capacityand does not systematically take into account of bottleneck activities. However, bottleneck activities create interruption smooth traffic flow along arterial streets, which in turns stimulate related problems, such as, excessive air pollution, additional energy consumption and driver’s frustration due to traffic jammed. This condition could happen simultaneously; mostly repetitive and predictable in same peak hour demands. Therefore, this paper carefully summarize on the existing methodologies considering required data, handled data processing and expected output of each proposed of analysis. We further notice that dynamic approach could be more appropriated for analyzing temporal congestion segments (median opening, on street parking, etc.. Method of oblique cumulative plot seems to be more applicable in terms of

  16. The ups and downs of coral reef fishes: the genetic characteristics of a formerly severely overfished but currently recovering Nassau grouper fish spawning aggregation

    Science.gov (United States)

    Bernard, A. M.; Feldheim, K. A.; Nemeth, R.; Kadison, E.; Blondeau, J.; Semmens, B. X.; Shivji, M. S.

    2016-03-01

    The Nassau grouper ( Epinephelus striatus) has sustained large declines across its distribution, including extirpation of many of its fish spawning aggregations (FSAs). Within US Virgin Islands (USVI) waters, Nassau grouper FSAs were overfished until their disappearance in the 1970s and 1980s. In the early 2000s, however, Nassau grouper were found gathering at Grammanik Bank, USVI, a mesophotic coral reef adjacent to one of the extinct aggregation sites, and regulatory protective measures were implemented to protect this fledgling FSA. The population genetic dynamics of this rapid FSA deterioration followed by protection-facilitated, incipient recovery are unknown. We addressed two objectives: (1) we explored which factors (i.e., local vs. external recruitment) might be key in shaping the USVI FSA recovery; and (2) we examined the consequences of severe past overfishing on this FSA's current genetic status. We genotyped individuals (15 microsatellites) from the USVI FSA comprising three successive spawning years (2008-2010), as well as individuals from a much larger, presumably less impacted, Nassau grouper FSA in the Cayman Islands, to assess their comparative population dynamics. No population structure was detected between the USVI and Cayman FSAs ( F ST = -0.0004); however, a temporally waning, genetic bottleneck signal was detected in the USVI FSA. Parentage analysis failed to identify any parent-offspring matches between USVI FSA adults and nearby juveniles, and relatedness analysis showed low levels of genetic relatedness among USVI FSA individuals. Genetic diversity across USVI FSA temporal collections was relatively high, and no marked differences were found between the USVI and Cayman FSAs. These collective results suggest that external recruitment is an important driver of the USVI FSA recovery. Furthermore, despite an apparent genetic bottleneck, the genetic diversity of USVI Nassau grouper has not been severely compromised. Our findings also provide a

  17. Population genetics of the black scar oyster, Crassostrea iredalei: repercussion of anthropogenic interference.

    Science.gov (United States)

    Zainal Abidin, Danial Hariz; Mustaffa, Suzana; Rahim, Masazurah A; Nair, Devakie M; Naim, Darlina Md; Mohd Nor, Siti Azizah

    2016-01-01

    Mitochondrial cytochrome oxidase subunit I (COI) gene was utilized to assess the population genetics of the commercially important black scar oyster, Crassostrea iredalei among 11 populations throughout the west and east coasts Peninsular Malaysia and Sabah (Malaysian Borneo). Overall, populations of C. iredalei demonstrated low nucleotide diversity π (0.000-0.004) and low-to-high haplotype diversity h (0.000-0.795) levels. Genetic structuring was detected between the Peninsular Malaysia and Sabah populations as revealed by the FST analysis. However, the COI gene analyses showed minimal and non-significant (p > 0.05) population differentiation within the east and west coasts Peninsular Malaysia and Sabah regions. This was attributed to both high larval dispersal along the east and west coasts and human-driven spat translocation between the two coastlines due to C. iredalei cultivation practices. Phylogeographic relationships inferences were also conducted to further support these hypotheses. The neutrality and mismatch distribution analyses suggested that C. iredalei had experienced a/several bottleneck event(s), followed by population expansion. The molecular information obtained from this study could be incorporated in a pragmatic aquaculture management strategy of wild broodstock and the hatchery lines of C. iredalei in Malaysia.

  18. The Canarian Camel: A Traditional Dromedary Population

    Directory of Open Access Journals (Sweden)

    Ursula Schulz

    2010-04-01

    Full Text Available The domestic camel (dromedary is the most important livestock species in the Canary Islands and the most important autochthonous European camel population. After six centuries of a successful adaptation process to the particular environment of the Canary Islands, the abandonment of traditional agriculture has led this population to a major bottleneck. Along with a lack of foreign genetic interchanges, this could lead the population to the brink of extinction. Genetic analysis using 13 microsatellites showed the closest genetic proximity to the North African (Tindouf, Algeria camel population and a certain degree of sub-division, with significant genetic differences among breeders. An important level of genetic differentiation among the different populations analyzed was found with a global FST value of 0.116.

  19. Achievements & bottlenecks in humanitarian demining EU-funded research: Final results from the EC DELVE project

    NARCIS (Netherlands)

    Sahli, H.; Bruschini, C.; Kempen, L. van; Schleijpen, H.M.A.; Breejen, E. den

    2008-01-01

    The EC DELVE Support Action project has analyzed the bottlenecks in the transfer of Humanitarian Demining (HD) technology from technology development to the use in the field, and drawn some lessons learned, basing itself on the assessment of the European Humanitarian Demining Research and Technology

  20. Urban park characteristics, genetic variation, and historical demography of white-footed mouse (Peromyscus leucopus populations in New York City

    Directory of Open Access Journals (Sweden)

    Jason Munshi-South

    2014-03-01

    Full Text Available Severe fragmentation is a typical fate of native remnant habitats in cities, and urban wildlife with limited dispersal ability are predicted to lose genetic variation in isolated urban patches. However, little information exists on the characteristics of urban green spaces required to conserve genetic variation. In this study, we examine whether isolation in New York City (NYC parks results in genetic bottlenecks in white-footed mice (Peromyscus leucopus, and test the hypotheses that park size and time since isolation are associated with genetic variability using nonlinear regression and information-theoretic model selection. White-footed mice have previously been documented to exhibit male-biased dispersal, which may create disparities in genetic variation between males and females in urban parks. We use genotypes of 18 neutral microsatellite data and four different statistical tests to assess this prediction. Given that sex-biased dispersal may create disparities between population genetic patterns inferred from bi- vs. uni-parentally inherited markers, we also sequenced a 324 bp segment of the mitochondrial D-loop for independent inferences of historical demography in urban P. leucopus. We report that isolation in urban parks does not necessarily result in genetic bottlenecks; only three out of 14 populations in NYC parks exhibited a signature of a recent bottleneck at 18 neutral microsatellite loci. Mouse populations in larger urban parks, or parks that have been isolated for shorter periods of time, also do not generally contain greater genetic variation than populations in smaller parks. These results suggest that even small networks of green spaces may be sufficient to maintain the evolutionary potential of native species with certain characteristics. We also found that isolation in urban parks results in weak to nonexistent sex-biased dispersal in a species known to exhibit male-biased dispersal in less fragmented environments. In

  1. Modelling of lane-changing behaviour integrating with merging effect before a city road bottleneck

    Science.gov (United States)

    Lv, Wei; Song, Wei-guo; Fang, Zhi-ming; Ma, Jian

    2013-10-01

    Merging behaviour is a compulsive action in a discretionary lane-changing traffic system, especially in a system with a bottleneck. This paper aims to investigate the generic lane-changing behaviour considering the merging effect before a city road bottleneck. Thus firstly the merging behaviour is distinguished from other generic lane-changing behaviour. Combining discretionary lane-changing and compulsive merging, we developed an integrative traffic model, in which a method to calculate the lane-changing probability and the merging probability was proposed. A simulation scenario derived from real life was conducted to validate the proposed programming algorithm. Finally, a discussion on the simulation findings shows that the merging influence can be expanded and the merging behaviour can increase the probability of local traffic jamming in its affected area of the adjacent lane. The distribution of the merging distance provides fundamental insights for actual traffic management. The result of the clearance time implies the position of the incident point has a significant effect on the clearing time and it is important to ensure the end (exit) of the road is unimpeded in traffic evacuation.

  2. HIV/AIDS: global trends, global funds and delivery bottlenecks

    Directory of Open Access Journals (Sweden)

    Hadingham Jacqui

    2005-08-01

    Full Text Available Abstract Globalisation affects all facets of human life, including health and well being. The HIV/AIDS epidemic has highlighted the global nature of human health and welfare and globalisation has given rise to a trend toward finding common solutions to global health challenges. Numerous international funds have been set up in recent times to address global health challenges such as HIV. However, despite increasingly large amounts of funding for health initiatives being made available to poorer regions of the world, HIV infection rates and prevalence continue to increase world wide. As a result, the AIDS epidemic is expanding and intensifying globally. Worst affected are undoubtedly the poorer regions of the world as combinations of poverty, disease, famine, political and economic instability and weak health infrastructure exacerbate the severe and far-reaching impacts of the epidemic. One of the major reasons for the apparent ineffectiveness of global interventions is historical weaknesses in the health systems of underdeveloped countries, which contribute to bottlenecks in the distribution and utilisation of funds. Strengthening these health systems, although a vital component in addressing the global epidemic, must however be accompanied by mitigation of other determinants as well. These are intrinsically complex and include social and environmental factors, sexual behaviour, issues of human rights and biological factors, all of which contribute to HIV transmission, progression and mortality. An equally important factor is ensuring an equitable balance between prevention and treatment programmes in order to holistically address the challenges presented by the epidemic.

  3. Steiner tree heuristic in the Euclidean d-space using bottleneck distances

    DEFF Research Database (Denmark)

    Lorenzen, Stephan Sloth; Winter, Pawel

    2016-01-01

    Some of the most efficient heuristics for the Euclidean Steiner minimal tree problem in the d-dimensional space, d ≥2, use Delaunay tessellations and minimum spanning trees to determine small subsets of geometrically close terminals. Their low-cost Steiner trees are determined and concatenated...... in a greedy fashion to obtain a low cost tree spanning all terminals. The weakness of this approach is that obtained solutions are topologically related to minimum spanning trees. To avoid this and to obtain even better solutions, bottleneck distances are utilized to determine good subsets of terminals...

  4. Curvature and bottlenecks control molecular transport in inverse bicontinuous cubic phases

    Science.gov (United States)

    Assenza, Salvatore; Mezzenga, Raffaele

    2018-02-01

    We perform a simulation study of the diffusion of small solutes in the confined domains imposed by inverse bicontinuous cubic phases for the primitive, diamond, and gyroid symmetries common to many lipid/water mesophase systems employed in experiments. For large diffusing domains, the long-time diffusion coefficient shows universal features when the size of the confining domain is renormalized by the Gaussian curvature of the triply periodic minimal surface. When bottlenecks are widely present, they become the most relevant factor for transport, regardless of the connectivity of the cubic phase.

  5. Only adding stationary storage to vaccine supply chains may create and worsen transport bottlenecks.

    Science.gov (United States)

    Haidari, Leila A; Connor, Diana L; Wateska, Angela R; Brown, Shawn T; Mueller, Leslie E; Norman, Bryan A; Schmitz, Michelle M; Paul, Proma; Rajgopal, Jayant; Welling, Joel S; Leonard, Jim; Claypool, Erin G; Weng, Yu-Ting; Chen, Sheng-I; Lee, Bruce Y

    2013-01-01

    Although vaccine supply chains in many countries require additional stationary storage and transport capacity to meet current and future needs, international donors tend to donate stationary storage devices far more often than transport equipment. To investigate the impact of only adding stationary storage equipment on the capacity requirements of transport devices and vehicles, we used HERMES (Highly Extensible Resource for Modeling Supply Chains) to construct a discrete event simulation model of the Niger vaccine supply chain. We measured the transport capacity requirement for each mode of transport used in the Niger vaccine cold chain, both before and after adding cold rooms and refrigerators to relieve all stationary storage constraints in the system. With the addition of necessary stationary storage, the average transport capacity requirement increased from 88% to 144% for cold trucks, from 101% to 197% for pickup trucks, and from 366% to 420% for vaccine carriers. Therefore, adding stationary storage alone may worsen or create new transport bottlenecks as more vaccines flow through the system, preventing many vaccines from reaching their target populations. Dynamic modeling can reveal such relationships between stationary storage capacity and transport constraints.

  6. Client-server computer architecture saves costs and eliminates bottlenecks

    International Nuclear Information System (INIS)

    Darukhanavala, P.P.; Davidson, M.C.; Tyler, T.N.; Blaskovich, F.T.; Smith, C.

    1992-01-01

    This paper reports that workstation, client-server architecture saved costs and eliminated bottlenecks that BP Exploration (Alaska) Inc. experienced with mainframe computer systems. In 1991, BP embarked on an ambitious project to change technical computing for its Prudhoe Bay, Endicott, and Kuparuk operations on Alaska's North Slope. This project promised substantial rewards, but also involved considerable risk. The project plan called for reservoir simulations (which historically had run on a Cray Research Inc. X-MP supercomputer in the company's Houston data center) to be run on small computer workstations. Additionally, large Prudhoe Bay, Endicott, and Kuparuk production and reservoir engineering data bases and related applications also would be moved to workstations, replacing a Digital Equipment Corp. VAX cluster in Anchorage

  7. The Addiction Severity Index: reliability and validity in a Dutch alcoholic population.

    Science.gov (United States)

    DeJong, C A; Willems, J C; Schippers, G M; Hendriks, V M

    1995-04-01

    The Addiction Severity Index (ASI) was evaluated for its psychometric qualities in a Dutch alcoholic population admitted to an addiction treatment center in The Netherlands. Its factorial structure in this population was found to be consistent with the established six factor structure of the ASI. Reliability analysis revealed that the homogeneity of the subscales was acceptable with the exception of the Alcohol Scale. The six subscales were not highly intercorrelated. The results of this study indicate that the ASI is a useful instrument for the assessment of several problems associated with alcoholism. However, the Alcohol Scale appears to be limited as a diagnostic and research instrument in the field of inpatient treatment of alcohol dependence in The Netherlands.

  8. Independent bottlenecks characterize colonization of systemic compartments and gut lymphoid tissue by salmonella.

    Science.gov (United States)

    Lim, Chee Han; Voedisch, Sabrina; Wahl, Benjamin; Rouf, Syed Fazle; Geffers, Robert; Rhen, Mikael; Pabst, Oliver

    2014-07-01

    Vaccination represents an important instrument to control typhoid fever in humans and protects mice from lethal infection with mouse pathogenic serovars of Salmonella species. Mixed infections with tagged Salmonella can be used in combination with probabilistic models to describe the dynamics of the infection process. Here we used mixed oral infections with tagged Salmonella strains to identify bottlenecks in the infection process in naïve and vaccinated mice. We established a next generation sequencing based method to characterize the composition of tagged Salmonella strains which offers a fast and reliable method to characterise the composition of genome-tagged Salmonella strains. We show that initial colonization of Salmonella was distinguished by a non-Darwinian selection of few bacteria setting up the infection independently in gut associated lymphoid tissue and systemic compartments. Colonization of Peyer's patches fuels the sustained spread of bacteria into mesenteric lymph nodes via dendritic cells. In contrast, infection of liver and spleen originated from an independent pool of bacteria. Vaccination only moderately reduced invasion of Peyer's patches but potently uncoupled bacterial populations present in different systemic compartments. Our data indicate that vaccination differentially skews the capacity of Salmonella to colonize systemic and gut immune compartments and provide a framework for the further dissection of infection dynamics.

  9. Independent bottlenecks characterize colonization of systemic compartments and gut lymphoid tissue by salmonella.

    Directory of Open Access Journals (Sweden)

    Chee Han Lim

    2014-07-01

    Full Text Available Vaccination represents an important instrument to control typhoid fever in humans and protects mice from lethal infection with mouse pathogenic serovars of Salmonella species. Mixed infections with tagged Salmonella can be used in combination with probabilistic models to describe the dynamics of the infection process. Here we used mixed oral infections with tagged Salmonella strains to identify bottlenecks in the infection process in naïve and vaccinated mice. We established a next generation sequencing based method to characterize the composition of tagged Salmonella strains which offers a fast and reliable method to characterise the composition of genome-tagged Salmonella strains. We show that initial colonization of Salmonella was distinguished by a non-Darwinian selection of few bacteria setting up the infection independently in gut associated lymphoid tissue and systemic compartments. Colonization of Peyer's patches fuels the sustained spread of bacteria into mesenteric lymph nodes via dendritic cells. In contrast, infection of liver and spleen originated from an independent pool of bacteria. Vaccination only moderately reduced invasion of Peyer's patches but potently uncoupled bacterial populations present in different systemic compartments. Our data indicate that vaccination differentially skews the capacity of Salmonella to colonize systemic and gut immune compartments and provide a framework for the further dissection of infection dynamics.

  10. Genetic Variation and Population Structure in Jamunapari Goats Using Microsatellites, Mitochondrial DNA, and Milk Protein Genes

    Science.gov (United States)

    Rout, P. K.; Thangraj, K.; Mandal, A.; Roy, R.

    2012-01-01

    Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation

  11. Phonon bottleneck identification in disordered nanoporous materials

    Science.gov (United States)

    Romano, Giuseppe; Grossman, Jeffrey C.

    2017-09-01

    Nanoporous materials are a promising platform for thermoelectrics in that they offer high thermal conductivity tunability while preserving good electrical properties, a crucial requirement for high-efficiency thermal energy conversion. Understanding the impact of the pore arrangement on thermal transport is pivotal to engineering realistic materials, where pore disorder is unavoidable. Although there has been considerable progress in modeling thermal size effects in nanostructures, it has remained a challenge to screen such materials over a large phase space due to the slow simulation time required for accurate results. We use density functional theory in connection with the Boltzmann transport equation to perform calculations of thermal conductivity in disordered porous materials. By leveraging graph theory and regressive analysis, we identify the set of pores representing the phonon bottleneck and obtain a descriptor for thermal transport, based on the sum of the pore-pore distances between such pores. This approach provide a simple tool to estimate phonon suppression in realistic porous materials for thermoelectric applications and enhance our understanding of heat transport in disordered materials.

  12. Landscape attributes and life history variability shape genetic structure of trout populations in a stream network

    Science.gov (United States)

    Neville, H.M.; Dunham, J.B.; Peacock, M.M.

    2006-01-01

    Spatial and temporal landscape patterns have long been recognized to influence biological processes, but these processes often operate at scales that are difficult to study by conventional means. Inferences from genetic markers can overcome some of these limitations. We used a landscape genetics approach to test hypotheses concerning landscape processes influencing the demography of Lahontan cutthroat trout in a complex stream network in the Great Basin desert of the western US. Predictions were tested with population- and individual-based analyses of microsatellite DNA variation, reflecting patterns of dispersal, population stability, and local effective population sizes. Complementary genetic inferences suggested samples from migratory corridors housed a mixture of fish from tributaries, as predicted based on assumed migratory life histories in those habitats. Also as predicted, populations presumed to have greater proportions of migratory fish or from physically connected, large, or high quality habitats had higher genetic variability and reduced genetic differentiation from other populations. Populations thought to contain largely non-migratory individuals generally showed the opposite pattern, suggesting behavioral isolation. Estimated effective sizes were small, and we identified significant and severe genetic bottlenecks in several populations that were isolated, recently founded, or that inhabit streams that desiccate frequently. Overall, this work suggested that Lahontan cutthroat trout populations in stream networks are affected by a combination of landscape and metapopulation processes. Results also demonstrated that genetic patterns can reveal unexpected processes, even within a system that is well studied from a conventional ecological perspective. ?? Springer 2006.

  13. Genetic diversity and population structure of 20 North European cattle breeds

    DEFF Research Database (Denmark)

    kantanen, J; Olsaker, Ingrid; Holm, Lars-Erik

    2000-01-01

    Blood samples were collected from 743 animals from 15 indigenous, 2 old imported, and 3 commercial North European cattle breeds. The samples were analyzed for 11 erythrocyte antigen systems, 8 proteins, and 10 microsatellites, and used to assess inter- and intrabreed genetic variation and genetic......, allelic diversity has been reduced in several breeds, which was explained by limited effective population sizes over the course of man-directed breed development and demographic bottlenecks of indigenous breeds. A tree showing genetic relationships between breeds was constructed from a matrix of random...... drift-based genetic distance estimates. The breeds were classified on the basis of the tree topology into four major breed groups, defined as Northern indigenous breeds, Southern breeds, Ayrshire and Friesian breeds, and Jersey. Grouping of Nordic breeds was supported by documented breed history...

  14. Phylogeography and population dynamics of the white-sided dolphin (Lagenorhynchus acutus) in the North Atlantic

    KAUST Repository

    Banguera-Hinestroza, E.; Evans, P. G H; Mirimin, L.; Reid, R. J.; Mikkelsen, B.; Couperus, A. S.; Deaville, R.; Rogan, E.; Hoelzel, A. R.

    2014-01-01

    Highly mobile species in the marine environment may be expected to show little differentiation at the population level, but this is often not the case. Instead cryptic population structure is common, and effective conservation will require an understanding of how these patterns evolve. Here we present an assessment from both sides of the North Atlantic of differentiation among populations of a dolphin species that inhabits mainly pelagic waters, the Atlantic white-sided dolphin. We compare eleven putative populations in the western and eastern North Atlantic at mtDNA and microsatellite DNA loci and find reduced nucleotide diversity and signals for historical bottlenecks and post-bottleneck expansions in all regions. We calculate expansion times to have occurred during the early Holocene, following the last glacial maximum (LGM). We find evidence for connectivity among populations from either side of the North Atlantic, and differentiation between putative populations in the far northeast compared with all other areas sampled. Some data suggest the possibility of separate refugia during the LGM explaining this pattern, although ongoing ecological processes may also be a factor. We discuss the implications for developing effective programs of conservation and management in the context of ongoing anthropogenic impact. © 2014 Springer Science+Business Media Dordrecht.

  15. Phylogeography and population dynamics of the white-sided dolphin (Lagenorhynchus acutus) in the North Atlantic

    KAUST Repository

    Banguera-Hinestroza, E.

    2014-02-27

    Highly mobile species in the marine environment may be expected to show little differentiation at the population level, but this is often not the case. Instead cryptic population structure is common, and effective conservation will require an understanding of how these patterns evolve. Here we present an assessment from both sides of the North Atlantic of differentiation among populations of a dolphin species that inhabits mainly pelagic waters, the Atlantic white-sided dolphin. We compare eleven putative populations in the western and eastern North Atlantic at mtDNA and microsatellite DNA loci and find reduced nucleotide diversity and signals for historical bottlenecks and post-bottleneck expansions in all regions. We calculate expansion times to have occurred during the early Holocene, following the last glacial maximum (LGM). We find evidence for connectivity among populations from either side of the North Atlantic, and differentiation between putative populations in the far northeast compared with all other areas sampled. Some data suggest the possibility of separate refugia during the LGM explaining this pattern, although ongoing ecological processes may also be a factor. We discuss the implications for developing effective programs of conservation and management in the context of ongoing anthropogenic impact. © 2014 Springer Science+Business Media Dordrecht.

  16. A POPULATION MEMETICS APPROACH TO CULTURAL EVOLUTION IN CHAFFINCH SONG: DIFFERENTIATION AMONG POPULATIONS.

    Science.gov (United States)

    Lynch, Alejandro; Baker, Allan J

    1994-04-01

    We investigated cultural evolution in populations of common chaffinches (Fringilla coelebs) in the Atlantic islands (Azores, Madeira, and Canaries) and neighboring continental regions (Morocco and Iberia) by employing a population-memetic approach. To quantify differentiation, we used the concept of a song meme, defined as a single syllable or a series of linked syllables capable of being transmitted. The levels of cultural differentiation are higher among the Canaries populations than among the Azorean ones, even though the islands are on average closer to each other geographically. This is likely the result of reduced levels of migration, lower population sizes, and bottlenecks (possibly during the colonization of these populations) in the Canaries; all these factors produce a smaller effective population size and therefore accentuate the effects of differentiation by random drift. Significant levels of among-population differentiation in the Azores, in spite of substantial levels of migration, attest to the differentiating effects of high mutation rates of memes, which allow the accumulation of new mutants in different populations before migration can disperse them throughout the entire region. © 1994 The Society for the Study of Evolution.

  17. Genetic diversity and conservation status of managed vicuña (Vicugna vicugna) populations in Argentina.

    Science.gov (United States)

    Anello, M; Daverio, M S; Romero, S R; Rigalt, F; Silbestro, M B; Vidal-Rioja, L; Di Rocco, F

    2016-02-01

    The vicuña (Vicugna vicugna) was indiscriminately hunted for more than 400 years and, by the end of 1960s, it was seriously endangered. At that time, a captive breeding program was initiated in Argentina by the National Institute of Agricultural Technology (INTA) with the aim of preserving the species. Nowadays, vicuñas are managed in captivity and in the wild to obtain their valuable fiber. The current genetic status of Argentinean vicuña populations is virtually unknown. Using mitochondrial DNA and microsatellite markers, we assessed levels of genetic diversity of vicuña populations managed in the wild and compared it with a captive population from INTA. Furthermore, we examined levels of genetic structure and evidence for historical bottlenecks. Overall, all populations revealed high genetic variability with no signs of inbreeding. Levels of genetic diversity between captive and wild populations were not significantly different, although the captive population showed the lowest estimates of allelic richness, number of mitochondrial haplotypes, and haplotype diversity. Significant genetic differentiation at microsatellite markers was found between free-living populations from Jujuy and Catamarca provinces. Moreover, microsatellite data also revealed genetic structure within the Catamarca management area. Genetic signatures of past bottlenecks were detected in wild populations by the Garza Williamson test. Results from this study are discussed in relation to the conservation and management of the species.

  18. Climate Change and Genetic Structure of Leading Edge and Rear End Populations in a Northwards Shifting Marine Fish Species, the Corkwing Wrasse (Symphodus melops).

    Science.gov (United States)

    Knutsen, Halvor; Jorde, Per Erik; Gonzalez, Enrique Blanco; Robalo, Joana; Albretsen, Jon; Almada, Vitor

    2013-01-01

    One mechanism by which marine organisms may respond to climate shifts is range shifts. The corkwing wrasse (Symphodus melops) is a temperate fish species, inhabiting the coasts of Europe, that show strong indications of current as well as historical (ice-age) range shifts towards the north. Nine neutral microsatellite DNA markers were screened to study genetic signatures and spatial population structure over the entire geographic and thermal gradient of the species from Portugal to Norway. A major genetic break (F ST  = 0.159 average among pairs) was identified between Scandinavian and more southern populations, with a marked reduction (30% or more) in levels of genetic variability in Scandinavia. The break is probably related to bottleneck(s) associated with post-glacial colonization of the Scandinavian coasts, and indicates a lack of present gene flow across the North Sea. The lack of gene flow can most likely be attributed to the species' need for rocky substrate for nesting and a relatively short pelagic larval phase, limiting dispersal by ocean currents. These findings demonstrate that long-distance dispersal may be severely limited in the corkwing wrasse, and that successful range-shifts following present climate change may be problematic for this and other species with limited dispersal abilities, even in the seemingly continuous marine environment.

  19. The Addiction Severity Index: Reliability and validity in a Dutch alcoholic population

    OpenAIRE

    Dejong, C.A.J.; Willems, J.C.E.W.; Schippers, G.M.; Hendriks, V.M.

    1995-01-01

    The Addiction Severity Index (ASI) was evaluated for its psychometric qualities in a Dutch alcoholic population admitted to an addiction treatment center in the Netherlands. Its factorial structure in this population was found to be consistent with the established six factor structure of the ASI. Reliability analysis revealed that the homogeneity of the subscales was acceptable with the exception of the Alcohol Scale. The six subscales were not highly intercorrelated. The results of this stud...

  20. Dynamics-Based Stranded-Crowd Model for Evacuation in Building Bottlenecks

    Directory of Open Access Journals (Sweden)

    Lidi Huang

    2013-01-01

    Full Text Available In high-density public buildings, it is difficult to evacuate. So in this paper, we propose a novel quantitative evacuation model to insure people’s safety and reduce the risk of crowding. We analyze the mechanism of arch-like clogging phenomena during evacuation and the influencing factors in emergency situations at bottleneck passages; then we design a model based on crowd dynamics and apply the model to a stadium example. The example is used to compare evacuation results of crowd density with different egress widths in stranded zones. The results show this model proposed can guide the safe and dangerous egress widths in performance design and can help evacuation routes to be selected and optimized.

  1. Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus.

    Science.gov (United States)

    Moncla, Louise H; Zhong, Gongxun; Nelson, Chase W; Dinis, Jorge M; Mutschler, James; Hughes, Austin L; Watanabe, Tokiko; Kawaoka, Yoshihiro; Friedrich, Thomas C

    2016-02-10

    Avian influenza virus reassortants resembling the 1918 human pandemic virus can become transmissible among mammals by acquiring mutations in hemagglutinin (HA) and polymerase. Using the ferret model, we trace the evolutionary pathway by which an avian-like virus evolves the capacity for mammalian replication and airborne transmission. During initial infection, within-host HA diversity increased drastically. Then, airborne transmission fixed two polymerase mutations that do not confer a detectable replication advantage. In later transmissions, selection fixed advantageous HA1 variants. Transmission initially involved a "loose" bottleneck, which became strongly selective after additional HA mutations emerged. The stringency and evolutionary forces governing between-host bottlenecks may therefore change throughout host adaptation. Mutations occurred in multiple combinations in transmitted viruses, suggesting that mammalian transmissibility can evolve through multiple genetic pathways despite phenotypic constraints. Our data provide a glimpse into avian influenza virus adaptation in mammals, with broad implications for surveillance on potentially zoonotic viruses. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Reducing Concurrency Bottlenecks in Parallel I/O Workloads

    Energy Technology Data Exchange (ETDEWEB)

    Manzanares, Adam C. [Los Alamos National Laboratory; Bent, John M. [Los Alamos National Laboratory; Wingate, Meghan [Los Alamos National Laboratory

    2011-01-01

    To enable high performance parallel checkpointing we introduced the Parallel Log Structured File System (PLFS). PLFS is middleware interposed on the file system stack to transform concurrent writing of one application file into many non-concurrently written component files. The promising effectiveness of PLFS makes it important to examine its performance for workloads other than checkpoint capture, notably the different ways that state snapshots may be later read, to make the case for using PLFS in the Exascale I/O stack. Reading a PLFS file involved reading each of its component files. In this paper we identify performance limitations on broader workloads in an early version of PLFS, specifically the need to build and distribute an index for the overall file, and the pressure on the underlying parallel file system's metadata server, and show how PLFS's decomposed components architecture can be exploited to alleviate bottlenecks in the underlying parallel file system.

  3. Bottleneck analysis and strategic planning using Tanahashi model for childhood diarrhea management in Gujarat, Western India.

    Science.gov (United States)

    Rupani, Mihir Prafulbhai; Gaonkar, Narayan T; Bhatt, Gneyaa S

    2016-10-01

    In spite of continued efforts, India is still lagging behind in achieving its MDG goals. The objectives of this study were to identify stake-holders who have a role to play in childhood diarrhea management, to identify gaps in childhood diarrhea management and to propose strategic options for relieving these gaps. Bottleneck analysis exercise was carried out based on the Tanahashi model in six High Priority Districts (HPDs) of Gujarat in period between July-November 2013. The major bottlenecks identified for Childhood Diarrhea management were poor demand generation, unsafe drinking water, poor access to improved sanitation facility and lack of equitable distribution and replenishment mechanisms for Oral Rehydration Solution (ORS) packets and Zinc tablets till the front-line worker level. The main strategic options that were suggested for relieving these bottlenecks were Zinc-ORS roll out in scale-up districts, develop Information Education Communication/Behaviour Change Communication (IEC/BCC) plan for childhood diarrhea management at state/district level, use of Drug Logistics Information Management System (DLIMS) software for supply chain management of Zinc-ORS, strengthening of chlorination activity at household level, monitoring implementation of Nirmal Bharat Abhiyaan (NBA) for constructing improved sanitation facilities at household level and to develop an IEC/BCC plan for hygiene promotion and usage of sanitary latrines. Use of Zinc tablets need to be intensified through an effective scale-up. Adequate demand generation activity is needed. There is need to address safe drinking water and improved sanitation measures at household levels. Multi-sectoral engagements and ownership of Zinc-ORS program is the need of the hour. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Supply Chain Management in The Brazilian Automobile Industry: Bottlenecks for Steadier Growth

    Directory of Open Access Journals (Sweden)

    W. F. Sorte Junior

    2011-06-01

    Full Text Available Taking the Lean Production System as the reference model, this paper analyses the supply chain management approach and the relationship between private and public sectors in the Brazilian automobile industry. Through a case study conducted from October 2006 to October 2008 in a private owned automaker, two bottlenecks in this Brazilian industrial sector are identified: (1 Emphasis on coordination rather than integration in supply chain management; and (2 Insufficient channels of communication between private and public sectors, resulting in inefficient policies to nurture automakers with low production volume.

  5. Juvenile bottlenecks and salinity shape grey mullet assemblages in Mediterranean estuaries

    Science.gov (United States)

    Cardona, Luis; Hereu, Bernat; Torras, Xavier

    2008-05-01

    Previous research has suggested that competitive bottlenecks may exist for the Mediterranean grey mullets (Osteichthyes, Mugilidae) at the fry stage with the exotic Cyprinus carpio (Osteichthyes, Cyprinidae) playing a central role. As a consequence, the structure of grey mullet assemblages at later stages is thought to reflect previous competition as well as differences in osmoregulatory skills. This paper tests that hypothesis by examining four predictions about the relative abundance of five grey mullet species in 42 Western Mediterranean estuary sites from three areas (Aiguamolls de l'Empordà, Ebro Delta and Minorca) differing in the salinity level and occurrence of C. carpio. Field data confirmed the predictions as: (1) Liza aurata and Mugil cephalus were scarce everywhere and never dominated the assemblage; (2) Liza saliens dominated the assemblage where the salinity level was higher than 13; (3) Liza ramado always dominated the assemblage where the salinity level was lower than 13 and C. carpio was present; and (4) Chelon labrosus dominated the assemblage only where the salinity level was lower than 13 and C. carpio was absent. The catch per unit effort of C. labrosus of any size was smaller in the presence of C. carpio than where it had not been introduced, which is in agreement with the juvenile competitive bottleneck hypothesis. Discriminant analysis confirmed that the assemblage structure was linked to the salinity level and the occurrence of C. carpio for both early juveniles and late juveniles as well as adults. The data reported here reveal that the structure of grey mullet assemblages inhabiting Mediterranean estuaries is determined by salinity and competitive interactions at the fry stage.

  6. Migratory connectivity magnifies the consequences of habitat loss from sea-level rise for shorebird populations.

    Science.gov (United States)

    Iwamura, Takuya; Possingham, Hugh P; Chadès, Iadine; Minton, Clive; Murray, Nicholas J; Rogers, Danny I; Treml, Eric A; Fuller, Richard A

    2013-06-22

    Sea-level rise (SLR) will greatly alter littoral ecosystems, causing habitat change and loss for coastal species. Habitat loss is widely used as a measurement of the risk of extinction, but because many coastal species are migratory, the impact of habitat loss will depend not only on its extent, but also on where it occurs. Here, we develop a novel graph-theoretic approach to measure the vulnerability of a migratory network to the impact of habitat loss from SLR based on population flow through the network. We show that reductions in population flow far exceed the proportion of habitat lost for 10 long-distance migrant shorebirds using the East Asian-Australasian Flyway. We estimate that SLR will inundate 23-40% of intertidal habitat area along their migration routes, but cause a reduction in population flow of up to 72 per cent across the taxa. This magnifying effect was particularly strong for taxa whose migration routes contain bottlenecks-sites through which a large fraction of the population travels. We develop the bottleneck index, a new network metric that positively correlates with the predicted impacts of habitat loss on overall population flow. Our results indicate that migratory species are at greater risk than previously realized.

  7. Strategic behavior and social outcomes in a bottleneck queue

    DEFF Research Database (Denmark)

    Breinbjerg, J.; Sebald, Alexander; Østerdal, L. P.

    2016-01-01

    the first-in-first-out (FIFO), last-in-first-out (LIFO), and service-in-random-order (SIRO) queue disciplines and compare these predictions to outcomes from a laboratory experiment. In line with our theoretical predictions, we find that people arrive with greater dispersion when participating under the LIFO......We theoretically and experimentally study the differential incentive effects of three well known queue disciplines in a strategic environment in which a bottleneck facility opens and impatient players decide when to arrive. For a class of three-player games, we derive equilibrium arrivals under...... discipline, whereas they tend to arrive immediately under FIFO and SIRO. As a consequence, shorter waiting times are obtained under LIFO as compared to FIFO and SIRO. However, while our theoretical predictions admit higher welfare under LIFO, this is not recovered experimentally as the queue disciplines...

  8. Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes.

    Science.gov (United States)

    Gómez-Brandón, María; Aira, Manuel; Lores, Marta; Domínguez, Jorge

    2011-01-01

    Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. To address these questions we determined the microbial community structure (phospholipid fatty acid profiles) and microbial activity (fluorescein diacetate hydrolysis) in the earthworm casts derived from three types of animal manure (cow, horse and pig manure), which differed in microbial composition. The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions within the decomposer food web influence on nutrient cycling.

  9. Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes.

    Directory of Open Access Journals (Sweden)

    María Gómez-Brandón

    Full Text Available BACKGROUND: Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. METHODOLOGY: To address these questions we determined the microbial community structure (phospholipid fatty acid profiles and microbial activity (fluorescein diacetate hydrolysis in the earthworm casts derived from three types of animal manure (cow, horse and pig manure, which differed in microbial composition. PRINCIPAL FINDINGS: The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. CONCLUSIONS/SIGNIFICANCE: Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions

  10. Genetic diversity and population genetic structure of the only population of Aoluguya Reindeer (Rangifer tarandus) in China.

    Science.gov (United States)

    Ju, Yan; Liu, Huamiao; Rong, Min; Zhang, Ranran; Dong, Yimeng; Zhou, Yongna; Xing, Xiumei

    2018-04-16

    Aoluguya Reindeer is the only reindeer species in China and currently approximately 1000 Aoluguya Reindeer remain semi-domesticated. A relative low diversity estimate was found by investigating genetic variability and demographic history of its population. Mismatch distribution curve of its nucleotide sequences and neutral test indicate its population has not experienced expansion. Genetic diversity and population structure were also analysed by using its mtDNA and microsatellites technology. Statistical results of these analyses showed there were varying degrees of population inbreeding and suggested that gene flow existed among its populations at one time. Three mutation models were also used to detect the bottleneck effect of reindeer population. The genetic variation of eight populations is relatively small. In addition, the clustering program STRUCTURE was used to analyse Aoluguya Reindeer population structure, to determine its optimal K and first time to analyse the phylogenetic status of Aoluguya Reindeer among other reindeer subspecies. It is recommended that the government establish a natural conservation area in Aoluguya Reindeer growing geography, forbade the trade and hunting of Aoluguya Reindeer, and strengthen the protection of this endangered species.

  11. Mask manufacturing improvement through capability definition and bottleneck line management

    Science.gov (United States)

    Strott, Al

    1994-02-01

    In 1989, Intel's internal mask operation limited itself to research and development activities and re-inspection and pellicle application of externally manufactured masks. Recognizing the rising capital cost of mask manufacturing at the leading edge, Intel's Mask Operation management decided to offset some of these costs by manufacturing more masks internally. This was the beginning of the challenge they set to manufacture at least 50% of Intel's mask volume internally, at world class performance levels. The first step in responding to this challenge was the completion of a comprehensive operation capability analysis. A series of bottleneck improvements by focus teams resulted in an average cycle time improvement to less than five days on all product and less than two days on critical products.

  12. Causes and evolutionary consequences of population subdivision of an Iberian mountain lizard, Iberolacerta monticola.

    Science.gov (United States)

    Remón, Nuria; Galán, Pedro; Vila, Marta; Arribas, Oscar; Naveira, Horacio

    2013-01-01

    The study of the factors that influence population connectivity and spatial distribution of genetic variation is crucial for understanding speciation and for predicting the effects of landscape modification and habitat fragmentation, which are considered severe threats to global biodiversity. This dual perspective is obtained from analyses of subalpine mountain species, whose present distribution may have been shaped both by cyclical climate changes over ice ages and anthropogenic perturbations of their habitats. Here, we examine the phylogeography, population structure and genetic diversity of the lacertid lizard Iberolacerta monticola, an endemism considered to be facing a high risk of extinction in several populations. Northwestern quadrant of the Iberian Peninsula. We analyzed the mtDNA variation at the control region (454 bp) and the cytochrome b (598 bp) loci, as well as at 10 nuclear microsatellite loci from 17 populations throughout the distribution range of the species. According to nuclear markers, most sampling sites are defined as distinct, genetically differentiated populations, and many of them show traces of recent bottlenecks. Mitochondrial data identify a relatively old, geographically restricted lineage, and four to six younger geographically vicariant sister clades, whose origin may be traced back to the mid-Pleistocene revolution, with several subclades possibly associated to the mid-Bruhnes transition. Geographic range fragmentation of one of these clades, which includes lowland sites, is very recent, and most likely due to the accelerated loss of Atlantic forests by human intervention. Altogether, the data fit a "refugia within refugia" model, some lack of pattern uniformity notwithstanding, and suggest that these mountains might be the cradles of new species of Iberolacerta. However, the changes operated during the Holocene severely compromise the long-term survival of those genetic lineages more exposed to the anthropogenic perturbations of

  13. Process-based Assignment-Setting Change for Support of Overcoming Bottlenecks in Learning by Problem-Posing in Arithmetic Word Problems

    Science.gov (United States)

    Supianto, A. A.; Hayashi, Y.; Hirashima, T.

    2017-02-01

    Problem-posing is well known as an effective activity to learn problem-solving methods. Monsakun is an interactive problem-posing learning environment to facilitate arithmetic word problems learning for one operation of addition and subtraction. The characteristic of Monsakun is problem-posing as sentence-integration that lets learners make a problem of three sentences. Monsakun provides learners with five or six sentences including dummies, which are designed through careful considerations by an expert teacher as a meaningful distraction to the learners in order to learn the structure of arithmetic word problems. The results of the practical use of Monsakun in elementary schools show that many learners have difficulties in arranging the proper answer at the high level of assignments. The analysis of the problem-posing process of such learners found that their misconception of arithmetic word problems causes impasses in their thinking and mislead them to use dummies. This study proposes a method of changing assignments as a support for overcoming bottlenecks of thinking. In Monsakun, the bottlenecks are often detected as a frequently repeated use of a specific dummy. If such dummy can be detected, it is the key factor to support learners to overcome their difficulty. This paper discusses how to detect the bottlenecks and to realize such support in learning by problem-posing.

  14. Contact transmission of influenza virus between ferrets imposes a looser bottleneck than respiratory droplet transmission allowing propagation of antiviral resistance

    Science.gov (United States)

    Frise, Rebecca; Bradley, Konrad; van Doremalen, Neeltje; Galiano, Monica; Elderfield, Ruth A.; Stilwell, Peter; Ashcroft, Jonathan W.; Fernandez-Alonso, Mirian; Miah, Shahjahan; Lackenby, Angie; Roberts, Kim L.; Donnelly, Christl A.; Barclay, Wendy S.

    2016-01-01

    Influenza viruses cause annual seasonal epidemics and occasional pandemics. It is important to elucidate the stringency of bottlenecks during transmission to shed light on mechanisms that underlie the evolution and propagation of antigenic drift, host range switching or drug resistance. The virus spreads between people by different routes, including through the air in droplets and aerosols, and by direct contact. By housing ferrets under different conditions, it is possible to mimic various routes of transmission. Here, we inoculated donor animals with a mixture of two viruses whose genomes differed by one or two reverse engineered synonymous mutations, and measured the transmission of the mixture to exposed sentinel animals. Transmission through the air imposed a tight bottleneck since most recipient animals became infected by only one virus. In contrast, a direct contact transmission chain propagated a mixture of viruses suggesting the dose transferred by this route was higher. From animals with a mixed infection of viruses that were resistant and sensitive to the antiviral drug oseltamivir, resistance was propagated through contact transmission but not by air. These data imply that transmission events with a looser bottleneck can propagate minority variants and may be an important route for influenza evolution. PMID:27430528

  15. Conservation genetics of extremely isolated urban populations of the northern dusky salamander (Desmognathus fuscus in New York City

    Directory of Open Access Journals (Sweden)

    Jason Munshi-South

    2013-04-01

    Full Text Available Urbanization is a major cause of amphibian decline. Stream-dwelling plethodontid salamanders are particularly susceptible to urbanization due to declining water quality and hydrological changes, but few studies have examined these taxa in cities. The northern dusky salamander (Desmognathus fuscus was once common in the New York City metropolitan area, but has substantially declined throughout the region in recent decades. We used five tetranucleotide microsatellite loci to examine population differentiation, genetic variation, and bottlenecks among five remnant urban populations of dusky salamanders in NYC. These genetic measures provide information on isolation, prevalence of inbreeding, long-term prospects for population persistence, and potential for evolutionary responses to future environmental change. All populations were genetically differentiated from each other, and the most isolated populations in Manhattan have maintained very little genetic variation (i.e. <20% heterozygosity. A majority of the populations also exhibited evidence of genetic bottlenecks. These findings contrast with published estimates of high genetic variation within and lack of structure between populations of other desmognathine salamanders sampled over similar or larger spatial scales. Declines in genetic variation likely resulted from population extirpations and the degradation of stream and terrestrial paths for dispersal in NYC. Loss of genetic variability in populations isolated by human development may be an underappreciated cause and/or consequence of the decline of this species in urbanized areas of the northeast USA.

  16. Population Structure Analysis of Bull Genomes of European and Western Ancestry

    DEFF Research Database (Denmark)

    Chung, Neo Christopher; Szyda, Joanna; Frąszczak, Magdalena

    2017-01-01

    Since domestication, population bottlenecks, breed formation, and selective breeding have radically shaped the genealogy and genetics of Bos taurus. In turn, characterization of population structure among diverse bull (males of Bos taurus) genomes enables detailed assessment of genetic resources...... and origins. By analyzing 432 unrelated bull genomes from 13 breeds and 16 countries, we demonstrate genetic diversity and structural complexity among the European/Western cattle population. Importantly, we relaxed a strong assumption of discrete or admixed population, by adapting latent variable models...... harboring largest genetic differentiation suggest positive selection underlying population structure. We carried out gene set analysis using SNP annotations to identify enriched functional categories such as energy-related processes and multiple development stages. Our population structure analysis of bull...

  17. X-linked MTMR8 diversity and evolutionary history of sub-Saharan populations.

    Directory of Open Access Journals (Sweden)

    Damian Labuda

    Full Text Available The genetic diversity within an 11 kb segment of the MTMR8 gene in a sample of 111 sub-Saharan and 49 non-African X chromosomes was investigated to assess the early evolutionary history of sub-Saharan Africans and the out-of-Africa expansion. The analyses revealed a complex genetic structure of the Africans that contributed to the emergence of modern humans. We observed partitioning of two thirds of old lineages among southern, west/central and east African populations indicating ancient population stratification predating the out of Africa migration. Age estimates of these lineages, older than coalescence times of uniparentally inherited markers, raise the question whether contemporary humans originated from a single population or as an amalgamation of different populations separated by years of independent evolution, thus suggesting a greater antiquity of our species than generally assumed. While the oldest sub-Saharan lineages, ~500 thousand years, are found among Khoe-San from southern-Africa, a distinct haplotype found among Biaka is likely due to admixture from an even older population. An East African population that gave rise to non-Africans underwent a selective sweep affecting the subcentromeric region where MTMR8 is located. This and similar sweeps in four other regions of the X chromosome, documented in the literature, effectively reduced genetic diversity of non-African chromosomes and therefore may have exacerbated the effect of the demographic bottleneck usually ascribed to the out of Africa migration. Our data is suggestive, however, that a bottleneck, occurred in Africa before range expansion.

  18. X-linked MTMR8 diversity and evolutionary history of sub-Saharan populations.

    Science.gov (United States)

    Labuda, Damian; Yotova, Vania; Lefebvre, Jean-François; Moreau, Claudia; Utermann, Gerd; Williams, Scott M

    2013-01-01

    The genetic diversity within an 11 kb segment of the MTMR8 gene in a sample of 111 sub-Saharan and 49 non-African X chromosomes was investigated to assess the early evolutionary history of sub-Saharan Africans and the out-of-Africa expansion. The analyses revealed a complex genetic structure of the Africans that contributed to the emergence of modern humans. We observed partitioning of two thirds of old lineages among southern, west/central and east African populations indicating ancient population stratification predating the out of Africa migration. Age estimates of these lineages, older than coalescence times of uniparentally inherited markers, raise the question whether contemporary humans originated from a single population or as an amalgamation of different populations separated by years of independent evolution, thus suggesting a greater antiquity of our species than generally assumed. While the oldest sub-Saharan lineages, ~500 thousand years, are found among Khoe-San from southern-Africa, a distinct haplotype found among Biaka is likely due to admixture from an even older population. An East African population that gave rise to non-Africans underwent a selective sweep affecting the subcentromeric region where MTMR8 is located. This and similar sweeps in four other regions of the X chromosome, documented in the literature, effectively reduced genetic diversity of non-African chromosomes and therefore may have exacerbated the effect of the demographic bottleneck usually ascribed to the out of Africa migration. Our data is suggestive, however, that a bottleneck, occurred in Africa before range expansion.

  19. Hierarchical Genetic Analysis of German Cockroach (Blattella germanica) Populations from within Buildings to across Continents

    Science.gov (United States)

    Vargo, Edward L.; Crissman, Jonathan R.; Booth, Warren; Santangelo, Richard G.; Mukha, Dmitry V.; Schal, Coby

    2014-01-01

    Understanding the population structure of species that disperse primarily by human transport is essential to predicting and controlling human-mediated spread of invasive species. The German cockroach (Blattella germanica) is a widespread urban invader that can actively disperse within buildings but is spread solely by human-mediated dispersal over longer distances; however, its population structure is poorly understood. Using microsatellite markers we investigated population structure at several spatial scales, from populations within single apartment buildings to populations from several cities across the U.S. and Eurasia. Both traditional measures of genetic differentiation and Bayesian clustering methods revealed increasing levels of genetic differentiation at greater geographic scales. Our results are consistent with active dispersal of cockroaches largely limited to movement within a building. Their low levels of genetic differentiation, yet limited active spread between buildings, suggests a greater likelihood of human-mediated dispersal at more local scales (within a city) than at larger spatial scales (within and between continents). About half the populations from across the U.S. clustered together with other U.S. populations, and isolation by distance was evident across the U.S. Levels of genetic differentiation among Eurasian cities were greater than those in the U.S. and greater than those between the U.S. and Eurasia, but no clear pattern of structure at the continent level was detected. MtDNA sequence variation was low and failed to reveal any geographical structure. The weak genetic structure detected here is likely due to a combination of historical admixture among populations and periodic population bottlenecks and founder events, but more extensive studies are needed to determine whether signatures of global movement may be present in this species. PMID:25020136

  20. On the impact of fiber-delay-lines (FDL) in an all-optical network (AON) bottleneck without wavelength conversion

    Science.gov (United States)

    Argibay-Losada, Pablo Jesus; Sahin, Gokhan

    2014-08-01

    Random access memories (RAM) are fundamental in conventional electronic switches and routers to manage short-term congestion and to decrease data loss probabilities. Switches in all-optical networks (AONs), however, do not have access to optical RAM, and therefore are prone to much higher loss levels than their electronic counterparts. Fiber-delay-lines (FDLs), able to delay an optical data packet a fixed amount of time, have been proposed in the literature as a means to alleviate those high loss levels. However, they are extremely bulky to manage, so their usage introduces a trade-off between practicality and performance in the design and operation of the AON. In this paper we study the influence that FDLs have in the performance of flows crossing an all-optical switch that acts as their bottleneck. We show how extremely low numbers of FDLs (e.g., 1 or 2) can help in reducing losses by several orders of magnitude in several illustrative scenarios with high aggregation levels. Our results therefore suggest that FDLs can be a practical means of dealing with congestion in AONs in the absence of optical RAM buffers or of suitable data interchange protocols specifically designed for AONs.

  1. Global drought and severe drought-affected populations in 1.5 and 2 °C warmer worlds

    Science.gov (United States)

    Liu, Wenbin; Sun, Fubao; Lim, Wee Ho; Zhang, Jie; Wang, Hong; Shiogama, Hideo; Zhang, Yuqing

    2018-03-01

    The 2015 Paris Agreement proposed a more ambitious climate change mitigation target on limiting global warming to 1.5 °C instead of 2 °C above preindustrial levels. Scientific investigations on environmental risks associated with these warming targets are necessary to inform climate policymaking. Based on the Coupled Model Intercomparison Project phase 5 (CMIP5) climate models, we present the first risk-based assessment of changes in global drought and the impact of severe drought on populations from additional 1.5 and 2 °C warming conditions. Our results highlight the risk of drought on a global scale and in several hotspot regions such as the Amazon, northeastern Brazil, southern Africa and Central Europe at both 1.5 and 2 °C global warming relative to the historical period, showing increases in drought durations from 2.9 to 3.2 months. Correspondingly, more total and urban populations would be exposed to severe droughts globally (+132.5 ± 216.2 million and +194.5 ± 276.5 million total population and +350.2 ± 158.8 million and +410.7 ± 213.5 million urban populations in 1.5 and 2 °C warmer worlds) and regionally (e.g., East Africa, West Africa and South Asia). Less rural populations (-217.7 ± 79.2 million and -216.2 ± 82.4 million rural populations in 1.5 and 2 °C warmer worlds) would be exposed to severe drought globally under climate warming, population growth and especially the urbanization-induced population migration. By keeping global warming at 1.5 °C above the preindustrial levels instead of 2 °C, there is a decrease in drought risks (i.e., less drought duration, less drought intensity and severity but relatively more frequent drought) and the affected total, urban and rural populations would decrease globally and in most regions. While challenging for both East Africa and South Asia, the benefits of limiting warming to below 1.5 °C in terms of global drought risk and impact reduction are significant.

  2. Situation awareness of active distribution network: roadmap, technologies, and bottlenecks

    DEFF Research Database (Denmark)

    Lin, Jin; Wan, Can; Song, Yonghua

    2016-01-01

    With the rapid development of local generation and demand response, the active distribution network (ADN), which aggregates and manages miscellaneous distributed resources, has moved from theory to practice. Secure and optimal operations now require an advanced situation awareness (SA) system so...... in the project of developing an SA system as the basic component of a practical active distribution management system (ADMS) deployed in Beijing, China, is presented. This paper reviews the ADN’s development roadmap by illustrating the changes that are made in elements, topology, structure, and control scheme....... Taking into consideration these hardware changes, a systematic framework is proposed for the main components and the functional hierarchy of an SA system for the ADN. The SA system’s implementation bottlenecks are also presented, including, but not limited to issues in big data platform, distribution...

  3. Scaling up quality care for mothers and newborns around the time of birth: an overview of methods and analyses of intervention-specific bottlenecks and solutions.

