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Sample records for extreme population bottleneck

  1. The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation

    DEFF Research Database (Denmark)

    Pedersen, Casper-Emil T; Lohmueller, Kirk E; Grarup, Niels;

    2016-01-01

    to a markedly more extreme distribution of allele frequencies than seen for any other human population, 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......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 here we show that the Inuit have undergone a severe ~20,000 year long bottleneck. This has led...... alleles, the Inuit show, at most, a slight increase in load compared to European, East Asian, and African populations. Specifically, we observe

  2. Consequences of extreme life history traits on population persistence: do short-lived gobies face demographic bottlenecks?

    Science.gov (United States)

    Lefèvre, Carine D.; Nash, Kirsty L.; González-Cabello, Alonso; Bellwood, David R.

    2016-06-01

    The majority of coral reef goby species are short-lived, with some highly abundant species living less than 100 d. To understand the role and consequences of this extreme life history in shaping coral reef fish populations, we quantitatively documented the structure of small reef fish populations over a 26-month period (>14 short-lived fish generations) at an inshore reef on the Great Barrier Reef, Australia. Most species with life spans >1 yr, such as pomacentrids, exhibited a peak in recruitment during the austral summer, driving seasonal changes in the small fish community composition. In contrast, there were no clear changes in goby community composition, despite the abundance of short-lived, high turnover species. Species of Eviota, the most abundant gobiid genus observed, showed remarkably similar demographic profiles year-round, with consistent densities of adults as well as recently recruited juveniles. Our results demonstrate ongoing recruitment of these small cryptic fishes, which appears to compensate for an exceptionally short life span on the reef. Our results suggest that gobiid populations are able to overcome demographic limitations, and by maintaining reproduction, larval survival and recruitment throughout the year, they may avoid population bottlenecks. These findings also underline the potential trophodynamic importance of these small species; because of this constant turnover, Eviota species and other short-lived fishes may be particularly valuable contributors to the flow of energy on coral reefs, underpinning the year-round trophic structure.

  3. Whole-genome sequencing of six Mauritian Cynomolgus macaques (Macaca fascicularis) reveals a genome-wide pattern of polymorphisms under extreme population bottleneck.

    Science.gov (United States)

    Osada, Naoki; Hettiarachchi, Nilmini; Adeyemi Babarinde, Isaac; Saitou, Naruya; Blancher, Antoine

    2015-03-23

    Cynomolgus macaques (Macaca fascicularis) were introduced to the island of Mauritius by humans around the 16th century. The unique demographic history of the Mauritian cynomolgus macaques provides the opportunity to not only examine the genetic background of well-established nonhuman primates for biomedical research but also understand the effect of an extreme population bottleneck on the pattern of polymorphisms in genomes. We sequenced the whole genomes of six Mauritian cynomolgus macaques and obtained an average of 20-fold coverage of the genome sequences for each individual. The overall level of nucleotide diversity was 23% smaller than that of the Malaysian cynomolgus macaques, and a reduction of low-frequency polymorphisms was observed. In addition, we also confirmed that the Mauritian cynomolgus macaques were genetically closer to a representative of the Malaysian population than to a representative of the Indochinese population. Excess of nonsynonymous polymorphisms in low frequency, which has been observed in many other species, was not very strong in the Mauritian samples, and the proportion of heterozygous nonsynonymous polymorphisms relative to synonymous polymorphisms is higher within individuals in Mauritian than Malaysian cynomolgus macaques. Those patterns indicate that the extreme population bottleneck made purifying selection overwhelmed by the power of genetic drift in the population. Finally, we estimated the number of founding individuals by using the genome-wide site frequency spectrum of the six samples. Assuming a simple demographic scenario with a single bottleneck followed by exponential growth, the estimated number of founders (∼20 individuals) is largely consistent with previous estimates.

  4. Population bottlenecks promote cooperation in bacterial biofilms.

    Directory of Open Access Journals (Sweden)

    Michael A Brockhurst

    Full Text Available Population bottlenecks are assumed to play a key role in the maintenance of social traits in microbes. Ecological parameters such as colonisation or disturbances can favour cooperation through causing population bottlenecks that enhance genetic structuring (relatedness. However, the size of the population bottleneck is likely to play a crucial role in determining the success of cooperation. Relatedness is likely to increase with decreasing bottleneck size thus favouring the evolution of cooperation. I used an experimental evolution approach to test this prediction with biofilm formation by the bacterium Pseudomonas fluorescens as the cooperative trait. Replicate populations were exposed to disturbance events every four days under one of six population bottleneck treatments (from 10(3 to 10(8 bacterial cells. In line with predictions, the frequency of evolved cheats within the populations increased with increasing bottleneck size. This result highlights the importance of ecologically mediated population bottlenecks in the maintenance of social traits in microbes.

  5. 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.

    2012-01-01

    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 popula

  6. The effect of population bottlenecks on mutation rate evolution in asexual populations.

    Science.gov (United States)

    Raynes, Y; Halstead, A L; Sniegowski, P D

    2014-01-01

    In the absence of recombination, a mutator allele can spread through a population by hitchhiking with beneficial mutations that appear in its genetic background. Theoretical studies over the past decade have shown that the survival and fixation probability of beneficial mutations can be severely reduced by population size bottlenecks. Here, we use computational modelling and evolution experiments with the yeast S. cerevisiae to examine whether population bottlenecks can affect mutator dynamics in adapting asexual populations. In simulation, we show that population bottlenecks can inhibit mutator hitchhiking with beneficial mutations and are most effective at lower beneficial mutation supply rates. We then subjected experimental populations of yeast propagated at the same effective population size to three different bottleneck regimes and observed that the speed of mutator hitchhiking was significantly slower at smaller bottlenecks, consistent with our theoretical expectations. Our results, thus, suggest that bottlenecks can be an important factor in mutation rate evolution and can in certain circumstances act to stabilize or, at least, delay the progressive elevation of mutation rates in asexual populations. Additionally, our findings provide the first experimental support for the theoretically postulated effect of population bottlenecks on beneficial mutations and demonstrate the usefulness of studying mutator frequency dynamics for understanding the underlying dynamics of fitness-affecting mutations.

  7. Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution

    OpenAIRE

    Vogwill, Tom; Phillips, Robyn L.; Gifford, Danna R.; MacLean, R. Craig

    2016-01-01

    There is growing evidence that parallel molecular evolution is common, but its causes remain poorly understood. Demographic parameters such as population bottlenecks are predicted to be major determinants of parallelism. Here, we test the hypothesis that bottleneck intensity shapes parallel evolution by elucidating the genomic basis of adaptation to antibiotic-supplemented media in hundreds of populations of the bacterium Pseudomonas fluorescens Pf0-1. As expected, bottlenecking decreased the...

  8. The effect of ancient population bottlenecks on human phenotypic variation.

    Science.gov (United States)

    Manica, Andrea; Amos, William; Balloux, François; Hanihara, Tsunehiko

    2007-07-19

    The origin and patterns of dispersal of anatomically modern humans are the focus of considerable debate. Global genetic analyses have argued for one single origin, placed somewhere in Africa. This scenario implies a rapid expansion, with a series of bottlenecks of small amplitude, which would have led to the observed smooth loss of genetic diversity with increasing distance from Africa. Analyses of cranial data, on the other hand, have given mixed results, and have been argued to support multiple origins of modern humans. Using a large data set of skull measurements and an analytical framework equivalent to that used for genetic data, we show that the loss in genetic diversity has been mirrored by a loss in phenotypic variability. We find evidence for an African origin, placed somewhere in the central/southern part of the continent, which harbours the highest intra-population diversity in phenotypic measurements. We failed to find evidence for a second origin, and we confirm these results on a large genetic data set. Distance from Africa accounts for an average 19-25% of heritable variation in craniometric measurements-a remarkably strong effect for phenotypic measurements known to be under selection.

  9. Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution

    Science.gov (United States)

    Phillips, Robyn L.; Gifford, Danna R.; MacLean, R. Craig

    2016-01-01

    There is growing evidence that parallel molecular evolution is common, but its causes remain poorly understood. Demographic parameters such as population bottlenecks are predicted to be major determinants of parallelism. Here, we test the hypothesis that bottleneck intensity shapes parallel evolution by elucidating the genomic basis of adaptation to antibiotic-supplemented media in hundreds of populations of the bacterium Pseudomonas fluorescens Pf0-1. As expected, bottlenecking decreased the rate of phenotypic and molecular adaptation. Surprisingly, bottlenecking had no impact on the likelihood of parallel adaptive molecular evolution at a genome-wide scale. However, bottlenecking had a profound impact on the genes involved in antibiotic resistance. Specifically, under either intense or weak bottlenecking, resistance predominantly evolved by strongly beneficial mutations which provide high levels of antibiotic resistance. In contrast with intermediate bottlenecking regimes, resistance evolved by a greater diversity of genetic mechanisms, significantly reducing the observed levels of parallel genetic evolution. Our results demonstrate that population bottlenecking can be a major predictor of parallel evolution, but precisely how may be more complex than many simple theoretical predictions. PMID:27466449

  10. Genome-wide signatures of population bottlenecks and diversifying selection in European wolves.

    Science.gov (United States)

    Pilot, M; Greco, C; vonHoldt, B M; Jędrzejewska, B; Randi, E; Jędrzejewski, W; Sidorovich, V E; Ostrander, E A; Wayne, R K

    2014-04-01

    Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European populations of grey wolves in comparison with other populations worldwide, and investigate genome-wide effects of demographic bottlenecks and signatures of selection. European wolves have a discontinuous range, with large and connected populations in Eastern Europe and relatively smaller, isolated populations in Italy and the Iberian Peninsula. Our results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population. The Italian and Iberian populations have low genetic variability and high linkage disequilibrium, but relatively few autozygous segments across the genome. This last characteristic clearly distinguishes them from populations that underwent recent drastic demographic declines or founder events, and implies long-term bottlenecks in these two populations. Although genetic drift due to spatial isolation and bottlenecks seems to be a major evolutionary force diversifying the European populations, we detected 35 loci that are putatively under diversifying selection. Two of these loci flank the canine platelet-derived growth factor gene, which affects bone growth and may influence differences in body size between wolf populations. This study demonstrates the power of population genomics for identifying genetic signals of demographic bottlenecks and detecting signatures of directional selection in bottlenecked populations, despite their low background variability.

  11. Evaluating ring-tailed lemurs (Lemur catta) from southwestern Madagascar for a genetic population bottleneck.

    Science.gov (United States)

    Parga, Joyce A; Sauther, Michelle L; Cuozzo, Frank P; Jacky, Ibrahim Antho Youssouf; Lawler, Richard R

    2012-01-01

    In light of historical and recent anthropogenic influences on Malagasy primate populations, in this study ring-tailed lemur (Lemur catta) samples from two sites in southwestern Madagascar, Beza Mahafaly Special Reserve (BMSR) and Tsimanampetsotsa National Park (TNP), were evaluated for the genetic signature of a population bottleneck. A total of 45 individuals (20 from BMSR and 25 from TNP) were genotyped at seven microsatellite loci. Three methods were used to evaluate these populations for evidence of a historical bottleneck: M-ratio, mode-shift, and heterozygosity excess tests. Three mutation models were used for heterozygosity excess tests: the stepwise mutation model (SMM), two-phase model (TPM), and infinite allele model (IAM). M-ratio estimations indicated a potential bottleneck in both populations under some conditions. Although mode-shift tests did not strongly indicate a population bottleneck in the recent historical past when samples from all individuals were included, a female-only analysis indicated a potential bottleneck in TNP. Heterozygosity excess was indicated under two of the three mutation models (IAM and TPM), with TNP showing stronger evidence of heterozygosity excess than BMSR. Taken together, these results suggest that a bottleneck may have occurred among L. catta in southwestern Madagascar in the recent past. Given knowledge of how current major stochastic climatic events and human-induced change can negatively impact extant lemur populations, it is reasonable that comparable events in the historical past could have caused a population bottleneck. This evaluation additionally functions to highlight the continuing environmental and anthropogenic challenges faced by lemurs in southwestern Madagascar. Copyright © 2011 Wiley Periodicals, Inc.

  12. Post-bottleneck genetic diversity of elephant populations in South Africa, revealed using microsatellite analysis.

    Science.gov (United States)

    Whitehouse, A M; Harley, E H

    2001-09-01

    Widespread hunting had fragmented and severely reduced elephant populations in South Africa by 1900. Elephant numbers increased during the 1900s, although rates of recovery of individual populations varied. The Kruger National Park elephant population increased rapidly, to more than 6000 by 1967, with recruitment boosted by immigration from Mozambique. The Addo Elephant National Park population was reduced to 11 elephants in 1931 and remains relatively small (n = 325). Loss of genetic variation is expected to occur whenever a population goes through a bottleneck, especially when post-bottleneck recovery is slow. Variation at nine polymorphic microsatellite loci was analysed for Kruger and Addo elephants, as well as museum specimens of Addo elephants shot prior to the population bottleneck. Significantly reduced genetic variation and heterozygosity were observed in Addo in comparison to Kruger (mean alleles/locus and H(E): Addo 1.89, 0.18; Kruger 3.89, 0.44). Two alleles not present in the current Addo population were observed in the museum specimens. Addo elephants represent a genetic subset of the Kruger population, with high levels of genetic differentiation resulting from rapid genetic drift. The Kruger population is low in genetic diversity in comparison to East African elephants, confirming this population also suffered an appreciable bottleneck.

  13. Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure.

    Science.gov (United States)

    Peter, Benjamin M; Wegmann, Daniel; Excoffier, Laurent

    2010-11-01

    Although most natural populations are genetically subdivided, they are often analysed as if they were panmictic units. In particular, signals of past demographic size changes are often inferred from genetic data by assuming that the analysed sample is drawn from a population without any internal subdivision. However, it has been shown that a bottleneck signal can result from the presence of some recent immigrants in a population. It thus appears important to contrast these two alternative scenarios in a model choice procedure to prevent wrong conclusions to be made. We use here an Approximate Bayesian Computation (ABC) approach to infer whether observed patterns of genetic diversity in a given sample are more compatible with it being drawn from a panmictic population having gone through some size change, or from one or several demes belonging to a recent finite island model. Simulations show that we can correctly identify samples drawn from a subdivided population in up to 95% of the cases for a wide range of parameters. We apply our model choice procedure to the case of the chimpanzee (Pan troglodytes) and find conclusive evidence that Western and Eastern chimpanzee samples are drawn from a spatially subdivided population. © 2010 Blackwell Publishing Ltd.

  14. 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

    variation for 15 microsatellite loci in each of nine populations in eastern Australia was used to estimate the size of the bottleneck, and to determine if any of these microsatellites marked genomic regions subject to recent selection. We estimate that on its introduction to Australia, D. buzzatii went...

  15. Population Bottlenecks Increase Additive Genetic Variance But Do Not Break a Selection Limit in Rainforest Drosophila

    DEFF Research Database (Denmark)

    van Heerwaarden, Belinda; Willi, Yvonne; Kristensen, Torsten N

    2008-01-01

    actually increase additive genetic variance. This has been an important issue in conservation genetics where it has been suggested that small population size might actually experience an increase rather than a decrease in the rate of adaptation. Here we test if bottlenecks can break a selection limit...... for desiccation resistance in the rain forest-restricted fly Drosophila bunnanda. After one generation of single-pair mating, additive genetic variance for desiccation resistance increased to a significant level, on average higher than for the control lines. Line crosses revealed that both dominance and epistatic...... effects were responsible for the divergence in desiccation resistance between the original control and a bottlenecked line exhibiting increased additive genetic variance for desiccation resistance. However, when bottlenecked lines were selected for increased desiccation resistance, there was only a small...

  16. On the prospect of identifying adaptive loci in recently bottlenecked populations.

    Directory of Open Access Journals (Sweden)

    Yu-Ping Poh

    Full Text Available Identifying adaptively important loci in recently bottlenecked populations - be it natural selection acting on a population following the colonization of novel habitats in the wild, or artificial selection during the domestication of a breed - remains a major challenge. Here we report the results of a simulation study examining the performance of available population-genetic tools for identifying genomic regions under selection. To illustrate our findings, we examined the interplay between selection and demography in two species of Peromyscus mice, for which we have independent evidence of selection acting on phenotype as well as functional evidence identifying the underlying genotype. With this unusual information, we tested whether population-genetic-based approaches could have been utilized to identify the adaptive locus. Contrary to published claims, we conclude that the use of the background site frequency spectrum as a null model is largely ineffective in bottlenecked populations. Results are quantified both for site frequency spectrum and linkage disequilibrium-based predictions, and are found to hold true across a large parameter space that encompasses many species and populations currently under study. These results suggest that the genomic footprint left by selection on both new and standing variation in strongly bottlenecked populations will be difficult, if not impossible, to find using current approaches.

  17. Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck.

    Science.gov (United States)

    Guo, Ya-Long; Bechsgaard, Jesper S; Slotte, Tanja; Neuffer, Barbara; Lascoux, Martin; Weigel, Detlef; Schierup, Mikkel H

    2009-03-31

    Flowering plants often prevent selfing through mechanisms of self-incompatibility (S.I.). The loss of S.I. has occurred many times independently, because it provides short-term advantages in situations where pollinators or mates are rare. The genus Capsella, which is closely related to Arabidopsis, contains a pair of closely related diploid species, the self-incompatible Capsella grandiflora and the self-compatible Capsella rubella. To elucidate the transition to selfing and its relationship to speciation of C. rubella, we have made use of comparative sequence information. Our analyses indicate that C. rubella separated from C. grandiflora recently ( approximately 30,000-50,000 years ago) and that breakdown of S.I. occurred at approximately the same time. Contrasting the nucleotide diversity patterns of the 2 species, we found that C. rubella has only 1 or 2 alleles at most loci, suggesting that it originated through an extreme population bottleneck. Our data are consistent with diploid speciation by a single, selfing individual, most likely living in Greece. The new species subsequently colonized the Mediterranean by Northern and Southern routes, at a time that also saw the spread of agriculture. The presence of phenotypic diversity within modern C. rubella suggests that this species will be an interesting model to understand divergence and adaptation, starting from very limited standing genetic variation.

  18. Circulating virus load determines the size of bottlenecks in viral populations progressing within a host.

    Directory of Open Access Journals (Sweden)

    Serafín Gutiérrez

    Full Text Available For any organism, population size, and fluctuations thereof, are of primary importance in determining the forces driving its evolution. This is particularly true for viruses--rapidly evolving entities that form populations with transient and explosive expansions alternating with phases of migration, resulting in strong population bottlenecks and associated founder effects that increase genetic drift. A typical illustration of this pattern is the progression of viral disease within a eukaryotic host, where such demographic fluctuations are a key factor in the emergence of new variants with altered virulence. Viruses initiate replication in one or only a few infection foci, then move through the vasculature to seed secondary infection sites and so invade distant organs and tissues. Founder effects during this within-host colonization might depend on the concentration of infectious units accumulating and circulating in the vasculature, as this represents the infection dose reaching new organs or "territories". Surprisingly, whether or not the easily measurable circulating (plasma virus load directly drives the size of population bottlenecks during host colonization has not been documented in animal viruses, while in plants the virus load within the sap has never been estimated. Here, we address this important question by monitoring both the virus concentration flowing in host plant sap, and the number of viral genomes founding the population in each successive new leaf. Our results clearly indicate that the concentration of circulating viruses directly determines the size of bottlenecks, which hence controls founder effects and effective population size during disease progression within a host.

  19. Multiple Population Theory: Extreme helium population problem

    OpenAIRE

    Yi, Sukyoung K.

    2009-01-01

    The spreads in chemical abundances inferred by recent precision observations suggest that some or possibly all globular clusters can no longer be considered as simple stellar populations. The most striking case is omega Cen in the sense that its bluest main-sequence despite its high metallicity demands an extreme helium abundance of Y > 0.4. I focus on this issue of "the extreme helium population problem" in this review.

  20. The effect of a population bottleneck on the evolution of genetic variance/covariance structure.

    Science.gov (United States)

    Jarvis, J P; Cropp, S N; Vaughn, T T; Pletscher, L S; King-Ellison, K; Adams-Hunt, E; Erickson, C; Cheverud, J M

    2011-10-01

    It is well known that standard population genetic theory predicts decreased additive genetic variance (V(a) ) following a population bottleneck and that theoretical models including interallelic and intergenic interactions indicate such loss may be avoided. However, few empirical data from multicellular model systems are available, especially regarding variance/covariance (V/CV) relationships. Here, we compare the V/CV structure of seventeen traits related to body size and composition between control (60 mating pairs/generation) and bottlenecked (2 mating pairs/generation; average F = 0.39) strains of mice. Although results for individual traits vary considerably, multivariate analysis indicates that V(a) in the bottlenecked populations is greater than expected. Traits with patterns and amounts of epistasis predictive of enhanced V(a) also show the largest deviations from additive expectations. Finally, the correlation structure of weekly weights is not significantly different between control and experimental lines but correlations between necropsy traits do differ, especially those involving the heart, kidney and tail length. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  1. Anatomy of a bottleneck: diagnosing factors limiting population growth in the Puerto Rican parrot

    Science.gov (United States)

    Beissenger, S.R.; Wunderle, J.M.; Meyers, J.M.; Saether, B.-E.; Engen, S.

    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 analysis, then examine evidence for the importance of specific processes maintaining the bottleneck using the multiple competing hypotheses approach, and finally integrate these results through a sensitivity analysis of a demographic model using life-stage simulation analysis (LSA) to determine the relative importance of genetic, demographic, environmental, and catastrophic processes on population growth. Annual population growth has been slow and variable (1.0 6 5.2 parrots per year, or an average k?1.05 6 0.19) from 16 parrots (1973) to a high of 40-42 birds (1997-1998). A risk analysis based on population prediction intervals (PPI) indicates great risk and large uncertainty, with a range of 22?83 birds in the 90% PPI only five years into the future. Four primary factors (reduced hatching success due to inbreeding, failure of adults to nest, nest failure due to nongenetic causes, and reduced survival of adults and juveniles) were responsible for maintaining the bottleneck. Egghatchability rates were low (70.6% per egg and 76.8% per pair), and hatchability increased after mate changes, suggesting inbreeding effects. Only an average of 34% of the population nested annually, which was well below the percentage of adults that should have reached an age of first breeding (41-56%). This chronic failure to nest appears to have been caused primarily by environmental and/or behavioral factors, and not by nest-site scarcity or a skewed sex ratio. Nest failure rates from nongenetic causes (i.e., predation, parasitism, and wet cavities) were low (29%) due to active management (protecting nests and fostering

  2. Host-Pathogen Checkpoints and Population Bottlenecks in Persistent and Intracellular Uropathogenic E. coli Bladder Infection

    Science.gov (United States)

    Hannan, Thomas J.; Totsika, Makrina; Mansfield, Kylie J.; Moore, Kate H.; Schembri, Mark A.; Hultgren, Scott J.

    2013-01-01

    Bladder infections affect millions of people yearly, and recurrent symptomatic infections (cystitis) are very common. The rapid increase in infections caused by multi-drug resistant uropathogens threatens to make recurrent cystitis an increasingly troubling public health concern. Uropathogenic E. coli (UPEC) cause the vast majority of bladder infections. Upon entry into the lower urinary tract, UPEC face obstacles to colonization that constitute population bottlenecks, reducing diversity and selecting for fit clones. A critical mucosal barrier to bladder infection is the epithelium (urothelium). UPEC bypass this barrier when they invade urothelial cells and form intracellular bacterial communities (IBCs), a process which requires type 1 pili. IBCs are transient in nature, occurring primarily during acute infection. Chronic bladder infection is common and can be either latent, in the form of the Quiescent Intracellular Reservoir (QIR), or active, in the form of asymptomatic bacteriuria (ASB/ABU) or chronic cystitis. In mice, the fate of bladder infection: QIR, ASB, or chronic cystitis, is determined within the first 24 hours of infection and constitutes a putative host-pathogen mucosal checkpoint that contributes to susceptibility to recurrent cystitis. Knowledge of these checkpoints and bottlenecks is critical for our understanding of bladder infection and efforts to devise novel therapeutic strategies. PMID:22404313

  3. Genetic analysis reveals population structuring and a bottleneck in the black-faced lion tamarin (Leontopithecus caissara).

    Science.gov (United States)

    Martins, M M; Nascimento, A T A; Nali, C; Velastin, G O; Mangini, P B; Valladares-Padua, C B; Galetti, P M

    2011-01-01

    The ability of a population to evolve in a changing environment may be compromised by human-imposed barriers to gene flow. We investigated the population structure and the possible occurrence of a genetic bottleneck in two isolated populations of the black-faced lion tamarin (Leontopithecus caissara), a species with very reduced numbers (less than 400) in a very restricted range in the Atlantic Forest of southeast Brazil. We determined the genotypes of 52 individuals across 9 microsatellite loci. We found genetic divergence between the populations, each exhibiting low genetic diversity. Analysis revealed broad- and fine-scale population structuring. Both populations have evidently experienced population reduction and a genetic bottleneck without presenting any apparent detrimental effect. Anyway, measures should be taken to effectively protect the forests where L. caissara occurs in order to allow its populations to increase and counteract the eventual effects of genetic impoverishment. Copyright © 2012 S. Karger AG, Basel.

  4. Reconstruction of a beech population bottleneck using archival demographic information and Bayesian analysis of genetic data.

    Science.gov (United States)

    Lander, Tonya A; Oddou-Muratorio, Sylvie; Prouillet-Leplat, Helene; Klein, Etienne K

    2011-12-01

    Range expansion and contraction has occurred in the history of most species and can seriously impact patterns of genetic diversity. Historical data about range change are rare and generally appropriate for studies at large scales, whereas the individual pollen and seed dispersal events that form the basis of geneflow and colonization generally occur at a local scale. In this study, we investigated range change in Fagus sylvatica on Mont Ventoux, France, using historical data from 1838 to the present and approximate Bayesian computation (ABC) analyses of genetic data. From the historical data, we identified a population minimum in 1845 and located remnant populations at least 200 years old. The ABC analysis selected a demographic scenario with three populations, corresponding to two remnant populations and one area of recent expansion. It also identified expansion from a smaller ancestral population but did not find that this expansion followed a population bottleneck, as suggested by the historical data. Despite a strong support to the selected scenario for our data set, the ABC approach showed a low power to discriminate among scenarios on average and a low ability to accurately estimate effective population sizes and divergence dates, probably due to the temporal scale of the study. This study provides an unusual opportunity to test ABC analysis in a system with a well-documented demographic history and identify discrepancies between the results of historical, classical population genetic and ABC analyses. The results also provide valuable insights into genetic processes at work at a fine spatial and temporal scale in range change and colonization.

  5. Molecular and pedigree measures of relatedness provide similar estimates of inbreeding depression in a bottlenecked population.

    Science.gov (United States)

    Townsend, S M; Jamieson, I G

    2013-04-01

    Individual-based estimates of the degree of inbreeding or parental relatedness from pedigrees provide a critical starting point for studies of inbreeding depression, but in practice wild pedigrees are difficult to obtain. Because inbreeding increases the proportion of genomewide loci that are identical by descent, inbreeding variation within populations has the potential to generate observable correlations between heterozygosity measured using molecular markers and a variety of fitness related traits. Termed heterozygosity-fitness correlations (HFCs), these correlations have been observed in a wide variety of taxa. The difficulty of obtaining wild pedigree data, however, means that empirical investigations of how pedigree inbreeding influences HFCs are rare. Here, we assess evidence for inbreeding depression in three life-history traits (hatching and fledging success and juvenile survival) in an isolated population of Stewart Island robins using both pedigree- and molecular-derived measures of relatedness. We found results from the two measures were highly correlated and supported evidence for significant but weak inbreeding depression. However, standardized effect sizes for inbreeding depression based on the pedigree-based kin coefficients (k) were greater and had smaller standard errors than those based on molecular genetic measures of relatedness (RI), particularly for hatching and fledging success. Nevertheless, the results presented here support the use of molecular-based measures of relatedness in bottlenecked populations when information regarding inbreeding depression is desired but pedigree data on relatedness are unavailable. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  6. Population genetics and the effects of a severe bottleneck in an ex situ population of critically endangered Hawaiian tree snails.

    Science.gov (United States)

    Price, Melissa R; Hadfield, Michael G

    2014-01-01

    As wild populations decline, ex situ propagation provides a potential bank of genetic diversity and a hedge against extinction. These programs are unlikely to succeed if captive populations do not recover from the severe bottleneck imposed when they are founded with a limited number of individuals from remnant populations. In small captive populations allelic richness may be lost due to genetic drift, leading to a decline in fitness. Wild populations of the Hawaiian tree snail Achatinella lila, a hermaphroditic snail with a long life history, have declined precipitously due to introduced predators and other human impacts. A captive population initially thrived after its founding with seven snails, exceeding 600 captive individuals in 2009, but drastically declined in the last five years. Measures of fitness were examined from 2,018 captive snails that died between 1998 and 2012, and compared with genotypic data for six microsatellite loci from a subset of these deceased snails (N = 335), as well as live captive snails (N = 198) and wild snails (N = 92). Surprisingly, the inbreeding coefficient (Fis) declined over time in the captive population, and is now approaching values observed in the 2013 wild population, despite a significant decrease in allelic richness. However, adult annual survival and fecundity significantly declined in the second generation. These measures of fitness were positively correlated with heterozygosity. Snails with higher measures of heterozygosity had more offspring, and third generation offspring with higher measures of heterozygosity were more likely to reach maturity. These results highlight the importance of maintaining genetic diversity in captive populations, particularly those initiated with a small number of individuals from wild remnant populations. Genetic rescue may allow for an increase in genetic diversity in the captive population, as measures of heterozygosity and rarified allelic richness were higher in wild tree

  7. 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.

  8. Population structure and genetic bottleneck in sweet cherry estimated with SSRs and the gametophytic self-incompatibility locus

    Directory of Open Access Journals (Sweden)

    Mariette Stéphanie

    2010-08-01

    Full Text Available Abstract Background Domestication and breeding involve the selection of particular phenotypes, limiting the genomic diversity of the population and creating a bottleneck. These effects can be precisely estimated when the location of domestication is established. Few analyses have focused on understanding the genetic consequences of domestication and breeding in fruit trees. In this study, we aimed to analyse genetic structure and changes in the diversity in sweet cherry Prunus avium L. Results Three subgroups were detected in sweet cherry, with one group of landraces genetically very close to the analysed wild cherry population. A limited number of SSR markers displayed deviations from the frequencies expected under neutrality. After the removal of these markers from the analysis, a very limited bottleneck was detected between wild cherries and sweet cherry landraces, with a much more pronounced bottleneck between sweet cherry landraces and modern sweet cherry varieties. The loss of diversity between wild cherries and sweet cherry landraces at the S-locus was more significant than that for microsatellites. Particularly high levels of differentiation were observed for some S-alleles. Conclusions Several domestication events may have happened in sweet cherry or/and intense gene flow from local wild cherry was probably maintained along the evolutionary history of the species. A marked bottleneck due to breeding was detected, with all markers, in the modern sweet cherry gene pool. The microsatellites did not detect the bottleneck due to domestication in the analysed sample. The vegetative propagation specific to some fruit trees may account for the differences in diversity observed at the S-locus. Our study provides insights into domestication events of cherry, however, requires confirmation on a larger sampling scheme for both sweet cherry landraces and wild cherry.

  9. 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.

  10. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima).

    Science.gov (United States)

    Nabholz, Benoit; Sarah, Gautier; Sabot, François; Ruiz, Manuel; Adam, Hélène; Nidelet, Sabine; Ghesquière, Alain; Santoni, Sylvain; David, Jacques; Glémin, Sylvain

    2014-05-01

    The African cultivated rice (Oryza glaberrima) was domesticated in West Africa 3000 years ago. Although less cultivated than the Asian rice (O. sativa), O. glaberrima landraces often display interesting adaptation to rustic environment (e.g. drought). Here, using RNA-seq technology, we were able to compare more than 12,000 transcripts between 9 O. glaberrima, 10 wild O. barthii and one O. meridionalis individuals. With a synonymous nucleotide diversity πs = 0.0006 per site, O. glaberrima appears as the least genetically diverse crop grass ever documented. Using approximate Bayesian computation, we estimated that O. glaberrima experienced a severe bottleneck during domestication. This demographic scenario almost fully accounts for the pattern of genetic diversity across O. glaberrima genome as we detected very few outliers regions where positive selection may have further impacted genetic diversity. Moreover, the large excess of derived nonsynonymous substitution that we detected suggests that the O. glaberrima population suffered from the 'cost of domestication'. In addition, we used this genome-scale data set to demonstrate that (i) O. barthii genetic diversity is positively correlated with recombination rate and negatively with gene density, (ii) expression level is negatively correlated with evolutionary constraint, and (iii) one region on chromosome 5 (position 4-6 Mb) exhibits a clear signature of introgression with a yet unidentified Oryza species. This work represents the first genome-wide survey of the African rice genetic diversity and paves the way for further comparison between the African and the Asian rice, notably regarding the genetics underlying domestication traits.

  11. Chikungunya virus 3' untranslated region: adaptation to mosquitoes and a population bottleneck as major evolutionary forces.

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    Rubing Chen

    Full Text Available The 3' untranslated genome region (UTR of arthropod-borne viruses is characterized by enriched direct repeats (DRs and stem-loop structures. Despite many years of theoretical and experimental study, on-going positive selection on the 3'UTR had never been observed in 'real-time,' and the role of the arbovirus 3'UTR remains poorly understood. We observed a lineage-specific 3'UTR sequence pattern in all available Asian lineage of the mosquito-borne alphavirus, chikungunya virus (CHIKV (1958-2009, including complicated mutation and duplication patterns of the long DRs. Given that a longer genome is usually associated with less efficient replication, we hypothesized that the fixation of these genetic changes in the Asian lineage 3'UTR was due to their beneficial effects on adaptation to vectors or hosts. Using reverse genetic methods, we examined the functional importance of each direct repeat. Our results suggest that adaptation to mosquitoes, rather than to mammalian hosts, is a major evolutionary force on the CHIKV 3'UTR. Surprisingly, the Asian 3'UTR appeared to be inferior to its predicted ancestral sequence for replication in both mammals and mosquitoes, suggesting that its fixation in Asia was not a result of directional selection. Rather, it may have resulted from a population bottleneck during its introduction from Africa to Asia. We propose that this introduction of a 3'UTR with deletions led to genetic drift and compensatory mutations associated with the loss of structural/functional constraints, followed by two independent beneficial duplications and fixation due to positive selection. Our results provide further evidence that the limited epidemic potential of the Asian CHIKV strains resulted from founder effects that reduced its fitness for efficient transmission by mosquitoes there.

  12. Meta-Analysis of Mitochondrial DNA Reveals Several Population Bottlenecks during Worldwide Migrations of Cattle

    Directory of Open Access Journals (Sweden)

    Johannes A. Lenstra

    2014-03-01

    Full Text Available Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a role.

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

    Science.gov (United States)

    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.

  14. Microsatellite analysis of a population crash and bottleneck in the Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense (Asteraceae), and its implications for reintroduction.

    Science.gov (United States)

    Friar, E A; Ladoux, T; Roalson, E H; Robichaux, R H

    2000-12-01

    The Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense, has experienced both a severe population crash associated with an increase in alien ungulate populations on Mauna Kea, and a population bottleneck associated with reintroduction. In this paper, we address the genetic consequences of both demographic events using eight microsatellite loci. The population crash was not accompanied by a significant reduction in number of alleles or heterozygosity. However, the population bottleneck was accompanied by significant reductions in observed number of alleles, effective number of alleles, and expected heterozygosity, though not in observed heterozygosity. The effective size of the population bottleneck was calculated using both observed heterozygosities and allele frequency variances. Both methods corroborated the historical census size of the population bottleneck of at most three individuals. The results suggest that: (i) small populations, even those that result from severe reductions in historical population size and extent, are not necessarily genetically depauperate; and (ii) species reintroduction plans need to be conceived and implemented carefully, with due consideration to the genetic impact of sampling for reintroduction.

  15. 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.

  16. 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.

  17. Beneficial Effects of Population Bottlenecks in an RNA Virus Evolving at Increased Error Rate

    OpenAIRE

    Cases-González, Clara E.; Arribas, María; Domingo, Esteban; Lázaro, Ester

    2008-01-01

    RNA viruses replicate their genomes with a very high error rate and constitute highly heterogeneous mutant distributions similar to the molecular quasispecies introduced to explain the evolution of prebiotic replicators. The genetic information included in a quasispecies can only be faithfully transmitted below a critical error rate. When the error threshold is crossed, the population structure disorganizes, and it is substituted by a randomly distributed mutant spectrum. For viral quasispeci...

  18. An extreme Population II dwarf without lithium

    Energy Technology Data Exchange (ETDEWEB)

    Hobbs, L.M.; Thorburn, J.A.; Welty, D.E. (Yerkes Observatory, Williams Bay, WI (USA) Chicago, University, IL (USA))

    1991-06-01

    G186 - 26 is an apparently normal, Population II dwarf with Fe/H = {minus} 2.9 and Te = 6220 K. A high-dispersion spectrogram of this extreme halo star recorded at the Li I 6707 line shows no detectable surface lithium, at an abundance upper limit N(Li) = 12 + log (Li/H) not greater than 1.23. In comparison with the uniform lithium abundance N(Li) of about 2.17 found previously in 11 other halo dwarfs with Fe/H less than about {minus}2.6, the minimum deficiency of surface lithium in G 186 {minus} 26 therefore exceeds a factor of 8. 19 refs.

  19. Vegetative propagation and its possible role as a genetic bottleneck in the shaping of the apple fruit crinkle viroid populations in apple and hop plants.

    Science.gov (United States)

    Sano, Teruo; Isono, Sayaka; Matsuki, Keigo; Kawaguchi-Ito, Yoko; Tanaka, Kazuaki; Kondo, Ken-ichi; Iijima, Akira; Bar-Joseph, Moshe

    2008-12-01

    Apple fruit crinkle viroid (AFCVd) infects apples and hops. To analyze the genetic diversity of AFCVd, nine apple and six hop isolates were collected from several locations in Japan. In total, 76 independent cDNA clones were used for sequencing and phylogenetic analyses. Two major population clusters were identified. The first consisted of all four hop isolates from Akita and some from Yamagata. The second cluster consisted of some Yamagata hop and all apple isolates. On the basis of the polymorphism found in the nucleotide insertion between positions 142/143 of the AFCVd genome and the history of hop cultivation in the region, it appears likely that one of the AFCVd populations that pre-existed in the Yamagata hops served as a "founder" for the Akita hop cluster. In this scenario, a genetic bottleneck caused by vegetative propagation played an important role in the shaping of viroid populations in a cultivated crop.

  20. 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.

  1. 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.

  2. When is a bottleneck a bottleneck?

    CERN Document Server

    Schadschneider, Andreas; Popkov, Vladislav

    2015-01-01

    Bottlenecks, i.e. local reductions of capacity, are one of the most relevant scenarios of traffic systems. The asymmetric simple exclusion process (ASEP) with a defect is a minimal model for such a bottleneck scenario. One crucial question is "What is the critical strength of the defect that is required to create global effects, i.e. traffic jams localized at the defect position". Intuitively one would expect that already an arbitrarily small bottleneck strength leads to global effects in the system, e.g. a reduction of the maximal current. Therefore it came as a surprise when, based on computer simulations, it was claimed that the reaction of the system depends in non-continuous way on the defect strength and weak defects do not have a global influence on the system. Here we reconcile intuition and simulations by showing that indeed the critical defect strength is zero. We discuss the implications for the analysis of empirical and numerical data.

  3. Population-based resequencing analysis of wild and cultivated barley revealed weak domestication signal of selection and bottleneck in the Rrs2 scald resistance gene region.

    Science.gov (United States)

    Fu, Yong-Bi

    2012-02-01

    Many plant disease resistance (R) genes have been cloned, but the potential of utilizing these plant R-gene genomic resources for genetic inferences of plant domestication history remains unexplored. A population-based resequencing analysis of the genomic region near the Rrs2 scald resistance gene was made in 51 accessions of wild and cultivated barley from 41 countries. Fifteen primer pairs were designed to sample the genomic region with a total length of 10 406 bp. More nucleotide diversity was found in wild (π = 0.01846) than cultivated (π = 0.01507) barley samples. Three distinct groups of 29 haplotypes were detected for all 51 samples, and they were well mixed with wild and cultivated barley samples from different countries and regions. The neutrality tests by Tajima's D were not significant, but a significant (P domestication. Together, the domestication signal in the genomic region was weak both in human selection and domestication bottleneck.

  4. Restriction of HIV-1 genotypes in breast milk does not account for the population transmission genetic bottleneck that occurs following transmission.

    Directory of Open Access Journals (Sweden)

    Laura Heath

    Full Text Available BACKGROUND: Breast milk transmission of HIV-1 remains a major route of pediatric infection. Defining the characteristics of viral variants to which breastfeeding infants are exposed is important for understanding the genetic bottleneck that occurs in the majority of mother-to-child transmissions. The blood-milk epithelial barrier markedly restricts the quantity of HIV-1 in breast milk, even in the absence of antiretroviral drugs. The basis of this restriction and the genetic relationship between breast milk and blood variants are not well established. METHODOLOGY/PRINCIPAL FINDINGS: We compared 356 HIV-1 subtype C gp160 envelope (env gene sequences from the plasma and breast milk of 13 breastfeeding women. A trend towards lower viral population diversity and divergence in breast milk was observed, potentially indicative of clonal expansion within the breast. No differences in potential N-linked glycosylation site numbers or in gp160 variable loop amino acid lengths were identified. Genetic compartmentalization was evident in only one out of six subjects in whom contemporaneously obtained samples were studied. However, in samples that were collected 10 or more days apart, six of seven subjects were classified as having compartmentalized viral populations, highlighting the necessity of contemporaneous sampling for genetic compartmentalization studies. We found evidence of CXCR4 co-receptor using viruses in breast milk and blood in nine out of the thirteen subjects, but no evidence of preferential localization of these variants in either tissue. CONCLUSIONS/SIGNIFICANCE: Despite marked restriction of HIV-1 quantities in milk, our data indicate intermixing of virus between blood and breast milk. Thus, we found no evidence that a restriction in viral genotype diversity in breast milk accounts for the genetic bottleneck observed following transmission. In addition, our results highlight the rapidity of HIV-1 env evolution and the importance of sample

  5. Extreme genetic diversity in asexual grass thrips populations.

    Science.gov (United States)

    Fontcuberta García-Cuenca, A; Dumas, Z; Schwander, T

    2016-05-01

    The continuous generation of genetic variation has been proposed as one of the main factors explaining the maintenance of sexual reproduction in nature. However, populations of asexual individuals may attain high levels of genetic diversity through within-lineage diversification, replicate transitions to asexuality from sexual ancestors and migration. How these mechanisms affect genetic variation in populations of closely related sexual and asexual taxa can therefore provide insights into the role of genetic diversity for the maintenance of sexual reproduction. Here, we evaluate patterns of intra- and interpopulation genetic diversity in sexual and asexual populations of Aptinothrips rufus grass thrips. Asexual A. rufus populations are found throughout the world, whereas sexual populations appear to be confined to few locations in the Mediterranean region. We found that asexual A. rufus populations are characterized by extremely high levels of genetic diversity, both in comparison with their sexual relatives and in comparison with other asexual species. Migration is extensive among asexual populations over large geographic distances, whereas close sexual populations are strongly isolated from each other. The combination of extensive migration with replicate evolution of asexual lineages, and a past demographic expansion in at least one of them, generated high local clone diversities in A. rufus. These high clone diversities in asexual populations may mimic certain benefits conferred by sex via genetic diversity and could help explain the extreme success of asexual A. rufus populations.

  6. Absence of a genetic bottleneck in a wild rabbit (Oryctolagus cuniculus) population exposed to a severe viral epizootic.

    Science.gov (United States)

    Queney, G; Ferrand, N; Marchandeau, S; Azevedo, M; Mougel, F; Branco, M; Monnerot, M

    2000-09-01

    Infectious diseases and their demographic consequences are thought to influence the genetic diversity of populations. In Europe, during the last 50 years, the European rabbit (Oryctolagus cuniculus) has suffered two important viral epizootics: myxomatosis and rabbit viral haemorraghic disease (RVHD). Although mortality rates were very high, the impact of these diseases on genetic diversity has never been assessed directly. The subject of this paper is a wild rabbit population in France, which has been studied since the beginning of the 1980s. The first outbreak of RVHD occurred in 1995 and provoked a demographic crash. The population, sampled for the first time in 1982 and 1994, was sampled again at the end of 1996 to examine the impact of the epizootic on genetic diversity. In spite of the observed high mortality rate ( approximately 90%), analysis of 14 polymorphic loci (allozymes and microsatellites) showed no loss in genetic diversity after the epizootic. Determination of temporal changes in allele frequencies indicated that the population evolved under genetic drift. The temporal method of Waples demonstrated a significant decrease in the effective population size (Ne) correlated with the demographic crash due to the epizootic. However, the population had only been studied for two generations after the epizootic and the remnant population size probably stayed high enough ( approximately 50 individuals) to keep its genetic diversity at the precrash level. These results suggest that, contrary to what is usually thought and in spite of the subsequent high mortality rates, past epizootics (especially myxomatosis) may have had little effect on the genetic diversity of wild rabbit populations in Europe.

  7. The Mouse-colored Tyrannulet (Phaeomyias murina) is a species complex that includes the Cocos Flycatcher (Nesotriccus ridgwayi), an island form that underwent a population bottleneck.

    Science.gov (United States)

    Zucker, Marc R; Harvey, Michael G; Oswald, Jessica A; Cuervo, Andrés; Derryberry, Elizabeth; Brumfield, Robb T

    2016-08-01

    Simultaneous examination of evolutionary history in island forms and closely related mainland relatives can provide reciprocal insight into the evolution of island and mainland faunas. The Cocos Flycatcher (Nesotriccus ridgwayi) is a small tyrant flycatcher (Tyrannidae) endemic to Cocos Island, an oceanic island in the eastern Pacific Ocean. We first established its close relationship to the mainland species Mouse-colored Tyrannulet (Phaeomyias murina) using a phylogeny from genome-wide ultraconserved elements and exons. We then used mitochondrial DNA to explore the relationships between Nesotriccus and Phaeomyias populations from across its distribution in Central and South America. We found that Nesotriccus is nested within the Phaeomyias evolutionary tree, and that Phaeomyias represents a complex of at least four evolutionarily distinct species that differ in plumage, voice, and habitat association. Nesotriccus underwent a population bottleneck subsequent to its divergence from Central American and northern South American Phaeomyias populations in the middle Pleistocene. The 46 UCE loci containing alleles that are fixed between the two species are widely distributed across the genome, which suggests that selective or neutral processes responsible for divergence have occurred genome-wide. Overall, our simultaneous examination of Phaeomyias and Nesotriccus revealed divergent levels of genetic diversity and evolutionary histories between island and mainland forms.

  8. Phylogeography of postglacial range expansion in Juglans mandshurica (Juglandaceae) reveals no evidence of bottleneck, loss of genetic diversity, or isolation by distance in the leading-edge populations.