    Science.gov (United States)

    Dickson, Kim E; Kinney, Mary V; Moxon, Sarah G; Ashton, Joanne; Zaka, Nabila; Simen-Kapeu, Aline; Sharma, Gaurav; Kerber, Kate J; Daelmans, Bernadette; Gülmezoglu, A; Mathai, Matthews; Nyange, Christabel; Baye, Martina; Lawn, Joy E

    2015-01-01

    The Every Newborn Action Plan (ENAP) and Ending Preventable Maternal Mortality targets cannot be achieved without high quality, equitable coverage of interventions at and around the time of birth. This paper provides an overview of the methodology and findings of a nine paper series of in-depth analyses which focus on the specific challenges to scaling up high-impact interventions and improving quality of care for mothers and newborns around the time of birth, including babies born small and sick. The bottleneck analysis tool was applied in 12 countries in Africa and Asia as part of the ENAP process. Country workshops engaged technical experts to complete a tool designed to synthesise "bottlenecks" hindering the scale up of maternal-newborn intervention packages across seven health system building blocks. We used quantitative and qualitative methods and literature review to analyse the data and present priority actions relevant to different health system building blocks for skilled birth attendance, emergency obstetric care, antenatal corticosteroids (ACS), basic newborn care, kangaroo mother care (KMC), treatment of neonatal infections and inpatient care of small and sick newborns. The 12 countries included in our analysis account for the majority of global maternal (48%) and newborn (58%) deaths and stillbirths (57%). Our findings confirm previously published results that the interventions with the most perceived bottlenecks are facility-based where rapid emergency care is needed, notably inpatient care of small and sick newborns, ACS, treatment of neonatal infections and KMC. Health systems building blocks with the highest rated bottlenecks varied for different interventions. Attention needs to be paid to the context specific bottlenecks for each intervention to scale up quality care. Crosscutting findings on health information gaps inform two final papers on a roadmap for improvement of coverage data for newborns and indicate the need for leadership for

  4. Population genetics of IFITM3 in Portugal and Central Africa reveals a potential modifier of influenza severity.

    Science.gov (United States)

    David, Susana; Correia, Vanessa; Antunes, Liliana; Faria, Ricardo; Ferrão, José; Faustino, Paula; Nunes, Baltazar; Maltez, Fernando; Lavinha, João; Rebelo de Andrade, Helena

    2018-03-01

    Influenza epidemics are a serious global public health and economic problem. The IFITM3 allele (rs12252-C) was suggested as a population-based genetic risk factor for severe influenza virus infection by A(H1N1)pdm09. We analyzed the population genetics of IFITM3 variants in the Portuguese general population (n = 200) and Central Africans (largely Angolan) (n = 148) as well as its association to influenza severity in Portuguese patients (n = 41). Seven SNPs, within the 352 bp IFITM3 amplicon around rs12252, were identified. SNP distributions in the Portuguese appeared at an intermediate level between the Africans and other Europeans. According to HapMap, rs34481144 belongs to the same linkage disequilibrium (LD) block as rs12252 and is in strong LD with rs6421983. A negative association with severe relative to mild disease was observed for allele rs34481144-A, indicating a protective effect under the dominant model. Moreover, haplotype Hap4 with rs34481144-A, not including rs12252-C, was significantly associated to mild influenza. Conversely, although with borderline significance, haplotype Hap1 with rs34481144-G, not including rs12252-C, was associated to severe disease. Moreover, in comparison to the general Portuguese population, statistical significant differences in the frequencies of the protective allele rs34481144-A in the severe disease group, the deleterious Hap1 in the mild disease group, and the protective Hap4 in the severe disease group were observed. The population attributable risk (PAR) for the targeted rs34481144 allele or genotype was of 55.91 and 64.44% in the general population and the mildly infected individuals, respectively. Implication of these variants in disease phenotype needs further validation, namely through functional analysis as is discussed.

  5. Direct structural mapping of organic field-effect transistors reveals bottlenecks to carrier transport

    KAUST Repository

    Li, Ruipeng

    2012-08-10

    X-ray microbeam scattering is used to map the microstructure of the organic semiconductor along the channel length of solution-processed bottom-contact OFET devices. Contact-induced nucleation is known to influence the crystallization behavior within the channel. We find that microstructural inhomogeneities in the center of the channel act as a bottleneck to charge transport. This problem can be overcome by controlling crystallization of the preferable texture, thus favoring more efficient charge transport throughout the channel. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Direct structural mapping of organic field-effect transistors reveals bottlenecks to carrier transport

    KAUST Repository

    Li, Ruipeng; Ward, Jeremy W.; Smilgies, Detlef Matthias; Payne, Marcia M.; Anthony, John Edward; Jurchescu, Oana D.; Amassian, Aram

    2012-01-01

    X-ray microbeam scattering is used to map the microstructure of the organic semiconductor along the channel length of solution-processed bottom-contact OFET devices. Contact-induced nucleation is known to influence the crystallization behavior within the channel. We find that microstructural inhomogeneities in the center of the channel act as a bottleneck to charge transport. This problem can be overcome by controlling crystallization of the preferable texture, thus favoring more efficient charge transport throughout the channel. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Lack of Population Structure in Coriander Populations Based on SDS (Seed Storage Protein Page Analysis

    Directory of Open Access Journals (Sweden)

    Gülsüm Yaldiz

    2016-08-01

    Full Text Available Genetic variation is prerequisite for plant breeding. Nothing information existed in the literature for available diversity of Coriander accession in Turkey. Plant breeding activities are negligible in Turkey. So in order to start effective plant breeding program in Turkey, information on the available genetic diversity is viable. Therefore we planned to study the genetic variation and population structure of 29 Coriander accessions by seed storage protein (SDS. SDS analysis elaborated the lack of population structure and genetic bottleneck in the Coriander accessions in Turkey. Based on the results of this study, it was clear that sampling strategy was not appropriate and plant introduction should be made from different sources and diverse genotypes should be used as parents to initialize the effective Turkish Coriander breeding program.

  8. Human Migration through Bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum Revealed by Y Chromosomes

    Science.gov (United States)

    Wen, Bo; Xu, Shuhua; Wang, Yi; Lu, Yan; Wei, Lanhai; Wang, Chuanchao; Li, Shilin; Huang, Xingqiu; Jin, Li; Li, Hui

    2011-01-01

    Molecular anthropological studies of the populations in and around East Asia have resulted in the discovery that most of the Y-chromosome lineages of East Asians came from Southeast Asia. However, very few Southeast Asian populations had been investigated, and therefore, little was known about the purported migrations from Southeast Asia into East Asia and their roles in shaping the genetic structure of East Asian populations. Here, we present the Y-chromosome data from 1,652 individuals belonging to 47 Mon-Khmer (MK) and Hmong-Mien (HM) speaking populations that are distributed primarily across Southeast Asia and extend into East Asia. Haplogroup O3a3b-M7, which appears mainly in MK and HM, indicates a strong tie between the two groups. The short tandem repeat network of O3a3b-M7 displayed a hierarchical expansion structure (annual ring shape), with MK haplotypes being located at the original point, and the HM and the Tibeto-Burman haplotypes distributed further away from core of the network. Moreover, the East Asian dominant haplogroup O3a3c1-M117 shows a network structure similar to that of O3a3b-M7. These patterns indicate an early unidirectional diffusion from Southeast Asia into East Asia, which might have resulted from the genetic drift of East Asian ancestors carrying these two haplogroups through many small bottle-necks formed by the complicated landscape between Southeast Asia and East Asia. The ages of O3a3b-M7 and O3a3c1-M117 were estimated to be approximately 19 thousand years, followed by the emergence of the ancestors of HM lineages out of MK and the unidirectional northward migrations into East Asia. PMID:21904623

  9. Role of population genetics in the sterile insect technique

    International Nuclear Information System (INIS)

    Krafsur, E.S.

    2005-01-01

    The detection and analysis of genetic variation in natural and laboratory populations are reviewed. The application of population genetic methods and theory can help to plan and evaluate the implementation of area-wide integrated pest management (AW-IPM) programmes that use the sterile insect technique (SIT). Population genetic studies can play an important role in estimating dispersal rates and thus gene flow among target populations, determining if sibling species exist, establishing the origin of outbreaks or reintroductions, and supporting the quality control of mass-reared colonies. The target's population history may be examined, in terms of 'bottlenecks', range fragmentations, and expansions. Genetic methods can be helpful in distinguishing wild insects from released sterile or substerile ones, and in ascertaining, together with mating cross-compatibility studies, the compatibility of mass-reared colonies with target wild insects. (author)

  10. Optimal design of future electricity supply systems. An analysis of potential bottlenecks in NW-Europe

    International Nuclear Information System (INIS)

    Joode, Jeroen de; Werven, Michiel van

    2005-01-01

    This paper analyses the potential bottlenecks that might emerge in the North-western European electricity supply system as a result of a number of (autonomous) long-term developments. The main long-term developments we identify are 1) a continuing increase in the demand for electricity, 2) a gradual shift from conventional electricity generation towards unconventional (green) generation, 3) a gradual shift from centralized generation towards decentralized generation and 4) a shift from national self-sufficient electricity supply systems towards a pan-European electricity system. Although it has been recognized that these developments might cause certain problems in some or more elements of the electricity supply chain, a coherent and comprehensive framework for the identification of these problems is lacking. More specific, governments and regulators seem to focus on certain parts of the electricity supply system separately, whereas certain interdependencies in the system have received relatively little attention. This paper presents such a framework and identifies some potential bottlenecks that receive relatively little attention from policy makers. These are 1) the increasing penetration of distributed generation, 2) an increasingly important role for demand response and 3) the lack of locational signals in the electricity supply system. The potential role of governments and markets in these issues is briefly explored. (Author)

  11. Bottleneck congestion and distribution of work start times: The economics of staggered work hours revisited

    OpenAIRE

    Takayama, Yuki

    2014-01-01

    Since the seminal work of Henderson (1981), a number of studies examined the effect of staggered work hours by analyzing models of work start time choice that consider the trade-off between negative congestion externalities and positive production externalities. However, these studies described traffic congestion using flow congestion models. This study develops a model of work start time choice with bottleneck congestion and discloses the intrinsic properties of the model. To this end, this ...

  12. Genetic and demographic responses of mosquitofish (Gambusia holbrooki) populations exposed to mercury for multiple generations

    Energy Technology Data Exchange (ETDEWEB)

    Tatara, C.P.; Mulvey, M.; Newman, M.C.

    1999-12-01

    Genetic and demographic responses of mosquitofish were examined after multiple generations of exposure to mercury. Previous studies of acute lethal exposures of mosquitofish to either mercury or arsenic demonstrated a consistent correlation between time to death and genotype at the glucosephosphate isomerase-2 (Gpi-2) locus. A mesocosm study involving mosquitofish populations exposed to mercury for 111 d showed significant female sexual selection and fecundity selection at the Gpi-2 locus. Here the mesocosm study was extended to populations exposed to mercury for several (approx. four) generations. After 2 years, control and mercury-exposed populations met Hardy-Weinberg expectations and showed no evidence of genetic bottlenecks. The mean number of heterozygous loci did not differ significantly between the mercury-exposed and control populations. Significant differences in allele frequencies at the Gpi-2 locus were observed between the mercury-exposed and control populations. Relative to the initial and control allele frequencies, the GPI-2{sup 100} allele frequency was lower, the Gpi-2{sup 66} allele frequency increased, but the Gpi-2{sup 38} allele frequency did not change in mercury-exposed populations. No significant differences were found in standard length, weight, sex ratio, or age class ratio between the control and mercury-exposed populations. Allele frequency changes at the Gpi-2 locus suggest population-level response to chronic mercury exposure. Changes in allele frequency may be useful as indicators of population response to contaminants, provided that the population in question is well understood.

  13. A Wide Range of 3243A>G/tRNALeu(UUR) (MELAS) Mutation Loads May Segregate in Offspring through the Female Germline Bottleneck

    Science.gov (United States)

    Pallotti, Francesco; Binelli, Giorgio; Fabbri, Raffaella; Valentino, Maria L.; Vicenti, Rossella; Macciocca, Maria; Cevoli, Sabina; Baruzzi, Agostino; DiMauro, Salvatore; Carelli, Valerio

    2014-01-01

    Segregation of mutant mtDNA in human tissues and through the germline is debated, with no consensus about the nature and size of the bottleneck hypothesized to explain rapid generational shifts in mutant loads. We investigated two maternal lineages with an apparently different inheritance pattern of the same pathogenic mtDNA 3243A>G/tRNALeu(UUR) (MELAS) mutation. We collected blood cells, muscle biopsies, urinary epithelium and hair follicles from 20 individuals, as well as oocytes and an ovarian biopsy from one female mutation carrier, all belonging to the two maternal lineages to assess mutant mtDNA load, and calculated the theoretical germline bottleneck size (number of segregating units). We also evaluated “mother-to-offspring” segregations from the literature, for which heteroplasmy assessment was available in at least three siblings besides the proband. Our results showed that mutation load was prevalent in skeletal muscle and urinary epithelium, whereas in blood cells there was an inverse correlation with age, as previously reported. The histoenzymatic staining of the ovarian biopsy failed to show any cytochrome-c-oxidase defective oocyte. Analysis of four oocytes and one offspring from the same unaffected mother of the first family showed intermediate heteroplasmic mutant loads (10% to 75%), whereas very skewed loads of mutant mtDNA (0% or 81%) were detected in five offspring of another unaffected mother from the second family. Bottleneck size was 89 segregating units for the first mother and 84 for the second. This was remarkably close to 88, the number of “segregating units” in the “mother-to-offspring” segregations retrieved from literature. In conclusion, a wide range of mutant loads may be found in offspring tissues and oocytes, resulting from a similar theoretical bottleneck size. PMID:24805791

  14. Genetic monitoring of western corn rootworm (Coleoptera: Chrysomelidae) populations on a microgeographic scale.

    Science.gov (United States)

    Ivkosic, S A; Gorman, J; Lemic, D; Mikac, K M

    2014-06-01

    Microsatellite and mitochondrial DNA genetic monitoring of the western corn rootworm, Diabrotica virgifera virgifera LeConte, was undertaken in Croatia and Serbia from 1996 to 2011 and in the United States in 2011. The seven U.S. populations displayed the greatest allelic diversity. In Europe, the highest number of alleles was found in Rugvica, Croatia, and Surčin, Serbia, the two sites closest to international airports. The highest number of mitochondrial (mt) DNA haplotypes was recorded from Croatia in 1996. From 2009 to 2011, haplotype diversity declined, and Croatia and Serbia had a single fixed haplotype. U.S. continuous maize locations had one haplotype, while three haplotypes were found at crop-rotated locations. Minimal temporal genetic differentiation was found within and between populations in Europe and the United States. Bayesian cluster analysis identified two genetic clusters that grouped western corn rootworm from Croatia and Serbia separately from U.S. populations; however, these clusters were not neat, and numerous U.S. individuals had both European and U.S. ancestry, suggesting bidirectional gene flow. Bottlenecks were identified within most Croatian populations sampled in 1996, only two populations in 2009, and in all populations in 2011. Bottlenecks were not identified from Serbia from 1996 to 2011 or from the United States in 2011. As suspected Serbia was identified as the geographic source of western corn rootworm in Croatia. The temporal genetic monitoring undertaken allowed a deeper understanding of the population genetics of western corn rootworm in Croatia, neighboring Serbia, and its geographic source in the United States. The data obtained can be used to inform western corn rootworm pest management strategies in Croatia and Europe.

  15. Bottle-Neck Feature Extraction Structures for Multilingual Training and Porting (Pub Version, Open Access)

    Science.gov (United States)

    2016-05-03

    set Language HA LA ZU LLP hours 7.9 8.1 8.4 LM sentences 9861 11577 10644 LM words 93131 93328 60832 dictionary 5333 3856 14962 # tied states 1257 1453... monolingual NNs, and having a (large) hidden layer between Bottle-Neck and output layers – we need to change the 149 František Grézl and Martin...In both cases the monolingual SBN hierarchy with desired DNN topology is obtained. Lower WER was achieved by the first variant which uses the tied

  16. Overcoming bottlenecks in the membrane protein structural biology pipeline.

    Science.gov (United States)

    Hardy, David; Bill, Roslyn M; Jawhari, Anass; Rothnie, Alice J

    2016-06-15

    Membrane proteins account for a third of the eukaryotic proteome, but are greatly under-represented in the Protein Data Bank. Unfortunately, recent technological advances in X-ray crystallography and EM cannot account for the poor solubility and stability of membrane protein samples. A limitation of conventional detergent-based methods is that detergent molecules destabilize membrane proteins, leading to their aggregation. The use of orthologues, mutants and fusion tags has helped improve protein stability, but at the expense of not working with the sequence of interest. Novel detergents such as glucose neopentyl glycol (GNG), maltose neopentyl glycol (MNG) and calixarene-based detergents can improve protein stability without compromising their solubilizing properties. Styrene maleic acid lipid particles (SMALPs) focus on retaining the native lipid bilayer of a membrane protein during purification and biophysical analysis. Overcoming bottlenecks in the membrane protein structural biology pipeline, primarily by maintaining protein stability, will facilitate the elucidation of many more membrane protein structures in the near future. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  17. Traffic jams without bottlenecks-experimental evidence for the physical mechanism of the formation of a jam

    International Nuclear Information System (INIS)

    Sugiyama, Yuki; Fukui, Minoru; Kikuchi, Macoto; Hasebe, Katsuya; Nakayama, Akihiro; Nishinari, Katsuhiro; Tadaki, Shin-ichi; Yukawa, Satoshi

    2008-01-01

    A traffic jam on a highway is a very familiar phenomenon. From the physical viewpoint, the system of vehicular flow is a non-equilibrium system of interacting particles (vehicles). The collective effect of the many-particle system induces the instability of a free flow state caused by the enhancement of fluctuations, and the transition to a jamming state occurs spontaneously if the average vehicle density exceeds a certain critical value. Thus, a bottleneck is only a trigger and not the essential origin of a traffic jam. In this paper, we present the first experimental evidence that the emergence of a traffic jam is a collective phenomenon like 'dynamical' phase transitions and pattern formation in a non-equilibrium system. We have performed an experiment on a circuit to show the emergence of a jam with no bottleneck. In the initial condition, all the vehicles are moving, homogeneously distributed on the circular road, with the same velocity. The average density of the vehicles is prepared for the onset of the instability. Even a tiny fluctuation grows larger and then the homogeneous movement cannot be maintained. Finally, a jam cluster appears and propagates backward like a solitary wave with the same speed as that of a jam cluster on a highway

  18. Traffic jams without bottlenecks-experimental evidence for the physical mechanism of the formation of a jam

    Energy Technology Data Exchange (ETDEWEB)

    Sugiyama, Yuki [Department of Complex Systems Science, Nagoya University, Nagoya 464-8601 (Japan); Fukui, Minoru [Nakanihon Automotive College, Sakahogi 505-0077 (Japan); Kikuchi, Macoto [Cybermedia Center, Osaka University, Toyonaka 560-0043 (Japan); Hasebe, Katsuya [Aichi University, Miyoshi 470-0296 (Japan); Nakayama, Akihiro [Faculty of Science and Technology, Meijo University, Nagoya 468-8502 (Japan); Nishinari, Katsuhiro [Department of Aeronautics and Astronautics, University of Tokyo, Bunkyo 113-8656 (Japan); Tadaki, Shin-ichi [Computer and Network Center, Saga University, Saga 840-8502 (Japan); Yukawa, Satoshi [Department of Earth and Space Science, Osaka University, Toyonaka 560-0043 (Japan)], E-mail: sugiyama@phys.cs.is.nagoya-u.ac.jp

    2008-03-15

    A traffic jam on a highway is a very familiar phenomenon. From the physical viewpoint, the system of vehicular flow is a non-equilibrium system of interacting particles (vehicles). The collective effect of the many-particle system induces the instability of a free flow state caused by the enhancement of fluctuations, and the transition to a jamming state occurs spontaneously if the average vehicle density exceeds a certain critical value. Thus, a bottleneck is only a trigger and not the essential origin of a traffic jam. In this paper, we present the first experimental evidence that the emergence of a traffic jam is a collective phenomenon like 'dynamical' phase transitions and pattern formation in a non-equilibrium system. We have performed an experiment on a circuit to show the emergence of a jam with no bottleneck. In the initial condition, all the vehicles are moving, homogeneously distributed on the circular road, with the same velocity. The average density of the vehicles is prepared for the onset of the instability. Even a tiny fluctuation grows larger and then the homogeneous movement cannot be maintained. Finally, a jam cluster appears and propagates backward like a solitary wave with the same speed as that of a jam cluster on a highway.

  19. Use of the Emergency Department for Severe Headache. A population-based study

    Science.gov (United States)

    Friedman, Benjamin W.; Serrano, Daniel; Reed, Michael; Diamond, Merle; Lipton, Richard B.

    2008-01-01

    Background Although headache is a common emergency department (ED) chief complaint, the role of the ED in the management of primary headache disorders has rarely been assessed from a population perspective. We determined frequency of ED use and risk factors for use among patients suffering severe headache. Methods As part of the American Migraine Prevalence and Prevention study, a validated self-administered questionnaire was mailed to 24,000 severe headache sufferers, who were randomly drawn from a larger sample constructed to be socio-demographically representative of the US population. Participants were asked a series of questions on headache management, healthcare system use, socio-demographic features, and number of ED visits for management of headache in the previous 12 months. In keeping with the work of others, “frequent” ED use was defined as a particpants report of four or more visits to the ED for treatment of a headache in the previous 12 months. Headaches were categorized into specific diagnoses using a validated methodology. Results Of 24,000 surveys, 18,514 were returned, and 13,451 (56%) provided complete data on ED use. Socio-demographic characteristics did not differ substantially between responders and non-responders. Among the 13,451 responders, over the course of the previous year, 12,592 (94%) did not visit the ED at all, 415 (3%) visited the ED once, and 444 (3%) visited the ED more than once. Patients with severe episodic tension-type headache were less likely to use the ED than patients with severe episodic migraine (OR 0.4 [95%CI 0.3, 0.6]). Frequent ED use was reported by 1% of the total sample or 19% (95%CI: 17, 22%) of subjects who used the ED in the previous year, though frequent users accounted for 51% (95%CI: 49, 53) of all ED visits. Predictors of ED use included markers of disease severity, elevated depression scores, low socio-economic status, and a predilection for ED use for conditions other than headache. Conclusions Most

  20. Density Estimation in Several Populations With Uncertain Population Membership

    KAUST Repository

    Ma, Yanyuan; Hart, Jeffrey D.; Carroll, Raymond J.

    2011-01-01

    sampled from any given population can be calculated. We develop general estimation procedures and bandwidth selection methods for our setting. We establish large-sample properties and study finite-sample performance using simulation studies. We illustrate

  1. Population genetic dynamics of three-spined sticklebacks (Gasterosteus aculeatus) in anthropogenic altered habitats.

    Science.gov (United States)

    Scharsack, Joern P; Schweyen, Hannah; Schmidt, Alexander M; Dittmar, Janine; Reusch, Thorsten Bh; Kurtz, Joachim

    2012-06-01

    In industrialized and/or agriculturally used landscapes, inhabiting species are exposed to a variety of anthropogenic changes in their environments. Genetic diversity may be reduced if populations encounter founder events, bottlenecks, or isolation. Conversely, genetic diversity may increase if populations adapt to changes in selective regimes in newly created habitats. With the present study, genetic variability of 918 sticklebacks from 43 samplings (21.3 ± 3.8 per sample) at 36 locations from cultivated landscapes in Northwest Germany was analyzed at nine neutral microsatellite loci. To test if differentiation is influenced by habitat alterations, sticklebacks were collected from ancient running waters and adjacent artificial stagnant waters, from brooks with salt water inflow of anthropogenic and natural origin and adjacent freshwater sites. Overall population structure was dominated by isolation by distance (IBD), which was significant across all populations, and analysis of molecular variance (AMOVA) revealed that 10.6% of the variation was explained by river catchment area. Populations in anthropogenic modified habitats deviated from the general IBD structure and in the AMOVA, grouping by habitat type running/stagnant water explained 4.9% of variation and 1.4% of the variation was explained by salt-/freshwater habitat. Sticklebacks in salt-polluted water systems seem to exhibit elevated migratory activity between fresh- and saltwater habitats, reducing IBD. In other situations, populations showed distinct signs of genetic isolation, which in some locations was attributed to mechanical migration barriers, but in others to potential anthropogenic induced bottleneck or founder effects. The present study shows that anthropogenic habitat alterations may have diverse effects on the population genetic structure of inhabiting species. Depending on the type of habitat change, increased genetic differentiation, diversification, or isolation are possible consequences.

  2. A case study of bats and white-nose syndrome demonstrating how to model population viability with evolutionary effects.

    Science.gov (United States)

    Maslo, Brooke; Fefferman, Nina H

    2015-08-01

    Ecological factors generally affect population viability on rapid time scales. Traditional population viability analyses (PVA) therefore focus on alleviating ecological pressures, discounting potential evolutionary impacts on individual phenotypes. Recent studies of evolutionary rescue (ER) focus on cases in which severe, environmentally induced population bottlenecks trigger a rapid evolutionary response that can potentially reverse demographic threats. ER models have focused on shifting genetics and resulting population recovery, but no one has explored how to incorporate those findings into PVA. We integrated ER into PVA to identify the critical decision interval for evolutionary rescue (DIER) under which targeted conservation action should be applied to buffer populations undergoing ER against extinction from stochastic events and to determine the most appropriate vital rate to target to promote population recovery. We applied this model to little brown bats (Myotis lucifugus) affected by white-nose syndrome (WNS), a fungal disease causing massive declines in several North American bat populations. Under the ER scenario, the model predicted that the DIER period for little brown bats was within 11 years of initial WNS emergence, after which they stabilized at a positive growth rate (λ = 1.05). By comparing our model results with population trajectories of multiple infected hibernacula across the WNS range, we concluded that ER is a potential explanation of observed little brown bat population trajectories across multiple hibernacula within the affected range. Our approach provides a tool that can be used by all managers to provide testable hypotheses regarding the occurrence of ER in declining populations, suggest empirical studies to better parameterize the population genetics and conservation-relevant vital rates, and identify the DIER period during which management strategies will be most effective for species conservation. © 2015 Society for Conservation

  3. The Relationship between Mating System and Genetic Diversity in Diploid Sexual Populations of Cyrtomium falcatum in Japan.

    Directory of Open Access Journals (Sweden)

    Ryosuke Imai

    Full Text Available The impact of variation in mating system on genetic diversity is a well-debated topic in evolutionary biology. The diploid sexual race of Cyrtomium falcatum (Japanese holly fern shows mating system variation, i.e., it displays two different types of sexual expression (gametangia formation in gametophytes: mixed (M type and separate (S type. We examined whether there is variation in the selfing rate among populations of this species, and evaluated the relationship between mating system, genetic diversity and effective population size using microsatellites. In this study, we developed eight new microsatellite markers and evaluated genetic diversity and structure of seven populations (four M-type and three S-type. Past effective population sizes (Ne were inferred using Approximate Bayesian computation (ABC. The values of fixation index (FIS, allelic richness (AR and gene diversity (h differed significantly between the M-type (FIS: 0.626, AR: 1.999, h: 0.152 and the S-type (FIS: 0.208, AR: 2.718, h: 0.367 populations (when admixed individuals were removed from two populations. Although evidence of past bottleneck events was detected in all populations by ABC, the current Ne of the M-type populations was about a third of that of the S-type populations. These results suggest that the M-type populations have experienced more frequent bottlenecks, which could be related to their higher colonization ability via gametophytic selfing. Although high population differentiation among populations was detected (FST = 0.581, F'ST = 0.739, there was no clear genetic differentiation between the M- and S-types. Instead, significant isolation by distance was detected among all populations. These results suggest that mating system variation in this species is generated by the selection for single spore colonization during local extinction and recolonization events and there is no genetic structure due to mating system.

  4. Bottlenecks, population differentiation and apparent selection at microsatellite loci in Australian Drosophila buzzatii

    DEFF Research Database (Denmark)

    Barker, J.S.F.; Frydenberg, Jane; González, J.

    2009-01-01

    Species colonizing new areas disjunct from their original habitat may be subject to novel selection pressures, and exhibit adaptive genetic changes. However, if colonization occurs through a small number of founders, the genetic composition of the colonized population may differ from that of the ...

  5. Global drought and severe drought-affected populations in 1.5 and 2 °C warmer worlds

    Directory of Open Access Journals (Sweden)

    W. Liu

    2018-03-01

    Full Text Available The 2015 Paris Agreement proposed a more ambitious climate change mitigation target on limiting global warming to 1.5 °C instead of 2 °C above preindustrial levels. Scientific investigations on environmental risks associated with these warming targets are necessary to inform climate policymaking. Based on the Coupled Model Intercomparison Project phase 5 (CMIP5 climate models, we present the first risk-based assessment of changes in global drought and the impact of severe drought on populations from additional 1.5 and 2 °C warming conditions. Our results highlight the risk of drought on a global scale and in several hotspot regions such as the Amazon, northeastern Brazil, southern Africa and Central Europe at both 1.5 and 2 °C global warming relative to the historical period, showing increases in drought durations from 2.9 to 3.2 months. Correspondingly, more total and urban populations would be exposed to severe droughts globally (+132.5 ± 216.2 million and +194.5 ± 276.5 million total population and +350.2 ± 158.8 million and +410.7 ± 213.5 million urban populations in 1.5 and 2 °C warmer worlds and regionally (e.g., East Africa, West Africa and South Asia. Less rural populations (−217.7 ± 79.2 million and −216.2 ± 82.4 million rural populations in 1.5 and 2 °C warmer worlds would be exposed to severe drought globally under climate warming, population growth and especially the urbanization-induced population migration. By keeping global warming at 1.5 °C above the preindustrial levels instead of 2 °C, there is a decrease in drought risks (i.e., less drought duration, less drought intensity and severity but relatively more frequent drought and the affected total, urban and rural populations would decrease globally and in most regions. While challenging for both East Africa and South Asia, the benefits of limiting warming to below 1.5 °C in terms of global drought risk

  6. Genetic Relatedness of African and United States Populations of Cercospora zeae-maydis.

    Science.gov (United States)

    Dunkle, L D; Levy, M

    2000-05-01

    recent or that the ancestral population experienced a severe bottleneck prior to secondary migration.

  7. Population genetic structure of the blue-fronted Amazon (Amazona aestiva, Psittacidae: Aves) based on nuclear microsatellite loci: implications for conservation.

    Science.gov (United States)

    Leite, K C E; Seixas, G H F; Berkunsky, I; Collevatti, R G; Caparroz, R

    2008-09-09

    The blue-fronted Amazon (Amazona aestiva) is a widely distributed Neotropical parrot and one of the most captured parrots in nature to supply the illegal trade of wild animals. The objectives of the present study were to analyze the genetic structure of A. aestiva to identify management units and support conservation planning and to verified if A. aestiva populations have undergone a recent bottleneck due to habitat loss and capture for the pet trade. The genetic structure was accessed by analyzing six microsatellite loci in 74 individuals of A. aestiva, including samples from the two subspecies (A. a. aestiva and A. a. xanthopteryx), from five populations: four in Brazil and one in Argentina. A significant genetic differentiation (theta = 0.007, p = 0.005) could be detected only between the most distant populations, Tocantins and Argentina, localized at the northeast and southwest limits of the sample sites, respectively. There was no evidence of inbreeding within or between populations, suggesting random mating among individuals. These results suggest a clinal distribution of genetic variability, as observed for variation in plumage color of the two A. aestiva subspecies. Bottleneck analysis did not show a recent reduction in population size. Thus, for the management and conservation of the species, the populations from Argentina and Tocantins should be considered as different management units, and the other populations from the center of the geographical distribution as another management unit.

  8. Genome-wide patterns of nucleotide polymorphism in domesticated rice

    DEFF Research Database (Denmark)

    Caicedo, Ana L; Williamson, Scott H; Hernandez, Ryan D

    2007-01-01

    Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments......, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models...... to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been...

  9. Catastrophic floods may pave the way for increased genetic diversity in endemic artesian spring snail populations.

    Directory of Open Access Journals (Sweden)

    Jessica Worthington Wilmer

    Full Text Available The role of disturbance in the promotion of biological heterogeneity is widely recognised and occurs at a variety of ecological and evolutionary scales. However, within species, the impact of disturbances that decimate populations are neither predicted nor known to result in conditions that promote genetic diversity. Directly examining the population genetic consequences of catastrophic disturbances however, is rarely possible, as it requires both longitudinal genetic data sets and serendipitous timing. Our long-term study of the endemic aquatic invertebrates of the artesian spring ecosystem of arid central Australia has presented such an opportunity. Here we show a catastrophic flood event, which caused a near total population crash in an aquatic snail species (Fonscochlea accepta endemic to this ecosystem, may have led to enhanced levels of within species genetic diversity. Analyses of individuals sampled and genotyped from the same springs sampled both pre (1988-1990 and post (1995, 2002-2006 a devastating flood event in 1992, revealed significantly higher allelic richness, reduced temporal population structuring and greater effective population sizes in nearly all post flood populations. Our results suggest that the response of individual species to disturbance and severe population bottlenecks is likely to be highly idiosyncratic and may depend on both their ecology (whether they are resilient or resistant to disturbance and the stability of the environmental conditions (i.e. frequency and intensity of disturbances in which they have evolved.

  10. Population structure of Nellore cattle in northeastern Brazil

    Directory of Open Access Journals (Sweden)

    Ana Carla Borges Barbosa

    2013-09-01

    Full Text Available The objective of this study was to evaluate the population genetic structure of Nellore cattle in northeastern Brazil. Pedigree information was collected from 175,231 animals born from 1967 to 2007. Probability of gene origin, inbreeding, average relatedness coefficient (AR, completeness pedigree, effective population size and generation interval were calculated. Generation interval was high due to the long period of time animals were used as reproducers. The bottleneck effect was evidenced as a result of intensive use of limited breeders over the last years. Low values were observed ​​in the effective number of founder animals (434 and ancestors (427 comparing with the number on the base (175,231 and reference populations (130,038. Generally, the variability explained by the founders and ancestors is considered low. The average coefficient of inbreeding (0.11% and AR (0.14% estimated for this population is considered low and can be partly explained by the increased population effective number in recent periods; however, it may be underestimated by shallow pedigree.

  11. Concurrent deployment of visual attention and response selection bottleneck in a dual-task: Electrophysiological and behavioural evidence.

    Science.gov (United States)

    Reimer, Christina B; Strobach, Tilo; Schubert, Torsten

    2017-12-01

    Visual attention and response selection are limited in capacity. Here, we investigated whether visual attention requires the same bottleneck mechanism as response selection in a dual-task of the psychological refractory period (PRP) paradigm. The dual-task consisted of an auditory two-choice discrimination Task 1 and a conjunction search Task 2, which were presented at variable temporal intervals (stimulus onset asynchrony, SOA). In conjunction search, visual attention is required to select items and to bind their features resulting in a serial search process around the items in the search display (i.e., set size). We measured the reaction time of the visual search task (RT2) and the N2pc, an event-related potential (ERP), which reflects lateralized visual attention processes. If the response selection processes in Task 1 influence the visual attention processes in Task 2, N2pc latency and amplitude would be delayed and attenuated at short SOA compared to long SOA. The results, however, showed that latency and amplitude were independent of SOA, indicating that visual attention was concurrently deployed to response selection. Moreover, the RT2 analysis revealed an underadditive interaction of SOA and set size. We concluded that visual attention does not require the same bottleneck mechanism as response selection in dual-tasks.

  12. Identifying bottlenecks in the iron and folic acid supply chain in Bihar, India: a mixed-methods study.

    Science.gov (United States)

    Wendt, Amanda S; Stephenson, Rob; Young, Melissa F; Verma, Pankaj; Srikantiah, Sridhar; Webb-Girard, Amy; Hogue, Carol J; Ramakrishnan, Usha; Martorell, Reynaldo

    2018-04-12

    Maternal anaemia prevalence in Bihar, India remains high despite government mandated iron supplementation targeting pregnant women. Inadequate supply has been identified as a potential barrier to iron and folic acid (IFA) receipt. Our study objective was to examine the government health system's IFA supply and distribution system and identify bottlenecks contributing to insufficient IFA supply. Primary data collection was conducted in November 2011 and July 2012 across 8 districts in Bihar, India. A cross-sectional, observational, mixed methods approach was utilized. Auxiliary Nurse Midwives were surveyed on current IFA supply and practices. In-depth interviews (n = 59) were conducted with health workers at state, district, block, health sub-centre, and village levels. Overall, 44% of Auxiliary Nurse Midwives were out of IFA stock. Stock levels and supply chain practices varied greatly across districts. Qualitative data revealed specific bottlenecks impacting IFA forecasting, procurement, storage, disposal, lack of personnel, and few training opportunities for key players in the supply chain. Inadequate IFA supply is a major constraint to the IFA supplementation program, the extent of which varies widely across districts. Improvements at all levels of infrastructure, practices, and effective monitoring will be critical to strengthen the IFA supply chain in Bihar.

  13. Environment construction and bottleneck breakthrough in the improvement of wisdom exhibition

    Science.gov (United States)

    Zhang, Jiankang

    2017-08-01

    Wisdom exhibition is an inexorable trend in convention and exhibition industry in China. Information technology must be utilized by exhibition industry to achieve intelligent application and wisdom management, breaking the limitation of time as well as space, which raise the quality of exhibition service and level of operation to a totally new standard. Accordingly, exhibition industry should optimize mobile internet, a fundamental technology platform, during the advancing process of wisdom exhibition and consummate the combination among three plates including wisdom connection of information, wisdom exhibition environment and wisdom application of technology. Besides, the industry should realize the wisdom of external environment including wisdom of exhibition city, exhibition place, exhibition resource deal etc and break through bottle-neck in construction of wisdom exhibition industry, which includes construction of big data center, development of Mobile Internet application platform, promotion of information construction, innovative design of application scenarios.

  14. From Bottleneck to Breakthrough: Urbanization and the Future of Biodiversity Conservation.

    Science.gov (United States)

    Sanderson, Eric W; Walston, Joseph; Robinson, John G

    2018-06-01

    For the first time in the Anthropocene, the global demographic and economic trends that have resulted in unprecedented destruction of the environment are now creating the necessary conditions for a possible renaissance of nature. Drawing reasonable inferences from current patterns, we can predict that 100 years from now, the Earth could be inhabited by between 6 and 8 billion people, with very few remaining in extreme poverty, most living in towns and cities, and nearly all participating in a technologically driven, interconnected market economy. Building on the scholarship of others in demography, economics, sociology, and conservation biology, here, we articulate a theory of social-environmental change that describes the simultaneous and interacting effects of urban lifestyles on fertility, poverty alleviation, and ideation. By recognizing the shifting dynamics of these macrodrivers, conservation practice has the potential to transform itself from a discipline managing declines ("bottleneck") to a transformative movement of recovery ("breakthrough").

  15. Fungal Beta-Glucosidases: A Bottleneck in Industrial Use of Lignocellulosic Materials

    Directory of Open Access Journals (Sweden)

    Peter S. Lübeck

    2013-09-01

    Full Text Available Profitable biomass conversion processes are highly dependent on the use of efficient enzymes for lignocellulose degradation. Among the cellulose degrading enzymes, beta-glucosidases are essential for efficient hydrolysis of cellulosic biomass as they relieve the inhibition of the cellobiohydrolases and endoglucanases by reducing cellobiose accumulation. In this review, we discuss the important role beta-glucosidases play in complex biomass hydrolysis and how they create a bottleneck in industrial use of lignocellulosic materials. An efficient beta-glucosidase facilitates hydrolysis at specified process conditions, and key points to consider in this respect are hydrolysis rate, inhibitors, and stability. Product inhibition impairing yields, thermal inactivation of enzymes, and the high cost of enzyme production are the main obstacles to commercial cellulose hydrolysis. Therefore, this sets the stage in the search for better alternatives to the currently available enzyme preparations either by improving known or screening for new beta-glucosidases.

  16. Lean thinking in the supply chain operations and its integration with customer order decoupling point and bottlenecks

    OpenAIRE

    Saeed, Muhammad

    2012-01-01

    The thesis study reveals that the position of bottleneck is a significant importance in supplychain process. The modern supply chain is characterized as having diverse products due tomass customization, dynamic production technology and ever changing customer demand.Usually customized supply chain process consists of an assemble to order (ATO) or make-to-order (MTO) type of operation. By controlling the supply constraints at upstream, a smoothmaterial flow achieved at downstream. Effective ma...

  17. Deep bottleneck features for spoken language identification.

    Directory of Open Access Journals (Sweden)

    Bing Jiang

    Full Text Available A key problem in spoken language identification (LID is to design effective representations which are specific to language information. For example, in recent years, representations based on both phonotactic and acoustic features have proven their effectiveness for LID. Although advances in machine learning have led to significant improvements, LID performance is still lacking, especially for short duration speech utterances. With the hypothesis that language information is weak and represented only latently in speech, and is largely dependent on the statistical properties of the speech content, existing representations may be insufficient. Furthermore they may be susceptible to the variations caused by different speakers, specific content of the speech segments, and background noise. To address this, we propose using Deep Bottleneck Features (DBF for spoken LID, motivated by the success of Deep Neural Networks (DNN in speech recognition. We show that DBFs can form a low-dimensional compact representation of the original inputs with a powerful descriptive and discriminative capability. To evaluate the effectiveness of this, we design two acoustic models, termed DBF-TV and parallel DBF-TV (PDBF-TV, using a DBF based i-vector representation for each speech utterance. Results on NIST language recognition evaluation 2009 (LRE09 show significant improvements over state-of-the-art systems. By fusing the output of phonotactic and acoustic approaches, we achieve an EER of 1.08%, 1.89% and 7.01% for 30 s, 10 s and 3 s test utterances respectively. Furthermore, various DBF configurations have been extensively evaluated, and an optimal system proposed.

  18. Secondary depression in severe anxiety disorders: a population-based cohort study in Denmark

    Science.gov (United States)

    Meier, Sandra M; Petersen, Liselotte; Mattheisen, Manuel; Mors, Ole; Mortensen, Preben B; Laursen, Thomas M

    2016-01-01

    Summary Background Depression and anxiety disorders are highly comorbid conditions and a worldwide disease burden; however, large-scale studies delineating their association are scarce. In this retrospective study, we aimed to assess the effect of severe anxiety disorders on the risk and course of depression. Methods We did a population-based cohort study with prospectively gathered data in Denmark using data from three Danish population registers: The Danish Civil Registration System, the Danish Psychiatric Central Register, and the Danish National Hospital Registry. We selected the cohort from people born in Denmark between Jan 1, 1955, and Dec 31, 2002, who we followed up from Jan 1, 1994, to Dec 31, 2012. The cohort was restricted to individuals with known parents. First, we investigated the effect of specific anxiety diagnoses on risk of single depressive episodes and recurrent depressive disorder. Second, we investigated the effect of comorbid anxiety on risk of readmission for depression, adjusting for sex, age, calendar year, parental age, place at residence at time of birth, and the interaction of age with sex. Findings We included 3 380 059 individuals in our study cohort. The adjusted incidence rate ratio (IRR) for single depressive episodes was 3·0 (95% CI 2·8–3·1, pdepressive disorder was 5·0 (4·8–5·2) in patients with severe anxiety disorders compared with the general population. Compared with control individuals, the offspring of parents with anxiety disorders were more likely to be diagnosed with single depressive episodes (1·9, 1·8–2·0) or recurrent depressive disorder (2·1, 1·9–2·2). Comorbid anxiety increased the readmission rates in both patients with single depressive episodes and patients with recurrent depressive disorder. Interpretation Severe anxiety constitutes a significant risk factor for depression. Focusing on specific anxiety disorders might help to identify individuals at risk of depression, thereby providing new

  19. Population Genetic Structure and Evidence of Demographic Expansion of the Ayu (Plecoglossus altivelis in East Asia

    Directory of Open Access Journals (Sweden)

    Ye-Seul Kwan

    2012-10-01

    Full Text Available Plecoglossus altivelis (ayu is an amphidromous fish widely distributed in Northeastern Asia from the East China Sea to the northern Japanese coastal waters, encompassing the Korean Peninsula within its range. The shore lines of northeastern region in Asia have severely fluctuated following glaciations in the Quaternary. In the present study, we investigate the population genetic structure and historical demographic change of P. altivelis at a population level in East Asia. Analysis of molecular variance (AMOVA based on 244 mitochondrial control region DNA sequences clearly showed that as the sampling scope extended to a larger geographic area, genetic differentiation began to become significant, particularly among Northeastern populations. A series of hierarchical AMOVA could detect the genetic relationship of three closely located islands between Korea and Japan that might have been tightly connected by the regional Tsushima current. Neutrality and mismatch distribution analyses revealed a strong signature of a recent population expansion of P. altivelis in East Asia, estimated at 126 to 391 thousand years ago during the late Pleistocene. Therefore it suggests that the present population of P. altivelis traces back to its approximate demographic change long before the last glacial maximum. This contrasts our a priori expectation that the most recent glacial event might have the most crucial effect on the present day demography of marine organisms through bottleneck and subsequent increase of effective population size in this region.

  20. Genetic structure analysis of a highly inbred captive population of the African antelope Addax nasomaculatus. Conservation and management implications.

    Science.gov (United States)

    Armstrong, E; Leizagoyen, C; Martínez, A M; González, S; Delgado, J V; Postiglioni, A

    2011-01-01

    The African antelope Addax nasomaculatus is a rare mammal at high risk of extinction, with no more than 300 individuals in the wild and 1,700 captive animals distributed in zoos around the world. In this work, we combine genetic data and genealogical information to assess the structure and genetic diversity of a captive population located at Parque Lecocq Zoo (N=27), originated from only two founders. We amplified 39 microsatellites previously described in other Artiodactyls but new to this species. Seventeen markers were polymorphic, with 2-4 alleles per locus (mean=2.71). Mean expected heterozygosity (He) per locus was between 0.050 (marker ETH3) and 0.650 (marker D5S2), with a global He of 0.43. The mean inbreeding coefficient of the population computed from pedigree records of all registered individuals (N=53) was 0.222. The mean coancestry of the population was 0.298 and F(IS) index was -0.108. These results reflect the importance of an adequate breeding management on a severely bottlenecked captive population, which would benefit by the incorporation of unrelated individuals. Thanks to the successful amplification of a large number of microsatellites commonly used in domestic bovids, this study will provide useful information for the management of this population and serve as future reference for similar studies in other captive populations of this species. © 2010 Wiley-Liss, Inc.

  1. Genetic evidence for a Paleolithic human population expansion in Africa

    Science.gov (United States)

    Reich, David E.; Goldstein, David B.

    1998-01-01

    Human populations have undergone dramatic expansions in size, but other than the growth associated with agriculture, the dates and magnitudes of those expansions have never been resolved. Here, we introduce two new statistical tests for population expansion, which use variation at a number of unlinked genetic markers to study the demographic histories of natural populations. By analyzing genetic variation in various aboriginal populations from throughout the world, we show highly significant evidence for a major human population expansion in Africa, but no evidence of expansion outside of Africa. The inferred African expansion is estimated to have occurred between 49,000 and 640,000 years ago, certainly before the Neolithic expansions, and probably before the splitting of African and non-African populations. In showing a significant difference between African and non-African populations, our analysis supports the unique role of Africa in human evolutionary history, as has been suggested by most other genetic work. In addition, the missing signal in non-African populations may be the result of a population bottleneck associated with the emergence of these populations from Africa, as postulated in the “Out of Africa” model of modern human origins. PMID:9653150

  2. Consequences of habitat fragmentation on genetic structure of Chamaedorea alternans (Arecaceae) palm populations in the tropical rain forests of Los Tuxtlas, Veracruz, Mexico

    OpenAIRE

    Peñaloza-Ramírez, Juan Manuel; Aguilar-Amezquita, Bernardo; Núñez-Farfán, Juan; Pérez-Nasser, Nidia; Albarrán-Lara, Ana Luisa; Oyama, Ken

    2016-01-01

    Abstract: Chamaedorea alternans is a palm species that has suffered from selective extraction, and habitat loss. We collected 11 populations from fragmented and conserved forest. We assess genetic variation of C. alternans, genetic exchange, differentiation, bottlenecks, effective population size and signals of natural selection. Genetic diversity was higher in conserved than in fragmented forest but not significant. Fragmentation did not play a significant role in genetic diversity, possibly...

  3. clubber: removing the bioinformatics bottleneck in big data analyses

    Science.gov (United States)

    Miller, Maximilian; Zhu, Chengsheng; Bromberg, Yana

    2018-01-01

    With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these “big data” analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber’s goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min) clearly illustrate the importance of clubber in the everyday computational biology environment. PMID:28609295

  4. clubber: removing the bioinformatics bottleneck in big data analyses.

    Science.gov (United States)

    Miller, Maximilian; Zhu, Chengsheng; Bromberg, Yana

    2017-06-13

    With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these "big data" analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber's goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min) clearly illustrate the importance of clubber in the everyday computational biology environment.

  5. clubber: removing the bioinformatics bottleneck in big data analyses

    Directory of Open Access Journals (Sweden)

    Miller Maximilian

    2017-06-01

    Full Text Available With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these “big data” analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber’s goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min clearly illustrate the importance of clubber in the everyday computational biology environment.

  6. Clogging transition of many-particle systems flowing through bottlenecks

    Science.gov (United States)

    Zuriguel, Iker; Parisi, Daniel Ricardo; Hidalgo, Raúl Cruz; Lozano, Celia; Janda, Alvaro; Gago, Paula Alejandra; Peralta, Juan Pablo; Ferrer, Luis Miguel; Pugnaloni, Luis Ariel; Clément, Eric; Maza, Diego; Pagonabarraga, Ignacio; Garcimartín, Angel

    2014-12-01

    When a large set of discrete bodies passes through a bottleneck, the flow may become intermittent due to the development of clogs that obstruct the constriction. Clogging is observed, for instance, in colloidal suspensions, granular materials and crowd swarming, where consequences may be dramatic. Despite its ubiquity, a general framework embracing research in such a wide variety of scenarios is still lacking. We show that in systems of very different nature and scale -including sheep herds, pedestrian crowds, assemblies of grains, and colloids- the probability distribution of time lapses between the passages of consecutive bodies exhibits a power-law tail with an exponent that depends on the system condition. Consequently, we identify the transition to clogging in terms of the divergence of the average time lapse. Such a unified description allows us to put forward a qualitative clogging state diagram whose most conspicuous feature is the presence of a length scale qualitatively related to the presence of a finite size orifice. This approach helps to understand paradoxical phenomena, such as the faster-is-slower effect predicted for pedestrians evacuating a room and might become a starting point for researchers working in a wide variety of situations where clogging represents a hindrance.

  7. No correlation between neonatal fitness and heterozygosity in a reintroduced population of Père David's deer

    Directory of Open Access Journals (Sweden)

    Yan ZENG, Chunwang LI, Linyuan ZHANG, Zhenyu ZHONG, Zhigang JIANG

    2013-04-01

    Full Text Available Considering the severe impacts of genetic bottlenecks and small numbers of founders in populations of reintroduced animals, it is necessary to study inbreeding and its effect on fitness in species of conservation concern. Père David’s deer is one of few large mammal species extinct in the wild but safely preserved in captivity. Its specific background gives us the opportunity to study the relationships between heterozygosity and neonatal fitness in relocated populations. We employed five microsatellite loci to explore heterozygosity-fitness correlations in a population of Père David’s deer at the Beijing Milu Ecological Research Center. We observed associations between microsatellite-based variables sMLH, IR, MD2 and HL, and two components of fitness expressed early in life (birth weight and the neonatal mortality of 123 Père David’s deer calves born over six consecutive years. We found that neonatal mortality was 19.1 ± 7.6%, not higher than the 19% or 18% reported in other ungulates. The heterozygosity of calves was not associated with neonatal mortality, nor birth weight. Our study implies that low genetic variability of microsatellite loci has no overt effect on birth weight and neonatal mortality in reintroduced populations of Père David’s deer [Current Zoology 59 (2: 249–256, 2013].

  8. Reduced population size does not affect the mating strategy of a vulnerable and endemic seabird

    Science.gov (United States)

    Nava, Cristina; Neves, Verónica C.; Andris, Malvina; Dubois, Marie-Pierre; Jarne, Philippe; Bolton, Mark; Bried, Joël

    2017-12-01

    Bottleneck episodes may occur in small and isolated animal populations, which may result in decreased genetic diversity and increased inbreeding, but also in mating strategy adjustment. This was evaluated in the vulnerable and socially monogamous Monteiro's Storm-petrel Hydrobates monteiroi, a seabird endemic to the Azores archipelago which has suffered a dramatic population decline since the XVth century. To do this, we conducted a genetic study (18 microsatellite markers) in the population from Praia islet, which has been monitored over 16 years. We found no evidence that a genetic bottleneck was associated with this demographic decline. Monteiro's Storm-petrels paired randomly with respect to genetic relatedness and body measurements. Pair fecundity was unrelated to genetic relatedness between partners. We detected only two cases of extra-pair parentage associated with an extra-pair copulation (out of 71 offspring). Unsuccessful pairs were most likely to divorce the next year, but genetic relatedness between pair mates and pair breeding experience did not influence divorce. Divorce enabled individuals to improve their reproductive performances after re-mating only when the new partner was experienced. Re-pairing with an experienced partner occurred more frequently when divorcees changed nest than when they retained their nest. This study shows that even in strongly reduced populations, genetic diversity can be maintained, inbreeding does not necessarily occur, and random pairing is not risky in terms of pair lifetime reproductive success. Given, however, that we found no clear phenotypic mate choice criteria, the part played by non-morphological traits should be assessed more accurately in order to better understand seabird mating strategies.

  9. Severely disabling chronic pain in young adults: prevalence from a population-based postal survey in North Staffordshire

    Directory of Open Access Journals (Sweden)

    Thomas Elaine

    2005-07-01

    Full Text Available Abstract Background Severely disabling chronic pain in the adult population is strongly associated with a range of negative health consequences for individuals and high health care costs, yet its prevalence in young adults is less clear. Methods All adults aged 18–25 years old registered with three general practices in North Staffordshire were invited to complete a postal questionnaire containing questions on pain within the last 6 months, pain location and duration. Severity of chronic pain was assessed by the Chronic Pain Grade. Severely disabling chronic pain was defined as pain within the last six months that had lasted for three months or more and was highly disabling-severely limiting (Grade IV. Results 858 responses from 2,389 were received (adjusted response = 37.0%. The prevalence of any pain within the previous six months was 66.9% (95%CI: 63.7%, 70.1%. Chronic pain was reported by 14.3% (95%CI: 12.0%, 16.8% of respondents with severely disabling chronic pain affecting 3.0% (95%CI: 2.0%, 4.4% of this population. Late responders were very similar to early responders in their prevalence of pain. Cross-checking the practice register against the electoral roll suggested register inaccuracies contributed to non-response. Conclusion Pain is a common phenomenon encountered by young adults, affecting 66.9% of this study population. Previously observed age-related trends in severely disabling chronic pain in older adults extend to younger adults. Although a small minority of younger adults are affected, they are likely to represent a group with particularly high health care needs. High levels of non-response in the present study means that these estimates should be interpreted cautiously although there was no evidence of non-response bias.

  10. Relationship of socioeconomic factors with vision-related quality of life on severe low vision and blind population in Indonesia

    Directory of Open Access Journals (Sweden)

    Habsyiyah Habsyiyah

    2015-12-01

    Full Text Available Background: Socioeconomic factors are known to be associated with visual impairment. Being someone who is visually impaired could affect his quality of life. The aim of this study is to evaluate the quality of life (QOL in severe low vision and blind population in Indonesia in relation to their socioeconomic status. Methods: A cross sectional population-based study was performed in 5 provinces, in Indonesia. Respondents of validation study on blindness data of national basic health survey 2013 (RISKESDAS 2013, who were above 18 years old with severe low vision (BCVA≥3/60 to 6/60 and blind (BCVA<3/60, were included in this study. Questionnaires for socioeconomic status and a questionnaire from the national eye institute visual function questionnaire 25 (NEI VFQ 25 for visual function were administered. Total  scores of NEI-VFQ25 were compared based on severity of visual impairment, educational level, occupation, literacy adequacy, income level, and residency. Data analysis was using independent T-test or Mann-Whitney test, and Chi square test.Results: A total of 134 subjects were enrolled in this study, most of them are  women (68.2%, aged >64 years old (64.9% with low education (65.7%, illiterate (52.2%, low income (71.6%, non working (63.4% and living in urban areas (58.2%. The blind population has lower VFQ scores than severe low vision (p=0.001. Different status of educational level, literacy adequacy, income level and residency did not show significant difference in VFQ scores, but those who have an occupation had better VFQ scores than those who do not (p=0.041.Conclusion: Visual related quality of life (VRQOL of severe low vision and blind population was associated significantly with occupational status. Because of culture and characteristics of Indonesian people, VRQOL of severe low vision and blind population in Indonesia was not affected by educational level, literacy, income level, and residency.

  11. A Selective Bottleneck Shapes the Evolutionary Mutant Spectra of Enterovirus A71 during Viral Dissemination in Humans.