    Science.gov (United States)

    Wang, Wen-Ting; Xu, Bing; Zhang, Da-Yong; Bai, Wei-Ning

    2016-09-01

    The past studies of postglacial recolonization patterns in high latitude regions have revealed a significant role of dispersal capacity in shaping the genetic diversity and population structure of temperate trees. However, most of these studies have focused on species with long-distance dispersal followed by exponential population growth and were therefore unable to reveal the patterns in the case of a gradual expansion. Here we studied the impacts of postglacial range expansions on the distribution of genetic diversity in the Manchurian walnut (Juglans mandshurica), a common tree of East Asian cool-temperate deciduous forests that apparently lacks long-distance seed dispersal ability. The genetic diversity and structure of 19 natural walnut populations in Northeast China and the Korean Peninsula were examined using 17 nuclear simple sequence repeat (SSR) loci. Potential habitats under current and past climatic conditions were predicted using the ecological niche modelling (ENM) method. Bayesian clustering analysis revealed three groups, which were inferred to have diverged through multiple glacial-interglacial cycles in multiple refugia during the Quaternary Period. ENM estimated a southward range shift at the LGM, but high suitability scores still occurred in the western parts of the Changbai Mountains (Northeast China), the Korean peninsula and the exposed seafloor of the Yellow Sea. In contrast to most other cool-temperate trees co-occurring in the same region, the Manchurian walnut did not show any evidence of a population bottleneck, loss of genetic diversity or isolation by distance during the postglacial expansion. Our study clearly indicates that current northern populations originated from one glacial lineage and recolonization via a gradually advancing front due to the lack of a long-distance seed dispersal mechanism led to no latitudinal decrease in genetic diversity.

  9. Bottlenecks in domestic animal populations can facilitate the emergence of Trypanosoma cruzi, the aetiological agent of Chagas disease

    Science.gov (United States)

    Levy, Michael Z.; Tustin, Aaron; Castillo-Neyra, Ricardo; Mabud, Tarub S.; Levy, Katelyn; Barbu, Corentin M.; Quispe-Machaca, Victor R.; Ancca-Juarez, Jenny; Borrini-Mayori, Katty; Naquira-Velarde, Cesar; Ostfeld, Richard S.

    2015-01-01

    Faeces-mediated transmission of Trypanosoma cruzi (the aetiological agent of Chagas disease) by triatomine insects is extremely inefficient. Still, the parasite emerges frequently, and has infected millions of people and domestic animals. We synthesize here the results of field and laboratory studies of T. cruzi transmission conducted in and around Arequipa, Peru. We document the repeated occurrence of large colonies of triatomine bugs (more than 1000) with very high infection prevalence (more than 85%). By inoculating guinea pigs, an important reservoir of T. cruzi in Peru, and feeding triatomine bugs on them weekly, we demonstrate that, while most animals quickly control parasitaemia, a subset of animals remains highly infectious to vectors for many months. However, we argue that the presence of these persistently infectious hosts is insufficient to explain the observed prevalence of T. cruzi in vector colonies. We posit that seasonal rains, leading to a fluctuation in the price of guinea pig food (alfalfa), leading to annual guinea pig roasts, leading to a concentration of vectors on a small subpopulation of animals maintained for reproduction, can propel T. cruzi through vector colonies and create a considerable force of infection for a pathogen whose transmission might otherwise fizzle out. PMID:26085582

  10. Bottlenecks in domestic animal populations can facilitate the emergence of Trypanosoma cruzi, the aetiological agent of Chagas disease.

    Science.gov (United States)

    Levy, Michael Z; Tustin, Aaron; Castillo-Neyra, Ricardo; Mabud, Tarub S; Levy, Katelyn; Barbu, Corentin M; Quispe-Machaca, Victor R; Ancca-Juarez, Jenny; Borrini-Mayori, Katty; Naquira-Velarde, Cesar; Ostfeld, Richard S

    2015-07-07

    Faeces-mediated transmission of Trypanosoma cruzi (the aetiological agent of Chagas disease) by triatomine insects is extremely inefficient. Still, the parasite emerges frequently, and has infected millions of people and domestic animals. We synthesize here the results of field and laboratory studies of T. cruzi transmission conducted in and around Arequipa, Peru. We document the repeated occurrence of large colonies of triatomine bugs (more than 1000) with very high infection prevalence (more than 85%). By inoculating guinea pigs, an important reservoir of T. cruzi in Peru, and feeding triatomine bugs on them weekly, we demonstrate that, while most animals quickly control parasitaemia, a subset of animals remains highly infectious to vectors for many months. However, we argue that the presence of these persistently infectious hosts is insufficient to explain the observed prevalence of T. cruzi in vector colonies. We posit that seasonal rains, leading to a fluctuation in the price of guinea pig food (alfalfa), leading to annual guinea pig roasts, leading to a concentration of vectors on a small subpopulation of animals maintained for reproduction, can propel T. cruzi through vector colonies and create a considerable force of infection for a pathogen whose transmission might otherwise fizzle out. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  11. Potentially Extreme Population Displacement and Concentration in the Tropics Under Non-Extreme Warming

    OpenAIRE

    Hsiang, Solomon M.; Sobel, Adam H.

    2016-01-01

    Evidence increasingly suggests that as climate warms, some plant, animal, and human populations may move to preserve their environmental temperature. The distances they must travel to do this depends on how much cooler nearby surfaces temperatures are. Because large-scale atmospheric dynamics constrain surface temperatures to be nearly uniform near the equator, these displacements can grow to extreme distances in the tropics, even under relatively mild warming scenarios. Here we show that in ...

  12. Bottleneck flows in networks

    CERN Document Server

    Punnen, Abraham P

    2007-01-01

    The bottleneck network flow problem (BNFP) is a generalization of several well-studied bottleneck problems such as the bottleneck transportation problem (BTP), bottleneck assignment problem (BAP), bottleneck path problem (BPP), and so on. In this paper we provide a review of important results on this topic and its various special cases. We observe that the BNFP can be solved as a sequence of $O(\\log n)$ maximum flow problems. However, special augmenting path based algorithms for the maximum flow problem can be modified to obtain algorithms for the BNFP with the property that these variations and the corresponding maximum flow algorithms have identical worst case time complexity. On unit capacity network we show that BNFP can be solved in $O(\\min \\{{m(n\\log n)}^{{2/3}}, m^{{3/2}}\\sqrt{\\log n}\\})$. This improves the best available algorithm by a factor of $\\sqrt{\\log n}$. On unit capacity simple graphs, we show that BNFP can be solved in $O(m \\sqrt {n \\log n})$ time. As a consequence we have an $O(m \\sqrt {n \\l...

  13. Economic analysis of production bottlenecks

    Directory of Open Access Journals (Sweden)

    Lawrence Stephen R.

    1995-01-01

    Full Text Available The management of bottlenecks has become a central topic in the planning and control of production systems. In this paper, we critically analyze bottlenecks from an economic perspective. Using a queueing network model, we demonstrate that bottlenecks are inevitable when there are differences in job arrival rates, processing rates, or costs of productive resources. These differences naturally lead to the creation of bottlenecks both for facilities design and demand planning problems. To evaluate bottlenecks from an economic perspective, we develop the notion of an “economic bottleneck,” which defines resources as bottlenecks based on economic, rather than physical, characteristics.

  14. Population genetic analysis of microsatellite variation of guppies (Poecilia reticulata) in Trinidad and Tobago: evidence for a dynamic source-sink metapopulation structure, founder events and population bottlenecks.

    Science.gov (United States)

    Barson, N J; Cable, J; Van Oosterhout, C

    2009-03-01

    Riverine fish populations are traditionally considered to be highly structured and subject to strong genetic drift. Here, we use microsatellites to analyse the population structure of the guppy (Poecilia reticulata), focussing on the headwater floodplain area of the Caroni drainage in Trinidad. We also analyse the population genetics of guppies in the Northern Drainage in Trinidad, a habitat characterized by rivers flowing directly into the sea, and a small isolated population in Tobago. Upland Caroni populations are highly differentiated and display low levels of genetic diversity. However, we found no evidence to suggest that these upland populations experienced recent population crashes and the populations appear to approach mutation-drift equilibrium. Dominant downstream migration over both short- and long-time frames has a strong impact on the population genetics of lowland Caroni populations. This drainage system could be considered a source-sink metapopulation, with the tributary furthest downstream representing a 'super sink', receiving immigrants from rivers upstream in the drainage. Moreover, the effective population size in the lowlands is surprisingly low in comparison with the apparently large census population sizes.

  15. Identifying covariates of population health using extreme bound analysis.

    Science.gov (United States)

    Carmignani, Fabrizio; Shankar, Sriram; Tan, Eng Joo; Tang, Kam Ki

    2014-06-01

    The literature is full of lively discussion on the determinants of population health outcomes. However, different papers focus on small and different sets of variables according to their research agenda. Because many of these variables are measures of different aspects of development and are thus correlated, the results for one variable can be sensitive to the inclusion/exclusion of others. We tested for the robustness of potential predictors of population health using the extreme bounds analysis. Population health was measured by life expectancy at birth and infant mortality rate. We found that only about half a dozen variables are robust predictors for life expectancy and infant mortality rate. Among them, adolescent fertility rate, improved water sources, and gender equality are the most robust. All institutional variables and environment variables are systematically non-robust predictors of population health. The results highlight the importance of robustness tests in identifying predictors or potential determinants of population health, and cast doubts on the findings of previous studies that fail to do so.

  16. Bottleneck Effect Analysis of Five Pony Populations in China%中国5个矮马品种的瓶颈效应分析

    Institute of Scientific and Technical Information of China (English)

    杨胜林; 徐龙鑫; 杨海兵; 李爱萍

    2013-01-01

    利用13个微卫星基因座对中国5个矮马品种(德保、贵州、宁强、四川、云南)群体进行了遗传平衡检测.根据微卫星等位基因频率,应用无限等位基因模型(infinite allele model,IAM)、双相突变模型(two-phased model of mutation,TPM)和逐步突变模型(step-wise mutation model,SMM)3种模型,符号和Wilcoxon符号—秩2种检验方法,对5个矮马群体的突变—漂移平衡进行分析.结果表明,在IAM下,Wilcoxon符号—秩检验中,德保矮马和云南矮马达到了显著性水平(P<0.05);在SMM下,宁强矮马在符号检验中达到了显著水平(P<0.05);在TPM下,5个群体均未达到显著水平(P>0.05).因此,德保、云南和宁强矮马近期可能经历了瓶颈效应.本研究结果对中国矮马的保护和利用具有重大意义.%Thirteen microsatellite loci were used to analyze genetic equilibrium of five pony populations in China (Debao, Guizhou, Ningqiang, Sichuan, Yunnan). According to the allele frequency, under IAM, TPM and SMM three models, the sign test and Wilcoxon sign-rank test were used to analyze bottleneck of five pony populations. The results showed that Debao and Yunnan pony were observed in the significant level under IAM and Wilcoxon sign-rank test(P0. 05). The results revealed significant level suggesting possible cryptic demographic in Debao, Yunnan and Ningqiang pony. The exploit and conservation priorities about pony populations in China were determined according to the result of the present study.

  17. Potentially Extreme Population Displacement and Concentration in the Tropics Under Non-Extreme Warming

    Science.gov (United States)

    Hsiang, Solomon M.; Sobel, Adam H.

    2016-06-01

    Evidence increasingly suggests that as climate warms, some plant, animal, and human populations may move to preserve their environmental temperature. The distances they must travel to do this depends on how much cooler nearby surfaces temperatures are. Because large-scale atmospheric dynamics constrain surface temperatures to be nearly uniform near the equator, these displacements can grow to extreme distances in the tropics, even under relatively mild warming scenarios. Here we show that in order to preserve their annual mean temperatures, tropical populations would have to travel distances greater than 1000 km over less than a century if global mean temperature rises by 2 °C over the same period. The disproportionately rapid evacuation of the tropics under such a scenario would cause migrants to concentrate in tropical margins and the subtropics, where population densities would increase 300% or more. These results may have critical consequences for ecosystem and human wellbeing in tropical contexts where alternatives to geographic displacement are limited.

  18. Potentially Extreme Population Displacement and Concentration in the Tropics Under Non-Extreme Warming.

    Science.gov (United States)

    Hsiang, Solomon M; Sobel, Adam H

    2016-06-09

    Evidence increasingly suggests that as climate warms, some plant, animal, and human populations may move to preserve their environmental temperature. The distances they must travel to do this depends on how much cooler nearby surfaces temperatures are. Because large-scale atmospheric dynamics constrain surface temperatures to be nearly uniform near the equator, these displacements can grow to extreme distances in the tropics, even under relatively mild warming scenarios. Here we show that in order to preserve their annual mean temperatures, tropical populations would have to travel distances greater than 1000 km over less than a century if global mean temperature rises by 2 °C over the same period. The disproportionately rapid evacuation of the tropics under such a scenario would cause migrants to concentrate in tropical margins and the subtropics, where population densities would increase 300% or more. These results may have critical consequences for ecosystem and human wellbeing in tropical contexts where alternatives to geographic displacement are limited.

  19. Bottlenecks drive temporal and spatial genetic changes in alpine caddisfly metapopulations

    Directory of Open Access Journals (Sweden)

    Jokela Jukka

    2011-09-01

    Full Text Available Abstract Background Extinction and re-colonisation of local populations is common in ephemeral habitats such as temporary streams. In most cases, such population turnover leads to reduced genetic diversity within populations and increased genetic differentiation among populations due to stochastic founder events, genetic drift, and bottlenecks associated with re-colonisation. Here, we examined the spatio-temporal genetic structure of 8 alpine caddisfly populations inhabiting permanent and temporary streams from four valleys in two regions of the Swiss Alps in years before and after a major stream drying event, the European heat wave in summer 2003. Results We found that population turnover after 2003 led to a loss of allelic richness and gene diversity but not to significant changes in observed heterozygosity. Within all valleys, permanent and temporary streams in any given year were not differentiated, suggesting considerable gene flow and admixture between streams with differing hydroperiods. Large changes in allele frequencies after 2003 resulted in a substantial increase in genetic differentiation among valleys within one to two years (1-2 generations driven primarily by drift and immigration. Signatures of genetic bottlenecks were detected in all 8 populations after 2003 using the M-ratio method, but in no populations when using a heterozygosity excess method, indicating differential sensitivity of bottleneck detection methods. Conclusions We conclude that genetic differentiation among A. uncatus populations changed markedly both temporally and spatially in response to the extreme climate event in 2003. Our results highlight the magnitude of temporal population genetic changes in response to extreme events. More specifically, our results show that extreme events can cause rapid genetic divergence in metapopulations. Further studies are needed to determine if recovery from this perturbation through gradual mixing of diverged populations by

  20. A recent bottleneck in the warthog and elephant populations of Queen Elizabeth National Park, revealed by a comparative study of four mammalian species in Uganda national parks

    DEFF Research Database (Denmark)

    Muwanika, Vincent B.; Siegismund, Hans Redlef; Okello, John Bosco A.

    2003-01-01

    Until 1972, Uganda's national parks boasted of large numbers of large mammal species. Following the breakdown of law and order between 1972 and 1985, large-scale poaching led to an unprecedented decline in numbers of most large mammals in Uganda's national parks. However, the extent of decline...... microsatellite loci (for elephant and warthog populations) and mitochondrial control sequence variation in the warthogs, elephants, buffaloes and hippopotamuses. Queen Elizabeth National Park showed extreme reduction in nucleotide diversity for two species, the common warthog (p= 0.0%) and African elephant (p= 0...... varied in the different parks across different animal species. We have investigated the genetic effects of these reductions in four mammalian species (the common warthog, African savannah elephant, savannah buffalo and common river hippopotamus) from the three major parks of Uganda using both...

  1. Estimating Bottleneck Bandwidth using TCP

    Science.gov (United States)

    Allman, Mark

    1998-01-01

    Various issues associated with estimating bottleneck bandwidth using TCP are presented in viewgraph form. Specific topics include: 1) Why TCP is wanted to estimate the bottleneck bandwidth; 2) Setting ssthresh to an appropriate value to reduce loss; 3) Possible packet-pair solutions; and 4) Preliminary results: ACTS and the Internet.

  2. Midcontinental Native American population dynamics and late Holocene hydroclimate extremes

    Science.gov (United States)

    Bird, Broxton W.; Wilson, Jeremy J.; Gilhooly, William P., III; Steinman, Byron A.; Stamps, Lucas

    2017-01-01

    Climate’s influence on late Pre-Columbian (pre-1492 CE), maize-dependent Native American populations in the midcontinental United States (US) is poorly understood as regional paleoclimate records are sparse and/or provide conflicting perspectives. Here, we reconstruct regional changes in precipitation source and seasonality and local changes in warm-season duration and rainstorm events related to the Pacific North American pattern (PNA) using a 2100-year-long multi-proxy lake-sediment record from the midcontinental US. Wet midcontinental climate reflecting negative PNA-like conditions occurred during the Medieval Climate Anomaly (950–1250 CE) as Native American populations adopted intensive maize agriculture, facilitating population aggregation and the development of urban centers between 1000–1200 CE. Intensifying midcontinental socio-political instability and warfare between 1250–1350 CE corresponded with drier positive PNA-like conditions, culminating in the staggered abandonment of many major Native American river valley settlements and large urban centers between 1350–1450 CE during an especially severe warm-season drought. We hypothesize that this sustained drought interval rendered it difficult to support dense populations and large urban centers in the midcontinental US by destabilizing regional agricultural systems, thereby contributing to the host of socio-political factors that led to population reorganization and migration in the midcontinent and neighboring regions shortly before European contact.

  3. Midcontinental Native American population dynamics and late Holocene hydroclimate extremes

    Science.gov (United States)

    Bird, Broxton W.; Wilson, Jeremy J.; Gilhooly III, William P.; Steinman, Byron A.; Stamps, Lucas

    2017-01-01

    Climate’s influence on late Pre-Columbian (pre-1492 CE), maize-dependent Native American populations in the midcontinental United States (US) is poorly understood as regional paleoclimate records are sparse and/or provide conflicting perspectives. Here, we reconstruct regional changes in precipitation source and seasonality and local changes in warm-season duration and rainstorm events related to the Pacific North American pattern (PNA) using a 2100-year-long multi-proxy lake-sediment record from the midcontinental US. Wet midcontinental climate reflecting negative PNA-like conditions occurred during the Medieval Climate Anomaly (950–1250 CE) as Native American populations adopted intensive maize agriculture, facilitating population aggregation and the development of urban centers between 1000–1200 CE. Intensifying midcontinental socio-political instability and warfare between 1250–1350 CE corresponded with drier positive PNA-like conditions, culminating in the staggered abandonment of many major Native American river valley settlements and large urban centers between 1350–1450 CE during an especially severe warm-season drought. We hypothesize that this sustained drought interval rendered it difficult to support dense populations and large urban centers in the midcontinental US by destabilizing regional agricultural systems, thereby contributing to the host of socio-political factors that led to population reorganization and migration in the midcontinent and neighboring regions shortly before European contact. PMID:28139698

  4. Effects of Bottlenecks in Vehicle Traffic

    CERN Document Server

    Yamamoto, S; Tadaki, S; Yamamoto, Syohei; Hieida, Yasuhiro; Tadaki, Shin-ichi

    2006-01-01

    Traffic congestion is usually observed at the upper streams of bottlenecks like tunnels. Congestion appears as stop-and-go waves and high density uniform flow. We perform simulations of traffic flow with a bottleneck using the coupled map optimal velocity model. The bottleneck is expressed as a road segment with speed reduction. The emergence of stop-and-go waves depends on the speed reduction in the bottleneck. A phenomenological theory of bottleneck effects is constructed.

  5. The Extremely Young Star Cluster Population In Haro 11

    CERN Document Server

    Adamo, Angela; Zackrisson, Erik; Hayes, Matthew

    2009-01-01

    We have performed a deep multi-band photometric analysis of the star cluster population of Haro 11. This starburst galaxy (log L_FUV = 10.3 L_sun) is considered a nearby analogue of Lyman break galaxies (LBGs) at high redshift. The study of the numerous star clusters in the systems is an effective way to investigate the formation and evolution of the starburst phase. In fact, the SED fitting models have revealed a surprisingly young star cluster population, with ages between 0.5 and 40 Myr, and estimated masses between 10^3 and 10^7 solar masses. An independent age estimation has been done with the EW(Halpha) analysis of each cluster. This last analysis has confirmed the young ages of the clusters. We noticed that the clusters with ages between 1 and 10 Myr show a flux excess in H (NIC3/F160W) and/or I (WFPC2/F814W) bands with respect to the evolutionary models. Once more Haro 11 represents a challenge to our understanding.

  6. Population exposure to heat-related extremes: Demographic change vs climate change

    Science.gov (United States)

    Jones, B.; O'Neill, B. C.; Tebaldi, C.; Oleson, K. W.

    2014-12-01

    Extreme heat events are projected to increase in frequency and intensity in the coming decades [1]. The physical effects of extreme heat on human populations are well-documented, and anticipating changes in future exposure to extreme heat is a key component of adequate planning/mitigation [2, 3]. Exposure to extreme heat depends not only on changing climate, but also on changes in the size and spatial distribution of the human population. Here we focus on systematically quantifying exposure to extreme heat as a function of both climate and population change. We compare exposure outcomes across multiple global climate and spatial population scenarios, and characterize the relative contributions of each to population exposure to extreme heat. We consider a 2 x 2 matrix of climate and population output, using projections of heat extremes corresponding to RCP 4.5 and RCP 8.5 from the NCAR community land model, and spatial population projections for SSP 3 and SSP 5 from the NCAR spatial population downscaling model. Our primary comparison is across RCPs - exposure outcomes from RCP 4.5 versus RCP 8.5 - paying particular attention to how variation depends on the choice of SSP in terms of aggregate global and regional exposure, as well as the spatial distribution of exposure. We assess how aggregate exposure changes based on the choice of SSP, and which driver is more important, population or climate change (i.e. does that outcome vary more as a result of RCP or SSP). We further decompose the population component to analyze the contributions of total population change, migration, and changes in local spatial structure. Preliminary results from a similar study of the US suggests a four-to-six fold increase in total exposure by the latter half of the 21st century. Changes in population are as important as changes in climate in driving this outcome, and there is regional variation in the relative importance of each. Aggregate population growth, as well as redistribution of

  7. Extreme lipoprotein(a) levels and risk of myocardial infarction in the general population

    DEFF Research Database (Denmark)

    Kamstrup, Pia R; Benn, Marianne; Tybjaerg-Hansen, Anne

    2008-01-01

    of absolute risk estimates in the general population. We tested the hypothesis that extreme lipoprotein(a) levels predict MI in the general population, measuring levels shortly after sampling, correcting for regression dilution bias, and calculating hazard ratios and absolute risk estimates....

  8. Continuous and discrete extreme climatic events affecting the dynamics of a high-arctic reindeer population.

    Science.gov (United States)

    Chan, Kung-Sik; Mysterud, Atle; Øritsland, Nils Are; Severinsen, Torbjørn; Stenseth, Nils Chr

    2005-10-01

    Climate at northern latitudes are currently changing both with regard to the mean and the temporal variability at any given site, increasing the frequency of extreme events such as cold and warm spells. Here we use a conceptually new modelling approach with two different dynamic terms of the climatic effects on a Svalbard reindeer population (the Brøggerhalvøya population) which underwent an extreme icing event ("locked pastures") with 80% reduction in population size during one winter (1993/94). One term captures the continuous and linear effect depending upon the Arctic Oscillation and another the discrete (rare) "event" process. The introduction of an "event" parameter describing the discrete extreme winter resulted in a more parsimonious model. Such an approach may be useful in strongly age-structured ungulate populations, with young and very old individuals being particularly prone to mortality factors during adverse conditions (resulting in a population structure that differs before and after extreme climatic events). A simulation study demonstrates that our approach is able to properly detect the ecological effects of such extreme climate events.

  9. 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.

  10. The differential effects of increasing frequency and magnitude of extreme events on coral populations

    OpenAIRE

    Fabina, NS; Baskett, ML; K. Gross

    2015-01-01

    © 2015 by the Ecological Society of America. Extreme events, which have profound ecological consequences, are changing in both frequency and magnitude with climate change. Because extreme temperatures induce coral bleaching, we can explore the relative impacts of changes in frequency and magnitude of high temperature events on coral reefs. Here, we combined climate projections and a dynamic population model to determine how changing bleaching regimes influence coral persistence. We additional...

  11. How to conserve threatened Chinese plant species with extremely small populations?

    Directory of Open Access Journals (Sweden)

    Sergei Volis

    2016-02-01

    Full Text Available The Chinese flora occupies a unique position in global plant diversity, but is severely threatened. Although biodiversity conservation in China has made significant progress over the past decades, many wild plant species have extremely small population sizes and therefore are in extreme danger of extinction. The concept of plant species with extremely small populations (PSESPs, recently adopted and widely accepted in China, lacks a detailed description of the methodology appropriate for conserving PSESPs. Strategies for seed sampling, reintroduction, protecting PSESP locations, managing interactions with the local human population, and other conservation aspects can substantially differ from those commonly applied to non-PSESPs. The present review is an attempt to provide a detailed conservation methodology with realistic and easy-to-follow guidelines for PSESPs in China.

  12. Extreme lipoprotein(a) levels and risk of myocardial infarction in the general population

    DEFF Research Database (Denmark)

    Kamstrup, Pia R; Benn, Marianne; Tybjaerg-Hansen, Anne

    2008-01-01

    Elevated lipoprotein(a) levels are associated with myocardial infarction (MI) in some but not all studies. Limitations of previous studies include lack of risk estimates for extreme lipoprotein(a) levels, measurements in long-term frozen samples, no correction for regression dilution bias, and lack...... of absolute risk estimates in the general population. We tested the hypothesis that extreme lipoprotein(a) levels predict MI in the general population, measuring levels shortly after sampling, correcting for regression dilution bias, and calculating hazard ratios and absolute risk estimates....

  13. Sales bottlenecks and their effect on profit

    NARCIS (Netherlands)

    Veltman, M.; Kooij, R.E.; Marban, S.

    2014-01-01

    This study introduces the term sales bottleneck, defined as a stage in a total production or service delivery process that limits sales. After analyzing the suitability of traditional methods to find sales bottlenecks, the study proposes the bottleneck accounting model as a method to determine sales

  14. Extreme polyandry aids the establishment of invasive populations of a social insect.

    Science.gov (United States)

    Ding, G; Xu, H; Oldroyd, B P; Gloag, R S

    2017-08-23

    Although monandry is believed to have facilitated the evolution of eusociality, many highly eusocial insects have since evolved extreme polyandry. The transition to extreme polyandry was likely driven by the benefits of within-colony genetic variance to task specialization and/or disease resistance, but the extent to which it confers secondary benefits, once evolved, is unclear. Here we investigate the consequences of extreme polyandry on the invasive potential of the Asian honey bee, Apis cerana. In honey bees and other Hymenoptera, small newly founded invasive populations must overcome the genetic constraint of their sex determination system that requires heterozygosity at a sex-determining locus to produce viable females. We find A. cerana queens in an invasive population mate with an average of 27 males (range 16-42) that would result in the founding queen/s carrying 75% of their source population's sex alleles in stored sperm. This mating frequency is similar to native-range Chinese A. cerana (mean 29 males, range 19-46). Simulations reveal that extreme polyandry reduces the risk, relative to monandry or moderate polyandry, that colonies produce a high incidence of inviable brood in populations that have experienced a founder event, that is, when sex allele diversity is low and/or allele frequencies are unequal. Thus, extreme polyandry aids the invasiveness of A. cerana in two ways: (1) by increasing the sex locus allelic richness carried to new populations with each founder, thereby increasing sex locus heterozygosity; and (2) by reducing the population variance in colony fitness following a founder event.Heredity advance online publication, 23 August 2017; doi:10.1038/hdy.2017.49.

  15. MODIFIED BOTTLENECK-BASED PROCEDURE FOR LARGE-SCALE FLOW-SHOP SCHEDULING PROBLEMS WITH BOTTLENECK

    Institute of Scientific and Technical Information of China (English)

    ZUO Yan; GU Hanyu; XI Yugeng

    2006-01-01

    A new bottleneck-based heuristic for large-scale flow-shop scheduling problems with a bottleneck is proposed, which is simpler but more tailored than the shifting bottleneck (SB)procedure. In this algorithm, a schedule for the bottleneck machine is first constructed optimally and then the non-bottleneck machines are scheduled around the bottleneck schedule by some effective dispatching rules. Computational results show that the modified bottleneck-based procedure can achieve a tradeoff between solution quality and computational time comparing with SB procedure for medium-size problems. Furthermore it can obtain a good solution in quite short time for large-scale scheduling problems.

  16. Dynamic Prediction Method of Production Logistics Bottleneck Based on Bottleneck Index

    Institute of Scientific and Technical Information of China (English)

    LIU Mingzhou; TANG Juan; GE Maogen; JIANG Zengqiang; HU Jing; LING Lin

    2009-01-01

    In modern manufacturing pattern, there are many uncertain factors in the modern manufacturing process, such as changes of product attribute, changes of manufacturing resources' state, and so on, which cause production logistics bottleneck frequently shift, and make decisions of production planning and control based on formed bottleneck deviated from practical production process. Considering these factors, present researches mainly apply afterwards control to optimize production process to passively adapt to bottleneck changes. If the direction of bottleneck shifting can be accurately forecasted, the transition from afterwards control of chasing bottleneck to beforehand control can be realized. Therefore, aiming at the phenomenon of production logistics bottleneck shifting under uncertain manufacturing circumstances, this paper starts off with dynamic property of capability and requirement and then builds the concepts of bottleneck degree and bottleneck index to describe dynamic bottleneck characteristic of production unit;taken production capability, production load and quality assurance capability into consideration, mathematical model of bottleneck index is established to measure bottleneck degree accurately, consequently, quantitative research on mechanism of production logistics shifting is achieved. Based on bottleneck index, the prediction model of production logistics bottleneck is founded to predict dynamic change of bottleneck accurately. Finally, an example of forecasting and monitoring the production logistics bottleneck in one manufacturing shop is given to testify the validation and practicability of the prediction method.

  17. General Population Knowledge about Extreme Heat: A Cross-Sectional Survey in Lisbon and Madrid.

    Science.gov (United States)

    Gil Cuesta, Julita; van Loenhout, Joris Adriaan Frank; Colaço, Maria da Conceição; Guha-Sapir, Debarati

    2017-01-28

    Extreme heat is associated with an increased mortality and morbidity. National heat plans have been implemented to minimize the effect of extreme heat. The population's awareness and knowledge of national heat plans and extreme heat is essential to improve the community's behavior and adaptation. A general population survey was conducted in Lisbon and in Madrid to assess this knowledge. We used a questionnaire to interview passers-by. Results were compared between Lisbon and Madrid and between locals and foreigners, using Pearson Chi-square tests and Fisher's exact test. We conducted 260 interviews in six locations of different socio-economic backgrounds in each city. The most frequently mentioned extreme heat-related risk groups were the elderly (79.2%), children (49.6%) and babies (21.5%). The most frequently reported protective measures were increased fluid intake (73.1%) and avoiding exposure to the sun (50.8%). Knowledge about the heat plan was higher in Lisbon (37.2%) than in Madrid (25.2%) (p-value = 0.03). Foreigners had less knowledge of risk groups compared to locals. Heat plans were not widely known in Madrid and Lisbon. Nonetheless, knowledge of practical concepts to face extreme heat, such as certain risk groups and protective measures, was found. Our results were similar to comparable surveys where specific respondents' groups were identified as less knowledgeable. This highlighted the importance of addressing these groups when communicating public health messages on heat. Foreigners should be specifically targeted to increase their awareness.

  18. Quantifying population exposure to airborne particulate matter during extreme events in California due to climate change

    Directory of Open Access Journals (Sweden)

    A. Mahmud

    2012-02-01

    Full Text Available The effect of climate change on population-weighted concentrations of particulate matter (PM during extreme events was studied using the Parallel Climate Model (PCM, the Weather Research and Forecasting (WRF model and the UCD/CIT 3-D photochemical air quality model. A "business as usual" (B06.44 global emissions scenario was dynamically downscaled for the entire state of California between the years 2000–2006 and 2047–2053. Air quality simulations were carried out for 1008 days in each of the present-day and future climate conditions using year-2000 emissions. Population-weighted concentrations of PM0.1, PM2.5, and PM10 total mass, components species, and primary source contributions were calculated for California and three air basins: the Sacramento Valley air basin (SV, the San Joaquin Valley air basin (SJV and the South Coast Air Basin (SoCAB. Results over annual-average periods were contrasted with extreme events.

    Climate change between 2000 vs. 2050 did not cause a statistically significant change in annual-average population-weighted PM2.5 mass concentrations within any major sub-region of California in the current study. Climate change did alter the annual-average composition of the airborne particles in the SoCAB, with notable reductions of elemental carbon (EC; −3% and organic carbon (OC; −3% due to increased annual-average wind speeds that diluted primary concentrations from gasoline combustion (−3% and food cooking (−4%. In contrast, climate change caused significant increases in population-weighted PM2.5 mass concentrations in central California during extreme events. The maximum 24-h average PM2.5 concentration experienced by an average person during a ten-year period in the SJV increased by 21% due to enhanced production of secondary particulate matter (manifested as NH4NO3. In general, climate change caused increased

  19. Maternal tobacco use and extremely premature birth - a population-based cohort study.

    Science.gov (United States)

    Dahlin, S; Gunnerbeck, A; Wikström, A-K; Cnattingius, S; Edstedt Bonamy, A-K

    2016-11-01

    To study the associations of maternal tobacco use (smoking or use of snuff) and risk of extremely preterm birth, and if tobacco cessation before antenatal booking influences this risk. To study the association between tobacco use and spontaneous or medically indicated onset of delivery. Population-based cohort study. Sweden. All live singleton births, registered in the Swedish Medical Birth Register, 1999-2012. Odds ratios (OR) with 95% confidence intervals (CI) were calculated using multiple logistic regression analysis. Extremely preterm birth (<28 weeks of gestation), very preterm birth (28-31 weeks), moderately preterm birth (32-36 weeks). Maternal snuff use (OR 1.58; 95% CI: 1.14-2.21) and smoking (OR 1.61; 95% CI: 1.39-1.87 and OR 1.91; 95% CI: 1.53-2.39 for moderate and heavy smoking, respectively) were associated with an increased risk of extremely preterm birth. When cessation of tobacco use was obtained there was no increased risk of preterm birth. Snuff use was associated with a twofold risk increase of medically indicated extremely preterm birth, whereas smoking was associated with increased risks of both medically indicated and spontaneous extremely preterm birth. Snuff use and smoking in pregnancy were associated with increased risks of extremely preterm birth. Women who stopped using tobacco before the antenatal booking had no increased risk. These findings indicate that nicotine, the common substance in cigarettes and snuff, is involved in the mechanisms behind preterm birth. The use of nicotine should be minimized in pregnancy. Tobacco use increases risk of extremely preterm birth. Cessation is preventive. Avoid nicotine in pregnancy. © 2016 Royal College of Obstetricians and Gynaecologists.

  20. [Hygienic problems of population health maintenance under the extremal conditions of North].

    Science.gov (United States)

    Potapov, A I; Istomin, A V; Shushkova, T S; Ustiushin, B V; Iudina, T V; Maĭmulov, V G; Raengulov, B M; Shagdarova, A N

    2005-01-01

    A range of multi-sided studies, carried out in various regions of Far North (Jamalo-Nenets autonomous region, Komi republic, Sakha republic (Yakutia)) have established the leading hygienic risk factors of population health deterioration, including those characteristic of small nationalities of North. The consideration of the obtained data, including regional alimentary status peculiarities, the condition of metabolic processes and antioxidant balance of the organism, allowed establishment of effective approaches to the maintenance of notherners' health. These approaches are based upon the optimization of nutrition as an element of population health control under extremal conditions.

  1. Evidence of population resistance to extreme low flows in a fluvial-dependent fish species

    Science.gov (United States)

    Katz, Rachel A.; Freeman, Mary C.

    2015-01-01

    Extreme low streamflows are natural disturbances to aquatic populations. Species in naturally intermittent streams display adaptations that enhance persistence during extreme events; however, the fate of populations in perennial streams during unprecedented low-flow periods is not well-understood. Biota requiring swift-flowing habitats may be especially vulnerable to flow reductions. We estimated the abundance and local survival of a native fluvial-dependent fish species (Etheostoma inscriptum) across 5 years encompassing historic low flows in a sixth-order southeastern USA perennial river. Based on capturemark-recapture data, the study shoal may have acted as a refuge during severe drought, with increased young-of-the-year (YOY) recruitment and occasionally high adult immigration. Contrary to expectations, summer and autumn survival rates (30 days) were not strongly depressed during low-flow periods, despite 25%-80% reductions in monthly discharge. Instead, YOY survival increased with lower minimum discharge and in response to small rain events that increased low-flow variability. Age-1+ fish showed the opposite pattern, with survival decreasing in response to increasing low-flow variability. Results from this population dynamics study of a small fish in a perennial river suggest that fluvial-dependent species can be resistant to extreme flow reductions through enhanced YOY recruitment and high survival

  2. BOTTLENECKS IN PRODUCTION NETWORKS: AN OVERVIEW

    Institute of Scientific and Technical Information of China (English)

    Yongcai WANG; Qianchuan ZHAO; Dazhong ZHENG

    2005-01-01

    Bottlenecks, the key ingredients for improving the performances of the production networks,have been profoundly studied during the last decade. Yet, because of the complexity of the research results, there is still a significant gap between theory and practice. In this paper, we review various bottleneck definitions, detection methods and the asymptotic results and provide a practical guidance for recognizing and utilizing the bottlenecks in production networks. Queueing theory works as the mathematical foundation in our study. Various definitions of the bottlenecks are classified as either Performance in Processing (PIP) based or sensitivity based definitions, which reflect the preferences of the managers. Detection methods are surveyed closely based on the definitions. These methods are used to recognize the bottlenecks and to provide diagnosis results to managers. Comparisons show that different detection methods may lead to vastly different conclusions. The recognition of the bottlenecks has another advantage: the ultimate phenomena of the bottlenecks can greatly reduce the computation complexity in calculating the system performances. Bottlenecks based approximation and asymptotic results are studied to exhibit the contribution of bottlenecks in performance estimation and theoretical analysis.

  3. Landscape genetics of alpine Sierra Nevada salamanders reveal extreme population subdivision in space and time.

    Science.gov (United States)

    Savage, Wesley K; Fremier, Alexander K; Shaffer, H Bradley

    2010-08-01

    Quantifying the influence of the landscape on the genetic structure of natural populations remains an important empirical challenge, particularly for poorly studied, ecologically cryptic species. We conducted an extensive microsatellite analysis to examine the population genetics of the southern long-toed salamander (Ambystoma macrodactylum sigillatum) in a naturally complex landscape. Using spatially explicit modelling, we investigated the influence of the Sierra Nevada topography on potential dispersal corridors between sampled populations. Our results indicate very high-genetic divergence among populations, high within-deme relatedness, and little evidence of recent migration or population admixture. We also discovered unexpectedly high between-year genetic differentiation (F(ST)) for breeding sites, suggesting that breeding groups vary over localized space and time. While environmental factors associated with high-elevation montane habitats apparently play an important role in shaping population differentiation, additional, species-specific biological processes must also be operating to account for observed deviations from temporal, among-year panmixia. Our study emphasizes the population-level insights that can be gained from high-density sampling in space and time, and the highly substructured population biology that may characterize amphibians in extreme montane habitats.

  4. Landscape composition creates a threshold influencing Lesser Prairie-Chicken population resilience to extreme drought

    Science.gov (United States)

    Ross, Beth E.; Haukos, David A.; Hagen, Christian A.; Pitman, James C.

    2016-01-01

    Habitat loss and degradation compound the effects of climate change on wildlife, yet responses to climate and land cover change are often quantified independently. The interaction between climate and land cover change could be intensified in the Great Plains region where grasslands are being converted to row-crop agriculture concurrent with increased frequency of extreme drought events. We quantified the combined effects of land cover and climate change on a species of conservation concern in the Great Plains, the Lesser Prairie-Chicken (Tympanuchus pallidicinctus  ). We combined extreme drought events and land cover change with lek count surveys in a Bayesian hierarchical model to quantify changes in abundance of male Lesser Prairie-Chickens from 1978 to 2014 in Kansas, the core of their species range. Our estimates of abundance indicate a gradually decreasing population through 2010 corresponding to drought events and reduced grassland areas. Decreases in Lesser Prairie-Chicken abundance were greatest in areas with increasing row-crop to grassland land cover ratio during extreme drought events, and decreased grassland reduces the resilience of Lesser Prairie-Chicken populations to extreme drought events. A threshold exists for Lesser Prairie-Chickens in response to the gradient of cropland:grassland land cover. When moving across the gradient of grassland to cropland, abundance initially increased in response to more cropland on the landscape, but declined in response to more cropland after the threshold (δ=0.096, or 9.6% cropland). Preservation of intact grasslands and continued implementation of initiatives to revert cropland to grassland should increase Lesser Prairie-Chicken resilience to extreme drought events due to climate change.

  5. Range of Motion of the Upper Extremity in a Healthy Pediatric Population: Introduction to Normative Data.

    Science.gov (United States)

    Da Paz, Stephanie Nunes; Stalder, Andreas; Berger, Steffen; Ziebarth, Kai

    2016-10-01

    Objective In the pediatric population traumatic injuries of the upper extremity are common. After therapy a decision has to be made if the mobility of the joint lies within a normal range. The purpose of this study was to give an introduction to normative data. We investigate if there is a significant difference in the range of motion (ROM) between male and female probands and furthermore, if an effect of the age can be detected. Methods We performed an institutional review board-approved study of healthy girls and boys aged between 2 and 16 years without any medical history of an upper extremity fracture. We investigated the active ROM of the elbow, wrist, metacarpophalangeal, and interphalangeal joints. Furthermore, age, handedness, weight, and height were recorded. A total of 171 adolescents with a mean age of 10.6 years were included and separated into four cohorts by age: 2 to 5, 6 to 10, 11 to 13, and 14 to 16 years. Results We found significant differences between the genders in the age group from 11 to 13 years for the flexion of the elbow, the pronation, the flexion of the interphalangeal joint of the thumb, as well as the flexion of the metacarpophalangeal joints of digitus II to V. Furthermore, a significant difference in the same joints except from the elbow flexion could be demonstrated between the genders. Conclusion Our study contributes normative data for upper extremity ROM in the pediatric population and presents a gender-related difference in certain joints. Clinical Relevance Normative data for the ROM of upper extremity joints in children is helpful for the evaluation of pediatric orthopedic patients and provides the framework for therapeutic resolution. Since a great number of traumatic injuries in children affect the upper extremity, this information may help the physician to estimate the impact of the injury and decide on the therapeutic management.

  6. Landscape composition creates a threshold influencing Lesser Prairie-Chicken population resilience to extreme drought

    Directory of Open Access Journals (Sweden)

    Beth E. Ross

    2016-04-01

    Full Text Available Habitat loss and degradation compound the effects of climate change on wildlife, yet responses to climate and land cover change are often quantified independently. The interaction between climate and land cover change could be intensified in the Great Plains region where grasslands are being converted to row-crop agriculture concurrent with increased frequency of extreme drought events. We quantified the combined effects of land cover and climate change on a species of conservation concern in the Great Plains, the Lesser Prairie-Chicken (Tympanuchus pallidicinctus. We combined extreme drought events and land cover change with lek count surveys in a Bayesian hierarchical model to quantify changes in abundance of male Lesser Prairie-Chickens from 1978 to 2014 in Kansas, the core of their species range. Our estimates of abundance indicate a gradually decreasing population through 2010 corresponding to drought events and reduced grassland areas. Decreases in Lesser Prairie-Chicken abundance were greatest in areas with increasing row-crop to grassland land cover ratio during extreme drought events, and decreased grassland reduces the resilience of Lesser Prairie-Chicken populations to extreme drought events. A threshold exists for Lesser Prairie-Chickens in response to the gradient of cropland:grassland land cover. When moving across the gradient of grassland to cropland, abundance initially increased in response to more cropland on the landscape, but declined in response to more cropland after the threshold (δ=0.096, or 9.6% cropland. Preservation of intact grasslands and continued implementation of initiatives to revert cropland to grassland should increase Lesser Prairie-Chicken resilience to extreme drought events due to climate change.

  7. Extreme High Prevalence of a Defective Mannose-Binding Lectin (MBL2) Genotype in Native South American West Andean Populations

    DEFF Research Database (Denmark)

    Sandoval, José Raul; Madsen, Hans O; De Stefano, Gianfranco

    2014-01-01

    ), and Ecuador (n = 182) (Region of Esmeraldas and Santo Domingo de los Colorados). The distribution of MBL2 genotypes among the populations showed that the defective variant LYPB haplotype was very common. It showed the highest frequencies in Puno (Taquile (0.80), Amantani (0.80) and Anapia (0.58) islander...... of the MBL2 LYPB variant causing low levels of functional MBL in serum may mainly reflect a random distribution due to a population bottleneck in the founder populations.......Mannose-binding lectin (MBL) is one of the five recognition molecules in the lectin complement pathway. Common variant alleles in the promoter and structural regions of the human MBL gene (MBL2) influence the stability and serum concentration of the protein. Epidemiological studies have shown...

  8. Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases.

    Directory of Open Access Journals (Sweden)

    Rong Chen

    Full Text Available Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may

  9. Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases.

    Science.gov (United States)

    Chen, Rong; Corona, Erik; Sikora, Martin; Dudley, Joel T; Morgan, Alex A; Moreno-Estrada, Andres; Nilsen, Geoffrey B; Ruau, David; Lincoln, Stephen E; Bustamante, Carlos D; Butte, Atul J

    2012-01-01

    Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D) demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed

  10. Microsurgical Reconstruction of Traumatic Lower Extremity Defects in the Pediatric Population.

    Science.gov (United States)

    Momeni, Arash; Lanni, Michael; Levin, L Scott; Kovach, Stephen J

    2017-04-01

    Few reports focus exclusively on microsurgical reconstruction of traumatic lower extremity defects in children. Hence, the authors felt it prudent to contribute to this area of clinical research. The authors hypothesized that reconstructive success would be comparable to success rates reported in adults, and that young age or concerns regarding vessel size or behavior do not negatively impact surgical outcome. A retrospective review of microsurgical lower extremity reconstruction cases at two academic medical centers was performed. All pediatric patients who underwent microsurgical reconstruction of traumatic lower extremity defects between 1997 and 2012 were included for analysis. Forty flaps transferred in 40 patients with a mean age of 11.4 years (range, 1 to 17 years) were included for analysis. Muscle flaps were predominantly used [n = 23 (57.5 percent)]; however, there was a recent increase in use of fasciocutaneous flaps [n = 16 (40 percent)]. Postoperative complications were seen in 25 percent of patients, with a total flap loss rate of 5 percent. No donor-site complications were observed. The mean postoperative length of hospital stay was 12.9 days (range, 4 to 41 days), with patients returning to full weight-bearing after a mean of 2.6 months (range, 1 to 8 months). Microsurgical reconstruction of traumatic lower extremity defects in the pediatric population is safe. Concerns related to patient age, vessel size, or vessel behavior (i.e., vasospasm) should not detract from offering free flap reconstruction, as they do not negatively impact outcomes. Therapeutic, IV.