    Science.gov (United States)

    Huang, Sheng-Wen; Huang, Yi-Hui; Tsai, Huey-Pin; Kuo, Pin-Hwa; Wang, Shih-Min; Liu, Ching-Chuan; Wang, Jen-Ren

    2017-12-01

    RNA viruses accumulate mutations to rapidly adapt to environmental changes. Enterovirus A71 (EV-A71) causes various clinical manifestations with occasional severe neurological complications. However, the mechanism by which EV-A71 evolves within the human body is unclear. Utilizing deep sequencing and haplotype analyses of viruses from various tissues of an autopsy patient, we sought to define the evolutionary pathway by which enterovirus A71 evolves fitness for invading the central nervous system in humans. Broad mutant spectra with divergent mutations were observed at the initial infection sites in the respiratory and digestive systems. After viral invasion, we identified a haplotype switch and dominant haplotype, with glycine at VP1 residue 31 (VP1-31G) in viral particles disseminated into the integumentary and central nervous systems. In vitro viral growth and fitness analyses indicated that VP1-31G conferred growth and a fitness advantage in human neuronal cells, whereas VP1-31D conferred enhanced replication in human colorectal cells. A higher proportion of VP1-31G was also found among fatal cases, suggesting that it may facilitate central nervous system infection in humans. Our data provide the first glimpse of EV-A71 quasispecies from oral tissues to the central nervous system within humans, showing broad implications for the surveillance and pathogenesis of this reemerging viral pathogen. IMPORTANCE EV-A71 continues to be a worldwide burden to public health. Although EV-A71 is the major etiological agent of hand, foot, and mouth disease, it can also cause neurological pulmonary edema, encephalitis, and even death, especially in children. Understanding selection processes enabling dissemination and accurately estimating EV-A71 diversity during invasion in humans are critical for applications in viral pathogenesis and vaccine studies. Here, we define a selection bottleneck appearing in respiratory and digestive tissues. Glycine substitution at VP1 residue 31

  12. Time-Contrastive Learning Based DNN Bottleneck Features for Text-Dependent Speaker Verification

    DEFF Research Database (Denmark)

    Sarkar, Achintya Kumar; Tan, Zheng-Hua

    2017-01-01

    In this paper, we present a time-contrastive learning (TCL) based bottleneck (BN) feature extraction method for speech signals with an application to text-dependent (TD) speaker verification (SV). It is well-known that speech signals exhibit quasi-stationary behavior in and only in a short interval......, and the TCL method aims to exploit this temporal structure. More specifically, it trains deep neural networks (DNNs) to discriminate temporal events obtained by uniformly segmenting speech signals, in contrast to existing DNN based BN feature extraction methods that train DNNs using labeled data...... to discriminate speakers or pass-phrases or phones or a combination of them. In the context of speaker verification, speech data of fixed pass-phrases are used for TCL-BN training, while the pass-phrases used for TCL-BN training are excluded from being used for SV, so that the learned features can be considered...

  13. Task-set inertia and memory-consolidation bottleneck in dual tasks.

    Science.gov (United States)

    Koch, Iring; Rumiati, Raffaella I

    2006-11-01

    Three dual-task experiments examined the influence of processing a briefly presented visual object for deferred verbal report on performance in an unrelated auditory-manual reaction time (RT) task. RT was increased at short stimulus-onset asynchronies (SOAs) relative to long SOAs, showing that memory consolidation processes can produce a functional processing bottleneck in dual-task performance. In addition, the experiments manipulated the spatial compatibility of the orientation of the visual object and the side of the speeded manual response. This cross-task compatibility produced relative RT benefits only when the instruction for the visual task emphasized overlap at the level of response codes across the task sets (Experiment 1). However, once the effective task set was in place, it continued to produce cross-task compatibility effects even in single-task situations ("ignore" trials in Experiment 2) and when instructions for the visual task did not explicitly require spatial coding of object orientation (Experiment 3). Taken together, the data suggest a considerable degree of task-set inertia in dual-task performance, which is also reinforced by finding costs of switching task sequences (e.g., AC --> BC vs. BC --> BC) in Experiment 3.

  14. En route to the conductivity bottleneck in p-type CuCr1-xMxO2-ySy (M = Li, Mg)

    Science.gov (United States)

    Mandal, P.; Mazumder, N.; Akhtar, A. J.; Roy, R.; Chattopadhyay, K. K.

    2017-05-01

    We extend our material design concept [P. Mandal et al. J. Phys. D: Appl. Phys. 49, 275109, (2016); N. Mazumder et al. J. Phys. Chem. Lett. 4, 3539, (2013)] further aiming to overcome the conductivity bottleneck (1 Scm-1) in p-type transparent conducting oxide (TCO). In this work, we execute the strategy of simultaneous cationic-anionic hole doping in the prototype p-TCO CuCrO2. CuCr1-xMxO2-ySy (M = Li, Mg) is prepared by solid state heating at 1150 °C. Using Rietveld analysis, the presence of Mgcr•, Licr • and SO×areconfirmed and quantified. The diffuse reflectance (DR) spectra are acquired to determine the dominant optical gap (˜ 3.5 eV) and found to be affected little upon site selective hole doping. From temperature dependence (80 - 300 K) of DC conductivity (σdc), (Licr •+SO×)dopingcan be identified to be the more plausible alternative to reach the bottleneck threshold compared to (Mgcr •+SO×) albeit of smaller σdc at 300 K.

  15. Ethnic Differences in Mental Illness Severity: A Population-Based Study of Chinese and South Asian Patients in Ontario, Canada.

    Science.gov (United States)

    Chiu, Maria; Lebenbaum, Michael; Newman, Alice M; Zaheer, Juveria; Kurdyak, Paul

    2016-09-01

    Little is known about the sociocultural determinants of mental illness at hospital presentation. Our objective was to examine ethnic differences in illness severity at hospital admission among Chinese, South Asian, and the general population living in Ontario, Canada. We conducted a large, population-based, cross-sectional study of psychiatric inpatients aged from 19 to 105 years who were discharged between 2006 and 2014. A total of 133,588 patients were classified as Chinese (n = 2,582), South Asian (n = 2,452), or the reference group (n = 128,554) using a validated surnames algorithm (specificity: 99.7%). Diagnoses were based on DSM-IV criteria. We examined the association between ethnicity and 4 measures of disease severity: involuntary admissions, aggressive behaviors, and the number and frequency of positive symptoms (ie, hallucinations, command hallucinations, delusions, and abnormal thought process) (Positive Symptoms Scale, Resident Assessment Instrument-Mental Health [RAI-MH]). After adjusting for sociodemographic characteristics, immigration status, and discharge diagnosis, Chinese patients had greater odds of involuntary admissions (odds ratio [OR] = 1.79; 95% CI, 1.64-1.95) and exhibiting severe aggressive behaviors (OR = 1.36; 95% CI, 1.23-1.51) and ≥ 3 positive symptoms (OR = 1.39; 95% CI, 1.24-1.56) compared to the general population. South Asian ethnicity was also an independent predictor of most illness severity measures. The association between Chinese ethnicity and illness severity was consistent across sex, diagnostic and immigrant categories, and first-episode hospitalization. Chinese and South Asian ethnicities are independent predictors of illness severity at hospital presentation. Understanding the role of patient, family, and health system factors in determining the threshold for hospitalization is an important future step in informing culturally specific care for these large and growing populations worldwide. © Copyright 2016 Physicians

  16. The Prevalence of Anemia and Moderate-Severe Anemia in the US Population (NHANES 2003-2012)

    Science.gov (United States)

    2016-01-01

    Since anemia is associated with poor health outcomes, the prevalence of anemia is a significant public health indicator. Even though anemia is primarily caused by iron deficiency, low oxygen-carrying capacity may result from other conditions such as chronic diseases, which remain a relevant health concern in the United States. However, studies examining current rates of anemia in the total US population and in more specific subgroups are limited. Data from five National Health and Nutrition Examination Surveys (NHANES) from 2003 to 2012 were analyzed to assess two outcomes: anemia and moderate-severe anemia, which were based upon serum hemoglobin levels (Hb) as per World Health Organization (WHO) definitions. Statistical analysis using SAS examined temporal trends and the prevalence of anemia among sexes, age groups, and races/ethnicities. The study estimated that an average of 5.6% of the U.S. population met the criteria for anemia and 1.5% for moderate-severe anemia during this 10-year period. High-risk groups such as pregnant women, elderly persons, women of reproductive age, non-Hispanic blacks, and Hispanics were identified, and relationships between multiple risk factors were examined. Rates of anemia in men increased monotonically with age, while that of women increased bimodally with peaks in age group 40–49 years and 80–85 years. The effect of risk factors was observed to compound. For instance, the prevalence of anemia in black women aged 80–85 years was 35.6%, 6.4 times higher than the population average. Moreover, anemia is a growing problem because of the increased prevalence of anemia (4.0% to 7.1%) and moderate-severe anemia (1.0% to 1.9%), which nearly doubled from 2003–2004 to 2011–2012. Thus, these results augment the current knowledge on anemia prevalence, severity, and distribution among subgroups in the US and raised anemia as an issue that requires urgent public health intervention. PMID:27846276

  17. Multiple bottlenecks in hierarchical control of action sequences: what does "response selection" select in skilled typewriting?

    Science.gov (United States)

    Yamaguchi, Motonori; Logan, Gordon D; Li, Vanessa

    2013-08-01

    Does response selection select words or letters in skilled typewriting? Typing performance involves hierarchically organized control processes: an outer loop that controls word level processing, and an inner loop that controls letter (or keystroke) level processing. The present study addressed whether response selection occurs in the outer loop or the inner loop by using the psychological refractory period (PRP) paradigm in which Task1 required typing single words and Task2 required vocal responses to tones. The number of letters (string length) in the words was manipulated to discriminate selection of words from selection of keystrokes. In Experiment 1, the PRP effect depended on string length of words in Task1, suggesting that response selection occurs in the inner loop. To assess contributions of the outer loop, the influence of string length was examined in a lexical-decision task that also involves word encoding and lexical access (Experiment 2), or to-be-typed words were preexposed so outer-loop processing could finish before typing started (Experiment 3). Response time for Task2 (RT2) did not depend on string length with lexical decision, and RT2 still depended on string length with typing preexposed strings. These results support the inner-loop locus of the PRP effect. In Experiment 4, typing was performed as Task2, and the effect of string length on typing RT interacted with stimulus onset asynchrony superadditively, implying that another bottleneck also exists in the outer loop. We conclude that there are at least two bottleneck processes in skilled typewriting. 2013 APA, all rights reserved

  18. Nonlinear analysis and synthesis of video images using deep dynamic bottleneck neural networks for face recognition.

    Science.gov (United States)

    Moghadam, Saeed Montazeri; Seyyedsalehi, Seyyed Ali

    2018-05-31

    Nonlinear components extracted from deep structures of bottleneck neural networks exhibit a great ability to express input space in a low-dimensional manifold. Sharing and combining the components boost the capability of the neural networks to synthesize and interpolate new and imaginary data. This synthesis is possibly a simple model of imaginations in human brain where the components are expressed in a nonlinear low dimensional manifold. The current paper introduces a novel Dynamic Deep Bottleneck Neural Network to analyze and extract three main features of videos regarding the expression of emotions on the face. These main features are identity, emotion and expression intensity that are laid in three different sub-manifolds of one nonlinear general manifold. The proposed model enjoying the advantages of recurrent networks was used to analyze the sequence and dynamics of information in videos. It is noteworthy to mention that this model also has also the potential to synthesize new videos showing variations of one specific emotion on the face of unknown subjects. Experiments on discrimination and recognition ability of extracted components showed that the proposed model has an average of 97.77% accuracy in recognition of six prominent emotions (Fear, Surprise, Sadness, Anger, Disgust, and Happiness), and 78.17% accuracy in the recognition of intensity. The produced videos revealed variations from neutral to the apex of an emotion on the face of the unfamiliar test subject which is on average 0.8 similar to reference videos in the scale of the SSIM method. Copyright © 2018 Elsevier Ltd. All rights reserved.

  19. Inferring the Mode of Selection from the Transient Response to Demographic Perturbations

    Science.gov (United States)

    Balick, Daniel; Do, Ron; Reich, David; Sunyaev, Shamil

    2014-03-01

    Despite substantial recent progress in theoretical population genetics, most models work under the assumption of a constant population size. Deviations from fixed population sizes are ubiquitous in natural populations, many of which experience population bottlenecks and re-expansions. The non-equilibrium dynamics introduced by a large perturbation in population size are generally viewed as a confounding factor. In the present work, we take advantage of the transient response to a population bottleneck to infer features of the mode of selection and the distribution of selective effects. We develop an analytic framework and a corresponding statistical test that qualitatively differentiates between alleles under additive and those under recessive or more general epistatic selection. This statistic can be used to bound the joint distribution of selective effects and dominance effects in any diploid sexual organism. We apply this technique to human population genetic data, and severely restrict the space of allowed selective coefficients in humans. Additionally, one can test a set of functionally or medically relevant alleles for the primary mode of selection, or determine the local regional variation in dominance coefficients along the genome.

  20. Perinatal risk factors in offenders with severe personality disorder: a population-based investigation.

    Science.gov (United States)

    Fazel, Seena; Bakiyeva, Liliya; Cnattingius, Sven; Grann, Martin; Hultman, Christina M; Lichtenstein, Paul; Geddes, John R

    2012-10-01

    Although perinatal factors are associated with the development of several psychiatric disorders, it is unknown whether these factors are linked with personality disorder. Cases of personality disorder were drawn from a national registry of all forensic psychiatric evaluations (n = 150). Two control groups were used: (1) A sample of forensic evaluations without any psychiatric disorder (n = 97) allowing for a nested case-control investigation; and (2) A population-based sample matched by age and gender with no history of psychiatric hospitalization (n = 1498). Prematurity (personality disorder, both in the nested and the population-based case-control comparisons with adjusted odds ratios (OR) for this risk factor ranging from 2 to 4. Asphyxia (adjusted OR = 2.4, 95% CI: 1.4-4.1) and complicated delivery (adjusted OR = 1.5, 1.0-2.1) were associated with personality disorder in the population-based study, and the former remained significant in multivariate models. Overall, perinatal complications were found to be associated with a later diagnosis of personality disorder in this selected sample. As with other psychiatric disorders where such associations have been demonstrated, changes during the perinatal period may lead to abnormal brain development and function.

  1. Effectiveness of microsatellite and SNP markers for parentage and identity analysis in species with low genetic diversity: the case of European bison

    DEFF Research Database (Denmark)

    Torskarska, M; Marshall, T; Kowalczyk, R

    2009-01-01

    The European bison (Bison bonasus) has recovered successfully after a severe bottleneck about 90 years ago. Pedigree analysis indicates that over 80% of the genes in the contemporary population descend from just 2 founder individuals and the pedigree-based inbreeding coefficient averages almost 0...

  2. Future trends in the prevalence of severe activity limitations among older adults in Europe: a cross-national population study using EU-SILC

    Science.gov (United States)

    Scherbov, Sergei; Weber, Daniela

    2017-01-01

    Objective To project the proportion of population 65+ years with severe long-term activity limitations from 2017 to 2047. Design Large population study. Setting Population living in private households of the European Union (EU) and neighbouring countries. Participants Participants from the EU Statistics on Income and Living Conditions aged 55 years and older and living in one of 26 EU and neighbouring countries, who answered the health section of the questionnaire. Outcome measures Prevalence of severe long-term activity limitations of particular subpopulations (ie, 55+, 65+, 75+ and 85+ years) by sex and country. Results We find a huge variation in the prevalence of self-reported severe long-term limitations across Europe for both sexes. However, in 2017, about 20% of the female population aged 65 years and above and about 16% of their male counterparts are expected to report severe long-term activity limitations after accounting for differences in reporting. Accounting for cultural differences in reporting, we expect that European countries will have about 21% (decile 1: 19.5%; decile 9: 22.9%) of female and about 16.8% (decile 1: 15.4%; decile 9: 18.1%) of male 65+ years population with severe long-term activity limitations by 2047. Conclusions Overall, despite the expected increase of life expectancy in European countries, our results suggest almost constant shares of older adults with severe long-term activity limitations within the next 30 years. PMID:29061570

  3. Severe MUPS in a sick-listed population: a cross-sectional study on prevalence, recognition, psychiatric co-morbidity and impairment

    Directory of Open Access Journals (Sweden)

    Koopmans Petra C

    2009-12-01

    Full Text Available Abstract Background Medically unexplained physical symptoms (MUPS have a high prevalence in the general population and are associated with psychiatric morbidity. There are indications that MUPS are an important determinant of frequent and long-term disability. The primary objective was to assess the prevalence of MUPS in sick-listed-employees and its associations with depressive disorders, anxiety disorders, health anxiety, distress and functional impairment. Secondary objectives were to investigate the classification of the occupational health physicians (OHPs, their opinions about the causes as well as the attributions of the employee. Methods In a cross-sectional study of 489 sick-listed employees from 5 OHP group practices, MUPS, depressive disorders, anxiety disorders, health anxiety, distress and functional impairment were assessed with the Patient Health Questionnaire (PHQ, the Whitely Index (WI, the Four- Dimensional Symptom Questionnaire (4DSQ and the Short-Form 36 Health Survey (SF-36. We used a cut off score of 15 on the PHQ for the categorisation of severe MUPS. The opinions of the OHPs were evaluated by means of a separate questionnaire with regard to the presence of employees physical symptoms, and the symptoms attributions, and the diagnoses of the OHPs. Results Severe MUPS had a prevalence of 15.1% in this population of sick-listed employees. These employees had 4-6 times more depressive and anxiety disorders, and were more impaired. Female gender and PHQ-9 scores were determinants of severe MUPS. Most of the time the OHPs diagnosed employees with severe MUPS as having a mental disorder. The employees attributed their physical symptoms in 66% to mental or to both mental and physical causes. Conclusion The prevalence of severe MUPS is higher in long-term sick-listed employees than in the non-sick- listed working population and at least equals the prevalence in the general practice population. Severe MUPS are associated with

  4. Genetic divergence in populations of Lutzomyia ayacuchensis, a vector of Andean-type cutaneous leishmaniasis, in Ecuador and Peru.

    Science.gov (United States)

    Kato, Hirotomo; Cáceres, Abraham G; Gomez, Eduardo A; Mimori, Tatsuyuki; Uezato, Hiroshi; Hashiguchi, Yoshihisa

    2015-01-01

    Haplotype and gene network analyses were performed on mitochondrial cytochrome oxidase I and cytochrome b gene sequences of Lutzomyia (Lu.) ayacuchensis populations from Andean areas of Ecuador and southern Peru where the sand fly species transmit Leishmania (Leishmania) mexicana and Leishmania (Viannia) peruviana, respectively, and populations from the northern Peruvian Andes, for which transmission of Leishmania by Lu. ayacuchensis has not been reported. The haplotype analyses showed higher intrapopulation genetic divergence in northern Peruvian Andes populations and less divergence in the southern Peru and Ecuador populations, suggesting that a population bottleneck occurred in the latter populations, but not in former ones. Importantly, both haplotype and phylogenetic analyses showed that populations from Ecuador consisted of clearly distinct clusters from southern Peru, and the two populations were separated from those of northern Peru. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

  5. Bottlenecks in deriving definitive hematopoietic stem cells from human pluripotent stem cells: a CIRM mini-symposium and workshop report.

    Science.gov (United States)

    Shepard, Kelly A; Talib, Sohel

    2014-07-01

    On August 29, 2013, the California Institute for Regenerative Medicine (CIRM) convened a small group of investigators in San Francisco, CA, to discuss a longstanding challenge in the stem cell field: the inability to derive fully functional, definitive hematopoietic stem cells (HSCs) from pluripotent stem cells (PSCs). To date, PSC-derived HSCs have been deficient in their developmental potential and their ability to self-renew and engraft upon transplantation. Tasked with identifying key challenges to overcoming this "HSC bottleneck", workshop participants identified critical knowledge gaps in two key areas: (a) understanding the ontogeny of human HSCs, and (b) understanding of the intrinsic and extrinsic factors that govern HSC behavior and function. They agreed that development of new methods and tools is critical for addressing these knowledge gaps. These include molecular profiling of key HSC properties, development of new model systems/assays for predicting and assessing HSC function, and novel technological advancements for manipulating cell culture conditions and genetic programs. The workshop produced tangible advances, including providing a current definition of the nature and challenge of the HSC bottleneck and identifying key mechanistic studies of HSC biology that should be prioritized for future funding initiatives (e.g., including higher risk approaches that have potential for high gain). ©AlphaMed Press.

  6. Bottleneck in secretion of α-amylase in Bacillus subtilis.

    Science.gov (United States)

    Yan, Shaomin; Wu, Guang

    2017-07-19

    Amylase plays an important role in biotechnology industries, and Gram-positive bacterium Bacillus subtilis is a major host to produce heterogeneous α-amylases. However, the secretion stress limits the high yield of α-amylase in B. subtilis although huge efforts have been made to address this secretion bottleneck. In this question-oriented review, every effort is made to answer the following questions, which look simple but are long-standing, through reviewing of literature: (1) Does α-amylase need a specific and dedicated chaperone? (2) What signal sequence does CsaA recognize? (3) Does CsaA require ATP for its operation? (4) Does an unfolded α-amylase is less soluble than a folded one? (5) Does α-amylase aggregate before transporting through Sec secretion system? (6) Is α-amylase sufficient stable to prevent itself from misfolding? (7) Does α-amylase need more disulfide bonds to be stabilized? (8) Which secretion system does PrsA pass through? (9) Is PrsA ATP-dependent? (10) Is PrsA reused after folding of α-amylase? (11) What is the fate of PrsA? (12) Is trigger factor (TF) ATP-dependent? The literature review suggests that not only the most of those questions are still open to answers but also it is necessary to calculate ATP budget in order to better understand how B. subtilis uses its energy for production and secretion.

  7. Founder representation and effective population size in old versus young breeds-genetic diversity of Finnish and Nordic Spitz.

    Science.gov (United States)

    Kumpulainen, M; Anderson, H; Svevar, T; Kangasvuo, I; Donner, J; Pohjoismäki, J

    2017-10-01

    Finnish Spitz is 130-year-old breed and has been highly popular in Finland throughout its history. Nordic Spitz is very similar to Finnish Spitz by origin and use, but is a relatively recent breed with much smaller population size. To see how breed age and breeding history have influenced the current population, we performed comprehensive population genetic analysis using pedigree data of 28,119 Finnish and 9,009 Nordic Spitzes combined with genomewide single nucleotide polymorphism (SNP) data from 135 Finnish and 110 Nordic Spitzes. We found that the Finnish Spitz has undergone repeated male bottlenecks resulting in dramatic loss of genetic diversity, reflected by 20 effective founders (f a ) and mean heterozygosity (Hz) of 0.313. The realized effective population size in the breed based on pedigree analysis (N¯ec) is 168, whereas the genetic effective population size (N eg ) computed the decay of linkage disequilibrium (r 2 ) is only 57 individuals. Nordic Spitz, although once been near extinction, has not been exposed to similar repeated bottlenecks than Finnish Spitz and had f a of 27 individuals. However, due to the smaller total population size, the breed has also smaller effective population size than Finnish Spitz (N¯ec = 98 and N eg  = 49). Interestingly, the r 2 data show that the effective population size has contracted dramatically since the establishment of the breed, emphasizing the role of breed standards as constrains for the breeding population. Despite the small population size, Nordic Spitz still maintains SNP heterozygosity levels similar to mixed breed dogs (mean Hz = 0.409). Our study demonstrates that although pedigree analyses cannot provide estimates of the present diversity within a breed, the effective population sizes inferred from them correlate with the genotyping results. The genetic relationships of the northern Spitz breeds and the benefits of the open breed registry are discussed. © 2017 Blackwell Verlag GmbH.

  8. Head-of-tide bottleneck of particulate material transport from watersheds to estuaries

    Science.gov (United States)

    Ensign, Scott H.; Noe, Gregory; Hupp, Cliff R.; Skalak, Katherine

    2015-01-01

    We measured rates of sediment, C, N, and P accumulation at four floodplain sites spanning the nontidal through oligohaline Choptank and Pocomoke Rivers, Maryland, USA. Ceramic tiles were used to collect sediment for a year and sediment cores were collected to derive decadal sedimentation rates using 137Cs. The results showed highest rates of short- and long-term sediment, C, N, and P accumulation occurred in tidal freshwater forests at the head of tide on the Choptank and the oligohaline marsh of the Pocomoke River, and lowest rates occurred in the downstream tidal freshwater forests in both rivers. Presumably, watershed material was mostly trapped at the head of tide, and estuarine material was trapped in oligohaline marshes. This hydrologic transport bottleneck at the head of tide stores most available watershed sediment, C, N, and P creating a sediment shadow in lower tidal freshwater forests potentially limiting their resilience to sea level rise.

  9. A Real-time Breakdown Prediction Method for Urban Expressway On-ramp Bottlenecks

    Science.gov (United States)

    Ye, Yingjun; Qin, Guoyang; Sun, Jian; Liu, Qiyuan

    2018-01-01

    Breakdown occurrence on expressway is considered to relate with various factors. Therefore, to investigate the association between breakdowns and these factors, a Bayesian network (BN) model is adopted in this paper. Based on the breakdown events identified at 10 urban expressways on-ramp in Shanghai, China, 23 parameters before breakdowns are extracted, including dynamic environment conditions aggregated with 5-minutes and static geometry features. Different time periods data are used to predict breakdown. Results indicate that the models using 5-10 min data prior to breakdown performs the best prediction, with the prediction accuracies higher than 73%. Moreover, one unified model for all bottlenecks is also built and shows reasonably good prediction performance with the classification accuracy of breakdowns about 75%, at best. Additionally, to simplify the model parameter input, the random forests (RF) model is adopted to identify the key variables. Modeling with the selected 7 parameters, the refined BN model can predict breakdown with adequate accuracy.

  10. Prevalence and severity of plaque-induced gingivitis in a Saudi adult population

    Science.gov (United States)

    Idrees, Majdy M.; Azzeghaiby, Saleh N.; Hammad, Mohammad M.; Kujan, Omar B.

    2014-01-01

    Objectives: To evaluate the prevalence and severity of plaque-induced gingivitis among a Saudi adult population in Riyadh region. Methods: Three hundred and eighty-five eligible participants in this cross-sectional study were recruited from routine dental patients attending the oral diagnosis clinic at Al-Farabi College in Riyadh, Saudi Arabia from June 2013 to December 2013. A clinical examination was performed by 2 dentists to measure the gingival and plaque indices of Löe and Silness for each participant. Results: The prevalence of gingivitis was 100% among adult subjects aged between 18-40 years old. Moreover, the mean gingival index was 1.68±0.31, which indicates a moderate gingival inflammation. In fact, males showed more severe signs of gingival inflammation compared with females (p=0.001). In addition, the mean plaque index was 0.875±0.49, which indicates a good plaque status of the participants. Interestingly, the age was not related either to the gingival inflammation (p=0.13), or to the amount of plaque accumulation (p=0.17). However, males were more affected than females (p=0.005). Conclusion: The results of this study show that plaque accumulation is strongly associated with high prevalence of moderate to severe gingivitis among Saudi subjects. PMID:25399215

  11. Demographic processes underlying subtle patterns of population structure in the scalloped hammerhead shark, Sphyrna lewini.

    Directory of Open Access Journals (Sweden)

    Holly A Nance

    Full Text Available Genetic diversity (θ, effective population size (N(e, and contemporary levels of gene flow are important parameters to estimate for species of conservation concern, such as the globally endangered scalloped hammerhead shark, Sphyrna lewini. Therefore, we have reconstructed the demographic history of S. lewini across its Eastern Pacific (EP range by applying classical and coalescent population genetic methods to a combination of 15 microsatellite loci and mtDNA control region sequences. In addition to significant population genetic structure and isolation-by-distance among seven coastal sites between central Mexico and Ecuador, the analyses revealed that all populations have experienced a bottleneck and that all current values of θ are at least an order of magnitude smaller than ancestral θ, indicating large decreases in N(e (θ = 4N(eμ, where μ is the mutation rate. Application of the isolation-with-migration (IM model showed modest but significant genetic connectivity between most sampled sites (point estimates of Nm = 0.1-16.7, with divergence times (t among all populations significantly greater than zero. Using a conservative (i.e., slow fossil-based taxon-specific phylogenetic calibration for mtDNA mutation rates, posterior probability distributions (PPDs for the onset of the decline in N(e predate modern fishing in this region. The cause of decline over the last several thousand years is unknown but is highly atypical as a post-glacial demographic history. Regardless of the cause, our data and analyses suggest that S. lewini was far more abundant throughout the EP in the past than at present.

  12. Microsatellite analysis of the natterjack toad (Bufo calamita) in Denmark: populations are islands in a fragmented landscape

    DEFF Research Database (Denmark)

    Allentoft, Morten Erik; Siegismund, Hans Redlef; Briggs, Lars

    2009-01-01

    The European natterjack toad (Bufo calamita) has declined rapidly in recent years, primarily due to loss of habitat, and in Denmark it is estimated that 50% of the isolated populations are lost each decade. To efficiently manage and conserve this species and its genetic diversity, knowledge...... of isolation by distance within major regions supported this apparent lack of a gene flow continuum. Indications of a genetic bottleneck were found in three populations. The analyses suggest that the remaining Bufo calamita populations in Denmark are genetically isolated, and represent independent units...... in a highly fragmented gene pool. Future conservation management of this species is discussed in light of these results....

  13. Genetic variants of STAT4 are associated with ankylosing spondylitis susceptibility and severity in a Chinese Han population.

    Science.gov (United States)

    Liu, Zhixiang; Zhang, Peisen; Dong, Jie

    2014-01-01

    Genetic factors play an important role in ankylosing spondylitis (AS) etiology and signal transducer and activator of transcription 4 (STAT4) gene polymorphisms may be involved. The aim of this study was to test whether STAT4 variants were associated with susceptibility to AS in a Chinese population. A total of 175 subjects who were diagnosed as AS and 249 healthy age-matched controls were enrolled in the present study. The rs7574865 G/T SNP in STAT4 gene was genotyped in all the subjects. The SPSS software was used to investigate the association between the rs7574865 genotypes and AS susceptibility or severity. Rs7574865 G/T was found to be significantly associated with increased risk and severity of AS. Our data demonstrated the STAT4 rs7574865 G/T SNP was significantly associated with increased AS susceptibility and severity in Chinese Han Population.

  14. Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity.

    Science.gov (United States)

    Patterson, Edward I; Khanipov, Kamil; Rojas, Mark M; Kautz, Tiffany F; Rockx-Brouwer, Dedeke; Golovko, Georgiy; Albayrak, Levent; Fofanov, Yuriy; Forrester, Naomi L

    2018-01-01

    Viral diversity is theorized to play a significant role during virus infections, particularly for arthropod-borne viruses (arboviruses) that must infect both vertebrate and invertebrate hosts. To determine how viral diversity influences mosquito infection and dissemination Culex taeniopus mosquitoes were infected with the Venezuelan equine encephalitis virus endemic strain 68U201. Bodies and legs/wings of the mosquitoes were collected individually and subjected to multi-parallel sequencing. Virus sequence diversity was calculated for each tissue. Greater diversity was seen in mosquitoes with successful dissemination versus those with no dissemination. Diversity across time revealed that bottlenecks influence diversity following dissemination to the legs/wings, but levels of diversity are restored by Day 12 post-dissemination. Specific minority variants were repeatedly identified across the mosquito cohort, some in nearly every tissue and time point, suggesting that certain variants are important in mosquito infection and dissemination. This study demonstrates that the interaction between the mosquito and the virus results in changes in diversity and the mutational spectrum and may be essential for successful transition of the bottlenecks associated with arbovirus infection.

  15. Analysis of registered CDM projects: potential removal of evidenced bottlenecks

    Energy Technology Data Exchange (ETDEWEB)

    Agosto, D.; Bombard, P.; Gostinelli, F.

    2007-07-01

    The Clean Development Mechanism (CDM) has developed during its first period of implementation, a distinctive set of patterns. The authors thought of concentrating on the CDM analysis in order to highlight potential remedies or reasons for given bottlenecks. In order to establish a sort of extensive SWOT analysis for CDMs, all the 356 projects actually (November 2006) registered at UNFCCC were examined, together with all the about 1000 PDDs presented to the UNFCCC but not registered yet. The CDM projects have been studied trying to cluster projects according to relevant characteristics, both from a technical and an economic point of view. Chosen indicators are meant to identify: more convenient/more diffused energy system for a CDM; reasons for a geographical distribution of different types of projects; potentials for a future exploitation of lower used technologies in CDM. Conclusions are drawn and appropriate tables and graphs presented. (1) the Baseline Emission Factor, combined to economic patterns, is the pivotal factor that characterizes both choices of host country and technology; (2) some technologies can exploit appropriately CDM scheme, whilst other technologies, are constrained by it. (3) there are still some important weak points: grouping of non Annex I countries; crediting period; criteria for the evaluation of sustainable development. (auth)

  16. Genome variability in European and American bison detected using the BovineSNP50 BeadChip

    DEFF Research Database (Denmark)

    Pertoldi, C.; Wójcik, Jan M; Tokarska, Małgorzata

    2010-01-01

     The remaining wild populations of bison have all been through severe bottlenecks. The genomic consequences of these bottlenecks present an interesting area to study. Using a very large panel of SNPs developed in Bos taurus we have carried out a genome-wide screening on the European bison (Bison...... bonasus; EB) and on two subspecies of American bison: the plains bison (B. bison bison; PB) and the wood bison (B. bison athabascae; WB). One hundred bison samples were genotyped for 52,978 SNPs along with seven breeds of domestic bovine Bos taurus. Only 2,209 of the SNPs were polymorphic in the bison...

  17. Topographic Steering of Enhanced Ice Flow at the Bottleneck Between East and West Antarctica

    DEFF Research Database (Denmark)

    Winter, Kate; Ross, Neil; Ferraccioli, Fausto

    2018-01-01

    Hypothesized drawdown of the East Antarctic Ice Sheet through the “bottleneck” zone between East and West Antarctica would have significant impacts for a large proportion of the Antarctic Ice Sheet. Earth observation satellite orbits and a sparseness of radio echo sounding data have restricted...... investigations of basal boundary controls on ice flow in this region until now. New airborne radio echo sounding surveys reveal complex topography of high relief beneath the southernmost Weddell/Ross ice divide, with three subglacial troughs connecting interior Antarctica to the Foundation and Patuxent Ice...... Streams and Siple Coast ice streams. These troughs route enhanced ice flow through the interior of Antarctica but limit potential drawdown of the East Antarctic Ice Sheet through the bottleneck zone. In a thinning or retreating scenario, these topographically controlled corridors of enhanced flow could...

  18. Population pharmacokinetics of recombinant coagulation factor VIII-SingleChain in patients with severe hemophilia A.

    Science.gov (United States)

    Zhang, Y; Roberts, J; Tortorici, M; Veldman, A; St Ledger, K; Feussner, A; Sidhu, J

    2017-06-01

    Essentials rVIII-SingleChain is a unique recombinant factor VIII (FVIII) molecule. A population pharmacokinetic model was based on FVIII activity of severe hemophilia A patients. The model was used to simulate factor VIII activity-time profiles for various dosing scenarios. The model supports prolonged dosing of rVIII-SingleChain with intervals of up to twice per week. Background Single-chain recombinant coagulation factor VIII (rVIII-SingleChain) is a unique recombinant coagulation factor VIII molecule. Objectives To: (i) characterize the population pharmacokinetics (PK) of rVIII-SingleChain in patients with severe hemophilia A; (ii) identify correlates of variability in rVIII-SingleChain PK; and (iii) simulate various dosing scenarios of rVIII-SingleChain. Patients/Methods A population PK model was developed, based on FVIII activity levels of 130 patients with severe hemophilia A (n = 91 for ≥ 12-65 years; n = 39 for  85% and > 93% of patients were predicted to maintain FVIII activity level above 1 IU dL -1 , at all times with three-times-weekly dosing (given on days 0, 2, and 4.5) at the lowest (20 IU kg -1 ) and highest (50 IU kg -1 ) doses, respectively. For twice weekly dosing (days 0 and 3.5) of 50 IU kg -1 rVIII-SingleChain, 62-80% of patients across all ages were predicted to maintain a FVIII activity level above 1 IU dL -1 at day 7. Conclusions The population PK model adequately characterized rVIII-SingleChain PK, and the model can be utilized to simulate FVIII activity-time profiles for various dosing scenarios. © 2017 The Authors. Journal of Thrombosis and Haemostasis published by Wiley Periodicals, Inc. on behalf of International Society on Thrombosis and Haemostasis.

  19. Lake trout demographics in relation to burbot and coregonine populations in the Algonquin Highlands, Ontario

    Science.gov (United States)

    Carl, L.M.

    2008-01-01

    The objective of the study was to test the hypothesis that lake trout populations change in relation to cisco, lake whitefish, round whitefish and burbot populations in lakes in the Algonquin Highlands region of Ontario. Lake trout population change is greatest where cisco and lake whitefish are present. Lake trout populations in lakes without either coregonine tend to have small adults and many juveniles. Where cisco or lake whitefish are present, adult lake trout are large, juvenile abundance is low, and the stock-recruit relationship appears to be uncoupled likely due to a larval bottleneck. Lake trout populations in these lakes may be sensitive to overfishing and recruitment failure. Lake trout populations do not appear to change in relation to round whitefish. There appears to be an indirect positive change on juvenile lake trout abundance through reductions in the density of benthic coregonines in the presence of large, hypolimnetic burbot. ?? 2007 Springer Science+Business Media B.V.

  20. Non-Selective Evolution of Growing Populations.

    Directory of Open Access Journals (Sweden)

    Karl Wienand

    Full Text Available Non-selective effects, like genetic drift, are an important factor in modern conceptions of evolution, and have been extensively studied for constant population sizes (Kimura, 1955; Otto and Whitlock, 1997. Here, we consider non-selective evolution in the case of growing populations that are of small size and have varying trait compositions (e.g. after a population bottleneck. We find that, in these conditions, populations never fixate to a trait, but tend to a random limit composition, and that the distribution of compositions "freezes" to a steady state. This final state is crucially influenced by the initial conditions. We obtain these findings from a combined theoretical and experimental approach, using multiple mixed subpopulations of two Pseudomonas putida strains in non-selective growth conditions (Matthijs et al, 2009 as model system. The experimental results for the population dynamics match the theoretical predictions based on the Pólya urn model (Eggenberger and Pólya, 1923 for all analyzed parameter regimes. In summary, we show that exponential growth stops genetic drift. This result contrasts with previous theoretical analyses of non-selective evolution (e.g. genetic drift, which investigated how traits spread and eventually take over populations (fixate (Kimura, 1955; Otto and Whitlock, 1997. Moreover, our work highlights how deeply growth influences non-selective evolution, and how it plays a key role in maintaining genetic variability. Consequently, it is of particular importance in life-cycles models (Melbinger et al, 2010; Cremer et al, 2011; Cremer et al, 2012 of periodically shrinking and expanding populations.

  1. Plasma sterols and depressive symptom severity in a population-based cohort.

    Directory of Open Access Journals (Sweden)

    Basar Cenik

    Full Text Available Convergent evidence strongly suggests major depressive disorder is heterogeneous in its etiology and clinical characteristics. Depression biomarkers hold potential for identifying etiological subtypes, improving diagnostic accuracy, predicting treatment response, and personalization of treatment. Human plasma contains numerous sterols that have not been systematically studied. Changes in cholesterol concentrations have been implicated in suicide and depression, suggesting plasma sterols may be depression biomarkers. Here, we investigated associations between plasma levels of 34 sterols (measured by mass spectrometry and scores on the Quick Inventory of Depressive Symptomatology-Self Report (QIDS-SR16 scale in 3117 adult participants in the Dallas Heart Study, an ethnically diverse, population-based cohort. We built a random forest model using feature selection from a pool of 43 variables including demographics, general health indicators, and sterol concentrations. This model comprised 19 variables, 13 of which were sterol concentrations, and explained 15.5% of the variation in depressive symptoms. Desmosterol concentrations below the fifth percentile (1.9 ng/mL, OR 1.9, 95% CI 1.2-2.9 were significantly associated with depressive symptoms of at least moderate severity (QIDS-SR16 score ≥10.5. This is the first study reporting a novel association between plasma concentrations cholesterol precursors and depressive symptom severity.

  2. Differential patterns of Batrachochytrium dendrobatidis infection in relict amphibian populations following severe disease-associated declines.

    Science.gov (United States)

    Whitfield, Steven M; Alvarado, Gilbert; Abarca, Juan; Zumbado, Hector; Zuñiga, Ibrahim; Wainwright, Mark; Kerby, Jacob

    2017-09-20

    Global amphibian biodiversity has declined dramatically in the past 4 decades, and many amphibian species have declined to near extinction as a result of emergence of the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd). However, persistent or recovering populations of several amphibian species have recently been rediscovered, and such populations may illustrate how amphibian species that are highly susceptible to chytridiomycosis may survive in the presence of Bd. We conducted field surveys for Bd infection in 7 species of Costa Rican amphibians (all species that have declined to near extinction but for which isolated populations persist) to characterize infection profiles in highly Bd-susceptible amphibians post-decline. We found highly variable patterns in infection, with some species showing low prevalence (~10%) and low infection intensity and others showing high infection prevalence (>80%) and either low or high infection intensity. Across sites, infection rates were negatively associated with mean annual precipitation, and infection intensity across sites was negatively associated with mean average temperatures. Our results illustrate that even the most Bd-susceptible amphibians can persist in Bd-enzootic ecosystems, and that multiple ecological or evolutionary mechanisms likely exist for host-pathogen co-existence between Bd and the most Bd-susceptible amphibian species. Continued monitoring of these populations is necessary to evaluate population trends (continuing decline, stability, or population growth). These results should inform efforts to mitigate impacts of Bd on amphibians in the field.

  3. Glycohemoglobin levels with severity of periodontitis in non-diabetic population.

    Science.gov (United States)

    Ghalaut, Pankaj; Sharma, Tarun Kumar; Ghalaut, Veena Singh; Singh, Ragini; Ghalaut, P S

    2013-01-01

    Periodontal disease is closely related to type 2 diabetes and is an important complication of diabetes. There are few studies about the relationship the glycohemoglobin levels with severity of periodontitis in non-diabetic population. We therefore planned this study to evaluate the glycohemoglobin levels with severity of periodontitis in non-diabetic population. This study was conducted on 50 age and gender matched subjects in each of the three groups (according to the grades of mobility in periodontitis), a total of 150 non-diabetic periodontitis patients (Grade 1, Grade 2, and Grade 3 mobility) and 50 non-diabetic periodontitis patients with Grade 0 mobility (controls), in collaboration with the Department of Periodontics of Dental College and Department of Biochemistry, PGIMS, Rohtak, Haryana. After obtaining informed consent, fasting venous blood samples of all the non-diabetic periodontitis patients of all grades were collected aseptically for HbA1c, plasma glucose, and serum C-reactive protein (CRP) estimation. A total of 150 non-diabetic periodontitis patients (Grade 1, Grade 2, and Grade 3 mobility) and 50 age and gender matched controls participated in the study. There was no significant difference in fasting plasma glucose and postprandial plasma glucose in non-diabetic periodontitis patients with Grade 1, Grade 2, and Grade 3 mobility as compared to controls, non-diabetic periodontitis patients with Grade 1 mobility as compared to Grade 2, non-diabetic periodontitis patients with Grade 1 mobility as compared to Grade 3 and non-diabetic periodontitis patients with Grade 2 mobility as compared to Grade 3. Glycohemoglobin and serum C-reactive protein levels were significantly increased in non-diabetic periodontitis patients with Grade 1, Grade 2, and Grade 3 mobility as compared to controls, non-diabetic periodontitis patients with Grade 1 mobility as compared to Grade 3 and non-diabetic periodontitis patients with Grade 2 mobility as compared to Grade 3

  4. Historical Processes and Contemporary Anthropogenic Activities Influence Genetic Population Dynamics of Nassau Grouper (Epinephelus striatus within The Bahamas

    Directory of Open Access Journals (Sweden)

    Krista D. Sherman

    2017-12-01

    Full Text Available Severe declines of endangered Nassau grouper (Epinephelus striatus across The Bahamas and Caribbean have spurred efforts to improve their fisheries management and population conservation. The Bahamas is reported to hold the majority of fish spawning aggregations for Nassau grouper, however, the status and genetic population structure of fish within the country is largely unknown, presenting a major knowledge gap for their sustainable management. Between August 2014–February 2017, 464 individual Nassau grouper sampled from The Bahamas were genotyped using 15 polymorphic microsatellite loci to establish measures of population structure, genetic diversity and effective population size (Ne. Nassau grouper were characterized by mostly high levels of genetic diversity, but we found no evidence for geographic population structure. Microsatellite analyses revealed weak, but significant genetic differentiation of Nassau grouper throughout the Bahamian archipelago (Global FST 0.00236, p = 0.0001. Temporal analyses of changes in Ne over the last 1,000 generations provide evidence in support of a pronounced historic decline in Bahamian Nassau grouper that appears to pre-date anthropogenic fishing activities. M-ratio results corroborate significant reductions in Ne throughout The Bahamas, with evidence for population bottlenecks in three islands and an active fish spawning aggregation along with apparent signs of inbreeding at two islands. Current estimates of Ne for Nassau grouper are considerably lower compared with historic levels. These findings represent important new contributions to our understanding of the evolutionary history, demographics and genetic connectivity of this endangered species, which are of critical importance for advancing their sustainable management.

  5. Traditional healers, faith healers and medical practitioners: the contribution of medical pluralism to bottlenecks along the cascade of care for HIV/AIDS in Eastern and Southern Africa.

    Science.gov (United States)

    Moshabela, Mosa; Bukenya, Dominic; Darong, Gabriel; Wamoyi, Joyce; McLean, Estelle; Skovdal, Morten; Ddaaki, William; Ondeng'e, Kenneth; Bonnington, Oliver; Seeley, Janet; Hosegood, Victoria; Wringe, Alison

    2017-07-01

    There are concerns that medical pluralism may delay patients' progression through the HIV cascade-of-care. However, the pathways of impact through which medical pluralism influence the care of people living with HIV (PLHIV) in African settings remain unclear. We sought to establish the manifestation of medical pluralism among PLHIV, and explore mechanisms through which medical pluralism contributes bottlenecks along the HIV care cascade. We conducted a multicountry exploratory qualitative study in seven health and demographic surveillance sites in six eastern and southern African countries: Uganda, Kenya, Tanzania, Malawi, Zimbabwe and South Africa. We interviewed 258 PLHIV at different stages of the HIV cascade-of-care, 48 family members of deceased PLHIV and 53 HIV healthcare workers. Interviews were conducted using shared standardised topic guides, and data managed through NVIVO 8/10/11. We conducted a thematic analysis of healthcare pathways and bottlenecks related to medical pluralism. Medical pluralism, manifesting across traditional, faith-based and biomedical health-worlds, contributed to the care cascade bottlenecks for PLHIV through three pathways of impact. First, access to HIV treatment was delayed through the nature of health-related beliefs, knowledge and patient journeys. Second, HIV treatment was interrupted by availability of alternative options, perceived failed treatment and exploitation of PLHIV by opportunistic traders and healers. Lastly, the mixing of biomedical healthcare providers and treatment with traditional and faith-based options fuelled tensions driven by fear of drug-to-drug interactions and mistrust between providers operating in different health-worlds. Medical pluralism contributes to delays and interruptions of care along the HIV cascade, and mistrust between health providers. Region-wide interventions and policies are urgently needed in sub-Saharan Africa to minimise potential harm and consequences of medical pluralism for PLHIV

  6. Identifying Rare Variation in Cases of Schizophrenia in the Isolated Population of the Faroe Islands using Whole-genome Sequencing

    DEFF Research Database (Denmark)

    Als, Thomas Damm; Lescai, Francesco; Dahl, Hans

    to map risk variants involved in complex traits. We aim at utilizing samples of cases and controls of the isolated population of the Faroe Islands to conduct whole-genome-sequence analysis in order to identify rare genetic variants associated with schizophrenia. We will search for rare genetic variants...... of developing SZ. However, these studies are designed to examining only “the common variant” proportion of the genomic landscape of SZ. Due to increased genetic drift during founding and potential bottlenecks, followed by population expansion, isolated populations may be particularly useful in identifying rare...... disease variants, that may appear at higher frequencies and/or within a more clearly distinct haplotype structure compared to outbred populations. Small isolated populations also typically show reduced phenotypic, genetic and environmental heterogeneity, thus making them advantageous in studies aiming...

  7. Determining causes of genetic isolation in a large carnivore (Ursus americanus population to direct contemporary conservation measures.

    Directory of Open Access Journals (Sweden)

    Agnès Pelletier

    Full Text Available The processes leading to genetic isolation influence a population's local extinction risk, and should thus be identified before conservation actions are implemented. Natural or human-induced circumstances can result in historical or contemporary barriers to gene flow and/or demographic bottlenecks. Distinguishing between these hypotheses can be achieved by comparing genetic diversity and differentiation in isolated vs. continuous neighboring populations. In Ontario, American black bears (Ursus americanus are continuously distributed, genetically diverse, and exhibit an isolation-by-distance structuring pattern, except on the Bruce Peninsula (BP. To identify the processes that led to the genetic isolation of BP black bears, we modelled various levels of historical and contemporary migration and population size reductions using forward simulations. We compared simulation results with empirical genetic indices from Ontario black bear populations under different levels of geographic isolation, and conducted additional simulations to determine if translocations could help achieve genetic restoration. From a genetic standpoint, conservation concerns for BP black bears are warranted because our results show that: i a recent demographic bottleneck associated with recently reduced migration best explains the low genetic diversity on the BP; and ii under sustained isolation, BP black bears could lose between 70% and 80% of their rare alleles within 100 years. Although restoring migration corridors would be the most effective method to enhance long-term genetic diversity and prevent inbreeding, it is unrealistic to expect connectivity to be re-established. Current levels of genetic diversity could be maintained by successfully translocating 10 bears onto the peninsula every 5 years. Such regular translocations may be more practical than landscape restoration, because areas connecting the peninsula to nearby mainland black bear populations have been

  8. Assessment of genetic diversity, population structure, and gene flow of tigers (Panthera tigris tigris) across Nepal's Terai Arc Landscape.

    Science.gov (United States)

    Thapa, Kanchan; Manandhar, Sulochana; Bista, Manisha; Shakya, Jivan; Sah, Govind; Dhakal, Maheshwar; Sharma, Netra; Llewellyn, Bronwyn; Wultsch, Claudia; Waits, Lisette P; Kelly, Marcella J; Hero, Jean-Marc; Hughes, Jane; Karmacharya, Dibesh

    2018-01-01

    With fewer than 200 tigers (Panthera tigris tigris) left in Nepal, that are generally confined to five protected areas across the Terai Arc Landscape, genetic studies are needed to provide crucial information on diversity and connectivity for devising an effective country-wide tiger conservation strategy. As part of the Nepal Tiger Genome Project, we studied landscape change, genetic variation, population structure, and gene flow of tigers across the Terai Arc Landscape by conducting Nepal's first comprehensive and systematic scat-based, non-invasive genetic survey. Of the 770 scat samples collected opportunistically from five protected areas and six presumed corridors, 412 were tiger (57%). Out of ten microsatellite loci, we retain eight markers that were used in identifying 78 individual tigers. We used this dataset to examine population structure, genetic variation, contemporary gene flow, and potential population bottlenecks of tigers in Nepal. We detected three genetic clusters consistent with three demographic sub-populations and found moderate levels of genetic variation (He = 0.61, AR = 3.51) and genetic differentiation (FST = 0.14) across the landscape. We detected 3-7 migrants, confirming the potential for dispersal-mediated gene flow across the landscape. We found evidence of a bottleneck signature likely caused by large-scale land-use change documented in the last two centuries in the Terai forest. Securing tiger habitat including functional forest corridors is essential to enhance gene flow across the landscape and ensure long-term tiger survival. This requires cooperation among multiple stakeholders and careful conservation planning to prevent detrimental effects of anthropogenic activities on tigers.

  9. Age and growth of European barbel Barbus barbus (Cyprinidae in the small, mesotrophic River Lee and relative to other populations in England

    Directory of Open Access Journals (Sweden)

    Vilizzi L.

    2013-08-01

    Full Text Available Suspected of being in decline, the European barbel Barbus barbus population of the River Lee, a heavily-modified river in South East England, has been the subject of investigations to identify factors associated with perceived population decreases. Population surveys between 1995 and 1999 captured a total of 912 individuals, and standard length (SL frequency analyses between years suggested that the population decline was not related to juvenile recruitment but rather to a recruitment bottleneck in fish 300–340 mm SL. This bottleneck probably results from insufficient available habitat suitable to this size class. Of the sampled fish, scales were removed from 764 and were used in a scale ageing exercise among three researchers. Analyses of their independent age estimates revealed variable interpretations, which arose from uncertainties relating to the difficulty of analysing scale patterns from relatively large, slow-growing fish. Nevertheless, error was within published acceptable margins, and age estimates revealed B. barbus in the river to age 10 years, lower than in many UK rivers. The SL-at-age growth curve was characterised by very fast growth in the initial years of life. Thus, the causal factors in the decline of this B. barbus population appear to have been in the adult life-stage habitat and were likely related to the loss of longitudinal connectivity, mainly due to the presence of water retention structures. River and aquatic ecosystem remediation strategies should therefore focus on enhancing longitudinal connectivity in conjunction with the ongoing improvement of water quality and ecosystem integrity.

  10. Metabolic Engineering of Yeast to Produce Fatty Acid-derived Biofuels: Bottlenecks and Solutions

    Directory of Open Access Journals (Sweden)

    Jiayuan eSheng

    2015-06-01

    Full Text Available Fatty acid-derived biofuels can be a better solution than bioethanol to replace petroleum fuel, since they have similar energy content and combustion properties as current transportation fuels. The environmentally friendly microbial fermentation process has been used to synthesize advanced biofuels from renewable feedstock. Due to their robustness as well as the high tolerance to fermentation inhibitors and phage contamination, yeast strains such as Saccharomyces cerevisiae and Yarrowia lipolytica have attracted tremendous attention in recent studies regarding the production of fatty acid-derived biofuels, including fatty acids, fatty acid ethyl esters, fatty alcohols, and fatty alkanes. However, the native yeast strains cannot produce fatty acids and fatty acid-derived biofuels in large quantities. To this end, we have summarized recent publications in this review on metabolic engineering of yeast strains to improve the production of fatty acid-derived biofuels, identified the bottlenecks that limit the productivity of biofuels, and categorized the appropriate approaches to overcome these obstacles.

  11. Variable Speed Limits: Strategies to Improve Safety and Traffic Parameters for a Bottleneck

    Directory of Open Access Journals (Sweden)

    M. Z. Hasanpour

    2017-04-01

    Full Text Available The primary purpose of the speed limit system is to enforce reasonable and safe speed. To reduce secondary problems such as accidents and queuing, Variable Speed Limits (VSL has been suggested. In this paper VSL is used to better safety and traffic parameters. Traffic parameters including speed, queue length and stopping time have been pondering. For VLS, an optimization decision tree algorithm with the function of microscopic simulation was used. The results in case of sub saturated, saturated and supersaturated at a bottleneck are examined and compared with the Allaby logic tree. The results show that the proposed decision tree shows an improved performance in terms of safety and comfort along the highway. The VSL pilot project is part of the Road Safety Improvement Program included in Iran’s road safety action plan that is in the research process in the BHRC Research Institute, Road and Housing & Urban Development Research that is planned for next 10-year Transportation safety view Plan.

  12. Museum DNA reveals the demographic history of the endangered Seychelles warbler.

    Science.gov (United States)

    Spurgin, Lewis G; Wright, David J; van der Velde, Marco; Collar, Nigel J; Komdeur, Jan; Burke, Terry; Richardson, David S

    2014-11-01

    The importance of evolutionary conservation - how understanding evolutionary forces can help guide conservation decisions - is widely recognized. However, the historical demography of many endangered species is unknown, despite the fact that this can have important implications for contemporary ecological processes and for extinction risk. Here, we reconstruct the population history of the Seychelles warbler (Acrocephalus sechellensis) - an ecological model species. By the 1960s, this species was on the brink of extinction, but its previous history is unknown. We used DNA samples from contemporary and museum specimens spanning 140 years to reconstruct bottleneck history. We found a 25% reduction in genetic diversity between museum and contemporary populations, and strong genetic structure. Simulations indicate that the Seychelles warbler was bottlenecked from a large population, with an ancestral N e of several thousands falling to Seychelles warbler, and our results will inform conservation practices. Reconstructing the population history of this species also allows us to better understand patterns of genetic diversity, inbreeding and promiscuity in the contemporary populations. Our approaches can be applied across species to test ecological hypotheses and inform conservation.

  13. Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA

    Science.gov (United States)

    Diefenbach, Duane R.; Hansen, Leslie A.; Bohling, Justin H.; Miller-Butterworth, Cassandra

    2015-01-01

    In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post-reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present-day population, as well as to quantify genetic diversity and inbreeding. We amplified 12 nuclear microsatellite loci from DNA isolated from scats to establish genetic profiles to identify individuals. We used spatially explicit capture–recapture population estimation to estimate abundance. From nine unique genetic profiles, we estimate a population size of 14.4 (SE = 3.052) bobcats, with an effective population size (Ne) of 5–8 breeding individuals. This is consistent with predictions of a population viability analysis conducted at the time of reintroduction, which estimated the population would average 12–13 bobcats after 10 years. We identified several pairs of related bobcats (parent-offspring and full siblings), but ~75% of the pairwise comparisons were typical of unrelated individuals, and only one individual appeared inbred. Despite the small population size and other indications that it has likely experienced a genetic bottleneck, levels of genetic diversity in the CUIS bobcat population remain high compared to other mammalian carnivores. The reintroduction of bobcats to CUIS provides an opportunity to study changes in genetic diversity in an insular population without risk to this common species. Opportunities for natural immigration to the island are limited; therefore, continued monitoring and supplemental bobcat reintroductions could be used to evaluate the effect of different management strategies to maintain genetic diversity and population viability. The successful reintroduction and maintenance of a

  14. Homology blocks of Plasmodium falciparum var genes and clinically distinct forms of severe malaria in a local population.