  11. Conservation genetics of the alligator snapping turtle: cytonuclear evidence of range-wide bottleneck effects and unusually pronounced geographic structure

    Science.gov (United States)

    Echelle, A.A.; Hackler, J.C.; Lack, Justin B.; Ballard, S. R.; Roman, J.; Fox, S. F.; Leslie,, David M.; Van Den Bussche, Ronald A.

    2010-01-01

    A previous mtDNA study indicated that female-mediated gene flow was extremely rare among alligator snapping turtle populations in different drainages of the Gulf of Mexico. In this study, we used variation at seven microsatellite DNA loci to assess the possibility of male-mediated gene flow, we augmented the mtDNA survey with additional sampling of the large Mississippi River System, and we evaluated the hypothesis that the consistently low within-population mtDNA diversity reflects past population bottlenecks. The results show that dispersal between drainages of the Gulf of Mexico is rare (F STmsat  = 0.43, ΦSTmtDNA = 0.98). Past range-wide bottlenecks are indicated by several genetic signals, including low diversity for microsatellites (1.1–3.9 alleles/locus; H e = 0.06–0.53) and mtDNA (h = 0.00 for most drainages; π = 0.000–0.001). Microsatellite data reinforce the conclusion from mtDNA that the Suwannee River population might eventually be recognized as a distinct taxonomic unit. It was the only population showing fixation or near fixation for otherwise rare microsatellite alleles. Six evolutionarily significant units are recommended on the basis of reciprocal mtDNA monophyly and high levels of microsatellite DNA divergence.

  12. Recovery trends of Scrobicularia plana populations after restoration measures, affected by extreme climate events.

    Science.gov (United States)

    Verdelhos, T; Cardoso, P G; Dolbeth, M; Pardal, M A

    2014-07-01

    The Mondego estuary (Portugal) went through different ecological scenarios over the last decades. An eutrophication process led to a decline in the ecosystem quality. The ensuing restoration plan resulted into a gradual ecological recovery, which was impaired by the occurrence of successive extreme climate events that affected dynamics and productivity of key species. In this study we assess the response of the bivalve Scrobicularia plana to the impacts of these events in a recovery scenario, by comparing populations in two different intertidal habitats: a seagrass bed and a sandflat area. As a general tendency, S. plana, which was negatively affected by eutrophication, responded positively to restoration. However, the occurrence of extreme climate events seemed to affect recruitment success, biomass and production, impairing the recovery process. In the seagrass bed, S. plana maintained a stable and structured population, while in the sandflat area recovery clearly reverted into a decline, mainly concerning biomass and production values. This sequence of multiple stressors might have reduced S. plana resilience to further impacts and therefore, understanding the behavior of biological populations following restoration initiatives requires acknowledgement that some changes may not be easily reversible.

  13. Large data centers interconnect bottlenecks.

    Science.gov (United States)

    Ghiasi, Ali

    2015-02-09

    Large data centers interconnect bottlenecks are dominated by the switch I/O BW and the front panel BW as a result of pluggable modules. To overcome the front panel BW and the switch ASIC BW limitation one approach is to either move the optics onto the mid-plan or integrate the optics into the switch ASIC. Over the last 4 years, VCSEL based optical engines have been integrated into the packages of large-scale HPC routers, moderate size Ethernet switches, and even FPGA's. Competing solutions based on Silicon Photonics (SiP) have also been proposed for integration into HPC and Ethernet switch packages but with better integration path through the use of TSV (Through Silicon Via) stack dies. Integrating either VCSEL or SiP based optical engines into complex ASIC package that operates at high temperatures, where the required reliability is not trivial, one should ask what is the technical or the economic advantage before embarking on such a complex integration. High density Ethernet switches addressing data centers currently in development are based on 25G NRZ signaling and QSFP28 optical module that can support up to 3.6 Tb of front panel bandwidth.

  14. Basic calibrations of the photographic RGU system. III - Intermediate and extreme Population II dwarf stars

    Science.gov (United States)

    Buser, R.; Fenkart, R. P.

    1990-11-01

    This paper presents an extended calibration of the color-magnitude and two-color diagrams and the metal-abundance parameter for the intermediate Population II and the extreme halo dwarfs observed in the Basel Palomar-Schmidt RGU three-color photometric surveys of the galaxy. The calibration covers the metallicity range between values +0.50 and -3.00. It is shown that the calibrations presented are sufficiently accurate to be useful for the future analyses of photographic survey data.

  15. Extreme climate, rather than population history, explains mid-facial morphology of Northern Asians.

    Science.gov (United States)

    Evteev, Andrej; Cardini, Andrea L; Morozova, Irina; O'Higgins, Paul

    2014-03-01

    Previous studies have examined mid-facial cold adaptation among either widely dispersed and genetically very diverse groups of humans isolated for tens of thousands of years, or among very closely related groups spread over climatically different regions. Here we present a study of one East Asian and seven North Asian populations in which we examine the evidence for convergent adaptations of the mid-face to a very cold climate. Our findings indicate that mid-facial morphology is strongly associated with climatic variables that contrast the temperate climate of East Asians and the very cold and dry climate of North Asians. This is also the case when either maxillary or nasal cavity measurements are considered alone. The association remains significant when mtDNA distances among populations are taken into account. The morphological contrasts between populations are consistent with physiological predictions and prior studies of mid-facial cold adaptation in more temperate regions, but among North Asians there appear to be some previously undescribed morphological features that might be considered as adaptive to extreme cold. To investigate this further, analyses of the seven North Asian populations alone suggest that mid-facial morphology remains strongly associated with climate, particularly winter precipitation, contrasting coastal Arctic and continental climates. However, the residual covariation among North Asian mid-facial morphology and climate when genetic distances are considered, is not significant. These findings point to modern adaptations to extreme climate that might be relevant to our understanding of the mid-facial morphology of fossil hominins that lived during glaciations.

  16. Extremity vascular trauma in civilian population: a seven-year review from North India.

    Science.gov (United States)

    Menakuru, Somasekhar R; Behera, Arunanshu; Jindal, Ravul; Kaman, Lileswar; Doley, Rudraprasad; Venkatesan, Rajarajan

    2005-03-01

    This is a retrospective study of the experience with extremity vascular trauma at a tertiary level referral centre in North India where the majority of the population lives in villages and the incidence of high-speed automobile accidents and civilian violence is low. The aim was to study the aetiology, pattern of injuries and the mortality and morbidity rates due to vascular trauma in our population. Data relating to 148 patients presenting with vascular trauma requiring surgical intervention other than amputation between January 1996 and December 2002 were collected retrospectively. There were 132 males and 16 females with a mean age of 39 years presenting to the casualty with a median delay of 9.3 h after injury. Blunt trauma accounted for 84% of the injuries with extremities involved in 88%. The brachial artery was the most common artery injured with the femoral next most common. Repair without graft interposition was done in 74% and autogenous vein grafts were used in 23% of cases. Comparison of our results with those that would have been obtained, had the recommendations of Mangled Extremity Severity Score (MESS) been followed, showed that this scoring system had low sensitivity and specificity for prediction of salvageability of limbs. Eight percent patients died due to associated visceral organ injuries. Complications occurred in 32% patients and amputation was required in 6% of patients after an initial surgical repair mainly due to inadequate functional recovery. Eighty-eight percent of the survivors with salvaged limbs were able to achieve full functional recovery. Judicious selection and appropriate intervention can result in satisfactory limb salvage with good functional outcomes even with delayed presentations.

  17. Environmental extremes versus ecological extremes: impact of a massive iceberg on the population dynamics of a high-level Antarctic marine predator†

    Science.gov (United States)

    Chambert, Thierry; Rotella, Jay J.; Garrott, Robert A.

    2012-01-01

    Extreme events have been suggested to play a disproportionate role in shaping ecological processes, but our understanding of the types of environmental conditions that elicit extreme consequences in natural ecosystems is limited. Here, we investigated the impact of a massive iceberg on the dynamics of a population of Weddell seals. Reproductive rates of females were reduced, but survival appeared unaffected. We also found suggestive evidence for a prolonged shift towards higher variability in reproductive rates. The annual number of females attending colonies showed unusual swings during the iceberg period, a pattern that was apparently the consequence of changes in sea-ice conditions. In contrast to the dramatic effects that were recorded in nearby populations of emperor penguins, our results suggest that this unusual environmental event did not have an extreme impact on the population of seals in the short-term, as they managed to avoid survival costs and were able to rapidly re-achieve high levels of reproduction by the end of the perturbation. Nevertheless, population projections suggest that even this modest impact on reproductive rates could negatively affect the population in the long run if such events were to occur more frequently, as is predicted by models of climate change. PMID:23015628

  18. Extreme heterogeneity in parasitism despite low population genetic structure among monarch butterflies inhabiting the Hawaiian Islands.

    Science.gov (United States)

    Pierce, Amanda A; de Roode, Jacobus C; Altizer, Sonia; Bartel, Rebecca A

    2014-01-01

    Host movement and spatial structure can strongly influence the ecology and evolution of infectious diseases, with limited host movement potentially leading to high spatial heterogeneity in infection. Monarch butterflies (Danaus plexippus) are best known for undertaking a spectacular long-distance migration in eastern North America; however, they also form non-migratory populations that breed year-round in milder climates such as Hawaii and other tropical locations. Prior work showed an inverse relationship between monarch migratory propensity and the prevalence of the protozoan parasite, Ophryocystis elektroscirrha. Here, we sampled monarchs from replicate sites within each of four Hawaiian Islands to ask whether these populations show consistently high prevalence of the protozoan parasite as seen for monarchs from several other non-migratory populations. Counter to our predictions, we observed striking spatial heterogeneity in parasite prevalence, with infection rates per site ranging from 4-85%. We next used microsatellite markers to ask whether the observed variation in infection might be explained by limited host movement and spatial sub-structuring among sites. Our results showed that monarchs across the Hawaiian Islands form one admixed population, supporting high gene flow among sites. Moreover, measures of individual-level genetic diversity did not predict host infection status, as might be expected if more inbred hosts harbored higher parasite loads. These results suggest that other factors such as landscape-level environmental variation or colonization-extinction processes might instead cause the extreme heterogeneity in monarch butterfly infection observed here.

  19. Extreme Heterogeneity in Parasitism Despite Low Population Genetic Structure among Monarch Butterflies Inhabiting the Hawaiian Islands

    Science.gov (United States)

    Pierce, Amanda A.; de Roode, Jacobus C.; Altizer, Sonia; Bartel, Rebecca A.

    2014-01-01

    Host movement and spatial structure can strongly influence the ecology and evolution of infectious diseases, with limited host movement potentially leading to high spatial heterogeneity in infection. Monarch butterflies (Danaus plexippus) are best known for undertaking a spectacular long-distance migration in eastern North America; however, they also form non-migratory populations that breed year-round in milder climates such as Hawaii and other tropical locations. Prior work showed an inverse relationship between monarch migratory propensity and the prevalence of the protozoan parasite, Ophryocystis elektroscirrha. Here, we sampled monarchs from replicate sites within each of four Hawaiian Islands to ask whether these populations show consistently high prevalence of the protozoan parasite as seen for monarchs from several other non-migratory populations. Counter to our predictions, we observed striking spatial heterogeneity in parasite prevalence, with infection rates per site ranging from 4–85%. We next used microsatellite markers to ask whether the observed variation in infection might be explained by limited host movement and spatial sub-structuring among sites. Our results showed that monarchs across the Hawaiian Islands form one admixed population, supporting high gene flow among sites. Moreover, measures of individual-level genetic diversity did not predict host infection status, as might be expected if more inbred hosts harbored higher parasite loads. These results suggest that other factors such as landscape-level environmental variation or colonization-extinction processes might instead cause the extreme heterogeneity in monarch butterfly infection observed here. PMID:24926796

  20. Extreme heterogeneity in parasitism despite low population genetic structure among monarch butterflies inhabiting the Hawaiian Islands.

    Directory of Open Access Journals (Sweden)

    Amanda A Pierce

    Full Text Available Host movement and spatial structure can strongly influence the ecology and evolution of infectious diseases, with limited host movement potentially leading to high spatial heterogeneity in infection. Monarch butterflies (Danaus plexippus are best known for undertaking a spectacular long-distance migration in eastern North America; however, they also form non-migratory populations that breed year-round in milder climates such as Hawaii and other tropical locations. Prior work showed an inverse relationship between monarch migratory propensity and the prevalence of the protozoan parasite, Ophryocystis elektroscirrha. Here, we sampled monarchs from replicate sites within each of four Hawaiian Islands to ask whether these populations show consistently high prevalence of the protozoan parasite as seen for monarchs from several other non-migratory populations. Counter to our predictions, we observed striking spatial heterogeneity in parasite prevalence, with infection rates per site ranging from 4-85%. We next used microsatellite markers to ask whether the observed variation in infection might be explained by limited host movement and spatial sub-structuring among sites. Our results showed that monarchs across the Hawaiian Islands form one admixed population, supporting high gene flow among sites. Moreover, measures of individual-level genetic diversity did not predict host infection status, as might be expected if more inbred hosts harbored higher parasite loads. These results suggest that other factors such as landscape-level environmental variation or colonization-extinction processes might instead cause the extreme heterogeneity in monarch butterfly infection observed here.

  1. Analytical approach to continuous and intermittent bottleneck flows

    DEFF Research Database (Denmark)

    Helbing, D.; Johansson, A.; Mathiesen, Joachim Kaj;

    2006-01-01

    Many-particle-inspired theory, Continuous and Intermittent Bottleneck Flows Udgivelsesdato: Oct. 20......Many-particle-inspired theory, Continuous and Intermittent Bottleneck Flows Udgivelsesdato: Oct. 20...

  2. 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.

  3. 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 p

  4. 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

  5. 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

    2017-01-01

    ABSTRACT 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

  6. Estimation of the bottleneck size in Florida panthers

    Science.gov (United States)

    Culver, M.; Hedrick, P.W.; Murphy, K.; O'Brien, S.; Hornocker, M.G.

    2008-01-01

    We have estimated the extent of genetic variation in museum (1890s) and contemporary (1980s) samples of Florida panthers Puma concolor coryi for both nuclear loci and mtDNA. The microsatellite heterozygosity in the contemporary sample was only 0.325 that in the museum samples although our sample size and number of loci are limited. Support for this estimate is provided by a sample of 84 microsatellite loci in contemporary Florida panthers and Idaho pumas Puma concolor hippolestes in which the contemporary Florida panther sample had only 0.442 the heterozygosity of Idaho pumas. The estimated diversities in mtDNA in the museum and contemporary samples were 0.600 and 0.000, respectively. Using a population genetics approach, we have estimated that to reduce either the microsatellite heterozygosity or the mtDNA diversity this much (in a period of c. 80years during the 20th century when the numbers were thought to be low) that a very small bottleneck size of c. 2 for several generations and a small effective population size in other generations is necessary. Using demographic data from Yellowstone pumas, we estimated the ratio of effective to census population size to be 0.315. Using this ratio, the census population size in the Florida panthers necessary to explain the loss of microsatellite variation was c .41 for the non-bottleneck generations and 6.2 for the two bottleneck generations. These low bottleneck population sizes and the concomitant reduced effectiveness of selection are probably responsible for the high frequency of several detrimental traits in Florida panthers, namely undescended testicles and poor sperm quality. The recent intensive monitoring both before and after the introduction of Texas pumas in 1995 will make the recovery and genetic restoration of Florida panthers a classic study of an endangered species. Our estimates of the bottleneck size responsible for the loss of genetic variation in the Florida panther completes an unknown aspect of this

  7. Urban traffic congestion propagation and bottleneck identification

    Institute of Scientific and Technical Information of China (English)

    LONG JianCheng; GAO ZiYou; REN HuaLing; LIAN AiPing

    2008-01-01

    Bottlenecks in urban traffic network are sticking points in restricting network col-lectivity traffic efficiency.To identify network bottlenecks effectively is a founda-tional work for improving network traffic condition and preventing traffic conges-tion.In this paper,a congestion propagation model of urban network traffic is proposed based on the cell transmission model (CTM).The proposed model in-cludes a link model,which describes flow propagation on links,and a node model,which represents link-to-link flow propagation.A new method of estimating average journey velocity (AJV) of both link and network is developed to identify network congestion bottlenecks.A numerical example is studied in Sioux Falls urban traffic network.The proposed model is employed in simulating network traffic propaga-tion and congestion bottleneck identification under different traffic demands.The simulation results show that continual increase of traffic demand is an immediate factor in network congestion bottleneck emergence and increase as well as re-ducing network collectivity capability.Whether a particular link will become a bot-tleneck is mainly determined by its position in network,its traffic flow (attributed to different OD pairs) component,and network traffic demand.

  8. The differential effects of increasing frequency and magnitude of extreme events on coral populations.

    Science.gov (United States)

    Fabina, Nicholas S; Baskett, Marissa L; Gross, Kevin

    2015-09-01

    Extreme events, which have profound ecological consequences, are changing in both frequency and magnitude with climate change. Because extreme temperatures induce coral bleaching, we can explore the relative impacts of changes in frequency and magnitude of high temperature events on coral reefs. Here, we combined climate projections and a dynamic population model to determine how changing bleaching regimes influence coral persistence. We additionally explored how coral traits and competition with macroalgae mediate changes in bleaching regimes. Our results predict that severe bleaching events reduce coral persistence more than frequent bleaching. Corals with low adult mortality and high growth rates are successful when bleaching is mild, but bleaching resistance is necessary to persist when bleaching is severe, regardless of frequency. The existence of macroalgae-dominated stable states reduces coral persistence and changes the relative importance of coral traits. Building on previous studies, our results predict that management efforts may need to prioritize protection of "weaker" corals with high adult mortality when bleaching is mild, and protection of "stronger" corals with high bleaching resistance when bleaching is severe. In summary, future reef projections and conservation targets depend on both local bleaching regimes and biodiversity.

  9. Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect.

    Science.gov (United States)

    Lozier, Jeffrey D; Jackson, Jason M; Dillon, Michael E; Strange, James P

    2016-02-01

    Geographic variation in insect coloration is among the most intriguing examples of rapid phenotypic evolution and provides opportunities to study mechanisms of phenotypic change and diversification in closely related lineages. The bumble bee Bombus bifarius comprises two geographically disparate color groups characterized by red-banded and black-banded abdominal pigmentation, but with a range of spatially and phenotypically intermediate populations across western North America. Microsatellite analyses have revealed that B. bifarius in the USA are structured into two major groups concordant with geography and color pattern, but also suggest ongoing gene flow among regional populations. In this study, we better resolve the relationships among major color groups to better understand evolutionary mechanisms promoting and maintaining such polymorphism. We analyze >90,000 and >25,000 single-nucleotide polymorphisms derived from transcriptome (RNAseq) and double digest restriction site associated DNA sequencing (ddRAD), respectively, in representative samples from spatial and color pattern extremes in B. bifarius as well as phenotypic and geographic intermediates. Both ddRAD and RNAseq data illustrate substantial genome-wide differentiation of the red-banded (eastern) color form from both black-banded (western) and intermediate (central) phenotypes and negligible differentiation among the latter populations, with no obvious admixture among bees from the two major lineages. Results thus indicate much stronger background differentiation among B. bifarius lineages than expected, highlighting potential challenges for revealing loci underlying color polymorphism from population genetic data alone. These findings will have significance for resolving taxonomic confusion in this species and in future efforts to investigate color-pattern evolution in B. bifarius and other polymorphic bumble bee species.

  10. More precisely biased : increasing the number of markers is not a silver bullet in genetic bottleneck testing

    NARCIS (Netherlands)

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

    2013-01-01

    In response to our review of the use of genetic bottleneck tests in the conservation literature (Peery etal. 2012, Molecular Ecology, 21, 3403-3418), Hoban etal. (2013, Molecular Ecology, in press) conducted population genetic simulations to show that the statistical power of genetic bottleneck test

  11. Microbial Diversity and Population Structure of Extremely Acidic Sulfur-Oxidizing Biofilms From Sulfidic Caves

    Science.gov (United States)

    Jones, D.; Stoffer, T.; Lyon, E. H.; Macalady, J. L.

    2005-12-01

    Extremely acidic (pH 0-1) microbial biofilms called snottites form on the walls of sulfidic caves where gypsum replacement crusts isolate sulfur-oxidizing microorganisms from the buffering action of limestone host rock. We investigated the phylogeny and population structure of snottites from sulfidic caves in central Italy using full cycle rRNA methods. A small subunit rRNA bacterial clone library from a Frasassi cave complex snottite sample contained a single sequence group (>60 clones) similar to Acidithiobacillus thiooxidans. Bacterial and universal rRNA clone libraries from other Frasassi snottites were only slightly more diverse, containing a maximum of 4 bacterial species and probably 2 archaeal species. Fluorescence in situ hybridization (FISH) of snottites from Frasassi and from the much warmer Rio Garrafo cave complex revealed that all of the communities are simple (low-diversity) and dominated by Acidithiobacillus and/or Ferroplasma species, with smaller populations of an Acidimicrobium species, filamentous fungi, and protists. Our results suggest that sulfidic cave snottites will be excellent model microbial ecosystems suited for ecological and metagenomic studies aimed at elucidating geochemical and ecological controls on microbial diversity, and at mapping the spatial history of microbial evolutionary events such as adaptations, recombinations and gene transfers.

  12. Testing the AGB Scenario as the Origin of the Extreme-Helium Population in omega Centauri

    CERN Document Server

    Choi, Ena

    2008-01-01

    The most massive Galactic globular cluster, Omega centauri, appears to have multiple populations. Its bluest main sequence and extended horizontal branch stars are suggested to have the common origin, that is, an extremely high helium abundance of Y ~ 0.4. The high helium abundance is most often attributed to asymptotic giant branch (AGB) stars. In this study we test the AGB hypothesis. We simulate the maximum-AGB models where the impact of AGB stars is maximised by assuming that supernova explosions do not affect the chemical evolution of the proto cloud. We compare the enrichment history of helium, metals, carbon and nitrogen to the observed values. Even under the most generous condition, the maximum-AGB models fail to reproduce the large values of helium Y ~ 0.4 and helium enrichment parameter Delta Y / Delta Z ~ 70 which were deduced from the colour-magnitude diagram fits. They also fail to reproduce the C and N contents of the blue population spectroscopically determined. We conclude that the AGB scenari...

  13. Pulse seedling recruitment on the population dynamics of a columnar cactus: Effect of an extreme rainfall event

    Science.gov (United States)

    Arroyo-Cosultchi, Gabriel; Golubov, Jordan; Mandujano, María C.

    2016-02-01

    Demographic studies on the Cactaceae have highlighted several threats which are clearly human induced (e.g., disturbance) or intrinsic to their biology (e.g., infrequent recruitment). Most demographic studies suggest that early life stages of germination and seedling recruitment are crucial and often a limitation for population growth. The population dynamics of Neobuxbaumia polylopha (DC) Backeb. was modeled for a three-year period to assess the contribution of the early life cycle stages on population growth rate (λ). Two annual size-classified matrix population models were constructed for standard analysis, applied a life table response experiment (LTRE) analysis to explore the contributions of demographic processes, plant size, and temporal variability (years) to λ, and changes in the matrix elements were simulated including a seed bank, and seed-to-seedling transition using observed and experimental data. The population growth rates for 2012-2013 and 2013-2014 were 0.9916 (0.9906-0.9929) and 1.0216 (1.011-1.0280) respectively, suggesting two opposite growth rates for the studied period. The increase in λ in 2013-2014 was driven primarily by the increased growth and seedling recruitment and survival of small individuals. The rate of recruitment was higher in 2013-2014 with a left-skewed stable size distribution. Elasticity values were high for matrix entries corresponding to individuals remaining in the same category (stasis), followed by growth, retrogression and fecundity. The simulations show that the seed bank has a minor effect in comparison with the seed-seedling transition which became the population bottleneck under the assumption that seeds are not limited, so programs designed to preserve N. polylopha populations must focus on seedling establishment.

  14. Controlling population evolution in the laboratory to evaluate methods of historical inference.

    Directory of Open Access Journals (Sweden)

    Patrick Mardulyn

    Full Text Available Natural populations of known detailed past demographic history are extremely valuable to evaluate methods of historical inference, yet are extremely rare. As an alternative approach, we have generated multiple replicate microsatellite data sets from laboratory-cultured populations of a gonochoric free-living nematode, Caenorhabditis remanei, that were constrained to pre-defined demographic histories featuring different levels of migration among populations or bottleneck events of different magnitudes. These data sets were then used to evaluate the performances of two recently developed population genetics methods, BayesAss+, that estimates recent migration rates among populations, and Bottleneck, that detects the occurrence of recent bottlenecks. Migration rates inferred by BayesAss+ were generally over-estimates, although these were often included within the confidence interval. Analyses of data sets simulated in-silico, using a model mimicking the laboratory experiments, produced less biased estimates of the migration rates, and showed increased efficiency of the program when the number of loci and sampled genotypes per population was higher. In the replicates for which the pre-bottleneck laboratory-cultured populations did not significantly depart from a mutation/drift equilibrium, an important assumption of the program Bottleneck, only a portion of the bottleneck events were detected. This result was confirmed by in-silico simulations mirroring the laboratory bottleneck experiments. More generally, our study demonstrates the feasibility, and highlights some of the limits, of the approach that consists in generating molecular genetic data sets by controlling the evolution of laboratory-reared nematode populations, for the purpose of validating methods inferring population history.

  15. Present limits to heat-adaptability in corals and population-level responses to climate extremes.

    Directory of Open Access Journals (Sweden)

    Bernhard M Riegl

    Full Text Available Climate change scenarios suggest an increase in tropical ocean temperature by 1-3°C by 2099, potentially killing many coral reefs. But Arabian/Persian Gulf corals already exist in this future thermal environment predicted for most tropical reefs and survived severe bleaching in 2010, one of the hottest years on record. Exposure to 33-35°C was on average twice as long as in non-bleaching years. Gulf corals bleached after exposure to temperatures above 34°C for a total of 8 weeks of which 3 weeks were above 35°C. This is more heat than any other corals can survive, providing an insight into the present limits of holobiont adaptation. We show that average temperatures as well as heat-waves in the Gulf have been increasing, that coral population levels will fluctuate strongly, and reef-building capability will be compromised. This, in combination with ocean acidification and significant local threats posed by rampant coastal development puts even these most heat-adapted corals at risk. WWF considers the Gulf ecoregion as "critically endangered". We argue here that Gulf corals should be considered for assisted migration to the tropical Indo-Pacific. This would have the double benefit of avoiding local extinction of the world's most heat-adapted holobionts while at the same time introducing their genetic information to populations naïve to such extremes, potentially assisting their survival. Thus, the heat-adaptation acquired by Gulf corals over 6 k, could benefit tropical Indo-Pacific corals who have <100 y until they will experience a similarly harsh climate. Population models suggest that the heat-adapted corals could become dominant on tropical reefs within ∼20 years.

  16. Differences in the rotational properties of multiple stellar populations in M 13: a faster rotation for the "extreme" chemical subpopulation

    CERN Document Server

    Cordero, M J; Pilachowski, C A; Balbinot, E; Johnson, C I; Varri, A L

    2016-01-01

    We use radial velocities from spectra of giants obtained with the WIYN telescope, coupled with existing chemical abundance measurements of Na and O for the same stars, to probe the presence of kinematic differences among the multiple populations of the globular cluster (GC) M13. To characterise the kinematics of various chemical subsamples, we introduce a method using Bayesian inference along with an MCMC algorithm to fit a six-parameter kinematic model (including rotation) to these subsamples. We find that the so-called "extreme" population (Na-enhanced and extremely O-depleted) exhibits faster rotation around the centre of the cluster than the other cluster stars, in particular when compared to the dominant "intermediate" population (moderately Na-enhanced and O-depleted). The most likely difference between the rotational amplitude of this extreme population and that of the intermediate population is found to be $\\sim$4 km s$^{-1}$, with a 98.4% probability that the rotational amplitude of the extreme popul...

  17. Cryoprotectants and extreme freeze tolerance in a subarctic population of the wood frog.

    Science.gov (United States)

    Costanzo, Jon P; Reynolds, Alice M; do Amaral, M Clara F; Rosendale, Andrew J; Lee, Richard E

    2015-01-01

    Wood frogs (Rana sylvatica) exhibit marked geographic variation in freeze tolerance, with subarctic populations tolerating experimental freezing to temperatures at least 10-13 degrees Celsius below the lethal limits for conspecifics from more temperate locales. We determined how seasonal responses enhance the cryoprotectant system in these northern frogs, and also investigated their physiological responses to somatic freezing at extreme temperatures. Alaskan frogs collected in late summer had plasma urea levels near 10 μmol ml-1, but this level rose during preparation for winter to 85.5 ± 2.9 μmol ml-1 (mean ± SEM) in frogs that remained fully hydrated, and to 186.9 ± 12.4 μmol ml-1 in frogs held under a restricted moisture regime. An osmolality gap indicated that the plasma of winter-conditioned frogs contained an as yet unidentified osmolyte(s) that contributed about 75 mOsmol kg-1 to total osmotic pressure. Experimental freezing to -8°C, either directly or following three cycles of freezing/thawing between -4 and 0°C, or -16°C increased the liver's synthesis of glucose and, to a lesser extent, urea. Concomitantly, organs shed up to one-half (skeletal muscle) or two-thirds (liver) of their water, with cryoprotectant in the remaining fluid reaching concentrations as high as 0.2 and 2.1 M, respectively. Freeze/thaw cycling, which was readily survived by winter-conditioned frogs, greatly increased hepatic glycogenolysis and delivery of glucose (but not urea) to skeletal muscle. We conclude that cryoprotectant accrual in anticipation of and in response to freezing have been greatly enhanced and contribute to extreme freeze tolerance in northern R. sylvatica.

  18. Cryoprotectants and extreme freeze tolerance in a subarctic population of the wood frog.

    Directory of Open Access Journals (Sweden)

    Jon P Costanzo

    Full Text Available Wood frogs (Rana sylvatica exhibit marked geographic variation in freeze tolerance, with subarctic populations tolerating experimental freezing to temperatures at least 10-13 degrees Celsius below the lethal limits for conspecifics from more temperate locales. We determined how seasonal responses enhance the cryoprotectant system in these northern frogs, and also investigated their physiological responses to somatic freezing at extreme temperatures. Alaskan frogs collected in late summer had plasma urea levels near 10 μmol ml-1, but this level rose during preparation for winter to 85.5 ± 2.9 μmol ml-1 (mean ± SEM in frogs that remained fully hydrated, and to 186.9 ± 12.4 μmol ml-1 in frogs held under a restricted moisture regime. An osmolality gap indicated that the plasma of winter-conditioned frogs contained an as yet unidentified osmolyte(s that contributed about 75 mOsmol kg-1 to total osmotic pressure. Experimental freezing to -8°C, either directly or following three cycles of freezing/thawing between -4 and 0°C, or -16°C increased the liver's synthesis of glucose and, to a lesser extent, urea. Concomitantly, organs shed up to one-half (skeletal muscle or two-thirds (liver of their water, with cryoprotectant in the remaining fluid reaching concentrations as high as 0.2 and 2.1 M, respectively. Freeze/thaw cycling, which was readily survived by winter-conditioned frogs, greatly increased hepatic glycogenolysis and delivery of glucose (but not urea to skeletal muscle. We conclude that cryoprotectant accrual in anticipation of and in response to freezing have been greatly enhanced and contribute to extreme freeze tolerance in northern R. sylvatica.

  19. Potential performance bottleneck in Linux TCP

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Wenji; Crawford, Matt; /Fermilab

    2006-12-01

    TCP is the most widely used transport protocol on the Internet today. Over the years, especially recently, due to requirements of high bandwidth transmission, various approaches have been proposed to improve TCP performance. The Linux 2.6 kernel is now preemptible. It can be interrupted mid-task, making the system more responsive and interactive. However, we have noticed that Linux kernel preemption can interact badly with the performance of the networking subsystem. In this paper we investigate the performance bottleneck in Linux TCP. We systematically describe the trip of a TCP packet from its ingress into a Linux network end system to its final delivery to the application; we study the performance bottleneck in Linux TCP through mathematical modeling and practical experiments; finally we propose and test one possible solution to resolve this performance bottleneck in Linux TCP.

  20. The Simulation Utilization for the Bottleneck Identification

    Directory of Open Access Journals (Sweden)

    Petra Vegnerová

    2009-12-01

    Full Text Available Advancing globalization increasingly leads to the creation of delivery systems. Increasing competition forces companies to reduce costs permanently. Both of these trends lead to the need to control material and information flows precisely. The target of this article is to describe and show one of ways of bottleneck determination in the supply system. This study deals with the computer simulation and its utilization for assessment of bottleneck. The foundation of the work is created a model of the supply system, it is used to compare the costs associated with the existence of stocks and stock levels in the individual partner of the system, depending on the location of the bottleneck. This article is published as a part of the research intention MSM 6046137306.

  1. Formation and erasure of population difference gratings in the coherent interaction of a resonant medium with extremely short optical pulses

    Science.gov (United States)

    Arkhipov, R. M.; Arkhipov, M. V.; Babushkin, I.; Rosanov, N. N.

    2016-11-01

    In the regime of coherent interaction of short optical pulses with a resonant medium, which is implemented with a pulse duration shorter than the relaxation times in the medium, the formation of population gratings can occur without overlapping the pulses therein. In this case, there are new possibilities for controlling optical pulses, which are especially pronounced for extremely short pulses. It is shown that, with the proper choice of the parameters of a sequence of extremely short optical pulses, not only the formation of population gratings, but also their erasure are possible. It is demonstrated that this effect can be used for the creation of an ultrahigh-speed optical deflector.

  2. Properties of Bottleneck on Complex Networks

    Institute of Scientific and Technical Information of China (English)

    WANG Chao-Yang; WU Jian-Jun; GAO Zi-You

    2011-01-01

    The traffic bottleneck plays a key role in most of the natural and artificial network.Here we present a simply model for bottleneck dynamical characteristics consideration the reliability on the complex network by taking into account the network topology characteristics and system size.We find that there is a critical rate of flow generation below which the network traffic is free but above which traffic congestion occurs.Also, it is found that random networks have larger critical flow generating rate than scale free ones.Analytical results may be practically useful for designing networks, especially for the urban traffic network.

  3. Genetic evidence for population expansion in Hydrotaea irritans (Fallèn) (Diptera: Muscidae)

    DEFF Research Database (Denmark)

    Loeschcke, V.; Nielsen, B. O.; Pedersen, A. Aa.;

    2004-01-01

    geographic variation, F-statistics, allozyme electrophoresis, skewed allele frequencies, bottleneck, population expansion......geographic variation, F-statistics, allozyme electrophoresis, skewed allele frequencies, bottleneck, population expansion...

  4. The spatial distribution of threats to plant species with extremely small populations

    Science.gov (United States)

    Wang, Chunjing; Zhang, Jing; Wan, Jizhong; Qu, Hong; Mu, Xianyun; Zhang, Zhixiang

    2016-04-01

    Many biological conservationists take actions to conserve plant species with extremely small populations (PSESP) in China; however, there have been few studies on the spatial distribution of threats to PSESP. Hence, we selected distribution data of PSESP and made a map of the spatial distribution of threats to PSESP in China. First, we used the weight assignment method to evaluate the threat risk to PSESP at both country and county scales. Second, we used a geographic information system to map the spatial distribution of threats to PSESP, and explored the threat factors based on linear regression analysis. Finally, we suggested some effective conservation options. We found that the PSESP with high values of protection, such as the plants with high scientific research values and ornamental plants, were threatened by over-exploitation and utilization, habitat fragmentation, and a small sized wild population in broad-leaved forests and bush fallows. We also identified some risk hotspots for PSESP in China. Regions with low elevation should be given priority for ex- and in-situ conservation. Moreover, climate change should be considered for conservation of PSESP. To avoid intensive over-exploitation or utilization and habitat fragmentation, in-situ conservation should be practiced in regions with high temperatures and low temperature seasonality, particularly in the high risk hotspots for PSESP that we proposed. Ex-situ conservation should be applied in these same regions, and over-exploitation and utilization of natural resources should be prevented. It is our goal to apply the concept of PSESP to the global scale in the future.

  5. The spatial distribution of threats to plant species with extremely small populations

    Science.gov (United States)

    Wang, Chunjing; Zhang, Jing; Wan, Jizhong; Qu, Hong; Mu, Xianyun; Zhang, Zhixiang

    2017-03-01

    Many biological conservationists take actions to conserve plant species with extremely small populations (PSESP) in China; however, there have been few studies on the spatial distribution of threats to PSESP. Hence, we selected distribution data of PSESP and made a map of the spatial distribution of threats to PSESP in China. First, we used the weight assignment method to evaluate the threat risk to PSESP at both country and county scales. Second, we used a geographic information system to map the spatial distribution of threats to PSESP, and explored the threat factors based on linear regression analysis. Finally, we suggested some effective conservation options. We found that the PSESP with high values of protection, such as the plants with high scientific research values and ornamental plants, were threatened by over-exploitation and utilization, habitat fragmentation, and a small sized wild population in broad-leaved forests and bush fallows. We also identified some risk hotspots for PSESP in China. Regions with low elevation should be given priority for ex- and in-situ conservation. Moreover, climate change should be considered for conservation of PSESP. To avoid intensive over-exploitation or utilization and habitat fragmentation, in-situ conservation should be practiced in regions with high temperatures and low temperature seasonality, particularly in the high risk hotspots for PSESP that we proposed. Ex-situ conservation should be applied in these same regions, and over-exploitation and utilization of natural resources should be prevented. It is our goal to apply the concept of PSESP to the global scale in the future.

  6. Extreme high prevalence of a defective mannose-binding lectin (MBL2 genotype in native South American West Andean populations.

    Directory of Open Access Journals (Sweden)

    José Raul Sandoval

    Full Text Available Mannose-binding lectin (MBL is one of the five recognition molecules in the lectin complement pathway. Common variant alleles in the promoter and structural regions of the human MBL gene (MBL2 influence the stability and serum concentration of the protein. Epidemiological studies have shown that MBL2 variant alleles are associated with susceptibility to and the course of different types of infectious and inflammatory conditions. However, it has been suggested that these alleles are maintained in different populations due to selected advantages for carriers. We investigated the MBL2 allelic variation in indigenous individuals from 12 different West Central South America localities spanning from the desert coast, high altitude Andean plates and the Amazon tropical forest within the territories of Peru (n = 249 (Departments of Loreto, Ucayali, Lambayeque, Junin, Ayacucho, Huancayo and Puno, and Ecuador (n = 182 (Region of Esmeraldas and Santo Domingo de los Colorados. The distribution of MBL2 genotypes among the populations showed that the defective variant LYPB haplotype was very common. It showed the highest frequencies in Puno (Taquile (0.80, Amantani (0.80 and Anapia (0.58 islander communities of the Lake Titicaca, but lower frequencies of 0.22 in Junin (Central Andean highland and Ucayali (Central Amazonian forest, as well as 0.27 and 0.24 in the Congoma and Cayapa/Chachis populations in the Amazonian forest in Ecuador were also observed. Our results suggest that the high prevalence of the MBL2 LYPB variant causing low levels of functional MBL in serum may mainly reflect a random distribution due to a population bottleneck in the founder populations.

  7. Extreme high prevalence of a defective mannose-binding lectin (MBL2) genotype in native South American West Andean populations.

    Science.gov (United States)

    Sandoval, José Raul; Madsen, Hans O; De Stefano, Gianfranco; Descailleaux-Dulanto, Jaime; Velazquez-Reinoso, Margarita; Ñique, Cesar; Fujita, Ricardo; Garred, Peter

    2014-01-01

    Mannose-binding lectin (MBL) is one of the five recognition molecules in the lectin complement pathway. Common variant alleles in the promoter and structural regions of the human MBL gene (MBL2) influence the stability and serum concentration of the protein. Epidemiological studies have shown that MBL2 variant alleles are associated with susceptibility to and the course of different types of infectious and inflammatory conditions. However, it has been suggested that these alleles are maintained in different populations due to selected advantages for carriers. We investigated the MBL2 allelic variation in indigenous individuals from 12 different West Central South America localities spanning from the desert coast, high altitude Andean plates and the Amazon tropical forest within the territories of Peru (n = 249) (Departments of Loreto, Ucayali, Lambayeque, Junin, Ayacucho, Huancayo and Puno), and Ecuador (n = 182) (Region of Esmeraldas and Santo Domingo de los Colorados). The distribution of MBL2 genotypes among the populations showed that the defective variant LYPB haplotype was very common. It showed the highest frequencies in Puno (Taquile (0.80), Amantani (0.80) and Anapia (0.58) islander communities of the Lake Titicaca), but lower frequencies of 0.22 in Junin (Central Andean highland) and Ucayali (Central Amazonian forest), as well as 0.27 and 0.24 in the Congoma and Cayapa/Chachis populations in the Amazonian forest in Ecuador were also observed. Our results suggest that the high prevalence of the MBL2 LYPB variant causing low levels of functional MBL in serum may mainly reflect a random distribution due to a population bottleneck in the founder populations.

  8. Plant species with extremely small populations (PSESP in China: A seed and spore biology perspective

    Directory of Open Access Journals (Sweden)

    Ellie Merrett Wade

    2016-10-01

    Full Text Available Approximately one fifth of the world's plants are at risk of extinction. Of these, a significant number exist as populations of few individuals, with limited distribution ranges and under enormous pressure due to habitat destruction. In China, these most-at-risk species are described as ‘plant species with extremely small populations’ (PSESP. Implementing conservation action for such listed species is urgent. Storing seeds is one of the main means of ex situ conservation for flowering plants. Spore storage could provide a simple and economical method for fern ex situ conservation. Seed and spore germination in nature is a critical step in species regeneration and thus in situ conservation. But what is known about the seed and spore biology (storage and germination of at-risk species? We have used China's PSESP (the first group listing as a case study to understand the gaps in knowledge on propagule biology of threatened plant species. We found that whilst germination information is available for 28 species (23% of PSESP, storage characteristics are only known for 8% of PSESP (10 species. Moreover, we estimate that 60% of the listed species may require cryopreservation for long-term storage. We conclude that comparative biology studies are urgently needed on the world's most threatened taxa so that conservation action can progress beyond species listing.

  9. An extreme paucity of second population AGB stars in the normal globular cluster M4

    CERN Document Server

    MacLean, B T; De Silva, G M; Lattanzio, J; DOrazi, V; Simpson, J D; Momany, Y

    2016-01-01

    Galactic Globular clusters (GCs) are now known to harbour multiple stellar populations, which are chemically distinct in many light element abundances. It is becoming increasingly clear that asymptotic giant branch (AGB) stars in GCs show different abundance distributions in light elements compared to those in the red giant branch (RGB) and other phases, skewing toward more primordial, field-star-like abundances, which we refer to as subpopulation one (SP1). As part of a larger program targeting giants in GCs, we obtained high-resolution spectra for a sample of 106 RGB and 15 AGB stars in Messier 4 (NGC 6121) using the 2dF+HERMES facility on the Anglo-Australian Telescope. In this Letter we report an extreme paucity of AGB stars with [Na/O] > -0.17 in M4, which contrasts with the RGB that has abundances up to [Na/O] =0.55. The AGB abundance distribution is consistent with all AGB stars being from SP1. This result appears to imply that all subpopulation two stars (SP2; Na-rich, O-poor) avoid the AGB phase. Thi...

  10. Extreme lipoprotein(a) levels and risk of myocardial infarction in the general population: the Copenhagen City Heart Study

    DEFF Research Database (Denmark)

    Kamstrup, P.R.; Benn, M.; Tybjaerg-Hansen, A.

    2008-01-01

    estimates. METHODS AND RESULTS: We examined 9330 men and women from the general population in the Copenhagen City Heart Study. During 10 years of follow-up, 498 participants developed MI. In women, multifactorially adjusted hazard ratios for MI for elevated lipoprotein(a) levels were 1.1 (95% CI, 0.6 to 1...... bias, and lack of absolute risk estimates in the general population. We tested the hypothesis that extreme lipoprotein(a) levels predict MI in the general population, measuring levels shortly after sampling, correcting for regression dilution bias, and calculating hazard ratios and absolute risk...... observed a stepwise increase in risk of MI with increasing levels of lipoprotein(a), with no evidence of a threshold effect. Extreme lipoprotein(a) levels predict a 3- to 4-fold increase in risk of MI in the general population and absolute 10-year risks of 20% and 35% in high-risk women and men...

  11. Genome-wide population-based association study of extremely overweight young adults--the GOYA study

    DEFF Research Database (Denmark)

    Paternoster, Lavinia; Evans, David M; Nøhr, Ellen Aagaard

    2011-01-01

    Thirty-two common variants associated with body mass index (BMI) have been identified in genome-wide association studies, explaining ∼1.45% of BMI variation in general population cohorts. We performed a genome-wide association study in a sample of young adults enriched for extremely overweight...

  12. Do changes in the frequency, magnitude and timing of extreme climatic events threaten the population viability of coastal birds?

    NARCIS (Netherlands)

    van de Pol, Martijn; Ens, Bruno J.; Heg, Dik; Brouwer, Lyanne; Krol, Johan; Maier, Martin; Exo, Klaus-Michael; Oosterbeek, Kees; Lok, Tamar; Eising, Corine M.; Koffijberg, Kees

    P>1. Climate change encompasses changes in both the means and the extremes of climatic variables, but the population consequences of the latter are intrinsically difficult to study. 2. We investigated whether the frequency, magnitude and timing of rare but catastrophic flooding events have changed

  13. Brief Report: No Association between Parental Age and Extreme Social-Communicative Autistic Traits in the General Population

    Science.gov (United States)

    Robinson, Elise B.; Munir, Kerim; McCormick, Marie C.; Koenen, Karestan C.; Santangelo, Susan L.

    2011-01-01

    This is the first investigation of the relationship between parental age and extreme social-communicative autistic traits in the general population. The parents of 5,246 children in the Avon Longitudinal Study of Parents and Children (ALSPAC) completed the Social and Communication Disorders Checklist (SCDC). The association between parental age…

  14. Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population

    Science.gov (United States)

    Flowering time is one of the major adaptive traits in domestication of maize and an important selection criterion in breeding. To detect more maize flowering time variants we evaluated flowering time traits using an extremely large multi- genetic background population that contained more than 8000 l...

  15. Extreme winter cyclones and the extinction of a reindeer population (Invited)

    Science.gov (United States)

    Walsh, J. E.; Klein, D. R.; Shulski, M.

    2009-12-01

    While strong cyclones are not unusual are not unusual in the subpolar North Pacific storm track, an exceptional series of storm events in early 1964 decimated the reindeer population of St. Matthew Island in the central Bering Sea. This case illustrates how severe winter storms can lead to species extinction when overpopulated species are restricted to islands or fractured habitats where dispersal is not an option. The strongest storm occurred in early February when a surface low pressure system that originated over the warm waters offshore of Japan tracked eastward from the warm waters offshore of Japan. The intensification of the low then accelerated as the storm approached the Aleutians, where the central pressure decreased to 957 hPa, a pressure typical of Category 3 hurricanes. The track and intensity of the low were such that St. Matthew Island was in the storm’s northwest quadrant during the peak-intensity phase. The pressure difference between the intense cyclone and the Siberian high exceeded 100 hPa -- a pressure difference between these two locations that was the largest in the entire 60-year period of the NCEP reanalysis. This record pressure difference led to extremely strong northerly winds that brought bitterly cold arctic air over St. Matthew Island, which was in the storm’s northwest quadrant. The wind chill temperature dropped to -50°C and remained colder than -40°C almost continuously for a full week. In this presentation, we examine the storm’s evolution and place the winter of early 1964 into the context of the historical cyclone climatological of the North Pacific.

  16. Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus.

    Science.gov (United States)

    Furlan, Elise; Stoklosa, J; Griffiths, J; Gust, N; Ellis, R; Huggins, R M; Weeks, A R

    2012-04-01

    Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (H(E)= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed.

  17. Genome-wide population-based association study of extremely overweight young adults--the GOYA study.

    Directory of Open Access Journals (Sweden)

    Lavinia Paternoster

    Full Text Available Thirty-two common variants associated with body mass index (BMI have been identified in genome-wide association studies, explaining ∼1.45% of BMI variation in general population cohorts. We performed a genome-wide association study in a sample of young adults enriched for extremely overweight individuals. We aimed to identify new loci associated with BMI and to ascertain whether using an extreme sampling design would identify the variants known to be associated with BMI in general populations.From two large Danish cohorts we selected all extremely overweight young men and women (n = 2,633, and equal numbers of population-based controls (n = 2,740, drawn randomly from the same populations as the extremes, representing ∼212,000 individuals. We followed up novel (at the time of the study association signals (p<0.001 from the discovery cohort in a genome-wide study of 5,846 Europeans, before attempting to replicate the most strongly associated 28 SNPs in an independent sample of Danish individuals (n = 20,917 and a population-based cohort of 15-year-old British adolescents (n = 2,418. Our discovery analysis identified SNPs at three loci known to be associated with BMI with genome-wide confidence (P<5×10(-8; FTO, MC4R and FAIM2. We also found strong evidence of association at the known TMEM18, GNPDA2, SEC16B, TFAP2B, SH2B1 and KCTD15 loci (p<0.001, and nominal association (p<0.05 at a further 8 loci known to be associated with BMI. However, meta-analyses of our discovery and replication cohorts identified no novel associations.Our results indicate that the detectable genetic variation associated with extreme overweight is very similar to that previously found for general BMI. This suggests that population-based study designs with enriched sampling of individuals with the extreme phenotype may be an efficient method for identifying common variants that influence quantitative traits and a valid alternative to genotyping all

  18. Individual Microscopic Results Of Bottleneck Experiments

    CERN Document Server

    Bukáček, Marek; Krbálek, Milan

    2016-01-01

    This contribution provides microscopic experimental study of pedestrian motion in front of the bottleneck, explains the high variance of individual travel time by the statistical analysis of trajectories. The analysis shows that this heterogeneity increases with increasing occupancy. Some participants were able to reach lower travel time due more efficient path selection and more aggressive behavior within the crowd. Based on this observations, linear model predicting travel time with respect to the aggressiveness of pedestrian is proposed.

  19. Reduced incidence of lower-extremity amputations in a Danish diabetes population from 2000 to 2011

    DEFF Research Database (Denmark)

    Jørgensen, M E; Almdal, T P; Faerch, K

    2014-01-01

    Diabetic foot disease and amputations severely reduce quality of life and have major economic consequences. The aim of this study was to estimate time trends in the incidence of lower-extremity amputations in Danish people with diabetes.......Diabetic foot disease and amputations severely reduce quality of life and have major economic consequences. The aim of this study was to estimate time trends in the incidence of lower-extremity amputations in Danish people with diabetes....

  20. Bottleneck effects on the bidirectional crowd dynamics

    Science.gov (United States)

    Yang, Xiao-Xia; Dong, Hai-Rong; Yao, Xiu-Ming; Sun, Xu-Bin

    2016-12-01

    The bottleneck effect on bidirectional crowd dynamics is of great theoretical and practical significance, especially for the designing of corridors in public places, such as subway stations or airports. Based on the famous social force model, this paper investigates the bottleneck effects on the free flow dynamics and breakdown phenomenon under different scenarios, in which different corridor shapes and inflow ratios are considered simultaneously. Numerical simulation finds an interesting self-organization phenomenon in the bidirectional flow, a typical characteristic of such a phenomenon is called lane formation, and the existence of which is independent of the corridor’s shape and inflow rate. However, the pattern of the lane formed by pedestrian flow is related to the corridor’s shape, and the free flow efficiency has close relationship with the inflow rate. Specifically, breakdown phenomenon occurs when inflows from both sides of the corridor are large enough, which mostly originates from the bottleneck and then gradually spreads to the other regions. Simulation results further indicate that the leaving efficiency becomes low as breakdown occurs, and the degree of congestion is proportional to the magnitude of inflow. The findings presented in this paper match well with some of our daily observations, hence it is possible to use them to provide us with theoretical suggestions in design of infrastructures. Project supported jointly by the National Natural Science Foundation of China (Grant Nos. 61322307 and 2016YJS023).

  1. The demographic impact of extreme events: stochastic weather drives survival and population dynamics in a long-lived seabird.

    Science.gov (United States)

    Frederiksen, M; Daunt, F; Harris, M P; Wanless, S

    2008-09-01

    1. Most scenarios for future climate change predict increased variability and thus increased frequency of extreme weather events. To predict impacts of climate change on wild populations, we need to understand whether this translates into increased variability in demographic parameters, which would lead to reduced population growth rates even without a change in mean parameter values. This requires robust estimates of temporal process variance, for example in survival, and identification of weather covariates linked to interannual variability. 2. The European shag Phalacrocorax aristotelis (L.) shows unusually large variability in population size, and large-scale mortality events have been linked to winter gales. We estimated first-year, second-year and adult survival based on 43 years of ringing and dead recovery data from the Isle of May, Scotland, using recent methods to quantify temporal process variance and identify aspects of winter weather linked to survival. 3. Survival was highly variable for all age groups, and for second-year and adult birds process variance declined strongly when the most extreme year was excluded. Survival in these age groups was low in winters with strong onshore winds and high rainfall. Variation in first-year survival was not related to winter weather, and process variance, although high, was less affected by extreme years. A stochastic population model showed that increasing process variance in survival would lead to reduced population growth rate and increasing probability of extinction. 4. As in other cormorants, shag plumage is only partially waterproof, presumably an adaptation to highly efficient underwater foraging. We speculate that this adaptation may make individuals vulnerable to rough winter weather, leading to boom-and-bust dynamics, where rapid population growth under favourable conditions allows recovery from periodic large-scale weather-related mortality. 5. Given that extreme weather events are predicted to become

  2. Extreme nonfasting remnant cholesterol vs extreme LDL cholesterol as contributors to cardiovascular disease and all-cause mortality in 90000 individuals from the general population

    DEFF Research Database (Denmark)

    Varbo, Anette; Freiberg, Jacob J; Nordestgaard, Børge G

    2015-01-01

    BACKGROUND: Increased nonfasting remnant cholesterol, like increased LDL cholesterol, is causally associated with increased risk for ischemic heart disease (IHD). We tested the hypothesis that extreme concentrations of nonfasting remnant and LDL cholesterol are equal contributors to the risk of IHD......, myocardial infarction (MI), and all-cause mortality. METHODS: We compared stepwise increasing concentrations of nonfasting remnant and LDL cholesterol for association with risk of IHD, MI, and all-cause mortality in approximately 90 000 individuals from the Danish general population. During up to 22 years...... of complete follow-up, 4435 participants developed IHD, 1722 developed MI, and 8121 died. RESULTS: Compared with participants with nonfasting remnant cholesterol cholesterol of 0.5-0.99 mmol/L (19.3-38.2 mg/dL) to 2...

  3. 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

  4. Widening inequality in extreme macrosomia between Indigenous and non-Indigenous populations of Québec, Canada.

    Science.gov (United States)

    Auger, Nathalie; Park, Alison L; Zoungrana, Hamado; Fon Sing, Mélanie; Lo, Ernest; Luo, Zhong-Cheng

    2013-02-01

    To evaluate trends in macrosomia by severity in Indigenous vs. non-Indigenous populations of Québec, Canada. We used a retrospective cohort of 2,298,332 singleton live births in the province of Québec, 1981-2008. Indigenous births were identified by community of residence (First Nations, Inuit, non-Indigenous) and language spoken (First Nations, Inuit, French/English). High birth weight (HBW) and large-for-gestational-age (LGA) births were categorised by severity (moderate, very, extreme). Time trends in HBW and LGA, by severity, were estimated using odds ratios (OR) and rate differences for Indigenous vs. non-Indigenous births, adjusting for maternal characteristics. Relative to non-Indigenous, First Nations (but not Inuit) had higher rates of extreme HBW (1.3% vs. 0.1%) and extreme LGA birth (12.6% vs. 2.2%), and rates increased over time. First Nations had progressively elevated ORs with greater severity of macrosomia, and associations were strongest for extreme HBW >5,000 g (OR=12.4) and LGA >97th percentile (OR=7.2). Inequalities in extreme macrosomia between First Nations and non-Indigenous Quebecers are pronounced and widened between 1981 and 2008. Studies are needed to determine why macrosomia rates are increasing in Québec's First Nations, and how they compare with Indigenous sub-groups of demographically similar countries, including Australia and New Zealand. © 2013 The Authors. ANZJPH © 2013 Public Health Association of Australia.

  5. Effect of extreme sea surface temperature events on the demography of an age-structured albatross population.

    Science.gov (United States)

    Pardo, Deborah; Jenouvrier, Stéphanie; Weimerskirch, Henri; Barbraud, Christophe

    2017-06-19

    Climate changes include concurrent changes in environmental mean, variance and extremes, and it is challenging to understand their respective impact on wild populations, especially when contrasted age-dependent responses to climate occur. We assessed how changes in mean and standard deviation of sea surface temperature (SST), frequency and magnitude of warm SST extreme climatic events (ECE) influenced the stochastic population growth rate log(λs) and age structure of a black-browed albatross population. For changes in SST around historical levels observed since 1982, changes in standard deviation had a larger (threefold) and negative impact on log(λs) compared to changes in mean. By contrast, the mean had a positive impact on log(λs). The historical SST mean was lower than the optimal SST value for which log(λs) was maximized. Thus, a larger environmental mean increased the occurrence of SST close to this optimum that buffered the negative effect of ECE. This 'climate safety margin' (i.e. difference between optimal and historical climatic conditions) and the specific shape of the population growth rate response to climate for a species determine how ECE affect the population. For a wider range in SST, both the mean and standard deviation had negative impact on log(λs), with changes in the mean having a greater effect than the standard deviation. Furthermore, around SST historical levels increases in either mean or standard deviation of the SST distribution led to a younger population, with potentially important conservation implications for black-browed albatrosses.This article is part of the themed issue 'Behavioural, ecological and evolutionary responses to extreme climatic events'. © 2017 The Author(s).

  6. Extreme prematurity in the UK and Denmark: population differences in viability

    OpenAIRE

    Field, D.; Petersen, S.; Clarke, M.; Draper, E

    2002-01-01

    Background: Previous studies comparing different models of neonatal intensive care have generally not been population based. The objective of this study was to compare the perinatal services of two total populations.

  7. A theory of traffic congestion at moving bottlenecks

    Science.gov (United States)

    Kerner, Boris S.; Klenov, Sergey L.

    2010-10-01

    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.

  8. Identification and optimization of traffic bottleneck with signal timing

    Directory of Open Access Journals (Sweden)

    Shaoxin Yuan

    2014-10-01

    Full Text Available In urban transportation network, traffic congestion is likely to occur at traffic bottlenecks. The signal timing at intersections together with static properties of left-turn and straight-through lanes of roads are two significant factors causing traffic bottlenecks. A discrete-time model of traffic bottleneck is hence developed to analyze these two factors, and a bottleneck indicator is introduced to estimate the comprehensive bottleneck degree of individual road in regional transportation networks universally, the identification approaches are presented to identify traffic bottlenecks, bottleneck-free roads, and bottleneck-prone roads. Based on above work, the optimization method applies ant colony algorithm with effective green time as decision variables to find out an optimal coordinated signal timing plan for a regional network. In addition, a real experimental transportation network is chosen to verify the validation of bottleneck identification. The bottleneck identification approaches can explain the features of occurrence and dissipation of traffic congestion in a certain extent, and the bottleneck optimization method provides a new way to coordinate signal timing at intersections to mitigate traffic congestion.

  9. High genetic variation in marginal fragmented populations at extreme climatic conditions of the Patagonian Cypress Austrocedrus chilensis.

    Science.gov (United States)

    Arana, María Verónica; Gallo, Leonardo A; Vendramin, Giovanni G; Pastorino, Mario J; Sebastiani, Federico; Marchelli, Paula

    2010-03-01

    Knowledge about current patterns of genetic structure of populations together with the evolutionary history of a species helps to understand and predict the adaptation of populations to future climate change. We assayed variation at nuclear microsatellite markers among peripheral vs. continuous populations of the temperate South American species Austrocedrus chilensis, to investigate the role of historical vs. demographical forces in shaping population genetic structure. This species occurs in continuous populations in the west and central distribution range, but becomes highly fragmented at the eastern limit, which comprised ice-free areas during Quaternary glaciations and has extreme climatic conditions at present times. Bayesian analysis methods identified two contrasting patterns of genetic structure; (I) populations from humid, mesic and peri-glacial regions formed a single deme with relatively low genetic differentiation and high admixture levels whereas (II) a highly heterogeneous genetic structure with low level of admixture was found in the steppe, towards the east and northeast limit of the distribution range. In the steppe, population fragmentation, restricted gene flow and isolation-by-distance were also inferred. In addition, several small steppe populations showed high genetic diversity and divergent gene pools, suggesting that they constitute ancient refuges from pre-Holocene glaciations with just a subgroup of them contributing significantly to post-glacial spread. These results are discussed in relation to patterns of genetic variation found for other temperate species and the contribution of the particular southern Andes topography and climate to post-glacial spread.

  10. Censusing natural microgametophyte populations: variable spatial mosaics and extreme fine-graininess in winter-flowering Helleborus foetidus (Ranunculaceae).

    Science.gov (United States)

    Herrera, Carlos M

    2002-10-01

    Little is known about patterns and correlates of variation in microgametophyte populations for naturally pollinated plants, yet this information is critical for evaluating the prevalence and potential evolutionary significance of gametophyte competition in the wild. This paper analyzes spatial and temporal variation in microgametophyte populations (= number of pollen tubes per style) for the winter-flowering, perennial herb Helleborus foetidus (Ranunculaceae), based on data from 29 populations in three regions of the Iberian Peninsula collected over two consecutive years. Mean size of microgametophyte populations varied significantly at a wide range of spatial scales, including among regions, among populations within regions, among individual plants within populations, among flowers of the same plant, and among pistils of the same flower (H. foetidus flowers are apocarpous). Differences between regions were quantitatively negligible. Differences between populations in the same region were moderate to low, and their sign and magnitude were inconsistent between years. Roughly half of total variance in microgametophyte numbers was accounted for by variation within individual plants, and the largest part of this component was due to differences between the pistils of the same flower. These results reveal extreme spatial fine-graininess and marked stochasticity in the spatial variation of H. foetidus microgametophyte populations and suggest that opportunities for consistent selection on male gametophyte competitive ability are probably negligible in this species.

  11. Eating Problems at Age 6 Years in a Whole Population Sample of Extremely Preterm Children

    Science.gov (United States)

    Samara, Muthanna; Johnson, Samantha; Lamberts, Koen; Marlow, Neil; Wolke, Dieter

    2010-01-01

    Aim: The aim of this study was to investigate the prevalence of eating problems and their association with neurological and behavioural disabilities and growth among children born extremely preterm (EPC) at age 6 years. Method: A standard questionnaire about eating was completed by parents of 223 children (125 males [56.1%], 98 females [43.9%])…

  12. Populating the Large-Wavevector Realm: Bloch Volume Plasmon Polaritons in Hyperbolic and Extremely Anisotropic Metamaterials

    DEFF Research Database (Denmark)

    Zhukovsky, Sergei; Babicheva, Viktoriia; Orlov, A. A.

    2014-01-01

    Optics of hyperbolic metamaterials is revisited in terms of large-wavevector waves, evanescent in isotropic media but propagating in presence of extreme anisotropy. Identifying the physical nature of these waves as Bloch volume plasmon polaritons, we derive their existence conditions and outline...... the strategy for tailoring their properties in multiscale metamaterials....

  13. Super Helium-Rich Population and the Origin of Extreme Horizontal-Branch Stars in Globular Clusters

    CERN Document Server

    Lee, Y W; Han, S I; Chung, C; Ree, C H; Sohn, Y J; Kim, Y C; Yoon, S J; Yi, S K; Demarque, P; Lee, Young-Wook; Joo, Seok-Joo; Han, Sang-Il; Chung, Chul; Ree, Chang H.; Sohn, Young-Jong; Kim, Yong-Cheol; Yoon, Suk-Jin; Yi, Sukyoung K.; Demarque, Pierre

    2005-01-01

    Recent observations for the color-magnitude diagrams (CMDs) of the massive globular cluster Omega Centauri have shown that it has a striking double main sequence (MS), with a minority population of bluer and fainter MS well separated from a majority population of MS stars. Here we confirm, with the most up-to-date Y2 isochrones, that this special feature can only be reproduced by assuming a large variation (Delta Y = 0.15) of primordial helium abundance among several distinct populations in this cluster. We further show that the same helium enhancement required for this special feature on the MS can by itself reproduce the extreme horizontal-branch (HB) stars observed in Omega Cen, which are hotter than normal HB stars. Similarly, the complex features on the HBs of other globular clusters, such as NGC 2808, are explained by large internal variations of helium abundance. Supporting evidence for the helium-rich population is also provided by the far-UV (FUV) observations of extreme HB stars in these clusters, w...

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

    Indian Academy of Sciences (India)

    A. K. Gupta; M. Chauhan; S. N. Tandon; Sonia

    2005-12-01

    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 (± 2.24), with a total of 133 alleles. A high level of genetic variability within this breed was observed in terms of high values of mean (± s.e.) effective number of alleles (3.3 ± 1.27), observed heterozygosity (0.5306 ± 0.22), expected Levene’s heterozygosity (0.6612 ± 0.15), expected Nei’s heterozygosity (0.6535 ± 0.14), and polymorphism information content (0.6120 ± 0.03). Low values of Wright’s fixation index, $F_{\\text{IS}}$ (0.2433 ± 0.05) indicated low levels of inbreeding. This basic study indicated the existence of substantial genetic diversity in the Marwari horse population. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A normal ‘L’ shaped distribution of mode–shift test, non-significant heterozygote excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests as well as non-significant ratio value suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders. This study also revealed that the Marwari breed can be differentiated from some other exotic breeds of horses on the basis of three microsatellite primers.

  15. Morphological variations of wild populations of Nile tilapia (Oreochromis niloticus) living in extreme environmental conditions in the Kenyan Rift-Valley

    OpenAIRE

    Ndiwa, T.C.; Nyingi, D. W.; Claude, J.; Agnèse, Jean-François

    2016-01-01

    In this study, we use geometric morphometric method to establish morphological differences between natural populations of Nile tilapia from two extreme environmental conditions (high temperature and salinity) in Kenya, and compare them to two populations from regions experiencing less extreme conditions. To determine genetic influence on morphology, we correlated genetic data with morphological data. The study observed significant morphological differences between all studied populations, inc...

  16. 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.

  17. Global and regional changes in exposure to extreme heat and the relative contributions of climate and population change

    Science.gov (United States)

    Liu, Zhao; Anderson, Bruce; Yan, Kai; Dong, Weihua; Liao, Hua; Shi, Peijun

    2017-03-01

    The frequency and intensity of extreme heat wave events have increased in the past several decades and are likely to continue to increase in the future under the influence of human-induced climate change. Exposure refers to people, property, systems, or other elements present in hazard zones that are thereby subject to potential losses. Exposure to extreme heat and changes therein are not just determined by climate changes but also population changes. Here we analyze output for three scenarios of greenhouse gas emissions and socio-economic growth to estimate future exposure change taking account of both climate and population factors. We find that for the higher emission scenario (RCP8.5-SSP3), the global exposure increases nearly 30-fold by 2100. The average exposure for Africa is over 118 times greater than it has been historically, while the exposure for Europe increases by only a factor of four. Importantly, in the absence of climate change, exposure is reduced by 75–95% globally and across all geographic regions, as compared with exposure under the high emission scenario. Under lower emission scenarios RCP4.5-SSP2 and RCP2.6-SSP1, the global exposure is reduced by 65% and 85% respectively, highlighting the efficacy of mitigation efforts in reducing exposure to extreme heat.

  18. Global and regional changes in exposure to extreme heat and the relative contributions of climate and population change.

    Science.gov (United States)

    Liu, Zhao; Anderson, Bruce; Yan, Kai; Dong, Weihua; Liao, Hua; Shi, Peijun

    2017-03-07

    The frequency and intensity of extreme heat wave events have increased in the past several decades and are likely to continue to increase in the future under the influence of human-induced climate change. Exposure refers to people, property, systems, or other elements present in hazard zones that are thereby subject to potential losses. Exposure to extreme heat and changes therein are not just determined by climate changes but also population changes. Here we analyze output for three scenarios of greenhouse gas emissions and socio-economic growth to estimate future exposure change taking account of both climate and population factors. We find that for the higher emission scenario (RCP8.5-SSP3), the global exposure increases nearly 30-fold by 2100. The average exposure for Africa is over 118 times greater than it has been historically, while the exposure for Europe increases by only a factor of four. Importantly, in the absence of climate change, exposure is reduced by 75-95% globally and across all geographic regions, as compared with exposure under the high emission scenario. Under lower emission scenarios RCP4.5-SSP2 and RCP2.6-SSP1, the global exposure is reduced by 65% and 85% respectively, highlighting the efficacy of mitigation efforts in reducing exposure to extreme heat.

  19. Temporal changes in allele frequencies in a small marble trout Salmo marmoratus population threatened by extreme flood events.

    Science.gov (United States)

    Pujolar, J M; Vincenzi, S; Zane, L; Crivelli, A J

    2016-03-01

    The effect of extreme floods on the genetic composition of marble trout Salmo marmoratus living in Lipovscek, a tributary of the Soca River in Slovenia, which has been affected by multiple destructive flood events for centuries was investigated. By monitoring genetic variability during the period 2004-2011, apparent signatures of genetic erosion including a decline in observed and expected heterozygosities and allelic richness were observed. Contemporary effective population size was estimated between 11 and 55 individuals, which is congruent with census data. The data suggest asymmetric gene flow between the two sections of the river. The existence of substantial downstream migration (15-19%) was confirmed by paternity analysis. A small (1-3%) upstream migration was also suggested, which was confirmed by tagging data. Overall, low genetic diversity has not prevented the survival of the Lipovscek population, which might be a common feature of salmonid freshwater populations.

  20. Desiccation and Mortality Dynamics in Seedlings of Different European Beech (Fagus sylvatica L.) Populations under Extreme Drought Conditions.

    Science.gov (United States)

    Bolte, Andreas; Czajkowski, Tomasz; Cocozza, Claudia; Tognetti, Roberto; de Miguel, Marina; Pšidová, Eva; Ditmarová, Ĺubica; Dinca, Lucian; Delzon, Sylvain; Cochard, Hervè; Ræbild, Anders; de Luis, Martin; Cvjetkovic, Branislav; Heiri, Caroline; Müller, Jürgen

    2016-01-01

    European beech (Fagus sylvatica L., hereafter beech), one of the major native tree species in Europe, is known to be drought sensitive. Thus, the identification of critical thresholds of drought impact intensity and duration are of high interest for assessing the adaptive potential of European beech to climate change in its native range. In a common garden experiment with one-year-old seedlings originating from central and marginal origins in six European countries (Denmark, Germany, France, Romania, Bosnia-Herzegovina, and Spain), we applied extreme drought stress and observed desiccation and mortality processes among the different populations and related them to plant water status (predawn water potential, ΨPD) and soil hydraulic traits. For the lethal drought assessment, we used a critical threshold of soil water availability that is reached when 50% mortality in seedling populations occurs (LD50SWA). We found significant population differences in LD50SWA (10.5-17.8%), and mortality dynamics that suggest a genetic difference in drought resistance between populations. The LD50SWA values correlate significantly with the mean growing season precipitation at population origins, but not with the geographic margins of beech range. Thus, beech range marginality may be more due to climatic conditions than to geographic range. The outcome of this study suggests the genetic variation has a major influence on the varying adaptive potential of the investigated populations.

  1. Desiccation and Mortality Dynamics in Seedlings of Different European Beech (Fagus sylvatica L.) Populations under Extreme Drought Conditions

    Science.gov (United States)

    Bolte, Andreas; Czajkowski, Tomasz; Cocozza, Claudia; Tognetti, Roberto; de Miguel, Marina; Pšidová, Eva; Ditmarová, Ĺubica; Dinca, Lucian; Delzon, Sylvain; Cochard, Hervè; Ræbild, Anders; de Luis, Martin; Cvjetkovic, Branislav; Heiri, Caroline; Müller, Jürgen

    2016-01-01

    European beech (Fagus sylvatica L., hereafter beech), one of the major native tree species in Europe, is known to be drought sensitive. Thus, the identification of critical thresholds of drought impact intensity and duration are of high interest for assessing the adaptive potential of European beech to climate change in its native range. In a common garden experiment with one-year-old seedlings originating from central and marginal origins in six European countries (Denmark, Germany, France, Romania, Bosnia-Herzegovina, and Spain), we applied extreme drought stress and observed desiccation and mortality processes among the different populations and related them to plant water status (predawn water potential, ΨPD) and soil hydraulic traits. For the lethal drought assessment, we used a critical threshold of soil water availability that is reached when 50% mortality in seedling populations occurs (LD50SWA). We found significant population differences in LD50SWA (10.5–17.8%), and mortality dynamics that suggest a genetic difference in drought resistance between populations. The LD50SWA values correlate significantly with the mean growing season precipitation at population origins, but not with the geographic margins of beech range. Thus, beech range marginality may be more due to climatic conditions than to geographic range. The outcome of this study suggests the genetic variation has a major influence on the varying adaptive potential of the investigated populations. PMID:27379105

  2. Defining Population Health Vulnerability Following an Extreme Weather Event in an Urban Pacific Island Environment: Honiara, Solomon Islands.

    Science.gov (United States)

    Natuzzi, Eileen S; Joshua, Cynthia; Shortus, Matthew; Reubin, Reginald; Dalipanda, Tenneth; Ferran, Karen; Aumua, Audrey; Brodine, Stephanie

    2016-08-03

    Extreme weather events are common and increasing in intensity in the southwestern Pacific region. Health impacts from cyclones and tropical storms cause acute injuries and infectious disease outbreaks. Defining population vulnerability to extreme weather events by examining a recent flood in Honiara, Solomon Islands, can help stakeholders and policymakers adapt development to reduce future threats. The acute and subacute health impacts following the April 2014 floods were defined using data obtained from hospitals and clinics, the Ministry of Health and in-country World Health Organization office in Honiara. Geographical information system (GIS) was used to assess morbidity and mortality, and vulnerability of the health system infrastructure and households in Honiara. The April flash floods were responsible for 21 acute deaths, 33 injuries, and a diarrhea outbreak that affected 8,584 people with 10 pediatric deaths. A GIS vulnerability assessment of the location of the health system infrastructure and households relative to rivers and the coastline identified 75% of the health infrastructure and over 29% of Honiara's population as vulnerable to future hydrological events. Honiara, Solomon Islands, is a rapidly growing, highly vulnerable urban Pacific Island environment. Evaluation of the mortality and morbidity from the April 2014 floods as well as the infectious disease outbreaks that followed allows public health specialists and policy makers to understand the health system and populations vulnerability to future shocks. Understanding the negative impacts natural disaster have on people living in urban Pacific environments will help the government as well as development partners in crafting resilient adaptation development.

  3. Extreme genetic differences among populations of Gazella granti, Grant's gazelle in Kenya

    DEFF Research Database (Denmark)

    Arctander, P; Kat, P W; Aman, R A

    1996-01-01

    Mitochondrial DNA (mtDNA) control region sequences from six Kenyan Grant's gazelle (Gazella granti) populations were highly divergent among locations. Neighbouring populations not separated by geographical or vegetational barriers exhibited and nucleotide sequence divergence about 14 per cent....... A similar level of divergence separates Grant's gazelles from a closely related species, the Soemmering's gazelle (G. soemmeringii). Nuclear microsatellite repeat number variation at two loci also indicated substantial population genetic differentiation. Despite high levels of sequence divergence...... populations of Grant's gazelles were more closely related to each other than to Soemmering's and Thompson's gazelles (G. thomsoni) as measured by nucleotide sequence divergence at the mtDNA protein coding cytochrome b gene and the nuclear alpha-lactalbumin gene. This pattern of extensive differentiation...

  4. Seasonal variations in microbial populations and environmental conditions in an extreme acid mine drainage environment.

    Science.gov (United States)

    Edwards, K J; Gihring, T M; Banfield, J F

    1999-08-01

    Microbial populations, their distributions, and their aquatic environments were studied over a year (1997) at an acid mine drainage (AMD) site at Iron Mountain, Calif. Populations were quantified by fluorescence in situ hybridizations with group-specific probes. Probes were used for the domains Eucarya, Bacteria, and Archaea and the two species most widely studied and implicated for their role in AMD production, Thiobacillus ferrooxidans and Leptospirillum ferrooxidans. Results show that microbial populations, in relative proportions and absolute numbers, vary spatially and seasonally and correlate with geochemical and physical conditions (pH, temperature, conductivity, and rainfall). Bacterial populations were in the highest proportion (>95%) in January. Conversely, archaeal populations were in the highest proportion in July and September ( approximately 50%) and were virtually absent in the winter. Bacterial and archaeal populations correlated with conductivity and rainfall. High concentrations of dissolved solids, as reflected by high conductivity values (up to 125 mS/cm), occurred in the summer and correlated with high archaeal populations and proportionally lower bacterial populations. Eukaryotes were not detected in January, when total microbial cell numbers were lowest (numbers of prokaryotes (10(8) to 10(9) cells/ml). T. ferrooxidans was in highest abundance (>30%) at moderate pHs and temperatures ( approximately 2.5 and 20 degrees C) in sites that were peripheral to primary acid-generating sites and lowest (0 to 5%) at low-pH sites (pH approximately 0.5) that were in contact with the ore body. L. ferrooxidans was more widely distributed with respect to geochemical conditions (pH = 0 to 3; 20 to 50 degrees C) but was more abundant at higher temperatures and lower pHs ( approximately 40 degrees C; pH approximately 0.5) than T. ferrooxidans.

  5. Spatial Ecology of the Critically Endangered Fijian Crested Iguana, Brachylophus vitiensis, in an Extremely Dense Population: Implications for Conservation

    Science.gov (United States)

    Morrison, Suzanne F.; Biciloa, Pita; Harlow, Peter S.; Keogh, J. Scott

    2013-01-01

    The Critically Endangered Fijian crested iguana, Brachylophus vitiensis, occurs at extreme density at only one location, with estimates of >10,000 iguanas living on the 70 hectare island of Yadua Taba in Fiji. We conducted a mark and recapture study over two wet seasons, investigating the spatial ecology and intraspecific interactions of the strictly arboreal Fijian crested iguana. This species exhibits moderate male-biased sexual size dimorphism, which has been linked in other lizard species to territoriality, aggression and larger male home ranges. We found that male Fijian crested iguanas exhibit high injury levels, indicative of frequent aggressive interactions. We did not find support for larger home range size in adult males relative to adult females, however male and female residents were larger than roaming individuals. Males with established home ranges also had larger femoral pores relative to body size than roaming males. Home range areas were small in comparison to those of other iguana species, and we speculate that the extreme population density impacts considerably on the spatial ecology of this population. There was extensive home range overlap within and between sexes. Intersexual overlap was greater than intrasexual overlap for both sexes, and continuing male-female pairings were observed among residents. Our results suggest that the extreme population density necessitates extensive home range overlap even though the underlying predictors of territoriality, such as male biased sexual size dimorphism and high aggression levels, remain. Our findings should be factored in to conservation management efforts for this species, particularly in captive breeding and translocation programs. PMID:24019902

  6. Spatial ecology of the critically endangered Fijian crested iguana, Brachylophus vitiensis, in an extremely dense population: implications for conservation.

    Science.gov (United States)

    Morrison, Suzanne F; Biciloa, Pita; Harlow, Peter S; Keogh, J Scott

    2013-01-01

    The Critically Endangered Fijian crested iguana, Brachylophus vitiensis, occurs at extreme density at only one location, with estimates of >10,000 iguanas living on the 70 hectare island of Yadua Taba in Fiji. We conducted a mark and recapture study over two wet seasons, investigating the spatial ecology and intraspecific interactions of the strictly arboreal Fijian crested iguana. This species exhibits moderate male-biased sexual size dimorphism, which has been linked in other lizard species to territoriality, aggression and larger male home ranges. We found that male Fijian crested iguanas exhibit high injury levels, indicative of frequent aggressive interactions. We did not find support for larger home range size in adult males relative to adult females, however male and female residents were larger than roaming individuals. Males with established home ranges also had larger femoral pores relative to body size than roaming males. Home range areas were small in comparison to those of other iguana species, and we speculate that the extreme population density impacts considerably on the spatial ecology of this population. There was extensive home range overlap within and between sexes. Intersexual overlap was greater than intrasexual overlap for both sexes, and continuing male-female pairings were observed among residents. Our results suggest that the extreme population density necessitates extensive home range overlap even though the underlying predictors of territoriality, such as male biased sexual size dimorphism and high aggression levels, remain. Our findings should be factored in to conservation management efforts for this species, particularly in captive breeding and translocation programs.

  7. Spatial ecology of the critically endangered Fijian crested iguana, Brachylophus vitiensis, in an extremely dense population: implications for conservation.

    Directory of Open Access Journals (Sweden)

    Suzanne F Morrison

    Full Text Available The Critically Endangered Fijian crested iguana, Brachylophus vitiensis, occurs at extreme density at only one location, with estimates of >10,000 iguanas living on the 70 hectare island of Yadua Taba in Fiji. We conducted a mark and recapture study over two wet seasons, investigating the spatial ecology and intraspecific interactions of the strictly arboreal Fijian crested iguana. This species exhibits moderate male-biased sexual size dimorphism, which has been linked in other lizard species to territoriality, aggression and larger male home ranges. We found that male Fijian crested iguanas exhibit high injury levels, indicative of frequent aggressive interactions. We did not find support for larger home range size in adult males relative to adult females, however male and female residents were larger than roaming individuals. Males with established home ranges also had larger femoral pores relative to body size than roaming males. Home range areas were small in comparison to those of other iguana species, and we speculate that the extreme population density impacts considerably on the spatial ecology of this population. There was extensive home range overlap within and between sexes. Intersexual overlap was greater than intrasexual overlap for both sexes, and continuing male-female pairings were observed among residents. Our results suggest that the extreme population density necessitates extensive home range overlap even though the underlying predictors of territoriality, such as male biased sexual size dimorphism and high aggression levels, remain. Our findings should be factored in to conservation management efforts for this species, particularly in captive breeding and translocation programs.

  8. Modeling interacting dynamic networks: III. Extraordinary properties in a population of extreme introverts and extroverts

    CERN Document Server

    Liu, Wenjia; Bassler, Kevin E; Schmittmann, Beate; Zia, Royce K P

    2014-01-01

    Recently, we introduced dynamic networks with preferred degrees, showing that interesting properties are present in a single, homogeneous system as well as one with two interacting networks. While simulations are readily performed, analytic studies are challenging, due mainly to the lack of detailed balance in the dynamics. Here, we consider the two-community case in a special limit: a system of extreme introverts and extroverts - the XIE model. Surprising phenomena appear, even in this minimal model, where the only control parameters are the numbers of each subgroup: $N_{I,E}$. Specifically, an extraordinary transition emerges when $N_I$ crosses $N_E$. For example, the fraction of total number of I-E links jumps from $\\thicksim 0$ to $\\thicksim 1$. In a $N_I=N_E$ system, this fraction performs a pure random walk so that its distribution displays a flat plateau across most of $[0,1]$, with the edges vanishing as $(N_{I,E})^{-0.38}$ for large systems. Thus, we believe the XIE model exhibits an extreme Thouless...

  9. Extreme femoral shortening: an approach to the chronically dislocated hip in the nonambulatory pediatric population.

    Science.gov (United States)

    Kalawadia, Jay V; Patel, Ronak M; Jensen, Layne; Sarwark, John

    2014-09-01

    There are many surgical techniques for treating the chronically dislocated, painful hip in patients with neuromuscular spasticity, but each has significant complication rates. We conducted a study to examine the outcomes of a novel technique, an extreme varus femoral shortening osteotomy, used in nonambulatory patients with neuromuscular spasticity. Patients who underwent the procedure were identified retrospectively by surgical codes. Medical records were reviewed for range of motion, pain and functional assessment, surgical indications, complications, and results. In addition, preoperative and postoperative radiographs were assessed, and caretaker questionnaires reviewed. Between 2001 and 2010, 1 surgeon performed 6 femoral shortening osteotomies in 5 nonambulatory patients with neuromuscular spasticity. In all 5 cases, there were improvements in pain, sitting tolerance, ease of hygiene, and ease of transfers at a minimum follow-up of 2 years (mean, 3.4 years). Postoperative complications included asymptomatic heterotopic ossification and recurrent subluxation. Extreme femoral shortening is a reproducible surgical technique that alleviates pain and makes hygiene easier in nonambulatory children with symptomatic hip dislocations caused by neuromuscular spasticity. Our complication rate was comparable to that of other procedures.

  10. [Genetic structure of the populations of Pallas pine (Pinus pallasiana D. Don) reforested in extreme conditions].

    Science.gov (United States)

    Korshikov, I I; Krasnoshtan, O V

    2010-01-01

    The paper reports on an intensive reforestation of Pallas pine (Pinus pallasiana D. Don) in post-fire sites in the native Mountainous Crimean populations and around the previously planted seed-producing trees in ore-mining dumps of the Krivoy Rog region. Self-sown progeny growing in the dump is characterized by a better growth and comes to the reproductive development phase earlier compared to that one growing in post-fire forest. Allele variability at 20 allozyme loci is less in self-sown progeny than in the native populations whereas its heterozygosity level is similar. Genetic distance (D(N)) among self-sown progenies in post-fire sites and ore-mining dump is comparable to that of the natural populations.

  11. Swift discoveries of new populations of extremely long duration high energy transient

    CERN Document Server

    Levan, A J

    2015-01-01

    Recent observations with Swift have begun to uncover $\\gamma$-ray transients whose total energies are comparable to those of gamma-ray bursts (GRB), but have a duration an order of magnitude or more longer than the bulk of the GRB population. Some are suggested to form a new population of ultra-long GRBs, with a mean duration around $10^4$s, while a further population with $\\gamma-$ray durations $>10^5$ s may represent manifestations of relativistic outflows from stars shredded around massive black holes in tidal disruption flares (TDFs). Here I review the observations of these new classes of events, discuss progress towards identifying their progenitors and suggest how new observations may both hone our understanding of the outbursts, and allow them to be used as probes, that offer both complementary and additional tools to GRBs.

  12. Document Clustering using Sequential Information Bottleneck Method

    CERN Document Server

    Gayathri, P J; Punithavalli, M

    2010-01-01

    This paper illustrates the Principal Direction Divisive Partitioning (PDDP) algorithm and describes its drawbacks and introduces a combinatorial framework of the Principal Direction Divisive Partitioning (PDDP) algorithm, then describes the simplified version of the EM algorithm called the spherical Gaussian EM (sGEM) algorithm and Information Bottleneck method (IB) is a technique for finding accuracy, complexity and time space. The PDDP algorithm recursively splits the data samples into two sub clusters using the hyper plane normal to the principal direction derived from the covariance matrix, which is the central logic of the algorithm. However, the PDDP algorithm can yield poor results, especially when clusters are not well separated from one another. To improve the quality of the clustering results problem, it is resolved by reallocating new cluster membership using the IB algorithm with different settings. IB Method gives accuracy but time consumption is more. Furthermore, based on the theoretical backgr...

  13. Modified bottleneck-based heuristic for large-scale job-shop scheduling problems with a single bottleneck

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A modified bottleneck-based (MB) heuristic for large-scale job-shop scheduling problems with a welldefined bottleneck is suggested,which is simpler but more tailored than the shifting bottleneck (SB) procedure.In this algorithm,the bottleneck is first scheduled optimally while the non-bottleneck machines are subordinated around the solutions of the bottleneck schedule by some effective dispatching rules.Computational results indicate that the MB heuristic can achieve a better tradeoff between solution quality and computational time compared to SB procedure for medium-size problems.Furthermore,it can obtain a good solution in a short time for large-scale job-shop scheduling problems.

  14. Extreme differences in SLCO1B3 functional polymorphisms in Roma and Hungarian populations.

    Science.gov (United States)

    Nagy, Agnes; Szalai, Renata; Magyari, Lili; Bene, Judit; Toth, Kalman; Melegh, Bela

    2015-05-01

    Variants in SLCO1B3 transporter are linked to disposition and uptake of drugs and show high degree of heterogeneity between populations. A total of 467 Roma and 448 Hungarian subjects were genotyped for SLCO1B3 c.334T>G and c.1683-5676A>G variant alleles by PCR-RFLP assay and direct sequencing. We found significant differences in the frequencies of homozygous variant genotypes of SLCO1B3 334GG (41.54% vs. 8.04%, pRomas and Hungarians. A significantly increased prevalence was found in SLCO1B3 1683-5676G allele frequency in Hungarians compared to the Roma population (15.07% vs. 3.43%, p≤0.001). The frequency of SLCO1B3 334G allele was significantly increased in Roma population compared to Hungarians (70.56% vs. 52.23%, p=0.001). The LD values between the examined SNPs were 80 and 90 in Roma and in Hungarian samples, respectively. Our results highlight notable pharmacogenetic differences between Roma and Hungarian populations, which may have therapeutic implications.

  15. Persistence of an extreme male-biased adult sex ratio in a natural population of polyandrous bird.

    Science.gov (United States)

    Kosztolányi, A; Barta, Z; Küpper, C; Székely, T

    2011-08-01

    In a number of insects, fishes and birds, the conventional sex roles are reversed: males are the main care provider, whereas females focus on matings. The reversal of typical sex roles is an evolutionary puzzle, because it challenges the foundations of sex roles, sexual selection and parental investment theory. Recent theoretical models predict that biased parental care may be a response to biased adult sex ratios (ASRs). However, estimating ASR is challenging in natural populations, because males and females often have different detectabilities. Here, we use demographic modelling with field data from 2101 individuals, including 579 molecularly sexed offspring, to provide evidence that ASR is strongly male biased in a polyandrous bird with male-biased care. The model predicts 6.1 times more adult males than females (ASR=0.860, proportion of males) in the Kentish plover Charadrius alexandrinus. The extreme male bias is consistent between years and concordant with experimental results showing strongly biased mating opportunity towards females. Based on these results, we conjecture that parental sex-role reversal may occur in populations that exhibit extreme male-biased ASR.

  16. Black Populations and Economic Growth: An Extreme Bounds Analysis of Mississippi County-Level Data

    OpenAIRE

    Young, Andrew; Higgins, Matthew; Levy, Daniel

    2007-01-01

    We use Mississippi county-level data on (per capita) income and the percentages of populations that are Black (henceforth "Black") to examine the relationship between race and economic growth. The analysis is also conditioned on 40 other economic and socio-demographic variables. Given a negative and statistically significant partial correlation between income growth and Black, we ask if it is robust to exhaustive combinations of other conditioning variables (taken 3 at a time). The evidence ...

  17. Extreme ("pathological") demand avoidance in autism: a general population study in the Faroe Islands.

    Science.gov (United States)

    Gillberg, Christopher; Gillberg, I Carina; Thompson, Lucy; Biskupsto, Rannvá; Billstedt, Eva

    2015-08-01

    Research into Pathological Demand Avoidance (PDA), which has been suggested to be a subgroup within the Autism Spectrum Disorder (ASD), is almost nonexistent in spite of the frequent reference to the condition in clinical practice. The total population of 15 to 24-year-olds in the Faroe Islands was screened for ASD, and 67 individuals were identified who met diagnostic criteria for ASD (corresponding to a general population prevalence of ASD of almost 1 %). Of these 67, 50 had parents who were interviewed using the Diagnostic Interview for Social and Communication Disorders (DISCO-11) which contains 15 "PDA-specific" items. Nine individuals met criteria for "possible clinical diagnosis of PDA", meaning that almost one in five of all with ASD also had indications of having had PDA in childhood, and that 0.18 % of the total population had had the combination of ASD and PDA. However, at the time of assessment, only one of the 9 individuals with possible PDA still met "full criteria". PDA possibly constitutes a considerable minority of all cases with ASD diagnosed in childhood, but criteria for the condition are unlikely to be still met in later adolescence and early adult life.

  18. 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

  19. Extreme genetic heterogeneity among the nine major tribal Taiwanese island populations detected with a new generation Y23 STR system.

    Science.gov (United States)

    Zeng, Zhaoshu; Garcia-Bertrand, Ralph; Calderon, Silvia; Li, Li; Zhong, Mingxia; Herrera, Rene J

    2014-09-01

    The Taiwanese aborigines have been regarded as the source populations for the Austronesian expansion that populated Oceania to the east and Madagascar off Africa to the West. Although a number of genetic studies have been performed on some of these important tribes, the scope of the investigations has been limited, varying in the specific populations examined as well as the maker systems employed. This has made direct comparison among studies difficult. In an attempt to alleviate this lacuna, we investigate, for the first time, the genetic diversity of all nine major Taiwanese aboriginal tribes (Ami, Atayal, Bunun, Rukai, Paiwan, Saisat, Puyuma, Tsou and Yami) utilizing a new generation multiplex Y-STR system that allows for the genotyping of 23 loci from a single amplification reaction. This comprehensive approach examining 293 individuals from all nine main tribes with the same battery of forensic markers provides for the much-needed equivalent data essential for comparative analyses. Our results have uncovered that these nine major aboriginal populations exhibit limited intrapopulation genetic diversity and are highly heterogeneous from each other, possibly the result of endogamy, isolation, drift and/or unique ancestral populations. Specifically, genetic diversity, discrimination capacity, fraction of unique haplotypes and the most frequent haplotypes differ among the nine tribes, with the Tsou possessing the lowest values for the first three of these parameters. The phylogenetic analyses performed indicate that the genetic diversity among all nine tribes is greater than the diversity observed among the worldwide reference populations examined, indicating an extreme case of genetic heterogeneity among these tribes that have lived as close neighbors for thousands of years confined to the limited geographical area of an island.