    Science.gov (United States)

    Rorick, Mary M; Rask, Thomas S; Baskerville, Edward B; Day, Karen P; Pascual, Mercedes

    2013-11-06

    The primary target of the human immune response to the malaria parasite Plasmodium falciparum, P. falciparum erythrocyte membrane protein 1 (PfEMP1), is encoded by the members of the hyper-diverse var gene family. The parasite exhibits antigenic variation via mutually exclusive expression (switching) of the ~60 var genes within its genome. It is thought that different variants exhibit different host endothelial binding preferences that in turn result in different manifestations of disease. Var sequences comprise ancient sequence fragments, termed homology blocks (HBs), that recombine at exceedingly high rates. We use HBs to define distinct var types within a local population. We then reanalyze a dataset that contains clinical and var expression data to investigate whether the HBs allow for a description of sequence diversity corresponding to biological function, such that it improves our ability to predict disease phenotype from parasite genetics. We find that even a generic set of HBs, which are defined for a small number of non-local parasites: capture the majority of local sequence diversity; improve our ability to predict disease severity from parasite genetics; and reveal a previously hypothesized yet previously unobserved parasite genetic basis for two forms of severe disease. We find that the expression rates of some HBs correlate more strongly with severe disease phenotypes than the expression rates of classic var DBLα tag types, and principal components of HB expression rate profiles further improve genotype-phenotype models. More specifically, within the large Kenyan dataset that is the focus of this study, we observe that HB expression differs significantly for severe versus mild disease, and for rosetting versus impaired consciousness associated severe disease. The analysis of a second much smaller dataset from Mali suggests that these HB-phenotype associations are consistent across geographically distant populations, since we find evidence suggesting

  15. Population Development of Several Species of Ants on the Cocoa Trees in South Sulawesi

    Directory of Open Access Journals (Sweden)

    Fatahuddin Fatahuddin

    2010-08-01

    Full Text Available Several species of ants with different behavior have been found in cocoa plantations and their behavior is important to be considered because it might be correlated with the degree of protection of cocoa plant from cocoa pests. The aim of this research is to manipulate and to develop ants population in environment, so they are able to establish permanently in cocoa trees. This research was conducted in Papakaju Regions Luwu Regency in Juli to November 2009. In this study, 10 cocoa trees with ants were sampled (each species of ant in 10 cocoa trees. A control of 10 tree samples without ant was also taken. In order to assess the abundance of ant population, it was grouped based on scoring, which score 1 for less than 20 ants, score 2 for 21–50 ants, score 3 for 51–200 ants, score 4 for 201–1000 ants, and score 5 for more than 1000 per tree. The results indicated that average of population score of the three ants species reached the highest population for the Oecophylla. smaragdina with average score 4.85 (>1000 ants, Dolichoderus thoracicus, with average score 3.90 (> 200 ants and Crematogaster. difformis with average score 3.10 (>200 ants. This research indicated that three species of ants, Oecophylla smaragdina (weaver ant, Dolichoderus thoracicus (cocoa black ant and Crematogaster difformis (cracking ant. in farmer cocoa plantations in South Sulawesi giving better performance against major pests of cocoa in particular cocoa pod borer (CPB. Key words: Ant Population, Oecophylla smaragdina, Dolichoderus thoracicus, Crematogaster difformis, artificial nest, cocoa.

  16. Poor man’s 1000 genome project: Recent human population expansion confounds the detection of disease alleles in 7,098 complete mitochondrial genomes

    Directory of Open Access Journals (Sweden)

    Hie Lim eKim

    2013-02-01

    Full Text Available Rapid growth of the human population has caused the accumulation of rare genetic variants that may play a role in the origin of genetic diseases. However, it is challenging to identify those rare variants responsible for specific diseases without genetic data from an extraordinarily large population sample. Here we focused on the accumulated data from the human mitochondrial (mt genome sequences because this data provided 7,098 whole genomes for analysis. In this dataset we identified 6,110 single nucleotide variants (SNVs and their frequency and determined that the best-fit demographic model for the 7,098 genomes included severe population bottlenecks and exponential expansions of the non-African population. Using this model, we simulated the evolution of mt genomes in order to ascertain the behavior of deleterious mutations. We found that such deleterious mutations barely survived during population expansion. We derived the threshold frequency of a deleterious mutation in separate African, Asian, and European populations and used it to identify pathogenic mutations in our dataset. Although threshold frequency was very low, the proportion of variants showing a lower frequency than that threshold was 82%, 83%, and 91% of the total variants for the African, Asian, and European populations, respectively. Within these variants, only 18 known pathogenic mutations were detected in the 7,098 genomes. This result showed the difficulty of detecting a pathogenic mutation within an abundance of rare variants in the human population, even with a large number of genomes available for study.

  17. Microsatellite DNA analysis of northern pike ( Esox lucius L.) populations: insights into the genetic structure and demographic history of a genetically depauperate species

    DEFF Research Database (Denmark)

    Jacobsen, B. H.; Hansen, Michael Møller; Loeschcke, V.

    2005-01-01

    The northern pike Esox lucius L. is a freshwater fish exhibiting pronounced population subdivision and low genetic variability. However, there is limited knowledge on phylogeographical patterns within the species, and it is not known whether the low genetic variability reflects primarily current...... low effective population sizes or historical bottlenecks. We analysed six microsatellite loci in ten populations from Europe and North America. Genetic variation was low, with the average number of alleles within populations ranging from 2.3 to 4.0 per locus. Genetic differentiation among populations...... was high (overall theta(ST) = 0.51; overall rho(ST) = 0.50). Multidimensional scaling analysis of genetic distances between populations and spatial analysis of molecular variance suggested a single phylogeographical race within the sampled populations from northern Europe, whereas North American...

  18. Population genetics and the evolution of geographic range limits in an annual plant.

    Science.gov (United States)

    Moeller, David A; Geber, Monica A; Tiffin, Peter

    2011-10-01

    Abstract Theoretical models of species' geographic range limits have identified both demographic and evolutionary mechanisms that prevent range expansion. Stable range limits have been paradoxical for evolutionary biologists because they represent locations where populations chronically fail to respond to selection. Distinguishing among the proposed causes of species' range limits requires insight into both current and historical population dynamics. The tools of molecular population genetics provide a window into the stability of range limits, historical demography, and rates of gene flow. Here we evaluate alternative range limit models using a multilocus data set based on DNA sequences and microsatellites along with field demographic data from the annual plant Clarkia xantiana ssp. xantiana. Our data suggest that central and peripheral populations have very large historical and current effective population sizes and that there is little evidence for population size changes or bottlenecks associated with colonization in peripheral populations. Whereas range limit populations appear to have been stable, central populations exhibit a signature of population expansion and have contributed asymmetrically to the genetic diversity of peripheral populations via migration. Overall, our results discount strictly demographic models of range limits and more strongly support evolutionary genetic models of range limits, where adaptation is prevented by a lack of genetic variation or maladaptive gene flow.

  19. Massive nest-box supplementation boosts fecundity, survival and even immigration without altering mating and reproductive behaviour in a rapidly recovered bird population.

    Directory of Open Access Journals (Sweden)

    Karine Berthier

    Full Text Available Habitat restoration measures may result in artificially high breeding density, for instance when nest-boxes saturate the environment, which can negatively impact species' demography. Potential risks include changes in mating and reproductive behaviour such as increased extra-pair paternity, conspecific brood parasitism, and polygyny. Under particular cicumstances, these mechanisms may disrupt reproduction, with populations dragged into an extinction vortex. With the use of nuclear microsatellite markers, we investigated the occurrence of these potentially negative effects in a recovered population of a rare secondary cavity-nesting farmland bird of Central Europe, the hoopoe (Upupa epops. High intensity farming in the study area has resulted in a total eradication of cavity trees, depriving hoopoes from breeding sites. An intensive nest-box campaign rectified this problem, resulting in a spectacular population recovery within a few years only. There was some concern, however, that the new, high artificially-induced breeding density might alter hoopoe mating and reproductive behaviour. As the species underwent a serious demographic bottleneck in the 1970-1990s, we also used the microsatellite markers to reconstitute the demo-genetic history of the population, looking in particular for signs of genetic erosion. We found i a low occurrence of extra-pair paternity, polygyny and conspecific brood parasitism, ii a high level of neutral genetic diversity (mean number of alleles and expected heterozygosity per locus: 13.8 and 83%, respectively and, iii evidence for genetic connectivity through recent immigration of individuals from well differentiated populations. The recent increase in breeding density did thus not induce so far any noticeable detrimental changes in mating and reproductive behaviour. The demographic bottleneck undergone by the population in the 1970s-1990s was furthermore not accompanied by any significant drop in neutral genetic

  20. Massive nest-box supplementation boosts fecundity, survival and even immigration without altering mating and reproductive behaviour in a rapidly recovered bird population.

    Science.gov (United States)

    Berthier, Karine; Leippert, Fabio; Fumagalli, Luca; Arlettaz, Raphaël

    2012-01-01

    Habitat restoration measures may result in artificially high breeding density, for instance when nest-boxes saturate the environment, which can negatively impact species' demography. Potential risks include changes in mating and reproductive behaviour such as increased extra-pair paternity, conspecific brood parasitism, and polygyny. Under particular cicumstances, these mechanisms may disrupt reproduction, with populations dragged into an extinction vortex. With the use of nuclear microsatellite markers, we investigated the occurrence of these potentially negative effects in a recovered population of a rare secondary cavity-nesting farmland bird of Central Europe, the hoopoe (Upupa epops). High intensity farming in the study area has resulted in a total eradication of cavity trees, depriving hoopoes from breeding sites. An intensive nest-box campaign rectified this problem, resulting in a spectacular population recovery within a few years only. There was some concern, however, that the new, high artificially-induced breeding density might alter hoopoe mating and reproductive behaviour. As the species underwent a serious demographic bottleneck in the 1970-1990s, we also used the microsatellite markers to reconstitute the demo-genetic history of the population, looking in particular for signs of genetic erosion. We found i) a low occurrence of extra-pair paternity, polygyny and conspecific brood parasitism, ii) a high level of neutral genetic diversity (mean number of alleles and expected heterozygosity per locus: 13.8 and 83%, respectively) and, iii) evidence for genetic connectivity through recent immigration of individuals from well differentiated populations. The recent increase in breeding density did thus not induce so far any noticeable detrimental changes in mating and reproductive behaviour. The demographic bottleneck undergone by the population in the 1970s-1990s was furthermore not accompanied by any significant drop in neutral genetic diversity. Finally

  1. Prevalence and impact of severe fatigue in adolescent and young adult cancer patients in comparison with population-based controls.

    Science.gov (United States)

    Poort, Hanneke; Kaal, Suzanne E J; Knoop, Hans; Jansen, Rosemarie; Prins, Judith B; Manten-Horst, Eveliene; Servaes, Petra; Husson, Olga; van der Graaf, Winette T A

    2017-09-01

    The current study determined the prevalence of severe fatigue in adolescent and young adult (AYA) cancer patients (aged 18-35 years at diagnosis) consulting a multidisciplinary AYA team in comparison with gender- and age-matched population-based controls. In addition, impact of severe fatigue on quality of life and correlates of fatigue severity were examined. AYAs with cancer (n = 83) completed questionnaires including the Checklist Individual Strength (CIS-fatigue), Quality of Life (QoL)-Cancer Survivor, Hospital Anxiety and Depression Scale (reflecting psychological distress), and the Cancer Worry Scale (reflecting fear of cancer recurrence or progression). The vast majority of participants had been treated with chemotherapy (87%) and had no active treatment at the time of participation (73.5%). Prevalence of severe fatigue (CIS-fatigue score ≥35) in AYAs with cancer (48%, n = 40/83) was significantly higher in comparison with matched population-based controls (20%, n = 49/249; p fatigued AYAs with cancer reported lower QoL compared to non-severely fatigued AYAs with cancer (p fatigue severity (p fatigue based on a validated cut-off score was highly prevalent in this group of AYAs with cancer. QoL is significantly affected by severe fatigue, stressing the importance of detection and management of this symptom in those patients affected by a life-changing diagnosis of cancer in late adolescence or young adulthood.

  2. Lack of association of interferon regulatory factor 1 with severe malaria in affected child-parental trio studies across three African populations.

    Directory of Open Access Journals (Sweden)

    Valentina D Mangano

    Full Text Available Interferon Regulatory Factor 1 (IRF-1 is a member of the IRF family of transcription factors, which have key and diverse roles in the gene-regulatory networks of the immune system. IRF-1 has been described as a critical mediator of IFN-gamma signalling and as the major player in driving TH1 type responses. It is therefore likely to be crucial in both innate and adaptive responses against intracellular pathogens such as Plasmodium falciparum. Polymorphisms at the human IRF1 locus have been previously found to be associated with the ability to control P. falciparum infection in populations naturally exposed to malaria. In order to test whether genetic variation at the IRF1 locus also affects the risk of developing severe malaria, we performed a family-based test of association for 18 Single Nucleotide Polymorphisms (SNPs across the gene in three African populations, using genotype data from 961 trios consisting of one affected child and his/her two parents (555 from The Gambia, 204 from Kenya and 202 from Malawi. No significant association with severe malaria or severe malaria subphenotypes (cerebral malaria and severe malaria anaemia was observed for any of the SNPs/haplotypes tested in any of the study populations. Our results offer no evidence that the molecular pathways regulated by the transcription factor IRF-1 are involved in the immune-based pathogenesis of severe malaria.

  3. Demographic changes and marker properties affect detection of human population differentiation

    Directory of Open Access Journals (Sweden)

    Sanichwankul Kittipong

    2007-05-01

    Full Text Available Abstract Background Differentiating genetically between populations is valuable for admixture and population stratification detection and in understanding population history. This is easy to achieve for major continental populations, but not for closely related populations. It has been claimed that a large marker panel is necessary to reliably distinguish populations within a continent. We investigated whether empirical genetic differentiation could be accomplished efficiently among three Asian populations (Hmong, Thai, and Chinese using a small set of highly variable markers (15 tetranucleotide and 17 dinucleotide repeats. Results Hmong could be differentiated from Thai and Chinese based on multi-locus genotypes, but Thai and Chinese were indistinguishable from each other. We found significant evidence for a recent population bottleneck followed by expansion in the Hmong that was not present in the Thai or Chinese. Tetranucleotide repeats were less useful than dinucleotide repeat markers in distinguishing between major continental populations (Asian, European, and African while both successfully distinguished Hmong from Thai and Chinese. Conclusion Demographic history contributes significantly to robust detection of intracontinental population structure. Populations having experienced a rapid size reduction may be reliably distinguished as a result of a genetic drift -driven redistribution of population allele frequencies. Tetranucleotide markers, which differ from dinucleotide markers in mutation mechanism and rate, are similar in information content to dinucleotide markers in this situation. These factors should be considered when identifying populations suitable for gene mapping studies and when interpreting interpopulation relationships based on microsatellite markers.

  4. Deep Learning for Population Genetic Inference.

    Science.gov (United States)

    Sheehan, Sara; Song, Yun S

    2016-03-01

    Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme.

  5. Treatment Options for Severe Obesity in the Pediatric Population: Current Limitations and Future Opportunities.

    Science.gov (United States)

    Ryder, Justin R; Fox, Claudia K; Kelly, Aaron S

    2018-06-01

    Severe obesity is the only obesity classification increasing in prevalence among children and adolescents. Treatment options that produce meaningful and sustained weight loss and comorbidity resolution are urgently needed. The purpose of this review is to provide a brief overview of the current treatment options for pediatric severe obesity and offer suggestions regarding future opportunities for accelerating the development and evaluation of innovative treatment strategies. At present, there are three treatment options for youth with severe obesity: lifestyle modification therapy, pharmacotherapy, and bariatric surgery. Lifestyle modification therapy can be useful for improving many chronic disease risk factors and comorbid conditions but often fails to achieve clinically meaningful and sustainable weight loss. Pharmacotherapy holds promise as an effective adjunctive treatment but remains in the primordial stages of development in the pediatric population. Bariatric surgery provides robust weight loss and risk factor/comorbidity improvements but is accompanied by higher risks and lower uptake compared to lifestyle modification therapy and pharmacotherapy. New areas worth pursuing include combination pharmacotherapy, device therapy, identification of predictors of response aimed at precision treatment, and interventions in the postbariatric surgical setting to improve long-term outcomes. Treating pediatric severe obesity effectively and safely is extremely challenging. Some progress has been made, but substantially more effort and innovation are needed in the future to combat this serious and ongoing medical and public health issue. © 2018 The Obesity Society.

  6. Parsing a cognitive task: a characterization of the mind's bottleneck.

    Directory of Open Access Journals (Sweden)

    Mariano Sigman

    2005-02-01

    Full Text Available Parsing a mental operation into components, characterizing the parallel or serial nature of this flow, and understanding what each process ultimately contributes to response time are fundamental questions in cognitive neuroscience. Here we show how a simple theoretical model leads to an extended set of predictions concerning the distribution of response time and its alteration by simultaneous performance of another task. The model provides a synthesis of psychological refractory period and random-walk models of response time. It merely assumes that a task consists of three consecutive stages-perception, decision based on noisy integration of evidence, and response-and that the perceptual and motor stages can operate simultaneously with stages of another task, while the central decision process constitutes a bottleneck. We designed a number-comparison task that provided a thorough test of the model by allowing independent variations in number notation, numerical distance, response complexity, and temporal asynchrony relative to an interfering probe task of tone discrimination. The results revealed a parsing of the comparison task in which each variable affects only one stage. Numerical distance affects the integration process, which is the only step that cannot proceed in parallel and has a major contribution to response time variability. The other stages, mapping the numeral to an internal quantity and executing the motor response, can be carried out in parallel with another task. Changing the duration of these processes has no significant effect on the variance.

  7. Influence of road network and population demand assumptions in evacuation modeling for distant tsunamis

    Science.gov (United States)

    Henry, Kevin; Wood, Nathan J.; Frazier, Tim G.

    2017-01-01

    Tsunami evacuation planning in coastal communities is typically focused on local events where at-risk individuals must move on foot in a matter of minutes to safety. Less attention has been placed on distant tsunamis, where evacuations unfold over several hours, are often dominated by vehicle use and are managed by public safety officials. Traditional traffic simulation models focus on estimating clearance times but often overlook the influence of varying population demand, alternative modes, background traffic, shadow evacuation, and traffic management alternatives. These factors are especially important for island communities with limited egress options to safety. We use the coastal community of Balboa Island, California (USA), as a case study to explore the range of potential clearance times prior to wave arrival for a distant tsunami scenario. We use a first-in–first-out queuing simulation environment to estimate variations in clearance times, given varying assumptions of the evacuating population (demand) and the road network over which they evacuate (supply). Results suggest clearance times are less than wave arrival times for a distant tsunami, except when we assume maximum vehicle usage for residents, employees, and tourists for a weekend scenario. A two-lane bridge to the mainland was the primary traffic bottleneck, thereby minimizing the effect of departure times, shadow evacuations, background traffic, boat-based evacuations, and traffic light timing on overall community clearance time. Reducing vehicular demand generally reduced clearance time, whereas improvements to road capacity had mixed results. Finally, failure to recognize non-residential employee and tourist populations in the vehicle demand substantially underestimated clearance time.

  8. Early Characterization of the Severity and Transmissibility of Pandemic Influenza Using Clinical Episode Data from Multiple Populations.

    Directory of Open Access Journals (Sweden)

    Pete Riley

    2015-09-01

    Full Text Available The potential rapid availability of large-scale clinical episode data during the next influenza pandemic suggests an opportunity for increasing the speed with which novel respiratory pathogens can be characterized. Key intervention decisions will be determined by both the transmissibility of the novel strain (measured by the basic reproductive number R0 and its individual-level severity. The 2009 pandemic illustrated that estimating individual-level severity, as described by the proportion pC of infections that result in clinical cases, can remain uncertain for a prolonged period of time. Here, we use 50 distinct US military populations during 2009 as a retrospective cohort to test the hypothesis that real-time encounter data combined with disease dynamic models can be used to bridge this uncertainty gap. Effectively, we estimated the total number of infections in multiple early-affected communities using the model and divided that number by the known number of clinical cases. Joint estimates of severity and transmissibility clustered within a relatively small region of parameter space, with 40 of the 50 populations bounded by: pC, 0.0133-0.150 and R0, 1.09-2.16. These fits were obtained despite widely varying incidence profiles: some with spring waves, some with fall waves and some with both. To illustrate the benefit of specific pairing of rapidly available data and infectious disease models, we simulated a future moderate pandemic strain with pC approximately ×10 that of 2009; the results demonstrating that even before the peak had passed in the first affected population, R0 and pC could be well estimated. This study provides a clear reference in this two-dimensional space against which future novel respiratory pathogens can be rapidly assessed and compared with previous pandemics.

  9. Risk of affective disorders following prenatal exposure to severe life events: a Danish population-based cohort study.

    LENUS (Irish Health Repository)

    Khashan, Ali S

    2012-01-31

    OBJECTIVE: To examine the effect of prenatal exposure to severe life events on risk of affective disorders in the offspring. METHODS: In a cohort of 1.1 million Danish births from May 1978 until December 1997, mothers were considered exposed if one (or more) of their close relatives died or was diagnosed with serious illness up to 6 months before conception or during pregnancy. Offspring were followed up from their 10th birthday until their death, migration, onset of affective disorder or 31 December 2007; hospital admissions were identified by linkage to the Central Psychiatric Register. Log-linear Poisson regression was used for data analysis. RESULTS: The risk of affective disorders was increased in male offspring whose mothers were exposed to severe life events during the second trimester (adjusted RR 1.55 [95% CI 1.05-2.28]). There was an increased risk of male offspring affective disorders in relation to maternal exposure to death of a relative in the second trimester (adjusted RR 1.74 [95% CI 1.06-2.84]) or serious illness in a relative before pregnancy (adjusted RR 1.44 [95% CI 1.02-2.05]). There was no evidence for an association between prenatal exposure to severe life events and risk of female offspring affective disorders. CONCLUSIONS: Our population-based study suggests that prenatal maternal exposure to severe life events may increase the risk of affective disorders in male offspring. These findings are consistent with studies of populations exposed to famine and earthquake disasters which indicate that prenatal environment may influence the neurodevelopment of the unborn child.

  10. Prevalence and risk factors for HIV, hepatitis B, and hepatitis C in people with severe mental illness: a total population study of Sweden.

    Science.gov (United States)

    Bauer-Staeb, Clarissa; Jörgensen, Lena; Lewis, Glyn; Dalman, Christina; Osborn, David P J; Hayes, Joseph F

    2017-09-01

    Severe mental illness is associated with increased morbidity and mortality. The elevated risk of blood-borne viruses (BBVs) in people with severe mental illness is of concern, but the full extent of this problem is unclear. We aimed to determine the prevalence of and risk factors for BBVs in people with severe mental illness. In this nationwide, population-based, cross-sectional study, we estimated the point prevalence of HIV, hepatitis B (HBV), and hepatitis C (HCV) in people with severe mental illness, including the total adult (≥18 years) Swedish population. We defined severe mental illness as a clinical diagnosis of schizophrenia, schizoaffective disorder, bipolar disorder, or other psychotic illness according to the Swedish version of the International Statistical Classification of Diseases version 8, 9, or 10. We used multivariable logistic regression to determine the odds of BBVs in individuals with severe mental illness, relative to the general population, and to identify independent risk factors (age, sex, immigration status, socioeconomic status, education, and substance misuse) for BBV infection. We also did a sensitivity analysis excluding BBV diagnoses made before the introduction of the Register for Infection Disease Control (1997). Of 6 815 931 adults in Sweden, 97 797 (1·43%) individuals had a diagnosis of severe mental illness. Prevalence of BBVs was elevated in people with severe mental illness, of which 230 (0·24%) had HIV, 518 (0·53%) had HBV, and 4476 (4·58%) had HCV. After accounting for sociodemographic characteristics, the odds of HIV were 2·57 (95% CI 2·25-2·94, pmental illness than in the general population, whereas the odds of HBV were 2·29 (2·09-2·51, pmental illness and identify interventions preventing infection. Targeting of comorbid substance misuse would have particular effect on reduction of BBV prevalence in this population. Medical Research Council and Swedish Research Council. Copyright © 2017 The Author

  11. Severe inbreeding depression in a wild wolf (Canis lupus) population.

    Science.gov (United States)

    Liberg, Olof; Andrén, Henrik; Pedersen, Hans-Christian; Sand, Håkan; Sejberg, Douglas; Wabakken, Petter; Kesson, Mikael; Bensch, Staffan

    2005-03-22

    The difficulty of obtaining pedigrees for wild populations has hampered the possibility of demonstrating inbreeding depression in nature. In a small, naturally restored, wild population of grey wolves in Scandinavia, founded in 1983, we constructed a pedigree for 24 of the 28 breeding pairs established in the period 1983-2002. Ancestry for the breeding animals was determined through a combination of field data (snow tracking and radio telemetry) and DNA microsatellite analysis. The population was founded by only three individuals. The inbreeding coefficient F varied between 0.00 and 0.41 for wolves born during the study period. The number of surviving pups per litter during their first winter after birth was strongly correlated with inbreeding coefficients of pups (R2=0.39, pwolf population.

  12. Genetic impact of a severe El Niño event on Galápagos marine iguanas (Amblyrhynchus cristatus).

    Science.gov (United States)

    Steinfartz, Sebastian; Glaberman, Scott; Lanterbecq, Deborah; Marquez, Cruz; Rassmann, Kornelia; Caccone, Adalgisa

    2007-12-12

    The El Niño-Southern Oscillation (ENSO) is a major source of climatic disturbance, impacting the dynamics of ecosystems worldwide. Recent models predict that human-generated rises in green-house gas levels will cause an increase in the strength and frequency of El Niño warming events in the next several decades, highlighting the need to understand the potential biological consequences of increased ENSO activity. Studies have focused on the ecological and demographic implications of El Niño in a range of organisms, but there have been few systematic attempts to measure the impact of these processes on genetic diversity in populations. Here, we evaluate whether the 1997-1998 El Niño altered the genetic composition of Galápagos marine iguana populations from eleven islands, some of which experienced mortality rates of up to 90% as a result of El Niño warming. Specifically, we measured the temporal variation in microsatellite allele frequencies and mitochondrial DNA diversity (mtDNA) in samples collected before (1991/1993) and after (2004) the El Niño event. Based on microsatellite data, only one island (Marchena) showed signatures of a genetic bottleneck, where the harmonic mean of the effective population size (N(e)) was estimated to be less than 50 individuals during the period between samplings. Substantial decreases in mtDNA variation between time points were observed in populations from just two islands (Marchena and Genovesa). Our results suggests that, for the majority of islands, a single, intense El Niño event did not reduce marine iguana populations to the point where substantial neutral genetic diversity was lost. In the case of Marchena, simultaneous changes to both nuclear and mitochondrial DNA variation may also be the result of a volcanic eruption on the island in 1991. Therefore, studies that seek to evaluate the genetic impact of El Niño must also consider the confounding or potentially synergistic effect of other environmental and biological

  13. Genetic impact of a severe El Niño event on Galápagos marine iguanas (Amblyrhynchus cristatus.

    Directory of Open Access Journals (Sweden)

    Sebastian Steinfartz

    2007-12-01

    Full Text Available The El Niño-Southern Oscillation (ENSO is a major source of climatic disturbance, impacting the dynamics of ecosystems worldwide. Recent models predict that human-generated rises in green-house gas levels will cause an increase in the strength and frequency of El Niño warming events in the next several decades, highlighting the need to understand the potential biological consequences of increased ENSO activity. Studies have focused on the ecological and demographic implications of El Niño in a range of organisms, but there have been few systematic attempts to measure the impact of these processes on genetic diversity in populations. Here, we evaluate whether the 1997-1998 El Niño altered the genetic composition of Galápagos marine iguana populations from eleven islands, some of which experienced mortality rates of up to 90% as a result of El Niño warming. Specifically, we measured the temporal variation in microsatellite allele frequencies and mitochondrial DNA diversity (mtDNA in samples collected before (1991/1993 and after (2004 the El Niño event. Based on microsatellite data, only one island (Marchena showed signatures of a genetic bottleneck, where the harmonic mean of the effective population size (N(e was estimated to be less than 50 individuals during the period between samplings. Substantial decreases in mtDNA variation between time points were observed in populations from just two islands (Marchena and Genovesa. Our results suggests that, for the majority of islands, a single, intense El Niño event did not reduce marine iguana populations to the point where substantial neutral genetic diversity was lost. In the case of Marchena, simultaneous changes to both nuclear and mitochondrial DNA variation may also be the result of a volcanic eruption on the island in 1991. Therefore, studies that seek to evaluate the genetic impact of El Niño must also consider the confounding or potentially synergistic effect of other environmental

  14. Interleukin 1β (+3954; −511) Genotype Polymorphism and its Association with Severe Chronic Generalized Periodontitis in the Malaysian Population

    Science.gov (United States)

    Arora, Shelly; Ramachandra, Srinivas Sulugodu; Abdullah, Fawzia; Gundavarapu, Kalyan C.

    2017-01-01

    Introduction: Single-nucleotide polymorphisms (SNPs) in interleukin 1β (IL-1β) gene have been known to be associated with increased susceptibility to chronic periodontitis among various ethnic populations. SNPs are more commonly observed at loci + 3954 and − 511. The aim of this study was to evaluate the role of IL-1β gene polymorphism at loci +3954 and − 511, and its association with severe chronic generalized periodontitis among the ethnic Malay, Chinese, and Indians within the Malaysian population. Materials and Methods: Saliva samples from 120 subjects (60 cases and 60 controls) in the age group of 25–50 years were collected for isolation of genetic material using Norgen technique. Clinical attachment loss of ≥5 mm was considered as severe chronic generalized periodontitis. SNP's at loci +3954 and − 511 were identified and analyzed using Kompetitive Allele Specific Polymerase Chain Reaction Genotyping System (KASP™). Differences in the allele/genotype frequencies were assessed by Chi-square test (P Malaysian population was similar. Conclusion: IL-1β genotype polymorphism at +3954 and − 511 was found to be not associated with severe chronic generalized periodontitis among the three ethnicities in Malaysia. Studies with larger sample size should be done to confirm the findings of this study. PMID:28566859

  15. Evaluation of institutional bottlenecks with the introduction of solar energy. Evaluatie van institutionele knelpunten bij de introductie van zonne-energie

    Energy Technology Data Exchange (ETDEWEB)

    1982-01-01

    Institutional bottlenecks are caused not only by the fact that statutory regulations, directions and procedures are not (yet) attuned to the application of solar energy, but also by lack of notion and ideas of people concerned with solar energy like architects, contractors, financers, authorities, etc. Juridical and economic aspects as well as motivation, information and education play important roles and they are often mutually interwoven. Since solar energy techniques are in full development, considerations of cost and efficiency are not of crucial importance, but this makes regulations for subsidy necessary. Lack of knowledge of responsible authorities may lead to technical problems. It is expected that these bottlenecks will become less important when the market for solar energy will develop further. The point of view: First good than cheap is dangerous, for reasons of high prices, but the idea of first cheap, than good will also cause an ousting from the market. All this makes subsidy regulations even more necessary. Within the building sector things are very difficult, due to a lot of complicated procedures, which are time and patience consuming. Better organization of building, cooperation of authorities, architects, urban planners and suppliers, better know how and education of builders are of vital importance. Also the end users need better information on solar energy systems. The general conclusion is that the introduction of solar energy systems is difficult and laborious because it is part of a complex of new factors which are sometimes contradictory to Dutch building traditions.

  16. Abraham's children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern Ancestry.

    Science.gov (United States)

    Atzmon, Gil; Hao, Li; Pe'er, Itsik; Velez, Christopher; Pearlman, Alexander; Palamara, Pier Francesco; Morrow, Bernice; Friedman, Eitan; Oddoux, Carole; Burns, Edward; Ostrer, Harry

    2010-06-11

    For more than a century, Jews and non-Jews alike have tried to define the relatedness of contemporary Jewish people. Previous genetic studies of blood group and serum markers suggested that Jewish groups had Middle Eastern origin with greater genetic similarity between paired Jewish populations. However, these and successor studies of monoallelic Y chromosomal and mitochondrial genetic markers did not resolve the issues of within and between-group Jewish genetic identity. Here, genome-wide analysis of seven Jewish groups (Iranian, Iraqi, Syrian, Italian, Turkish, Greek, and Ashkenazi) and comparison with non-Jewish groups demonstrated distinctive Jewish population clusters, each with shared Middle Eastern ancestry, proximity to contemporary Middle Eastern populations, and variable degrees of European and North African admixture. Two major groups were identified by principal component, phylogenetic, and identity by descent (IBD) analysis: Middle Eastern Jews and European/Syrian Jews. The IBD segment sharing and the proximity of European Jews to each other and to southern European populations suggested similar origins for European Jewry and refuted large-scale genetic contributions of Central and Eastern European and Slavic populations to the formation of Ashkenazi Jewry. Rapid decay of IBD in Ashkenazi Jewish genomes was consistent with a severe bottleneck followed by large expansion, such as occurred with the so-called demographic miracle of population expansion from 50,000 people at the beginning of the 15th century to 5,000,000 people at the beginning of the 19th century. Thus, this study demonstrates that European/Syrian and Middle Eastern Jews represent a series of geographical isolates or clusters woven together by shared IBD genetic threads.

  17. Homogeneity of Powassan virus populations in naturally infected Ixodes scapularis

    International Nuclear Information System (INIS)

    Brackney, Doug E.; Brown, Ivy K.; Nofchissey, Robert A.; Fitzpatrick, Kelly A.; Ebel, Gregory D.

    2010-01-01

    Powassan virus (POWV, Flaviviridae: Flavivirus) is the sole North American member of the tick-borne encephalitis complex and consists of two distinct lineages that are maintained in ecologically discrete enzootic transmission cycles. The underlying genetic mechanisms that lead to niche partitioning in arboviruses are poorly understood. Therefore, intra- and interhost genetic diversity was analyzed to determine if POWV exists as a quasispecies in nature and quantify selective pressures within and between hosts. In contrast to previous reports for West Nile virus (WNV), significant intrahost genetic diversity was not observed. However, pN (0.238) and d N /d S ratios (0.092) for interhost diversity were similar to those of WNV. Combined, these data suggest that purifying selection and/or population bottlenecks constrain quasispecies diversity within ticks. These same selective and stochastic mechanisms appear to drive minor sequence changes between ticks. Moreover, Powassan virus populations seem not to be structured as quasispecies in naturally infected adult deer ticks.

  18. Evaluation of sweet sorghum (Sorghum bicolor L. [Moench]) on several population density for bioethanol production

    Science.gov (United States)

    Suwarti; Efendi, R.; Massinai, R.; Pabendon, M. B.

    2018-03-01

    Sweet sorghum (Sorghum bicolor L. [Moench]) crop management that is use for raw source of bioethanol for industrial purpose in Indonesia is less developed. The aim of this research was to evaluated sweet sorghum variety at several population to determine optimum density for juice production. Experiment design was set on split-plot design with three replications, conducted on August to December 2016 at the Indonesian Cereals Research Institute Research Station, Maros South Sulawesi. Main plot were six variation of plant row, and sub plot were three sweet sorghum varieties. Result of the study showed that plant population was high significanty affect to stalk weight, total biomass yield, leaf weight, and also significantly affect bagass weight and juice volume. Varieties were high significantly different in plant height, juice volume, and number of nodes. Super 1 variety on population at 166,667 plants/ha (P1) was obtained the highest juice volume (19,445 lHa-1), meanwhile the highest brix value obtained from Numbu at the same plants population. Furthermore juice volume had significant correlation with biomass weight at the r=0.73. Based on ethanol production, Super 2 and Numbu had the highest volume at 83.333 plants/ha density (P3) and Super 1 at 166.667 plants/ha density with the ethanol volume were 827.68 l Ha-1, 1116.50 l/ha and 993.62 l Ha-1 respectively.

  19. Severe maternal morbidity: A population-based study of an expanded measure and associated factors.

    Directory of Open Access Journals (Sweden)

    Victoria Lazariu

    Full Text Available Severe maternal morbidity conditions such as sepsis, embolism and cardiac arrest during the delivery hospitalization period can lead to extended length of hospital stays, life-long maternal health problems, and high medical costs. Most importantly, these conditions also contribute to the risk of maternal death. This population-based observational study proposed and evaluated the impact of expanding the Centers for Disease Control and Prevention (CDC measure of severe maternal morbidity by including additional comorbidities and intensive care admissions during delivery hospitalizations and examined associated factors. A New York State linked hospitalization and birth record database was used. Study participants included all New York State female residents, ages 10 to 55 years, who delivered a live infant in a New York acute care hospital between 2008 and 2013, inclusive. Incidence trends for both severe maternal morbidity measures were evaluated longitudinally. Associations between covariates and the two severe maternal morbidity measures were examined with logistic regression models, solved using generalized estimating equations and stratified by method of delivery. The New York expanded severe maternal morbidity measure identified 34,478 cases among 1,352,600 hospital deliveries (estimated incidence 2.55% representing a 3% increase in the number of cases compared to the CDC measure. Both estimates increased over the study period (p 1.5 included most measured comorbidities (e.g., pregnancy-induced hypertension, placentation disorder, multiple births, preterm birth, no prenatal care, hospitalization prior to delivery, higher levels of perinatal care birthing facilities and race/ethnicity. Expanding the measure for severe maternal morbidity during delivery to capture intensive care admissions provides a more sensitive estimate of disease burden. Perinatal regionalization in New York appears effective in routing high risk pregnancies to higher

  20. Near neutrality: leading edge of the neutral theory of molecular evolution.

    Science.gov (United States)

    Hughes, Austin L

    2008-01-01

    The nearly neutral theory represents a development of Kimura's neutral theory of molecular evolution that makes testable predictions that go beyond a mere null model. Recent evidence has strongly supported several of these predictions, including the prediction that slightly deleterious variants will accumulate in a species that has undergone a severe bottleneck or in cases where recombination is reduced or absent. Because bottlenecks often occur in speciation and slightly deleterious mutations in coding regions will usually be nonsynonymous, we should expect that the ratio of nonsynonymous to synonymous fixed differences between species should often exceed the ratio of nonsynonymous to synonymous polymorphisms within species. Many data support this prediction, although they have often been wrongly interpreted as evidence for positive Darwinian selection. The use of conceptually flawed tests for positive selection has become widespread in recent years, seriously harming the quest for an understanding of genome evolution. When properly analyzed, many (probably most) claimed cases of positive selection will turn out to involve the fixation of slightly deleterious mutations by genetic drift in bottlenecked populations. Slightly deleterious variants are a transient feature of evolution in the long term, but they have substantially affected contemporary species, including our own.

  1. Resolving relationships between several Neolithic and Mesolithic populations in Northern Eurasia using geometric morphometrics.

    Science.gov (United States)

    Stansfield Bulygina, Ekaterina; Rasskasova, Anna; Berezina, Natalia; Soficaru, Andrei D

    2017-09-01

    Remains from several Eastern European and Siberian Mesolithic and Neolithic sites are analysed to clarify their biological relationships. We assume that groups' geographical distances correlate with genetic and, therefore, morphological distances between them. Material includes complete male crania from several Mesolithic and Neolithic burial sites across Northern Eurasia and from several modern populations. Geometric morphometrics and multivariate statistical techniques are applied to explore morphological trends, group distances, and correlations with their geographical position, climate, and the time of origin. Despite an overlap in the morphology among the modern and archeological groups, some of them show significant morphological distances. Geographical parameters account for only a small proportion of cranial variation in the sample, with larger variance explained by geography and age together. Expectations of isolation by distance are met in some but not in all cases. Climate accounts for a large proportion of autocorrelation with geography. Nearest-neighbor joining trees demonstrate group relationships predicted by the regression on geography and on climate. The obtained results are discussed in application to relationships between particular groups. Unlike the Ukrainian Mesolithic, the Yuzhny Oleni Ostrov Mesolithic displays a high morphological affinity with several groups from Northern Eurasia of both European and Asian origin. A possibility of a common substrate for the Yuzhny Oleni Ostrov Mesolithic and Siberian Neolithic groups is reviewed. The Siberian Neolithic is shown to have morphological connection with both modern Siberian groups and the Native North Americans. © 2017 Wiley Periodicals, Inc.

  2. MHC class II diversity of koala (Phascolarctos cinereus) populations across their range.

    Science.gov (United States)

    Lau, Q; Jaratlerdsiri, W; Griffith, J E; Gongora, J; Higgins, D P

    2014-10-01

    Major histocompatibility complex class II (MHCII) genes code for proteins that bind and present antigenic peptides and trigger the adaptive immune response. We present a broad geographical study of MHCII DA β1 (DAB) and DB β1 (DBB) variants of the koala (Phascolarctos cinereus; n=191) from 12 populations across eastern Australia, with a total of 13 DAB and 7 DBB variants found. We identified greater MHCII variation and, possibly, additional gene copies in koala populations in the north (Queensland and New South Wales) relative to the south (Victoria), confirmed by STRUCTURE analyses and genetic differentiation using analysis of molecular variance. The higher MHCII diversity in the north relative to south could potentially be attributed to (i) significant founder effect in Victorian populations linked to historical translocation of bottlenecked koala populations and (ii) increased pathogen-driven balancing selection and/or local genetic drift in the north. Low MHCII genetic diversity in koalas from the south could reduce their potential response to disease, although the three DAB variants found in the south had substantial sequence divergence between variants. This study assessing MHCII diversity in the koala with historical translocations in some populations contributes to understanding the effects of population translocations on functional genetic diversity.

  3. Influence of drift and admixture on population structure of American black bears (Ursus americanus) in the Central Interior Highlands, USA, 50 years after translocation.

    Science.gov (United States)

    Puckett, Emily E; Kristensen, Thea V; Wilton, Clay M; Lyda, Sara B; Noyce, Karen V; Holahan, Paula M; Leslie, David M; Beringer, Jeff; Belant, Jerrold L; White, Don; Eggert, Lori S

    2014-05-01

    Bottlenecks, founder events, and genetic drift often result in decreased genetic diversity and increased population differentiation. These events may follow abundance declines due to natural or anthropogenic perturbations, where translocations may be an effective conservation strategy to increase population size. American black bears (Ursus americanus) were nearly extirpated from the Central Interior Highlands, USA by 1920. In an effort to restore bears, 254 individuals were translocated from Minnesota, USA, and Manitoba, Canada, into the Ouachita and Ozark Mountains from 1958 to 1968. Using 15 microsatellites and mitochondrial haplotypes, we observed contemporary genetic diversity and differentiation between the source and supplemented populations. We inferred four genetic clusters: Source, Ouachitas, Ozarks, and a cluster in Missouri where no individuals were translocated. Coalescent models using approximate Bayesian computation identified an admixture model as having the highest posterior probability (0.942) over models where the translocation was unsuccessful or acted as a founder event. Nuclear genetic diversity was highest in the source (AR = 9.11) and significantly lower in the translocated populations (AR = 7.07-7.34; P = 0.004). The Missouri cluster had the lowest genetic diversity (AR = 5.48) and served as a natural experiment showing the utility of translocations to increase genetic diversity following demographic bottlenecks. Differentiation was greater between the two admixed populations than either compared to the source, suggesting that genetic drift acted strongly over the eight generations since the translocation. The Ouachitas and Missouri were previously hypothesized to be remnant lineages. We observed a pretranslocation remnant signature in Missouri but not in the Ouachitas. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

  4. The world's most isolated and distinct whale population? Humpback whales of the Arabian Sea.

    Science.gov (United States)

    Pomilla, Cristina; Amaral, Ana R; Collins, Tim; Minton, Gianna; Findlay, Ken; Leslie, Matthew S; Ponnampalam, Louisa; Baldwin, Robert; Rosenbaum, Howard

    2014-01-01

    A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as "Endangered" on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to "Critically Endangered" on the IUCN Red List.

  5. The world's most isolated and distinct whale population? Humpback whales of the Arabian Sea.

    Directory of Open Access Journals (Sweden)

    Cristina Pomilla

    Full Text Available A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as "Endangered" on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to "Critically Endangered" on the IUCN Red List.

  6. INFLUENCE OF NPK AND LIME APLICATION ON ERVA-MATE GROWTH, ROOT-ROT SEVERITY AND SOIL FUNGI POPULATION1

    Directory of Open Access Journals (Sweden)

    Igor Poletto

    2011-09-01

    Full Text Available The present work evaluated the influence of the application of NPK and liming doses in the soil, on the growth of Erva-mate, the severity of rot-root and the fungi population of the soil. To do so, an experiment was installed at the green house, in the Forest Nursery of UFSM, using an experimental design completely randomized factorial 4x3x4 (Factor F: Fusarium spp. inoculation; Factor C: soil limestone; Factor A: NPK doses , totaling 48 treatments. The seedlings were cultivated in vases containing 2 kg of soil, classified as ‘Red-Yellow Argisoil’ (clay soil. At the end of the experiment was measured the stem diameter, height of the aerial part, leaves number, aerial dry biomass, root dry biomass and total dry biomass of the seedlings. Also, the soil was collected, from each treatment, for the chemical analysis and the counting of the fungi population. It was observed that the association among application of NPK and liming in the soil hampered the development of Erva-mate seedlings. The analysis of some variables suggests that the limestone absence provided greater resistance of seedlings to the attack of Fusarium spp. or the severity of Fusarium spp. was reduced in lower pH. The fungi population of the soil presented varied behavior depending on the applied treatments.

  7. Deep Learning for Population Genetic Inference.

    Directory of Open Access Journals (Sweden)

    Sara Sheehan

    2016-03-01

    Full Text Available Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data to the output (e.g., population genetic parameters of interest. We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history. Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme.

  8. Deep Learning for Population Genetic Inference

    Science.gov (United States)

    Sheehan, Sara; Song, Yun S.

    2016-01-01

    Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme. PMID:27018908

  9. Development and bottlenecks of renewable electricity generation in China: a critical review.

    Science.gov (United States)

    Hu, Yuanan; Cheng, Hefa

    2013-04-02

    This review provides an overview on the development and status of electricity generation from renewable energy sources, namely hydropower, wind power, solar power, biomass energy, and geothermal energy, and discusses the technology, policy, and finance bottlenecks limiting growth of the renewable energy industry in China. Renewable energy, dominated by hydropower, currently accounts for more than 25% of the total electricity generation capacity. China is the world's largest generator of both hydropower and wind power, and also the largest manufacturer and exporter of photovoltaic cells. Electricity production from solar and biomass energy is at the early stages of development in China, while geothermal power generation has received little attention recently. The spatial mismatch in renewable energy supply and electricity demand requires construction of long-distance transmission networks, while the intermittence of renewable energy poses significant technical problems for feeding the generated electricity into the power grid. Besides greater investment in research and technology development, effective policies and financial measures should also be developed and improved to better support the healthy and sustained growth of renewable electricity generation. Meanwhile, attention should be paid to the potential impacts on the local environment from renewable energy development, despite the wider benefits for climate change.

  10. Meal replacements as a weight loss tool in a population with severe mental illness.

    Science.gov (United States)

    Gelberg, Hollie A; Kwan, Crystal L; Mena, Shirley J; Erickson, Zachary D; Baker, Matthew R; Chamberlin, Valery; Nguyen, Charles; Rosen, Jennifer A; Shah, Chandresh; Ames, Donna

    2015-12-01

    Weight gain and worsening metabolic parameters are often side effects of antipsychotic medications used by individuals with severe mental illness. To address this, a randomized, controlled research study of a behavioral weight management program for individuals with severe mental illness was undertaken to assess its efficacy. Patients unable to meet weight loss goals during the first portion of the year-long study were given the option of using meal replacement shakes in an effort to assist with weight loss. Specific requirements for use of meal replacement shakes were specified in the study protocol; only five patients were able to use the shakes in accordance with the protocol and lose weight while improving metabolic parameters. Case studies of two subjects are presented, illustrating the challenges and obstacles they faced, as well as their successes. Taking responsibility for their own weight loss, remaining motivated through the end of the study, and incorporating the meal replacement shakes into a daily routine were factors found in common with these patients. Use of meal replacements shakes with this population may be effective. Published by Elsevier Ltd.

  11. Technology Transfer Bottlenecks and Lessons Learned in Humanitarian Demining EU-funded Research: Analysis and Results from the EC DELVE Project

    International Nuclear Information System (INIS)

    Bruschini, C.; Sahli, H.; Van Kempen, L.; Schleijpen, R.; Breejen, E. den

    2010-01-01

    The EC DELVE Support Action (www.delve.vub.ac.be) has analyzed the bottlenecks in the transfer of Humanitarian Demining (HD) technology from technology development to the use in the field, basing itself on the assessment of the European HD Research and Technology Development (RTD) situation from early 1990 until 2006. The developments in HD during the last 10 years underline the fact that in a number of cases demining related developments have been terminated or at least put on hold. A number of lessons learned were drawn, bottlenecks identified and broadly classified as either Confidence, Cost, or Communication related. The study also showed that the funding provided by the European Commission (EC) has led directly to the creation of an extensive portfolio of HD technology development projects. However, the range of instruments available to the EC to finance the necessary R and D was limited to pre-competitive research. The EC had no tools or programs to fund actual product development. The corresponding consequences are detailed in the study. The separation of the Mine Action and RTD funding streams in the EC did also negatively affect the take-up of new technologies. As a main conclusion, creating coherence between: (1) the EC policy based on political decisions, (2) RTD, testing and industrialization of equipment, and (3) timely deployment, requires a new way of coordinated thinking: 'end-to-end planning' has to be supported by a well organized and coordinated organizational structure involving different DGs (Directorate General) and even extending beyond the EU. This was not the case for Mine Action. (author)

  12. Distribution and medical impact of loss-of-function variants in the Finnish founder population.

    Directory of Open Access Journals (Sweden)

    Elaine T Lim

    2014-07-01

    Full Text Available Exome sequencing studies in complex diseases are challenged by the allelic heterogeneity, large number and modest effect sizes of associated variants on disease risk and the presence of large numbers of neutral variants, even in phenotypically relevant genes. Isolated populations with recent bottlenecks offer advantages for studying rare variants in complex diseases as they have deleterious variants that are present at higher frequencies as well as a substantial reduction in rare neutral variation. To explore the potential of the Finnish founder population for studying low-frequency (0.5-5% variants in complex diseases, we compared exome sequence data on 3,000 Finns to the same number of non-Finnish Europeans and discovered that, despite having fewer variable sites overall, the average Finn has more low-frequency loss-of-function variants and complete gene knockouts. We then used several well-characterized Finnish population cohorts to study the phenotypic effects of 83 enriched loss-of-function variants across 60 phenotypes in 36,262 Finns. Using a deep set of quantitative traits collected on these cohorts, we show 5 associations (p<5×10⁻⁸ including splice variants in LPA that lowered plasma lipoprotein(a levels (P = 1.5×10⁻¹¹⁷. Through accessing the national medical records of these participants, we evaluate the LPA finding via Mendelian randomization and confirm that these splice variants confer protection from cardiovascular disease (OR = 0.84, P = 3×10⁻⁴, demonstrating for the first time the correlation between very low levels of LPA in humans with potential therapeutic implications for cardiovascular diseases. More generally, this study articulates substantial advantages for studying the role of rare variation in complex phenotypes in founder populations like the Finns and by combining a unique population genetic history with data from large population cohorts and centralized research access to National Health

  13. Mental distress in treatment seeking young adults (18-25 years) with severe obesity compared with population controls of different body mass index levels: cohort study.

    Science.gov (United States)

    Dreber, H; Reynisdottir, S; Angelin, B; Tynelius, P; Rasmussen, F; Hemmingsson, E

    2017-02-01

    Young adults (18-25) with severe obesity constitute a challenging patient group, and there is limited evidence about their mental health status compared to population controls. Mental distress in treatment seeking young adults with severe obesity (n = 121, mean body mass index [BMI] = 39.8 kg m -2 ) was compared with matched (1:3 for age, gender and socioeconomic status) population controls of normal weight (n = 363, mean BMI = 22.4 kg m -2 ), as well as unmatched population controls with class I obesity (n = 105, mean BMI = 32.1 kg m -2 ) or severe obesity (n = 41, mean BMI = 39.7 kg m -2 ). Mental distress was measured by the General Health Questionnaire-12 (GHQ-12), and we quantified physician-diagnosed depression, present anxiety and suicide attempts. Poisson regression and linear regression analysis were used for analysing differences in mental distress between groups. Treatment seekers experienced more mental distress than normal weight controls as measured by continuous (adjusted mean: 3.9 vs. 2.2 points, P obesity (adjusted mean: 2.3 points) or severe obesity (adjusted mean: 2.1; both, P Young adult treatment seekers with severe obesity constitute a risk group for mental distress compared to population controls of different BMI levels. © 2017 World Obesity Federation.

  14. Population profiles associated with severe functioning difficulties and disability among two to four years old children in Mexico

    Directory of Open Access Journals (Sweden)

    Rosalba Rojas-Martínez

    2017-07-01

    Full Text Available Objective. To describe the prevalence and factors associated with severe child functioning difficulties and disability (CFD among two to four year old children in Mexico, and estimates the probability of presenting CFD based on specific population profiles. Materials and methods. The sample consists of 5 104 children who participated in the National Survey of Children and Women 2015 (ENIM. We used postestimation exploration by computing predicted values of CFD to interpret the logistic models for discrete combinations of the independent variables. Results. CFD prevalence is 2%,which means at least 130 000 two to four year-old children are at risk of experiencing severely limited participation in an unaccommodating environment. The probability of presenting CFD is dramatically higher in specific sub-groups of the population, in particular, male children of women with low education, who live in the poorest households. Conclusions. A significant proportion of Mexican children face important challenges due to functioning difficulties and disability. Public policies must be developed to accommodate the needs of these children and provide a proper environment for their development.

  15. Correction: Forrester, N.L.; Coffey, L.L.; Weaver, S.C. Arboviral Bottlenecks and Challenges to Maintaining Diversity and Fitness during Mosquito Transmission. Viruses 2014, 6, 3991–4004

    Directory of Open Access Journals (Sweden)

    Naomi L. Forrester

    2014-11-01

    Full Text Available In the original manuscript, Forrester, N.L.; Coffey, L.L.; Weaver, S.C. Arboviral Bottlenecks and Challenges to Maintaining Diversity and Fitness during Mosquito Transmission. Viruses 2014, 6, 3991–4004, Figure 1 contains an error, the third bottle was absent from the figure:[...

  16. Quantifying the severity of hurricanes on extinction probabilities of a primate population: Insights into "Island" extirpations.