  20. Exploring the active galactic nuclei population with extreme X-ray-to-optical flux ratios (fx/fo > 50)

    Science.gov (United States)

    Della Ceca, R.; Carrera, F. J.; Caccianiga, A.; Severgnini, P.; Ballo, L.; Braito, V.; Corral, A.; Del Moro, A.; Mateos, S.; Ruiz, A.; Watson, M. G.

    2015-03-01

    The cosmic history of the growth of supermassive black holes in galactic centres parallels that of star formation in the Universe. However, an important fraction of this growth occurs inconspicuously in obscured objects, where ultraviolet/optical/near-infrared emission is heavily obscured by dust. Since the X-ray flux is less attenuated, a high X-ray-to-optical flux ratio (fx/fo) is expected to be an efficient tool to find out these obscured accreting sources. We explore here via optical spectroscopy, X-ray spectroscopy and infrared photometry the most extreme cases of this population (those with fx/fo > 50, EXO50 sources hereafter), using a well-defined sample of seven X-ray sources extracted from the 2XMM catalogue. Five EXO50 sources (˜70 per cent of the sample) in the bright flux regime explored by our survey (f(2-10 keV) ≥ 1.5 × 10-13 erg cm-2 s-1) are associated with obscured AGN (NH > 1022 cm-2), spanning a redshift range between 0.75 and 1 and characterized by 2-10 keV intrinsic luminosities in the QSO regime (e.g. well in excess to 1044 erg s-1). We did not find compelling evidence of Compton thick active galacic nuclei (AGN). Overall, the EXO50 type 2 QSOs do not seem to be different from standard X-ray-selected type 2 QSOs in terms of nuclear absorption; a very high AGN/host galaxy ratio seems to play a major role in explaining their extreme properties. Interestingly, three out of five EXO50 type 2 QSO objects can be classified as extreme dust-obscured galaxies (EDOGs, f24 μm/fR ≥ 2000), suggesting that a very high AGN/host ratios (along with the large amount of dust absorption) could be the natural explanation also for a part of the EDOG population. The remaining two EXO50 sources are classified as BL Lac objects, having rather extreme properties, and which are good candidates for TeV emission.

  1. Deep Complementary Bottleneck Features for Visual Speech Recognition

    NARCIS (Netherlands)

    Petridis, Stavros; Pantic, Maja

    2016-01-01

    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 auto

  2. 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

  3. Galactic Dark Matter Halos and Globular Cluster Populations. III. Extension to Extreme Environments

    Science.gov (United States)

    Harris, William E.; Blakeslee, John P.; Harris, Gretchen L. H.

    2017-02-01

    The total mass {M}{GCS} in the globular cluster (GC) system of a galaxy is empirically a near-constant fraction of the total mass {M}h\\equiv {M}{bary}+{M}{dark} of the galaxy across a range of 105 in galaxy mass. This trend is radically unlike the strongly nonlinear behavior of total stellar mass M ⋆ versus M h . We discuss extensions of this trend to two more extreme situations: (a) entire clusters of galaxies and (b) the ultra-diffuse galaxies (UDGs) recently discovered in Coma and elsewhere. Our calibration of the ratio {η }M={M}{GCS}/{M}h from normal galaxies, accounting for new revisions in the adopted mass-to-light ratio for GCs, now gives {η }M=2.9× {10}-5 as the mean absolute mass fraction. We find that the same ratio appears valid for galaxy clusters and UDGs. Estimates of {η }M in the four clusters we examine tend to be slightly higher than for individual galaxies, but more data and better constraints on the mean GC mass in such systems are needed to determine if this difference is significant. We use the constancy of {η }M to estimate total masses for several individual cases; for example, the total mass of the Milky Way is calculated to be {M}h=1.1× {10}12 {M}ȯ . Physical explanations for the uniformity of {η }M are still descriptive, but point to a picture in which massive dense star clusters in their formation stages were relatively immune to the feedback that more strongly influenced lower-density regions where most stars form.

  4. 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.

  5. Desiccation and Mortality Dynamics in Seedlings of Different European Beech (Fagus sylvatica L.) Populations under Extreme Drought Conditions

    DEFF Research Database (Denmark)

    Bolte, Andreas; Czajkowski, Tomasz; Cocozza, Claudia

    2016-01-01

    , but not with the geographic margins of beech range. Thus, beech range marginality may be more due to climatic conditions than to geographic range. The outcome of this study suggests the genetic variation has a major influence on the varying adaptive potential of the investigated populations.......European beech (Fagus sylvatica L., hereafter beech), one of the major native tree species in Europe, is known to be drought sensitive. Thus, the identification of critical thresholds of drought impact intensity and duration are of high interest for assessing the adaptive potential of European...... beech to climate change in its native range. In a common garden experiment with one-year-old seedlings originating from central and marginal origins in six European countries (Denmark, Germany, France, Romania, Bosnia-Herzegovina, and Spain), we applied extreme drought stress and observed desiccation...

  6. The extremely populated globular cluster system of the lenticular galaxy NGC 6861

    CERN Document Server

    Escudero, Carlos G; Bassino, Lilia P; Calderon, Juan Pablo; Caso, Juan Pablo

    2015-01-01

    We present a photometric study of the globular cluster (GC) system associated to the lenticular galaxy (S0) NGC 6861, which is located in a relatively low density environment. It is based on GEMINI/GMOS images in the filters g', r', i' of three fields, obtained under good seeing conditions. Analyzing the colour-magnitude and colour-colour diagrams, we find a large number of GC candidates, which extends out to 100 kpc, and we estimate a total population of 3000+/-300 GCs. Besides the well known blue and red subpopulations, the colour distribution shows signs of the possible existence of a third subpopulation with intermediate colours. This could be interpreted as evidence of a past interaction or fusion event. Other signs of interactions presented by the galaxy, are the non-concentric isophotes and the asymmetric spatial distribution of GC candidates with colours (g'-i')_0>1.16. As observed in other galaxies, the red GCs show a steeper radial distribution than the blue GCs. In addition, the spatial distributio...

  7. Low-energy Population III supernovae and the origin of extremely metal-poor stars

    Science.gov (United States)

    Chen, Ke-Jung; Heger, Alexander; Whalen, Daniel J.; Moriya, Takashi J.; Bromm, Volker; Woosley, S. E.

    2017-06-01

    Some ancient, dim, metal-poor stars may have formed in the ashes of the first supernovae (SNe). If their chemical abundances can be reconciled with the elemental yields of specific Population III (Pop III) explosions, they could reveal the properties of primordial stars. But multidimensional simulations of such explosions are required to predict their yields because dynamical instabilities can dredge material up from deep in the ejecta that would otherwise be predicted to fall back on to the central remnant and be lost in one-dimensional (1D) models. We have performed two-dimensional (2D) numerical simulations of two low-energy Pop III SNe, a 12.4 M⊙ explosion and a 60 M⊙ explosion, and find that they produce elemental yields that are a good fit to those measured in the most iron-poor star discovered to date, SMSS J031300.36-670839.3 (J031300). Fallback on to the compact remnant in these weak explosions accounts for the lack of measurable iron in J031300 and its low iron-group abundances in general. Our 2D explosions produce higher abundances of heavy elements (atomic number Z > 20) than their 1D counterparts due to dredge-up by fluid instabilities. Since almost no 56Ni is ejected by these weak SNe, their low luminosities will prevent their detection in the near-infrared with the James Webb Space Telescope and future 30-m telescopes on the ground. The only evidence that they ever occurred will be in the fossil abundance record.

  8. Effects of elevated mean and extremely high temperatures on the physio-ecological characteristics of geographically distinctive populations of Cunninghamia lanceolata

    Science.gov (United States)

    Zhou, Ting; Jia, Xiaorong; Liao, Huixuan; Peng, Shijia; Peng, Shaolin

    2016-12-01

    Conventional models for predicting species distribution under global warming scenarios often treat one species as a homogeneous whole. In the present study, we selected Cunninghamia lanceolata (C. lanceolata), a widely distributed species in China, to investigate the physio-ecological responses of five populations under different temperature regimes. The results demonstrate that increased mean temperatures induce increased growth performance among northern populations, which exhibited the greatest germination capacity and largest increase in the overlap between the growth curve and the monthly average temperature. However,tolerance of the southern population to extremely high temperatures was stronger than among the population from the northern region,shown by the best growth and the most stable photosynthetic system of the southern population under extremely high temperature. This result indicates that the growth advantage among northern populations due to increased mean temperatures may be weakened by lower tolerance to extremely high temperatures. This finding is antithetical to the predicted results. The theoretical coupling model constructed here illustrates that the difference in growth between populations at high and low latitudes and altitudes under global warming will decrease because of the frequent occurrence of extremely high temperatures.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    Marc Ciosi

    2014-02-01

    Full Text Available BACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. CONCLUSIONS/SIGNIFICANCE: 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.

  11. Critical Bottleneck Size for Jamless Particle Flows in Two Dimensions

    Science.gov (United States)

    Masuda, Takumi; Nishinari, Katsuhiro; Schadschneider, Andreas

    2014-04-01

    We propose a simple microscopic model for arching phenomena at bottlenecks. The dynamics of particles in front of a bottleneck is described by a one-dimensional stochastic cellular automaton on a semicircular geometry. The model reproduces oscillation phenomena due to the formation and collapsing of arches. It predicts the existence of a critical bottleneck size for continuous particle flows. The dependence of the jamming probability on the system size is approximated by the Gompertz function. The analytical results are in good agreement with simulations.

  12. A Design Framework for Metaheuristics: Problem Types and Avoiding Bottlenecking

    OpenAIRE

    2006-01-01

    This paper is concerned with an aspect of the design of metaheuristic algorithms, such as evolutionary algorithms, tabu search and ant colony optimization. The topic that is considered is how problems can be represented when they are given to a metaheuristic algorithm. A particular difficulty is presented, viz. the ''bottleneck'', where the problem is artificially converted into a new representation in order to fit the standard input to the metaheuristic. Such bottlenecks cause problems in in...

  13. Analysis of moving bottlenecks considering a triangular fundamental diagram

    Directory of Open Access Journals (Sweden)

    Karim Fadhloun

    2016-10-01

    Full Text Available A significant number of research efforts have studied and analyzed the case in which a vehicle is moving slower than the traffic stream. This phenomenon, known as a moving bottleneck, results in a disruption of traffic flow and may significantly impact the traffic stream behavior upstream, downstream and abreast the slow moving vehicle. In this paper, a macroscopic approach for modeling moving bottlenecks is developed using microscopically derived data considering a triangular fundamental diagram. The passing flow rates of different moving bottleneck scenarios are determined using a previously developed microscopic model based on simulated data derived from the INTEGRATION software. Using the simulation results, an explicit expression of the bottleneck diagram, a flow-density relationship that defines the phenomenon macroscopically is proposed and the behavior of the traffic stream downstream and abreast the moving obstruction is depicted. It is demonstrated that the behavior of the traffic stream downstream of the slow vehicle as well as the acceleration behavior while passing is governed by the demand level. Such a result is coherent and consistent, to a significant extent, with two decades of research related to modeling moving bottlenecks and constitutes a potential feasible and more detailed description of the phenomenon in the case of a triangular fundamental diagram. Finally, it is noteworthy that the research subject of this paper could be considered as a first step in developing a numerical and practitioner-friendly framework for the analysis of moving bottlenecks that does not involve approaching the problem from its theoretical perspective.

  14. Thermal discomfort with cold extremities in relation to age, gender, and body mass index in a random sample of a Swiss urban population

    Directory of Open Access Journals (Sweden)

    Orgül Selim

    2010-06-01

    Full Text Available Abstract Background The aim of this epidemiological study was to investigate the relationship of thermal discomfort with cold extremities (TDCE to age, gender, and body mass index (BMI in a Swiss urban population. Methods In a random population sample of Basel city, 2,800 subjects aged 20-40 years were asked to complete a questionnaire evaluating the extent of cold extremities. Values of cold extremities were based on questionnaire-derived scores. The correlation of age, gender, and BMI to TDCE was analyzed using multiple regression analysis. Results A total of 1,001 women (72.3% response rate and 809 men (60% response rate returned a completed questionnaire. Statistical analyses revealed the following findings: Younger subjects suffered more intensely from cold extremities than the elderly, and women suffered more than men (particularly younger women. Slimmer subjects suffered significantly more often from cold extremities than subjects with higher BMIs. Conclusions Thermal discomfort with cold extremities (a relevant symptom of primary vascular dysregulation occurs at highest intensity in younger, slimmer women and at lowest intensity in elderly, stouter men.

  15. Exploring the Active Galactic Nuclei population with extreme X-ray to optical flux ratios (Fx/Fo >50)

    CERN Document Server

    Della Ceca, R; Caccianiga, A; Severgnini, P; Ballo, L; Braito, V; Corral, A; Del Moro, A; Mateos, S; Ruiz, A; Watson, M G

    2015-01-01

    The cosmic history of the growth of supermassive black holes in galactic centers parallels that of star-formation in the Universe. However, an important fraction of this growth occurs inconspicuously in obscured objects, where ultraviolet/optical/near-infrared emission is heavily obscured by dust. Since the X-ray flux is less attenuated, a high X-ray-to-optical flux ratio (Fx/Fo) is expected to be an efficient tool to find out these obscured accreting sources. We explore here via optical spectroscopy, X-ray spectroscopy and infrared photometry the most extreme cases of this population (those with Fx/Fo >50, EXO50 sources hereafter), using a well defined sample of seven X-ray sources extracted from the 2XMM catalogue. Five EXO50 sources (about 70 percent of the sample) in the bright flux regime explored by our survey (f(2-10 keV) > 1.5E-13 cgs) are associated with obscured AGN (Nh > 1.0E22 cm-2), spanning a redshift range between 0.75 and 1 and characterised by 2-10 keV intrinsic luminosities in the QSO regime...

  16. Extreme variation in migration strategies between and within wandering albatross populations during their sabbatical year, and their fitness consequences.

    Science.gov (United States)

    Weimerskirch, Henri; Delord, Karine; Guitteaud, Audrey; Phillips, Richard A; Pinet, Patrick

    2015-03-09

    Migratory behavior, routes and zones used during the non-breeding season are assumed to have been selected to maximize fitness, and can lead to genetic differentiation. Yet, here we show that migration strategies differ markedly between and within two genetically similar populations of wandering albatross Diomedea exulans from the Crozet and Kerguelen archipelagos in the Indian Ocean. Wandering albatrosses usually breed biennially if successful, and during the sabbatical year, all birds from Kerguelen migrate to the Pacific Ocean, whereas most from Crozet are sedentary. Instead of taking the shortest routes, which would involve a return against headwinds, migratory birds fly with the westerly winds, requiring detours of 10,000 s km. In total, migrants circumnavigate Antarctica 2 to 3 times, covering more than 120,000 km in a single sabbatical year. Our results indicate strong links between migratory behavior and fitness; all birds from Kerguelen breed biennially, whereas a significant proportion of those from Crozet, especially females, are sedentary and breed in consecutive calendar years. To breed annually, these females temporarily change mate, but return to their original partner in the following year. This extreme variation in migratory behavior has important consequences in term of life history evolution and susceptibility to climate change and fisheries.

  17. Asymbiotic seed germination and in vitro seedling development of Paphiopedilum spicerianum: An orchid with an extremely small population in China

    Directory of Open Access Journals (Sweden)

    Ying Chen

    2015-01-01

    Full Text Available Paphiopedilum spicerianum  is listed as one of the country’s Wild Plants with Extremely Small Populations (PSESP. Procedures were developed for asymbiotic seed germination and seedling development aimed at producing seedlings for reintroduction. The highest germination was achieved in RECW with a 24 h dark cycle after pretreatment with 1% NaOCl for 40 min after 30 days from germination. However, these protocorms remained white and did not develop further. Although germination was lower under the same conditions in MSCW, it resulted in healthier and greener protocorms. Of four suitable media tested to promote seedling formation, Hyponex No 1 medium with 1.0mgl−1α-naphthalene acetic acid, 0.5gl−1 activated charcoal and 10% banana homogenate was the most effective. Advanced seedling development was seen in all six tested media during a 4 month growing period, with the highest leaf growth rate seen in the same media used for seedling formation, supplemented with 1.0mgl−16-benzyladenine added to promote leaf growth. Fluorescein diacetate (FDA tests on seeds showed that higher salt concentrations in the medium and longer duration of exposure to NaOCl reduce germination because of damaging effects on the testa and the embryo cells.

  18. Bottlenecks in serial production lines: A system-theoretic approach

    Directory of Open Access Journals (Sweden)

    C.-T. Kuo

    1996-01-01

    Full Text Available In this work, a new definition of production systems bottlenecks is formulated and analyzed. Specifically, a machine is defined as the bottleneck if the sensitivity of the system's performance index to this machine's production rate in isolation is the largest. Although appealing from the systems point of view, this definition suffers a deficiency due to the fact that the sensitivities involved cannot be either measured on-line or efficiently calculated off-line. To avoid this, the paper develops a method based on indirect but real-time data. From this point of view, the main result of the work is as follows: The bottleneck machine in a serial production line can be identified by analyzing relationships between the so-called manufacturing blockage and manufacturing starvation of each machine. This leads to a simple rule for bottleneck identification. The rule requires neither the calculation of the production rate sensitivities nor the production rate itself. When the probabilities of manufacturing blockages and starvations are not available from on-line measurements, the paper presents their analytical estimates which, under certain conditions, can be used for bottleneck identification. Finally, a case study at an automotive component plant is described.

  19. c-Bottlenecks in serial production lines: Identification and application

    Directory of Open Access Journals (Sweden)

    Chiang S.-Y.

    2001-01-01

    Full Text Available The bottleneck of a production line is a machine that impedes the system performance in the strongest manner. In production lines with the so-called Markovian model of machine reliability, bottlenecks with respect to the downtime, uptime, and the cycle time of the machines can be introduced. The two former have been addressed in recent publications [1] and [2]. The latter is investigated in this paper. Specifically, using a novel aggregation procedure for performance analysis of production lines with Markovian machines having different cycle time, we develop a method for c-bottleneck identification and apply it in a case study to a camshaft production line at an automotive engine plant.

  20. Steady State of Pedestrian Flow in Bottleneck Experiments

    CERN Document Server

    Liao, Weichen; Seyfried, Armin; Chraibi, Mohcine; Drzycimski, Kevin; Zheng, Xiaoping; Zhao, Ying

    2015-01-01

    Experiments with pedestrians could depend strongly on initial conditions. Comparisons of the results of such experiments require to distinguish carefully between transient state and steady state. In this work, a feasible algorithm - Cumulative Sum Control Chart - is proposed and improved to automatically detect steady states from density and speed time series of bottleneck experiments. The threshold of the detection parameter in the algorithm is calibrated using an autoregressive model. Comparing the detected steady states with previous manually selected ones, the modified algorithm gives more reproducible results. For the applications, three groups of bottleneck experiments are analysed and the steady states are detected. The study about pedestrian flow shows that the difference between the flows in all states and in steady state mainly depends on the ratio of pedestrian number to bottleneck width. When the ratio is higher than a critical value (approximately 115 persons/m), the flow in all states is almost ...

  1. Associating emergency room visits with first and prolonged extreme temperature event in Taiwan: A population-based cohort study.

    Science.gov (United States)

    Wang, Yu-Chun; Lin, Yu-Kai; Chuang, Chun-Yu; Li, Ming-Hsu; Chou, Chang-Hung; Liao, Chun-Hui; Sung, Fung-Chang

    2012-02-01

    The present study evaluated emergency room visit (ERV) risks for all causes and cardiopulmonary diseases associated with temperature and long-lasting extreme temperatures from 2000 to 2009 in four major cities in Taiwan. The city-specific daily average temperatures at the high 95th, 97th, and 99th percentiles, and the low 10th, 5th, and 1st percentiles were defined as extreme heat and cold. A distributed lag non-linear model was used to estimate the cumulative relative risk (RR) of ERV for morbidities associated with temperatures (0 to 3-day lags), extreme heat and cold lasting for 2 to 9 days or longer, and with the annual first extreme heat or cold event after controlling for covariates. Low temperatures were associated with slightly higher ERV risks than high temperatures for circulatory diseases. After accounting for 4-day cumulative temperature effect, the ERV risks for all causes and respiratory diseases were found to be associated with extreme cold at the 5th percentile lasting for >8 days and 1st percentile lasting for >3 days. The annual first extreme cold event of 5th percentile or lower temperatures was also significantly associated with ERV, with RRs ranging from 1.09 to 1.12 for all causes and from 1.15 to 1.26 for respiratory diseases. The annual first extreme heat event of 99th percentile temperature was associated with higher ERV for all causes and circulatory diseases. Annual first extreme temperature event and intensified prolonged extreme cold events are associated with increased ERVs in Taiwan.

  2. Symbiotic bacterial communities in ants are modified by invasion pathway bottlenecks and alter host behavior.

    Science.gov (United States)

    Lester, Philip J; Sébastien, Alexandra; Suarez, Andrew V; Barbieri, Rafael F; Gruber, Monica A M

    2017-03-01

    Biological invasions are a threat to global biodiversity and provide unique opportunities to study ecological processes. Population bottlenecks are a common feature of biological invasions and the severity of these bottlenecks is likely to be compounded as an invasive species spreads from initial invasion sites to additional locations. Despite extensive work on the genetic consequences of bottlenecks, we know little about how they influence microbial communities of the invaders themselves. Due to serial bottlenecks, invasive species may lose microbial symbionts including pathogenic taxa (the enemy release hypothesis) and/or may accumulate natural enemies with increasing time after invasion (the pathogen accumulation and invasive decline hypothesis). We tested these alternate hypotheses by surveying bacterial communities of Argentine ants (Linepithema humile). We found evidence for serial symbiont bottlenecks: the bacterial community richness declined over the invasion pathway from Argentina to New Zealand. The abundance of some genera, such as Lactobacillus, also significantly declined over the invasion pathway. Argentine ants from populations in the United States shared the most genera with ants from their native range in Argentina, while New Zealand shared the least (120 vs. 57, respectively). Nine genera were present in all sites around the globe possibly indicating a core group of obligate microbes. In accordance with the pathogen accumulation and invasive decline hypothesis, Argentine ants acquired genera unique to each specific invaded country. The United States had the most unique genera, though even within New Zealand these ants acquired symbionts. In addition to our biogeographic sampling, we administered antibiotics to Argentine ants to determine if changes in the micro-symbiont community could influence behavior and survival in interspecific interactions. Treatment with the antibiotics spectinomycin and kanamycin only slightly increased Argentine ant

  3. Kinetic description of bottleneck effects in traffic flow

    Institute of Scientific and Technical Information of China (English)

    Peng ZHANG; Dong-yan WU; S. C. WONG; Yi-zhou TAO

    2009-01-01

    This paper deals with the effects of traffic bottlenecks using an extended Lighthill-Whitham-Richards (LWR) model. The solution structure is analytically indi-cated by the study of the Riemann problem characterized by a discontinuous flux. This leads to a typical solution describing a queue upstream of the bottleneck and its width and height, and informs the design of a 5-mapping algorithm. More significantly, it is found that the kinetic model is able to reproduce stop-and-go waves for a triangular fun-damental diagram. Some simulation examples, which are in agreement with the analytical solutions, are given to support these conclusions.

  4. The "Bottleneck" Behaviours in Linear FNNCs and Their Breakthrough

    Institute of Scientific and Technical Information of China (English)

    HUANG Deshuang

    1999-01-01

    The classification mechanisms of linear feed forward neural network classifiers (FNNC), whose hidden layer performs the Fisher lineartrans formation of the input patterns, under the supervision of outer-supervised signals are investigated. The "bottleneck" behavioursin linear FNNCs are observed and analyzed. In addition, the structure stabilities of the linear FNNCs are also discussed. It is pointed out that the key point to break through the "bottleneck" behaviours forlinear FNNCs is to change linear hidden neurons into nonlinear hiddenones. Finally, the experimental results, taking the parity 3 problem asexample, are given.

  5. Extreme Elevations in Blood Pressure and All-Cause Mortality in a Referred CKD Population: Results from the CRISIS Study.

    Science.gov (United States)

    Ritchie, James; Rainone, Francesco; Green, Darren; Alderson, Helen; Chiu, Diana; Middleton, Rachel; O'Donoghue, Donal; Kalra, Philip A

    2013-01-01

    Hypertension frequently complicates chronic kidney disease (CKD), with studies showing clinical benefit from blood pressure lowering. Subgroups of patients with severe hypertension exist. We aimed to identify patients with the greatest mortality risk from uncontrolled hypertension to define the prevalence and phenotype of patients who might benefit from adjunctive therapies. 1691 all-cause CKD patients from the CRISIS study were grouped by baseline blood pressure-target (extreme (>190 and/or 100 mmHg). Groups were well matched for age, eGFR, and comorbidities. 77 patients had extreme hypertension at recruitment but no increased mortality risk (HR 0.9, P = 0.9) over a median follow-up period of 4.5 years. The 1.2% of patients with extreme hypertension at recruitment and at 12-months had a significantly increased mortality risk (HR 4.3, P = 0.01). This association was not seen in patients with baseline extreme hypertension and improved 12-month blood pressures (HR 0.86, P = 0.5). Most CKD patients with extreme hypertension respond to pharmacological blood pressure control, reducing their risk for death. Patients with extreme hypertension in whom blood pressure control cannot be achieved have an approximate prevalence of 1%. These patients have an increased mortality risk and may be an appropriate group to consider for further therapies, including renal nerve ablation.

  6. Shallow gene pools in the high intertidal: extreme loss of genetic diversity in viviparous sea stars (Parvulastra).

    Science.gov (United States)

    Keever, Carson C; Puritz, Jonathan B; Addison, Jason A; Byrne, Maria; Grosberg, Richard K; Toonen, Robert J; Hart, Michael W

    2013-10-23

    We document an extreme example of reproductive trait evolution that affects population genetic structure in sister species of Parvulastra cushion stars from Australia. Self-fertilization by hermaphroditic adults and brood protection of benthic larvae causes strong inbreeding and range-wide genetic poverty. Most samples were fixed for a single allele at nearly all nuclear loci; heterozygotes were extremely rare (0.18%); mitochondrial DNA sequences were more variable, but few populations shared haplotypes in common. Isolation-with-migration models suggest that these patterns are caused by population bottlenecks (relative to ancestral population size) and low gene flow. Loss of genetic diversity and low potential for dispersal between high-intertidal habitats may have dire consequences for extinction risk and potential for future adaptive evolution in response to climate and other selective agents.

  7. A single origin and moderate bottleneck during domestication of soybean (Glycine max): implications from microsatellites and nucleotide sequences.

    Science.gov (United States)

    Guo, Juan; Wang, Yunsheng; Song, Chi; Zhou, Jianfeng; Qiu, Lijuan; Huang, Hongwen; Wang, Ying

    2010-09-01

    Background and Aims It is essential to illuminate the evolutionary history of crop domestication in order to understand further the origin and development of modern cultivation and agronomy; however, despite being one of the most important crops, the domestication origin and bottleneck of soybean (Glycine max) are poorly understood. In the present study, microsatellites and nucleotide sequences were employed to elucidate the domestication genetics of soybean. Methods The genomes of 79 landrace soybeans (endemic cultivated soybeans) and 231 wild soybeans (G. soja) that represented the species-wide distribution of wild soybean in East Asia were scanned with 56 microsatellites to identify the genetic structure and domestication origin of soybean. To understand better the domestication bottleneck, four nucleotide sequences were selected to simulate the domestication bottleneck. Key Results Model-based analysis revealed that most of the landrace genotypes were assigned to the inferred wild soybean cluster of south China, South Korea and Japan. Phylogeny for wild and landrace soybeans showed that all landrace soybeans formed a single cluster supporting a monophyletic origin of all the cultivars. The populations of the nearest branches which were basal to the cultivar lineage were wild soybeans from south China. The coalescent simulation detected a bottleneck severity of K' = 2 during soybean domestication, which could be explained by a foundation population of 6000 individuals if domestication duration lasted 3000 years. Conclusions As a result of integrating geographic distribution with microsatellite genotype assignment and phylogeny between landrace and wild soybeans, a single origin of soybean in south China is proposed. The coalescent simulation revealed a moderate genetic bottleneck with an effective wild soybean population used for domestication estimated to be approximately 2 % of the total number of ancestral wild soybeans. Wild soybeans in Asia, especially in

  8. Bottleneck Accumulation of Hybrid Magnetoelastic Bosons

    Science.gov (United States)

    Bozhko, Dmytro A.; Clausen, Peter; Melkov, Gennadii A.; L'vov, Victor S.; Pomyalov, Anna; Vasyuchka, Vitaliy I.; Chumak, Andrii V.; Hillebrands, Burkard; Serga, Alexander A.

    2017-06-01

    An ensemble of magnons, quanta of spin waves, can be prepared as a Bose gas of weakly interacting quasiparticles. Furthermore, the thermalization of the overpopulated magnon gas through magnon-magnon scattering processes, which conserve the number of particles, can lead to the formation of a Bose-Einstein condensate at the bottom of a spin-wave spectrum. However, magnon-phonon scattering can significantly modify this scenario and new quasiparticles are formed—magnetoelastic bosons. Our observations of a parametrically populated magnon gas in a single-crystal film of yttrium iron garnet by means of wave-vector-resolved Brillouin light scattering spectroscopy evidence a novel condensation phenomenon: A spontaneous accumulation of hybrid magnetoelastic bosonic quasiparticles at the intersection of the lowest magnon mode and a transversal acoustic wave.

  9. 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.

  10. 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.

  11. Mitigating the controller performance bottlenecks in Software Defined Networks

    DEFF Research Database (Denmark)

    Caba, Cosmin Marius; Soler, José

    2016-01-01

    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...

  12. Energetic bottlenecks and other design constraints in avian annual cycles

    NARCIS (Netherlands)

    Piersma, T

    2002-01-01

    The flexible phenotypes of birds and mammals often appear to represent adjustments to alleviate some energetic bottleneck or another. By increasing the size of the organs involved in digestion and assimilation of nutrients (gut and liver), an individual bird can increase its ability to process nutri

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

    NARCIS (Netherlands)

    Keijzer, B. de; Schäfer, G.; Telelis, O.; Kontogiannis, S.; Koutsoupias, E.; Spirakis, P.G.

    2010-01-01

    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 (weigh

  14. Step by step: Revisiting step tolling in the bottleneck model

    NARCIS (Netherlands)

    Lindsey, C.R.; Berg, van den V.A.C.; Verhoef, E.T.

    2010-01-01

    In most dynamic traffic congestion models, congestion tolls must vary continuously over time to achieve the full optimum. This is also the case in Vickrey's (1969) 'bottleneck model'. To date, the closest approximations of this ideal in practice have so-called 'step tolls', in which the toll takes o

  15. 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

  16. Demographic effects of extreme weather events: snow storms, breeding success, and population growth rate in a long-lived Antarctic seabird.

    Science.gov (United States)

    Descamps, Sébastien; Tarroux, Arnaud; Varpe, Øystein; Yoccoz, Nigel G; Tveraa, Torkild; Lorentsen, Svein-Håkon

    2015-01-01

    Weather extremes are one important element of ongoing climate change, but their impacts are poorly understood because they are, by definition, rare events. If the frequency and severity of extreme weather events increase, there is an urgent need to understand and predict the ecological consequences of such events. In this study, we aimed to quantify the effects of snow storms on nest survival in Antarctic petrels and assess whether snow storms are an important driver of annual breeding success and population growth rate. We used detailed data on daily individual nest survival in a year with frequent and heavy snow storms, and long term data on petrel productivity (i.e., number of chicks produced) at the colony level. Our results indicated that snow storms are an important determinant of nest survival and overall productivity. Snow storm events explained 30% of the daily nest survival within the 2011/2012 season and nearly 30% of the interannual variation in colony productivity in period 1985-2014. Snow storms are a key driver of Antarctic petrel breeding success, and potentially population dynamics. We also found state-dependent effects of snow storms and chicks in poor condition were more likely to die during a snow storm than chicks in good condition. This stresses the importance of considering interactions between individual heterogeneity and extreme weather events to understand both individual and population responses to climate change.

  17. Bulinus globosus (Planorbidae; Gastropoda) populations in the Lake Victoria basin and coastal Kenya show extreme nuclear genetic differentiation

    DEFF Research Database (Denmark)

    Nyakaana, Silvester; Stothard, J. Russell; Nalugwa, Allen

    2013-01-01

    -fertilizing, this species has been reported to be preferentially out crossing. In this study, we characterized the population genetic structure of 19 B. globosus populations sampled across the Lake Victoria basin and coastal Kenya using four polymorphic microsatellite loci. Population genetic structure was characterized...

  18. Population-based resequencing of APOA1 in 10,330 individuals: spectrum of genetic variation, phenotype, and comparison with extreme phenotype approach.

    Science.gov (United States)

    Haase, Christiane L; Frikke-Schmidt, Ruth; Nordestgaard, Børge G; Tybjærg-Hansen, Anne

    2012-01-01

    Rare genetic variants, identified by in-detail resequencing of loci, may contribute to complex traits. We used the apolipoprotein A-I gene (APOA1), a major high-density lipoprotein (HDL) gene, and population-based resequencing to determine the spectrum of genetic variants, the phenotypic characteristics of these variants, and how these results compared with results based on resequencing only the extremes of the apolipoprotein A-I (apoA-I) distribution. First, we resequenced APOA1 in 10,330 population-based participants in the Copenhagen City Heart Study. The spectrum and distribution of genetic variants was determined as a function of the number of individuals resequenced. Second, apoA-I and HDL cholesterol phenotypes were determined for nonsynonymous (NS) and synonymous (S) variants and were validated in the Copenhagen General Population Study (n = 45,239). Third, observed phenotypes were compared with those predicted using an extreme phenotype approach based on the apoA-I distribution. Our results are as follows: First, population-based resequencing of APOA1 identified 40 variants of which only 7 (18%) had minor allele frequencies >1%, and most were exceedingly rare. Second, 0.27% of individuals in the general population were heterozygous for NS variants which were associated with substantial reductions in apoA-I (up to 39 mg/dL) and/or HDL cholesterol (up to 0.9 mmol/L) and, surprisingly, 0.41% were heterozygous for variants predisposing to amyloidosis. NS variants associated with a hazard ratio of 1.72 (1.09-2.70) for myocardial infarction (MI), largely driven by A164S, a variant not associated with apoA-I or HDL cholesterol levels. Third, using the extreme apoA-I phenotype approach, NS variants correctly predicted the apoA-I phenotype observed in the population-based resequencing. However, using the extreme approach, between 79% (screening 0-1(st) percentile) and 21% (screening 0-20(th) percentile) of all variants were not identified; among these were variants

  19. Incidence and prevalence of lower extremity tendinopathy in a Dutch general practice population : a cross sectional study

    NARCIS (Netherlands)

    Albers, Iris Sophie; Zwerver, Johannes; Diercks, Ronald Leo; Dekker, Janny Hendrika; Van den Akker-Scheek, Inge

    2016-01-01

    Background: Lower extremity tendinopathy is a common sports injury, but it can also affect non-athletes. Because tendinopathy is difficult to treat and has negative effects on the ability to work and quality of life, development of preventive interventions is important. The first step in the Van Mec

  20. Incidence and prevalence of lower extremity tendinopathy in a Dutch general practice population: A cross sectional study

    NARCIS (Netherlands)

    Albers, Iris Sophie; Zwerver, Johannes; Diercks, Ronald Leo; Dekker, Janny Hendrika; Van den Akker-Scheek, Inge

    2016-01-01

    Background: Lower extremity tendinopathy is a common sports injury, but it can also affect non-athletes. Because tendinopathy is difficult to treat and has negative effects on the ability to work and quality of life, development of preventive interventions is important. The first step in the Van Mec

  1. Incidence and prevalence of lower extremity tendinopathy in a Dutch general practice population : a cross sectional study

    NARCIS (Netherlands)

    Albers, Iris Sophie; Zwerver, Johannes; Diercks, Ronald Leo; Dekker, Janny Hendrika; Van den Akker-Scheek, Inge

    2016-01-01

    Background: Lower extremity tendinopathy is a common sports injury, but it can also affect non-athletes. Because tendinopathy is difficult to treat and has negative effects on the ability to work and quality of life, development of preventive interventions is important. The first step in the Van

  2. Incidence and prevalence of lower extremity tendinopathy in a Dutch general practice population: A cross sectional study

    NARCIS (Netherlands)

    Albers, Iris Sophie; Zwerver, Johannes; Diercks, Ronald Leo; Dekker, Janny Hendrika; Van den Akker-Scheek, Inge

    2016-01-01

    Background: Lower extremity tendinopathy is a common sports injury, but it can also affect non-athletes. Because tendinopathy is difficult to treat and has negative effects on the ability to work and quality of life, development of preventive interventions is important. The first step in the Van Mec

  3. Incidence and prevalence of lower extremity tendinopathy in a Dutch general practice population : a cross sectional study

    NARCIS (Netherlands)

    Albers, Iris Sophie; Zwerver, Johannes; Diercks, Ronald Leo; Dekker, Janny Hendrika; Van den Akker-Scheek, Inge

    2016-01-01

    Background: Lower extremity tendinopathy is a common sports injury, but it can also affect non-athletes. Because tendinopathy is difficult to treat and has negative effects on the ability to work and quality of life, development of preventive interventions is important. The first step in the Van Mec

  4. Bulinus globosus (Planorbidae; Gastropoda) populations in the Lake Victoria basin and coastal Kenya show extreme nuclear genetic differentiation.

    Science.gov (United States)

    Nyakaana, Silvester; Stothard, J Russell; Nalugwa, Allen; Webster, Bonnie L; Lange, Charles N; Jørgensen, Aslak; Rollinson, David; Kristensen, Thomas K

    2013-11-01

    Bulinus globosus, a key intermediate host for Schistosoma haematobium that causes urinary schistosomiasis, is a hermaphroditic freshwater Planorbid snail species that inhabits patchy and transient water bodies prone to large seasonal variations in water availability. Although capable of self-fertilizing, this species has been reported to be preferentially out crossing. In this study, we characterized the population genetic structure of 19 B. globosus populations sampled across the Lake Victoria basin and coastal Kenya using four polymorphic microsatellite loci. Population genetic structure was characterized and quantified using FST statistics and Bayesian clustering algorithms. The four loci used in this study contained sufficient statistical power to detect low levels of population genetic differentiation and were highly polymorphic with the number of alleles per locus across populations ranging from 16 to 22. Average observed and expected heterozygosities across loci in each population ranged from 0.13 to 0.69 and from 0.39 to 0.79, respectively. Twenty-five of the seventy-six possible population-locus comparisons significantly deviated from Hardy-Weinberg equilibrium proportions after Bonferroni corrections, mostly due to the deficiency of heterozygotes. Significant genetic differentiation was observed between populations and Bayesian inferences identified 15 genetic clusters. The excess homozygosity, significant inbreeding and population genetic differentiation observed in B. globosus populations are likely to be due to the habitat patchiness, mating system and the proneness to cyclic extinction and recolonization in transient habitats.

  5. How extreme are extremes?

    Science.gov (United States)

    Cucchi, Marco; Petitta, Marcello; Calmanti, Sandro

    2016-04-01

    High temperatures have an impact on the energy balance of any living organism and on the operational capabilities of critical infrastructures. Heat-wave indicators have been mainly developed with the aim of capturing the potential impacts on specific sectors (agriculture, health, wildfires, transport, power generation and distribution). However, the ability to capture the occurrence of extreme temperature events is an essential property of a multi-hazard extreme climate indicator. Aim of this study is to develop a standardized heat-wave indicator, that can be combined with other indices in order to describe multiple hazards in a single indicator. The proposed approach can be used in order to have a quantified indicator of the strenght of a certain extreme. As a matter of fact, extremes are usually distributed in exponential or exponential-exponential functions and it is difficult to quickly asses how strong was an extreme events considering only its magnitude. The proposed approach simplify the quantitative and qualitative communication of extreme magnitude

  6. Whole-genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations.

    Science.gov (United States)

    Kardos, Marty; Husby, Arild; McFarlane, S Eryn; Qvarnström, Anna; Ellegren, Hans

    2016-05-01

    Dissecting the genetic basis of phenotypic variation in natural populations is a long-standing goal in evolutionary biology. One open question is whether quantitative traits are determined only by large numbers of genes with small effects, or whether variation also exists in large-effect loci. We conducted genomewide association analyses of forehead patch size (a sexually selected trait) on 81 whole-genome-resequenced male collared flycatchers with extreme phenotypes, and on 415 males sampled independent of patch size and genotyped with a 50K SNP chip. No SNPs were genomewide statistically significantly associated with patch size. Simulation-based power analyses suggest that the power to detect large-effect loci responsible for 10% of phenotypic variance was 0.8 for resequencing of extreme phenotypes (N = 243), but power remained 0.8 when analysing 415 randomly sampled phenotypes. However, power of the 50K SNP chip to detect large-effect loci was nearly 0.8 in simulations with a small effective population size of 1500. These results suggest that reliably detecting large-effect trait loci in large natural populations will often require thousands of individuals and near complete sampling of the genome. Encouragingly, far fewer individuals and loci will often be sufficient to reliably detect large-effect loci in small populations with widespread strong linkage disequilibrium.

  7. Extreme patterns of variance in small populations: placing limits on human Y-chromosome diversity through time in the Vanuatu Archipelago.

    Science.gov (United States)

    Cox, M

    2007-05-01

    Small populations are dominated by unique patterns of variance, largely characterized by rapid drift of allele frequencies. Although the variance components of genetic datasets have long been recognized, most population genetic studies still treat all sampling locations equally despite differences in sampling and effective population sizes. Because excluding the effects of variance can lead to significant biases in historical reconstruction, variance components should be incorporated explicitly into population genetic analyses. The possible magnitude of variance effects in small populations is illustrated here via a case study of Y-chromosome haplogroup diversity in the Vanuatu Archipelago. Deme-based modelling is used to simulate allele frequencies through time, and conservative confidence bounds are placed on the accumulation of stochastic variance effects, including diachronic genetic drift and contemporary sampling error. When the information content of the dataset has been ascertained, demographic models with parameters falling outside the confidence bounds of the variance components can then be accepted with some statistical confidence. Here I emphasize how aspects of the demographic history of a population can be disentangled from stochastic variance effects, and I illustrate the extreme roles of genetic drift and sampling error for many small human population datasets.

  8. Microsatellite variation and rare alleles in a bottlenecked Hawaiian Islands endemic: implications for reintroductions

    Science.gov (United States)

    Reynolds, Michelle H.; Pearce, John M.; Lavretsky, Philip; Seixas, Pedro P.; Courtot, Karen

    2015-01-01

    Conservation of genetic biodiversity in endangered wildlife populations is an important challenge to address since the loss of alleles and genetic drift may influence future adaptability. Reintroduction aims to re-establish species to restored or protected ecosystems; however, moving a subset of individuals may result in loss of gene variants during the management-induced bottleneck (i.e. translocation). The endangered Laysan teal Anas laysanensis was once widespread across the Hawaiian archipelago, but became isolated on Laysan Island (415 ha) from the mid-1800s until 2004 when a translocation to Midway Atoll (596 ha) was undertaken to reduce extinction risks. We compared genetic diversity and quantified variation at microsatellite loci sampled from 230 individuals from the wild populations at Laysan (1999 to 2009) and Midway (2007 to 2010; n = 133 Laysan, n = 96 Midway birds). We identified polymorphic markers by screening nuclear microsatellites (N = 83). Low nuclear variation was detected, consistent with the species’ insular isolation and historical bottleneck. Six of 83 microsatellites were polymorphic. We found limited but similar estimates of allelic richness (2.58 alleles per locus) and heterozygosity within populations. However, 2 rare alleles found in the Laysan source population were not present in Midway’s reintroduced population, and a unique allele was discovered in an individual on Midway. Differentiation between island populations was low (FST = 0.6%), but statistically significant. Our results indicate that genetic drift had little effect on offspring generations 3 to 6 yr post-release and demonstrate the utility of using known founder events to help quantify genetic capture during translocations and to inform management decisions.

  9. Upper extremity proprioception in healthy aging and stroke populations, and the effects of therapist- and robot-based rehabilitation therapies on proprioceptive function

    Directory of Open Access Journals (Sweden)

    Charmayne Mary Lee Hughes

    2015-03-01

    Full Text Available The world’s population is aging, with the number of people ages 65 or older expected to surpass 1.5 billion people, or 16% of the global total. As people age, there are notable declines in proprioception due to changes in the central and peripheral nervous systems. Moreover, the risk of stroke increases with age, with approximately two-thirds of stroke-related hospitalizations occurring in people over the age of 65. In this literature review we first summarize behavioral studies investigating proprioceptive deficits in normally aging older adults and stroke patients, and discuss the differences in proprioceptive function between these populations. We then provide a state of the art review the literature regarding therapist- and robot-based rehabilitation of the upper extremity proprioceptive dysfunction in stroke populations and discuss avenues of future research.

  10. Upper extremity proprioception in healthy aging and stroke populations, and the effects of therapist- and robot-based rehabilitation therapies on proprioceptive function.

    Science.gov (United States)

    Hughes, Charmayne Mary Lee; Tommasino, Paolo; Budhota, Aamani; Campolo, Domenico

    2015-01-01

    The world's population is aging, with the number of people ages 65 or older expected to surpass 1.5 billion people, or 16% of the global total. As people age, there are notable declines in proprioception due to changes in the central and peripheral nervous systems. Moreover, the risk of stroke increases with age, with approximately two-thirds of stroke-related hospitalizations occurring in people over the age of 65. In this literature review, we first summarize behavioral studies investigating proprioceptive deficits in normally aging older adults and stroke patients, and discuss the differences in proprioceptive function between these populations. We then provide a state of the art review the literature regarding therapist- and robot-based rehabilitation of the upper extremity proprioceptive dysfunction in stroke populations and discuss avenues of future research.

  11. Upper Extremity Proprioception in Healthy Aging and Stroke Populations, and the Effects of Therapist- and Robot-Based Rehabilitation Therapies on Proprioceptive Function

    Science.gov (United States)

    Hughes, Charmayne Mary Lee; Tommasino, Paolo; Budhota, Aamani; Campolo, Domenico

    2015-01-01

    The world’s population is aging, with the number of people ages 65 or older expected to surpass 1.5 billion people, or 16% of the global total. As people age, there are notable declines in proprioception due to changes in the central and peripheral nervous systems. Moreover, the risk of stroke increases with age, with approximately two-thirds of stroke-related hospitalizations occurring in people over the age of 65. In this literature review, we first summarize behavioral studies investigating proprioceptive deficits in normally aging older adults and stroke patients, and discuss the differences in proprioceptive function between these populations. We then provide a state of the art review the literature regarding therapist- and robot-based rehabilitation of the upper extremity proprioceptive dysfunction in stroke populations and discuss avenues of future research. PMID:25784872

  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. Nonlocal bottleneck effect in two-dimensional turbulence

    CERN Document Server

    Biskamp, D; Schwarz, E

    1998-01-01

    The bottleneck pileup in the energy spectrum is investigated for several two-dimensional (2D) turbulence systems by numerical simulation using high-order diffusion terms to amplify the effect, which is weak for normal diffusion. For 2D magnetohydrodynamic (MHD) turbulence, 2D electron MHD (EMHD) turbulence and 2D thermal convection, which all exhibit direct energy cascades, a nonlocal behavior is found resulting in a logarithmic enhancement of the spectrum.