    Science.gov (United States)

    Ameca y Juárez, Eric I; Ellis, Edward A; Rodríguez-Luna, Ernesto

    2015-07-01

    Long-term studies quantifying impacts of hurricane activity on growth and trajectory of primate populations are rare. Using a 14-year monitored population of Alouatta palliata mexicana as a study system, we developed a modeling framework to assess the relative contribution of hurricane disturbance and two types of human impacts, habitat loss, and hunting, on quasi-extinction risk. We found that the scenario with the highest level of disturbance generated a 21% increase in quasi-extinction risk by 40 years compared to scenarios of intermediate disturbance, and around 67% increase relative to that found in low disturbance scenarios. We also found that the probability of reaching quasi-extinction due to human disturbance alone was below 1% by 40 years, although such scenarios reduced population size by 70%, whereas the risk of quasi-extinction ranged between 3% and 65% for different scenarios of hurricane severity alone, in absence of human impacts. Our analysis moreover found that the quasi-extinction risk driven by hunting and hurricane disturbance was significantly lower than the quasi-extinction risk posed by human-driven habitat loss and hurricane disturbance. These models suggest that hurricane disturbance has the potential to exceed the risk posed by human impacts, and, in particular, to substantially increase the speed of the extinction vortex driven by habitat loss relative to that driven by hunting. Early mitigation of habitat loss constituted the best method for reducing quasi-extinction risk: the earlier habitat loss is halted, the less vulnerable the population becomes to hurricane disturbance. By using a well-studied population of A. p. mexicana, we help understand the demographic impacts that extreme environmental disturbance can trigger on isolated populations of taxa already endangered in other systems where long-term demographic data are not available. For those experiencing heavy anthropogenic pressure and lacking sufficiently evolved coping

  17. Effect of geographical and ethnic variation on Dysphonia Severity Index: a study of Indian population.

    Science.gov (United States)

    Jayakumar, T; Savithri, S R

    2012-01-01

    Dysphonia Severity Index (DSI) is a widely used multiparametric approach to objectively quantify the voice quality. Few research groups have investigated the test-retest, interobserver variability, and influence of age and gender. They have also verified the application of DSI in various voice rehabilitation conditions. However, all these studies have been conducted on European population. There is a possibility of variation in the basic parameters of DSI across geographical and ethnic groups. Hence, the present study evaluated DSI in Indian population. One hundred twenty voluntary participants (60 males, 60 females) who had G(0) on the Grade, Roughness, Breathiness, Aesthenia, Strain (GRBAS) scale participated in the study (age range of 18-25 years, M=21.8, standard deviation=2.7). Maximum phonation time (MPT), frequency intensity, and jitter measurements were made using CSL 4500 (Kay Elemetrics, Pine Brook, NJ). Results showed noticeable difference between Indian and European population on MPT, Highest frequency (F(0)-High), and DSI values. Significant gender difference was also observed on MPT and F(0)-High. Test-retest reliability showed >95% for all the parameters. The MPT decrement lead to a reduction in the overall DSI value in both the genders. These results of the study caution voice professionals to reinvestigate and establish their own norms for their geographical and ethnic groups. Copyright © 2012 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

  18. Neutron capture cross section of $^{90}$Zr Bottleneck in the s-process reaction flow

    CERN Document Server

    Tagliente, G; Milazzo, P M; Moreau, C; Aerts, G; Abbondanno, U; Alvarez, H; Alvarez-Velarde, F; Andriamonje, Samuel A; Andrzejewski, J; Assimakopoulos, Panayiotis; Audouin, L; Badurek, G; Baumann, P; Bečvář, F; Berthoumieux, E; Bisterzo, S; Calviño, F; Calviani, M; Cano-Ott, D; Capote, R; Carrapiço, C; Cennini, P; Chepel, V; Chiaveri, Enrico; Colonna, N; Cortés, G; Couture, A; Cox, J; Dahlfors, M; David, S; Dillman, I; Domingo-Pardo, C; Dridi, W; Durán, I; Eleftheriadis, C; Embid-Segura, M; Ferrant, L; Ferrari, A; Ferreira-Marques, R; Furman, W; Gallino, R; Gonçalves, I; Gonzalez-Romero, E; Gramegna, F; Guerrero, C; Gunsing, F; Haas, B; Haight, R; Heil, M; Herrera-Martínez, A; Igashira, M; Jericha, E; Käppeler, F; Kadi, Y; Karadimos, D; Karamanis, D; Kerveno, M; Köhler, P; Kossionides, E; Krtička, M; Lamboudis, C; Leeb, H; Lindote, A; Lopes, I; Lozano, M; Lukic, S; Marganiec, J; Marrone, S; Martínez, T; Massimi, C; Mastinu, P; Mengoni, A; Mosconi, M; Neves, F; Oberhummer, Heinz; O'Brien, S; Pancin, J; Papachristodoulou, C; Papadopoulos, C; Paradela, C; Patronis, N; Pavlik, A; Pavlopoulos, P; Perrot, L; Pigni, M T; Plag, R; Plompen, A; Plukis, A; Poch, A; Praena, J; Pretel, C; Quesada, J; Rauscher, T; Reifarth, R; Rubbia, Carlo; Rudolf, G; Rullhusen, P; Salgado, J; Santos, J; Sarchiapone, L; Savvidis, I; Stéphan, C; Taín, J L; Tassan-Got, L; Tavora, L; Terlizzi, R; Vannini, G; Vaz, P; Ventura, A; Villamarín, D; Vincente, M, C; Vlachoudis, V; Vlastou, R; Voss, F; Walter, S; Wendler, H; Wiescher, M; Wisshak, K

    2008-01-01

    The neutron capture cross sections of the Zr isotopes have important implications in nuclear astrophysics and for reactor design. The small cross section of the neutron magic nucleus 90Zr, which accounts for more than 50% of natural zirconium represents one of the key isotopes for the stellar s-process, because it acts as a bottleneck in the neutron capture chain between the Fe seed and the heavier isotopes. The same element, Zr, also is an important component of the structural materials used in traditional and advanced nuclear reactors. The (n,γ) cross section has been measured at CERN, using the n_TOF spallation neutron source. In total, 45 resonances could be resolved in the neutron energy range below 70 keV, 10 being observed for the first time thanks to the high resolution and low backgrounds at n_TOF. On average, the Γγ widths obtained in resonance analyses with the R-matrix code SAMMY were 15% smaller than reported previously. By these results, the accuracy of the Maxwellian averaged cross section f...

  19. Photodegradation alleviates the lignin bottleneck for carbon turnover in terrestrial ecosystems.

    Science.gov (United States)

    Austin, Amy T; Méndez, M Soledad; Ballaré, Carlos L

    2016-04-19

    A mechanistic understanding of the controls on carbon storage and losses is essential for our capacity to predict and mitigate human impacts on the global carbon cycle. Plant litter decomposition is an important first step for carbon and nutrient turnover, and litter inputs and losses are essential in determining soil organic matter pools and the carbon balance in terrestrial ecosystems. Photodegradation, the photochemical mineralization of organic matter, has been recently identified as a mechanism for previously unexplained high rates of litter mass loss in arid lands; however, the global significance of this process as a control on carbon cycling in terrestrial ecosystems is not known. Here we show that, across a wide range of plant species, photodegradation enhanced subsequent biotic degradation of leaf litter. Moreover, we demonstrate that the mechanism for this enhancement involves increased accessibility to plant litter carbohydrates for microbial enzymes. Photodegradation of plant litter, driven by UV radiation, and especially visible (blue-green) light, reduced the structural and chemical bottleneck imposed by lignin in secondary cell walls. In leaf litter from woody species, specific interactions with UV radiation obscured facilitative effects of solar radiation on biotic decomposition. The generalized effect of sunlight exposure on subsequent microbial activity, mediated by increased accessibility to cell wall polysaccharides, suggests that photodegradation is quantitatively important in determining rates of mass loss, nutrient release, and the carbon balance in a broad range of terrestrial ecosystems.

  20. Evolution and Adaptation of Wild Emmer Wheat Populations to Biotic and Abiotic Stresses.

    Science.gov (United States)

    Huang, Lin; Raats, Dina; Sela, Hanan; Klymiuk, Valentina; Lidzbarsky, Gabriel; Feng, Lihua; Krugman, Tamar; Fahima, Tzion

    2016-08-04

    The genetic bottlenecks associated with plant domestication and subsequent selection in man-made agroecosystems have limited the genetic diversity of modern crops and increased their vulnerability to environmental stresses. Wild emmer wheat, the tetraploid progenitor of domesticated wheat, distributed along a wide range of ecogeographical conditions in the Fertile Crescent, has valuable "left behind" adaptive diversity to multiple diseases and environmental stresses. The biotic and abiotic stress responses are conferred by series of genes and quantitative trait loci (QTLs) that control complex resistance pathways. The study of genetic diversity, genomic organization, expression profiles, protein structure and function of biotic and abiotic stress-resistance genes, and QTLs could shed light on the evolutionary history and adaptation mechanisms of wild emmer populations for their natural habitats. The continuous evolution and adaptation of wild emmer to the changing environment provide novel solutions that can contribute to safeguarding food for the rapidly growing human population.

  1. Perceived causes of severe mental disturbance and preferred interventions by the Borana semi-nomadic population in southern Ethiopia: a qualitative study

    Science.gov (United States)

    2012-01-01

    Background Culture affects the way people conceptualize causes of severe mental disturbance which may lead to a variation in the preferred intervention methods. There is a seemingly dichotomous belief regarding what causes severe mental disturbance: people living in western countries tend to focus mainly on biological and psychosocial risk factors; whereas, in non-western countries the focus is mainly on supernatural and religious factors. These belief systems about causation potentially dictate the type of intervention preferred. Studying such belief systems in any society is expected to help in planning and implementation of appropriate mental health services. Methods A qualitative study was conducted among the Borana semi-nomadic population in southern Ethiopia to explore perceived causes of severe mental disturbance and preferred interventions. We selected, using purposive sampling, key informants from three villages and conducted a total of six focus group discussions: three for males and three for females. Results The views expressed regarding the causes of mental disturbance were heterogeneous encompassing supernatural causes such as possession by evil spirits, curse, bewitchment, ‘exposure to wind’ and subsequent attack by evil spirit in postnatal women and biopsychosocial causes such as infections (malaria), loss, ‘thinking too much’, and alcohol and khat abuse. The preferred interventions for severe mental disturbance included mainly indigenous approaches, such as consulting Borana wise men or indigenous healers, prayer, holy water treatment and seeking modern mental health care as a last resort. Conclusions These findings will be of value for health care planners who wish to expand modern mental health care to this population, indicating the need to increase awareness about the causes of severe mental disturbance and their interventions and collaborate with influential people and indigenous healers to increase acceptability of modern mental

  2. Microsatellite genetic diversity and differentiation of native and introduced grass carp populations in three continents

    Science.gov (United States)

    Chapman, Duane C.; Chen, Qin; Wang, Chenghui; Zhao, Jinlian; Lu, Guoqing; Zsigmond, Jeney; Li, Si-Fa

    2012-01-01

    Grass carp (Ctenopharyngodon idella), a freshwater species native to China, has been introduced to about 100 countries/regions and poses both biological and environmental challenges to the receiving ecosystems. In this study, we analyzed genetic variation in grass carp from three introduced river systems (Mississippi River Basin in US, Danube River in Hungary, and Tone River in Japan) as well as its native ranges (Yangtze, Pearl, and Amur Rivers) in China using 21 novel microsatellite loci. The allelic richness, observed heterozygosity, and within-population gene diversity were found to be lower in the introduced populations than in the native populations, presumably due to the small founder population size of the former. Significant genetic differentiation was found between all pairwise populations from different rivers. Both principal component analysis and Bayesian clustering analysis revealed obvious genetic distinction between the native and introduced populations. Interestingly, genetic bottlenecks were detected in the Hungarian and Japanese grass carp populations, but not in the North American population, suggesting that the Mississippi River Basin grass carp has experienced rapid population expansion with potential genetic diversification during the half-century since its introduction. Consequently, the combined forces of the founder effect, introduction history, and rapid population expansion help explaining the observed patterns of genetic diversity within and among both native and introduced populations of the grass carp.

  3. Mycoplasma ovipneumoniae - A Primary Cause of Severe Pneumonia Epizootics in the Norwegian Muskox (Ovibos moschatus) Population

    DEFF Research Database (Denmark)

    Handeland, Kjell; Tengs, Torstein; Kokotovic, Branko

    2014-01-01

    The Norwegian muskox (Ovibos moschatus) population lives on the high mountain plateau of Dovre and originates from animals introduced from Greenland. In the late summers of 2006 and 2012, severe outbreaks of pneumonia with mortality rates of 25-30% occurred. During the 2012 epidemic high quality...... heavy consolidations primarily in the cranial parts of the lungs and it also identified one case of otitis media. Histologically, lung lesions were characterized as acute to subacute mixed exudative and moderately proliferative bronchoalveolar pneumonia. Immunohistochemical (IHC) examination revealed...

  4. Genome sequencing highlights the dynamic early history of dogs.

    Directory of Open Access Journals (Sweden)

    Adam H Freedman

    2014-01-01

    Full Text Available To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow. In dogs, the domestication bottleneck involved at least a 16-fold reduction in population size, a much more severe bottleneck than estimated previously. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was substantially larger than represented by modern wolf populations. We narrow the plausible range for the date of initial dog domestication to an interval spanning 11-16 thousand years ago, predating the rise of agriculture. In light of this finding, we expand upon previous work regarding the increase in copy number of the amylase gene (AMY2B in dogs, which is believed to have aided digestion of starch in agricultural refuse. We find standing variation for amylase copy number variation in wolves and little or no copy number increase in the Dingo and Husky lineages. In conjunction with the estimated timing of dog origins, these results provide additional support to archaeological finds, suggesting the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that, surprisingly, none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog

  5. Heterozygosity in an isolated population of a large mammal founded by four individuals is predicted by an individual-based genetic model.

    Directory of Open Access Journals (Sweden)

    Jaana Kekkonen

    Full Text Available Within-population genetic diversity is expected to be dramatically reduced if a population is founded by a low number of individuals. Three females and one male white-tailed deer Odocoileus virginianus, a North American species, were successfully introduced in Finland in 1934 and the population has since been growing rapidly, but remained in complete isolation from other populations.Based on 14 microsatellite loci, the expected heterozygosity H was 0.692 with a mean allelic richness (AR of 5.36, which was significantly lower than what was found in Oklahoma, U.S.A. (H = 0.742; AR = 9.07, demonstrating that a bottleneck occurred. Observed H was in line with predictions from an individual-based model where the genealogy of the males and females in the population were tracked and the population's demography was included.Our findings provide a rare within-population empirical test of the founder effect and suggest that founding a population by a small number of individuals need not have a dramatic impact on heterozygosity in an iteroparous species.

  6. Patterns of circulating corticosterone in a population of rattlesnakes afflicted with snake fungal disease: Stress hormones as a potential mediator of seasonal cycles in disease severity and outcomes

    Science.gov (United States)

    Lind, Craig M.; Moore, Ignacio T.; Akçay, Çağlar; Vernasco, Ben J.; Lorch, Jeffrey M.; Farrell, Terence M.

    2018-01-01

    Snake fungal disease (SFD) is an emerging threat to snake populations in the United States. Fungal pathogens are often associated with a physiological stress response mediated by the hypothalamo-pituitary-adrenal axis (HPA), and afflicted individuals may incur steep coping costs. The severity of SFD can vary seasonally; however, little is known regarding (1) how SFD infection relates to HPA activity and (2) how seasonal shifts in environment, life history, or HPA activity may interact to drive seasonal patterns of infection severity and outcomes. To test the hypothesis that SFD is associated with increased HPA activity and to identify potential environmental or physiological drivers of seasonal infection, we monitored baseline corticosterone, SFD infection severity, foraging success, body condition, and reproductive status in a field-active population of pigmy rattlesnakes. Both plasma corticosterone and the severity of clinical signs of SFD peaked in the winter. Corticosterone levels were also elevated in the fall before the seasonal rise in SFD severity. Severely symptomatic snakes were in low body condition and had elevated corticosterone levels compared to moderately infected and uninfected snakes. The monthly mean severity of SFD in the population was negatively related to population-wide estimates of body condition and temperature measured in the precedent month and positively correlated with corticosterone levels measured in the precedent month. Symptomatic females were less likely to enter reproductive bouts compared to asymptomatic females. We propose the hypothesis that the seasonal interplay among environment, host energetics, and HPA activity initiates trade-offs in the fall that drive the increase in SFD prevalence, symptom severity, and decline in condition observed in the population through winter.

  7. Reducing Bottlenecks to Improve the Efficiency of the Lung Cancer Care Delivery Process: A Process Engineering Modeling Approach to Patient-Centered Care.

    Science.gov (United States)

    Ju, Feng; Lee, Hyo Kyung; Yu, Xinhua; Faris, Nicholas R; Rugless, Fedoria; Jiang, Shan; Li, Jingshan; Osarogiagbon, Raymond U

    2017-12-01

    The process of lung cancer care from initial lesion detection to treatment is complex, involving multiple steps, each introducing the potential for substantial delays. Identifying the steps with the greatest delays enables a focused effort to improve the timeliness of care-delivery, without sacrificing quality. We retrospectively reviewed clinical events from initial detection, through histologic diagnosis, radiologic and invasive staging, and medical clearance, to surgery for all patients who had an attempted resection of a suspected lung cancer in a community healthcare system. We used a computer process modeling approach to evaluate delays in care delivery, in order to identify potential 'bottlenecks' in waiting time, the reduction of which could produce greater care efficiency. We also conducted 'what-if' analyses to predict the relative impact of simulated changes in the care delivery process to determine the most efficient pathways to surgery. The waiting time between radiologic lesion detection and diagnostic biopsy, and the waiting time from radiologic staging to surgery were the two most critical bottlenecks impeding efficient care delivery (more than 3 times larger compared to reducing other waiting times). Additionally, instituting surgical consultation prior to cardiac consultation for medical clearance and decreasing the waiting time between CT scans and diagnostic biopsies, were potentially the most impactful measures to reduce care delays before surgery. Rigorous computer simulation modeling, using clinical data, can provide useful information to identify areas for improving the efficiency of care delivery by process engineering, for patients who receive surgery for lung cancer.

  8. Interleukin 1β (+3954; −511 genotype polymorphism and its association with severe chronic generalized periodontitis in the Malaysian Population

    Directory of Open Access Journals (Sweden)

    Shelly Arora

    2017-01-01

    Full Text Available Introduction: Single-nucleotide polymorphisms (SNPs in interleukin 1β (IL-1β gene have been known to be associated with increased susceptibility to chronic periodontitis among various ethnic populations. SNPs are more commonly observed at loci + 3954 and − 511. The aim of this study was to evaluate the role of IL-1β gene polymorphism at loci +3954 and − 511, and its association with severe chronic generalized periodontitis among the ethnic Malay, Chinese, and Indians within the Malaysian population. Materials and Methods: Saliva samples from 120 subjects (60 cases and 60 controls in the age group of 25–50 years were collected for isolation of genetic material using Norgen technique. Clinical attachment loss of ≥5 mm was considered as severe chronic generalized periodontitis. SNP's at loci +3954 and − 511 were identified and analyzed using Kompetitive Allele Specific Polymerase Chain Reaction Genotyping System (KASP™. Differences in the allele/genotype frequencies were assessed by Chi-square test (P < 0.05. Results: On the comparison between cases and controls of IL-1β genotype polymorphism (+3954 and − 511, the difference in the genotype frequencies was statistically insignificant in all the three ethnicities. The genotype frequency in both groups in all three ethnicities of the Malaysian population was similar. Conclusion: IL-1β genotype polymorphism at +3954 and − 511 was found to be not associated with severe chronic generalized periodontitis among the three ethnicities in Malaysia. Studies with larger sample size should be done to confirm the findings of this study.

  9. The oriental fruit fly, Bactrocera dorsalis, in China: origin and gradual inland range expansion associated with population growth.

    Science.gov (United States)

    Wan, Xuanwu; Nardi, Francesco; Zhang, Bin; Liu, Yinghong

    2011-01-01

    The oriental fruit fly, Bactrocera dorsalis, expanded throughout mainland China in the last century to become one of the most serious pests in the area, yet information on this process are fragmentary. Three mitochondrial genes (nad1, cytb and nad5) were used to infer the genetic diversity, population structure and demographic history of the oriental fruit fly from its entire distribution range in China. High levels of genetic diversity, as well as a significant correspondence between genetic and geographic distances, suggest that the invasion process might have been gradual, with no associated genetic bottlenecks. Three population groups could be identified, nevertheless the overall genetic structure was weak. The effective number of migrants between populations, estimated using the coalescent method, suggested asymmetric gene flow from the costal region of Guangdong to most inland regions. The demographic analysis indicates the oriental fruit fly underwent a recent population expansion in the Central China. We suggest the species originated in the costal region facing the South China Sea and gradually expanded to colonize mainland China, expanding here to high population numbers.

  10. Genetic consequences of anagenetic speciation in Acer okamotoanum (Sapindaceae) on Ullung Island, Korea.

    Science.gov (United States)

    Takayama, Koji; Sun, Byung-Yun; Stuessy, Tod F

    2012-02-01

    Anagenesis (also known as phyletic speciation) is an important process of speciation in endemic species of oceanic islands. We investigated genetic variation in Acer okamotoanum, an anagenetically derived species endemic to Ullung Island, South Korea, to infer genetic consequences of anagenesis in comparison with other groups that have undergone cladogenesis (and adaptive radiation). We examined genetic variation based on eight polymorphic microsatellite markers from 145 individuals of A. okamotoanum and 134 individuals of its putative progenitor A. mono. We employed standard population genetic analyses, clustering analyses, Bayesian clustering analyses in STRUCTURE and bottleneck analyses. Based on both the Neighbor-Joining tree and Bayesian clustering analyses, clear genetic distinctions were found between the two species. Genetic diversity in terms of allelic richness and heterozygosity shows slightly lower levels in A. okamotoanum in comparison with A. mono. Bayesian clustering analyses showed a relatively high F-value in the cluster of A. okamotoanum, suggesting a strong episode of genetic drift during colonization and speciation. There was no clear evidence of a bottleneck based on allelic frequency distribution and excess of observed heterozygotes, but the M-ratio indicated a historical bottleneck in several populations of A. okamotoanum. No geographical genetic structure within the island was found, and the genetic variation among populations of A. okamotoanum was quite low. We hypothesized that genetic consequences of oceanic-endemic plants derived via anagenesis would be quite different from those derived via cladogenesis. Populations of A. okamotoanum form a cluster and are clearly differentiated from A. mono, which suggests a single origin for the anagenetically derived island endemic. No pattern of geographical differentiation of populations occurs in A. okamotoanum, which supports the concept of initial founder populations diverging through time by

  11. Risk factors associated with hospitalisation for influenza-associated severe acute respiratory illness in South Africa: A case-population study.

    Science.gov (United States)

    Abadom, Tochukwu Raphael; Smith, Adrian D; Tempia, Stefano; Madhi, Shabir A; Cohen, Cheryl; Cohen, Adam L

    2016-11-04

    Influenza is a common cause of severe respiratory illness, but risk factors for hospitalisation in low income settings with a high HIV prevalence are not well described. We aimed to assess risk factors associated with influenza-associated severe acute respiratory illness (SARI) hospitalisation in South Africa. We conducted a case-population study using data on risk conditions in patients hospitalised with SARI and the national prevalence of these conditions. Data on hospitalised cases were from the national SARI surveillance program while data on the referent population were from the latest national census or health and demographic surveillance surveys. From 2009 to 2012, we identified 3646 (7.9%) of 46,031 enrolled cases of SARI that were associated with influenza infection. Risk factors associated with hospitalisation included previous history of smoking [case-population ratio (CPR) 3.82, 95% confidence interval (CI) 3.5-4.16], HIV infection (CPR 3.61, 95% CI 3.5-3.71), asthma (CPR 2.45, 95% CI 2.19-2.73), previous history of hospital admission in the past 12months (CPR 2.07, 95% CI 1.92-2.23), and tuberculosis (CPR 1.85, 95% CI 1.68-2.02). When stratified by age, there is increased risk of hospitalisation in those ⩽5yearsof age (CPR 3.07, 95% CI 2.93-3.21) and among those 35yearsof age and above (CPR 1.23, 95% CI 1.28-1.18). Male sex (CPR 0.85, 95% CI 0.82-0.88) and completion of pneumococcal conjugate vaccination schedule in children <5yearsof age (CPR 0.74, 95% CI 0.71-0.77) were associated with decreased risk of hospitalisation. These results identify groups at high-risk for severe influenza who should be considered potential targets for influenza vaccination in South Africa and similar settings. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Comparative population genetics of the German shepherd dog in South Africa

    Directory of Open Access Journals (Sweden)

    N. J. Coutts

    2010-01-01

    Full Text Available Modern breeding practices strive to achieve distinctive phenotypic uniformity in breeds of dogs, but these strategies are associated with the inevitable loss of genetic diversity. Thus, in parallel with the morphological variation displayed by breeds, purebred dogs commonly express genetic defects as a result of the inbreeding associated with artificial selection and the reduction of selection against disease phenotypes. Microsatellite marker analyses of 15 polymorphic canine loci were used to investigate measures of genetic diversity and population differentiation within and between German-bred and South African-bred German shepherd dogs. These data were quantified by comparison with typically outbred mongrel or crossbred dogs. Both the imported and locally-bred German shepherd dogs exhibited similar levels of genetic diversity. The breed is characterised by only a moderate loss of genetic diversity relative to outbred dogs, despite originating from a single founding sire and experiencing extensive levels of inbreeding throughout the history of the breed. Non-significant population differentiation between the ancestral German and derived South African populations indicates sufficient contemporary gene flow between these populations, suggesting that migration resulting from the importation of breeding stock has mitigated the effects of random genetic drift and a population bottleneck caused by the original founder event in South Africa. Significant differentiation between the combined German shepherd dog population and the outbred dogs illustrates the effects of selection and genetic drift on the breed since its establishment just over 100 years ago.

  13. Frequency of rare mutations and common genetic variations in severe hypertriglyceridemia in the general population of Spain.

    Science.gov (United States)

    Lamiquiz-Moneo, Itziar; Blanco-Torrecilla, Cristian; Bea, Ana M; Mateo-Gallego, Rocío; Pérez-Calahorra, Sofía; Baila-Rueda, Lucía; Cenarro, Ana; Civeira, Fernando; de Castro-Orós, Isabel

    2016-04-23

    Hypertriglyceridemia (HTG) is a common complex metabolic trait that results of the accumulation of relatively common genetic variants in combination with other modifier genes and environmental factors resulting in increased plasma triglyceride (TG) levels. The majority of severe primary hypertriglyceridemias is diagnosed in adulthood and their molecular bases have not been fully defined yet. The prevalence of HTG is highly variable among populations, possibly caused by differences in environmental factors and genetic background. However, the prevalence of very high TG and the frequency of rare mutations causing HTG in a whole non-selected population have not been previously studied. The total of 23,310 subjects over 18 years from a primary care-district in a middle-class area of Zaragoza (Spain) with TG >500 mg/dL were selected to establish HTG prevalence. Those affected of primary HTG were considered for further genetic analysis. The promoters, coding regions and exon-intron boundaries of LPL, LMF1, APOC2, APOA5, APOE and GPIHBP1 genes were sequenced. The frequency of rare variants identified was studied in 90 controls. One hundred ninety-four subjects (1.04%) had HTG and 90 subjects (46.4%) met the inclusion criteria for primary HTG. In this subgroup, nine patients (12.3%) were carriers of 7 rare variants in LPL, LMF1, APOA5, GPIHBP1 or APOE genes. Three of these mutations are described for the first time in this work. The presence of a rare pathogenic mutation did not confer a differential phenotype or a higher family history of HTG. The prevalence of rare mutations in candidate genes in subjects with primary HTG is low. The low frequency of rare mutations, the absence of a more severe phenotype or the dominant transmission of the HTG would not suggest the use of genetic analysis in the clinical practice in this population.

  14. Structure and genetic diversity of natural Brazilian pepper populations (Schinus terebinthifolius Raddi).

    Science.gov (United States)

    Álvares-Carvalho, S V; Duarte, J F; Santos, T C; Santos, R M; Silva-Mann, R; Carvalho, D

    2016-06-17

    In the face of a possible loss of genetic diversity in plants due the environmental changes, actions to ensure the genetic variability are an urgent necessity. The extraction of Brazilian pepper fruits is a cause of concern because it results in the lack of seeds in soil, hindering its distribution in space and time. It is important to address this concern and explore the species, used by riparian communities and agro-factories without considering the need for keeping the seeds for natural seed banks and for species sustainability. The objective of this study was to evaluate the structure and the genetic diversity in natural Brazilian pepper populations (Schinus terebinthifolius Raddi). Twenty-two alleles in 223 individuals were identified from eight forest remnants located in the states of Minas Gerais, Espírito Santo, and Sergipe. All populations presented loci in Hardy-Weinberg equilibrium deviation. Four populations presented six combinations of loci in linkage disequilibrium. Six exclusive alleles were detected in four populations. Analysis of molecular variance showed the absence of diversity between regions and that between the populations (GST) was 41%. Genetic diversity was structured in seven clusters (ΔK7). Brazilian pepper populations were not structured in a pattern of isolation by distance and present genetic bottleneck. The populations São Mateus, Canastra, Barbacena, and Ilha das Flores were identified as management units and may support conservation projects, ecological restoration and in implementation of management plans for Brazilian pepper in the State of Sergipe.

  15. HLA-B*44 Is Associated with Dengue Severity Caused by DENV-3 in a Brazilian Population

    Directory of Open Access Journals (Sweden)

    Liciana Xavier Eurico de Alencar

    2013-01-01

    Full Text Available Human leukocyte antigen (HLA alleles have been correlated with susceptibility or resistance to severe dengue; however, few immunogenetic studies have been performed in Latin American (LA populations. We have conducted immunogenetic studies of HLA class I and II alleles in a cohort of 187 patients with DENV-3 infection and confirmed clinical diagnosis of either severe dengue, known as dengue hemorrhagic fever (DHF, or the less severe form, dengue fever (DF, in Recife, Pernambuco, Brazil. An association analysis was performed using Fisher’s association test, with odds ratios (ORs calculated using conditional maximum likelihood estimates. HLA-B*44 (P=0.047, OR = 2.025, 95% CI = 0.97–4.24 was found to be associated with increased susceptibility to DHF in response to DENV-3 infection. In addition, HLA-B*07 (P=0.048, OR = 0.501, one-sided 95% CI = 0–0.99 and HLA-DR*13 (P=0.028, OR = 0.511, one-sided 95% CI = 0–0.91 were found to be associated with resistance to secondary dengue infection by DENV-3. These results suggest that HLA-B*44 supertype alleles and their respective T-cell responses might be involved in susceptibility to severe dengue infections, whereas the HLA-B*07 supertype alleles and DR*13 might be involved in cross-dengue serotype immunity.

  16. "out of The Cold": On Late Neanderthal Population Dynamics In Central Europe

    Science.gov (United States)

    Jöris, O.

    During the last several years, analyses of fossil Neanderthal DNA have shown not only the degree to which the genetic fingerprints of Neanderthals differ from those of anatomically modern humans, but have also lent credibility to the hotly debated "Out- of-Africa" hypothesis. Perhaps more important than the observed genetic differences is the fact that Neanderthals - according to their reconstructed DNA sequences - were genetically highly homogeneous, indicating rapid population growth that may have followed a demographic 'bottleneck' during the first cold maximum (CM-1 = second part of OIS 4) of the last glacial, some 60 to 70 ka ago. Central European Middle Palaeolithic sites characterised by broad spectra of bifacially-worked tools, namely different forms of backed knives ("Keilmesser") com- monly attributed to Neanderthals, fall within the age-range 85 and 45 ka calBP and thus both pre- and post-date the proposed 'bottleneck' that occurred during CM-1. Di- rectly comparable sites dating within this critical period are lacking. Based on strati- graphic, palaeoenvironmental, and radiometric evidence, a series of sites can tenta- tively be age-calibrated with the high-resolution GISP2 Greenland ice core record of last glacial climate change. With the aid of improved chronological frameworks and additional palaeoenvironmen- tal information (e.g. glacier mass balance models), we have developed a three-step model with which to investigate this period. We begin with (1) pre-CM-1 populations in Central and northern Central Europe which (2) were forced into southern Euro- pean refugia (i.e. SW France and the Pannonian Basins) by the rapid expansion of the northern hemispheric ice-cover at the beginning of CM-1 (a process that could be named 'preglacial dislocation'). Finally, some 10 ka later, their descendants may have re-occupied the southern part of Central Europe during the climatic amelioration (OIS 3) following CM-1. Changes in lithic technology, as expressed in

  17. Engineering oilseeds for sustainable production of industrial and nutritional feedstocks: solving bottlenecks in fatty acid flux.

    Science.gov (United States)

    Cahoon, Edgar B; Shockey, Jay M; Dietrich, Charles R; Gidda, Satinder K; Mullen, Robert T; Dyer, John M

    2007-06-01

    Oilseeds provide a unique platform for the production of high-value fatty acids that can replace non-sustainable petroleum and oceanic sources of specialty chemicals and aquaculture feed. However, recent efforts to engineer the seeds of crop and model plant species to produce new types of fatty acids, including hydroxy and conjugated fatty acids for industrial uses and long-chain omega-3 polyunsaturated fatty acids for farmed fish feed, have met with only modest success. The collective results from these studies point to metabolic 'bottlenecks' in the engineered plant seeds that substantially limit the efficient or selective flux of unusual fatty acids between different substrate pools and ultimately into storage triacylglycerol. Evidence is emerging that diacylglycerol acyltransferase 2, which catalyzes the final step in triacylglycerol assembly, is an important contributor to the synthesis of unusual fatty acid-containing oils, and is likely to be a key target for future oilseed metabolic engineering efforts.

  18. Interaction of malaria with a common form of severe thalassemia in an Asian population

    Science.gov (United States)

    O'Donnell, A.; Premawardhena, A.; Arambepola, M.; Samaranayake, R.; Allen, S. J.; Peto, T. E. A.; Fisher, C. A.; Cook, J.; Corran, P. H.; Olivieri, Nancy F.; Weatherall, D. J.

    2009-01-01

    In many Asian populations, the commonest form of severe thalassemia results from the coinheritance of HbE and β thalassemia. The management of this disease is particularly difficult because of its extreme clinical diversity; although some genetic and adaptive factors have been identified as phenotypic modifiers, the reasons remain unclear. Because the role of the environment in the course of severe thalassemia has been neglected completely and because malaria due to both Plasmodium falciparum and Plasmodium vivax has been prevalent in Sri Lanka, we carried out a pilot study of patients with HbE β thalassemia that showed high frequencies of antibodies to both parasite species and that 28.6% of the children had DNA-based evidence of current infection with P. vivax. Malarial antibodies then were assessed in patients with HbE β thalassemia compared with those in age-matched controls. There was a significant increase in the frequency of antibodies in the thalassemic patients, particularly against P. vivax and in young children. There was also a higher frequency in those who had been splenectomized compared with those with intact spleens, although in the latter it was still higher than that in the controls. The thalassemic patients showed significant correlations between malaria antibody status and phenotype. Patients with HbE β thalassemia may be more prone to malaria, particularly P. vivax, which is reflected in their clinical severity. Because P. vivax malaria is widespread in Asia, further studies of its interaction with HbE β thalassemia and related diseases are required urgently as a part of ongoing thalassemia control programs. PMID:19841268

  19. The Effect of Recurrent Floods on Genetic Composition of Marble Trout Populations

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    Pujolar, José Martin; Vincenzi, Simone; Zane, Lorenzo; Jesensek, Dusan; De Leo, Giulio A.; Crivelli, Alain J.

    2011-01-01

    A changing global climate can threaten the diversity of species and ecosystems. We explore the consequences of catastrophic disturbances in determining the evolutionary and demographic histories of secluded marble trout populations in Slovenian streams subjected to weather extremes, in particular recurrent flash floods and debris flows causing massive mortalities. Using microsatellite data, a pattern of extreme genetic differentiation was found among populations (global F ST of 0.716), which exceeds the highest values reported in freshwater fish. All locations showed low levels of genetic diversity as evidenced by low heterozygosities and a mean of only 2 alleles per locus, with few or no rare alleles. Many loci showed a discontinuous allele distribution, with missing alleles across the allele size range, suggestive of a population contraction. Accordingly, bottleneck episodes were inferred for all samples with a reduction in population size of 3–4 orders of magnitude. The reduced level of genetic diversity observed in all populations implies a strong impact of genetic drift, and suggests that along with limited gene flow, genetic differentiation might have been exacerbated by recurrent mortalities likely caused by flash flood and debris flows. Due to its low evolutionary potential the species might fail to cope with an intensification and altered frequency of flash flood events predicted to occur with climate change. PMID:21931617

  20. Trends in adverse maternal outcomes during childbirth: a population-based study of severe maternal morbidity.

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    Roberts, Christine L; Ford, Jane B; Algert, Charles S; Bell, Jane C; Simpson, Judy M; Morris, Jonathan M

    2009-02-25

    Maternal mortality is too rare in high income countries to be used as a marker of the quality of maternity care. Consequently severe maternal morbidity has been suggested as a better indicator. Using the maternal morbidity outcome indicator (MMOI) developed and validated for use in routinely collected population health data, we aimed to determine trends in severe adverse maternal outcomes during the birth admission and in particular to examine the contribution of postpartum haemorrhage (PPH). We applied the MMOI to the linked birth-hospital discharge records for all women who gave birth in New South Wales, Australia from 1999 to 2004 and determined rates of severe adverse maternal outcomes. We used frequency distributions and contingency table analyses to examine the association between adverse outcomes and maternal, pregnancy and birth characteristics, among all women and among only those with PPH. Using logistic regression, we modelled the effects of these characteristics on adverse maternal outcomes. The impact of adverse outcomes on duration of hospital admission was also examined. Of 500,603 women with linked birth and hospital records, 6242 (12.5 per 1,000) suffered an adverse outcome, including 22 who died. The rate of adverse maternal outcomes increased from 11.5 in 1999 to 13.8 per 1000 deliveries in 2004, an annual increase of 3.8% (95%CI 2.3-5.3%). This increase occurred almost entirely among women with a PPH. Changes in pregnancy and birth factors during the study period did not account for increases in adverse outcomes either overall, or among the subgroup of women with PPH. Among women with severe adverse outcomes there was a 12% decrease in hospital days over the study period, whereas women with no severe adverse outcome occupied 23% fewer hospital days in 2004 than in 1999. Severe adverse maternal outcomes associated with childbirth have increased in Australia and the increase was entirely among women who experienced a PPH. Reducing or stabilising

  1. Trends in adverse maternal outcomes during childbirth: a population-based study of severe maternal morbidity

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    Algert Charles S

    2009-02-01

    Full Text Available Abstract Background Maternal mortality is too rare in high income countries to be used as a marker of the quality of maternity care. Consequently severe maternal morbidity has been suggested as a better indicator. Using the maternal morbidity outcome indicator (MMOI developed and validated for use in routinely collected population health data, we aimed to determine trends in severe adverse maternal outcomes during the birth admission and in particular to examine the contribution of postpartum haemorrhage (PPH. Methods We applied the MMOI to the linked birth-hospital discharge records for all women who gave birth in New South Wales, Australia from 1999 to 2004 and determined rates of severe adverse maternal outcomes. We used frequency distributions and contingency table analyses to examine the association between adverse outcomes and maternal, pregnancy and birth characteristics, among all women and among only those with PPH. Using logistic regression, we modelled the effects of these characteristics on adverse maternal outcomes. The impact of adverse outcomes on duration of hospital admission was also examined. Results Of 500,603 women with linked birth and hospital records, 6242 (12.5 per 1,000 suffered an adverse outcome, including 22 who died. The rate of adverse maternal outcomes increased from 11.5 in 1999 to 13.8 per 1000 deliveries in 2004, an annual increase of 3.8% (95%CI 2.3–5.3%. This increase occurred almost entirely among women with a PPH. Changes in pregnancy and birth factors during the study period did not account for increases in adverse outcomes either overall, or among the subgroup of women with PPH. Among women with severe adverse outcomes there was a 12% decrease in hospital days over the study period, whereas women with no severe adverse outcome occupied 23% fewer hospital days in 2004 than in 1999. Conclusion Severe adverse maternal outcomes associated with childbirth have increased in Australia and the increase was

  2. Genetic diversity and population structure of Sitodiplosis mosellana in Northern China.

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    Yun Duan

    Full Text Available The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups, broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (F ST = 0.117 between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (F ST = 0.116, Nm = 1.89 than those in the eastern group (F ST = 0.049, Nm = 4.91. Genetic distance between populations was positively and significantly correlated with geographic distance (r = 0.56, P<0.001. The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.

  3. Disentangling the roles of natural selection and genetic drift in shaping variation at MHC immunity genes.

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    Sutton, Jolene T; Nakagawa, Shinichi; Robertson, Bruce C; Jamieson, Ian G

    2011-11-01

    The major histocompatibility complex (MHC) forms an integral component of the vertebrate immune response and, due to strong selection pressures, is one of the most polymorphic regions of the entire genome. Despite over 15 years of research, empirical studies offer highly contradictory explanations of the relative roles of different evolutionary forces, selection and genetic drift, acting on MHC genes during population bottlenecks. Here, we take a meta-analytical approach to quantify the results of studies into the effects of bottlenecks on MHC polymorphism. We show that the consequences of selection acting on MHC loci prior to a bottleneck event, combined with drift during the bottleneck, will result in overall loss of MHC polymorphism that is ∼15% greater than loss of neutral genetic diversity. These results are counter to general expectations that selection should maintain MHC polymorphism, but do agree with the results of recent simulation models and at least two empirical studies. Notably, our results suggest that negative frequency-dependent selection could be more important than overdominance for maintaining high MHC polymorphism in pre-bottlenecked populations. © 2011 Blackwell Publishing Ltd.

  4. Consequences of severe habitat fragmentation on density, genetics, and spatial capture-recapture analysis of a small bear population.

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    Sean M Murphy

    Full Text Available Loss and fragmentation of natural habitats caused by human land uses have subdivided several formerly contiguous large carnivore populations into multiple small and often isolated subpopulations, which can reduce genetic variation and lead to precipitous population declines. Substantial habitat loss and fragmentation from urban development and agriculture expansion relegated the Highlands-Glades subpopulation (HGS of Florida, USA, black bears (Ursus americanus floridanus to prolonged isolation; increasing human land development is projected to cause ≥ 50% loss of remaining natural habitats occupied by the HGS in coming decades. We conducted a noninvasive genetic spatial capture-recapture study to quantitatively describe the degree of contemporary habitat fragmentation and investigate the consequences of habitat fragmentation on population density and genetics of the HGS. Remaining natural habitats sustaining the HGS were significantly more fragmented and patchier than those supporting Florida's largest black bear subpopulation. Genetic diversity was low (AR = 3.57; HE = 0.49 and effective population size was small (NE = 25 bears, both of which remained unchanged over a period spanning one bear generation despite evidence of some immigration. Subpopulation density (0.054 bear/km2 was among the lowest reported for black bears, was significantly female-biased, and corresponded to a subpopulation size of 98 bears in available habitat. Conserving remaining natural habitats in the area occupied by the small, genetically depauperate HGS, possibly through conservation easements and government land acquisition, is likely the most important immediate step to ensuring continued persistence of bears in this area. Our study also provides evidence that preferentially placing detectors (e.g., hair traps or cameras primarily in quality habitat across fragmented landscapes poses a challenge to estimating density-habitat covariate relationships using spatial

  5. Genetic Pattern and Demographic History of Salminus brasiliensis: Population Expansion in the Pantanal Region during the Pleistocene

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    Lívia A. de Carvalho Mondin

    2018-01-01

    Full Text Available Pleistocene climate changes were major historical events that impacted South American biodiversity. Although the effects of such changes are well-documented for several biomes, it is poorly known how these climate shifts affected the biodiversity of the Pantanal floodplain. Fish are one of the most diverse groups in the Pantanal floodplains and can be taken as a suitable biological model for reconstructing paleoenvironmental scenarios. To identify the effects of Pleistocene climate changes on Pantanal’s ichthyofauna, we used genetic data from multiple populations of a top-predator long-distance migratory fish, Salminus brasiliensis. We specifically investigated whether Pleistocene climate changes affected the demography of this species. If this was the case, we expected to find changes in population size over time. Thus, we assessed the genetic diversity of S. brasiliensis to trace the demographic history of nine populations from the Upper Paraguay basin, which includes the Pantanal floodplain, that form a single genetic group, employing approximate Bayesian computation (ABC to test five scenarios: constant population, old expansion, old decline, old bottleneck following by recent expansion, and old expansion following by recent decline. Based on two mitochondrial DNA markers, our inferences from ABC analysis, the results of Bayesian skyline plot, the implications of star-like networks, and the patterns of genetic diversity (high haplotype diversity and low-to-moderate nucleotide diversity indicated a sudden population expansion. ABC allowed us to make strong quantitative inferences about the demographic history of S. brasiliensis. We estimated a small ancestral population size that underwent a drastic fivefold expansion, probably associated with the colonization of newly formed habitats. The estimated time of this expansion was consistent with a humid and warm phase as inferred by speleothem growth phases and travertine records during

  6. Genetic Population Structure and Demographic History of the Widespread Common Shipworm Teredo navalis Linnaeus 1758 (Mollusca: Bivalvia: Teredinidae in European Waters Inferred from Mitochondrial COI Sequence Data

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    Ronny Weigelt

    2017-06-01

    Full Text Available The first documented scientific reports of the common marine shipworm Teredo navalis (Bivalvia for Central European waters date back to the time between 1700 and 1730 in the Netherlands. During the following centuries there were several irregular mass occurrences reported for both the North Sea and the Baltic Sea. These events were accompanied by massive destruction of wooden ships and coastal protection structures. In this study, the first population analysis of T. navalis is presented with the aim to detect the genetic population structure in the waters of Central Europe. The mtDNA COI (cytochrome c oxidase subunit I locus was found as suitable molecular marker and hence a 675 bp gene fragment was studied. A total of 352 T. navalis specimens from 13 different sampling sites distributed across Central Europe were examined. Subsequently, various population genetic indices including FST values and an AMOVA analysis were applied for the description of the population structure. To visualize the distribution of haplotypes at the different sampling sites two median-joining networks were calculated. In addition, the past demographic structure of the T. navalis population was analyzed, among others by calculating Tajima's D, Fu's F and the mismatch distribution. Finally, all computations of the population genetic indices could not reveal differentiated populations or any kind of distinct population structure in T. navalis. The network analyses revealed “star-like” patterns without differentiated substructures or demes. Therefore, it can be assumed that a sudden expansion of this species took place without any indications of neither a bottleneck nor a founder effect for the study area. The results of this study support the concept of a regional panmictic population in the waters of Central Europe with unhindered migration of individuals (e.g., via pelagic larvae between the various sampling sites as reflected by a high gene flow.

  7. Unravelling the genetic history of Negritos and indigenous populations of Southeast Asia.

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    Aghakhanian, Farhang; Yunus, Yushima; Naidu, Rakesh; Jinam, Timothy; Manica, Andrea; Hoh, Boon Peng; Phipps, Maude E

    2015-04-14

    Indigenous populations of Malaysia known as Orang Asli (OA) show huge morphological, anthropological, and linguistic diversity. However, the genetic history of these populations remained obscure. We performed a high-density array genotyping using over 2 million single nucleotide polymorphisms in three major groups of Negrito, Senoi, and Proto-Malay. Structural analyses indicated that although all OA groups are genetically closest to East Asian (EA) populations, they are substantially distinct. We identified a genetic affinity between Andamanese and Malaysian Negritos which may suggest an ancient link between these two groups. We also showed that Senoi and Proto-Malay may be admixtures between Negrito and EA populations. Formal admixture tests provided evidence of gene flow between Austro-Asiatic-speaking OAs and populations from Southeast Asia (SEA) and South China which suggest a widespread presence of these people in SEA before Austronesian expansion. Elevated linkage disequilibrium (LD) and enriched homozygosity found in OAs reflect isolation and bottlenecks experienced. Estimates based on Ne and LD indicated that these populations diverged from East Asians during the late Pleistocene (14.5 to 8 KYA). The continuum in divergence time from Negritos to Senoi and Proto-Malay in combination with ancestral markers provides evidences of multiple waves of migration into SEA starting with the first Out-of-Africa dispersals followed by Early Train and subsequent Austronesian expansions. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  8. Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion

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    Boomsma Jacobus J

    2011-07-01

    Full Text Available Abstract Background Fragmentation of terrestrial ecosystems has had detrimental effects on metapopulations of habitat specialists. Maculinea butterflies have been particularly affected because of their specialized lifecycles, requiring both specific food-plants and host-ants. However, the interaction between dispersal, effective population size, and long-term genetic erosion of these endangered butterflies remains unknown. Using non-destructive sampling, we investigated the genetic diversity of the last extant population of M. arion in Denmark, which experienced critically low numbers in the 1980s. Results Using nine microsatellite markers, we show that the population is genetically impoverished compared to nearby populations in Sweden, but less so than monitoring programs suggested. Ten additional short repeat microsatellites were used to reconstruct changes in genetic diversity and population structure over the last 77 years from museum specimens. We also tested amplification efficiency in such historical samples as a function of repeat length and sample age. Low population numbers in the 1980s did not affect genetic diversity, but considerable turnover of alleles has characterized this population throughout the time-span of our analysis. Conclusions Our results suggest that M. arion is less sensitive to genetic erosion via population bottlenecks than previously thought, and that managing clusters of high quality habitat may be key for long-term conservation.

  9. Neutral polymorphisms in putative housekeeping genes and tandem repeats unravels the population genetics and evolutionary history of Plasmodium vivax in India.

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    Surendra K Prajapati

    Full Text Available The evolutionary history and age of Plasmodium vivax has been inferred as both recent and ancient by several studies, mainly using mitochondrial genome diversity. Here we address the age of P. vivax on the Indian subcontinent using selectively neutral housekeeping genes and tandem repeat loci. Analysis of ten housekeeping genes revealed a substantial number of SNPs (n = 75 from 100 P. vivax isolates collected from five geographical regions of India. Neutrality tests showed a majority of the housekeeping genes were selectively neutral, confirming the suitability of housekeeping genes for inferring the evolutionary history of P. vivax. In addition, a genetic differentiation test using housekeeping gene polymorphism data showed a lack of geographical structuring between the five regions of India. The coalescence analysis of the time to the most recent common ancestor estimate yielded an ancient TMRCA (232,228 to 303,030 years and long-term population history (79,235 to 104,008 of extant P. vivax on the Indian subcontinent. Analysis of 18 tandem repeat loci polymorphisms showed substantial allelic diversity and heterozygosity per locus, and analysis of potential bottlenecks revealed the signature of a stable P. vivax population, further corroborating our ancient age estimates. For the first time we report a comparable evolutionary history of P. vivax inferred by nuclear genetic markers (putative housekeeping genes to that inferred from mitochondrial genome diversity.

  10. Neutral polymorphisms in putative housekeeping genes and tandem repeats unravels the population genetics and evolutionary history of Plasmodium vivax in India.

    Science.gov (United States)

    Prajapati, Surendra K; Joshi, Hema; Carlton, Jane M; Rizvi, M Alam

    2013-01-01

    The evolutionary history and age of Plasmodium vivax has been inferred as both recent and ancient by several studies, mainly using mitochondrial genome diversity. Here we address the age of P. vivax on the Indian subcontinent using selectively neutral housekeeping genes and tandem repeat loci. Analysis of ten housekeeping genes revealed a substantial number of SNPs (n = 75) from 100 P. vivax isolates collected from five geographical regions of India. Neutrality tests showed a majority of the housekeeping genes were selectively neutral, confirming the suitability of housekeeping genes for inferring the evolutionary history of P. vivax. In addition, a genetic differentiation test using housekeeping gene polymorphism data showed a lack of geographical structuring between the five regions of India. The coalescence analysis of the time to the most recent common ancestor estimate yielded an ancient TMRCA (232,228 to 303,030 years) and long-term population history (79,235 to 104,008) of extant P. vivax on the Indian subcontinent. Analysis of 18 tandem repeat loci polymorphisms showed substantial allelic diversity and heterozygosity per locus, and analysis of potential bottlenecks revealed the signature of a stable P. vivax population, further corroborating our ancient age estimates. For the first time we report a comparable evolutionary history of P. vivax inferred by nuclear genetic markers (putative housekeeping genes) to that inferred from mitochondrial genome diversity.

  11. Genome-Wide Search for Quantitative Trait Loci Controlling Important Plant and Flower Traits in Petunia Using an Interspecific Recombinant Inbred Population of Petunia axillaris and Petunia exserta.

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    Cao, Zhe; Guo, Yufang; Yang, Qian; He, Yanhong; Fetouh, Mohammed; Warner, Ryan M; Deng, Zhanao

    2018-05-15

    A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia. An F 7 recombinant inbred population derived between Petunia axillaris and P. exserta was phenotyped for plant height, plant spread, plant size, flower counts, flower diameter, flower length, and days to anthesis, in Florida in two consecutive years. Transgressive segregation was observed for all seven traits in both years. The broad-sense heritability estimates for the traits ranged from 0.20 (days to anthesis) to 0.62 (flower length). A genome-wide genetic linkage map consisting 368 single nucleotide polymorphism bins and extending over 277 cM was searched to identify QTL for these traits. Nineteen QTL were identified and localized to five linkage groups. Eleven of the loci were identified consistently in both years; several loci explained up to 34.0% and 24.1% of the phenotypic variance for flower length and flower diameter, respectively. Multiple loci controlling different traits are co-localized in four intervals in four linkage groups. These intervals contain desirable alleles that can be introgressed into commercial petunia germplasm to expand the genetic base and improve plant performance and flower characteristics in petunia. Copyright © 2018, G3: Genes, Genomes, Genetics.

  12. Frequent beneficial mutations during single-colony serial transfer of Streptococcus pneumoniae.

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    Kathleen E Stevens

    2011-08-01

    Full Text Available The appearance of new mutations within a population provides the raw material for evolution. The consistent decline in fitness observed in classical mutation accumulation studies has provided support for the long-held view that deleterious mutations are more common than beneficial mutations. Here we present results of a study using a mutation accumulation design with the bacterium Streptococcus pneumoniae in which the fitness of the derived populations increased. This rise in fitness was associated specifically with adaptation to survival during brief stationary phase periods between single-colony population bottlenecks. To understand better the population dynamics behind this unanticipated adaptation, we developed a maximum likelihood model describing the processes of mutation and stationary-phase selection in the context of frequent population bottlenecks. Using this model, we estimate that the rate of beneficial mutations may be as high as 4.8×10(-4 events per genome for each time interval corresponding to the pneumococcal generation time. This rate is several orders of magnitude higher than earlier estimates of beneficial mutation rates in bacteria but supports recent results obtained through the propagation of small populations of Escherichia coli. Our findings indicate that beneficial mutations may be relatively frequent in bacteria and suggest that in S. pneumoniae, which develops natural competence for transformation, a steady supply of such mutations may be available for sampling by recombination.

  13. Tremor severity and age: a cross-sectional, population-based study of 2,524 young and midlife normal adults.

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    Louis, Elan D; Hafeman, Danella; Parvez, Faruque; Liu, Xinhua; Alcalay, Roy N; Islam, Tariqul; Ahmed, Alauddin; Siddique, Abu Bakar; Patwary, Tazul Islam; Melkonian, Stephanie; Argos, Maria; Levy, Diane; Ahsan, Habibul

    2011-07-01

    Mild action tremor occurs in most normal people. Yet this tremor mainly has been studied within the context of advanced age rather than among the vast bulk of adults who are not elderly. Whether this tremor worsens during young and middle age is unknown. Using cross-sectional data from a large population-based study of young and midlife normal adults (age range, 18-60 years), we assessed whether increasing age is associated with more severe action tremor. Two thousand five hundred and twenty-four adults in Araihazar, Bangladesh, drew an Archimedes spiral with each hand. Tremor in spirals was rated (0-3) by a blinded neurologist, and a spiral score (range, 0-6) was assigned. Spiral score was correlated with age (r = 0.06, P = .004). With each advancing decade, the spiral score increased (P = .002) so that the spiral score in participants in the highest age group (age 60) was approximately twice that of participants in the youngest age group (age 18-19); P = .003. In the regression model that adjusted for potential confounders (sex, cigarettes, medications, asthma inhalers, and tea and betel nut use), spiral score was associated with age (P = .0045). In this cross-sectional, population-based study of more than 2500 young and midlife normal adults, there was a clear association between age and tremor severity. Although the magnitude of the correlation coefficient was modest, tremor severity was higher with each passing decade. These data suggest that age-dependent increase in tremor amplitude is not restricted to older people but occurs in all adult age groups. Copyright © 2011 Movement Disorder Society.

  14. The value of some Corsican sub-populations for genetic association studies

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    Vona Giuseppe

    2008-07-01

    Full Text Available Abstract Background Genetic isolates with a history of a small founder population, long-lasting isolation and population bottlenecks represent exceptional resources in the identification of disease genes. In these populations the disease allele reveals Linkage Disequilibrium (LD with markers over significant genetic intervals, therefore facilitating disease locus identification. In a previous study we examined the LD extension on the Xq13 region in three Corsican sub-populations from the inner mountainous region of the island. On the basis of those previous results we have proposed a multistep procedure to carry out studies aimed at the identification of genes involved in complex diseases in Corsica. A prerequisite to carry out the proposed multi-step procedure was the presence of different degrees of LD on the island and a common genetic derivation of the different Corsican sub-populations. In order to evaluate the existence of these conditions in the present paper we extended the analysis to the Corsican coastal populations. Methods Samples were analyzed using seven dinucleotide microsatellite markers on chromosome Xq13-21: DXS983, DXS986, DXS8092, DXS8082, DXS1225, DXS8037 and DXS995 spanning approximately 4.0 cM (13.3 Mb. We have also investigated the distribution of the DXS1225-DXS8082 haplotype which has been recently proposed as a good marker of population genetic history due to its low recombination rate. Results the results obtained indicate a decrease of LD on the island from the central mountainous toward the coastal sub-populations. In addition the analysis of the DXS1225-DXS8082 haplotype revealed: 1 the presence of a particular haplotype with high frequency; 2 the derivation from a common genetic pool of the sub-populations examined in the present study. Conclusion These results indicate the Corsican sub-populations useful for the fine mapping of genes contributing to complex diseases.