  14. 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.

  15. Bottleneck on Supply Chain of Organic Agricultural Products and Countermeasures

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xin-min

    2012-01-01

    Organic agriculture is one of successful models of low-carbon agriculture, and plays an important role in alleviating and adapting to climate change. However, the development of supply chain of organic agricultural products lags behind, which seriously restricts development of organic agricultural product market. In this paper, major models and bottleneck of supply chain of organic agricultural products are analyzed, and finally countermeasures are put forward.

  16. ON THE BOTTLENECK CAPACITY EXPANSION PROBLEMS ON NETWORKS

    Institute of Scientific and Technical Information of China (English)

    Yang Chao; Zhang Jianzhong

    2006-01-01

    This article considers a class of bottleneck capacity expansion problems. Such problems aim to enhance bottleneck capacity to a certain level with minimum cost. Given a network G(V, A,(-C)) consisting of a set of nodes V = {v1, v2,………, vn}, a set of arcs A(∪-){(vi, vj) | i = 1, 2,………, n; j = 1, 2,………, n} and a capacity vector (-C). The component (-C)ij of (-C) is the capacity of arc (vi, vj). Define the capacity of a subset A' of A as the minimum capacity of the arcs in A, the capacity of a family F of subsets of A is the maximum capacity of its members. There axe two types of expanding models. In the arc-expanding model, the unit cost to increase the capacity of arc (vi, vj) is wij. In the node-expanding model, it is assumed that the capacities of all arcs (vi, vi) which start at the same node vi should be increased by the same amount and that the unit cost to make such expansion is wi. This article considers three kinds of bottleneck capacity expansion problems (path,spanning arborescence and maximum flow) in both expanding models. For each kind of expansion problems, this article discusses the characteristics of the problems and presents several results on the complexity of the problems.

  17. A Macro Model for Traffic Flow with Consideration of Static Bottleneck

    Institute of Scientific and Technical Information of China (English)

    唐铁桥; 李鹏; 吴永洪; 黄海军

    2012-01-01

    In this paper, we develop a macro model for traffic flow with consideration of static bottleneck to explore the impacts of static bottleneck on traffic flow. The analytical and numerical results show that the proposed model can qualitatively describe the equilibrium flux, uniform flow and small perturbation under the action of a static bottleneck.

  18. Censusing natural Microgametophyte populations:variable spatial mosaics and extreme fine-graininess in winter-flowering Helleborus foetidus (Ranunculaceae)

    OpenAIRE

    Carlos M Herrera

    2002-01-01

    Little is known about patterns and correlates of variation in microgametophyte populations for naturally pollinated plants, yet this information is critical for evaluating the prevalence and potential evolutionary significance of gametophyte competition in the wild. This paper analyzes spatial and temporal variation in microgametophyte populations (= number of pollen tubes per style) for the winter-flowering, perennial herb Helleborus foetidus (Ranunculaceae), based on data from 29 populatio...

  19. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

    DEFF Research Database (Denmark)

    Abascal, Federico; Corvelo, André; Cruz, Fernando;

    2016-01-01

    BACKGROUND: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and...

  20. Local adaptations to frost in marginal and central populations of the dominant forest tree Fagus sylvatica L. as affected by temperature and extreme drought in common garden experiments.

    Science.gov (United States)

    Kreyling, Juergen; Buhk, Constanze; Backhaus, Sabrina; Hallinger, Martin; Huber, Gerhard; Huber, Lukas; Jentsch, Anke; Konnert, Monika; Thiel, Daniel; Wilmking, Martin; Beierkuhnlein, Carl

    2014-03-01

    Local adaptations to environmental conditions are of high ecological importance as they determine distribution ranges and likely affect species responses to climate change. Increased environmental stress (warming, extreme drought) due to climate change in combination with decreased genetic mixing due to isolation may lead to stronger local adaptations of geographically marginal than central populations. We experimentally observed local adaptations of three marginal and four central populations of Fagus sylvaticaL., the dominant native forest tree, to frost over winter and in spring (late frost). We determined frost hardiness of buds and roots by the relative electrolyte leakage in two common garden experiments. The experiment at the cold site included a continuous warming treatment; the experiment at the warm site included a preceding summer drought manipulation. In both experiments, we found evidence for local adaptation to frost, with stronger signs of local adaptation in marginal populations. Winter frost killed many of the potted individuals at the cold site, with higher survival in the warming treatment and in those populations originating from colder environments. However, we found no difference in winter frost tolerance of buds among populations, implying that bud survival was not the main cue for mortality. Bud late frost tolerance in April differed between populations at the warm site, mainly because of phenological differences in bud break. Increased spring frost tolerance of plants which had experienced drought stress in the preceding summer could also be explained by shifts in phenology. Stronger local adaptations to climate in geographically marginal than central populations imply the potential for adaptation to climate at range edges. In times of climate change, however, it needs to be tested whether locally adapted populations at range margins can successfully adapt further to changing conditions.

  1. Evidence for an invasive aphid "superclone": extremely low genetic diversity in Oleander aphid (Aphis nerii populations in the southern United States.

    Directory of Open Access Journals (Sweden)

    John Scott Harrison

    Full Text Available BACKGROUND: The importance of genetic diversity in successful biological invasions is unclear. In animals, but not necessarily plants, increased genetic diversity is generally associated with successful colonization and establishment of novel habitats. The Oleander aphid, Aphis nerii, though native to the Mediterranean region, is an invasive pest species throughout much of the world. Feeding primarily on Oleander (Nerium oleander and Milkweed (Asclepias spp. under natural conditions, these plants are unlikely to support aphid populations year round in the southern US. The objective of this study was to describe the genetic variation within and among US populations of A. nerii, during extinction/recolonization events, to better understand the population ecology of this invasive species. METHODOLOGY/PRINCIPAL FINDINGS: We used five microsatellite markers to assess genetic diversity over a two year period within and among three aphid populations separated by small (100 km and large (3,700 km geographic distances on two host plant species. Here we provide evidence for A. nerii "superclones". Genotypic variation was absent in all populations (i.e., each population consisted of a single multilocus genotype (MLG or "clone" and the genetic composition of only one population completely changed across years. There was no evidence of sexual reproduction or host races on different plant species. CONCLUSIONS/SIGNIFICANCE: Aphis nerii is a well established invasive species despite having extremely low genetic diversity. As this aphid appears to be obligatorily asexual, it may share more similarities with clonally reproducing invasive plants, than with other animals. Patterns of temporal and geographic genetic variation, viewed in the context of its population dynamics, have important implications for the management of invasive pests and the evolutionary biology of asexual species.

  2. [Adaptive reactions of lipid metabolism in native and alien female representatives of Tofalaria population living under extreme environmental conditions].

    Science.gov (United States)

    Kolesnikova, L I; Darenskaya, M A; Grebenkina, L A; Dolgikh, M I; Semenova, N V

    2014-01-01

    Peculiarities of the state of lipid metabolism and of processes of lipid peroxidation--the antioxidant protection have been considered in female representatives of the native and alien population of Tofalaria in the age aspects. The obtained data indicate specificity of changes of level of parameters lipid metabolism not only in response to duration of effect of climatic factors, but also depending on belonging to different ethnic groups. Thus, in girls of the natural population of Tofalaria there is noted activation of adaptational-compensatory processes as compared with the alien ones, which is expressed as a significant decrease of atherogenic blood fractions and the general activation of the system of antioxidant protection. However, with age, in both ethnic groups a change of character of reactions of lipid peroxidation and lipid metabolism is noted, which is more expressed in the alien population.

  3. Chronic pain in the pelvic area or lower extremities after rectal cancer treatment and its impact on quality of life: a population-based cross-sectional study.

    Science.gov (United States)

    Feddern, Marie-Louise; Jensen, Troels Staehelin; Laurberg, Søren

    2015-09-01

    The aim of this investigation was to examine the prevalence of and factors associated with chronic pain in the pelvic area or lower extremities after rectal cancer treatment and its impact on quality of life (QoL). This is a population-based cross-sectional study of chronic pain and QoL in patients treated for rectal cancer from 2001 to 2007. A modified version of the Brief Descriptive Danish Pain Questionnaire and the European Organization for Research and Treatment of Cancer QLQ-C30 questionnaire were mailed to 1713 Danish patients. Informative answers were obtained from 1369 patients (80%). A total of 426 patients (31%) reported chronic pain in the pelvic area or lower extremities, 173 (41%) of whom had daily pain. Pain in other parts of the body was associated with the presence of pain in the pelvic region (odds ratio [OR] 4.81 [3.63-6.38], P pain in female patients (OR 1.91 [1.51-2.43], P pelvic pain. Chronic pain in the pelvic region or lower extremities after rectal cancer treatment is a common but largely neglected problem that is associated with female gender, type of surgery, radio(chemo)therapy, and young age, all of which impact the patient's QoL.

  4. Genetic diversity of native Turkish cattle breeds: Mantel, AMOVA and bottleneck analysis

    Directory of Open Access Journals (Sweden)

    Yusuf Özşensoy

    2014-09-01

    Full Text Available This study was conducted to evaluate potential extinction risk of Turkish native cattle breeds using Mantel and AMOVA tests and Bottleneck analysis. A total of 271 DNA samples were isolated from Anatolian Black, Anatolian Grey, South Anatolian Red, Native Southern Anatolian Yellow, East Anatolian Red, and Zavot cattle. In this study, genotypes of 20 microsatellites were determined by capillary electrophoresis and fragment analysis. A total of 269 different alleles were detected. The maximum and minimum numbers of total alleles were observed in TGLA122 (n=26 and INRA005 (n=7 loci, respectively. The highest average observed and expected heterozygosity values were determined as 0.619–0.852 and 0.669–0.877, respectively. The average FIS value was 0.068. Results of AMOVA and Mantel tests illustrated statistically significant differences in populations (p<0.001 and correlation (p<0.01. Bottleneck analysis revealed a normal distribution of L–shaped curve indicating that there was no recent risk of extinction for these breeds.

  5. DUSTiNGS. III. Distribution of Intermediate-age and Old Stellar Populations in Disks and Outer Extremities of Dwarf Galaxies

    Science.gov (United States)

    McQuinn, Kristen B.; Boyer, Martha; DUSTiNGS Team

    2017-06-01

    As part of the DUST in Nearby Galaxies with Spitzer (DUSTiNGS) survey, we have traced the spatial distributions of intermediate-age and old stars in nine dwarf galaxies in the distant parts of the Local Group. We find intermediate age stars are well mixed with the older populations and extend to large radii, indicating that chemical enrichment from these dust-producing stars may occur in the outer regions of galaxies with some frequency. Theories of structure formation in dwarf galaxies must account for the lack of radial gradients in intermediate-age populations and the presence of these stars in the outer extremities of dwarfs. We also identify the tip of the red giant branch (TRGB) in Spitzer IRAC 3.6 μm photometry. Unlike the constant TRGB in the I band, at 3.6 μm, the TRGB magnitude varies by ˜0.7 mag and is not a metallicity independent distance indicator.

  6. Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level

    Science.gov (United States)

    2010-01-01

    Background Targeted re-sequencing of candidate genes in individuals at the extremes of a quantitative phenotype distribution is a method of choice to gain information on the contribution of rare variants to disease susceptibility. The endocannabinoid system mediates signaling in the brain and peripheral tissues involved in the regulation of energy balance, is highly active in obese patients, and represents a strong candidate pathway to examine for genetic association with body mass index (BMI). Results We sequenced two intervals (covering 188 kb) encoding the endocannabinoid metabolic enzymes fatty-acid amide hydrolase (FAAH) and monoglyceride lipase (MGLL) in 147 normal controls and 142 extremely obese cases. After applying quality filters, we called 1,393 high quality single nucleotide variants, 55% of which are rare, and 143 indels. Using single marker tests and collapsed marker tests, we identified four intervals associated with BMI: the FAAH promoter, the MGLL promoter, MGLL intron 2, and MGLL intron 3. Two of these intervals are composed of rare variants and the majority of the associated variants are located in promoter sequences or in predicted transcriptional enhancers, suggesting a regulatory role. The set of rare variants in the FAAH promoter associated with BMI is also associated with increased level of FAAH substrate anandamide, further implicating a functional role in obesity. Conclusions Our study, which is one of the first reports of a sequence-based association study using next-generation sequencing of candidate genes, provides insights into study design and analysis approaches and demonstrates the importance of examining regulatory elements rather than exclusively focusing on exon sequences. PMID:21118518

  7. Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level.

    Science.gov (United States)

    Harismendy, Olivier; Bansal, Vikas; Bhatia, Gaurav; Nakano, Masakazu; Scott, Michael; Wang, Xiaoyun; Dib, Colette; Turlotte, Edouard; Sipe, Jack C; Murray, Sarah S; Deleuze, Jean Francois; Bafna, Vineet; Topol, Eric J; Frazer, Kelly A

    2010-01-01

    Targeted re-sequencing of candidate genes in individuals at the extremes of a quantitative phenotype distribution is a method of choice to gain information on the contribution of rare variants to disease susceptibility. The endocannabinoid system mediates signaling in the brain and peripheral tissues involved in the regulation of energy balance, is highly active in obese patients, and represents a strong candidate pathway to examine for genetic association with body mass index (BMI). We sequenced two intervals (covering 188 kb) encoding the endocannabinoid metabolic enzymes fatty-acid amide hydrolase (FAAH) and monoglyceride lipase (MGLL) in 147 normal controls and 142 extremely obese cases. After applying quality filters, we called 1,393 high quality single nucleotide variants, 55% of which are rare, and 143 indels. Using single marker tests and collapsed marker tests, we identified four intervals associated with BMI: the FAAH promoter, the MGLL promoter, MGLL intron 2, and MGLL intron 3. Two of these intervals are composed of rare variants and the majority of the associated variants are located in promoter sequences or in predicted transcriptional enhancers, suggesting a regulatory role. The set of rare variants in the FAAH promoter associated with BMI is also associated with increased level of FAAH substrate anandamide, further implicating a functional role in obesity. Our study, which is one of the first reports of a sequence-based association study using next-generation sequencing of candidate genes, provides insights into study design and analysis approaches and demonstrates the importance of examining regulatory elements rather than exclusively focusing on exon sequences. © 2010 Harismendy et al.; licensee BioMed Central Ltd.

  8. 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.

  9. Extreme population differences in the human zinc transporter ZIP4 (SLC39A4) are explained by positive selection in Sub-Saharan Africa.

    Science.gov (United States)

    Engelken, Johannes; Carnero-Montoro, Elena; Pybus, Marc; Andrews, Glen K; Lalueza-Fox, Carles; Comas, David; Sekler, Israel; de la Rasilla, Marco; Rosas, Antonio; Stoneking, Mark; Valverde, Miguel A; Vicente, Rubén; Bosch, Elena

    2014-02-01

    Extreme differences in allele frequency between West Africans and Eurasians were observed for a leucine-to-valine substitution (Leu372Val) in the human intestinal zinc uptake transporter, ZIP4, yet no further evidence was found for a selective sweep around the ZIP4 gene (SLC39A4). By interrogating allele frequencies in more than 100 diverse human populations and resequencing Neanderthal DNA, we confirmed the ancestral state of this locus and found a strong geographical gradient for the derived allele (Val372), with near fixation in West Africa. In extensive coalescent simulations, we show that the extreme differences in allele frequency, yet absence of a classical sweep signature, can be explained by the effect of a local recombination hotspot, together with directional selection favoring the Val372 allele in Sub-Saharan Africans. The possible functional effect of the Leu372Val substitution, together with two pathological mutations at the same codon (Leu372Pro and Leu372Arg) that cause acrodermatitis enteropathica (a disease phenotype characterized by extreme zinc deficiency), was investigated by transient overexpression of human ZIP4 protein in HeLa cells. Both acrodermatitis mutations cause absence of the ZIP4 transporter cell surface expression and nearly absent zinc uptake, while the Val372 variant displayed significantly reduced surface protein expression, reduced basal levels of intracellular zinc, and reduced zinc uptake in comparison with the Leu372 variant. We speculate that reduced zinc uptake by the ZIP4-derived Val372 isoform may act by starving certain pathogens of zinc, and hence may have been advantageous in Sub-Saharan Africa. Moreover, these functional results may indicate differences in zinc homeostasis among modern human populations with possible relevance for disease risk.

  10. Extreme population differences in the human zinc transporter ZIP4 (SLC39A4 are explained by positive selection in Sub-Saharan Africa.

    Directory of Open Access Journals (Sweden)

    Johannes Engelken

    2014-02-01

    Full Text Available Extreme differences in allele frequency between West Africans and Eurasians were observed for a leucine-to-valine substitution (Leu372Val in the human intestinal zinc uptake transporter, ZIP4, yet no further evidence was found for a selective sweep around the ZIP4 gene (SLC39A4. By interrogating allele frequencies in more than 100 diverse human populations and resequencing Neanderthal DNA, we confirmed the ancestral state of this locus and found a strong geographical gradient for the derived allele (Val372, with near fixation in West Africa. In extensive coalescent simulations, we show that the extreme differences in allele frequency, yet absence of a classical sweep signature, can be explained by the effect of a local recombination hotspot, together with directional selection favoring the Val372 allele in Sub-Saharan Africans. The possible functional effect of the Leu372Val substitution, together with two pathological mutations at the same codon (Leu372Pro and Leu372Arg that cause acrodermatitis enteropathica (a disease phenotype characterized by extreme zinc deficiency, was investigated by transient overexpression of human ZIP4 protein in HeLa cells. Both acrodermatitis mutations cause absence of the ZIP4 transporter cell surface expression and nearly absent zinc uptake, while the Val372 variant displayed significantly reduced surface protein expression, reduced basal levels of intracellular zinc, and reduced zinc uptake in comparison with the Leu372 variant. We speculate that reduced zinc uptake by the ZIP4-derived Val372 isoform may act by starving certain pathogens of zinc, and hence may have been advantageous in Sub-Saharan Africa. Moreover, these functional results may indicate differences in zinc homeostasis among modern human populations with possible relevance for disease risk.

  11. Bottlenecks to vibrational energy flow in OCS: Structures and mechanisms

    CERN Document Server

    Paškauskas, R; Uzer, T

    2008-01-01

    Finding the causes for the nonstatistical vibrational energy relaxation in the planar carbonyl sulfide (OCS) molecule is a longstanding problem in chemical physics: Not only is the relaxation incomplete long past the predicted statistical relaxation time, but it also consists of a sequence of abrupt transitions between long-lived regions of localized energy modes. We report on the phase space bottlenecks responsible for this slow and uneven vibrational energy flow in this Hamiltonian system with three degrees of freedom. They belong to a particular class of two-dimensional invariant tori which are organized around elliptic periodic orbits. We relate the trapping and transition mechanisms with the linear stability of these structures.

  12. Congestion in a city with a central bottleneck

    DEFF Research Database (Denmark)

    Fosgerau, Mogens; Palma, André de

    2010-01-01

    , travelers sort according to their distance to the destination. We construct a welfare maximizing tolling regime, which eliminates congestion. All travelers located beyond a critical distance from the CBD gain from tolling, even when toll revenues are not redistributed, while nearby travelers lose. We......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 equilibrium...

  13. 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

  14. Clustered Bottlenecks in mRNA Translation and Protein Synthesis

    Science.gov (United States)

    Chou, Tom; Lakatos, Greg

    2004-11-01

    Using a model based on the totally asymmetric exclusion process, we investigate the effects of slow codons along messenger RNA. Ribosome density profiles near neighboring clusters of slow codons interact, enhancing suppression of ribosome throughput when such bottlenecks are closely spaced. Increasing the slow codon cluster size beyond ˜3 4 codons does not significantly reduce the ribosome current. Our results are verified by both extensive MonteCarlo simulations and numerical calculation, and provide a biologically motivated explanation for the experimentally observed clustering of low-usage codons.

  15. 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 equilibrium......, travelers sort according to their distance to the destination. We construct a welfare maximizing tolling regime, which eliminates congestion. All travelers located beyond a critical distance from the CBD gain from tolling, even when toll revenues are not redistributed, while nearby travelers lose. We...

  16. A cellular automaton model for a bridge traffic bottleneck

    Institute of Scientific and Technical Information of China (English)

    Shifa Xiao; Lingjiang Kong; Muren Liu

    2005-01-01

    A cellular automaton (CA) model is proposed in this paper to analyze a bridge traffic bottleneck. The simulation results with this model show that there are several phase transitions in the traffic average density, velocity and flow for each lane under a periodic boundary condition. An unstable phase in the traffic average density and velocity for the upstream and downstream lanes of the bridge is shown in a range of initial traffic densities. The critical points of the phase transitions and the phenomenon of the unstable phase found in the simulation are also explained with the mean-field theory.

  17. OPTIMISATION OF JOB SHOP SCHEDULING USING SHIFTING BOTTLENECK TECHNIQUE

    Directory of Open Access Journals (Sweden)

    Katuru Phani Raja Kumar

    2013-07-01

    Full Text Available In manufacturing system the problem of scheduling machines is a difficult task to reach the due date of the productivity. The Job Shop Scheduling have been solved by different algorithms and methods based on the sequence operation constraints and processing times for small size problems. The JSSP with m machines and n jobs is represented to determine an optimal solution by using the shortest processing time technique and Gantt chart is drawn to visually represent the total makespan. The shifting bottleneck method has been used to reduce the total flow time of the JSSP and arrive at an optimal solution.

  18. 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.

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

    Science.gov (United States)

    Chou, Tom; Wang, Yu

    2015-05-01

    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.

  20. GENETIC DIVERSITY, PARENTAGE VERIFICATION AND GENETIC BOTTLENECKS EVALUATION IN IRANIAN TURKMEN HORSE BREED.

    Science.gov (United States)

    Rahimi-Mianji, G; Nejati-Javaremi, A; Farhadi, A

    2015-09-01

    The present study was undertaken to genetically evaluate Turkmen horses for genetic diversity and to evaluate whether they have experienced any recent genetic bottlenecks. A total of 565 individuals from Turkmen horses were characterized for within breed diversity using 12 microsatellite markers. The estimated mean allelic diversity was (9.42 ± 1.78) per locus, with a total of 131 alleles in genotyped samples. A high level of genetic variability within this breed was observed in terms of high values of effective number of alleles (4.70 ± 1.36), observed heterozygosity (0.757 ± 0.19), expected Nei's heterozygosity (0.765 ± 0.13), and polymorphism information content (0.776 ± 0.17). The estimated cumulative probability of exclusion of wrongly named parents (PE) was high, with an average value of 99.96% that indicates the effectiveness of applied markers in resolving of parentage typing in Turkmen horse population. The paternity testing results did not show any misidentification and all selected animals were qualified based on genotypic information using a likelihood-based method. Low values of Wright's fixation index, F(IS) (0.012) indicated low levels of inbreeding. A significant heterozygote excess on the basis of different models, as revealed from Sign and Wilcoxon sign rank test suggested that Turkmen horse population is not in mutation-drift equilibrium. But, the Mode-shift indicator test showed a normal 'L' shaped distribution for allelic class and proportion of alleles, thus indicating the absence of bottleneck events in the recent past history of this breed. Further research work should be carrying out to clarify the cause of discrepancy observed forbottleneck results in this breed. In conclusion, despite unplanned breeding in Turkmen horse population, this breed still has sufficient genetic variability and could provide a valuable source of genetic material that may use for meeting the demands of future breeding programs.

  1. Extreme late chronotypes and social jetlag challenged by Antarctic conditions in a population of university students from Uruguay.

    Science.gov (United States)

    Tassino, Bettina; Horta, Stefany; Santana, Noelia; Levandovski, Rosa; Silva, Ana

    2016-01-01

    In humans, a person's chronotype depends on environmental cues and on individual characteristics, with late chronotypes prevailing in youth. Social jetlag (SJL), the misalignment between an individual׳s biological clock and social time, is higher in late chronotypes. Strong SJL is expected in Uruguayan university students with morning class schedules and very late entertainment activities. Sleep disorders have been reported in Antarctic inhabitants, that might be a response to the extreme environment or to the strictness of Antarctic life. We evaluated, for the first time in Uruguay, the chronotypes and SJL of 17 undergraduate students of the First Uruguayan Summer School on Antarctic Research, using Munich Chronotype Questionnaire (MCTQ) and sleep logs (SL) recorded during 3 phases: pre-Antarctic, Antarctic, and post-Antarctic. The midsleep point of free days corrected for sleep debt on work days (MSFsc,) was used as proxy of individuals' chronotype, whose values (around 6 a.m.) are the latest ever reported. We found a SJL of around 2 h in average, which correlated positively with MSFsc, confirming that late chronotypes generate a higher sleep debt during weekdays. Midsleep point and sleep duration significantly decreased between pre-Antarctic and Antarctic phases, and sleep duration rebounded to significant higher values in the post-Antarctic phase. Waking time, but not sleep onset time, significantly varied among phases. This evidence suggests that sleep schedules more likely depended on the social agenda than on the environmental light-dark shifts. High motivation of students towards Antarctic activities likely induced a subjective perception of welfare non-dependent on sleep duration.

  2. Extreme late chronotypes and social jetlag challenged by Antarctic conditions in a population of university students from Uruguay

    Science.gov (United States)

    Tassino, Bettina; Horta, Stefany; Santana, Noelia; Levandovski, Rosa; Silva, Ana

    2016-01-01

    In humans, a person’s chronotype depends on environmental cues and on individual characteristics, with late chronotypes prevailing in youth. Social jetlag (SJL), the misalignment between an individual׳s biological clock and social time, is higher in late chronotypes. Strong SJL is expected in Uruguayan university students with morning class schedules and very late entertainment activities. Sleep disorders have been reported in Antarctic inhabitants, that might be a response to the extreme environment or to the strictness of Antarctic life. We evaluated, for the first time in Uruguay, the chronotypes and SJL of 17 undergraduate students of the First Uruguayan Summer School on Antarctic Research, using Munich Chronotype Questionnaire (MCTQ) and sleep logs (SL) recorded during 3 phases: pre-Antarctic, Antarctic, and post-Antarctic. The midsleep point of free days corrected for sleep debt on work days (MSFsc,) was used as proxy of individuals’ chronotype, whose values (around 6 a.m.) are the latest ever reported. We found a SJL of around 2 h in average, which correlated positively with MSFsc, confirming that late chronotypes generate a higher sleep debt during weekdays. Midsleep point and sleep duration significantly decreased between pre-Antarctic and Antarctic phases, and sleep duration rebounded to significant higher values in the post-Antarctic phase. Waking time, but not sleep onset time, significantly varied among phases. This evidence suggests that sleep schedules more likely depended on the social agenda than on the environmental light–dark shifts. High motivation of students towards Antarctic activities likely induced a subjective perception of welfare non-dependent on sleep duration. PMID:27226819

  3. A bottleneck model of set-specific capture.

    Science.gov (United States)

    Moore, Katherine Sledge; Weissman, Daniel H

    2014-01-01

    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.

  4. The Effects of Juvenile Competitive Bottleneck on Dynamic Behavior%幼年竞争瓶颈对动力学行为的影响

    Institute of Scientific and Technical Information of China (English)

    唐光耀

    2011-01-01

    The effect of juvenile competitive bottlenecks on population dynamics is investigated by formulating food web models with a nonlinear maturation rate.The food web system consists of a resource (R),an intermediate consumer (N) and a predator (P).Our results show,with weak bottlenecks,that a juvenile bottleneck in the predator's life history has a larger impact than a bottleneck in the consumer.In the food web model with bottleneck for the predator,there are two possible internal steady states,and the system can exhibit consumer-predator equilibrium and consumer equilibrium as two alternative stable states,as well as the consumer equilibrium and predator equilibrium as two alternative stable states.No bistable phenomenon induced by bottleneck can be detected,and nothing new happens in system with consumer bottlenecks.Further,we show that a bottleneck can change the net effect of the intermediate consumer on predator from facilitation to inhibition or from inhibition to facilitation,which case occurs depends on both the choice of bottleneck and the initial states of systems.%通过建立具有非线性成熟率的食物网模型研究了幼年竞争瓶颈对种群动力学行为的影响,结论显示当竞争瓶颈比较弱的时,捕食者生活史中的幼年瓶颈对系统的影响要大于成年.模型存在两种可能的共存态或双稳定性,即消费者-捕食者和消费者平衡态共存,但是瓶颈不能诱导系统的双稳定性.进一步研究说明了选择不同的瓶颈或初始条件,瓶颈能够改变次级消费者对捕食者的净影响.

  5. 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

  6. The influence of extreme winds on coastal oceanography and its implications for coral population connectivity in the southern Arabian Gulf.

    Science.gov (United States)

    Cavalcante, Geórgenes H; Feary, David A; Burt, John A

    2016-04-30

    Using long-term oceanographic surveys and a 3-D hydrodynamic model we show that localized peak winds (known as shamals) cause fluctuation in water current speed and direction, and substantial oscillations in sea-bottom salinity and temperature in the southern Persian/Arabian Gulf. Results also demonstrate that short-term shamal winds have substantial impacts on oceanographic processes along the southern Persian/Arabian Gulf coastline, resulting in formation of large-scale (52 km diameter) eddies extending from the coast of the United Arab Emirates (UAE) to areas near the off-shore islands of Iran. Such eddies likely play an important role in transporting larvae from well-developed reefs of the off-shore islands to the degraded reef systems of the southern Persian/Arabian Gulf, potentially maintaining genetic and ecological connectivity of these geographically distant populations and enabling enhanced recovery of degraded coral communities in the UAE.

  7. Enzymatic regulation of glycogenolysis in a subarctic population of the wood frog: implications for extreme freeze tolerance.

    Directory of Open Access Journals (Sweden)

    M Clara F do Amaral

    Full Text Available The wood frog, Rana sylvatica, from Interior Alaska survives freezing at -16°C, a temperature 10-13°C below that tolerated by its southern conspecifics. We investigated the hepatic freezing response in this northern phenotype to determine if its profound freeze tolerance is associated with an enhanced glucosic cryoprotectant system. Alaskan frogs had a larger liver glycogen reserve that was mobilized faster during early freezing as compared to conspecifics from a cool-temperate region (southern Ohio, USA. In Alaskan frogs the rapid glucose production in the first hours of freezing was associated with a 7-fold increase in glycogen phosphorylase activity above unfrozen frog levels, and the activity of this enzyme was higher than that of frozen Ohioan frogs. Freezing of Ohioan frogs induced a more modest (4-fold increase in glycogen phosphorylase activity above unfrozen frog values. Relative to the Ohioan frogs, Alaskan frogs maintained a higher total protein kinase A activity throughout an experimental freezing/thawing time course, and this may have potentiated glycogenolysis during early freezing. We found populational variation in the activity and protein level of protein kinase A which suggested that the Alaskan population had a more efficient form of this enzyme. Alaskan frogs modulated their glycogenolytic response by decreasing the activity of glycogen phosphorylase after cryoprotectant mobilization was well under way, thereby conserving their hepatic glycogen reserve. Ohioan frogs, however, sustained high glycogen phosphorylase activity until early thawing and consumed nearly all their liver glycogen. These unique hepatic responses of Alaskan R. sylvatica likely contribute to this phenotype's exceptional freeze tolerance, which is necessary for their survival in a subarctic climate.

  8. Enzymatic regulation of glycogenolysis in a subarctic population of the wood frog: implications for extreme freeze tolerance.

    Science.gov (United States)

    do Amaral, M Clara F; Lee, Richard E; Costanzo, Jon P

    2013-01-01

    The wood frog, Rana sylvatica, from Interior Alaska survives freezing at -16°C, a temperature 10-13°C below that tolerated by its southern conspecifics. We investigated the hepatic freezing response in this northern phenotype to determine if its profound freeze tolerance is associated with an enhanced glucosic cryoprotectant system. Alaskan frogs had a larger liver glycogen reserve that was mobilized faster during early freezing as compared to conspecifics from a cool-temperate region (southern Ohio, USA). In Alaskan frogs the rapid glucose production in the first hours of freezing was associated with a 7-fold increase in glycogen phosphorylase activity above unfrozen frog levels, and the activity of this enzyme was higher than that of frozen Ohioan frogs. Freezing of Ohioan frogs induced a more modest (4-fold) increase in glycogen phosphorylase activity above unfrozen frog values. Relative to the Ohioan frogs, Alaskan frogs maintained a higher total protein kinase A activity throughout an experimental freezing/thawing time course, and this may have potentiated glycogenolysis during early freezing. We found populational variation in the activity and protein level of protein kinase A which suggested that the Alaskan population had a more efficient form of this enzyme. Alaskan frogs modulated their glycogenolytic response by decreasing the activity of glycogen phosphorylase after cryoprotectant mobilization was well under way, thereby conserving their hepatic glycogen reserve. Ohioan frogs, however, sustained high glycogen phosphorylase activity until early thawing and consumed nearly all their liver glycogen. These unique hepatic responses of Alaskan R. sylvatica likely contribute to this phenotype's exceptional freeze tolerance, which is necessary for their survival in a subarctic climate.

  9. Extreme population inversion in the fragments formed by UV photoinduced S-H bond fission in 2-thiophenethiol.

    Science.gov (United States)

    Ingle, Rebecca A; Karsili, Tolga N V; Dennis, Gregg J; Staniforth, Michael; Stavros, Vasilios G; Ashfold, Michael N R

    2016-04-28

    H atom loss following near ultraviolet photoexcitation of gas phase 2-thiophenethiol molecules has been studied experimentally, by photofragment translational spectroscopy (PTS) methods, and computationally, by ab initio electronic structure calculations. The long wavelength (277.5 ≥ λ(phot) ≥ 240 nm) PTS data are consistent with S-H bond fission after population of the first (1)πσ* state. The partner thiophenethiyl (R) radicals are formed predominantly in their first excited Ã(2)A' state, but assignment of a weak signal attributable to H + R(X˜(2)A'') products allows determination of the S-H bond strength, D0 = 27,800 ± 100 cm(-1) and the Ã-X˜ state splitting in the thiophenethiyl radical (ΔE = 3580 ± 100 cm(-1)). The deduced population inversion between the à and X˜ states of the radical reflects the non-planar ground state geometry (wherein the S-H bond is directed near orthogonal to the ring plane) which, post-photoexcitation, is unable to planarise sufficiently prior to bond fission. This dictates that the dissociating molecules follow the adiabatic fragmentation pathway to electronically excited radical products. π* ← π absorption dominates at shorter excitation wavelengths. Coupling to the same (1)πσ* potential energy surface (PES) remains the dominant dissociation route, but a minor yield of H atoms attributable to a rival fragmentation pathway is identified. These products are deduced to arise via unimolecular decay following internal conversion to the ground (S0) state PES via a conical intersection accessed by intra-ring C-S bond extension. The measured translational energy disposal shows a more striking change once λ(phot) ≤ 220 nm. Once again, however, the dominant decay pathway is deduced to be S-H bond fission following coupling to the (1)πσ* PES but, in this case, many of the evolving molecules are deduced to have sufficiently near-planar geometries to allow passage through the conical intersection at extended S-H bond

  10. 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.

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

    Science.gov (United States)

    Tully, Damien C.; Ogilvie, Colin B.; Batorsky, Rebecca E.; Bean, David J.; Power, Karen A.; Ghebremichael, Musie; Bedard, Hunter E.; Gladden, Adrianne D.; Seese, Aaron M.; Amero, Molly A.; Lane, Kimberly; McGrath, Graham; Bazner, Suzane B.; Tinsley, Jake; Lennon, Niall J.; Henn, Matthew R.; Brumme, Zabrina L.; Norris, Philip J.; Rosenberg, Eric S.; Mayer, Kenneth H.; Jessen, Heiko; Kosakovsky Pond, Sergei L.; Walker, Bruce D.; Altfeld, Marcus; Carlson, Jonathan M.; Allen, Todd M.

    2016-01-01

    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. PMID:27163788

  12. 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.

  13. Distinct variants of extreme psychopathic individuals in society at large: evidence from a population-based sample.

    Science.gov (United States)

    Drislane, Laura E; Patrick, Christopher J; Sourander, Andre; Sillanmäki, Lauri; Aggen, Steven H; Elonheimo, Henrik; Parkkola, Kai; Multimäki, Petteri; Kendler, Kenneth S

    2014-04-01

    This study used model-based cluster analysis to identify subtypes of men who scored high in overall psychopathy (i.e., ≥ 95th percentile on the Triarchic Psychopathy Measure; n = 193) from a larger sample evaluated for service in the Finnish military (N = 4043). Cluster variates consisted of scores on distinct facets of psychopathy together with a measure of negative affectivity. The best-fitting model specified 2 clusters, representing "primary" (n = 110) and "secondary" psychopathy (n = 83) groups. Compared to a low-psychopathy comparison group (n = 1878), both psychopathy subgroups showed markedly elevated levels of externalizing symptoms and criminal behavior. Secondary psychopathic participants also reported high levels of internalizing problems including anxiousness, depression, and somatization, and scored higher on the disinhibition facet of psychopathy relative to the primary group. By contrast, primary psychopathic individuals reported fewer internalizing problems than either the secondary psychopathy or comparison groups and scored higher on the boldness facet of psychopathy. Primary psychopathic participants also had higher rates of violent crimes than the secondary psychopaths. Implications for conceptualizing and studying psychopathy in nonforensic populations are discussed.

  14. Surviving in isolation: genetic variation, bottlenecks and reproductive strategies in the Canarian endemic Limonium macrophyllum (Plumbaginaceae).

    Science.gov (United States)

    Jiménez, Ares; Weigelt, Barbara; Santos-Guerra, Arnoldo; Caujapé-Castells, Juli; Fernández-Palacios, José María; Conti, Elena

    2017-02-01

    Oceanic archipelagos are typically rich in endemic taxa, because they offer ideal conditions for diversification and speciation in isolation. One of the most remarkable evolutionary radiations on the Canary Islands comprises the 16 species included in Limonium subsection Nobiles, all of which are subject to diverse threats, and legally protected. Since many of them are single-island endemics limited to one or a few populations, there exists a risk that a loss of genetic variation might limit their long-term survival. In this study, we used eight newly developed microsatellite markers to characterize the levels of genetic variation and inbreeding in L. macrophyllum, a species endemic to the North-east of Tenerife that belongs to Limonium subsection Nobiles. We detected generally low levels of genetic variation over all populations (H T = 0.363), and substantial differentiation among populations (F ST = 0.188; R ST = 0.186) coupled with a negligible degree of inbreeding (F = 0.042). Obligate outcrossing may have maintained L. macrophyllum relatively unaffected by inbreeding despite the species' limited dispersal ability and the genetic bottlenecks likely caused by a prolonged history of grazing. Although several factors still constitute a risk for the conservation of L. macrophyllum, the lack of inbreeding and the recent positive demographic trends observed in the populations of this species are factors that favour its future persistence.

  15. 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......, at equilibrium, travelers sort according to their distance to the destination; the queue is always unimodal regardless of the spatial distribution of trip origins. We construct a welfare maximizing tolling regime, which eliminates congestion. All travelers located beyond a critical distance from the CBD gain...... from tolling, even when toll revenues are not redistributed, while nearby travelers lose. We discuss our results in the context of acceptability of tolling policies....

  16. On Bottleneck Product Rate Variation Problem with Batching

    Directory of Open Access Journals (Sweden)

    Shree Khadka

    2013-07-01

    Full Text Available The product rate variation problem minimizes the variation in the rate at which different models of a common base product are produced on the assembly lines with the assumption of negligible switch-over cost and unit processing time for each copy of each model. The assumption of significant setup and arbitrary processing times forces the problem to be a two phase problem. The first phase determines the size and the number of batches and the second one sequences the batches of models. In this paper, the bottleneck case i.e. the min-max case of the problem with a generalized objective function is formulated. A Pareto optimal solution is proposed and a relation between optimal sequences for the problem with different objective functions is investigated.

  17. Queuing model of a traffic bottleneck with bimodal arrival rate

    Science.gov (United States)

    Woelki, Marko

    2016-06-01

    This paper revisits the problem of tuning the density in a traffic bottleneck by reduction of the arrival rate when the queue length exceeds a certain threshold, studied recently for variants of totally asymmetric simple exclusion process (TASEP) and Burgers equation. In the present approach, a simple finite queuing system is considered and its contrasting “phase diagram” is derived. One can observe one jammed region, one low-density region and one region where the queue length is equilibrated around the threshold. Despite the simplicity of the model the physics is in accordance with the previous approach: The density is tuned at the threshold if the exit rate lies in between the two arrival rates.

  18. Traffic Flow States in a Freeway with Bottleneck

    Institute of Scientific and Technical Information of China (English)

    PENG Zi-Hui; SUN Gang; ZHU Jing-Yi

    2009-01-01

    The system of mixture of single lane and double lane is studied by a cellular automata model, which is developed by us based on the Nagel and Schreckenberg's models. We justify that the model can reach a stable states quickly. The density distributions of the stable state is presented for several cases, which illustrate the manner of the congestion. The relationship between the outflow rate and the total number of vehicles and that between the outflow rate and the density just before the bottleneck are both given. Comparing with the relationship that occurring in the granular flow, we conclude that the transition from the free traffic flow to the congested traffic flow can also be attributed to the abrupt variation through unstable flow state, which can naturally explain the discontinuities and the complex time variation behavior observed in the traffic flow experiments.

  19. 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.

  20. MHC-DRB3 variation in a free-living population of the European bison, Bison bonasus.

    Science.gov (United States)

    Radwan, J; Kawałko, A; Wójcik, J M; Babik, W

    2007-02-01

    MHC genes play a crucial role in pathogen recognition and are the most polymorphic genes in vertebrates. Loss of variation in these genes in bottlenecked species is thought to put their survival at risk. We examined variation at the MHC II DRB3 locus in the European bison, Bison bonasus, a species that has undergone an extreme bottleneck: the current population originated from only 12 founders. We also tested for the association of DRB3 genes with the incidence of posthitis, a disease affecting the reproductive organs of bulls and posing a new threat to the survival of the species. We found very limited MHC diversity, with only four alleles segregating in a sample of 172 individuals from a free-ranging Białowieza population. The alleles were highly divergent and revealed the hallmark of positive selection acting on them in the past, that is, a significant excess of nonsynonymous substitutions. This excess was concentrated in putative antigen-binding sites, suggesting that selection was driven by pathogens. However, we did not observe departures from Hardy-Weinberg equilibrium, an indicator of strong ongoing selection. Neither have we found a significant association between DRB3 alleles or genotypes and susceptibility to posthitis. Alleles conferring resistance to males may have been lost during the extreme bottleneck the species had undergone.

  1. DUSTiNGS III: Distribution of Intermediate-Age and Old Stellar Populations in Disks and Outer Extremities of Dwarf Galaxies

    CERN Document Server

    McQuinn, Kristen B W; Mitchell, Mallory B; Skillman, Evan D; Gehrz, R D; Groenewegen, Martin A T; McDonald, Iain; Sloan, G C; van Loon, Jacco Th; Whitelock, Patricia A; Zijlstra, Albert A

    2016-01-01

    We have traced the spatial distributions of intermediate-age and old stars in nine dwarf galaxies in the distant parts of the Local Group, using multi-epoch 3.6 and 4.5 micron data from the DUST in Nearby Galaxies with Spitzer (DUSTiNGS) survey. Using complementary optical imaging from the Hubble Space Telescope, we identify the tip of the red giant branch (TRGB) in the 3.6 micron photometry, separating thermally-pulsating asymptotic giant branch (TP-AGB) stars from the larger red giant branch (RGB) populations. Unlike the constant TRGB in the I-band, at 3.6 micron the TRGB magnitude varies by ~0.7 mag, making it unreliable as a distance indicator. The intermediate-age and old stars are well mixed in two-thirds of the sample with no evidence of a gradient in the ratio of the intermediate-age to old stellar populations outside the central ~1-2'. Variable AGB stars are detected in the outer extremities of the galaxies, indicating that chemical enrichment from these dust-producing stars may occur in the outer re...

  2. Extreme Heat

    Science.gov (United States)

    ... Landslides & Debris Flow Nuclear Blast Nuclear Power Plants Power Outages Pandemic Radiological Dispersion Device Severe Weather Snowstorms & Extreme ... Landslides & Debris Flow Nuclear Blast Nuclear Power Plants Power Outages Pandemic Radiological Dispersion Device Severe Weather Snowstorms & Extreme ...

  3. Mandelbrot's Extremism

    NARCIS (Netherlands)

    Beirlant, J.; Schoutens, W.; Segers, J.J.J.

    2004-01-01

    In the sixties Mandelbrot already showed that extreme price swings are more likely than some of us think or incorporate in our models.A modern toolbox for analyzing such rare events can be found in the field of extreme value theory.At the core of extreme value theory lies the modelling of maxima

  4. Discovery of a population of bulgeless galaxies with extremely red MID-IR colors: Obscured AGN activity in the low-mass regime?

    Energy Technology Data Exchange (ETDEWEB)

    Satyapal, S.; Secrest, N. J.; McAlpine, W.; Rosenberg, J. L. [School of Physics, Astronomy, and Computational Sciences, George Mason University, MS 3F3, 4400 University Drive, Fairfax, VA 22030 (United States); Ellison, S. L. [Department of Physics and Astronomy, University of Victoria, Victoria, BC V8P 1A1 (Canada); Fischer, J., E-mail: satyapal@physics.gmu.edu [Naval Research Laboratory, Remote Sensing Division, 4555 Overlook Avenue SW, Washington, DC 20375 (United States)

    2014-04-01

    In contrast to massive, bulge hosting galaxies, very few supermassive black holes (SMBHs) are known in either low-mass or bulgeless galaxies. Such a population could provide clues to the origins of SMBHs and to secular pathways for their growth. Using the all-sky Wide-field Infrared Survey Explorer (WISE ) survey, and bulge-to-disk decompositions from the Sloan Digital Sky Survey (SDSS) Data Release 7, we report the discovery of a population of local (z < 0.3) bulgeless disk galaxies with extremely red mid-infrared colors which are highly suggestive of a dominant active galactic nucleus (AGN), despite having no optical AGN signatures in their SDSS spectra. Using various mid-infrared selection criteria from the literature, there are between 30 and over 300 bulgeless galaxies with possible AGNs. Other known scenarios that can heat the dust to high temperatures do not appear to explain the observed colors of this sample. If these galaxies are confirmed to host AGNs, this study will provide a breakthrough in characterizing the properties of SMBHs in the low bulge mass regime and in understanding their relation with their host galaxies. Mid-infrared selection identifies AGNs that dominate their host galaxy's emission and therefore reveal a different AGN population than that uncovered by optical studies. We find that the fraction of all galaxies identified as candidate AGNs by WISE is highest at lower stellar masses and drops dramatically in higher mass galaxies, in striking contrast to the findings from optical studies.