  15. DnaSAM: Software to perform neutrality testing for large datasets with complex null models.

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    Eckert, Andrew J; Liechty, John D; Tearse, Brandon R; Pande, Barnaly; Neale, David B

    2010-05-01

    Patterns of DNA sequence polymorphisms can be used to understand the processes of demography and adaptation within natural populations. High-throughput generation of DNA sequence data has historically been the bottleneck with respect to data processing and experimental inference. Advances in marker technologies have largely solved this problem. Currently, the limiting step is computational, with most molecular population genetic software allowing a gene-by-gene analysis through a graphical user interface. An easy-to-use analysis program that allows both high-throughput processing of multiple sequence alignments along with the flexibility to simulate data under complex demographic scenarios is currently lacking. We introduce a new program, named DnaSAM, which allows high-throughput estimation of DNA sequence diversity and neutrality statistics from experimental data along with the ability to test those statistics via Monte Carlo coalescent simulations. These simulations are conducted using the ms program, which is able to incorporate several genetic parameters (e.g. recombination) and demographic scenarios (e.g. population bottlenecks). The output is a set of diversity and neutrality statistics with associated probability values under a user-specified null model that are stored in easy to manipulate text file. © 2009 Blackwell Publishing Ltd.

  16. Evolving trends in the epidemiology, resource utilization, and outcomes of pregnancy-associated severe sepsis: a population-based cohort study.

    Science.gov (United States)

    Oud, Lavi; Watkins, Phillip

    2015-06-01

    Infections are a well-known complication of pregnancy. However, pregnancy-associated severe sepsis (PASS) has not been as well-characterized, with limited population-level data reported to date. We performed a population-based study of the evolving patterns of the epidemiology, clinical characteristics, resource utilization, and outcomes of PASS in Texas over the past decade. The Texas Inpatient Public Use Data File was used to identify pregnancy-associated hospitalizations and PASS hospitalizations for the years 2001 - 2010. The Texas Center for Health Statistics reports of live births, abortions and fetal deaths, and a previously reported population-based, age-specific linkage study on miscarriage were used to derive the annual total estimated pregnancies (TEPs). The incidence, demographics, clinical characteristics, resource utilization and outcomes of PASS were examined. Logistic regression modeling was used to explore the predictors of PASS and its associated mortality. There were 4,060,201 pregnancy-associated hospitalizations and 1,007 PASS hospitalizations during study period. The incidence of PASS was increased by 236% over the past decade, rising from 11 to 26 hospitalizations per 100,000 TEPs. The key changes between 2001 - 2002 and 2009 - 2010 within PASS hospitalizations included: admission to ICU 78% vs. 90% (P = 0.002); development of ≥ 3 organ failures 9% vs. 35% (P < 0.0001); and inflation-adjusted median hospital charges (2,010 dollars) $64,034 vs. $89,895 (P = 0.0141). Hospital mortality (11%) remained unchanged during study period. Chronic liver disease (adjusted odds ratio (aOR) 41.4) and congestive heart failure (CHF) (aOR 20.5) were associated with the highest risk of PASS, in addition to black race, poverty, drug abuse, and lack of health insurance. The highest risk of death was among women with HIV infection (aOR 45.5), need for mechanical ventilation (aOR 4.5), drug abuse (aOR 3.0), and lacking health insurance (aOR 2.9). The incidence

  17. Protracted outbreak of severe delta hepatitis: experience in an isolated Amerindian population of the Upper Orinoco basin.

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    Torres, J R; Mondolfi, A

    1991-01-01

    In an investigation of a 21-year-old epidemic of severe hepatitis, 80 serum samples were studied from two isolated Yanomami Amerindian populations of the Upper Orinoco basin in Venezuela. Of the assayed samples, 30.6% were positive for hepatitis B surface antigen (HBsAg), 53.7% were considered to reflect immunity to infection with hepatitis B virus (HBV), and only 16.2% were believed to reflect susceptibility to HBV infection; 82.5% of the samples tested positive for any marker of HBV infection. Thirty-one (39.7%) of 78 samples were also positive for antibody to delta antigen, including 91.6% of those positive for HBsAg and 20.9% of those immune to HBV. Our findings provide evidence of a high prevalence of HBV infection in this population. Furthermore, the high prevalence of antibody to delta antigen strongly suggests that coinfections with HBV or superinfections with hepatitis delta virus (HDV) in HBV carriers may be an important factor in the occurrence of an unusually high number of cases of fulminant hepatitis and of chronic liver disease. Serum samples obtained at the beginning of the outbreak 13 years earlier from 36 selected cases in the same population revealed a high rate of HBV infection (96.5%). All six HBsAg carriers from whom enough serum remained to be assayed were positive for antibody to delta antigen. Our findings indicate that the outbreak coincided with the introduction of HDV into a population with an already-high prevalence of HBV infection.

  18. Population growth enhances the mean fixation time of neutral mutations and the persistence of neutral variation.

    Science.gov (United States)

    Waxman, D

    2012-06-01

    A fundamental result of population genetics states that a new mutation, at an unlinked neutral locus in a randomly mating diploid population, has a mean time of fixation of ∼4N(e) generations, where N(e) is the effective population size. This result is based on an assumption of fixed population size, which does not universally hold in natural populations. Here, we analyze such neutral fixations in populations of changing size within the framework of the diffusion approximation. General expressions are derived for the mean and variance of the fixation time in changing populations. Some explicit results are given for two cases: (i) the effective population size undergoes a sudden change, representing a sudden population expansion or a sudden bottleneck; (ii) the effective population changes linearly for a limited period of time and then remains constant. Additionally, a lower bound for the mean time of fixation is obtained for an effective population size that increases with time, and this is applied to exponentially growing populations. The results obtained in this work show, among other things, that for populations that increase in size, the mean time of fixation can be enhanced, sometimes substantially so, over 4N(e,0) generations, where N(e,0) is the effective population size at the time the mutation arises. Such an enhancement is associated with (i) an increased probability of neutral polymorphism in a population and (ii) an enhanced persistence of high-frequency neutral variation, which is the variation most likely to be observed.

  19. Demographic collapse and low genetic diversity of the Irrawaddy dolphin population inhabiting the Mekong River.

    Science.gov (United States)

    Krützen, Michael; Beasley, Isabel; Ackermann, Corinne Y; Lieckfeldt, Dietmar; Ludwig, Arne; Ryan, Gerard E; Bejder, Lars; Parra, Guido J; Wolfensberger, Rebekka; Spencer, Peter B S

    2018-01-01

    In threatened wildlife populations, it is important to determine whether observed low genetic diversity may be due to recent anthropogenic pressure or the consequence of historic events. Historical size of the Irrawaddy dolphin (Orcaella brevirostris) population inhabiting the Mekong River is unknown and there is significant concern for long-term survival of the remaining population as a result of low abundance, slow reproduction rate, high neonatal mortality, and continuing anthropogenic threats. We investigated population structure and reconstructed the demographic history based on 60 Irrawaddy dolphins samples collected between 2001 and 2009. The phylogenetic analysis indicated reciprocal monophyly of Mekong River Orcaella haplotypes with respect to haplotypes from other populations, suggesting long-standing isolation of the Mekong dolphin population from other Orcaella populations. We found that at least 85% of all individuals in the two main study areas: Kratie and Stung Treng, bore the same mitochondrial haplotype. Out of the 21 microsatellite loci tested, only ten were polymorphic and exhibited very low levels of genetic diversity. Both individual and frequency-based approaches suggest very low and non-significant genetic differentiation of the Mekong dolphin population. Evidence for recent bottlenecks was equivocal. Some results suggested a recent exponential decline in the Mekong dolphin population, with the current size being only 5.2% of the ancestral population. In order for the Mekong dolphin population to have any potential for long-term survival, it is imperative that management priorities focus on preventing any further population fragmentation or genetic loss, reducing or eliminating anthropogenic threats, and promoting connectivity between all subpopulations.

  20. Genetic variability in mitochondrial and nuclear genes of Larus dominicanus (Charadriiformes, Laridae from the Brazilian coast

    Directory of Open Access Journals (Sweden)

    Gisele Pires de Mendonça Dantas

    2012-01-01

    Full Text Available Several phylogeographic studies of seabirds have documented low genetic diversity that has been attributed to bottleneck events or individual capacity for dispersal. Few studies have been done in seabirds on the Brazilian coast and all have shown low genetic differentiation on a wide geographic scale. The Kelp Gull is a common species with a wide distribution in the Southern Hemisphere. In this study, we used mitochondrial and nuclear markers to examine the genetic variability of Kelp Gull populations on the Brazilian coast and compared this variability with that of sub-Antarctic island populations of this species. Kelp Gulls showed extremely low genetic variability for mitochondrial markers (cytb and ATPase and high diversity for a nuclear locus (intron 7 of the β-fibrinogen. The intraspecific evolutionary history of Kelp Gulls showed that the variability found in intron 7 of the β-fibrinogen gene was compatible with the variability expected under neutral evolution but suggested an increase in population size during the last 10,000 years. However, none of the markers revealed evidence of a bottleneck population. These findings indicate that the recent origin of Kelp Gulls is the main explanation for their nuclear diversity, although selective pressure on the mtDNA of this species cannot be discarded.

  1. Effects of Freshwater Pollution on the Genetics of Zebra Mussels (Dreissena polymorpha at the Molecular and Population Level

    Directory of Open Access Journals (Sweden)

    Emilia G. Thomas

    2014-01-01

    Full Text Available Revealing long-term effects of contaminants on the genetic structure of organisms inhabiting polluted environments should encompass analyses at the population, molecular, and cellular level. Following this concept, we studied the genetic constitution of zebra mussel populations from a polluted (Dp and reference sites (Cl at the river Drava, Croatia, and applied microsatellite and DNA damage analyses (Comet assay, micronucleus test (MNT. Additionally, mussels from both populations were exposed to polluted wastewater in the laboratory for three days, and DNA damage was analyzed to evaluate acclimatization and genetic adaptation of the investigated populations to the polluted environment. The two populations differed in their genetic constitution. Microsatellite analysis suggested that Dp had undergone a genetic bottleneck. Comet assay did not indicate any difference in DNA damage between the two populations, but MNT revealed that Dp had an increased percentage of micronuclei in hemocytes in comparison to Cl. The laboratory experiment revealed that Dp had a lower percentage of tail DNA and a higher percentage of micronuclei than Cl. These differences between populations were possibly caused by an overall decreased fitness of Dp due to genetic drift and by an enhanced DNA repair mechanism due to acclimatization to pollution in the source habitat.

  2. Effects of freshwater pollution on the genetics of zebra mussels (Dreissena polymorpha) at the molecular and population level.

    Science.gov (United States)

    Thomas, Emilia G; Srut, Maja; Stambuk, Anamaria; Klobučar, Göran I V; Seitz, Alfred; Griebeler, Eva Maria

    2014-01-01

    Revealing long-term effects of contaminants on the genetic structure of organisms inhabiting polluted environments should encompass analyses at the population, molecular, and cellular level. Following this concept, we studied the genetic constitution of zebra mussel populations from a polluted (Dp) and reference sites (Cl) at the river Drava, Croatia, and applied microsatellite and DNA damage analyses (Comet assay, micronucleus test (MNT)). Additionally, mussels from both populations were exposed to polluted wastewater in the laboratory for three days, and DNA damage was analyzed to evaluate acclimatization and genetic adaptation of the investigated populations to the polluted environment. The two populations differed in their genetic constitution. Microsatellite analysis suggested that Dp had undergone a genetic bottleneck. Comet assay did not indicate any difference in DNA damage between the two populations, but MNT revealed that Dp had an increased percentage of micronuclei in hemocytes in comparison to Cl. The laboratory experiment revealed that Dp had a lower percentage of tail DNA and a higher percentage of micronuclei than Cl. These differences between populations were possibly caused by an overall decreased fitness of Dp due to genetic drift and by an enhanced DNA repair mechanism due to acclimatization to pollution in the source habitat.

  3. Historical and contemporary population genetic connectivity of the European short-snouted seahorse Hippocampus hippocampus and implications for management.

    Science.gov (United States)

    Woodall, L C; Koldewey, H J; Shaw, P W

    2011-06-01

    This first genetic study of Hippocampus hippocampus covers the species' entire geographic range and employs two mtDNA markers (control region and cytochrome b) to establish patterns of population structuring. A total of 255 specimens from 21 locations were used to obtain 89 concatenated haplotypes. The common haplotype was present in all but one population, however, most haplotypes were unique. The haplotype network had a star-like construction, suggesting expansion from a bottleneck event. F(ST) and AMOVA revealed population subdivision into three geographic regions (English Channel + Bay of Biscay, Mediterranean Sea + Atlantic Ocean Iberian coast + Macaronesian Islands, and West Africa) with barriers to gene flow indentified at Cape Finisterre and the Cape Verde frontal zone. Neutrality tests and nested clade analysis suggest a complex demographic history, with both historic events and contemporary processes shaping patterns of genetic differentiation. The genetic population subdivision detected in this study indicates that H. hippocampus should be managed as three separate units. This is especially pertinent as H. hippocampus populations within the West African region are the only ones known to be specifically targeted for exploitation. © 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.

  4. Change in genetic size of small-closed populations: lessons from a domestic mammal population

    Directory of Open Access Journals (Sweden)

    Farhad Ghafouri-Kesbi

    2010-01-01

    Full Text Available The aim of this study was to monitor changes in genetic size of a small-closed population of Iranian Zandi sheep, by using pedigree information from animals born between 1991 and 2005. The genetic size was assessed by using measures based on the probability of identity-by-descend of genes (coancestry, f, and effective population size, Ne, as well as measures based on probability of gene origin (effective number of founders, f e, effective number of founder genomes, f g, and effective number of non-founder genomes, f ne. Average coancestry, or the degree of genetic similarity of individuals, increased from 0.81% to 1.44% during the period 1993 to 2005, at the same time that Ne decreased from 263 to 93. The observed trend for f e was irregular throughout the experiment in a way that f e was 68, 87, 77, 92, and 80 in 1993, 1996, 1999, 2002, and 2005, respectively. Simultaneously, f g, the most informative effective number, decreased from 61 to 35. The index of genetic diversity (GD which was obtained from estimates of f g,decreased about 2% throughout the period studied. In addition, a noticeable reduction was observed in the estimates of f ne from 595 in 1993 to 61 in 2005. The higher than 1 ratio of f e to f g indicated the presence of bottlenecks and genetic drift in the development of this population of Zandi sheep. From 1993 to 1999, f ne was much higher than f e, thereby indicating that with respect to loss of genetic diversity, the unequal contribution of founders was more important than the random genetic drift in non-founder generations. Subsequently, random genetic drift in non-founder generations was the major reason for f e> f ne. The minimization of average coancestry in new reproductive individuals was recommended as a means of preserving the population against a further loss in genetic diversity.

  5. Change in genetic size of small-closed populations: Lessons from a domestic mammal population.

    Science.gov (United States)

    Ghafouri-Kesbi, Farhad

    2010-10-01

    The aim of this study was to monitor changes in genetic size of a small-closed population of Iranian Zandi sheep, by using pedigree information from animals born between 1991 and 2005. The genetic size was assessed by using measures based on the probability of identity-by-descend of genes (coancestry, f, and effective population size, N(e) ), as well as measures based on probability of gene origin (effective number of founders, f(e) , effective number of founder genomes, f(g) , and effective number of non-founder genomes, f(ne) ). Average coancestry, or the degree of genetic similarity of individuals, increased from 0.81% to 1.44% during the period 1993 to 2005, at the same time that N(e) decreased from 263 to 93. The observed trend for f(e) was irregular throughout the experiment in a way that f(e) was 68, 87, 77, 92, and 80 in 1993, 1996, 1999, 2002, and 2005, respectively. Simultaneously, f(g) , the most informative effective number, decreased from 61 to 35. The index of genetic diversity (GD) which was obtained from estimates of f(g) , decreased about 2% throughout the period studied. In addition, a noticeable reduction was observed in the estimates of f(ne) from 595 in 1993 to 61 in 2005. The higher than 1 ratio of f(e) to f(g) indicated the presence of bottlenecks and genetic drift in the development of this population of Zandi sheep. From 1993 to 1999, f(ne) was much higher than f(e) , thereby indicating that with respect to loss of genetic diversity, the unequal contribution of founders was more important than the random genetic drift in non-founder generations. Subsequently, random genetic drift in non-founder generations was the major reason for f(e) > f(ne) . The minimization of average coancestry in new reproductive individuals was recommended as a means of preserving the population against a further loss in genetic diversity.

  6. Beyond a mask and against the bottleneck: retroactive dual-task interference during working memory consolidation of a masked visual target.

    Science.gov (United States)

    Nieuwenstein, Mark; Wyble, Brad

    2014-06-01

    While studies on visual memory commonly assume that the consolidation of a visual stimulus into working memory is interrupted by a trailing mask, studies on dual-task interference suggest that the consolidation of a stimulus can continue for several hundred milliseconds after a mask. As a result, estimates of the time course of working memory consolidation differ more than an order of magnitude. Here, we contrasted these opposing views by examining if and for how long the processing of a masked display of visual stimuli can be disturbed by a trailing 2-alternative forced choice task (2-AFC; a color discrimination task or a visual or auditory parity judgment task). The results showed that the presence of the 2-AFC task produced a pronounced retroactive interference effect that dissipated across stimulus onset asynchronies of 250-1,000 ms, indicating that the processing elicited by the 2-AFC task interfered with the gradual consolidation of the earlier shown stimuli. Furthermore, this interference effect occurred regardless of whether the to-be-remembered stimuli comprised a string of letters or an unfamiliar complex visual shape, and it occurred regardless of whether these stimuli were masked. Conversely, the interference effect was reduced when the memory load for the 1st task was reduced, or when the 2nd task was a color detection task that did not require decision making. Taken together, these findings show that the formation of a durable and consciously accessible working memory trace for a briefly shown visual stimulus can be disturbed by a trailing 2-AFC task for up to several hundred milliseconds after the stimulus has been masked. By implication, the current findings challenge the common view that working memory consolidation involves an immutable central processing bottleneck, and they also make clear that consolidation does not stop when a stimulus is masked. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  7. Bottlenecks and Solution of New Urbanization Construction%我国新型城镇化建设瓶颈及解决途径

    Institute of Scientific and Technical Information of China (English)

    徐君; 王育红; 张娜

    2014-01-01

    分析我国城镇化建设存在的土地浪费严重、户籍制度障碍、社会保障不足、公共服务不均等诸多问题,并从因地制宜进行城镇化、大中小城市合理发展、新四化协调发展、土地与户籍制度改革、完善社会保障、公共服务均等化、生态环境保护、区域协调发展和政府调控与管理九个方面提出我国新型城镇化建设路径。%This paper analyzed some bottlenecks of new urbanization development such as severe waste of land,residence system obstacle,lack of social security,public service inequality,and so on.Then,the solutions of the new urbanization are proposed from nine aspects including urbanization based on local conditions,the reasonable development of large,medi-um and small cities,new modernization coordinated development,system reform of land and household register,perfection of the social security,equalization of public services,protection of ecological environment,regional coordinated develop-ment,administration and regulation of government.

  8. Policy redesign for solving the financial bottleneck in demand side management (DSM) in China

    International Nuclear Information System (INIS)

    Yu, Yongzhen

    2010-01-01

    DSM is one of the best and most practical policy tools for China to balance environmental protection and economic growth. However, the bottleneck lies in the lack of long-term, stable, sufficient and gradually increasing funds to flow into DSM projects. The author redesigns the practical 'system benefit charge (SBC)' policy, which will provide long-term and stable funding for DSM, the policy to facilitate the financial support from banking sector and capital market, and investigates the possibility of DSM funding from CDM projects. SBC is the best way to boost long-term stable and sufficient funding for DSM at present in China. The current low inflation rate and natural resource price are favored to expedite the implementation of SBC and DSM developments. With regard to the uneven development, China needs to design relative policies to offset the impact in different areas, such as tax reduction and fiscal subsides. It is time for China to develop a definite and clear target and timetable to implement DSM, which will give the public and enterprises a definite and clear expectation for the future. The government should publicize a clear and integrated DSM development plan and relative policy outline in the near, medium, and long term. (author)

  9. Population genetic structure of the endemic rosewoods Dalbergia cochinchinensis and D. oliveri at a regional scale reflects the Indochinese landscape and life-history traits

    DEFF Research Database (Denmark)

    Hartvig, Ida; So, Thea; Changtragoon, Suchitra

    2018-01-01

    of the distribution area, particularly in Cambodia. We suggest that this pattern is ancient, reflecting the demographic history of the species and possible location of refugia during earlier time periods with limited forest cover, which was supported by signs of old genetic bottlenecks. The D. oliveri populations had......Indochina is a biodiversity hot spot and harbors a high number of endemic species, most of which are poorly studied. This study explores the genetic structure and reproductive system of the threatened endemic timber species Dalbergia cochinchinensis and Dalbergia oliveri using microsatellite data...... from populations across Indochina and relates it to landscape characteristics and life-history traits. We found that the major water bodies in the region, Mekong and Tonle Sap, represented barriers to gene flow and that higher levels of genetic diversity were found in populations in the center...

  10. Addressing an I/O Bottleneck in a Web-Based CERES QC Tool

    Science.gov (United States)

    Heckert, E.; Sun-Mack, S.; Chen, Y.; Chu, C.; Smith, R. A.

    2016-12-01

    In this poster, we explore the technologies we have used to overcome the problem of transmitting and analyzing large datasets in our web-based CERES Quality Control tool and consider four technologies to potentially adopt for future performance improvements. The CERES team uses this tool to validate pixel-level data from Terra, Aqua, SNPP, MSG, MTSAT, and many geostationary GOES satellites, as well as to develop cloud retrieval algorithms. The tool includes a histogram feature that allows the user to aggregate data from many different timestamps and different scenes globally or locally selected by the user by drawing bounding boxes. In order to provide a better user experience, the tool passes a large amount of data to the user's browser. The browser then processes the data in order to present it to users in various formats, for example as a histogram. In addition to using multiple servers to subset data and pass a smaller set of data to the browser, the tool also makes use of a compression technology, Gzip, to reduce the size of the data. However, sometimes the application in the browser is still slow when dealing with these large sets of data due to the delay in the browser receiving the server's response. To address this I/O bottleneck, we will investigate four alternatives and present the results in this poster: 1) sending uncompressed data, 2) ESRI's Limited Error Raster Compression (LERC), 3) Gzip, and 4) WebSocket protocol. These approaches are compared to each other and to the uncompressed control to determine the optimal solution.

  11. Several aspects of descriptive epidemiology of hematological malignancies in adult population of Ukraine, Belarus and Russian Federation after Chornobyl accident.

    Science.gov (United States)

    Guslitser, N; Zavelevich, M P; Koval, S V; Gluzman, D F

    2016-12-01

    Chornobyl impact on the health of adult population in Ukraine, Belarus and Russian Federation was a subject of several studies. However, the studies of the effects of Chornobyl on leukemia in adult populations in post-Soviet countries are scarce and the results are contradictory up to present. The results of the epidemiological studies of the oncohematological consequences of Chornobyl accident are briefly reviewed with particular focus on pre-Chornobyl and post-Chornobyl trends in leukemia incidence in Ukraine, Belarus and Russian Federation as well as in small territories of these countries with various levels of radionuclide contamination. This article is a part of a Special Issue entitled "The Chornobyl Nuclear Accident: Thirty Years After".

  12. Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.

    Science.gov (United States)

    Senol Cali, Damla; Kim, Jeremie S; Ghose, Saugata; Alkan, Can; Mutlu, Onur

    2018-04-02

    Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance, as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we (1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and (2) provide guidelines for determining the appropriate tools for each step. Based on our analyses, we make four key observations: (1) the choice of the tool for basecalling plays a critical role in overcoming the high error rates of nanopore sequencing technology. (2) Read-to-read overlap finding tools, GraphMap and Minimap, perform similarly in terms of accuracy. However, Minimap has a lower memory usage, and it is faster than GraphMap. (3) There is a trade-off between accuracy and performance when deciding on the appropriate tool for the assembly step. The fast but less accurate assembler Miniasm can be used for quick initial assembly, and further polishing can be applied on top of it to increase the accuracy, which leads to faster overall assembly. (4) The state-of-the-art polishing tool, Racon, generates high-quality consensus sequences while providing a significant speedup over another polishing tool, Nanopolish. We analyze various combinations of different tools and expose the trade-offs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious

  13. Food insecurity among people with severe mental disorder in a rural Ethiopian setting: a comparative, population-based study.

    Science.gov (United States)

    Tirfessa, K; Lund, C; Medhin, G; Hailemichael, Y; Fekadu, A; Hanlon, C

    2017-11-16

    In low-income African countries, ensuring food security for all segments of the population is a high priority. Mental illness is associated consistently with poverty, but there is little evidence regarding the association with food insecurity. The aim of this study was to compare the levels of food insecurity in people with severe mental disorders (SMD) with the general population in a rural African setting with a high burden of food insecurity. Households of 292 community-ascertained people with a specialist-confirmed diagnosis of SMD (including schizophrenia and bipolar disorder) were compared with 284 households without a person with SMD in a rural district in south Ethiopia. At the time of the study, no mental health services were available within the district. Food insecurity was measured using a validated version of the Household Food Insecurity Access Scale. Disability was measured using the World Health Organisation Disability Assessment Schedule 2.0. Severe household food insecurity was reported by 32.5% of people with SMD and 15.9% of respondents from comparison households: adjusted odds ratio 2.82 (95% confidence interval 1.62 to 4.91). Higher annual income was associated independently with lower odds of severe food insecurity. When total disability scores were added into the model, the association between SMD and food insecurity became non-significant, indicating a possible mediating role of disability. Efforts to alleviate food insecurity need to target people with SMD as a vulnerable group. Addressing the disabling effects of SMD would also be expected to reduce food insecurity. Access to mental health care integrated into primary care is being expanded in this district as part of the Programme for Improving Mental health carE (PRIME). The impact of treatment on disability and food insecurity will be evaluated.

  14. At the Origin of a Worldwide Invasion: Unraveling the Genetic Makeup of the Caribbean Bridgehead Populations of the Dengue Vector Aedes aegypti.

    Science.gov (United States)

    Sherpa, Stéphanie; Rioux, Delphine; Goindin, Daniella; Fouque, Florence; François, Olivier; Després, Laurence

    2018-01-01

    Human-driven global environmental changes have considerably increased the risk of biological invasions, especially the spread of human parasites and their vectors. Among exotic species that have major impacts on public health, the dengue fever mosquito Aedes aegypti originating from Africa has spread worldwide during the last three centuries. Although considerable progress has been recently made in understanding the history of this invasion, the respective roles of human and abiotic factors in shaping patterns of genetic diversity remain largely unexplored. Using a genome-wide sample of genetic variants (3,530 ddRAD SNPs), we analyzed the genetic structure of Ae. aegypti populations in the Caribbean, the first introduced territories in the Americas. Fourteen populations were sampled in Guyane and in four islands of the Antilles that differ in climatic conditions, intensity of urbanization, and vector control history. The genetic diversity in the Caribbean was low (He = 0.14-0.17), as compared with a single African collection from Benin (He = 0.26) and site-frequency spectrum analysis detected an ancient bottleneck dating back ∼300 years ago, supporting a founder event during the introduction of Ae. aegypti. Evidence for a more recent bottleneck may be related to the eradication program undertaken on the American continent in the 1950s. Among 12 loci detected as FST-outliers, two were located in candidate genes for insecticide resistance (cytochrome P450 and voltage-gated sodium channel). Genome-environment association tests identified additional loci associated with human density and/or deltamethrin resistance. Our results highlight the high impact of human pressures on the demographic history and genetic variation of Ae. aegypti Caribbean populations. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  15. Historical and contemporary DNA indicate fisher decline and isolation occurred prior to the European settlement of California.

    Directory of Open Access Journals (Sweden)

    Jody M Tucker

    Full Text Available Establishing if species contractions were the result of natural phenomena or human induced landscape changes is essential for managing natural populations. Fishers (Martes pennanti in California occur in two geographically and genetically isolated populations in the northwestern mountains and southern Sierra Nevada. Their isolation is hypothesized to have resulted from a decline in abundance and distribution associated with European settlement in the 1800s. However, there is little evidence to establish that fisher occupied the area between the two extant populations at that time. We analyzed 10 microsatellite loci from 275 contemporary and 21 historical fisher samples (1880-1920 to evaluate the demographic history of fisher in California. We did not find any evidence of a recent (post-European bottleneck in the northwestern population. In the southern Sierra Nevada, genetic subdivision within the population strongly influenced bottleneck tests. After accounting for genetic subdivision, we found a bottleneck signal only in the northern and central portions of the southern Sierra Nevada, indicating that the southernmost tip of these mountains may have acted as a refugium for fisher during the anthropogenic changes of the late 19(th and early 20(th centuries. Using a coalescent-based Bayesian analysis, we detected a 90% decline in effective population size and dated the time of decline to over a thousand years ago. We hypothesize that fisher distribution in California contracted to the two current population areas pre-European settlement, and that portions of the southern Sierra Nevada subsequently experienced another more recent bottleneck post-European settlement.

  16. An automated microfluidic multiplexer for fast delivery of C. elegans populations from multiwells.

    Directory of Open Access Journals (Sweden)

    Navid Ghorashian

    Full Text Available Automated biosorter platforms, including recently developed microfluidic devices, enable and accelerate high-throughput and/or high-resolution bioassays on small animal models. However, time-consuming delivery of different organism populations to these systems introduces a major bottleneck to executing large-scale screens. Current population delivery strategies rely on suction from conventional well plates through tubing periodically exposed to air, leading to certain disadvantages: 1 bubble introduction to the sample, interfering with analysis in the downstream system, 2 substantial time drain from added bubble-cleaning steps, and 3 the need for complex mechanical systems to manipulate well plate position. To address these concerns, we developed a multiwell-format microfluidic platform that can deliver multiple distinct animal populations from on-chip wells using multiplexed valve control. This Population Delivery Chip could operate autonomously as part of a relatively simple setup that did not require any of the major mechanical moving parts typical of plate-handling systems to address a given well. We demonstrated automatic serial delivery of 16 distinct C. elegans worm populations to a single outlet without introducing any bubbles to the samples, causing cross-contamination, or damaging the animals. The device achieved delivery of more than 90% of the population preloaded into a given well in 4.7 seconds; an order of magnitude faster than delivery modalities in current use. This platform could potentially handle other similarly sized model organisms, such as zebrafish and drosophila larvae or cellular micro-colonies. The device's architecture and microchannel dimensions allow simple expansion for processing larger numbers of populations.

  17. Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates

    Science.gov (United States)

    Charruau, P; Fernandes, C; Orozco-terWengel, P; Peters, J; Hunter, L; Ziaie, H; Jourabchian, A; Jowkar, H; Schaller, G; Ostrowski, S; Vercammen, P; Grange, T; Schlötterer, C; Kotze, A; Geigl, E-M; Walzer, C; Burger, P A

    2011-01-01

    The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity. PMID:21214655

  18. Is the Partners in Recovery program connecting with the intended population of people living with severe and persistent mental illness? What are their prioritised needs?

    Science.gov (United States)

    Hancock, Nicola; Smith-Merry, Jennifer; Gillespie, James A; Yen, Ivy

    2017-10-01

    Objective The Partners in Recovery (PIR) program is an Australian government initiative designed to make the mental health and social care sectors work in more coordinated ways to meet the needs of those with severe and complex mental illness. Herein we reflect on demographic data collected during evaluation of PIR implementation in two Western Sydney sites. The aims of the present study were to: (1) explore whether two Sydney-based PIR programs had recruited their intended population, namely people living with severe and persistent mental illness; and (2) learn more about this relatively unknown population and their self-identified need priorities. Methods Routinely collected initial client assessment data were analysed descriptively. Results The data suggest that the two programs are engaging the intended population. The highest unmet needs identified included psychological distress, lack of daytime activities and company, poor physical health and inadequate accommodation. Some groups remain hard to connect, including people from Aboriginal and other culturally diverse communities. Conclusions The data confirm that the PIR program, at least in the two regions evaluated, is mostly reaching its intended audience. Some data were being collected inconsistently, limiting the usefulness of the data and the ability to build on PIR findings to develop ongoing support for this population. What is known about the topic? PIR is a unique national program funded to engage with and address the needs of Australians living with severe and persistent mental illness by facilitating service access. What does this paper add? This paper reports on recruitment of people living with severe and persistent mental illness, their need priorities and data collection. These are three central elements to successful roll-out of the much anticipated mental health component of the National Disability Insurance Scheme, as well as ongoing PIR operation. What are the implications for practitioners

  19. Fractured genetic connectivity threatens a southern california puma (Puma concolor population.

    Directory of Open Access Journals (Sweden)

    Holly B Ernest

    Full Text Available Pumas (Puma concolor; also known as mountain lions and cougars in southern California live among a burgeoning human population of roughly 20 million people. Yet little is known of the consequences of attendant habitat loss and fragmentation, and human-caused puma mortality to puma population viability and genetic diversity. We examined genetic status of pumas in coastal mountains within the Peninsular Ranges south of Los Angeles, in San Diego, Riverside, and Orange counties. The Santa Ana Mountains are bounded by urbanization to the west, north, and east, and are separated from the eastern Peninsular Ranges to the southeast by a ten lane interstate highway (I-15. We analyzed DNA samples from 97 pumas sampled between 2001 and 2012. Genotypic data for forty-six microsatellite loci revealed that pumas sampled in the Santa Ana Mountains (n = 42 displayed lower genetic diversity than pumas from nearly every other region in California tested (n = 257, including those living in the Peninsular Ranges immediately to the east across I-15 (n = 55. Santa Ana Mountains pumas had high average pairwise relatedness, high individual internal relatedness, a low estimated effective population size, and strong evidence of a bottleneck and isolation from other populations in California. These and ecological findings provide clear evidence that Santa Ana Mountains pumas have been experiencing genetic impacts related to barriers to gene flow, and are a warning signal to wildlife managers and land use planners that mitigation efforts will be needed to stem further genetic and demographic decay in the Santa Ana Mountains puma population.

  20. Solar radiation uncorks the lignin bottleneck on plant litter decomposition in terrestrial ecosystems

    Science.gov (United States)

    Austin, A.; Ballare, C. L.; Méndez, M. S.

    2015-12-01

    Plant litter decomposition is an essential process in the first stages of carbon and nutrient turnover in terrestrial ecosystems, and together with soil microbial biomass, provide the principal inputs of carbon for the formation of soil organic matter. Photodegradation, the photochemical mineralization of organic matter, has been recently identified as a mechanism for previously unexplained high rates of litter mass loss in low rainfall ecosystems; however, the generality of this process as a control on carbon cycling in terrestrial ecosystems is not known, and the indirect effects of photodegradation on biotic stimulation of carbon turnover have been debated in recent studies. We demonstrate that in a wide range of plant species, previous exposure to solar radiation, and visible light in particular, enhanced subsequent biotic degradation of leaf litter. Moreover, we demonstrate that the mechanism for this enhancement involves increased accessibility for microbial enzymes to plant litter carbohydrates due to a reduction in lignin content. Photodegradation of plant litter reduces the structural and chemical bottleneck imposed by lignin in secondary cell walls. In litter from woody plant species, specific interactions with ultraviolet radiation obscured facilitative effects of solar radiation on biotic decomposition. The generalized positive effect of solar radiation exposure on subsequent microbial activity is mediated by increased accessibility to cell wall polysaccharides, which suggests that photodegradation is quantitatively important in determining rates of mass loss, nutrient release and the carbon balance in a broad range of terrestrial ecosystems.

  1. Severe Anemia in Malawian Children

    NARCIS (Netherlands)

    Calis, J.C.J.; Kamija, S.P.; Faragher, E.B.; Brabin, B.J.; Bates, I.; Cuevas, L.E.; Haan, de R.J.; Phiri, A.I.; Malange, P.; Khoka, M.; Hulshof, P.J.M.; Lieshout, L.; Beld, M.G.H.M.; Teo, Y.Y.; Rockett, K.A.; Richardson, A.; Kwiatkowski, D.P.; Molyneux, M.E.; Hensbroek, van M.B.

    2008-01-01

    Background Severe anemia is a major cause of sickness and death in African children, yet the causes of anemia in this population have been inadequately studied. Methods We conducted a case¿control study of 381 preschool children with severe anemia (hemoglobin concentration,

  2. Application of the asthma phenotype algorithm from the Severe Asthma Research Program to an urban population.

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    Paru Patrawalla

    Full Text Available Identification and characterization of asthma phenotypes are challenging due to disease complexity and heterogeneity. The Severe Asthma Research Program (SARP used unsupervised cluster analysis to define 5 phenotypically distinct asthma clusters that they replicated using 3 variables in a simplified algorithm. We evaluated whether this simplified SARP algorithm could be used in a separate and diverse urban asthma population to recreate these 5 phenotypic clusters.The SARP simplified algorithm was applied to adults with asthma recruited to the New York University/Bellevue Asthma Registry (NYUBAR to classify patients into five groups. The clinical phenotypes were summarized and compared.Asthma subjects in NYUBAR (n = 471 were predominantly women (70% and Hispanic (57%, which were demographically different from the SARP population. The clinical phenotypes of the five groups generated by the simplified SARP algorithm were distinct across groups and distributed similarly to those described for the SARP population. Groups 1 and 2 (6 and 63%, respectively had predominantly childhood onset atopic asthma. Groups 4 and 5 (20% were older, with the longest duration of asthma, increased symptoms and exacerbations. Group 4 subjects were the most atopic and had the highest peripheral eosinophils. Group 3 (10% had the least atopy, but included older obese women with adult-onset asthma, and increased exacerbations.Application of the simplified SARP algorithm to the NYUBAR yielded groups that were phenotypically distinct and useful to characterize disease heterogeneity. Differences across NYUBAR groups support phenotypic variation and support the use of the simplified SARP algorithm for classification of asthma phenotypes in future prospective studies to investigate treatment and outcome differences between these distinct groups.Clinicaltrials.gov NCT00212537.

  3. Are habitat fragmentation, local adaptation and isolation-by-distance driving population divergence in wild rice Oryza rufipogon?

    Science.gov (United States)

    Zhao, Yao; Vrieling, Klaas; Liao, Hui; Xiao, Manqiu; Zhu, Yongqing; Rong, Jun; Zhang, Wenju; Wang, Yuguo; Yang, Ji; Chen, Jiakuan; Song, Zhiping

    2013-11-01

    Habitat fragmentation weakens the connection between populations and is accompanied with isolation by distance (IBD) and local adaptation (isolation by adaptation, IBA), both leading to genetic divergence between populations. To understand the evolutionary potential of a population and to formulate proper conservation strategies, information on the roles of IBD and IBA in driving population divergence is critical. The putative ancestor of Asian cultivated rice (Oryza sativa) is endangered in China due to habitat loss and fragmentation. We investigated the genetic variation in 11 Chinese Oryza rufipogon populations using 79 microsatellite loci to infer the effects of habitat fragmentation, IBD and IBA on genetic structure. Historical and current gene flows were found to be rare (mh  = 0.0002-0.0013, mc  = 0.007-0.029), indicating IBD and resulting in a high level of population divergence (FST  = 0.343). High within-population genetic variation (HE  = 0.377-0.515), relatively large effective population sizes (Ne  = 96-158), absence of bottlenecks and limited gene flow were found, demonstrating little impact of recent habitat fragmentation on these populations. Eleven gene-linked microsatellite loci were identified as outliers, indicating local adaptation. Hierarchical AMOVA and partial Mantel tests indicated that population divergence of Chinese O. rufipogon was significantly correlated with environmental factors, especially habitat temperature. Common garden trials detected a significant adaptive population divergence associated with latitude. Collectively, these findings imply that IBD due to historical rather than recent fragmentation, followed by local adaptation, has driven population divergence in O. rufipogon. © 2013 John Wiley & Sons Ltd.

  4. Gene flow connects coastal populations of a habitat specialist, the Clapper Rail Rallus crepitans

    Science.gov (United States)

    Coster, Stephanie S.; Welsh, Amy B.; Costanzo, Gary R.; Harding, Sergio R.; Anderson, James T.; Katzner, Todd

    2018-01-01

    Examining population genetic structure can reveal patterns of reproductive isolation or population mixing and inform conservation management. Some avian species are predicted to exhibit minimal genetic differentiation among populations as a result of the species high mobility, with habitat specialists tending to show greater fine‐scale genetic structure. To explore the relationship between habitat specialization and gene flow, we investigated the genetic structure of a saltmarsh specialist with high potential mobility across a wide geographic range of fragmented habitat. Little variation among mitochondrial sequences (620 bp from ND2) was observed among 149 individual Clapper Rails Rallus crepitans sampled along the Atlantic coast of North America, with the majority of individuals at all sampling sites sharing a single haplotype. Genotyping of nine microsatellite loci across 136 individuals revealed moderate genetic diversity, no evidence of bottlenecks, and a weak pattern of genetic differentiation that increased with geographic distance. Multivariate analyses, Bayesian clustering and an AMOVA all suggested a lack of genetic structuring across the North American Atlantic coast, with all individuals grouped into a single interbreeding population. Spatial autocorrelation analyses showed evidence of weak female philopatry and a lack of male philopatry. We conclude that high gene flow connecting populations of this habitat specialist may result from the interaction of ecological and behavioral factors that promote dispersal and limit natal philopatry and breeding‐site fidelity. As climate change threatens saltmarshes, the genetic diversity and population connectivity of Clapper Rails may promote resilience of their populations. This finding helps inform about potential fates of other similarly behaving saltmarsh specialists on the Atlantic coast.

  5. Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish.

    Science.gov (United States)

    Coleman, R A; Gauffre, B; Pavlova, A; Beheregaray, L B; Kearns, J; Lyon, J; Sasaki, M; Leblois, R; Sgro, C; Sunnucks, P

    2018-01-12

    Habitat loss and fragmentation often result in small, isolated populations vulnerable to environmental disturbance and loss of genetic diversity. Low genetic diversity can increase extinction risk of small populations by elevating inbreeding and inbreeding depression, and reducing adaptive potential. Due to their linear nature and extensive use by humans, freshwater ecosystems are especially vulnerable to habitat loss and fragmentation. Although the effects of fragmentation on genetic structure have been extensively studied in migratory fishes, they are less understood in low-mobility species. We estimated impacts of instream barriers on genetic structure and diversity of the low-mobility river blackfish (Gadopsis marmoratus) within five streams separated by weirs or dams constructed 45-120 years ago. We found evidence of small-scale (barriers, as expected for a fish with low mobility. Genetic diversity was lower above barriers in small streams only, regardless of barrier age. In particular, one isolated population showed evidence of a recent bottleneck and inbreeding. Differentiation above and below the barrier (F ST  = 0.13) was greatest in this stream, but in other streams did not differ from background levels. Spatially explicit simulations suggest that short-term barrier effects would not be detected with our data set unless effective population sizes were very small (barriers is reduced and requires more genetic markers compared to panmictic populations. We also demonstrate the importance of accounting for natural population genetic structure in fragmentation studies.

  6. Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency.

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    Max Schelker

    2016-10-01

    Full Text Available After endocytic uptake, influenza viruses transit early endosomal compartments and eventually reach late endosomes. There, the viral glycoprotein hemagglutinin (HA triggers fusion between endosomal and viral membrane, a critical step that leads to release of the viral segmented genome destined to reach the cell nucleus. Endosomal maturation is a complex process involving acidification of the endosomal lumen as well as endosome motility along microtubules. While the pH drop is clearly critical for the conformational change and membrane fusion activity of HA, the effect of intracellular transport dynamics on the progress of infection remains largely unclear. In this study, we developed a comprehensive mathematical model accounting for the first steps of influenza virus infection. We calibrated our model with experimental data and challenged its predictions using recombinant viruses with altered pH sensitivity of HA. We identified the time point of virus-endosome fusion and thereby the diffusion distance of the released viral genome to the nucleus as a critical bottleneck for efficient virus infection. Further, we concluded and supported experimentally that the viral RNA is subjected to cytosolic degradation strongly limiting the probability of a successful genome import into the nucleus.

  7. Gene and process level modulation to overcome the bottlenecks of recombinant proteins expression in Pichia pastoris.

    Science.gov (United States)

    Prabhu, Ashish A; Boro, Bibari; Bharali, Biju; Chakraborty, Shuchishloka; Dasu, V Venkata

    2018-03-28

    Process development involving system metabolic engineering and bioprocess engineering has become one of the major thrust for the development of therapeutic proteins or enzymes. Pichia pastoris has emerged as a prominent host for the production of therapeutic protein or enzymes. Despite of producing high protein titers, various cellular and process level bottlenecks hinders the expression of recombinant proteins in P. pastoris. In the present review, we have summarized the recent developments in the expression of foreign proteins in P. pastoris. Further, we have discussed various cellular engineering strategies which include codon optimization, pathway engineering, signal peptide processing, development of protease deficient strain and glyco-engineered strains for the high yield protein secretion of recombinant protein. Bioprocess development of recombinant proteins in large scale bioreactor including medium optimization, optimum feeding strategy and co-substrate feeding in fed batch as well as continuous cultivation have been described. The recent advances in system and synthetic biology studies including metabolic flux analysis in understanding the phenotypic characteristics of recombinant Pichia and genome editing with CRISPR-CAS system have also been summarized. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  8. A population-based nested case control study on recurrent pneumonias in children with severe generalized cerebral palsy: ethical considerations of the design and representativeness of the study sample

    Directory of Open Access Journals (Sweden)

    Benninga Marc A

    2005-07-01

    Full Text Available Abstract Background In children with severe generalized cerebral palsy, pneumonias are a major health issue. Malnutrition, dysphagia, gastro-oesophageal reflux, impaired respiratory function and constipation are hypothesized risk factors. Still, no data are available on the relative contribution of these possible risk factors in the described population. This paper describes the initiation of a study in 194 children with severe generalized cerebral palsy, on the prevalence and on the impact of these hypothesized risk factors of recurrent pneumonias. Methods/Design A nested case-control design with 18 months follow-up was chosen. Dysphagia, respiratory function and constipation will be assessed at baseline, malnutrition and gastro-oesophageal reflux at the end of the follow-up. The study population consists of a representative population sample of children with severe generalized cerebral palsy. Inclusion was done through care-centres in a predefined geographical area and not through hospitals. All measurements will be done on-site which sets high demands on all measurements. If these demands were not met in "gold standard" methods, other methods were chosen. Although the inclusion period was prolonged, the desired sample size of 300 children was not met. With a consent rate of 33%, nearly 10% of all eligible children in the Netherlands are included (n = 194. The study population is subtly different from the non-participants with regard to severity of dysphagia and prevalence rates of pneumonias and gastro-oesophageal reflux. Discussion Ethical issues complicated the study design. Assessment of malnutrition and gastro-oesophageal reflux at baseline was considered unethical, since these conditions can be easily treated. Therefore, we postponed these diagnostics until the end of the follow-up. In order to include a representative sample, all eligible children in a predefined geographical area had to be contacted. To increase the consent rate, on

  9. One-year outcome after first-ever stroke according to stroke subtype, severity, risk factors and pre-stroke treatment. A population-based study from Tartu, Estonia.

    Science.gov (United States)

    Vibo, R; Kõrv, J; Roose, M

    2007-04-01

    The aim of the current study was to evaluate the outcome at 1 year following a first-ever stroke based on a population-based registry from 2001 to 2003 in Tartu, Estonia. The outcome of first-ever stroke was assessed in 433 patients by stroke risk factors, demographic data and stroke severity at onset using the Barthel Index (BI) score and the modified Rankin Score (mRS) at seventh day, 6 months and 1 year. Female sex, older age, blood glucose value >10 mmol/l on admission and more severe stroke on admission were the best predictors of dependency 1 year following the first-ever stroke. At 1 year, the percentage of functionally dependent patients was 20% and the survival rate was 56%. The use of antihypertensive/antithrombotic medication prior to stroke did not significantly affect the outcome. The survival rate of stroke patients in Tartu is lower compared with other studied populations. The outcome of stroke was mainly determined by the initial severity of stroke and by elevated blood glucose value on admission. Patients with untreated hypertension had more severe stroke and trend for unfavourable outcome compared with those who were on treatment.

  10. Severe anemia in Malawian children

    NARCIS (Netherlands)

    Calis, Job C. J.; Phiri, Kamija S.; Faragher, E. Brian; Brabin, Bernard J.; Bates, Imelda; Cuevas, Luis E.; de Haan, Rob J.; Phiri, Ajib I.; Malange, Pelani; Khoka, Mirriam; Hulshof, Paul J. M.; van Lieshout, Lisette; Beld, Marcel G. H. M.; teo, Yik Y.; Rockett, Kirk A.; Richardson, Anna; Kwiatkowski, Dominic P.; Molyneux, Malcolm E.; Boele van Hensbroek, Michael

    2008-01-01

    Background Severe anemia is a major cause of sickness and death in African children, yet the causes of anemia in this population have been inadequately studied. Methods We conducted a case-control study of 381 preschool children with severe anemia (hemoglobin concentration, <5.0 g per deciliter) and

  11. Severe anemia in Malawian children

    NARCIS (Netherlands)

    Calis, Job Cj; Phiri, Kamija S.; Faragher, E. Brian; Brabin, Bernard J.; Bates, Imelda; Cuevas, Luis E.; de Haan, Rob J.; Phiri, Ajib I.; Malange, Pelani; Khoka, Mirriam; Hulshof, Paul Jm; van Lieshout, Lisette; Beld, Marcel Ghm; teo, Yik Y.; Rockett, Kirk A.; Richardson, Anna; Kwiatkowski, Dominic P.; Molyneux, Malcolm E.; van Hensbroek, Michaël Boele

    2016-01-01

    Severe anemia is a major cause of sickness and death in African children, yet the causes of anemia in this population have been inadequately studied. We conducted a case-control study of 381 preschool children with severe anemia (hemoglobin concentration, <5.0 g per deciliter) and 757 preschool

  12. Machine Learning Based Classification of Microsatellite Variation: An Effective Approach for Phylogeographic Characterization of Olive Populations.

    Science.gov (United States)

    Torkzaban, Bahareh; Kayvanjoo, Amir Hossein; Ardalan, Arman; Mousavi, Soraya; Mariotti, Roberto; Baldoni, Luciana; Ebrahimie, Esmaeil; Ebrahimi, Mansour; Hosseini-Mazinani, Mehdi

    2015-01-01

    Finding efficient analytical techniques is overwhelmingly turning into a bottleneck for the effectiveness of large biological data. Machine learning offers a novel and powerful tool to advance classification and modeling solutions in molecular biology. However, these methods have been less frequently used with empirical population genetics data. In this study, we developed a new combined approach of data analysis using microsatellite marker data from our previous studies of olive populations using machine learning algorithms. Herein, 267 olive accessions of various origins including 21 reference cultivars, 132 local ecotypes, and 37 wild olive specimens from the Iranian plateau, together with 77 of the most represented Mediterranean varieties were investigated using a finely selected panel of 11 microsatellite markers. We organized data in two '4-targeted' and '16-targeted' experiments. A strategy of assaying different machine based analyses (i.e. data cleaning, feature selection, and machine learning classification) was devised to identify the most informative loci and the most diagnostic alleles to represent the population and the geography of each olive accession. These analyses revealed microsatellite markers with the highest differentiating capacity and proved efficiency for our method of clustering olive accessions to reflect upon their regions of origin. A distinguished highlight of this study was the discovery of the best combination of markers for better differentiating of populations via machine learning models, which can be exploited to distinguish among other biological populations.

  13. Lack of Population Genetic Structuring in Ocelots (Leopardus pardalis in a Fragmented Landscape

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    Marina G. Figueiredo

    2015-07-01

    Full Text Available Habitat fragmentation can promote patches of small and isolated populations, gene flow disruption between those populations, and reduction of local and total genetic variation. As a consequence, these small populations may go extinct in the long-term. The ocelot (Leopardus pardalis, originally distributed from Texas to southern Brazil and northern Argentina, has been impacted by habitat fragmentation throughout much of its range. To test whether habitat fragmentation has already induced genetic differentiation in an area where this process has been documented for a larger felid (jaguars, we analyzed molecular variation in ocelots inhabiting two Atlantic Forest fragments, Morro do Diabo (MD and Iguaçu Region (IR. Analyses using nine microsatellites revealed mean observed and expected heterozygosity of 0.68 and 0.70, respectively. The MD sampled population showed evidence of a genetic bottleneck under two mutational models (TPM = 0.03711 and SMM = 0.04883. Estimates of genetic structure (FST = 0.027; best fit of k = 1 with STRUCTURE revealed no meaningful differentiation between these populations. Thus, our results indicate that the ocelot populations sampled in these fragments are still not significantly different genetically, a pattern that strongly contrasts with that previously observed in jaguars for the same comparisons. This observation is likely due to a combination of two factors: (i larger effective population size of ocelots (relative to jaguars in each fragment, implying a slower effect of drift-induced differentiation; and (ii potentially some remaining permeability of the anthropogenic matrix for ocelots, as opposed to the observed lack of permeability for jaguars. The persistence of ocelot gene flow between these areas must be prioritized in long-term conservation planning on behalf of these felids.

  14. Severity of cotton whitefly (bemisia tabaci genn.) population with special reference to abiotic factors

    International Nuclear Information System (INIS)

    Zia, K.; Bashir, M.H.; Khan, B.S.; Khan, R.R.; Hafeez, F.

    2013-01-01

    Bemisia tabaci is serious insect and constantly destabilizing the cotton production. The research was conducted to evaluate cotton cultivars (transgenic and non transgenic) for resistance against whitefly and further correlated with weather factors such as temperature, relative humidity and rainfall, during the cropping seasons 2010 and 2011. However, peak population (6.36 per leaf) was recorded from FH-113 followed FH-167 and FH-114, whereas minimum population was recorded from FH-4243 in transgenic group whereas peak population (5.24 per leaf) was recorded from FH- 941 followed by FH-100 and FH- 901 while minimum population was recorded from FH-207, in non transgenic group of cultivars in the year 2010. The incidence and abundance was much high and reaching towards two folds in the year 2011 but the trend of whitefly varied with peak population (11.03 per leaf) recorded from FH -167 followed by FH- 4243 and FH113 (from transgenic group of cultivars) whereas a peak of 10.77 per leaf population of whitefly, recorded followed by FH-901 and FH-941 (from non transgenic group of cultivars). FH-207 found more resistant from all ten cultivars studied in 2011. Correlation among weather factors and whitefly population showed that rainfall was negatively correlated while temperature and relative humidity were positively correlated with whitefly population. In addition to that situation is becoming worse because of shifting from conventional to more advanced transgenic cultivars that are susceptible and serve as host. Moreover, climatic conditions provide addition favor and helps in population buildup, abundance and incidence. (author)

  15. Diallel analyze of yield and progress of the severity of leaf diseases in maize hybrids in two population density

    Directory of Open Access Journals (Sweden)

    Marcos Ventura Faria

    2015-02-01

    Full Text Available Seven commercial maize hybrids (AS1575, 2B688, Penta, GNZ2004, AG8021, Sprint e P30F53 were intercrossed in a complete diallel, excluded reciprocal, obtaining 21 crosses. The 28 treatments were evaluated in two environments characterized by different densities (62,500 and 90,000 plants ha-1, with the aim of selecting the most promising parents for generating base population to obtain lines. Two experiments were carried out in Guarapuava-PR, at randomized block design with three replications. We estimated the general (GCA and specific (SCA combining abilities for yield and disease severity assessed by the area under the common rust (Puccinia sorghi progress curve (AURPC and the area under the leaf spot (Cercospora zeae-maydis progress curve (AULPC. The effects of GCA and SCA were significant for grain yield and diseases severity in both densities, revealing the importance of both additive and non-additive effects. There GCA x densities interaction was significant only for grain yield. Crossings P30F53 x AG8021 and P30F53 x Penta had negative estimates of SCA for AURPC and AULPC on the environments average. Hybrids GNZ 2004 and P30F53 stood out showing positive GCA for grain yield and negative for AURPC and AULPC in both densities and therefore are recommended for generating base populations for obtaining lines adapted for both densities, conventional and denser plantings, given the current trends in management of maize.