  5. Widening Synthesis Bottlenecks: Realization of Ultrafast and Continuous-Flow Synthesis of High-Silica Zeolite SSZ-13 for NOx Removal.

    Science.gov (United States)

    Liu, Zhendong; Wakihara, Toru; Oshima, Kazunori; Nishioka, Daisuke; Hotta, Yuusuke; Elangovan, Shanmugam P; Yanaba, Yutaka; Yoshikawa, Takeshi; Chaikittisilp, Watcharop; Matsuo, Takeshi; Takewaki, Takahiko; Okubo, Tatsuya

    2015-05-04

    Characteristics of zeolite formation, such as being kinetically slow and thermodynamically metastable, are the main bottlenecks that obstruct a fast zeolite synthesis. We present an ultrafast route, the first of its kind, to synthesize high-silica zeolite SSZ-13 in 10 min, instead of the several days usually required. Fast heating in a tubular reactor helps avoid thermal lag, and the synergistic effect of addition of a SSZ-13 seed, choice of the proper aluminum source, and employment of high temperature prompted the crystallization. Thanks to the ultra-short period of synthesis, we established a continuous-flow preparation of SSZ-13. The fast-synthesized SSZ-13, after copper-ion exchange, exhibits outstanding performance in the ammonia selective catalytic reduction (NH3 -SCR) of nitrogen oxides (NOx ), showing it to be a superior catalyst for NOx removal. Our results indicate that the formation of high-silica zeolites can be extremely fast if bottlenecks are effectively widened.

  6. Breaking the carrier injection bottleneck of phosphor-free nanowire white light-emitting diodes.

    Science.gov (United States)

    Nguyen, Hieu Pham Trung; Zhang, Shaofei; Connie, Ashfiqua T; Kibria, Md Golam; Wang, Qi; Shih, Ishiang; Mi, Zetian

    2013-01-01

    We have examined the carrier injection process of axial nanowire light-emitting diode (LED) structures and identified that poor carrier injection efficiency, due to the large surface recombination, is the primary cause for the extremely low output power of phosphor-free nanowire white LEDs. We have further developed InGaN/GaN/AlGaN dot-in-a-wire core-shell white LEDs on Si substrate, which can break the carrier injection efficiency bottleneck, leading to a massive enhancement in the output power. At room temperature, the devices can exhibit an output power of ~1.5 mW, which is more than 2 orders of magnitude stronger than nanowire LEDs without shell coverage. Additionally, such phosphor-free nanowire white LEDs can deliver an unprecedentedly high color rendering index of ~92-98 in both the warm and cool white regions, with the color rendering capability approaching that of an ideal light source, i.e. a blackbody.

  7. Bottleneck Analysis of the Minimum Coat Problem for the Generalized Network Based on Augmented Forest Structure

    Institute of Scientific and Technical Information of China (English)

    江永亨; 王军; 等

    2003-01-01

    The bottleneck analysis of the minimum coat problem for the generalized netwok(MCPGN) is discussed.The analysis is based on the network simplex algorithm,which gains negative cost graphs by constructing augmented forest structure,then augments flows on the negative cost graphs until the optimal revolution is gained Bottleneck structure is presented after analyzing the augmented forest structure.The negative cost augmented graphs are constructed with the bottleneck structure.The arcs that block the negative cost augmented graph are the elements of the bottleneck.The bottleneck analysis for the generalized circulation problem,the minimum circulation problem and the circulation problem are discussed respectively as the basal problems,then that for MCPGN is achieved.An example is presented at the end.

  8. 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.

  9. Metabolic rates in five animal populations after prolonged exposure to weak extremely low frequency electromagnetic fields in nature. [Lambricus terrestris, L. rubellus, Arion sp. , Oniscus asellus, Plettrodon cinereus

    Energy Technology Data Exchange (ETDEWEB)

    Greenberg, B.; Ash, N.

    1976-08-01

    Five species of soil-dwelling animals were collected under or some distance from the Navy's Project Sanguine extremely low frequency experimental antenna in September 1974 and in summer 1975, and their oxygen consumption and respiratory quotient (RQ) were tested and compared. The species were: earthworms, Lumbricus terrestris L. and Lumbricus rubellus Hoffmeister; slug, Arion sp.; wood louse, Oniscus asellus L.; and redbacked salamander, Plethodon cinereus cinereus (Green). Controls were collected on the same or next day, 6 to 13 miles from the nearest antenna. Test and control animals were tested simultaneously. In September 1974 there were no significant differences in O/sub 2/ consumption and RQ, except for a marginal difference (0.05 greater than P greater than 0.025) in O/sub 2/ consumption of L. rubellus; in 1975, there were no significant differences. Comparisons of metabolic rates between exposed and control groups in fall 1974 and between fall and summer (1973 and 1975) populations show no seasonally linked change in sensitivity to the electromagnetic fields. Controls showed an autumnal increase in metabolic rate of wood lice and salamanders. Oxygen consumption of wood lice is significantly (P less than 0.05) affected by method of shipment but there is no evidence that exposed and control animals react differently from each other to shipment by air or by car. Short-term (1 week) exposure of earthworms to the electromagnetic fields did not alter metabolic rate; however, confinement in nylon bags and translocation did, thereby limiting meaningful conclusions. No abnormalities in behavior, habitat selection, or external features and pigmentation have been observed in any of the exposed populations during 4 yr of collecting and observation.

  10. New approaches for itaconic acid production: bottlenecks and possible remedies.

    Science.gov (United States)

    Bafana, Richa; Pandey, R A

    2017-04-20

    Currently, growing attention is being devoted to the conversion of biomass into value-added products, such as itaconic acid (IA), which is considered as the cleanest alternative to petroleum-based acrylic acid. IA is an unsaturated dicarboxylic acid that is used as a building block chemical for the production of several value-added products such as poly-itaconic acid. IA and its derivatives have a wide range of potential applications in textile, paint, pharmaceutical and chemical industries. Presently, industries are producing IA on the large scale by fermentation from glucose. However, due to the primary utility of glucose as a food, it cannot meet the global demand for IA production in an economical way. The main challenge, so far, has been the production technology, which does not support cost-effective and competitive production of IA. This review discusses the various bottlenecks faced during each step of IA production, along with possible remedies to deal with these problems. Furthermore, it reviews the recent progress in fermentative IA production and sheds light on different microorganisms used, potential substrates and fermentation conditions. The review also covers market potential for IA, which indicates that IA can be produced cost-effectively from sustainable substrates, and it has the potential to replace petrochemicals in the near future.

  11. 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.

  12. 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.

  13. 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

    2014-12-04

    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.

  14. 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)

  15. Photonic ADC: overcoming the bottleneck of electronic jitter.

    Science.gov (United States)

    Khilo, Anatol; Spector, Steven J; Grein, Matthew E; Nejadmalayeri, Amir H; Holzwarth, Charles W; Sander, Michelle Y; Dahlem, Marcus S; Peng, Michael Y; Geis, Michael W; DiLello, Nicole A; Yoon, Jung U; Motamedi, Ali; Orcutt, Jason S; Wang, Jade P; Sorace-Agaskar, Cheryl M; Popović, Miloš A; Sun, Jie; Zhou, Gui-Rong; Byun, Hyunil; Chen, Jian; Hoyt, Judy L; Smith, Henry I; Ram, Rajeev J; Perrott, Michael; Lyszczarz, Theodore M; Ippen, Erich P; Kärtner, Franz X

    2012-02-13

    Accurate conversion of wideband multi-GHz analog signals into the digital domain has long been a target of analog-to-digital converter (ADC) developers, driven by applications in radar systems, software radio, medical imaging, and communication systems. Aperture jitter has been a major bottleneck on the way towards higher speeds and better accuracy. Photonic ADCs, which perform sampling using ultra-stable optical pulse trains generated by mode-locked lasers, have been investigated for many years as a promising approach to overcome the jitter problem and bring ADC performance to new levels. This work demonstrates that the photonic approach can deliver on its promise by digitizing a 41 GHz signal with 7.0 effective bits using a photonic ADC built from discrete components. This accuracy corresponds to a timing jitter of 15 fs - a 4-5 times improvement over the performance of the best electronic ADCs which exist today. On the way towards an integrated photonic ADC, a silicon photonic chip with core photonic components was fabricated and used to digitize a 10 GHz signal with 3.5 effective bits. In these experiments, two wavelength channels were implemented, providing the overall sampling rate of 2.1 GSa/s. To show that photonic ADCs with larger channel counts are possible, a dual 20-channel silicon filter bank has been demonstrated.

  16. 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.

  17. Resistance of virus to extinction on bottleneck passages: Study of a decaying and fluctuating pattern of fitness loss

    Science.gov (United States)

    Lázaro, Ester; Escarmís, Cristina; Pérez-Mercader, Juan; Manrubia, Susanna C.; Domingo, Esteban

    2003-01-01

    RNA viruses display high mutation rates and their populations replicate as dynamic and complex mutant distributions, termed viral quasispecies. Repeated genetic bottlenecks, which experimentally are carried out through serial plaque-to-plaque transfers of the virus, lead to fitness decrease (measured here as diminished capacity to produce infectious progeny). Here we report an analysis of fitness evolution of several low fitness foot-and-mouth disease virus clones subjected to 50 plaque-to-plaque transfers. Unexpectedly, fitness decrease, rather than being continuous and monotonic, displayed a fluctuating pattern, which was influenced by both the virus and the state of the host cell as shown by effects of recent cell passage history. The amplitude of the fluctuations increased as fitness decreased, resulting in a remarkable resistance of virus to extinction. Whereas the frequency distribution of fitness in control (independent) experiments follows a log-normal distribution, the probability of fitness values in the evolving bottlenecked populations fitted a Weibull distribution. We suggest that multiple functions of viral genomic RNA and its encoded proteins, subjected to high mutational pressure, interact with cellular components to produce this nontrivial, fluctuating pattern. PMID:12960384

  18. Resistance of virus to extinction on bottleneck passages: study of a decaying and fluctuating pattern of fitness loss

    Science.gov (United States)

    Lazaro, Ester; Escarmis, Cristina; Perez-Mercader, Juan; Manrubia, Susanna C.; Domingo, Esteban

    2003-01-01

    RNA viruses display high mutation rates and their populations replicate as dynamic and complex mutant distributions, termed viral quasispecies. Repeated genetic bottlenecks, which experimentally are carried out through serial plaque-to-plaque transfers of the virus, lead to fitness decrease (measured here as diminished capacity to produce infectious progeny). Here we report an analysis of fitness evolution of several low fitness foot-and-mouth disease virus clones subjected to 50 plaque-to-plaque transfers. Unexpectedly, fitness decrease, rather than being continuous and monotonic, displayed a fluctuating pattern, which was influenced by both the virus and the state of the host cell as shown by effects of recent cell passage history. The amplitude of the fluctuations increased as fitness decreased, resulting in a remarkable resistance of virus to extinction. Whereas the frequency distribution of fitness in control (independent) experiments follows a log-normal distribution, the probability of fitness values in the evolving bottlenecked populations fitted a Weibull distribution. We suggest that multiple functions of viral genomic RNA and its encoded proteins, subjected to high mutational pressure, interact with cellular components to produce this nontrivial, fluctuating pattern.

  19. 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.

  20. Deep sequencing reveals persistence of intra- and inter-host genetic diversity in natural and greenhouse populations of zucchini yellow mosaic virus.

    Science.gov (United States)

    Simmons, H E; Dunham, J P; Stack, J C; Dickins, B J A; Pagán, I; Holmes, E C; Stephenson, A G

    2012-08-01

    The genetic diversity present in populations of RNA viruses is likely to be strongly modulated by aspects of their life history, including mode of transmission. However, how transmission mode shapes patterns of intra- and inter-host genetic diversity, particularly when acting in combination with de novo mutation, population bottlenecks and the selection of advantageous mutations, is poorly understood. To address these issues, this study performed ultradeep sequencing of zucchini yellow mosaic virus in a wild gourd, Cucurbita pepo ssp. texana, under two infection conditions: aphid vectored and mechanically inoculated, achieving a mean coverage of approximately 10 ,000×. It was shown that mutations persisted during inter-host transmission events in both the aphid vectored and mechanically inoculated populations, suggesting that the vector-imposed transmission bottleneck is not as extreme as previously supposed. Similarly, mutations were found to persist within individual hosts, arguing against strong systemic bottlenecks. Strikingly, mutations were seen to go to fixation in the aphid-vectored plants, suggestive of a major fitness advantage, but remained at low frequency in the mechanically inoculated plants. Overall, this study highlights the utility of ultradeep sequencing in providing high-resolution data capable of revealing the nature of virus evolution, particularly as the full spectrum of genetic diversity within a population may not be uncovered without sequence coverage of at least 2500-fold.

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

    Science.gov (United States)

    Griffis, Joseph C; Nenert, Rodolphe; Allendorfer, Jane B; Szaflarski, Jerzy P

    2017-01-01

    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.

  2. Microscopic theory of spatial-temporal congested traffic patterns at highway bottlenecks.

    Science.gov (United States)

    Kerner, Boris S; Klenov, Sergey L

    2003-09-01

    A microscopic theory of spatial-temporal congested traffic patterns at highway bottlenecks due to on-ramps, merge bottlenecks (a reduction of highway lanes), and off-ramps is presented. The basic postulate of three-phase traffic theory is used, which claims that homogeneous (in space and time) model solutions (steady states) of synchronized flow cover a two dimensional region in the flow-density plane [B. S. Kerner, Phys. Rev. Lett. 81, 3797 (1998); Trans. Res. Rec. 1678, 160 (1999)]. Phase transitions leading to diverse congested patterns, pattern evolution, and pattern nonlinear features have been found. Diagrams of congested patterns, i.e., regions of the pattern emergence dependent on traffic demand, have been derived. Diverse effects of metastability with respect to the pattern formation have been found. The microscopic theory allows us to explain the main empirical pattern features at on-ramps and off-ramps which have recently been found [B. S. Kerner, Phys. Rev. E 65, 046138 (2002)]. (i) Rather than moving jams, synchronized flow first occurs at bottlenecks if the flow rate is slowly increasing. Wide moving jams can spontaneously occur only in synchronized flow. (ii) General patterns (GP) and synchronized flow patterns (SP) can spontaneously emerge at the bottlenecks. There can be the widening SP (WSP), the moving SP (MSP), and the localized SP. (iii) At on-ramps cases of "weak" and "strong" congestion should be distinguished. In contrast to weak congestion, under strong congestion the flow rate in synchronized flow in GP reaches a limit flow rate, the frequency of the moving jam emergence reaches a maximum, i.e., the GP characteristics under strong congestion do not depend on traffic demand. (iv) At the off-ramp GP with weak congestion occur. (v) A study of the pattern formation on a highway with two bottlenecks shows that diverse expanded patterns can occur, which cover both bottlenecks. SP first emerged at the downstream bottleneck can be caught at the

  3. Study on the Protection Countermeasures to Extremely Small Population of Wild Plant of Guangxi%广西极小种群野生植物保护对策探讨

    Institute of Scientific and Technical Information of China (English)

    黎德丘; 彭定人

    2009-01-01

    This paper gave a full description of the current situation of 20 extremely small population of wild plant of population quantities and distribution in Guangxi. Based on the threat analysis of population decline and habitat loss were faced, some countermeasures to strengthen protection was discussed.%全面阐述了广西分布的20种极小种群野生植物的种群数量、分布等现状,在分析其面临的种群衰退、生境丧失等主要威胁的基础上,探讨了加强保护的对策.

  4. Extreme cosmos

    CERN Document Server

    Gaensler, Bryan

    2011-01-01

    The universe is all about extremes. Space has a temperature 270°C below freezing. Stars die in catastrophic supernova explosions a billion times brighter than the Sun. A black hole can generate 10 million trillion volts of electricity. And hypergiants are stars 2 billion kilometres across, larger than the orbit of Jupiter. Extreme Cosmos provides a stunning new view of the way the Universe works, seen through the lens of extremes: the fastest, hottest, heaviest, brightest, oldest, densest and even the loudest. This is an astronomy book that not only offers amazing facts and figures but also re

  5. Development of control strategy of variable speed limits for improving traffic operations at freeway bottlenecks

    Institute of Scientific and Technical Information of China (English)

    李志斌; 刘攀; 王炜; 徐铖铖

    2014-01-01

    A control strategy of variable speed limits (VSL) was developed to reduce the travel time at freeway recurrent bottleneck areas. The proposed control strategy particularly focused on preventing the capacity drop and increasing the discharge flow. A cell transmission model (CTM) was developed to evaluate the effects of the proposed VSL control strategy on the traffic operations. The results show that the total travel time is reduced by 25.5% and the delay is reduced by 56.1%. The average travel speed is increased by 34.3% and the queue length is reduced by 31.0%. The traffic operation is improved by the proposed VSL control strategy. The way to use the proposed VSL control strategy in different types of freeway bottlenecks was also discussed by considering different traffic flow characteristics. It is concluded that the VSL control strategy is effective for merge bottlenecks but is less effective for diverge bottlenecks.

  6. 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.

  7. 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.

  8. 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.

  9. 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

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

    Science.gov (United States)

    2015-01-01

    Background 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 hospital discharge with follow-up. The World Health Organization has endorsed KMC for stabilised newborns in health facilities in both high-income and low-resource settings. The objectives of this paper are to: (1) use a 12-country analysis to explore health system bottlenecks affecting the scale-up of KMC; (2) propose solutions to the most significant bottlenecks; and (3) outline priority actions for scale-up. Methods The bottleneck analysis tool was applied in 12 countries in Africa and 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. Results 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. Conclusions There are at least a dozen countries worldwide with national KMC programmes, and we identify three pathways to scale: (1

  11. Selectivity of fish ladders: a bottleneck in Neotropical fish movement

    Directory of Open Access Journals (Sweden)

    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.

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

    DEFF Research Database (Denmark)

    Mourier, Tobias; Ho, Simon; Gilbert, M Thomas P;

    2012-01-01

    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...... 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...... post-bottleneck recoveries. In contrast, nuclear SNPs can detect bottlenecks followed by rapid recovery, although bottlenecks involving reduction of less than half the population are generally detected with low power unless extensive genetic information from ancient individuals is available. Our...

  13. On the Accurate Identification of Network Paths Having a Common Bottleneck

    Directory of Open Access Journals (Sweden)

    Muhammad Murtaza Yousaf

    2013-01-01

    Full Text Available We present a new mechanism for detecting shared bottlenecks between end-to-end paths in a network. Our mechanism, which only needs one-way delays from endpoints as an input, is based on the well-known linear algebraic approach: singular value decomposition (SVD. Clusters of flows which share a bottleneck are extracted from SVD results by applying an outlier detection method. Simulations with varying topologies and different network conditions show the high accuracy of our technique.

  14. 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…

  15. A Preliminary Survey of Extremely Small Populations of Wild Plants in Bawangling,Hainan Island%海南岛霸王岭极小种群野生植物调查初报

    Institute of Scientific and Technical Information of China (English)

    许洋瑜; 罗文; 韩文涛; 彭慧

    2014-01-01

    According to the existing literature's analysis, there are 17 kinds of extremely small populations of wild plants in Bawangling , through the survey of 17 kinds of extremely small populations of wild plants, has got a preliminary understanding about the distribution of small populations in Bawangling ,and analyzed the correlation between the distribution of extremely small populations and the altitude, slope direction, slope, veg-etation habitat factors , the main threats factors. Found that the extremely small populations in Bawangling was at risk, which need protected timely, and at the same time put forward some suggestions for protection.%根据已有文献资料分析统计,霸王岭地区有分布记录的极小种群野生植物17种,通过对17种极小种群野生植物的调查,初步了解霸王岭地区极小种群的分布资源状况,并分析极小种群的分布与海拔、坡向、坡度、植被等生境因子的相关性以及所面临的主要威胁,据此可知霸王岭保护区的极小种群植物资源已处于亟待保护的危险状态,并提出了一些保护建议。

  16. Evidence of low genetic variation and rare alleles in a bottlenecked endangered island endemic, the Lasan Teal (Anas laysanensis)

    Science.gov (United States)

    Reynolds, Michelle H.; Pearce, John M.; Lavretsky, Philip; Peters Jeffrey L,; Courtot, Karen; Seixas, Pedro P.

    2015-01-01

    Genetic diversity is assumed to reflect the evolutionary potential and adaptability of populations, and thus quantifying the genetic diversity of endangered species is useful for recovery programs. In particular, if conservation strategies include reintroductions, periodic genetic assessments are useful to evaluate whether management efforts have resulted in the maximization or loss of genetic variation within populations over generations. In this study, we collected blood, feather, and tissue samples during 1999–2009 and quantified genetic diversity for a critically endangered waterfowl species endemic to the Hawaiian archipelago, the Laysan teal or duck (Anas laysanensis; n = 239 individual birds sampled). The last extant population of this species at Laysan Island was sourced in 2004–2005 for a ‘wild to wild’ translocation of 42 individuals for an experimental reintroduction to Midway Atoll. To inform future management strategies, we compared genetic diversity sampled from the source population (n = 133 Laysan birds) including 23 of Midway’s founders and offspring of the translocated population 2–5 years post release (n = 96 Midway birds). We attempted to identify polymorphic markers by screening nuclear microsatellite (N = 83) and intronic loci (N = 19), as well as the mitochondrial control region (mtDNA) for a subset of samples. Among 83 microsatellite loci screened, six were variable. We found low nuclear variation consistent with the species’ historical population bottlenecks and sequence variation was observed at a single intron locus. We detected no variation within the mtDNA. We found limited but similar estimates of allelic richness (2.58 alleles per locus) and heterozygosity within islands. Two rare alleles found in the Laysan Island source population were not present in the Midway translocated group, and a rare allele was discovered in an individual on Midway in 2008. We found similar genetic diversity and low, but statistically

  17. 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

  18. 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

    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 within the decomposer

  19. 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;

    is nowhere less than 4.3x and is on average 6.7x. More than 10 million Single Nucleotide Variants (SNVs) were identified based multi-sample calling of the aligned sequences. Identified risk alleles may, however, either appear to be private to the isolated population and not observed elsewhere or extremely...... 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...

  20. Local mate competition and transmission bottlenecks: a new model for understanding malaria parasite and other sex ratios.

    Science.gov (United States)

    Neal, Allison T; Taylor, Peter D

    2014-12-21

    The local mate competition model from sex ratio theory predicts female-biased sex ratios in populations that are highly subdivided during mating, and is thought to accord well with the population structure of malaria parasites. However, the selective advantage of female-biased sex ratios comes from the resulting increase in total reproductive output, an advantage the transmission biology of malaria parasite likely reduces. We develop a mathematical model to determine how bottlenecks in transmission that cause diminishing fitness returns from female production affect sex ratio evolution. We develop four variations of this model that incorporate whether or not parasite clones have the ability to detect others that occupy the same host and whether or not the number of clones affects the total mating population size. Our model indicates that transmission bottlenecks favor less female-biased sex ratios than those predicted under LMC. This effect is particularly pronounced if clones have no information about the presence of coexisting clones and the number of mating individuals per patch is fixed. The model could extend our understanding of malaria parasite sex ratios in three main ways. First, it identifies inconsistencies between the theoretical predictions and the data presented in a previous study, and proposes revised predictions that are more consistent with underlying biology of the parasite. Second, it may account for the positive association between parasite density and sex ratio observed within and between some species. Third, it predicts a relationship between mortality rates in the vector and sex ratios, which appears to be supported by the little existing data we have. While the inspiration for this model came from malaria parasites, it should apply to any system in which per capita dispersal success diminishes with increasing numbers of females in a patch.

  1. 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

  2. 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.

  3. Selectivity of fish ladders: a bottleneck in Neotropical fish movement

    Directory of Open Access Journals (Sweden)

    Carlos Sérgio Agostinho

    2007-01-01

    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.Dezenas de escadas de peixes foram construídas em barragens de reservatórios brasileiros, mas são raros os estudos acerca de suas eficiências como instrumentos de conservação da ictiofauna Neotropical, em especial de espécies migradoras. Neste contexto, o presente estudo teve como objetivo avaliar a seletividade específica no ingresso e ascensão de peixes na escada localizada junto à barragem de Lajeado (UHE Luis Eduardo Magalhães, rio Tocantins. Amostragens foram realizadas mensalmente de novembro de 2002 a outubro de 2003 nos tanques de descanso da escada, utilizando tarrafas, e no trecho a jusante, utilizando redes de espera. A avaliação da seletividade no ingresso da escada foi realizada através da comparação da ocorrência, abundância relativa, dominância e congruência dos ranks de abundância de espécies migradoras e não migradoras na escada e no trecho imediatamente a jusante. A riqueza e abundância específica nos diferentes tanques de descanso foram utilizadas para avaliar a seletividade ao longo da escada. Os efeitos das variações temporais do nível hidrométrico de jusante e da velocidade de fluxo na seletividade foram também analisados. Das 130 espécies registradas a jusante, 63,2% foram capturadas na escada, com claro favorecimento das espécies migradoras. Entretanto, mais de 2/3 das capturas pertenceram a apenas três espécies (Rhaphiodon vulpinus, Psectrogaster amazonica e Oxydoras niger. Embora a maioria das espécies que ingressa na escada possa alcançar seu topo, constatou

  4. Brown world forests: increased ungulate browsing keeps temperate trees in recruitment bottlenecks in resource hotspots.

    Science.gov (United States)

    Churski, Marcin; Bubnicki, Jakub W; Jędrzejewska, Bogumiła; Kuijper, Dries P J; Cromsigt, Joris P G M

    2017-04-01

    Plant biomass consumers (mammalian herbivory and fire) are increasingly seen as major drivers of ecosystem structure and function but the prevailing paradigm in temperate forest ecology is still that their dynamics are mainly bottom-up resource-controlled. Using conceptual advances from savanna ecology, particularly the demographic bottleneck model, we present a novel view on temperate forest dynamics that integrates consumer and resource control. We used a fully factorial experiment, with varying levels of ungulate herbivory and resource (light) availability, to investigate how these factors shape recruitment of five temperate tree species. We ran simulations to project how inter- and intraspecific differences in height increment under the different experimental scenarios influence long-term recruitment of tree species. Strong herbivore-driven demographic bottlenecks occurred in our temperate forest system, and bottlenecks were as strong under resource-rich as under resource-poor conditions. Increased browsing by herbivores in resource-rich patches strongly counteracted the increased escape strength of saplings in these patches. This finding is a crucial extension of the demographic bottleneck model which assumes that increased resource availability allows plants to more easily escape consumer-driven bottlenecks. Our study demonstrates that a more dynamic understanding of consumer-resource interactions is necessary, where consumers and plants both respond to resource availability.

  5. 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.

  6. Bottlenecks and hubs in inferred networks are important for virulence in Salmonella typhimurium.

    Science.gov (United States)

    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, 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, examining cellular response to environmental conditions and effects of 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 and hub genes were identified from these inferred networks, and we show for the first time that these genes are significantly more likely to be essential for virulence than their non-bottleneck or non-hub counterparts. Networks generated using simple similarity metrics (correlation and mutual information) 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.

  7. Extremely low microsatellite diversity but distinct population structure in a long-lived threatened species, the Australian lungfish Neoceratodus forsteri (Dipnoi).

    Science.gov (United States)

    Hughes, Jane M; Schmidt, Daniel J; Huey, Joel A; Real, Kathryn M; Espinoza, Thomas; McDougall, Andrew; Kind, Peter K; Brooks, Steven; Roberts, David T

    2015-01-01

    The Australian lungfish is a unique living representative of an ancient dipnoan lineage, listed as 'vulnerable' to extinction under Australia's Environment Protection and Biodiversity Conservation Act 1999. Historical accounts indicate this species occurred naturally in two adjacent river systems in Australia, the Burnett and Mary. Current day populations in other rivers are thought to have arisen by translocation from these source populations. Early genetic work detected very little variation and so had limited power to answer questions relevant for management including how genetic variation is partitioned within and among sub-populations. In this study, we use newly developed microsatellite markers to examine samples from the Burnett and Mary Rivers, as well as from two populations thought to be of translocated origin, Brisbane and North Pine. We test whether there is significant genetic structure among and within river drainages; assign putatively translocated populations to potential source populations; and estimate effective population sizes. Eleven polymorphic microsatellite loci genotyped in 218 individuals gave an average within-population heterozygosity of 0.39 which is low relative to other threatened taxa and for freshwater fishes in general. Based on FST values (average over loci = 0.11) and STRUCTURE analyses, we identify three distinct populations in the natural range, one in the Burnett and two distinct populations in the Mary. These analyses also support the hypothesis that the Mary River is the likely source of translocated populations in the Brisbane and North Pine rivers, which agrees with historical published records of a translocation event giving rise to these populations. We were unable to obtain bounded estimates of effective population size, as we have too few genotype combinations, although point estimates were low, ranging from 29 - 129. We recommend that, in order to preserve any local adaptation in the three distinct populations that

  8. Meta-Analysis of mitochondrial DNA reveals several population bottlenecks during worldwide migrations of cattle

    NARCIS (Netherlands)

    Lenstra, Johannes A.; Ajmone-Marsan, Paolo; Beja-Pereira, Albano; Bollongino, Ruth; Bradley, Daniel G.; Colli, Licia; De Gaetano, Anna; Edwards, Ceiridwen J.; Felius, Marleen; Ferretti, Luca; Ginja, Catarina; Hristov, Peter; Kantanen, Juha; Lirón, Juan Pedro; Magee, David A.; Negrini, Riccardo; Radoslavov, Georgi A.

    2014-01-01

    Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle ha

  9. Bottlenecks and Multiple Introductions: Population Genetics of the Vector of Avian Malaria in Hawaii

    Science.gov (United States)

    2000-01-01

    extinction . Likewise, a high degree of genetic diversity in the parasite may hinder the development of resistance (May & Nowak 1994). Key in this...survive outside the mosquito zone. Although several factors may have contributed to the extinction and endangerment of the endemic species of...remote locations in the Big Island collected in hapuu cavities in the Hawaiian rainforest . Four unique haplotypes were found there. Overall, the low

  10. IDENTIFYING BOTTLENECKS FOR APPROPRIATE INFANT FEEDING IN URBAN SLUMS, ALIGARH CITY.

    Directory of Open Access Journals (Sweden)

    Saira Mehnaz

    2012-04-01

    Full Text Available Introduction: Urban population is increasing rapidly. Majority of these families are poor or landless farmers and labourers, who settle down in peri-urban areas, creating slums. Urban slums are thus growing at an alarming rate. The present study was carried out with the general objective of identifying factors which prevent access to health services. Objectives: 1. To determine the prevalence of stunting, wasting, and underweight in infants and young children. 2. To determine presence of certain micro-environmental and socioeconomic factors associated with poor nutritional status of infants and children. Methodology: Baseline study was carried out in Oct –Nov 2009 (as a part of another ongoing study and data was collected in 110 Mothers who had delivered children during the last one month. In Oct 2010 these families were visited again the infants were followed up. 39 families had shifted to another location or emigrated back to their parent state or village mostly in search of seasonal employment as reported by neighbours. One family refused to cooperate. . Two infants had died. Remaining 68 Mothers were interviewed in friendly informal manner after taking consent for study. Results: (35.4% study subjects had migrated to other areas, as reported by neighbours. Of the 68 mothers interviewed during follow up visit, previous baseline record showed that a majority were 20-30 years of age. , only 2 mothers (2.9% had exclusively breastfed for 6 months. 46 (67.6% said they had not been contacted by any health worker during the last 3 months. All 68 children were malnourished. Immunization status was poor and 94.1% children had suffered from some illness in the last one month. Conclusion: Migration is a problem which makes it difficult for providers to give continuity of care. Capacity building of the community can reduce the the bottlenecks leading to marginalization and exclusion of slum mothers from the mainstream urban health services.

  11. Dynamic bottleneck elimination in mattress manufacturing line using theory of constraints.

    Science.gov (United States)

    Gundogar, Emin; Sari, Murat; Kokcam, Abdullah H

    2016-01-01

    There is a tough competition in the furniture sector like other sectors. Along with the varying product range, production system should also be renewed on a regular basis and the production costs should be kept under control. In this study, spring mattress manufacturing line of a furniture manufacturing company is analyzed. The company wants to increase its production output with new investments. The objective is to find the bottlenecks in production line in order to balance the semi-finished material flow. These bottlenecks are investigated and several different scenarios are tested to improve the current manufacturing system. The problem with a main theme based on the elimination of the bottleneck is solved using Goldratt and Cox's theory of constraints with a simulation based heuristic method. Near optimal alternatives are determined by system models built in Arena 13.5 simulation software. Results show that approximately 46 % capacity enhancements with 2 buffer stocks have increased average production by 88.8 %.

  12. Effects of speed bottleneck on traffic flow with feedback control signal

    Science.gov (United States)

    Zhu, Kangli; Bi, Jiantao; Wu, Jianjun; Li, Shubin

    2016-09-01

    Various car-following models (CMs) have been developed to capture the complex characteristics of microscopic traffic flow, among which the coupled map CM can better reveal and reflect various phenomena of practical traffic flow. Capacity change at bottleneck contributes to high-density traffic flow upstream the bottleneck and contains very complex dynamic behavior. In this paper, we analyze the effect of speed bottleneck on the spatial-temporal evolution characteristics of traffic flow, and propose a method to reduce traffic congestion with the feedback control signal based on CM. Simulation results highlight the potential of using the feedback signal to control the stop-and-go wave and furthermore to alleviate the traffic congestion effectively.

  13. Comparative analyses of genetic risk prediction methods reveal extreme diversity of genetic predisposition to nonalcoholic fatty liver disease (NAFLD) among ethnic populations of India.

    Science.gov (United States)

    Chatterjee, Ankita; Basu, Analabha; Chowdhury, Abhijit; Das, Kausik; Sarkar-Roy, Neeta; Majumder, Partha P; Basu, Priyadarshi

    2015-03-01

    Nonalcoholic fatty liver disease (NAFLD) is a distinct pathologic condition characterized by a disease spectrum ranging from simple steatosis to steato-hepatitis, cirrhosis and hepatocellular carcinoma. Prevalence of NAFLD varies in different ethnic groups, ranging from 12% in Chinese to 45% in Hispanics. Among Indian populations, the diversity in prevalence is high, ranging from 9% in rural populations to 32% in urban populations, with geographic differences as well. Here, we wished to find out if this difference is reflected in their genetic makeup. To date, several candidate genes and a few genomewide association studies (GWAS) have been carried out, and many associations between single nucleotide polymorphisms (SNPs) and NAFLD have been observed. In this study, the risk allele frequencies (RAFs) of NAFLD-associated SNPs in 20 Indian ethnic populations (376 individuals) were analysed. We used two different measures for calculating genetic risk scores and compared their performance. The correlation of additive risk scores of NAFLD for three Hapmap populations with their weighted mean prevalence was found to be high (R(2) = 0.93). Later we used this method to compare NAFLD risk among ethnic Indian populations. Based on our observation, the Indian caste populations have high risk scores compared to Caucasians, who are often used as surrogate and similar to Indian caste population in disease gene association studies, and is significantly higher than the Indian tribal populations.

  14. Comparative analyses of genetic risk prediction methods reveal extreme diversity of genetic predisposition to nonalcoholic fatty liver disease (NAFLD) among ethnic populations of India

    Indian Academy of Sciences (India)

    Ankita Chatterjee; Analabha Basu; Abhijit Chowdhury; Kausik Das; Neeta Sarkar-Roy; Partha P. Majumder; Priyadarshi Basu

    2015-03-01

    Nonalcoholic fatty liver disease (NAFLD) is a distinct pathologic condition characterized by a disease spectrum ranging from simple steatosis to steato-hepatitis, cirrhosis and hepatocellular carcinoma. Prevalence of NAFLD varies in different ethnic groups, ranging from 12% in Chinese to 45% in Hispanics. Among Indian populations, the diversity in prevalence is high, ranging from 9% in rural populations to 32% in urban populations, with geographic differences as well. Here, we wished to find out if this difference is reflected in their genetic makeup. To date, several candidate genes and a few genomewide association studies (GWAS) have been carried out, and many associations between single nucleotide polymorphisms (SNPs) and NAFLD have been observed. In this study, the risk allele frequencies (RAFs) of NAFLD-associated SNPs in 20 Indian ethnic populations (376 individuals) were analysed. We used two different measures for calculating genetic risk scores and compared their performance. The correlation of additive risk scores of NAFLD for three Hapmap populations with their weighted mean prevalence was found to be high (2 = 0.93). Later we used this method to compare NAFLD risk among ethnic Indian populations. Based on our observation, the Indian caste populations have high risk scores compared to Caucasians, who are often used as surrogate and similar to Indian caste population in disease gene association studies, and is significantly higher than the Indian tribal populations.

  15. Urban population vulnerability to climate extremes: mitigating urban heat through technology and water-sensitive urban design in Australian cities (Invited)

    Science.gov (United States)

    Tapper, N. J.

    2013-12-01

    Australia recently endured what was arguably its worst drought in 200 years. The 'Millennium Drought' lasted from 1999 until 2009, producing acute water shortages for several major Australian cities. Towards the end of the drought an extreme heat wave with temperatures approaching 50 C claimed the lives of several hundred people in Melbourne and Adelaide. One outcome of the extreme conditions was that the spectre of climate change and its impacts became very real for most Australians and contributed to the 2007 signing of the Kyoto Protocol by the Australian Government. Issues of extreme heat and water security also led to increased interest in adapting Australian cities to climate change. These concerns ultimately led to the establishment of the Australian Cooperative Research Centre (CRC) for Water Sensitive Cities, a $110 million research initiative to utilise storm water in Australian cities to create cooler and more liveable environments with increased levels of water security. This paper provides an overview of the work being undertaken within the urban climate program of the CRC to identify heat-health vulnerability in our cities and to evaluate the efficacy of irrigated green infrastructure to produce more liveable environments. This papers discusses some of the early research outputs that involve measurement, modelling and remote sensing at a range of scales in Australian cities.

  16. "BOTTLENECK" AND COUNTERMEASURE OF HIGH-TECHNOLOGIZATION OF MARINE INDUSTRY IN CHINA

    Institute of Scientific and Technical Information of China (English)

    LUAN Wei-xin

    2004-01-01

    This article deeply researched into the existent five problems and four main "bottlenecks" in the high-technologization of marine industry in China on the basis of analyzing the new trends in international marine problems and the necessity of implementing the strategy of developing China based on marine. This article brought up specific measures to the five "bottlenecks" according to the situations, and pointed out that new marine industry should be high-technologization and the traditional marine industry should be reformed by high-technique. The research results may provide the scientific basis for realizing the high-technologization of marine industry in China.

  17. Reducing the Analytical Bottleneck for Domain Scientists: Lessons from a Climate Data Visualization Case Study

    Energy Technology Data Exchange (ETDEWEB)

    Dasgupta, Aritra; Poco, Jorge; Bertini, Enrico; Silva, Claudio T.

    2016-01-31

    The gap between large-scale data production rate and the rate of generation of data-driven scientific insights has led to an analytical bottleneck in scientific domains like climate, biology, etc. This is primarily due to the lack of innovative analytical tools that can help scientists efficiently analyze and explore alternative hypotheses about the data, and communicate their findings effectively to a broad audience. In this paper, by reflecting on a set of successful collaborative research efforts between with a group of climate scientists and visualization researchers, we introspect how interactive visualization can help reduce the analytical bottleneck for domain scientists.

  18. Desiccation and Mortality Dynamics in Seedlings of Different European Beech (Fagus sylvatica L.) Populations under Extreme Drought Conditions

    DEFF Research Database (Denmark)

    Bolte, Andreas; Czajkowski, Tomasz; Cocozza, Claudia;

    2016-01-01

    and mortality processes among the different populations and related them to plant water status (predawn water potential, 9PD) and soil hydraulic traits. For the lethal drought assessment, we used a critical threshold of soil water availability that is reached when 50% mortality in seedling populations occurs...

  19. Research on polymorphism of production logistics bottleneck based on bottleneck index%基于瓶颈指数的生产物流瓶颈多态性研究

    Institute of Scientific and Technical Information of China (English)

    唐娟; 刘志

    2011-01-01

    Aiming at the shifting phenomenon of production logistics in the manufacturing shop under uncertain environments, the conceptual model which is composed of main bottleneck, second bottleneck, sensitive bottleneck and insensitive bottleneck is built;taken production capability,production load,quality assurance capability and production cost of manufacturing unit into con-sideration ,mathematical model of bottleneck index is established to measure bottleneck degree accurately;based on bottleneck in-dex, the prediction mechanism is established to identify bottleneck and non-bottleneck,main bottleneck and second bottleneck, then sensitive coefficient of bottleneck shifting is founded to accurately judge sensitive bottleneck and insensitive bottleneck of the manufacturing shop,which provide a method support for forecasting and monitoring the phenomenon of bottleneck shifting.%针对不确定性环境下制造车间生产物流瓶颈漂移现象,建立以主瓶颈、次瓶颈、灵敏型瓶颈和迟钝型瓶颈为主的瓶颈多态性概念模型;综合考虑制造单元的生产能力、生产负荷、质量保证能力和生产成本,构建瓶颈指数数学模型,以实现制造单元瓶颈度的准确度量;以瓶颈指数为基础,构建瓶颈及主次瓶颈的预测机制,并构建瓶颈漂移敏感系数,以实现制造车间生产物流瓶颈与非瓶颈、主瓶颈和次瓶颈、灵敏型瓶颈和迟钝型瓶颈的准确判别,进而为实现瓶颈漂移现象的预测和监控提供一种方法.

  20. 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.

  1. 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.

  2. 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

  3. 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

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

    NARCIS (Netherlands)

    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

  5. Effect of force and location of bottleneck for particle moving through window under encapsulation

    Indian Academy of Sciences (India)

    ANIRBAN SHARMA; PRADIP KR GHORAI

    2017-08-01

    One of the central assumptions to explain appearance of an anomalous diffusion regime in microporous materials is the cancellation of forces experienced by a moving particle at the bottleneck. In this work, we examine this issue of force cancellation inside a microporous material exploring the diffusion path and cross-checking bottleneck associated with diffusion. Conventional wisdom is that window of a microporous material is the bottleneck for diffusion. Our study reveals that bottleneck for diffusion is not at the window, it is always 2.6 Å to 3.0 Å away from the window plane and depending on guest size, it lies in different partsof the inner surface of α-cage. Window has significant effect in diffusion process only when diffusing particle size is comparable or larger than the window free diameter. Window does not play any role if particle size is smaller than window free diameter. We show that in the anomalous diffusion regime there is no signature of force cancellation at the window. Activation energy and total force along the diffusion path are responsible for the existence of anomalous diffusion regime in microporous materials.

  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

    2016-09-01

    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. Bottlenecks in Two-Hop Ad Hoc Networks - Dividing Radio Capacity in a Smart Way

    NARCIS (Netherlands)

    Remke, Anne Katharina Ingrid; Haverkort, Boudewijn R.H.M.; Cloth, L.; Mandjes, M.; van der Mei, R.; Nunez Queija, R.

    In two-hop ad hoc networks the available radio capacity tends to be equally shard among the contending stations, which may lead to bottleneck situations in case of unbalanced traffic routing. We propose a generic model for evaluating adaptive capacity sharing strategies. We use infinite-state

  8. Evaluation of bottlenecks in the late stages of protein secretion in Bacillus subtilis

    NARCIS (Netherlands)

    Bolhuis, A; Tjalsma, H; Smith, H.E; Meima, R.; Venema, G; Bron, S; van Dijl, J.M

    1999-01-01

    Despite a high capacity for secretion of homologous proteins, the secretion of heterologous proteins by Bacillus subtilis is frequently inefficient. In the present studies, we have investigated and compared bottlenecks in the secretion of four heterologous proteins: Bacillus lichenifomis alpha-amyla

  9. South West Georgia: an important bottleneck for raptor migration during autumn

    NARCIS (Netherlands)

    Verhelst, B.; Jansen, J.; Vansteelant, W.

    2011-01-01

    Counts of migrating raptors at Batumi, Georgia, revealed the eastern Black Sea coast to form one of the most important bottlenecks for raptor migration during autumn in the Eurasian-African migration system. Totals for 10 species (European Honey-buzzard Pernis apivorus, Steppe Buzzard Buteo buteo vu

  10. Avoiding the problem state bottleneck by strategic use of the environment

    NARCIS (Netherlands)

    Borst, Jelmer P.; Buwalda, Trudy A.; van Rijn, Hedderik; Taatgen, Niels A.

    2013-01-01

    We investigated whether environmental support can be used to circumvent the problem state bottleneck in human multitasking. Previously, it was shown that people can only maintain a single chunk of information in their problem state resource, the central part of working memory. Consequently, when the

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

    DEFF Research Database (Denmark)

    Lorenzen, Stephan Sloth; Winter, Pawel

    2016-01-01

    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...

  12. Bottleneck distances and Steiner trees in the Euclidean d-space

    DEFF Research Database (Denmark)

    Winter, Pawel; Lorenzen, Stephan Sloth

    fashion to obtain low cost trees spanning all terminals. The weakness of this approach is that obtained solutions are topologically related to minimum spanning trees. To obtain better solutions, bottleneck distances are utilized to determine good subsets of terminals without being constrained...

  13. 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…

  14. Analysis of a generic model for a bottleneck link in an integrated services communications network

    NARCIS (Netherlands)

    Al-Begain, K.; Heindl, A.; Telek, M.; Litjens, R.; Boucherie, R.J.

    2007-01-01

    We develop and analyse a generic model for performance evaluation, parameter optimisation and dimensioning of a bottleneck link in an integrated services communications network. Possible application areas include ip, atm and gsm/gprs networks. The model enables analytical evaluation for a scenario o

  15. Lake restoration studies: failures, bottlenecks and prospects of new ecotechnological measures

    NARCIS (Netherlands)

    Gulati, R.D.; Dionisio Pires, L.M.; Van Donk, E.

    2008-01-01

    This paper critically reviews the published works on lake restoration in north-western Europe, with the aim to highlight the causes of failures of lake biomanipulation, and to identify the main bottlenecks that have impeded progress. More importantly, we explore the prospects of applying new ecotech

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

    NARCIS (Netherlands)

    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

  17. Genetic Signatures of Demographic Changes in an Avian Top Predator during the Last Century: Bottlenecks and Expansions of the Eurasian Eagle Owl in the Iberian Peninsula.