  16. Interleukin 1β (+3954; −511) genotype polymorphism and its association with severe chronic generalized periodontitis in the Malaysian Population

    OpenAIRE

    Shelly Arora; Srinivas Sulugodu Ramachandra; Fawzia Abdullah; Kalyan C Gundavarapu

    2017-01-01

    Introduction: Single-nucleotide polymorphisms (SNPs) in interleukin 1? (IL-1?) gene have been known to be associated with increased susceptibility to chronic periodontitis among various ethnic populations. SNPs are more commonly observed at loci + 3954 and ? 511. The aim of this study was to evaluate the role of IL-1? gene polymorphism at loci +3954 and ? 511, and its association with severe chronic generalized periodontitis among the ethnic Malay, Chinese, and Indians within the Malaysian po...

  17. Recurrent Reverse Evolution Maintains Polymorphism after Strong Bottlenecks in Commensal Gut Bacteria.

    Science.gov (United States)

    Sousa, Ana; Ramiro, Ricardo S; Barroso-Batista, João; Güleresi, Daniela; Lourenço, Marta; Gordo, Isabel

    2017-11-01

    The evolution of new strains within the gut ecosystem is poorly understood. We used a natural but controlled system to follow the emergence of intraspecies diversity of commensal Escherichia coli, during three rounds of adaptation to the mouse gut (∼1,300 generations). We previously showed that, in the first round, a strongly beneficial phenotype (loss-of-function for galactitol consumption; gat-negative) spread to >90% frequency in all colonized mice. Here, we show that this loss-of-function is repeatedly reversed when a gat-negative clone colonizes new mice. The regain of function occurs via compensatory mutation and reversion, the latter leaving no trace of past adaptation. We further show that loss-of-function adaptive mutants reevolve, after colonization with an evolved gat-positive clone. Thus, even under strong bottlenecks a regime of strong-mutation-strong-selection dominates adaptation. Coupling experiments and modeling, we establish that reverse evolution recurrently generates two coexisting phenotypes within the microbiota that can or not consume galactitol (gat-positive and gat-negative, respectively). Although the abundance of the dominant strain, the gat-negative, depends on the microbiota composition, gat-positive abundance is independent of the microbiota composition and can be precisely manipulated by supplementing the diet with galactitol. These results show that a specific diet is able to change the abundance of specific strains. Importantly, we find polymorphism for these phenotypes in indigenous Enterobacteria of mice and man. Our results demonstrate that natural selection can greatly overwhelm genetic drift at structuring the strain diversity of gut commensals and that competition for limiting resources may be a key mechanism for maintaining polymorphism in the gut. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Geographic origins and population genetics of bats killed at wind-energy facilities.

    Science.gov (United States)

    Pylant, Cortney L; Nelson, David M; Fitzpatrick, Matthew C; Gates, J Edward; Keller, Stephen R

    2016-07-01

    An unanticipated impact of wind-energy development has been large-scale mortality of insectivorous bats. In eastern North America, where mortality rates are among the highest in the world, the hoary bat (Lasiurus cinereus) and the eastern red bat (L. borealis) comprise the majority of turbine-associated bat mortality. Both species are migratory tree bats with widespread distributions; however, little is known regarding the geographic origins of bats killed at wind-energy facilities or the diversity and population structure of affected species. We addressed these unknowns by measuring stable hydrogen isotope ratios (δ 2 H) and conducting population genetic analyses of bats killed at wind-energy facilities in the central Appalachian Mountains (USA) to determine the summering origins, effective size, structure, and temporal stability of populations. Our results indicate that ~1% of hoary bat mortalities and ~57% of red bat mortalities derive from non-local sources, with no relationship between the proportion of non-local bats and sex, location of mortality, or month of mortality. Additionally, our data indicate that hoary bats in our sample consist of an unstructured population with a small effective size (N e ) and either a stable or declining history. Red bats also showed no evidence of population genetic structure, but in contrast to hoary bats, the diversity contained in our red bat samples is consistent with a much larger N e that reflects a demographic expansion after a bottleneck. These results suggest that the impacts of mortality associated with intensive wind-energy development may affect bat species dissimilarly, with red bats potentially better able to absorb sustained mortality than hoary bats because of their larger N e . Our results provide important baseline data and also illustrate the utility of stable isotopes and population genetics for monitoring bat populations affected by wind-energy development. © 2016 by the Ecological Society of America.

  19. Vertical Transmission of Hepatitis C Virus: Variable Transmission Bottleneck and Evidence of Midgestation In Utero Infection.

    Science.gov (United States)

    Fauteux-Daniel, Sébastien; Larouche, Ariane; Calderon, Virginie; Boulais, Jonathan; Béland, Chanel; Ransy, Doris G; Boucher, Marc; Lamarre, Valérie; Lapointe, Normand; Boucoiran, Isabelle; Le Campion, Armelle; Soudeyns, Hugo

    2017-12-01

    Hepatitis C virus (HCV) can be transmitted from mother to child during pregnancy and childbirth. However, the timing and precise biological mechanisms that are involved in this process are incompletely understood, as are the determinants that influence transmission of particular HCV variants. Here we report results of a longitudinal assessment of HCV quasispecies diversity and composition in 5 cases of vertical HCV transmission, including 3 women coinfected with human immunodeficiency virus type 1 (HIV-1). The population structure of HCV variant spectra based on E2 envelope gene sequences (nucleotide positions 1491 to 1787), including hypervariable regions 1 and 2, was characterized using next-generation sequencing and median-joining network analysis. Compatible with a loose transmission bottleneck, larger numbers of shared HCV variants were observed in the presence of maternal coinfection. Coalescent Bayesian Markov chain Monte Carlo simulations revealed median times of transmission between 24.9 weeks and 36.1 weeks of gestation, with some confidence intervals ranging into the 1st trimester, considerably earlier than previously thought. Using recombinant autologous HCV pseudoparticles, differences were uncovered in HCV-specific antibody responses between coinfected mothers and mothers infected with HCV alone, in whom generalized absence of neutralization was observed. Finally, shifts in HCV quasispecies composition were seen in children around 1 year of age, compatible with the disappearance of passively transferred maternal immunoglobulins and/or the development of HCV-specific humoral immunity. Taken together, these results provide insights into the timing, dynamics, and biologic mechanisms involved in vertical HCV transmission and inform preventative strategies. IMPORTANCE Although it is well established that hepatitis C virus (HCV) can be transmitted from mother to child, the manner and the moment at which transmission operates have been the subject of

  20. Temporal Dynamics and Resource Availability for Drosophilid Fruit Flies (Insecta, Diptera in a Gallery Forest in the Brazilian Savanna

    Directory of Open Access Journals (Sweden)

    Henrique Valadão

    2010-01-01

    Full Text Available Seasonality can cause severe bottlenecks in natural populations, even leading to local extinction. Large variation in resource availability may explain the bottlenecks, but the role of these variations is still poorly understood. The goal of this study was to analyze if temporal variations in the guild of drosophilids breeding in fruits of Mauritia flexuosa (Arecaceae can be explained by the shortage of this resource during the dry season. Fruits of M. flexuosa were collected over one year in a gallery forest located in the Central Brazilian Savanna. The drosophilid assemblage varied over time, with a lower density of species and of individuals in the dry season, when the percentage of colonized fruits was also smaller. These findings suggest that although the fruits were available during the dry season, they were underused. This way, the resource availability does not seem to regulate the community in the dry season.

  1. Temporal Dynamics and Resource Availability for Drosophilid Fruit Flies (Insect, Diptera) in a Gallery Forest in the Brazilian Savanna

    International Nuclear Information System (INIS)

    Valadao, H.; Du Vall Hay, J.; Tidon, R.

    2010-01-01

    Seasonality can cause severe bottlenecks in natural populations, even leading to local extinction. Large variation in resource availability may explain the bottlenecks, but the role of these variations is still poorly understood. The goal of this study was to analyze if temporal variations in the guild of drosophilids breeding in fruits of Mauritia flexuosa (Arecaceae) can be explained by the shortage of this resource during the dry season. Fruits of M. flexuosa were collected over one year in a gallery forest located in the Central Brazilian Savanna. The drosophilid assemblage varied over time, with a lower density of species and of individuals in the dry season, when the percentage of colonized fruits was also smaller. These findings suggest that although the fruits were available during the dry season, they were under used. This way, the resource availability does not seem to regulate the community in the dry season.

  2. Intimate Partner Violence and Depression Symptom Severity among South African Women during Pregnancy and Postpartum: Population-Based Prospective Cohort Study.

    Directory of Open Access Journals (Sweden)

    Alexander C Tsai

    2016-01-01

    Full Text Available Violence against women by intimate partners remains unacceptably common worldwide. The evidence base for the assumed psychological impacts of intimate partner violence (IPV is derived primarily from studies conducted in high-income countries. A recently published systematic review identified 13 studies linking IPV to incident depression, none of which were conducted in sub-Saharan Africa. To address this gap in the literature, we analyzed longitudinal data collected during the course of a 3-y cluster-randomized trial with the aim of estimating the association between IPV and depression symptom severity.We conducted a secondary analysis of population-based, longitudinal data collected from 1,238 pregnant women during a 3-y cluster-randomized trial of a home visiting intervention in Cape Town, South Africa. Surveys were conducted at baseline, 6 mo, 18 mo, and 36 mo (85% retention. The primary explanatory variable of interest was exposure to four types of physical IPV in the past year. Depression symptom severity was measured using the Xhosa version of the ten-item Edinburgh Postnatal Depression Scale. In a pooled cross-sectional multivariable regression model adjusting for potentially confounding time-fixed and time-varying covariates, lagged IPV intensity had a statistically significant association with depression symptom severity (regression coefficient b = 1.04; 95% CI, 0.61-1.47, with estimates from a quantile regression model showing greater adverse impacts at the upper end of the conditional depression distribution. Fitting a fixed effects regression model accounting for all time-invariant confounding (e.g., history of childhood sexual abuse yielded similar findings (b = 1.54; 95% CI, 1.13-1.96. The magnitudes of the coefficients indicated that a one-standard-deviation increase in IPV intensity was associated with a 12.3% relative increase in depression symptom severity over the same time period. The most important limitations of our study

  3. End-Devonian extinction and a bottleneck in the early evolution of modern jawed vertebrates.

    Science.gov (United States)

    Sallan, Lauren Cole; Coates, Michael I

    2010-06-01

    The Devonian marks a critical stage in the early evolution of vertebrates: It opens with an unprecedented diversity of fishes and closes with the earliest evidence of limbed tetrapods. However, the latter part of the Devonian has also been characterized as a period of global biotic crisis marked by two large extinction pulses: a "Big Five" mass extinction event at the Frasnian-Famennian stage boundary (374 Ma) and the less well-documented Hangenberg event some 15 million years later at the Devonian-Carboniferous boundary (359 Ma). Here, we report the results of a wide-ranging analysis of the impact of these events on early vertebrate evolution, which was obtained from a database of vertebrate occurrences sampling over 1,250 taxa from 66 localities spanning Givetian to Serpukhovian stages (391 to 318 Ma). We show that major vertebrate clades suffered acute and systematic effects centered on the Hangenberg extinction involving long-term losses of over 50% of diversity and the restructuring of vertebrate ecosystems worldwide. Marine and nonmarine faunas were equally affected, precluding the existence of environmental refugia. The subsequent recovery of previously diverse groups (including placoderms, sarcopterygian fish, and acanthodians) was minimal. Tetrapods, actinopterygians, and chondrichthyans, all scarce within the Devonian, undergo large diversification events in the aftermath of the extinction, dominating all subsequent faunas. The Hangenberg event represents a previously unrecognized bottleneck in the evolutionary history of vertebrates as a whole and a historical contingency that shaped the roots of modern biodiversity.

  4. Developing Off-site Emergency Preparedness and Response Model (OEPRM) for Severe Accident of NPP in a Densely Populated Country Using System Dynamics Approach

    Energy Technology Data Exchange (ETDEWEB)

    Hossena, Muhammed Mufazzal; Kang, Kyoung Ho; Song, Jin Ho [KAERI, Deajeon (Korea, Republic of)

    2016-05-15

    The main objectives of this study are to find the influencing factors of systems and sub-systems of OEPRM, to find the interdependency among the influencing factors, and to develop a conceptual qualitative OEPRM for densely populated NPP country in case of SA using system dynamics (SD). NPP accidents are classified as nuclear accidents and incidents depending on the severity. Severe accident (SA) is certain low probability accident that are beyond design basis accident which may arise due to multiple failures of safety systems leading to significant core degradation and jeopardize the integrity of many or all of the barriers to the release of radioactive material. The weakness to the off-site emergency response in the time of Fukushima accident was observed. So, it is crucial to develop an off-site emergency preparedness and responses model (OEPRM) for radiological emergency in densely populated country from the Fukushima emergency response lesson. In this study, an OEPRM is developed for densely populated NPP country to mitigate radiological effects in case of SA using SD approach. Besides, this study focuses the weakness of emergency response in Fukushima accident and proposed solution approach. The development of OEPRM in case of SA of NPP is very complex because of the involvement of various organization and it requires highly specialized agencies and technical experts. Moreover, if the country is agriculture based, it will make completely sophisticated.

  5. Developing Off-site Emergency Preparedness and Response Model (OEPRM) for Severe Accident of NPP in a Densely Populated Country Using System Dynamics Approach

    International Nuclear Information System (INIS)

    Hossena, Muhammed Mufazzal; Kang, Kyoung Ho; Song, Jin Ho

    2016-01-01

    The main objectives of this study are to find the influencing factors of systems and sub-systems of OEPRM, to find the interdependency among the influencing factors, and to develop a conceptual qualitative OEPRM for densely populated NPP country in case of SA using system dynamics (SD). NPP accidents are classified as nuclear accidents and incidents depending on the severity. Severe accident (SA) is certain low probability accident that are beyond design basis accident which may arise due to multiple failures of safety systems leading to significant core degradation and jeopardize the integrity of many or all of the barriers to the release of radioactive material. The weakness to the off-site emergency response in the time of Fukushima accident was observed. So, it is crucial to develop an off-site emergency preparedness and responses model (OEPRM) for radiological emergency in densely populated country from the Fukushima emergency response lesson. In this study, an OEPRM is developed for densely populated NPP country to mitigate radiological effects in case of SA using SD approach. Besides, this study focuses the weakness of emergency response in Fukushima accident and proposed solution approach. The development of OEPRM in case of SA of NPP is very complex because of the involvement of various organization and it requires highly specialized agencies and technical experts. Moreover, if the country is agriculture based, it will make completely sophisticated

  6. The population structure of Glossina palpalis gambiensis from island and continental locations in Coastal Guinea.

    Directory of Open Access Journals (Sweden)

    Philippe Solano

    Full Text Available We undertook a population genetics analysis of the tsetse fly Glossina palpalis gambiensis, a major vector of sleeping sickness in West Africa, using microsatellite and mitochondrial DNA markers. Our aims were to estimate effective population size and the degree of isolation between coastal sites on the mainland of Guinea and Loos Islands. The sampling locations encompassed Dubréka, the area with the highest Human African Trypanosomosis (HAT prevalence in West Africa, mangrove and savannah sites on the mainland, and two islands, Fotoba and Kassa, within the Loos archipelago. These data are discussed with respect to the feasibility and sustainability of control strategies in those sites currently experiencing, or at risk of, sleeping sickness.We found very low migration rates between sites except between those sampled around the Dubréka area that seems to contain a widely dispersed and panmictic population. In the Kassa island samples, various effective population size estimates all converged on surprisingly small values (10bottleneck, and/or other biological or ecological factors such as strong variance in the reproductive success of individuals.Whatever their origin, the small effective population sizes suggest high levels of inbreeding in tsetse flies within the island samples in marked contrast to the large diffuse deme in Dubréka zones. We discuss how these genetic results suggest that different tsetse control strategies should be applied on the mainland and islands.

  7. Koalas (Phascolarctos cinereus) From Queensland Are Genetically Distinct From 2 Populations in Victoria.

    Science.gov (United States)

    Ruiz-Rodriguez, Christina T; Ishida, Yasuko; Murray, Neil D; O'Brien, Stephen J; Graves, Jennifer A M; Greenwood, Alex D; Roca, Alfred L

    2016-01-01

    The koala (Phascolarctos cinereus) suffered population declines and local extirpation due to hunting in the early 20th century, especially in southern Australia. Koalas were subsequently reintroduced to the Brisbane Ranges (BR) and Stony Rises (SR) by translocating individuals from a population on French Island descended from a small number of founders. To examine genetic diversity and north-south differentiation, we genotyped 13 microsatellite markers in 46 wild koalas from the BR and SR, and 27 Queensland koalas kept at the US zoos. The Queensland koalas displayed much higher heterozygosity (H O = 0.73) than the 2 southern Australian koala populations examined: H O = 0.49 in the BR, whereas H O = 0.41 in the SR. This is consistent with the historical accounts of bottlenecks and founder events affecting the southern populations and contrasts with reports of high genetic diversity in some southern populations. The 2 southern Australian koala populations were genetically similar (F ST = 0.018, P = 0.052). By contrast, northern and southern Australian koalas were highly differentiated (F ST = 0.27, P < 0.001), thereby suggesting that geographic structuring should be considered in the conservation management of koalas. Sequencing of 648bp of the mtDNA control region in Queensland koalas found 8 distinct haplotypes, one of which had not been previously detected among koalas. Queensland koalas displayed high mitochondrial haplotype diversity (H = 0.753) and nucleotide diversity (π = 0.0072), indicating along with the microsatellite data that North American zoos have maintained high levels of genetic diversity among their Queensland koalas. © The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  8. An integrated approach to historical population assessment of the great whales: case of the New Zealand southern right whale.

    Science.gov (United States)

    Jackson, Jennifer A; Carroll, Emma L; Smith, Tim D; Zerbini, Alexandre N; Patenaude, Nathalie J; Baker, C Scott

    2016-03-01

    Accurate estimation of historical abundance provides an essential baseline for judging the recovery of the great whales. This is particularly challenging for whales hunted prior to twentieth century modern whaling, as population-level catch records are often incomplete. Assessments of whale recovery using pre-modern exploitation indices are therefore rare, despite the intensive, global nature of nineteenth century whaling. Right whales (Eubalaena spp.) were particularly exploited: slow swimmers with strong fidelity to sheltered calving bays, the species made predictable and easy targets. Here, we present the first integrated population-level assessment of the whaling impact and pre-exploitation abundance of a right whale, the New Zealand southern right whale (E. australis). In this assessment, we use a Bayesian population dynamics model integrating multiple data sources: nineteenth century catches, genetic constraints on bottleneck size and individual sightings histories informing abundance and trend. Different catch allocation scenarios are explored to account for uncertainty in the population's offshore distribution. From a pre-exploitation abundance of 28 800-47 100 whales, nineteenth century hunting reduced the population to approximately 30-40 mature females between 1914 and 1926. Today, it stands at less than 12% of pre-exploitation abundance. Despite the challenges of reconstructing historical catches and population boundaries, conservation efforts of historically exploited species benefit from targets for ecological restoration.

  9. LONG-ORBITAL-PERIOD PREPOLARS CONTAINING EARLY K-TYPE DONOR STARS. BOTTLENECK ACCRETION MECHANISM IN ACTION

    International Nuclear Information System (INIS)

    Tovmassian, G.; González–Buitrago, D.; Zharikov, S.; Reichart, D. E.; Haislip, J. B.; Ivarsen, K. M.; LaCluyze, A. P.; Moore, J. P.; Miroshnichenko, A. S.

    2016-01-01

    We studied two objects identified as cataclysmic variables (CVs) with periods exceeding the natural boundary for Roche-lobe-filling zero-age main sequence (ZAMS) secondary stars. We present observational results for V1082 Sgr with a 20.82 hr orbital period, an object that shows a low luminosity state when its flux is totally dominated by a chromospherically active K star with no signs of ongoing accretion. Frequent accretion shutoffs, together with characteristics of emission lines in a high state, indicate that this binary system is probably detached, and the accretion of matter on the magnetic white dwarf takes place through stellar wind from the active donor star via coupled magnetic fields. Its observational characteristics are surprisingly similar to V479 And, a 14.5 hr binary system. They both have early K-type stars as donor stars. We argue that, similar to the shorter-period prepolars containing M dwarfs, these are detached binaries with strong magnetic components. Their magnetic fields are coupled, allowing enhanced stellar wind from the K star to be captured and channeled through the bottleneck connecting the two stars onto the white dwarf’s magnetic pole, mimicking a magnetic CV. Hence, they become interactive binaries before they reach contact. This will help to explain an unexpected lack of systems possessing white dwarfs with strong magnetic fields among detached white+red dwarf systems

  10. LONG-ORBITAL-PERIOD PREPOLARS CONTAINING EARLY K-TYPE DONOR STARS. BOTTLENECK ACCRETION MECHANISM IN ACTION

    Energy Technology Data Exchange (ETDEWEB)

    Tovmassian, G.; González–Buitrago, D.; Zharikov, S. [Instituto de Astronomía, Universidad Nacional Autónoma de México, Apartado Postal 877, Ensenada, Baja California, 22800 México (Mexico); Reichart, D. E.; Haislip, J. B.; Ivarsen, K. M.; LaCluyze, A. P.; Moore, J. P. [Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Campus Box 3255, Chapel Hill, NC 27599 (United States); Miroshnichenko, A. S., E-mail: gag@astro.unam.mx, E-mail: dgonzalez@astro.unam.mx, E-mail: zhar@astro.unam.mx [Department of Physics and Astronomy, University of North Carolina at Greensboro, Greensboro, NC 27402-6170 (United States)

    2016-03-01

    We studied two objects identified as cataclysmic variables (CVs) with periods exceeding the natural boundary for Roche-lobe-filling zero-age main sequence (ZAMS) secondary stars. We present observational results for V1082 Sgr with a 20.82 hr orbital period, an object that shows a low luminosity state when its flux is totally dominated by a chromospherically active K star with no signs of ongoing accretion. Frequent accretion shutoffs, together with characteristics of emission lines in a high state, indicate that this binary system is probably detached, and the accretion of matter on the magnetic white dwarf takes place through stellar wind from the active donor star via coupled magnetic fields. Its observational characteristics are surprisingly similar to V479 And, a 14.5 hr binary system. They both have early K-type stars as donor stars. We argue that, similar to the shorter-period prepolars containing M dwarfs, these are detached binaries with strong magnetic components. Their magnetic fields are coupled, allowing enhanced stellar wind from the K star to be captured and channeled through the bottleneck connecting the two stars onto the white dwarf’s magnetic pole, mimicking a magnetic CV. Hence, they become interactive binaries before they reach contact. This will help to explain an unexpected lack of systems possessing white dwarfs with strong magnetic fields among detached white+red dwarf systems.

  11. Teacher Diversity in Canada: Leaky Pipelines, Bottlenecks, and Glass Ceilings

    Science.gov (United States)

    Ryan, James; Pollock, Katina; Antonelli, Fab

    2009-01-01

    This article examines the racial diversity of the teacher population in Canada. In particular, we compare the number of teachers of colour in Canadian elementary and secondary schools from the 2001 and 2006 Census data with the diversity of the student and general populations. We also explore ways to understand the gap between the proportion of…

  12. Chronic obstructive pulmonary disease severity is associated with severe pneumonia

    Directory of Open Access Journals (Sweden)

    Jung Seop Eom

    2015-01-01

    Full Text Available CONTEXT: Chronic obstructive pulmonary disease (COPD is a heterogeneous disorder, and various aspects of COPD may be associated with the severity of pneumonia in such patients. AIMS: We examined the risk factors associated with severe pneumonia in a COPD population. MATERIALS AND METHODS: We performed a retrospective observational study using a prospectively collected database of pneumonia patients who were admitted to our hospital through emergency department between 2008 and 2012. Patients with hospital-acquired pneumonia and those with an immunocompromised status were excluded. RESULTS: Of 148 pneumonia patients with COPD for whom chest computed tomography (CT scans were available, 106 (71.6% and 42 (28.4% were classified as non-severe and severe pneumonia, respectively. Multivariate logistic regression analysis revealed that the severity of airflow limitation [odds ratio (OR, 2.751; 95% confidence interval (CI, 1.074-7.050; P = 0.035] and the presence of emphysema on a chest CT scan (OR, 3.366; 95% CI, 1.104-10.265; P = 0.033 were independently associated with severe pneumonia in patients with COPD. CONCLUSIONS: The severity of COPD including the airflow limitation grade and the presence of pulmonary emphysema were independently associated with the development of severe pneumonia.

  13. Oxytocin during labour and risk of severe postpartum haemorrhage: a population-based, cohort-nested case–control study

    Science.gov (United States)

    Belghiti, Jérémie; Kayem, Gilles; Dupont, Corinne; Rudigoz, René-Charles; Bouvier-Colle, Marie-Hélène

    2011-01-01

    Objectives Postpartum haemorrhage (PPH) is a major cause of maternal mortality and morbidity worldwide. Experimental studies support the hypothesis that oxytocin administration during labour, a common although not evidence-based practice, may increase the risk of atonic PPH. The clinical studies, however, are inconclusive. The objectives of this study was to investigate the association between the level of oxytocin exposure during labour and the risk of severe PPH and to explore whether the prophylactic use of oxytocin after birth modifies this association. Design Population-based, cohort-nested case–control study. Setting 106 French hospitals from December 2004 through November 2006. Participants Women with term singleton vaginal deliveries, after an uncomplicated pregnancy. Cases were 1483 women with severe PPH, defined by peripartum change in haemoglobin of ≥4 g/dl or need for blood transfusion. Controls were 1758 women from a random sample of parturients without PPH. Main outcome measures The independent association between the level of oxytocin during labour and the risk of severe PPH was tested and quantified with ORs through two-level multivariable logistic regression modelling. Results Oxytocin was administered during labour to 73% of cases and 61% of controls (crude OR: 1.7, 95% CI 1.5 to 2.0). After adjustment for all potential confounders, oxytocin during labour was associated with a significantly higher risk of severe PPH (adjusted OR: 1.8, 95% CI 1.3 to 2.6) in women who did not receive prophylactic oxytocin after delivery; the OR for haemorrhage increased from 1 to 5 according to the level of oxytocin exposure. In women who had prophylactic oxytocin after delivery, this association was significant only for the highest exposure categories. Conclusions Oxytocin during labour appears to be an independent risk factor for severe PPH. The results emphasise the need for guidelines clarifying the evidence-based indications for this procedure and the

  14. Pathways of Lipid Metabolism in Marine Algae, Co-Expression Network, Bottlenecks and Candidate Genes for Enhanced Production of EPA and DHA in Species of Chromista

    Directory of Open Access Journals (Sweden)

    Alice Mühlroth

    2013-11-01

    Full Text Available The importance of n-3 long chain polyunsaturated fatty acids (LC-PUFAs for human health has received more focus the last decades, and the global consumption of n-3 LC-PUFA has increased. Seafood, the natural n-3 LC-PUFA source, is harvested beyond a sustainable capacity, and it is therefore imperative to develop alternative n-3 LC-PUFA sources for both eicosapentaenoic acid (EPA, 20:5n-3 and docosahexaenoic acid (DHA, 22:6n-3. Genera of algae such as Nannochloropsis, Schizochytrium, Isochrysis and Phaedactylum within the kingdom Chromista have received attention due to their ability to produce n-3 LC-PUFAs. Knowledge of LC-PUFA synthesis and its regulation in algae at the molecular level is fragmentary and represents a bottleneck for attempts to enhance the n-3 LC-PUFA levels for industrial production. In the present review, Phaeodactylum tricornutum has been used to exemplify the synthesis and compartmentalization of n-3 LC-PUFAs. Based on recent transcriptome data a co-expression network of 106 genes involved in lipid metabolism has been created. Together with recent molecular biological and metabolic studies, a model pathway for n-3 LC-PUFA synthesis in P. tricornutum has been proposed, and is compared to industrialized species of Chromista. Limitations of the n-3 LC-PUFA synthesis by enzymes such as thioesterases, elongases, acyl-CoA synthetases and acyltransferases are discussed and metabolic bottlenecks are hypothesized such as the supply of the acetyl-CoA and NADPH. A future industrialization will depend on optimization of chemical compositions and increased biomass production, which can be achieved by exploitation of the physiological potential, by selective breeding and by genetic engineering.

  15. Inferences on the population structure and colonization process of the invasive oriental fruit fly, Bactrocera dorsalis (Hendel).

    Science.gov (United States)

    Aketarawong, N; Bonizzoni, M; Thanaphum, S; Gomulski, L M; Gasperi, G; Malacrida, A R; Gugliemino, C R

    2007-09-01

    The phytophagous insects of the Tephritidae family offer different case histories of successful invasions. An example is Bactrocera dorsalis sensu stricto, the oriental fruit fly which has been recognized as a key pest of Asia and the Pacific. It is known to have the potential to establish adventive populations in various tropical and subtropical areas. Despite the economic risk associated with a putative stable presence of this fly, the genetic aspects of its invasion process have remained relatively unexplored. Using microsatellite markers we have investigated the population structure and genetic variability in 14 geographical populations across the four areas of the actual species range: Far East Asia, South Asia, Southeast Asia and the Pacific Area. Results of clustering and admixture, associated with phylogenetic and migration analyses, were used to evaluate the changes in population genetic structure that this species underwent during its invasion process and establishment in the different areas. The colonization process of this fly is associated with a relatively stable population demographic structure, especially in an unfragmented habitat, rich in intensive cultivation such as in Southeast Asia. In this area, the results suggest a lively demographic history, characterized by evolutionary recent demographic expansions and no recent bottlenecks. Cases of genetic isolation attributable to geographical factors, fragmented habitats and/or fruit trade restrictions were observed in Bangladesh, Myanmar and Hawaii. Regarding the pattern of invasion, the overall genetic profile of the considered populations suggests a western orientated migration route from China to the West.

  16. Mortality Associated with Severe Sepsis Among Age-Similar Women with and without Pregnancy-Associated Hospitalization in Texas: A Population-Based Study.

    Science.gov (United States)

    Oud, Lavi

    2016-06-10

    BACKGROUND The reported mortality among women with pregnancy-associated severe sepsis (PASS) has been considerably lower than among severely septic patients in the general population, with the difference being attributed to the younger age and lack of chronic illness among the women with PASS. However, no comparative studies were reported to date between patients with PASS and age-similar women with severe sepsis not associated with pregnancy (NPSS). MATERIAL AND METHODS We used the Texas Inpatient Public Use Data File to compare the crude and adjusted hospital mortality between women with severe sepsis, aged 20-34 years, with and without pregnancy-associated hospitalizations during 2001-2010, following exclusion of those with reported chronic comorbidities, as well as alcohol and drug abuse. RESULTS Crude hospital mortality among PASS vs. NPSS hospitalizations was lower for the whole cohort (6.7% vs. 14.1% [p<0.0001]) and those with ≥3 organ failures (17.6% vs. 33.2% [p=0.0100]). Adjusted PASS mortality (odds ratio [95% CI]) was 0.57 (0.38-0.86) [p=0.0070]. CONCLUSIONS Hospital mortality was unexpectedly markedly and consistently lower among women with severe sepsis associated with pregnancy, as compared with contemporaneous, age-similar women with severe sepsis not associated with pregnancy, without reported chronic comorbidities. Further studies are warranted to examine the sources of the observed differences and to corroborate our findings.

  17. A wild 'albino' bilberry (Vaccinium myrtillus L. from Slovenia shows three bottlenecks in the anthocyanin pathway and significant differences in the expression of several regulatory genes compared to the common blue berry type.

    Directory of Open Access Journals (Sweden)

    Zala Zorenc

    Full Text Available Relative expressions of structural genes and a number of transcription factors of the anthocyanin pathway relevant in Vaccinium species, and related key enzyme activities were compared with the composition and content of metabolites in skins of ripe fruits of wild albino and blue bilberry (Vaccinium myrtillus found in Slovenia. Compared to the common blue type, the albino variant had a 151-fold lower total anthocyanin and a 7-fold lower total phenolic content in their berry skin, which correlated with lower gene expression of flavonoid 3-O-glycosyltransferase (FGT; 33-fold, flavanone 3-hydroxylase (FHT; 18-fold, anthocyanidin synthase (ANS; 11-fold, chalcone synthase (CHS, 7.6-fold and MYBPA1 transcription factor (22-fold. The expression of chalcone isomerase (CHI, dihydroflavonol 4-reductase (DFR, leucoanthocyanidin reductase (LAR, anthocyanidin reductase (ANR and MYBC2 transcription factor was reduced only by a factor of 1.5-2 in the albino berry skins, while MYBR3 and flavonoid 3',5'-hydroxylase (F3'5'H were increased to a similar extent. Expression of the SQUAMOSA class transcription factor TDR4, in contrast, was independent of the color type and does therefore not seem to be correlated with anthocyanin formation in this variant. At the level of enzymes, significantly lower FHT and DFR activities, but not of phenylalanine ammonia-lyase (PAL and CHS/CHI, were observed in the fruit skins of albino bilberries. A strong increase in relative hydroxycinnamic acid derivative concentrations indicates the presence of an additional bottleneck in the general phenylpropanoid pathway at a so far unknown step between PAL and CHS.

  18. Surfing the vegetal pole in a small population: extracellular vertical transmission of an 'intracellular' deep-sea clam symbiont.

    Science.gov (United States)

    Ikuta, Tetsuro; Igawa, Kanae; Tame, Akihiro; Kuroiwa, Tsuneyoshi; Kuroiwa, Haruko; Aoki, Yui; Takaki, Yoshihiro; Nagai, Yukiko; Ozawa, Genki; Yamamoto, Masahiro; Deguchi, Ryusaku; Fujikura, Katsunori; Maruyama, Tadashi; Yoshida, Takao

    2016-05-01

    Symbiont transmission is a key event for understanding the processes underlying symbiotic associations and their evolution. However, our understanding of the mechanisms of symbiont transmission remains still fragmentary. The deep-sea clam Calyptogena okutanii harbours obligate sulfur-oxidizing intracellular symbiotic bacteria in the gill epithelial cells. In this study, we determined the localization of their symbiont associating with the spawned eggs, and the population size of the symbiont transmitted via the eggs. We show that the symbionts are located on the outer surface of the egg plasma membrane at the vegetal pole, and that each egg carries approximately 400 symbiont cells, each of which contains close to 10 genomic copies. The very small population size of the symbiont transmitted via the eggs might narrow the bottleneck and increase genetic drift, while polyploidy and its transient extracellular lifestyle might slow the rate of genome reduction. Additionally, the extracellular localization of the symbiont on the egg surface may increase the chance of symbiont exchange. This new type of extracellular transovarial transmission provides insights into complex interactions between the host and symbiont, development of both host and symbiont, as well as the population dynamics underlying genetic drift and genome evolution in microorganisms.

  19. Incomplete Selective Sweeps of Microcystis Population Detected by the Leader-End CRISPR Fragment Analysis in a Natural Pond

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    Shigeko Kimura

    2018-03-01

    , resulting that Microcystis populations experience a bottleneck once a year, and thereby founder effects following a bottleneck mean that older CTs have an equal chance of increasing in prevalence as the CTs generated following acquisition of newer spacers.

  20. Selectivity of fish ladders: a bottleneck in Neotropical fish movement

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    Carlos Sérgio Agostinho

    their proportions in the downriver stretch: fish samples in the ladder were clearly dominated by a few species, including some that do not need to be translocated. Thus, selectivity constitutes an important bottleneck to initiatives for translocating fish aimed at conserving their stocks or biodiversity. It is urgent to review the decision-making process for the construction of fish passages and to evaluate the functioning of those already operating.

  1. The Best Prediction Model for Trauma Outcomes of the Current Korean Population: a Comparative Study of Three Injury Severity Scoring Systems

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    Kyoungwon Jung

    2016-08-01

    Full Text Available Background: Injury severity scoring systems that quantify and predict trauma outcomes have not been established in Korea. This study was designed to determine the best system for use in the Korean trauma population. Methods: We collected and analyzed the data from trauma patients admitted to our institution from January 2010 to December 2014. Injury Severity Score (ISS, Revised Trauma Score (RTS, and Trauma and Injury Severity Score (TRISS were calculated based on the data from the enrolled patients. Area under the receiver operating characteristic (ROC curve (AUC for the prediction ability of each scoring system was obtained, and a pairwise comparison of ROC curves was performed. Additionally, the cut-off values were estimated to predict mortality, and the corresponding accuracy, positive predictive value, and negative predictive value were obtained. Results: A total of 7,120 trauma patients (6,668 blunt and 452 penetrating injuries were enrolled in this study. The AUCs of ISS, RTS, and TRISS were 0.866, 0.894, and 0.942, respectively, and the prediction ability of the TRISS was significantly better than the others (p < 0.001, respectively. The cut-off value of the TRISS was 0.9082, with a sensitivity of 81.9% and specificity of 92.0%; mortality was predicted with an accuracy of 91.2%; its positive predictive value was the highest at 46.8%. Conclusions: The results of our study were based on the data from one institution and suggest that the TRISS is the best prediction model of trauma outcomes in the current Korean population. Further study is needed with more data from multiple centers in Korea.

  2. French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives

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    Guillaume eMinard

    2015-09-01

    Full Text Available The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the 21st century. Originating from Asia, it has invaded a wide range of eco-climatic regions worldwide. The insect-associated microbiota is now recognized to play a significant role in host biology. While genetic diversity bottlenecks are known to result from biological invasions, the resulting shifts in host-associated microbiota diversity has not been thoroughly investigated. To address this subject, we compared four autochthonous Ae. albopictus populations in Vietnam, the native area of Ae. albopictus, and three populations recently introduced to Metropolitan France, with the aim of documenting whether these populations display differences in host genotype and bacterial microbiota. Population-level genetic diversity (microsatellite markers and COI haplotype and bacterial diversity (16S rDNA metabarcoding were compared between field-caught mosquitoes. Bacterial microbiota from the whole insect bodies were largely dominated by Wolbachia pipientis. Targeted analysis of the gut microbiota revealed a greater bacterial diversity in which a fraction was common between French and Vietnamese populations. The genus Dysgonomonas was the most prevalent and abundant across all studied populations. Overall genetic diversities of both hosts and bacterial microbiota were significantly reduced in recently established populations of France compared to the autochthonous populations of Vietnam. These results open up many important avenues of investigation in order to link the process of geographical invasion to shifts in commensal and symbiotic microbiome communities, as such shifts may have dramatic impacts on the biology and/or vector competence of invading hematophagous insects.

  3. Gaian bottlenecks and planetary habitability maintained by evolving model biospheres: the ExoGaia model

    Science.gov (United States)

    Nicholson, Arwen E.; Wilkinson, David M.; Williams, Hywel T. P.; Lenton, Timothy M.

    2018-06-01

    The search for habitable exoplanets inspires the question - how do habitable planets form? Planet habitability models traditionally focus on abiotic processes and neglect a biotic response to changing conditions on an inhabited planet. The Gaia hypothesis postulates that life influences the Earth's feedback mechanisms to form a self-regulating system, and hence that life can maintain habitable conditions on its host planet. If life has a strong influence, it will have a role in determining a planet's habitability over time. We present the ExoGaia model - a model of simple `planets' host to evolving microbial biospheres. Microbes interact with their host planet via consumption and excretion of atmospheric chemicals. Model planets orbit a `star' that provides incoming radiation, and atmospheric chemicals have either an albedo or a heat-trapping property. Planetary temperatures can therefore be altered by microbes via their metabolisms. We seed multiple model planets with life while their atmospheres are still forming and find that the microbial biospheres are, under suitable conditions, generally able to prevent the host planets from reaching inhospitable temperatures, as would happen on a lifeless planet. We find that the underlying geochemistry plays a strong role in determining long-term habitability prospects of a planet. We find five distinct classes of model planets, including clear examples of `Gaian bottlenecks' - a phenomenon whereby life either rapidly goes extinct leaving an inhospitable planet or survives indefinitely maintaining planetary habitability. These results suggest that life might play a crucial role in determining the long-term habitability of planets.

  4. Evolutionary bottlenecks in brackish water habitats drive the colonization of fresh water by stingrays.

    Science.gov (United States)

    Kirchhoff, K N; Hauffe, T; Stelbrink, B; Albrecht, C; Wilke, T

    2017-08-01

    Species richness in freshwater bony fishes depends on two main processes: the transition into and the diversification within freshwater habitats. In contrast to bony fishes, only few cartilaginous fishes, mostly stingrays (Myliobatoidei), were able to colonize fresh water. Respective transition processes have been mainly assessed from a physiological and morphological perspective, indicating that the freshwater lifestyle is strongly limited by the ability to perform osmoregulatory adaptations. However, the transition history and the effect of physiological constraints on the diversification in stingrays remain poorly understood. Herein, we estimated the geographic pathways of freshwater colonization and inferred the mode of habitat transitions. Further, we assessed habitat-related speciation rates in a time-calibrated phylogenetic framework to understand factors driving the transition of stingrays into and the diversification within fresh water. Using South American and Southeast Asian freshwater taxa as model organisms, we found one independent freshwater colonization event by stingrays in South America and at least three in Southeast Asia. We revealed that vicariant processes most likely caused freshwater transition during the time of major marine incursions. The habitat transition rates indicate that brackish water species switch preferably back into marine than forth into freshwater habitats. Moreover, our results showed significantly lower diversification rates in brackish water lineages, whereas freshwater and marine lineages exhibit similar rates. Thus, brackish water habitats may have functioned as evolutionary bottlenecks for the colonization of fresh water by stingrays, probably because of the higher variability of environmental conditions in brackish water. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  5. Survival in individuals with severe alpha 1-antitrypsin deficiency (PiZZ) in comparison to a general population with known smoking habits.

    Science.gov (United States)

    Tanash, Hanan A; Ekström, Magnus; Rönmark, Eva; Lindberg, Anne; Piitulainen, Eeva

    2017-09-01

    Knowledge about the natural history of severe alpha 1-antitrypsin (AAT) deficiency (PiZZ) is limited. Our aim was to compare the survival of PiZZ individuals with randomly selected controls from the Swedish general population.The PiZZ subjects (n=1585) were selected from the Swedish National AATD Register. The controls (n=5999) were randomly selected from the Swedish population register. Smoking habits were known for all subjects.Median follow-up times for the PiZZ subjects (731 never-smokers) and controls (3179 never-smokers) were 12 and 17 years, respectively (psmoking habits and presence of respiratory symptoms, the risk of death was still significantly higher for the PiZZ individuals than for the controls, hazard ratio (HR) 3.2 (95% CI 2.8-3.6; psmoking PiZZ individuals identified by screening, compared to never-smoking controls, HR 1.2 (95% CI 0.6-2.2).The never-smoking PiZZ individuals identified by screening had a similar life expectancy to the never-smokers in the Swedish general population. Early diagnosis of AAT deficiency is of utmost importance. Copyright ©ERS 2017.

  6. Comparative population genomics of latitudinal variation in Drosophila simulans and Drosophila melanogaster.

    Science.gov (United States)

    Machado, Heather E; Bergland, Alan O; O'Brien, Katherine R; Behrman, Emily L; Schmidt, Paul S; Petrov, Dmitri A

    2016-02-01

    Examples of clinal variation in phenotypes and genotypes across latitudinal transects have served as important models for understanding how spatially varying selection and demographic forces shape variation within species. Here, we examine the selective and demographic contributions to latitudinal variation through the largest comparative genomic study to date of Drosophila simulans and Drosophila melanogaster, with genomic sequence data from 382 individual fruit flies, collected across a spatial transect of 19 degrees latitude and at multiple time points over 2 years. Consistent with phenotypic studies, we find less clinal variation in D. simulans than D. melanogaster, particularly for the autosomes. Moreover, we find that clinally varying loci in D. simulans are less stable over multiple years than comparable clines in D. melanogaster. D. simulans shows a significantly weaker pattern of isolation by distance than D. melanogaster and we find evidence for a stronger contribution of migration to D. simulans population genetic structure. While population bottlenecks and migration can plausibly explain the differences in stability of clinal variation between the two species, we also observe a significant enrichment of shared clinal genes, suggesting that the selective forces associated with climate are acting on the same genes and phenotypes in D. simulans and D. melanogaster. © 2015 John Wiley & Sons Ltd.

  7. Socio-economic factors associated with the 1‑year prevalence of severe pain and pain-related sickness absence in the Austrian population.

    Science.gov (United States)

    Mittendorfer-Rutz, Ellenor; Dorner, Thomas Ernst

    2018-01-01

    The aim of this study was to (1) investigate the relation of socio-economic status (SES), measured as education, occupation, and income, with the 12-month prevalence of severe pain and with pain-related sickness absence, and (2) analyse to what extent sociodemographic and medical factors influence these associations. The study population comprised 8084 subjects aged between 15 and 65 years from the Austrian Health Interview Survey in 2006/07. Associations of SES with the 1‑year prevalence of severe pain and sickness absence due to pain in those with severe pain was assessed with logistic regression analysis and adjusted for socio-demographic and chronic medical conditions. The 1‑year prevalence of severe pain was 33.7%. Among those with severe pain, 32.9% were on sickness absence due to pain. SES was significantly associated with the prevalence of severe pain and even more strongly with sickness absence due to pain. Stepwise adjustment for socio-demographics and medical factors had only marginal effects on these associations. Multivariate odds ratios (ORs) for severe pain were 1.14; 1.18 and 1.32 for low income, blue-collar workers, and low education, respectively. Related ORs for sickness absence due to pain were 1.52; 1.14 and 2.05. There was an association between SES, particularly measured as educational level, and the prevalence of severe pain, which was even stronger with sickness absence due to pain.

  8. Genome-Wide Meta-Analysis of Sciatica in Finnish Population.

    Science.gov (United States)

    Lemmelä, Susanna; Solovieva, Svetlana; Shiri, Rahman; Benner, Christian; Heliövaara, Markku; Kettunen, Johannes; Anttila, Verneri; Ripatti, Samuli; Perola, Markus; Seppälä, Ilkka; Juonala, Markus; Kähönen, Mika; Salomaa, Veikko; Viikari, Jorma; Raitakari, Olli T; Lehtimäki, Terho; Palotie, Aarno; Viikari-Juntura, Eira; Husgafvel-Pursiainen, Kirsti

    2016-01-01

    Sciatica or the sciatic syndrome is a common and often disabling low back disorder in the working-age population. It has a relatively high heritability but poorly understood molecular mechanisms. The Finnish population is a genetic isolate where small founder population and bottleneck events have led to enrichment of certain rare and low frequency variants. We performed here the first genome-wide association (GWAS) and meta-analysis of sciatica. The meta-analysis was conducted across two GWAS covering 291 Finnish sciatica cases and 3671 controls genotyped and imputed at 7.7 million autosomal variants. The most promising loci (psciatica patients and 18,489 controls. We identified five intragenic variants, with relatively low frequencies, at two novel loci associated with sciatica at genome-wide significance. These included chr9:14344410:I (rs71321981) at 9p22.3 (NFIB gene; p = 1.30x10-8, MAF = 0.08) and four variants at 15q21.2: rs145901849, rs80035109, rs190200374 and rs117458827 (MYO5A; p = 1.34x10-8, MAF = 0.06; p = 2.32x10-8, MAF = 0.07; p = 3.85x10-8, MAF = 0.06; p = 4.78x10-8, MAF = 0.07, respectively). The most significant association in the meta-analysis, a single base insertion rs71321981 within the regulatory region of the transcription factor NFIB, replicated in an independent Finnish population sample (p = 0.04). Despite identifying 15q21.2 as a promising locus, we were not able to replicate it. It was differentiated; the lead variants within 15q21.2 were more frequent in Finland (6-7%) than in other European populations (1-2%). Imputation accuracies of the three significantly associated variants (chr9:14344410:I, rs190200374, and rs80035109) were validated by genotyping. In summary, our results suggest a novel locus, 9p22.3 (NFIB), which may be involved in susceptibility to sciatica. In addition, another locus, 15q21.2, emerged as a promising one, but failed to replicate.

  9. Genetic structure, diversity, and interisland dispersal in the endangered Mariana Common Moorhen (Gallinula chloropus guami)

    Science.gov (United States)

    Miller, Mark P.; Mullins, Thomas D.; Haig, Susan M.; Takano, Leilani L.; Garcia, Karla

    2015-01-01

    The Mariana Common Moorhen (Gallinula chloropus guami) is a highly endangered taxon, with fewer than 300 individuals estimated to occur in the wild. The subspecies is believed to have undergone population declines attributable to loss of wetland habitats on its native islands in the Mariana Islands. We analyzed mitochondrial DNA (mtDNA) sequences (control region and ND2 genes) and nuclear microsatellite loci in Mariana Common Moorhens from Guam and Saipan, the two most distal islands inhabited by the subspecies. Our analyses revealed similar nuclear genetic diversity and effective population size estimates on Saipan and Guam. Birds from Guam and Saipan were genetically differentiated (microsatellites: FST = 0.152; control region: FST = 0.736; ND2: FST= 0.390); however, assignment tests revealed the presence of first-generation dispersers from Guam onto Saipan (1 of 27 sampled birds) and from Saipan onto Guam (2 of 28 sampled birds), suggesting the capability for long-distance interpopulation movements within the subspecies. The observed dispersal rate was consistent with long-term estimates of effective numbers of migrants per generation between islands, indicating that movement between islands has been an ongoing process in this system. Despite known population declines, bottleneck tests revealed no signature of historical bottleneck events, suggesting that the magnitude of past population declines may have been comparatively small relative to the severity of declines that can be detected using genetic data.

  10. Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice

    Directory of Open Access Journals (Sweden)

    Olsen Kenneth M

    2010-06-01

    Full Text Available Abstract Background Weedy rice (red rice, a conspecific weed of cultivated rice (Oryza sativa L., is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution. Results We find greater population structure than has been previously reported for U.S. weedy rice, and that the multiple, genetically divergent populations have separate origins. The two main U.S. weedy rice populations share genetic backgrounds with cultivated O. sativa varietal groups not grown commercially in the U.S., suggesting weed origins from domesticated ancestors. Hybridization between weedy groups and between weedy rice and local crops has also led to the evolution of distinct U.S. weedy rice populations. Demographic simulations indicate differences among the main weedy groups in the impact of bottlenecks on their establishment in the U.S., and in the timing of divergence from their cultivated relatives. Conclusions Unlike prior research, we did not find unambiguous evidence for U.S. weedy rice originating via hybridization between cultivated and wild Oryza species. Our results demonstrate the potential for weedy life-histories to evolve directly from within domesticated lineages. The diverse origins of U.S. weedy rice populations demonstrate the multiplicity of evolutionary forces that can influence the emergence of weeds from a single species complex.

  11. The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three-spine sticklebacks in divergent environments.

    Science.gov (United States)

    Ferchaud, Anne-Laure; Hansen, Michael M

    2016-01-01

    Heterogeneous genomic divergence between populations may reflect selection, but should also be seen in conjunction with gene flow and drift, particularly population bottlenecks. Marine and freshwater three-spine stickleback (Gasterosteus aculeatus) populations often exhibit different lateral armour plate morphs. Moreover, strikingly parallel genomic footprints across different marine-freshwater population pairs are interpreted as parallel evolution and gene reuse. Nevertheless, in some geographic regions like the North Sea and Baltic Sea, different patterns are observed. Freshwater populations in coastal regions are often dominated by marine morphs, suggesting that gene flow overwhelms selection, and genomic parallelism may also be less pronounced. We used RAD sequencing for analysing 28 888 SNPs in two marine and seven freshwater populations in Denmark, Europe. Freshwater populations represented a variety of environments: river populations accessible to gene flow from marine sticklebacks and large and small isolated lakes with and without fish predators. Sticklebacks in an accessible river environment showed minimal morphological and genomewide divergence from marine populations, supporting the hypothesis of gene flow overriding selection. Allele frequency spectra suggested bottlenecks in all freshwater populations, and particularly two small lake populations. However, genomic footprints ascribed to selection could nevertheless be identified. No genomic regions were consistent freshwater-marine outliers, and parallelism was much lower than in other comparable studies. Two genomic regions previously described to be under divergent selection in freshwater and marine populations were outliers between different freshwater populations. We ascribe these patterns to stronger environmental heterogeneity among freshwater populations in our study as compared to most other studies, although the demographic history involving bottlenecks should also be considered in the

  12. The effect of genetic bottlenecks and inbreeding on the incidence of two major autoimmune diseases in standard poodles, sebaceous adenitis and Addison's disease.

    Science.gov (United States)

    Pedersen, Niels C; Brucker, Lynn; Tessier, Natalie Green; Liu, Hongwei; Penedo, Maria Cecilia T; Hughes, Shayne; Oberbauer, Anita; Sacks, Ben

    2015-01-01

    Sebaceous adenitis (SA) and Addison's disease (AD) increased rapidly in incidence among Standard Poodles after the mid-twentieth century. Previous attempts to identify specific genetic causes using genome wide association studies and interrogation of the dog leukocyte antigen (DLA) region have been non-productive. However, such studies led us to hypothesize that positive selection for desired phenotypic traits that arose in the mid-twentieth century led to intense inbreeding and the inadvertent amplification of AD and SA associated traits. This hypothesis was tested with genetic studies of 761 Standard, Miniature, and Miniature/Standard Poodle crosses from the USA, Canada and Europe, coupled with extensive pedigree analysis of thousands more dogs. Genome-wide diversity across the world-wide population was measured using a panel of 33 short tandem repeat (STR) loci. Allele frequency data were also used to determine the internal relatedness of individual dogs within the population as a whole. Assays based on linkage between STR genomic loci and DLA genes were used to identify class I and II haplotypes and disease associations. Genetic diversity statistics based on genomic STR markers indicated that Standard Poodles from North America and Europe were closely related and reasonably diverse across the breed. However, genetic diversity statistics, internal relatedness, principal coordinate analysis, and DLA haplotype frequencies showed a marked imbalance with 30 % of the diversity in 70 % of the dogs. Standard Poodles with SA and AD were strongly linked to this inbred population, with dogs suffering with SA being the most inbred. No single strong association was found between STR defined DLA class I or II haplotypes and SA or AD in the breed as a whole, although certain haplotypes present in a minority of the population appeared to confer moderate degrees of risk or protection against either or both diseases. Dogs possessing minor DLA class I haplotypes were half as

  13. Relationship between seasonal weather changes, risk of dehydration, and incidence of severe bradyarrhythmias requiring urgent temporary transvenous cardiac pacing in an elderly population

    Science.gov (United States)

    Palmisano, Pietro; Accogli, Michele; Zaccaria, Maria; Vergari, Alessandra; De Luca De Masi, Gabriele; Negro, Luca; De Blasi, Sergio

    2014-09-01

    There is little information on any seasonal variations or meteorological factors associated with symptomatic bradyarrhythmias requiring cardiac pacing. The aim of this single-center study was to investigate the seasonal distribution of the incidence of severe, life-threatening bradyarrhythmias requiring urgent temporary transvenous cardiac pacing in an elderly population. Consecutive patients who underwent urgent temporary transvenous cardiac pacing between 2007 and 2012 were enrolled. The baseline characteristics of the patients and some meteorological parameters, including the calculation the daily heat index (HI), were recorded. During the study period, 79 consecutive patients (mean age 82 ± 8 years, 41 % male) underwent urgent temporary transvenous cardiac pacing, mainly for third-degree atrioventricular block (79 %). The incidence of bradyarrhythmias was significantly higher in summer than in the other seasons ( P 90 °F for >3 h per day for at least 10 days ( P renal function impairment and hyperkalemia (all P < 0.05). This study showed an increased incidence of severe bradyarrhythmias in an elderly population during the hottest months of the year. In these months, in subjects characterized by increased susceptibility to dehydration, the risk of developing bradyarrhythmias was increased significantly.

  14. Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action

    Directory of Open Access Journals (Sweden)

    Ruth McNerney

    2017-03-01

    Full Text Available Whole genome sequencing (WGS can provide a comprehensive analysis of Mycobacterium tuberculosis mutations that cause resistance to anti-tuberculosis drugs. With the deployment of bench-top sequencers and rapid analytical software, WGS is poised to become a useful tool to guide treatment. However, direct sequencing from clinical specimens to provide a full drug resistance profile remains a serious challenge. This article reviews current practices for extracting M. tuberculosis DNA and possible solutions for sampling sputum. Techniques under consideration include enzymatic digestion, physical disruption, chemical degradation, detergent solubilization, solvent extraction, ligand-coated magnetic beads, silica columns, and oligonucleotide pull-down baits. Selective amplification of genomic bacterial DNA in sputum prior to WGS may provide a solution, and differential lysis to reduce the levels of contaminating human DNA is also being explored. To remove this bottleneck and accelerate access to WGS for patients with suspected drug-resistant tuberculosis, it is suggested that a coordinated and collaborative approach be taken to more rapidly optimize, compare, and validate methodologies for sequencing from patient samples.

  15. Genetic diversity and a population structure analysis of accessions in the Chinese cowpea [Vigna unguiculata (L. Walp.] germplasm collection

    Directory of Open Access Journals (Sweden)

    Honglin Chen

    2017-10-01

    Full Text Available Cowpea (Vigna unguiculata is an important legume crop with diverse uses. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, a total of 200 genic and 100 genomic simple sequence repeat (SSR markers were developed from cowpea unigene and genome sequences, respectively. Among them, 27 genic and 27 genomic SSR markers were polymorphic and were used for assessment of genetic diversity and population structure in 105 selected cowpea accessions. A total of 155 alleles and 2.9 alleles per marker were identified, and the average polymorphic information content (PIC value was 0.3615. The average PIC of genomic SSRs (0.3996 was higher than that of genic SSRs (0.3235, and most of the polymorphic genomic SSRs were composed of di- and trinucleotide repeats (51.9% and 37.0% of all loci, respectively. The low level of detected genetic diversity may be attributed to a severe genetic bottleneck that occurred during the cowpea domestication process. The accessions were classified by structure and cluster analysis into four subgroups that correlated well with their geographic origins or collection sites. The classification results were also consistent with the results from principal coordinate analysis and can be used as a guide during future germplasm collection and selection of accessions as breeding materials for cultivar improvement. The newly developed genic and genomic SSR markers described in this study will be valuable genomic resources for the assessment of genetic diversity, population structure, evaluation of germplasm accessions, construction of genetic maps, identification of genes of interest, and application of marker-assisted selection in cowpea breeding programs.

  16. Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery.

    Science.gov (United States)

    Scott, Eric M; Halees, Anason; Itan, Yuval; Spencer, Emily G; He, Yupeng; Azab, Mostafa Abdellateef; Gabriel, Stacey B; Belkadi, Aziz; Boisson, Bertrand; Abel, Laurent; Clark, Andrew G; Alkuraya, Fowzan S; Casanova, Jean-Laurent; Gleeson, Joseph G

    2016-09-01

    The Greater Middle East (GME) has been a central hub of human migration and population admixture. The tradition of consanguinity, variably practiced in the Persian Gulf region, North Africa, and Central Asia, has resulted in an elevated burden of recessive disease. Here we generated a whole-exome GME variome from 1,111 unrelated subjects. We detected substantial diversity and admixture in continental and subregional populations, corresponding to several ancient founder populations with little evidence of bottlenecks. Measured consanguinity rates were an order of magnitude above those in other sampled populations, and the GME population exhibited an increased burden of runs of homozygosity (ROHs) but showed no evidence for reduced burden of deleterious variation due to classically theorized 'genetic purging'. Applying this database to unsolved recessive conditions in the GME population reduced the number of potential disease-causing variants by four- to sevenfold. These results show variegated genetic architecture in GME populations and support future human genetic discoveries in Mendelian and population genetics.

  17. Felbamate in an adult population with severe refractory epilepsy.

    LENUS (Irish Health Repository)

    Kearney, H

    2011-04-05

    Felbamate (FBM) is efficacious in treating patients with refractory epilepsy but was withdrawn due to cases of aplastic anaemia, hepatic failure and five reported deaths. FBM is currently used in specialist centres and is only being used in one Irish centre to date. This papers aim is to review the efficacy and safety experience of FBM in Irish adult patients with refractory epilepsy. A retrospective chart review was done on patients\\' medical records. Patients were subdivided into responders and non responders based on change in seizure frequency and side effects were recorded for all. Of the 13 patients on FBM nine patients responded to FBM, four patients did not. FBM is a safe and efficacious alternative in an Irish adult population with refractory epilepsy. However close monitoring is still required given the potential fatal side effects that are possible with this anticonvulsant.

  18. Combinatorial analysis of enzymatic bottlenecks of L-tyrosine pathway by p-coumaric acid production in Saccharomyces cerevisiae.

    Science.gov (United States)

    Mao, Jiwei; Liu, Quanli; Song, Xiaofei; Wang, Hesuiyuan; Feng, Hui; Xu, Haijin; Qiao, Mingqiang

    2017-07-01

    To identify new enzymatic bottlenecks of L-tyrosine pathway for further improving the production of L-tyrosine and its derivatives. When ARO4 and ARO7 were deregulated by their feedback resistant derivatives in the host strains, the ARO2 and TYR1 genes, coding for chorismate synthase and prephenate dehydrogenase were further identified as new important rate-limiting steps. The yield of p-coumaric acid in the feedback-resistant strain overexpressing ARO2 or TYR1, was significantly increased from 6.4 to 16.2 and 15.3 mg l -1 , respectively. Subsequently, we improved the strain by combinatorial engineering of pathway genes increasing the yield of p-coumaric acid by 12.5-fold (from 1.7 to 21.3 mg l -1 ) compared with the wild-type strain. Batch cultivations revealed that p-coumaric acid production was correlated with cell growth, and the formation of by-product acetate of the best producer NK-M6 increased to 31.1 mM whereas only 19.1 mM acetate was accumulated by the wild-type strain. Combinatorial metabolic engineering provides a new strategy for further improvement of L-tyrosine or other metabolic biosynthesis pathways in S. cerevisiae.

  19. Population. Headline Series.

    Science.gov (United States)

    Oppenheimer, Valerie K.

    Useful as background reading or secondary classroom material, this pamphlet reviews several dimensions of world population growth and control. The first of seven chapters, World Population Growth: Past, Present and Future, discusses some of the reasons for the greatly accelerated growth since 1950, and points out that even significantly rapid…

  20. Hunter-gatherer genomic diversity suggests a southern African origin for modern humans.

    Science.gov (United States)

    Henn, Brenna M; Gignoux, Christopher R; Jobin, Matthew; Granka, Julie M; Macpherson, J M; Kidd, Jeffrey M; Rodríguez-Botigué, Laura; Ramachandran, Sohini; Hon, Lawrence; Brisbin, Abra; Lin, Alice A; Underhill, Peter A; Comas, David; Kidd, Kenneth K; Norman, Paul J; Parham, Peter; Bustamante, Carlos D; Mountain, Joanna L; Feldman, Marcus W

    2011-03-29

    Africa is inferred to be the continent of origin for all modern human populations, but the details of human prehistory and evolution in Africa remain largely obscure owing to the complex histories of hundreds of distinct populations. We present data for more than 580,000 SNPs for several hunter-gatherer populations: the Hadza and Sandawe of Tanzania, and the ≠Khomani Bushmen of South Africa, including speakers of the nearly extinct N|u language. We find that African hunter-gatherer populations today remain highly differentiated, encompassing major components of variation that are not found in other African populations. Hunter-gatherer populations also tend to have the lowest levels of genome-wide linkage disequilibrium among 27 African populations. We analyzed geographic patterns of linkage disequilibrium and population differentiation, as measured by F(ST), in Africa. The observed patterns are consistent with an origin of modern humans in southern Africa rather than eastern Africa, as is generally assumed. Additionally, genetic variation in African hunter-gatherer populations has been significantly affected by interaction with farmers and herders over the past 5,000 y, through both severe population bottlenecks and sex-biased migration. However, African hunter-gatherer populations continue to maintain the highest levels of genetic diversity in the world.

  1. Middle Stone Age bedding construction and settlement patterns at Sibudu, South Africa.

    Science.gov (United States)

    Wadley, Lyn; Sievers, Christine; Bamford, Marion; Goldberg, Paul; Berna, Francesco; Miller, Christopher

    2011-12-09

    The Middle Stone Age (MSA) is associated with early behavioral innovations, expansions of modern humans within and out of Africa, and occasional population bottlenecks. Several innovations in the MSA are seen in an archaeological sequence in the rock shelter Sibudu (South Africa). At ~77,000 years ago, people constructed plant bedding from sedges and other monocotyledons topped with aromatic leaves containing insecticidal and larvicidal chemicals. Beginning at ~73,000 years ago, bedding was burned, presumably for site maintenance. By ~58,000 years ago, bedding construction, burning, and other forms of site use and maintenance intensified, suggesting that settlement strategies changed. Behavioral differences between ~77,000 and 58,000 years ago may coincide with population fluctuations in Africa.

  2. Predictors of childhood severe malaria in a densely populated area ...

    African Journals Online (AJOL)

    Coma, convulsions and unconsciousness were more indicative of cerebral malaria. Hemoglobin and blood glucose levels decreased significantly in severe malaria patients compared with uncomplicated malaria patients or controls (P < 0.001). On the contrary, blood transaminases and CRP levels increased significantly in ...

  3. [Association study between 834+7G/A and +1332C/T polymorphisms in the growth arrest specific 6 gene and risk of severe preeclampsia in Chinese population].

    Science.gov (United States)

    Ye, Liyan; Guan, Linbo; Fan, Ping; Liu, Xinghui; Liu, Rui; Chen, Jinxin; Zhu, Yue; Wei, Xin; Liu, Yu; Bai, Huai

    2017-02-10

    To investigate the relationship between polymorphisms of the growth arrest specific 6 (GAS6) gene and severe preeclampsia in a South West Han Chinese population. Blood samples from 167 patients with severe preeclampsia and 312 normal pregnant women as controls from Han Chinese in Chengdu area were analyzed by polymerase chain reaction-restriction fragment length polymorphisms. C and T allele frequencies for +1332C/T site were 85.63% and 14.37% in the patient group, respectively, and 78.04% and 21.96% in control group, respectively. The TT genotype and variant T allelic frequencies of the +1332C/T polymorphism were significantly lower in patients with severe preeclampsia than in the control group (both Ppreeclampsia was 0.602 (95%CI: 0.401-0.904) in carriers for the variant T allele (χ 2 =6.045, P=0.014). G and A allele frequencies for 834+7G/A site were 72.75% and 27.25% in case group, respectively, and 74.36% and 25.64% in control group, respectively. The genotype and allele frequencies of the 834+7G/A polymorphism in patients with severe preeclampsia and controls showed no significant differences (both P>0.05). In addition, there was no significant association between the polymorphisms and blood pressure levels in the patient or control groups. The variant GAS6+1332 T allele is associated with a decreased risk for severe preeclampsia in a South West Han Chinese population. On the other hand, the 834+7G/A polymorphism has no effect on the severe preeclampsia.

  4. Evidence of high inbreeding in a population of the endangered giant anteater, Myrmecophaga tridactyla (Myrmecophagidae, from Emas National Park, Brazil

    Directory of Open Access Journals (Sweden)

    Rosane G. Collevatti

    2007-01-01

    Full Text Available We report the genetic structure, relatedness and mating structure of a population of the endangered giant anteater Myrmecophaga tridactyla Linnaeus, 1758 in the Emas National Park, Brazil, based on variability at five microsatellite loci. Additionally, we addressed the hypothesis that the M. tridactyla population studied has low levels of polymorphism and high levels of inbreeding and relatedness and that animals with overlapping home range are highly related. All five microsatellite loci displayed low levels of polymorphism and of expected and observed heterozygosity. The low level of polymorphism and high inbreeding showed by the population studied may be the outcome of high mortality and reduction in population size due to recurrent fire events in the Emas National Park, as reported in 1994. The reduction in population size may have led to a higher frequency of mating between closely related animals, augmented by the isolation of the population in the park because of the expansion of agricultural land and fragmentation of the Cerrado environment. The natural history of M. tridactyla and the phylopatric (sex-biased dispersal behavior of females should increase the effects of isolation and bottlenecking, decreasing gene flow and increasing inbreeding. However, the low levels of polymorphism found in this population may simply be due to the natural history and evolution of M. tridactyla as reported for other species. The genetic structure and dynamics of this population needs to be investigated more profoundly in order to provide sound data for the design of conservation strategies for M. tridactyla in the Emas National Park.

  5. On the expected relationship between inbreeding, fitness, and extinction

    Directory of Open Access Journals (Sweden)

    Couvet Denis

    2006-06-01

    Full Text Available Abstract We assessed the expected relationship between the level and the cost of inbreeding, measured either in terms of fitness, inbreeding depression or probability of extinction. First, we show that the assumption of frequent, slightly deleterious mutations do agree with observations and experiments, on the contrary to the assumption of few, moderately deleterious mutations. For the same inbreeding coefficient, populations can greatly differ in fitness according to the following: (i population size; larger populations show higher fitness (ii the history of population size; in a population that recovers after a bottleneck, higher inbreeding can lead to higher fitness and (iii population demography; population growth rate and carrying capacity determine the relationship between inbreeding and extinction. With regards to the relationship between inbreeding depression and inbreeding coefficient, the population size that minimizes inbreeding depression depends on the level of inbreeding: inbreeding depression can even decrease when population size increases. It is therefore clear that to infer the costs of inbreeding, one must know both the history of inbreeding (e.g. past bottlenecks and population demography.

  6. Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics.

    Science.gov (United States)

    Yang, Lulu; Chen, Jianjun; Hu, Weiming; Yang, Tianshun; Zhang, Yanjun; Yukiyoshi, Tamura; Zhou, Yanyang; Wang, Ying

    2016-01-01

    Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been shaped by habitat

  7. Single-photon emission computed tomography myocardial perfusion imaging-assessed stress perfusion defect severity is associated with mortality independent of ethnicity in an Asian population.

    Science.gov (United States)

    Chin, Chee Tang; Gao, Fei; Keng, Felix Y J; Shah, Bimal R; Koh, Angela S; Tan, Ru San; Chua, Terrance S J

    2014-12-01

    Ischemic heart disease is growing by epidemic proportions in Asia. Among patients in Western populations with similar myocardial perfusion imaging (MPI) ischemia severity, ethnicity is independently associated with mortality. We aimed to determine the differential prognostic value of MPI abnormality severity among three major Asian ethnic groups. From 16,921 consecutive patients, we used summed stress score to define increasing abnormal scan severity groups (minimal, mild, moderate, and severe) among Chinese, Indian, and Malay patients. We determined mortality from the national death registry. Using multivariable Cox regression models, we examined the association between ethnicity and mortality. Chinese patients were older than Indians or Malays. Annual all-cause death rates increased with increasing abnormal scan severity in all three ethnicities. After adjustment, ethnicity was not associated with mortality. With Chinese as the reference group, adjusted hazard ratio and 95% CI for Malays and Indians were 1.29 (0.95-1.77) and 1.06 (0.74-1.50) in the minimally abnormal scan group, and 1.20 (0.75-1.91) and 0.82 (0.47-1.45) in the severely abnormal scan group, respectively. Mortality risk is related to the severity of scan abnormality and is independent of ethnicity in Asians. Our findings emphasize the continued utility of MPI in guiding risk stratification in Asia.

  8. Population genetic structure in natural and reintroduced beaver (Castor fiber populations in Central Europe

    Directory of Open Access Journals (Sweden)

    Kautenburger, R.

    2008-12-01

    Full Text Available Castor fiber Linnaeus, 1758 is the only indigenous species of the genus Castor in Europe and Asia. Due to extensive hunting until the beginning of the 20th century, the distribution of the formerly widespread Eurasian beaver was dramatically reduced. Only a few populations remained and these were in isolated locations, such as the region of the German Elbe River. The loss of genetic diversity in small or captive populations throughgenetic drift and inbreeding is a severe conservation problem. However, the reintroduction of beaver populations from several regions in Europe has shown high viability and populations today are growing fast. In the present study we analysed the population genetic structure of a natural and two reintroduced beaver populations in Germany and Austria. Furthermore, we studied the genetic differentiation between two beaver species, C. fiber and the American beaver (C. canadensis, using RAPD (Random Amplified Polymorphic DNA as a genetic marker. The reintroduced beaver populations of different origins and the autochthonous population of the Elbe River showed a similar low genetic heterogeneity. There was an overall high genetic similarity in the species C. fiber, and no evidence was found for a clear subspecific structure in the populations studied.

  9. Accelerated fetal growth in early pregnancy and risk of severe large-for-gestational-age and macrosomic infant: a cohort study in a low-risk population.

    Science.gov (United States)

    Simic, Marija; Wikström, Anna-Karin; Stephansson, Olof

    2017-10-01

    Our objective was to examine the association between fetal growth in early pregnancy and risk of severe large-for-gestational-age (LGA) and macrosomia at birth in a low-risk population. Cohort study that included 68 771 women with non-anomalous singleton pregnancies, without history of diabetes or hypertension, based on an electronic database on pregnancies and deliveries in Stockholm-Gotland Region, Sweden, 2008-2014. We performed multivariable logistic regression to estimate the association between accelerated fetal growth occurring in the first through early second trimester as measured by ultrasound and LGA and macrosomia at birth. Restricted analyses were performed in the groups without gestational diabetes and with normal body mass index (18.5-24.9 kg/m 2 ). When adjusting for confounders, the odds of having a severely LGA or macrosomic infant were elevated in mothers with fetuses that were at least 7 days larger than expected as compared with mothers without age discrepancy at the second-trimester scan (adjusted odds ratio 1.80; 95% CI 1.23-2.64 and adjusted odds ratio 2.15; 95% CI 1.55-2.98, respectively). Additionally, mothers without gestational diabetes and mothers with normal weight had an elevated risk of having a severely LGA or macrosomic infant when the age discrepancy by second-trimester ultrasound was at least 7 days. In a low-risk population, ultrasound-estimated accelerated fetal growth in early pregnancy was associated with an increased risk of having a severely LGA or macrosomic infant. © 2017 Nordic Federation of Societies of Obstetrics and Gynecology.

  10. [Collective immunity against poliomyelitis among the population of several regions of Russia].

    Science.gov (United States)

    Seybil, V B; Malyshkina, L P; Ageeva, O T; Kosolapova, E I; Mnozhina, E G; Groshenkova, E V; Krivtsov, N V; Gurianova, N I; Daltsaeva, M K; Fomina, N S

    2015-01-01

    The goal of this work was to estimate the collective immunity against poliomyelitis among the population of 8 regions and republics of Russia. The rates of the collective immunity against poliomyelitis allow the polio vaccination quality to be estimated and the population protection rate to be simultaneously demonstrated. A total of 8 regions (2138 people) were tested. The antibodies to the polioviruses of 1-3 types were determined against the vaccine Sabin strains in the neutralization test in the RD cell line. As a result, we found that vaccination against poliomyelitis in all observed regions was maintained at the required high level. Thus, the number of people with antibodies to the polio in most regions and age groups approximates or reaches 100%, while GMT is also high. This work demonstrated the necessity of the continuation of vaccination against poliomyelitis and control over collective immunity.

  11. Enriching the Metadata on CERN Document Server And Implementation of a Book Acquisition System To Predict the potential bottlenecks in availability of records in Library

    CERN Document Server

    Ahuja, Chakshu

    2015-01-01

    The automated script for data acquisition project ( bibtasklet ) which aims to enhance existing metadata in our CERN Document Server with data from Springer was implemented. An implicit part of this task is to manage disambiguation (within incoming data), removal of multiple entries, handle replications between new and existing records and further automate the latest file upload task to CDS. All such elements and their corresponding changes are integrated within Invenio to make the upgraded metadata available on the CDS. Another implementation was to make a web interface for the invenio software to calculate the normalized loan period to help the librarians to predict bottleneck on the books on loan over certain period of time and facilitate their decision to buy the new records accordingly.

  12. Genetic structure and conservation of Mountain Lions in the South-Brazilian Atlantic Rain Forest

    Directory of Open Access Journals (Sweden)

    Camila S. Castilho

    2012-01-01

    Full Text Available The Brazilian Atlantic Rain Forest, one of the most endangered ecosystems worldwide, is also among the most important hotspots as regards biodiversity. Through intensive logging, the initial area has been reduced to around 12% of its original size. In this study we investigated the genetic variability and structure of the mountain lion, Puma concolor. Using 18 microsatellite loci we analyzed evidence of allele dropout, null alleles and stuttering, calculated the number of allele/locus, PIC, observed and expected heterozygosity, linkage disequilibrium, Hardy-Weinberg equilibrium, F IS, effective population size and genetic structure (MICROCHECKER, CERVUS, GENEPOP, FSTAT, ARLEQUIN, ONESAMP, LDNe, PCAGEN, GENECLASS software,we also determine whether there was evidence of a bottleneck (HYBRIDLAB, BOTTLENECK software that might influence the future viability of the population in south Brazil. 106 alleles were identified, with the number of alleles/locus ranging from 2 to 11. Mean observed heterozygosity, mean number of alleles and polymorphism information content were 0.609, 5.89, and 0.6255, respectively. This population presented evidence of a recent bottleneck and loss of genetic variation. Persistent regional poaching constitutes an increasing in the extinction risk.

  13. Estuary wader capacity following severe weather mortality

    International Nuclear Information System (INIS)

    Clark, J.A.; Baillie, S.R.; Clark, N.A.; Langston, R.H.W.

    1993-01-01

    The building of a tidal power barrage across an estuary may lead to substantial changes in its ecology. Many of Britain's estuaries hold internationally important numbers of waders. Careful consideration, therefore, needs to be given to the likely effects of tidal power barrages on wader populations. The opportunity for increased understanding of the mechanisms which govern wader populations was provided by a period of severe winter weather in 1991, which resulted in a substantial mortality of waders in eastern England. Such conditions are known to be stressful to birds and the study objectives were to investigate both the effects of and recovery from severe weather. (author)

  14. Genetic composition of captive panda population.

    Science.gov (United States)

    Yang, Jiandong; Shen, Fujun; Hou, Rong; Da, Yang

    2016-10-03

    A major function of the captive panda population is to preserve the genetic diversity of wild panda populations in their natural habitats. Understanding the genetic composition of the captive panda population in terms of genetic contributions from the wild panda populations provides necessary knowledge for breeding plans to preserve the genetic diversity of the wild panda populations. The genetic contributions from different wild populations to the captive panda population were highly unbalanced, with Qionglai accounting for 52.2 % of the captive panda gene pool, followed by Minshan with 21.5 %, Qinling with 10.6 %, Liangshan with 8.2 %, and Xiaoxiangling with 3.6 %, whereas Daxiangling, which had similar population size as Xiaoxiangling, had no genetic representation in the captive population. The current breeding recommendations may increase the contribution of some small wild populations at the expense of decreasing the contributions of other small wild populations, i.e., increasing the Xiaoxiangling contribution while decreasing the contribution of Liangshan, or sharply increasing the Qinling contribution while decreasing the contributions of Xiaoxiangling and Liangshan, which were two of the three smallest wild populations and were already severely under-represented in the captive population. We developed three habitat-controlled breeding plans that could increase the genetic contributions from the smallest wild populations to 6.7-11.2 % for Xiaoxiangling, 11.5-12.3 % for Liangshan and 12.9-20.0 % for Qinling among the offspring of one breeding season while reducing the risk of hidden inbreeding due to related founders from the same habitat undetectable by pedigree data. The three smallest wild panda populations of Daxiangling, Xiaoxiangling and Liangshan either had no representation or were severely unrepresented in the current captive panda population. By incorporating the breeding goal of increasing the genetic contributions from the smallest wild

  15. Co-morbidities in severe asthma

    DEFF Research Database (Denmark)

    Porsbjerg, Celeste; Menzies-Gow, Andrew

    2017-01-01

    Patients with severe asthma represent a minority of the total asthma population, but carry a majority of the morbidity and healthcare costs. Achieving better asthma control in this group of patients is therefore of key importance. Systematic assessment of patients with possible severe asthma...... to identify treatment barriers and triggers of asthma symptoms, including co-morbidities, improves asthma control and reduces healthcare costs and is recommended by international guidelines on management of severe asthma. This review provides the clinician with an overview of the prevalence and clinical...... impact of the most common co-morbidities in severe asthma, including chronic rhinosinusitis, nasal polyposis, allergic rhinitis, dysfunctional breathing, vocal cord dysfunction, anxiety and depression, obesity, obstructive sleep apnoea syndrome (OSAS), gastroesophageal reflux disease (GERD...

  16. Processes shaping gut microbiota diversity in allopatric populations of the endemic lizard Podarcis lilfordi from Menorcan islets (Balearic Islands).

    Science.gov (United States)

    Baldo, Laura; Riera, Joan Lluís; Mitsi, Konstantina; Pretus, Joan Lluís

    2018-02-01

    Compositional variation of the gut microbiota across host allopatric populations can reflect both adaptation and stochasticity since the time of separation. Major factors shaping this variation include the host phylogeographic and demographic history, the microbiota inheritance, environmental inputs and dispersal of bacteria. Here we explored the impact of these factors in driving gut community diversity in seven allopatric populations of the omnivorous lizard Podarcis lilfordi from the Menorcan coastal islets, all descending from an ancestral mainland population. Using 16S rRNA Illumina sequencing, we showed that 'islet' and 'age' (time since islet separation from mainland) were the only significant variables in microbial community clustering, suggesting a partial islet-restricted diversification following these lizards phylogeography. Despite a significant variation, islets/populations were characterized by a remarkably low bacterial uniqueness (2.4% of total OTUs) and a minor differential enrichment of taxa, indicating a negligible impact of local inputs and important host common constraints. Overall, the extant pattern of similarity/dissimilarity among islets is compatible with partial retention of the ancestral mainland microbial pool, with differences among islets potentially explained by a differential loss of bacteria following population fragmentation and bottlenecks (i.e. ecological drift). While more quantitative data are needed to validate this hypothesis, this study unveils the importance of considering both neutral and niche-driven processes in driving contemporary patterns of gut metacommunity diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. Population Genetics as a Tool to Select Tsetse Control Strategies: Suppression or Eradication of Glossina palpalis gambiensis in the Niayes of Senegal

    International Nuclear Information System (INIS)

    Solano, Philippe; Kaba, Dramane; Ravel, Sophie; Sall, Baba; Mathu Ndung'u, Joseph

    2010-01-01

    The Government of Senegal has initiated the ''Projet de lutte contre les glossines dans les Niayes'' to remove the trypanosomosis problem from this area in a sustainable way. Due to past failures to sustainably eradicate Glossina palpalis gambiensis from the Niayes area, controversies remain as to the best strategy implement, i.e. ''eradication'' versus ''supression''.To inform this debate, we used population genetics to measure genetic differentiation between G. palpalis gambiensis from the Niayes and those from the southern tsetse belt (Missira).Three different markers (microsatellite DNA, mitochondrial CO1 DNA, and geometric morphometrics of the wings) were used on 153 individuals and revealed that the G. p. gambiensis populations of the Niayes were genetically isolated from the nearest proximate known population of Missira. The genetic differentiation measured between these two areas (h=0.12 using microsatellites) was equivalent to a between-taxa differentiation. We also demonstrated that within the Niayes, the population from Dakar Hann was isolated from the others and had probably experienced a bottleneck.The information presented in this paper leads to the recommendation that an eradication strategy for the Niayes populations is advisable. This kind of study may be repeated in other habitats and for other tsetse species to help decision on appropriate tsetse control strategies and find other possible discontinuities in tsetse distribution.

  18. Aetiology and severity of gingival recession in an adult population sample in Greece

    Directory of Open Access Journals (Sweden)

    Nikolaos Andreas Chrysanthakopoulos

    2011-01-01

    Full Text Available Background: Gingival recession is the most common and undesirable condition of the gingiva. The aim of study was to investigate the aetiology and severity of gingival recession in a Greek adult population sample. Methods : The study was performed on 165 males and 179 females, 18-68 years old who sought dental treatment in a private dental practice and showed gingival recession. All subjects were clinically examined and answered questions regarding their oral hygiene habits such as the type of toothbrush, frequency of brushing and method of brushing. The association between gingival recession and the following parameters was assessed: plaque score, gingival score and tooth position. Statistical analysis of the results was accomplished using chi-square test (α = 0.05. Results: The majority (79.4% of the patients showed grade I gingival recession and 15.3% showed grade II gingival recession. The maxillary 1 st and 2 nd molars (35.3% and the mandibular 1 st and 2 nd molars (28.7% were the teeth most frequently affected by root surface exposure. Patients with sub-gingival calculus, bacterial plaque and gingival inflammation (P < 0.05, malpositioned teeth (P < 0.001, horizontal brushing method, medium type of toothbrush (P < 0.001 and brushing once daily (P < 0.001 appeared to be the most common precipitating aetiological factor for gingival recession. Conclusion: According to the results of the present study, gingival recession was the result of more than one factor acting together. Horizontal brushing method, usage of medium type toothbrush and tooth brushing once daily were found to be more associated with gingival recession.

  19. How influenza vaccination policy may affect vaccine logistics.

    Science.gov (United States)

    Assi, Tina-Marie; Rookkapan, Korngamon; Rajgopal, Jayant; Sornsrivichai, Vorasith; Brown, Shawn T; Welling, Joel S; Norman, Bryan A; Connor, Diana L; Chen, Sheng-I; Slayton, Rachel B; Laosiritaworn, Yongjua; Wateska, Angela R; Wisniewski, Stephen R; Lee, Bruce Y

    2012-06-22

    When policymakers make decision about the target populations and timing of influenza vaccination, they may not consider the impact on the vaccine supply chains, which may in turn affect vaccine availability. Our goal is to explore the effects on the Thailand vaccine supply chain of introducing influenza vaccines and varying the target populations and immunization time-frames. We Utilized our custom-designed software HERMES (Highly Extensible Resource for Modeling Supply Chains), we developed a detailed, computational discrete-event simulation model of the Thailand's National Immunization Program (NIP) supply chain in Trang Province, Thailand. A suite of experiments simulated introducing influenza vaccines for different target populations and over different time-frames prior to and during the annual influenza season. Introducing influenza vaccines creates bottlenecks that reduce the availability of both influenza vaccines as well as the other NIP vaccines, with provincial to district transport capacity being the primary constraint. Even covering only 25% of the Advisory Committee on Immunization Practice-recommended population while administering the vaccine over six months hinders overall vaccine availability so that only 62% of arriving patients can receive vaccines. Increasing the target population from 25% to 100% progressively worsens these bottlenecks, while increasing influenza vaccination time-frame from 1 to 6 months decreases these bottlenecks. Since the choice of target populations for influenza vaccination and the time-frame to deliver this vaccine can substantially affect the flow of all vaccines, policy-makers may want to consider supply chain effects when choosing target populations for a vaccine. Copyright © 2012 Elsevier Ltd. All rights reserved.

  20. Tobacco addiction in the psychiatric population and in the general population

    Directory of Open Access Journals (Sweden)

    Renata Marques de Oliveira

    2017-12-01

    Full Text Available ABSTRACT Objective: To estimate the degree of tobacco addiction and identify independently associated factors by comparing the psychiatric population of secondary and tertiary care with the general population of the primary healthcare network. Method: This is a cross-sectional epidemiological study, conducted in a municipality of São Paulo, with 134 smokers of a Mental Health Outpatient Unit (MHOU, a Psychiatric Hospital (PH, and a Primary Healthcare Unit (PHU. Data were collected by means of individual interviews, recorded on a mobile device. Data were statistically processed using Stata/12 Results: Of the 134 participants, 54.5% were women. While 49.1% of the psychiatric population (MHOU/PH had medium/high nicotine addiction, 58.3% of smokers of the general population had very low/low dependency. The Poisson regression model indicated a higher prevalence of smokers with high dependence among men (PR = 1.41, people aged 49 years or less (15 - 29 years, PR = 4.06, 30 - 39 PR = 2.96 years, 40 - 49 years PR = 1.84, with severe mental disorders (PR = 3.05, with anxiety disorders/other (PR = 3.98, and with high suicide risk (PR = 1.55. Conclusion: Nicotine dependence was greater in the psychiatric population than in the general population. The independent factors associated with severe dependence were sex, age group, diagnosis, and current risk of suicide. These results trigger reflection among nurses on the need to focus more attention on a neglected subject in mental health services.

  1. Genome-Wide Meta-Analysis of Sciatica in Finnish Population.

    Directory of Open Access Journals (Sweden)

    Susanna Lemmelä

    Full Text Available Sciatica or the sciatic syndrome is a common and often disabling low back disorder in the working-age population. It has a relatively high heritability but poorly understood molecular mechanisms. The Finnish population is a genetic isolate where small founder population and bottleneck events have led to enrichment of certain rare and low frequency variants. We performed here the first genome-wide association (GWAS and meta-analysis of sciatica. The meta-analysis was conducted across two GWAS covering 291 Finnish sciatica cases and 3671 controls genotyped and imputed at 7.7 million autosomal variants. The most promising loci (p<1x10-6 were replicated in 776 Finnish sciatica patients and 18,489 controls. We identified five intragenic variants, with relatively low frequencies, at two novel loci associated with sciatica at genome-wide significance. These included chr9:14344410:I (rs71321981 at 9p22.3 (NFIB gene; p = 1.30x10-8, MAF = 0.08 and four variants at 15q21.2: rs145901849, rs80035109, rs190200374 and rs117458827 (MYO5A; p = 1.34x10-8, MAF = 0.06; p = 2.32x10-8, MAF = 0.07; p = 3.85x10-8, MAF = 0.06; p = 4.78x10-8, MAF = 0.07, respectively. The most significant association in the meta-analysis, a single base insertion rs71321981 within the regulatory region of the transcription factor NFIB, replicated in an independent Finnish population sample (p = 0.04. Despite identifying 15q21.2 as a promising locus, we were not able to replicate it. It was differentiated; the lead variants within 15q21.2 were more frequent in Finland (6-7% than in other European populations (1-2%. Imputation accuracies of the three significantly associated variants (chr9:14344410:I, rs190200374, and rs80035109 were validated by genotyping. In summary, our results suggest a novel locus, 9p22.3 (NFIB, which may be involved in susceptibility to sciatica. In addition, another locus, 15q21.2, emerged as a promising one, but failed to replicate.

  2. Shift within age-groups of mumps incidence, hospitalizations and severe complications in a highly vaccinated population. Spain, 1998-2014.

    Science.gov (United States)

    López-Perea, Noemí; Masa-Calles, Josefa; Torres de Mier, María de Viarce; Fernández-García, Aurora; Echevarría, Juan E; De Ory, Fernando; Martínez de Aragón, María Victoria

    2017-08-03

    The mumps vaccine (Jeryl-Lynn-strain) was introduced in Spain in 1981, and a vaccination policy which included a second dose was added in 1995. From 1992-1999, a Rubini-strain based vaccine was administered in many regions but later withdrawn due to lack of effectiveness. Despite high levels of vaccination coverage, epidemics have continued to appear. We characterized the three epidemic waves of mumps between 1998 and 2014, identifying major changes in susceptible populations using Poisson regression. For the period 1998-2003 (P1), the most affected group was from 1 to 4years old (y) [Incidence Rate (IR)=71.7 cases/100,000 population]; in the periods 2004-2009 (P2) and 2010-2014 (P3) IR ratio (IRR) increased among 15-24y (P2=1.46; P3=2.68) and 25-34y (P2=2.17; P3=4.05). Hospitalization rate (HR), complication rate (CR) and neurological complication rate (NR) among hospitalized subjects decreased across the epidemics, except for 25-34y which increased: HR ratio (HRR) (P2=2.18; P3=2.16), CRR (P3=2.48), NRR (P3=2.41). In Spain mumps incidence increased, while an overall decrease of hospitalizations and severe complications occurred across the epidemics. Cohorts born during periods of low vaccination coverage and those vaccinated with Rubini-strain were the most affected populations, leading to a shift in mumps cases from children to adolescents and young adults; this also reveals the waning immunity provided by the mumps vaccine. Despite not preventing all mumps cases, the vaccine appears to prevent serious forms of the disease. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  3. Making sense of mobile health data: an open architecture to improve individual- and population-level health.

    Science.gov (United States)

    Chen, Connie; Haddad, David; Selsky, Joshua; Hoffman, Julia E; Kravitz, Richard L; Estrin, Deborah E; Sim, Ida

    2012-08-09

    Mobile phones and devices, with their constant presence, data connectivity, and multiple intrinsic sensors, can support around-the-clock chronic disease prevention and management that is integrated with daily life. These mobile health (mHealth) devices can produce tremendous amounts of location-rich, real-time, high-frequency data. Unfortunately, these data are often full of bias, noise, variability, and gaps. Robust tools and techniques have not yet been developed to make mHealth data more meaningful to patients and clinicians. To be most useful, health data should be sharable across multiple mHealth applications and connected to electronic health records. The lack of data sharing and dearth of tools and techniques for making sense of health data are critical bottlenecks limiting the impact of mHealth to improve health outcomes. We describe Open mHealth, a nonprofit organization that is building an open software architecture to address these data sharing and "sense-making" bottlenecks. Our architecture consists of open source software modules with well-defined interfaces using a minimal set of common metadata. An initial set of modules, called InfoVis, has been developed for data analysis and visualization. A second set of modules, our Personal Evidence Architecture, will support scientific inferences from mHealth data. These Personal Evidence Architecture modules will include standardized, validated clinical measures to support novel evaluation methods, such as n-of-1 studies. All of Open mHealth's modules are designed to be reusable across multiple applications, disease conditions, and user populations to maximize impact and flexibility. We are also building an open community of developers and health innovators, modeled after the open approach taken in the initial growth of the Internet, to foster meaningful cross-disciplinary collaboration around new tools and techniques. An open mHealth community and architecture will catalyze increased mHealth efficiency

  4. Population genetic structure of the freshwater snail, Bulinus globosus, (Gastropoda: Planorbidae) from selected habitats of KwaZulu-Natal, South Africa.

    Science.gov (United States)

    Mkize, Lwamkelekile Sitshilelo; Mukaratirwa, Samson; Zishiri, Oliver Tendayi

    2016-09-01

    The freshwater snail Bulinus globosus is an important intermediate host of Schistosoma haematobium, the causative agent of urinary schistosomiasis. This disease is of major health concern, especially in Africa where the majority of cases have been reported. In this study the inter- and intra-genetic diversity and population genetic structure of B. globosus from nine locations in the KwaZulu-Natal province of South Africa was studied using four polymorphic microsatellite loci (BgZ1-BgZ4). Moderate genetic diversity was detected within populations with a mean diversity (HE) of 0.49±0.09. The majority of populations significantly deviated from Hardy-Weinberg equilibrium (p<0.05), due to a deficit of heterozygotes. Such deviations may be due to founder events that were caused by bottlenecks that occurred as a result of frequent droughts and flooding that these snails' habitats are exposed to. Overall, the populations studied seem to be partially inbreeders/selfers with mean estimates of 0.24/0.38. A discernable genetic structure was elucidated among populations as evident by the mean pairwise FST of 0.58±0.13. There was no significant association between genetic and geographical distance among populations, an indication of limited gene flow. This increases the chances of populations losing alleles due to genetic drift. Populations in close proximity demonstrated high genetic differentiation (58.77% total variation) due to allelic differences between them. The sample populations fell into 12 clusters, however, the populations from uMkhanyakude and uThungulu exhibited no discernable genetic structure. Genetically, the Bhobhoyi site found within the uGu district was equidistant to the two main sampling regions. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. White Sea's Severe Winter Hydrological Hazard and Its Effect On Decrease of Population of Greenland Seals (1998/99 Winter Ecological Catastrophe)

    Science.gov (United States)

    Melentyev, Konstantin V.; Chernook, Vladimir I.

    Types of hydrological hazards are various but its agencies are especially diversified . At this study hazard effects will be assessed for White Sea population of Greenland seals - a representatives of high level of marine fodder chains and the prime part of the Arctic nature. Number of population and type of their migration are strongly depended from different meteorological and hydrological parameters and processes, climate change and anthropogenical press, including pollution and fur-seal fishery, create additional problems. Especially hard situation happens now with the ice- associated sea mammals (p olar bear, seal, walrus, etc.). Mass destruction of seals in the White Sea (ecological catastrophe) which happens periodically is close connected with different kind of meteorological and hydrological hazard. Greenland seals selected these water areas for whelping where a rookeries are organized on pack ice. But severe winter conditions (long-run severe frosts and NE winds) can modify ice regime of the White Sea which lead to effect "blocking" of pack ice (and whelping rookeries) inside the "Basin". These features stimulated strong reduction number ofseals (especially pups). Marine biology use modelling of the system "sea mammal-media", study "behavior factors" and mammals biodiversity at the different natural conditions. But the main critical goal is the development of special observational network for the White Sea and contiguous regions. A contemporary technologies assume integration of remote sensing and in situ hydro-chemical measurements. Airborne IR and visible observation of the marginal Arctic seas became now an indispensable part of marine ecological investigations. Application of satellite data for monitoring of sea mammals has been attractive also but practical use is restrained by its small spatial resolution, daytime illumination and cloud influence in the Arctic. Launching ERS synthetic aperture radar (SAR) in 1991, which provides global all- weather

  6. Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers.

    Directory of Open Access Journals (Sweden)

    Dong-Xiu Xue

    Full Text Available The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure. Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene and current gene flow (through larval dispersal were responsible for the weak level of genetic structure detected in A. pectinata.

  7. A gut-homing, oligoclonal CD4+ T cell population in severe-combined immunodeficient mice expressing a rearranged, transgenic class I-restricted alpha beta T cell receptor

    DEFF Research Database (Denmark)

    Reimann, J; Rudolphi, A; Spiess, S

    1995-01-01

    We studied the peripheral T cell compartment of H-2b severe combined immunodeficient (scid) mice that express a transgenic (tg) alpha beta T cell receptor (TcR) specific for the H-Y (male) epitope presented by the H-2 class I Db molecule. Large populations of CD3+ NK1.1-TCR beta T+ T cells were...

  8. MIF functional polymorphisms (-794 CATT5-8 and -173 G>C) are associated with MIF serum levels, severity and progression in male multiple sclerosis from western Mexican population.

    Science.gov (United States)

    Castañeda-Moreno, V A; De la Cruz-Mosso, U; Torres-Carrillo, N; Macías-Islas, M A; Padilla-De la Torre, O; Mireles-Ramírez, M A; González-Pérez, O; Ruiz-Sandoval, J L; Huerta, M; Trujillo, X; Ortuño-Sahagún, D; Jf, Muñoz-Valle

    2018-07-15

    Macrophage migration inhibitory factor (MIF) is a cytokine associated with tissue damage in multiple autoimmune diseases such as systemic lupus erythematosus, rheumatoid arthritis and psoriatic arthritis. The role of MIF in multiple sclerosis (MS) and the contribution of its polymorphisms are unknown in our population. Therefore, we decided to investigate the genetic association of -794 CATT 5-8 (rs5844572) and -173 G>C (rs755622) MIF polymorphisms with MS, clinical variables and MIF serum levels in the population of western Mexico. 230 MS patients diagnosed according to McDonald criteria and 248 control subjects (CS) were recruited for this study, both polymorphisms were genotyped by PCR and PCR-RFLP and MIF serum levels were measured by ELISA kit. Severity and progression of MS were evaluated by EDSS and MSSS scores, respectively. Genotypes carrying the 5 repeats alleles of -794 CATT 5-8 MIF polymorphism present higher MIF serum levels in comparison with no carriers, and the presence of 5,7 heterozygous genotype contribute to the increase of disease severity and damage progression in MS patients. Notably when we stratified by sex, an effect of risk alleles (7 repeats and -173*C) of both MIF polymorphisms on EDSS and MSSS scores on males was found (p < 0.01). This study suggests that polymorphic alleles of MIF polymorphisms could act as sex-specific disease modifiers that increase the severity and progression of MS in male Mexican-Mestizo western population. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations

    Science.gov (United States)

    Kang, Hongzhang; Sun, Xiao; Yin, Shan; Du, Hongmei; Yamanaka, Norikazu; Gapare, Washington; Wu, Harry X.; Liu, Chunjiang

    2012-01-01

    The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (N ST = 0.751> G ST = 0.690, Ptree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia. PMID:23115642

  10. Museum samples reveal rapid evolution by wild honey bees exposed to a novel parasite.

    Science.gov (United States)

    Mikheyev, Alexander S; Tin, Mandy M Y; Arora, Jatin; Seeley, Thomas D

    2015-08-06

    Understanding genetic changes caused by novel pathogens and parasites can reveal mechanisms of adaptation and genetic robustness. Using whole-genome sequencing of museum and modern specimens, we describe the genomic changes in a wild population of honey bees in North America following the introduction of the ectoparasitic mite, Varroa destructor. Even though colony density in the study population is the same today as in the past, a major loss of haplotypic diversity occurred, indicative of a drastic mitochondrial bottleneck, caused by massive colony mortality. In contrast, nuclear genetic diversity did not change, though hundreds of genes show signs of selection. The genetic diversity within each bee colony, particularly as a consequence of polyandry by queens, may enable preservation of genetic diversity even during population bottlenecks. These findings suggest that genetically diverse honey bee populations can recover from introduced diseases by evolving rapid tolerance, while maintaining much of the standing genetic variation.

  11. Genetic Variability of Bovine Viral Diarrhea Virus and Evidence for a Possible Genetic Bottleneck during Vertical Transmission in Persistently Infected Cattle.

    Directory of Open Access Journals (Sweden)

    Natalie Dow

    Full Text Available Bovine viral diarrhea virus (BVDV, a Pestivirus in the family Flaviviridae, is an economically important pathogen of cattle worldwide. The primary propagators of the virus are immunotolerant persistently infected (PI cattle, which shed large quantities of virus throughout life. Despite the absence of an acquired immunity against BVDV in these PI cattle there are strong indications of viral variability that are of clinical and epidemiological importance. In this study the variability of E2 and NS5B sequences in multiple body compartments of PI cattle were characterized using clonal sequencing. Phylogenetic analyses revealed that BVDV exists as a quasispecies within PI cattle. Viral variants were clustered by tissue compartment significantly more often than expected by chance alone with the central nervous system appearing to be a particularly important viral reservoir. We also found strong indications for a genetic bottleneck during vertical transmission from PI animals to their offspring. These quasispecies analyses within PI cattle exemplify the role of the PI host in viral propagation and highlight the complex dynamics of BVDV pathogenesis, transmission and evolution.

  12. PREVALENCE, CLINICAL PRESENTATION, DIAGNOSIS AND TREATMENT OF ACUTE PULMONARY OEDEMA IN SEVERE PREGNANCY-INDUCED HYPERTENSION AND ECLAMPSIA CASES IN TRIBAL POPULATION OF SOUTH RAJASTHAN

    Directory of Open Access Journals (Sweden)

    (Brig. Pradeep Kuma

    2016-05-01

    Full Text Available BACKGROUND Pulmonary oedema in severe pregnancy-induced hypertension is a life threatening complication with high maternal mortality, particularly in tribal population of South Rajasthan. METHODS Thirteen cases which occurred in the duration of two and half years were analysed through medical records and findings were recorded. RESULTS Maximum cases 10(76.92% were in less than 20 years of age. 12 (92.30% cases were nulliparous. Out of 13 cases of PIH, pulmonary oedema developed in 5 (38.46% cases of eclampsia and 8 (61.54% cases of severe pregnancy-induced hypertension. 10 (76.92%cases were 28 to 30 weeks of gestation and 3 (23.08% were 31 to 34 weeks of gestation. 8 (61.54% cases were severely anaemic. 12 (92.30% were unbooked cases. CONCLUSION Regular antenatal checkups, early diagnosis, prompt treatment of hypertension and pulmonary oedema and termination of pregnancy is required to prevent maternal death.

  13. Population genetic structure and demographic history of the freshwater crab Potamon elbursi (Brachyura: Potamidae from the Alborz Mountains in northern Iran

    Directory of Open Access Journals (Sweden)

    Alireza Keikhosravi

    2015-04-01

    Full Text Available Hydrographically separated populations of the freshwater crab Potamon elbursi Pretzmann, 1976 were genetically investigated to assess their local diversity and to reconstruct the possible role of Quaternary glaciations in shaping current diversity in the Alborz Mountains, northern Iran. A total of 61 specimens from six rivers were collected from the two different drainage systems of the Alborz Mountains, Namak Lake and the South Caspian watershed. A comparative analysis of a partial sequence of the mitochondrial cytochrome oxidase subunit I gene revealed relatively high overall haplotype diversity and low nucleotide diversity. In four populations, there is no association between the haplotype network and the geographical separation between drainages, whereas the remaining two populations consist of private haplotypes. Gene flow among rivers was estimated using pairwise differences of Φst; in almost all cases gene flow was significantly restricted, regardless of association to a particular river system. Surprisingly, the only exception was the pairwise comparison of two distant rivers belonging to different drainages; this lack of differentiation may be attributed to incomplete lineage sorting or secondary introduction events. The mismatch distribution analysis, together with the shape of the haplotype network and the nucleotide and haplotype diversity indices, indicates that the studied metapopulation show the signature of recent population bottlenecks followed by demographic or spatial expansion and dating back to Pleistocene climatic fluctuations. 

  14. Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks

    Science.gov (United States)

    Chiappino-Pepe, Anush; Ataman, Meriç

    2017-01-01

    Novel antimalarial therapies are urgently needed for the fight against drug-resistant parasites. The metabolism of malaria parasites in infected cells is an attractive source of drug targets but is rather complex. Computational methods can handle this complexity and allow integrative analyses of cell metabolism. In this study, we present a genome-scale metabolic model (iPfa) of the deadliest malaria parasite, Plasmodium falciparum, and its thermodynamics-based flux analysis (TFA). Using previous absolute concentration data of the intraerythrocytic parasite, we applied TFA to iPfa and predicted up to 63 essential genes and 26 essential pairs of genes. Of the 63 genes, 35 have been experimentally validated and reported in the literature, and 28 have not been experimentally tested and include previously hypothesized or novel predictions of essential metabolic capabilities. Without metabolomics data, four of the genes would have been incorrectly predicted to be non-essential. TFA also indicated that substrate channeling should exist in two metabolic pathways to ensure the thermodynamic feasibility of the flux. Finally, analysis of the metabolic capabilities of P. falciparum led to the identification of both the minimal nutritional requirements and the genes that can become indispensable upon substrate inaccessibility. This model provides novel insight into the metabolic needs and capabilities of the malaria parasite and highlights metabolites and pathways that should be measured and characterized to identify potential thermodynamic bottlenecks and substrate channeling. The hypotheses presented seek to guide experimental studies to facilitate a better understanding of the parasite metabolism and the identification of targets for more efficient intervention. PMID:28333921

  15. Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks.

    Directory of Open Access Journals (Sweden)

    Anush Chiappino-Pepe

    2017-03-01

    Full Text Available Novel antimalarial therapies are urgently needed for the fight against drug-resistant parasites. The metabolism of malaria parasites in infected cells is an attractive source of drug targets but is rather complex. Computational methods can handle this complexity and allow integrative analyses of cell metabolism. In this study, we present a genome-scale metabolic model (iPfa of the deadliest malaria parasite, Plasmodium falciparum, and its thermodynamics-based flux analysis (TFA. Using previous absolute concentration data of the intraerythrocytic parasite, we applied TFA to iPfa and predicted up to 63 essential genes and 26 essential pairs of genes. Of the 63 genes, 35 have been experimentally validated and reported in the literature, and 28 have not been experimentally tested and include previously hypothesized or novel predictions of essential metabolic capabilities. Without metabolomics data, four of the genes would have been incorrectly predicted to be non-essential. TFA also indicated that substrate channeling should exist in two metabolic pathways to ensure the thermodynamic feasibility of the flux. Finally, analysis of the metabolic capabilities of P. falciparum led to the identification of both the minimal nutritional requirements and the genes that can become indispensable upon substrate inaccessibility. This model provides novel insight into the metabolic needs and capabilities of the malaria parasite and highlights metabolites and pathways that should be measured and characterized to identify potential thermodynamic bottlenecks and substrate channeling. The hypotheses presented seek to guide experimental studies to facilitate a better understanding of the parasite metabolism and the identification of targets for more efficient intervention.

  16. Mortality caused by intracranial bleeding in non-severe hemophilia A patients.

    Science.gov (United States)

    Loomans, J I; Eckhardt, C L; Reitter-Pfoertner, S E; Holmström, M; van Gorkom, B Laros; Leebeek, F W G; Santoro, C; Haya, S; Meijer, K; Nijziel, M R; van der Bom, J G; Fijnvandraat, K

    2017-06-01

    Essentials Data on bleeding-related causes of death in non-severe hemophilia A (HA) patients are scarce. Such data may provide new insights into areas of care that can be improved. Non-severe HA patients have an increased risk of dying from intracranial bleeding. This demonstrates the need for specialized care for non-severe HA patients. Background Non-severe hemophilia (factor VIII concentration [FVIII:C] of 2-40 IU dL -1 ) is characterized by a milder bleeding phenotype than severe hemophilia A. However, some patients with non-severe hemophilia A suffer from severe bleeding complications that may result in death. Data on bleeding-related causes of death, such as fatal intracranial bleeding, in non-severe patients are scarce. Such data may provide new insights into areas of care that can be improved. Aims To describe mortality rates, risk factors and comorbidities associated with fatal intracranial bleeding in non-severe hemophilia A patients. Methods We analyzed data from the INSIGHT study, an international cohort study of all non-severe hemophilia A patients treated with FVIII concentrates during the observation period between 1980 and 2010 in 34 participating centers across Europe and Australia. Clinical data and vital status were collected from 2709 patients. We report the standardized mortality rate for patients who suffered from fatal intracranial bleeding, using a general European male population as a control population. Results Twelve per cent of the 148 deceased patients in our cohort of 2709 patients died from intracranial bleeding. The mortality rate between 1996 and 2010 for all ages was 3.5-fold higher than that in the general population (95% confidence interval [CI] 2.0-5.8). Patients who died from intracranial bleeding mostly presented with mild hemophilia without clear comorbidities. Conclusion Non-severe hemophilia A patients have an increased risk of dying from intracranial bleeding in comparison with the general population. This demonstrates the

  17. Population Education in Africa. English Version.

    Science.gov (United States)

    Sankale-Semeteys, Eva, Ed.

    1985-01-01

    National conferences on population and development have recommended the integration of population issues into development planning by national governments. This book presents several ideas of practitioners in the field of population and family life education. Five articles in Part I focus on solutions to problems of introducing population…

  18. Nature-assisted rehabilitation for reactions to severe stress and/or depression in a rehabilitation garden: long-term follow-up including comparisons with a matched population-based reference cohort.

    Science.gov (United States)

    Währborg, Peter; Petersson, Ingemar F; Grahn, Patrik

    2014-03-01

    To determine the effect of a nature-assisted rehabilitation programme in a group of patients with reactions to severe stress and/or mild to moderate depression. Changes in sick-leave status and healthcare consumption in these patients were compared with those in a matched population-based reference cohort (treatment as usual). Retrospective cohort study with a matched reference group from the general population. A total of 118 participants referred to a nature-assisted rehabilitation programme, and 678 controls recruited from the Skåne Health Care Register. For both groups, information on sick leave was extracted from the National Social Insurance Register and on healthcare consumption data from the Skåne Health Care Register. The interventional rehabilitation programme was designed as a multimodal programme involving professionals from horticulture and medicine. The programme was conducted in a rehabilitation garden, designed especially for this purpose. A significant reduction in healthcare consumption was noted among participants in the programme compared with the reference population. The main changes were a reduction in outpatient visits to primary healthcare and a reduction in inpatient psychiatric care. No significant difference in sick-leave status was found. A structured, nature-based rehabilitation programme for patients with reactions to severe stress and/or depression could be beneficial, as reflected in reduced healthcare consumption.

  19. [On the extinction of populations with several types in a random environment].

    Science.gov (United States)

    Bacaër, Nicolas

    2018-03-01

    This study focuses on the extinction rate of a population that follows a continuous-time multi-type branching process in a random environment. Numerical computations in a particular example inspired by an epidemic model suggest an explicit formula for this extinction rate, but only for certain parameter values. Copyright © 2018 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

  20. Juvenile competitive bottleneck in the production of brown trout in hydroelectric reservoirs due to intraspecific habitat segregation

    International Nuclear Information System (INIS)

    Hegge, O.; Hesthagen, T.; Skurdal, J.

    1993-01-01

    Resource utilization and growth of brown trout were studied in four deep (mean depths 16.2 - 37.5 m) Norwegian hydroelectric reservoirs by benthic and pelagic gillnet sampling. In all the reservoirs supplementary stockings are carried out. The brown trout were spatially segregated according to size as the habitat use of small individuals (< 180-220 mm) was completely restricted to benthic habitats, whereas larger individuals mainly utilized the upper strata of pelagic waters. It is argued that the pelagic habitat is the more rewarding, and that small-sized brown trout are forced into the less favourable benthic habitat through social interactions with larger specimens. This is supported by an increase in growth of brown trout from their third to fifth year of life, which seems to be related to the shift from benthic to pelagic behaviour. It is also argued that the conditions for small-sized brown trout may be a bottleneck in the capacity to produce brown trout in hydroelectric reservoirs with limited benthic feeding conditions, despite ample access to food in pelagic habitats. When evaluating the possibility of increasing the yield of brown trout through supplementary stockings, it is therefore important to consider food and growth conditions for all age and size groups of brown trout. In reservoirs with poor benthic feeding conditions it may be necessary to stock with brown trout of sizes that are large enough to utilize pelagic habitat, to avoid the limiting benthic living stage. (Author)