    Science.gov (United States)

    Graciá, Eva; Ortego, Joaquín; Godoy, José Antonio; Pérez-García, Juan Manuel; Blanco, Guillermo; Delgado, María del Mar; Penteriani, Vincenzo; Almodóvar, Irene; Botella, Francisco; Sánchez-Zapata, José Antonio

    2015-01-01

    The study of the demographic history of species can help to understand the negative impact of recent population declines in organisms of conservation concern. Here, we use neutral molecular markers to explore the genetic consequences of the recent population decline and posterior recovery of the Eurasian eagle owl (Bubo bubo) in the Iberian Peninsula. During the last century, the species was the object of extermination programs, suffering direct persecution by hunters until the 70's. Moreover, during the last decades the eagle owl was severely impacted by increased mortality due to electrocution and the decline of its main prey species, the European rabbit (Oryctolagus cuniculus). In recent times, the decrease of direct persecution and the implementation of some conservation schemes have allowed the species' demographic recovery. Yet, it remains unknown to which extent the past population decline and the later expansion have influenced the current species' pattern of genetic diversity. We used eight microsatellite markers to genotype 235 eagle owls from ten Spanish subpopulations and analyse the presence of genetic signatures attributable to the recent population fluctuations experienced by the species. We found moderate levels of differentiation among the studied subpopulations and Bayesian analyses revealed the existence of three genetic clusters that grouped subpopulations from central, south-western and south-eastern Spain. The observed genetic structure could have resulted from recent human-induced population fragmentation, a patchy distribution of prey populations and/or the philopatric behaviour and habitat selection of the species. We detected an old population bottleneck, which occurred approximately 10,000 years ago, and significant signatures of recent demographic expansions. However, we did not find genetic signatures for a recent bottleneck, which may indicate that population declines were not severe enough to leave detectable signals on the species

  18. Genetic Signatures of Demographic Changes in an Avian Top Predator during the Last Century: Bottlenecks and Expansions of the Eurasian Eagle Owl in the Iberian Peninsula.

    Directory of Open Access Journals (Sweden)

    Eva Graciá

    Full Text Available The study of the demographic history of species can help to understand the negative impact of recent population declines in organisms of conservation concern. Here, we use neutral molecular markers to explore the genetic consequences of the recent population decline and posterior recovery of the Eurasian eagle owl (Bubo bubo in the Iberian Peninsula. During the last century, the species was the object of extermination programs, suffering direct persecution by hunters until the 70's. Moreover, during the last decades the eagle owl was severely impacted by increased mortality due to electrocution and the decline of its main prey species, the European rabbit (Oryctolagus cuniculus. In recent times, the decrease of direct persecution and the implementation of some conservation schemes have allowed the species' demographic recovery. Yet, it remains unknown to which extent the past population decline and the later expansion have influenced the current species' pattern of genetic diversity. We used eight microsatellite markers to genotype 235 eagle owls from ten Spanish subpopulations and analyse the presence of genetic signatures attributable to the recent population fluctuations experienced by the species. We found moderate levels of differentiation among the studied subpopulations and Bayesian analyses revealed the existence of three genetic clusters that grouped subpopulations from central, south-western and south-eastern Spain. The observed genetic structure could have resulted from recent human-induced population fragmentation, a patchy distribution of prey populations and/or the philopatric behaviour and habitat selection of the species. We detected an old population bottleneck, which occurred approximately 10,000 years ago, and significant signatures of recent demographic expansions. However, we did not find genetic signatures for a recent bottleneck, which may indicate that population declines were not severe enough to leave detectable signals

  19. Fungal specificity bottlenecks during orchid germination and development.

    Science.gov (United States)

    Bidartondo, Martin I; Read, David J

    2008-08-01

    Fungus-subsidized growth through the seedling stage is the most critical feature of the life history for the thousands of mycorrhizal plant species that propagate by means of 'dust seeds.' We investigated the extent of specificity towards fungi shown by orchids in the genera Cephalanthera and Epipactis at three stages of their life cycle: (i) initiation of germination, (ii) during seedling development, and (iii) in the mature photosynthetic plant. It is known that in the mature phase, plants of these genera can be mycorrhizal with a number of fungi that are simultaneously ectomycorrhizal with the roots of neighbouring forest trees. The extent to which earlier developmental stages use the same or a distinctive suite of fungi was unclear. To address this question, a total of 1500 packets containing orchid seeds were buried for up to 3 years in diverse European forest sites which either supported or lacked populations of helleborine orchids. After harvest, the fungi associated with the three developmental stages, and with tree roots, were identified via cultivation-independent molecular methods. While our results show that most fungal symbionts are ectomycorrhizal, differences were observed between orchids in the representation of fungi at the three life stages. In Cephalanthera damasonium and C. longifolia, the fungi detected in seedlings were only a subset of the wider range seen in germinating seeds and mature plants. In Epipactis atrorubens, the fungi detected were similar at all three life stages, but different fungal lineages produced a difference in seedling germination performance. Our results demonstrate that there can be a narrow checkpoint for mycorrhizal range during seedling growth relative to the more promiscuous germination and mature stages of these plants' life cycle.

  20. Hydrological extremes and security

    Science.gov (United States)

    Kundzewicz, Z. W.; Matczak, P.

    2015-04-01

    Economic losses caused by hydrological extremes - floods and droughts - have been on the rise. Hydrological extremes jeopardize human security and impact on societal livelihood and welfare. Security can be generally understood as freedom from threat and the ability of societies to maintain their independent identity and their functional integrity against forces of change. Several dimensions of security are reviewed in the context of hydrological extremes. The traditional interpretation of security, focused on the state military capabilities, has been replaced by a wider understanding, including economic, societal and environmental aspects that get increasing attention. Floods and droughts pose a burden and serious challenges to the state that is responsible for sustaining economic development, and societal and environmental security. The latter can be regarded as the maintenance of ecosystem services, on which a society depends. An important part of it is water security, which can be defined as the availability of an adequate quantity and quality of water for health, livelihoods, ecosystems and production, coupled with an acceptable level of water-related risks to people, environments and economies. Security concerns arise because, over large areas, hydrological extremes - floods and droughts - are becoming more frequent and more severe. In terms of dealing with water-related risks, climate change can increase uncertainties, which makes the state's task to deliver security more difficult and more expensive. However, changes in population size and development, and level of protection, drive exposure to hydrological hazards.

  1. 基于瓶颈多态性的生产物流瓶颈闭环预测方法%Close-loop prediction method of logistics bottleneck based on bottleneck polymorphism

    Institute of Scientific and Technical Information of China (English)

    刘志; 唐娟; 费志敏

    2012-01-01

    针对不确定性环境下的生产物流瓶颈漂移预测问题,提出一种基于瓶颈多态性的瓶颈闭环预测方法。建立灵敏型瓶颈、迟钝型瓶颈、渐向型瓶颈和渐离型瓶颈的概念,以定性描述制造系统的物流瓶颈多态性;以瓶颈指数为基础,以制造单元时问和质量为参数,构建瓶颈漂移指数数学模型,并以此为依据构建瓶颈多态性判定机制,以实现瓶颈多态性的定量描述,进而为瓶颈漂移规律的研究提供技术支持;构建包含数据统计分析、瓶颈预测机制、瓶颈多态性分析和瓶颈指数迭代预测四项内容的瓶颈闭环预测方法,以实现生产物流瓶颈的动态连续预测。通过对某汽车装配车间生产物流瓶颈的动态预测和监控,验证了该方法的有效性和准确性。%Aiming at the prediction problem of production logistics bottleneck shifting under uncertain environment, a closed-loop prediction method of bottleneck was proposed based on bottleneck polymorphisrrL The concepts of sensi- tive bottleneck, obtuse bottleneck, growing bottleneck and decreasing bottleneck were formulated to describe the lo- gistics bottleneck polymorphism of manufacturing system qualitatively. Based on bottleneck index, mathematical model of bottleneck shifting index was established by taking time and quality of manufacturing unit as parameters. Decision mechanism of bottleneck polymorphism was constructed to realize bottleneck polymorphism description on the basis of bottleneck shifting index quantitatively, which provided technological support for studying on bottleneck shifting rule. The bottleneck closed-loop prediction method which was composed of data statistic analysis, bottle- neck prediction mechanism, bottleneck polymorphism analysis and bottleneck index iterative prediction was founded to realize dynamic and continuous prediction of production logistics bottleneck. An example of dynamically forecas- ting

  2. 基于两种瓶颈度的制造车间多瓶颈动态预测方法%Dynamic Prediction Method of Multi-bottleneck in Manufacturing Shop Based on Two Bottleneck Degrees

    Institute of Scientific and Technical Information of China (English)

    刘志; 蒋增强; 龚本刚

    2014-01-01

    针对制造车间多瓶颈预测问题,提出一种基于两种瓶颈度的多瓶颈动态预测方法,以在合理认定瓶颈责任的前提下实现系统多瓶颈的连续准确预测。首先,建立综合瓶颈度和独立瓶颈度的概念模型,并以时间、质量和成本为参数,构建其数学模型;然后,构建包含多瓶颈双层预测机制、瓶颈多态性分析和瓶颈指数迭代预测模型的多瓶颈动态预测方法;最后,将多瓶颈动态预测方法、单瓶颈度法和PBM 法运用至某汽车产品总装线,以验证该方法有效性。%Aiming at the prediction problem of multi-bottleneck in complex manufacturing shop , a dynamic prediction method of multi-bottleneck was proposed based on two bottleneck degrees ,which can forecast bottleneck accurately under conditions that bottleneck responsibility was verified reasona-bly .Firstly ,conceptual models about general bottleneck degree and independent bottleneck degree were built ,and then taking time ,quality and cost as parameters ,their mathematical models were es-tablished .Secondly ,one dynamic prediction method of multi-bottleneck was come up with ,which con-tained dual-layer multi-bottleneck prediction mechanism ,bottleneck polymorphism analysis and the it-erative prediction of bottleneck index .Finally ,it is proved to be superior and credible by comparison to the method of single bottleneck degree and the method of PBM for production bottleneck prediction problem of one vehicle assembly line .

  3. Extremely low nucleotide diversity in the X-linked region of papaya caused by a strong selective sweep.

    Science.gov (United States)

    VanBuren, Robert; Wai, Ching Man; Zhang, Jisen; Han, Jennifer; Arro, Jie; Lin, Zhicong; Liao, Zhenyang; Yu, Qingyi; Wang, Ming-Li; Zee, Francis; Moore, Richard C; Charlesworth, Deborah; Ming, Ray

    2016-11-28

    The papaya Y-linked region showed clear population structure, resulting in the detection of the ancestral male population that domesticated hermaphrodite papayas were selected from. The same populations were used to study nucleotide diversity and population structure in the X-linked region. Diversity is very low for all genes in the X-linked region in the wild dioecious population, with nucleotide diversity π syn = 0.00017, tenfold lower than the autosomal region (π syn = 0.0017) and 12-fold lower than the Y-linked region (π syn = 0.0021). Analysis of the X-linked sequences shows an undivided population, suggesting a geographically wide diversity-reducing event, whereas two subpopulations were observed in the autosomes separating gynodioecy and dioecy and three subpopulations in the Y-linked region separating three male populations. The extremely low diversity in the papaya X-linked region was probably caused by a recent, strong selective sweep before domestication, involving either the spread of a recessive mutation in an X-linked gene that is beneficial to males or a partially dominant mutation that benefitted females or both sexes. Nucleotide diversity in the domesticated X samples is about half that in the wild Xs, probably due to the bottleneck when hermaphrodites were selected during domestication. The extreme low nucleotide diversity in the papaya X-linked region is much greater than observed in humans, great apes, and the neo-X chromosome of Drosophila miranda, which show the expected pattern of Y-linked genes X-linked genes genes; papaya shows an unprecedented pattern of X-linked genes genes genes.

  4. Maintaining population persistence in the face of an extremely altered hydrograph: implications for three sensitive fishes in a tributary of the Green River, Utah

    Science.gov (United States)

    Bottcher, Jared L.

    2009-01-01

    The ability of an organism to disperse to suitable habitats, especially in modified and fragmented systems, determines individual fitness and overall population viability. The bluehead sucker (Catostomus discobolus), flannelmouth sucker (Catostomus latipinnis), and roundtail chub (Gila robusta) are three species native to the upper Colorado River Basin that now occupy only 50% of their historic range. Despite these distributional declines, populations of all three species are present in the San Rafael River, a highly regulated tributary of the Green River, Utah, providing an opportunity for research. Our goal was to determine the timing and extent of movement, habitat preferences, and limiting factors, ultimately to guide effective management and recovery of these three species. In 2007-2008, we sampled fish from 25 systematically selected, 300-m reaches in the lower 64 km of the San Rafael River, spaced to capture the range of species, life-stages, and habitat conditions present. We implanted all target species with a passive integrated transponder (PIT) tag, installed a passive PIT tag antennae, and measured key habitat parameters throughout each reach and at the site of native fish capture. We used random forest modeling to identify and rank the most important abiotic and biotic predictor variables, and reveal potential limiting factors in the San Rafael River. While flannelmouth sucker were relatively evenly distributed within our study area, highest densities of roundtail chub and bluehead sucker occurred in isolated, upstream reaches characterized by complex habitat. In addition, our movement and length-frequency data indicate downstream drift of age-0 roundtail chub, and active upstream movement of adult flannelmouth sucker, both from source populations, providing the lower San Rafael River with colonists. Our random forest analysis highlights the importance of pools, riffles, and distance-to-source populations, suggesting that bluehead sucker and roundtail

  5. Peripatric differentiation among adjacent marine lake and lagoon populations of a coastal fish, Sphaeramia orbicularis (Apogonidae, Perciformes, Teleostei).

    Science.gov (United States)

    Gotoh, Ryo O; Sekimoto, Hidekatsu; Chiba, Satoru N; Hanzawa, Naoto

    2009-08-01

    The effect of geographical isolation on speciation, particularly within short geographical ranges, is poorly understood among marine organisms. Focusing on marine lakes of the Palau Islands, we investigated the effect of geographical isolation on Sphaeramia orbicularis, a coastal fish inhabiting marine lakes and lagoons. We collected a total of 157 individuals from three meromictic marine lakes and three lagoon sites, and analyzed the genetic diversity and differentiation of the populations based on complete sequences of the mitochondrial control region (824 bp). The analyses show that the genetic diversity of marine lake populations is much lower than that of lagoon populations. Moreover, a mismatch distribution analysis suggests that marine lake populations have experienced a decrease followed by a rapid expansion of their population size. These results reveal that marine lake populations have experienced severe founder and/or bottleneck events during the last thousand to tens of thousand years. Pairwise Phi(ST )values ranged from 0.531 to 0.848 between marine lake and lagoon populations and from 0.429 to 0.870 among marine lake populations, indicating a high degree of genetic differentiation. We speculate that such peripatric differentiation between marine lake and lagoon populations was caused by a small number of individuals colonizing the lakes from the lagoon (founder event) followed by repetitive bottleneck events, such as those generated by the El Niño-Southern Oscillation (ENSO). So far, such high genetic divergences in extremely short geographical ranges (approximately 150-250 m) have scarcely been reported for marine organisms. We suggest that the marine lake is one of the good model of geographical isolation in marine organisms and each marine lake population is in the early stages of speciation.

  6. 现代媒体环境对流动人口反抗方式类型极端化趋向的影响%Effects of Types of Modern Media Environment on the Floating Population Against the Extreme Trend

    Institute of Scientific and Technical Information of China (English)

    马征

    2013-01-01

      新生代流动人口成长在不同于老一代流动人口的社会情境下,成为社会转型时期研究的关注点,而转型期的中国社会正在逐步适应和完成媒体环境的革新,当前媒体环境的多元化及其内涵特性正在使流动人口群体的反抗方式类型发生转变,新生代流动人口反抗信息获取优于老一代流动人口,反抗方式偏好差别大,有极端化发展倾向。%The new generation of migrant population, growing in different from the older generation of floating population's social context, becomes the research focus in the period of social transformation. And the transformation period of China society is being fit and finished the media environment innovation. The diversity and inclusion characteristics of current media environment is changing in the resistance of floating population type, the new generation of migrant population against information is overmatch than the old generation, and has the extreme development tendency.

  7. Unexpected island effects at an extreme: reduced Y chromosome and mitochondrial DNA diversity in Nias

    NARCIS (Netherlands)

    M. van Oven (Mannis); J.M. Hämmerle (Johannes); M. van Schoor (Marja); G. Kushnick (Geoff); P. Pennekamp (Petra); I. Zega (Idaman); O. Lao Grueso (Oscar); L. Brown (Lea); I. Kennerknecht (Ingo); M.H. Kayser (Manfred)

    2011-01-01

    textabstractThe amount of genetic diversity in a population is determined by demographic and selection events in its history. Human populations which exhibit greatly reduced overall genetic diversity, presumably resulting from severe bottlenecks or founder events, are particularly interesting, not

  8. Rapid Mitochondrial DNA Segregation in Primate Preimplantation Embryos Precedes Somatic and Germline Bottleneck

    Directory of Open Access Journals (Sweden)

    Hyo-Sang Lee

    2012-05-01

    Full Text Available The timing and mechanisms of mitochondrial DNA (mtDNA segregation and transmission in mammals are poorly understood. Genetic bottleneck in female germ cells has been proposed as the main phenomenon responsible for rapid intergenerational segregation of heteroplasmic mtDNA. We demonstrate here that mtDNA segregation occurs during primate preimplantation embryogenesis resulting in partitioning of mtDNA variants between daughter blastomeres. A substantial shift toward homoplasmy occurred in fetuses and embryonic stem cells (ESCs derived from these heteroplasmic embryos. We also observed a wide range of heteroplasmic mtDNA variants distributed in individual oocytes recovered from these fetuses. Thus, we present here evidence for a previously unknown mtDNA segregation and bottleneck during preimplantation embryo development, suggesting that return to the homoplasmic condition can occur during development of an individual organism from the zygote to birth, without a passage through the germline.

  9. Rapid mitochondrial DNA segregation in primate preimplantation embryos precedes somatic and germline bottleneck.

    Science.gov (United States)

    Lee, Hyo-Sang; Ma, Hong; Juanes, Rita Cervera; Tachibana, Masahito; Sparman, Michelle; Woodward, Joy; Ramsey, Cathy; Xu, Jing; Kang, Eun-Ju; Amato, Paula; Mair, Georg; Steinborn, Ralf; Mitalipov, Shoukhrat

    2012-05-31

    The timing and mechanisms of mitochondrial DNA (mtDNA) segregation and transmission in mammals are poorly understood. Genetic bottleneck in female germ cells has been proposed as the main phenomenon responsible for rapid intergenerational segregation of heteroplasmic mtDNA. We demonstrate here that mtDNA segregation occurs during primate preimplantation embryogenesis resulting in partitioning of mtDNA variants between daughter blastomeres. A substantial shift toward homoplasmy occurred in fetuses and embryonic stem cells (ESCs) derived from these heteroplasmic embryos. We also observed a wide range of heteroplasmic mtDNA variants distributed in individual oocytes recovered from these fetuses. Thus, we present here evidence for a previously unknown mtDNA segregation and bottleneck during preimplantation embryo development, suggesting that return to the homoplasmic condition can occur during development of an individual organism from the zygote to birth, without a passage through the germline.

  10. 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.

  11. 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.

  12. Zero-temperature quantum annealing bottlenecks in the spin-glass phase.

    Science.gov (United States)

    Knysh, Sergey

    2016-08-05

    A promising approach to solving hard binary optimization problems is quantum adiabatic annealing in a transverse magnetic field. An instantaneous ground state-initially a symmetric superposition of all possible assignments of N qubits-is closely tracked as it becomes more and more localized near the global minimum of the classical energy. Regions where the energy gap to excited states is small (for instance at the phase transition) are the algorithm's bottlenecks. Here I show how for large problems the complexity becomes dominated by O(log N) bottlenecks inside the spin-glass phase, where the gap scales as a stretched exponential. For smaller N, only the gap at the critical point is relevant, where it scales polynomially, as long as the phase transition is second order. This phenomenon is demonstrated rigorously for the two-pattern Gaussian Hopfield model. Qualitative comparison with the Sherrington-Kirkpatrick model leads to similar conclusions.

  13. Zero-temperature quantum annealing bottlenecks in the spin-glass phase

    Science.gov (United States)

    Knysh, Sergey

    2016-08-01

    A promising approach to solving hard binary optimization problems is quantum adiabatic annealing in a transverse magnetic field. An instantaneous ground state--initially a symmetric superposition of all possible assignments of N qubits--is closely tracked as it becomes more and more localized near the global minimum of the classical energy. Regions where the energy gap to excited states is small (for instance at the phase transition) are the algorithm's bottlenecks. Here I show how for large problems the complexity becomes dominated by O(log N) bottlenecks inside the spin-glass phase, where the gap scales as a stretched exponential. For smaller N, only the gap at the critical point is relevant, where it scales polynomially, as long as the phase transition is second order. This phenomenon is demonstrated rigorously for the two-pattern Gaussian Hopfield model. Qualitative comparison with the Sherrington-Kirkpatrick model leads to similar conclusions.

  14. The bottleneck 2-connected $k$-Steiner network problem for $k\\leq 2$

    CERN Document Server

    Brazil, M; Thomas, D A

    2011-01-01

    The geometric bottleneck Steiner network problem on a set of vertices $X$ embedded in a normed plane requires one to construct a graph $G$ spanning $X$ and a variable set of $k\\geq 0$ additional points, such that the length of the longest edge is minimised. If no other constraints are placed on $G$ then a solution always exists which is a tree. In this paper we consider the Euclidean bottleneck Steiner network problem for $k\\leq 2$, where $G$ is constrained to be 2-connected. By taking advantage of relative neighbourhood graphs, Voronoi diagrams, and the tree structure of block cut-vertex decompositions of graphs, we produce exact algorithms of complexity $O(n^2)$ and $O(n^2\\log n)$ for the cases $k=1$ and $k=2$ respectively. Our algorithms can also be extended to other norms such as the $L_p$ planes.

  15. Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes.

    Science.gov (United States)

    Cai, Xiaoyun; Qin, Zhendong; 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.

  16. Bottleneck of Farmers’ Quality in New Socialist Countryside Construction and Countermeasures

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    We analyzed problems of farmers’ quality in the new socialist countryside construction,including low educational level,poor specialized skills,and low ideological and ethical quality.These problems become bottleneck of the socialist countryside construction.In view of these problems,we put forward following countermeasures:speeding up urbanization development,consolidating rural basic education,strengthening rural vocational education,and developing new approaches to improve farmers’ ideological and ethical quality.

  17. 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

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

    Directory of Open Access Journals (Sweden)

    Poobalan Pillay

    2017-01-01

    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.

  19. 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.

  20. Bottleneck genes and community structure in the cell cycle network of S. pombe.

    Directory of Open Access Journals (Sweden)

    Cécile Caretta-Cartozo

    2007-06-01

    Full Text Available The identification of cell cycle-related genes is still a difficult task, even for organisms with relatively few genes such as the fission yeast. Several gene expression studies have been published on S. pombe showing similarities but also discrepancies in their results. We introduce a network in which the weight of each link is a function of the phase difference between the expression peaks of two genes. The analysis of the stability of the clustering through the computation of an entropy parameter reveals a structure made of four clusters, the first one corresponding to a robustly connected M-G1 component, the second to genes in the S phase, and the third and fourth to two G2 components. They are separated by bottleneck structures that appear to correspond to cell cycle checkpoints. We identify a number of genes that are located on these bottlenecks. They represent a novel group of cell cycle regulatory genes. They all show interesting functions, and they are supposed to be involved in the regulation of the transition from one phase to the next. We therefore present a comparison of the available studies on the fission yeast cell cycle and a general statistical bioinformatics methodology to find bottlenecks and gene community structures based on recent developments in network theory.

  1. Mine production index (MPI)-extension of OEE for bottleneck detection in mining

    Institute of Scientific and Technical Information of China (English)

    Amol Arun Lanke; Seyed Hadi Hoseinie; Behzad Ghodrati

    2016-01-01

    Although mining production depends on various equipments, significant amount of production loss can be attributed a specific equipment or fleet. Bottleneck is defined not only by production loss but also by our satisfaction from the equipment. The user satisfaction could be measured as machine effectiveness. Mining literatures on performance improvement and optimization of equipment operations assert importance of availability, utilization and production performance as key parameters. These three param-eters are useful for evaluating effectiveness of equipment. Mine production index (MPI), which can rep-resent the effect of these factors, has been applied for continuous operation in mining. MPI uses Fuzzy Delphi Analytical Hierarchy Process to determine importance of each three parameter for individual equipment. A case study in a Swedish open pit mine was done to evaluate the field application of MPI. The results reveal that crusher is the bottleneck equipment in studied mine. As a methodical approach, an algorithm which uses MPI and detects bottleneck in continuous mining operation has been proposed.

  2. Lagrangian-averaged model for magnetohydrodynamic turbulence and the absence of bottlenecks.

    Science.gov (United States)

    Pietarila Graham, Jonathan; Mininni, Pablo D; Pouquet, Annick

    2009-07-01

    We demonstrate that, for the case of quasiequipartition between the velocity and the magnetic field, the Lagrangian-averaged magnetohydrodynamics (LAMHD) alpha model reproduces well both the large-scale and the small-scale properties of turbulent flows; in particular, it displays no increased (superfilter) bottleneck effect with its ensuing enhanced energy spectrum at the onset of the subfilter scales. This is in contrast to the case of the neutral fluid in which the Lagrangian-averaged Navier-Stokes alpha model is somewhat limited in its applications because of the formation of spatial regions with no internal degrees of freedom and subsequent contamination of superfilter-scale spectral properties. We argue that, as the Lorentz force breaks the conservation of circulation and enables spectrally nonlocal energy transfer (associated with Alfvén waves), it is responsible for the absence of a viscous bottleneck in magnetohydrodynamics (MHD), as compared to the fluid case. As LAMHD preserves Alfvén waves and the circulation properties of MHD, there is also no (superfilter) bottleneck found in LAMHD, making this method capable of large reductions in required numerical degrees of freedom; specifically, we find a reduction factor of approximately 200 when compared to a direct numerical simulation on a large grid of 1536;{3} points at the same Reynolds number.

  3. Empirical Features of Spontaneous and Induced Traffic Breakdowns in Free Flow at Highway Bottlenecks

    CERN Document Server

    Kerner, Boris S; Klenov, Sergey L; Rehborn, Hubert; Leibel, Michael

    2015-01-01

    Based on an empirical study of real field traffic data measured in 1996--2014 through road detectors installed on German freeways, we reveal physical features of empirical nuclei for spontaneous traffic breakdown in free flow at highway bottlenecks. It is shown that the source of a nucleus for traffic breakdown is the solely difference between empirical spontaneous and induced traffic breakdowns at a highway bottleneck. Microscopic traffic simulations with a stochastic traffic flow model in the framework of three-phase theory explain the empirical findings. It turns out that in the most cases, a nucleus for empirical spontaneous traffic breakdown occurs through an interaction of one of waves in free flow with an empirical permanent speed disturbance localized at a highway bottleneck. The wave is a localized structure in free flow, in which the total flow rate is larger and the speed averaged across the highway is smaller than outside the wave. The waves in free flow appear due to oscilations in the percentage...

  4. Incident and Traffic-Bottleneck Detection Algorithm in High-Resolution Remote Sensing Imagery

    Directory of Open Access Journals (Sweden)

    S.M.M. Kahaki

    2012-09-01

    Full Text Available One of the most important methods to solve traffic congestion is to detect the incident state of a roadway. This paper describes the development of a method for road traffic monitoring aimed at the acquisition and analysis of remote sensing imagery. We propose a strategy for road extraction, vehicle detection and incident detection from remote sensing imagery using techniques based on neural networks, Radon transform for angle detection and traffic-flow measurements. Traffic-bottleneck detection is another method that is proposed for recognizing incidents in both offline and real-time mode. Traffic flows and incidents are extracted from aerial images of bottleneck zones. The results show that the proposed approach has a reasonable detection performance compared to other methods. The best performance of the learning system was a detection rate of 87% and a false alarm rate of less than 18% on 45 aerial images of roadways. The performance of the traffic-bottleneck detection method had a detection rate of 87.5%.

  5. Incident and Traffic-Bottleneck Detection Algorithm in High-Resolution Remote Sensing Imagery

    Directory of Open Access Journals (Sweden)

    Sayed M.M. Kahaki

    2013-09-01

    Full Text Available One  of  the  most  important  methods  to  solve  traffic  congestion  is  to detect the incident state of a roadway. This paper describes the development of a method  for  road  traffic  monitoring  aimed  at  the  acquisition  and  analysis  of remote  sensing  imagery.  We  propose  a  strategy  for  road  extraction,  vehicle detection  and incident detection  from remote sensing imagery using techniques based on neural networks, Radon transform  for angle detection and traffic-flow measurements.  Traffic-bottleneck  detection  is  another  method  that  is  proposed for recognizing incidents in both offline and real-time mode. Traffic flows and incidents are extracted from aerial images of bottleneck zones. The results show that the proposed approach has a reasonable detection performance compared to other methods. The best performance of the learning system was a detection rate of 87% and a false alarm rate of less than 18% on 45 aerial images of roadways. The performance of the traffic-bottleneck detection  method had a detection rate of 87.5%.

  6. 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

    2013-08-22

    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.

  7. 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

  8. Treatment of neonatal infections: a multi-country analysis of health system bottlenecks and potential solutions.

    Science.gov (United States)

    Simen-Kapeu, Aline; Seale, Anna C; Wall, Steve; Nyange, Christabel; Qazi, Shamim A; Moxon, Sarah G; Young, Mark; Liu, Grace; Darmstadt, Gary L; Dickson, Kim E; Lawn, Joy E

    2015-01-01

    Around one-third of the world's 2.8 million neonatal deaths are caused by infections. Most of these deaths are preventable, but occur due to delays in care-seeking, and access to effective antibiotic treatment with supportive care. Understanding variation in health system bottlenecks to scale-up of case management of neonatal infections and identifying solutions is essential to reduce mortality, and also morbidity. A standardised bottleneck analysis tool was applied in 12 countries in Africa and Asia as part of the development of the Every Newborn Action Plan. Country workshops involved technical experts to complete a survey tool, to grade health system "bottlenecks" hindering scale up of maternal-newborn intervention packages. Quantitative and qualitative methods were used to analyse the data, combined with literature review, to present priority bottlenecks and synthesise actions to improve case management of newborn infections. For neonatal infections, the health system building blocks most frequently graded as major or significant bottlenecks, irrespective of mortality context and geographical region, were health workforce (11 out of 12 countries), and community ownership and partnership (11 out of 12 countries). Lack of data to inform decision making, and limited funding to increase access to quality neonatal care were also major challenges. Rapid recognition of possible serious bacterial infection and access to care is essential. Inpatient hospital care remains the first line of treatment for neonatal infections. In situations where referral is not possible, the use of simplified antibiotic regimens for outpatient management for non-critically ill young infants has recently been reported in large clinical trials; WHO is developing a guideline to treat this group of young infants. Improving quality of care through more investment in the health workforce at all levels of care is critical, in addition to ensuring development and dissemination of national

  9. The effect of recurrent floods on genetic composition of marble trout populations.

    Directory of Open Access Journals (Sweden)

    José Martin Pujolar

    Full Text Available 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.

  10. The Effect of Recurrent Floods on Genetic Composition of Marble Trout Populations

    Science.gov (United States)

    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 FST 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

  11. Work conditions as risk factors for varicose veins of the lower extremities in certain professions of the working population of Rijeka.

    Directory of Open Access Journals (Sweden)

    Kontosić I

    2000-02-01

    Full Text Available This research aims to establish the effect of working conditions on the appearance of varicose veins. The epidemiological study was carried out on 1,324 examinees, 530 males and 794 females, employed in 5 highly represented groups of professional activities in Rijeka (catering, trade, light industry, heavy industry and finances. The data were collected by survey and clinical examination. Varicose veins were more prevalent in the trade than in the office workers (odds ratio (OR = 2.08; 95% confidence interval (CI = 1.31-3.31, and more prevalent in catering industries than in the office workers (OR = 1.56; 95% CI = 1.001-2.43. chi 2-testing suggested that standing in the workplace (OR = 1.35; 95% CI = 0.95-1.92, weight handling while working (OR = 1.29; 95% CI = 1.01-1.64 and working indoors (OR = 1.61; 95% CI = 1.02-2.53 were risk factors for varicose veins. By multiple logistic regression, the following risk factors were isolated in the total population: female sex (OR = 1.92; 95% CI = 1.37-2.67, workplace (OR = 0.89; 95% CI = 0.78-0.99, age (OR = 1.05; 95% CI = 1.03-1.07, body mass index (OR = 1.04; 95% CI = 1.01-1.07 and family history of the disease (OR = 1.99; 95% CI = 1.55-2.57.

  12. Extremely low prevalence of Batrachochytrium dendrobatidis in frog populations from neotropical dry forest of Costa Rica supports the existence of a climatic refuge from disease.

    Science.gov (United States)

    Zumbado-Ulate, Héctor; Bolaños, Federico; Gutiérrez-Espeleta, Gustavo; Puschendorf, Robert

    2014-12-01

    Population declines and extinctions of numerous species of amphibians, especially stream-breeding frogs, have been linked to the emerging infectious disease chytridiomycosis, caused by the chytrid fungus, Batrachochytrium dendrobatidis. In Central America, most of the 34 species of the Craugastor punctariolus species group have disappeared in recent years in high- and low-elevation rainforests. Distribution models for B. dendrobatidis and the continuous presence of the extirpated stream-dwelling species, Craugastor ranoides, in the driest site of Costa Rica (Santa Elena Peninsula), suggest that environmental conditions might restrict the growth and development of B. dendrobatidis, existing as a refuge from chytridiomycosis-driven extinction. We conducted field surveys to detect and quantify the pathogen using Real-time PCR in samples from 15 species of frogs in two locations of tropical dry forest. In Santa Elena Peninsula, we swabbed 310 frogs, and only one sample of the species, C. ranoides, tested positive for B. dendrobatidis (prevalence refuges from chytridiomycosis and highlights the importance of tropical dry forest conservation for amphibians in the face of epidemic disease.

  13. Osmoregulatory strategies in natural populations of the black-chinned tilapia Sarotherodon melanotheron exposed to extreme salinities in West African estuaries.

    Science.gov (United States)

    Lorin-Nebel, Catherine; Avarre, Jean-Christophe; Faivre, Nicolas; Wallon, Sophie; Charmantier, Guy; Durand, Jean-Dominique

    2012-08-01

    The effect of salinity was studied in natural populations of the black-chinned tilapia (Sarotherodon melanotheron) from West Africa. This euryhaline species colonizes nearly all coastal environments from bays to lagoons characterized by salinities ranging from fresh water to hypersaline water over 100 ‰. Individuals were sampled during the dry season at several locations characterized by different levels of salinity (3-102 ‰). Their osmotic status and their gills were analyzed. The branchial mitochondria-rich cells (MRC), localized at the basis of the filaments and along the lamellae in fish taken from the saline stations, showed a wide plasticity with significant differences in their number and size. The most striking results were a significant larger area (≈3x) and a higher number (≈55x) of MRC at high salinity (102 ‰) compared to low salinity (3 ‰). The major ion transporters and channels were localized by immunocytochemistry and different expression patterns have been recorded between stations. Despite an increased Na⁺/K⁺-ATPase (NKA) α-subunit expression and NKA activity, pointing to an increased monovalent ion excretion, a severe osmotic imbalance was recorded in animals living in hypersaline environments.

  14. Bottleneck Prediction Method Based on Improved Adaptive Network-based Fuzzy Inference System (ANFIS) in Semiconductor Manufacturing System%Bottleneck Prediction Method Based on Improved Adaptive Network-based Fuzzy Inference System (ANFIS) in Semiconductor Manufacturing System

    Institute of Scientific and Technical Information of China (English)

    曹政才; 邓积杰; 刘民; 王永吉

    2012-01-01

    Semiconductor manufacturing (SM) system is one of the most complicated hybrid processes involved continuously variable dynamical systems and discrete event dynamical systems. The optimization and scheduling of semiconductor fabrication has long been a hot research direction in automation. Bottleneck is the key factor to a SM system, which seriously influences the throughput rate, cycle time, time-delivery rate, etc. Efficient prediction for the bottleneck of a SM system provides the best support for the consequent scheduling. Because categorical data (product types, releasing strategies) and numerical data (work in process, processing time, utilization rate, buffer length, etc.) have significant effect on bottleneck, an improved adaptive network-based fuzzy inference system (ANFIS) was adopted in this study to predict bottleneck since conventional neural network-based methods accommodate only numerical inputs. In this improved ANFIS, the contribution of categorical inputs to firing strength is reflected through a transformation matrix. In order to tackle high-dimensional inputs, reduce the number of fuzzy rules and obtain high prediction accuracy, a fuzzy c-means method combining binary tree linear division method was applied to identify the initial structure of fuzzy inference system. According to the experimental results, the main-bottleneck and sub-bottleneck of SM system can be predicted accurately with the proposed method.

  15. Extremely Preterm Birth

    Science.gov (United States)

    ... Events Advocacy For Patients About ACOG Extremely Preterm Birth Home For Patients Search FAQs Extremely Preterm Birth ... Spanish FAQ173, June 2016 PDF Format Extremely Preterm Birth Pregnancy When is a baby considered “preterm” or “ ...

  16. Risk-based water resources planning: Coupling water allocation and water quality management under extreme droughts

    Science.gov (United States)

    Mortazavi-Naeini, M.; Bussi, G.; Hall, J. W.; Whitehead, P. G.

    2016-12-01

    The main aim of water companies is to have a reliable and safe water supply system. To fulfil their duty the water companies have to consider both water quality and quantity issues and challenges. Climate change and population growth will have an impact on water resources both in terms of available water and river water quality. Traditionally, a distinct separation between water quality and abstraction has existed. However, water quality can be a bottleneck in a system since water treatment works can only treat water if it meets certain standards. For instance, high turbidity and large phytoplankton content can increase sharply the cost of treatment or even make river water unfit for human consumption purposes. It is vital for water companies to be able to characterise the quantity and quality of water under extreme weather events and to consider the occurrence of eventual periods when water abstraction has to cease due to water quality constraints. This will give them opportunity to decide on water resource planning and potential changes to reduce the system failure risk. We present a risk-based approach for incorporating extreme events, based on future climate change scenarios from a large ensemble of climate model realisations, into integrated water resources model through combined use of water allocation (WATHNET) and water quality (INCA) models. The annual frequency of imposed restrictions on demand is considered as measure of reliability. We tested our approach on Thames region, in the UK, with 100 extreme events. The results show increase in frequency of imposed restrictions when water quality constraints were considered. This indicates importance of considering water quality issues in drought management plans.

  17. 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.

  18. 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.

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

    Science.gov (United States)

    Rebolledo-Jaramillo, Boris; Su, Marcia Shu-Wei; Stoler, Nicholas; McElhoe, Jennifer A; Dickins, Benjamin; Blankenberg, Daniel; Korneliussen, Thorfinn S; Chiaromonte, Francesca; Nielsen, Rasmus; Holland, Mitchell M; Paul, Ian M; Nekrutenko, Anton; Makova, Kateryna D

    2014-10-28

    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. For deleterious heteroplasmies, a severe bottleneck may abruptly transform a benign (low) frequency in a mother into a disease-causing (high) frequency in her child. Here we present a high-resolution study of heteroplasmy transmission conducted on blood and buccal mtDNA of 39 healthy mother-child pairs of European ancestry (a total of 156 samples, each sequenced at ∼20,000× per site). On average, each individual carried one heteroplasmy, and one in eight individuals carried a disease-associated heteroplasmy, with minor allele frequency ≥1%. We observed frequent drastic heteroplasmy frequency shifts between generations and estimated the effective size of the germ-line mtDNA bottleneck at only ∼30-35 (interquartile range from 9 to 141). Accounting for heteroplasmies, we estimated the mtDNA germ-line mutation rate at 1.3 × 10(-8) (interquartile range from 4.2 × 10(-9) to 4.1 × 10(-8)) mutations per site per year, 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.

  20. Alpha-band suppression in the visual word form area as a functional bottleneck to consciousness.

    Science.gov (United States)

    Levy, Jonathan; Vidal, Juan R; Oostenveld, Robert; FitzPatrick, Ian; Démonet, Jean-François; Fries, Pascal

    2013-09-01

    The current state of empirical investigations refers to consciousness as an all-or-none phenomenon. However, a recent theoretical account opens up this perspective by proposing a partial level (between nil and full) of conscious perception. In the well-studied case of single-word reading, short-lived exposure can trigger incomplete word-form recognition wherein letters fall short of forming a whole word in one's conscious perception thereby hindering word-meaning access and report. Hence, the processing from incomplete to complete word-form recognition straightforwardly mirrors a transition from partial to full-blown consciousness. We therefore hypothesized that this putative functional bottleneck to consciousness (i.e. the perceptual boundary between partial and full conscious perception) would emerge at a major key hub region for word-form recognition during reading, namely the left occipito-temporal junction. We applied a real-time staircase procedure and titrated subjective reports at the threshold between partial (letters) and full (whole word) conscious perception. This experimental approach allowed us to collect trials with identical physical stimulation, yet reflecting distinct perceptual experience levels. Oscillatory brain activity was monitored with magnetoencephalography and revealed that the transition from partial-to-full word-form perception was accompanied by alpha-band (7-11 Hz) power suppression in the posterior left occipito-temporal cortex. This modulation of rhythmic activity extended anteriorly towards the visual word form area (VWFA), a region whose selectivity for word-forms in perception is highly debated. The current findings provide electrophysiological evidence for a functional bottleneck to consciousness thereby empirically instantiating a recently proposed partial perspective on consciousness. Moreover, the findings provide an entirely new outlook on the functioning of the VWFA as a late bottleneck to full-blown conscious word

  1. Testing founder effect speciation: Divergence population genetics of the Spoonbills Platalea regia and Pl. minor (Threskiornithidae, Aves)

    Science.gov (United States)

    Yeung, Carol K.L.; Tsai, Pi-Wen; Chesser, R. Terry; Lin, Rong-Chien; Yao, Cheng-Te; Tian, Xiu-Hua; Li, Shou-Hsien

    2011-01-01

    Although founder effect speciation has been a popular theoretical model for the speciation of geographically isolated taxa, its empirical importance has remained difficult to evaluate due to the intractability of past demography, which in a founder effect speciation scenario would involve a speciational bottleneck in the emergent species and the complete cessation of gene flow following divergence. Using regression-weighted approximate Bayesian computation, we tested the validity of these two fundamental conditions of founder effect speciation in a pair of sister species with disjunct distributions: the royal spoonbill Platalea regia in Australasia and the black-faced spoonbill Pl. minor in eastern Asia. When compared with genetic polymorphism observed at 20 nuclear loci in the two species, simulations showed that the founder effect speciation model had an extremely low posterior probability (1.55 × 10-8) of producing the extant genetic pattern. In contrast, speciation models that allowed for postdivergence gene flow were much more probable (posterior probabilities were 0.37 and 0.50 for the bottleneck with gene flow and the gene flow models, respectively) and postdivergence gene flow persisted for a considerable period of time (more than 80% of the divergence history in both models) following initial divergence (median = 197,000 generations, 95% credible interval [CI]: 50,000-478,000, for the bottleneck with gene flow model; and 186,000 generations, 95% CI: 45,000-477,000, for the gene flow model). Furthermore, the estimated population size reduction in Pl. regia to 7,000 individuals (median, 95% CI: 487-12,000, according to the bottleneck with gene flow model) was unlikely to have been severe enough to be considered a bottleneck. Therefore, these results do not support founder effect speciation in Pl. regia but indicate instead that the divergence between Pl. regia and Pl. minor was probably driven by selection despite continuous gene flow. In this light, we

  2. Phonon bottleneck in GaAs/AlxGa1−xAs quantum dots

    Directory of Open Access Journals (Sweden)

    Y. C. Chang

    2015-06-01

    Full Text Available We report low-temperature photoluminescence measurements on highly-uniform GaAs/AlxGa1−xAs quantum dots grown by droplet epitaxy. Recombination between confined electrons and holes bound to carbon acceptors in the dots allow us to determine the energies of the confined states in the system, as confirmed by effective mass calculations. The presence of acceptor-bound holes in the quantum dots gives rise to a striking observation of the phonon-bottleneck effect.

  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...... without being constrained by the topologies of minimum spanning trees. Computational experiments show a significant solution quality improvement....

  4. Breaking CFD Bottlenecks in Gas-Turbine Flow-Path Design

    Science.gov (United States)

    Davis, Roger L.; Dannenhoffer, John F., III; Clark, John P.

    2010-01-01

    New ideas are forthcoming to break existing bottlenecks in using CFD during design. CAD-based automated grid generation. Multi-disciplinary use of embedded, overset grids to eliminate complex gridding problems. Use of time-averaged detached-eddy simulations as norm instead of "steady" RANS to include effects of self-excited unsteadiness. Combined GPU/Core parallel computing to provide over an order of magnitude increase in performance/price ratio. Gas-turbine applications are shown here but these ideas can be used for other Air Force, Navy, and NASA applications.

  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. 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...... without being constrained by the topologies of minimum spanning trees. Computational experiments show a significant solution quality improvement....

  7. Global change ecotoxicology: Identification of early life history bottlenecks in marine invertebrates, variable species responses and variable experimental approaches.

    Science.gov (United States)

    Byrne, M

    2012-05-01

    Climate change is a threat to marine biota because increased atmospheric CO₂ is causing ocean warming, acidification, hypercapnia and decreased carbonate saturation. These stressors have toxic effects on invertebrate development. The persistence and success of populations requires all ontogenetic stages be completed successfully and, due to their sensitivity to environmental stressors, developmental stages may be a population bottleneck in a changing ocean. Global change ecotoxicology is being used to identify the marine invertebrate developmental stages vulnerable to climate change. This overview of research, and the methodologies used, shows that most studies focus on acidification, with few studies on ocean warming, despite a long history of research on developmental thermotolerance. The interactive effects of stressors are poorly studied. Experimental approaches differ among studies. Fertilization in many species exhibits a broad tolerance to warming and/or acidification, although different methodologies confound inter-study comparisons. Early development is susceptible to warming and most calcifying larvae are sensitive to acidification/increased pCO₂. In multistressor studies moderate warming diminishes the negative impact of acidification on calcification in some species. Development of non-calcifying larvae appears resilient to near-future ocean change. Although differences in species sensitivities to ocean change stressors undoubtedly reflect different tolerance levels, inconsistent handling of gametes, embryos and larvae probably influences different research outcomes. Due to the integrative 'developmental domino effect', life history responses will be influenced by the ontogenetic stage at which experimental incubations are initiated. Exposure to climate change stressors from early development (fertilization where possible) in multistressor experiments is needed to identify ontogenetic sensitivities and this will be facilitated by more consistent

  8. Multidimensional extremal dependence coefficients

    OpenAIRE

    2017-01-01

    Extreme values modeling has attracting the attention of researchers in diverse areas such as the environment, engineering, or finance. Multivariate extreme value distributions are particularly suitable to model the tails of multidimensional phenomena. The analysis of the dependence among multivariate maxima is useful to evaluate risk. Here we present new multivariate extreme value models, as well as, coefficients to assess multivariate extremal dependence.

  9. The European Extreme Right and Religious Extremism

    Directory of Open Access Journals (Sweden)

    Jean-Yves Camus

    2007-12-01

    Full Text Available The ideology of the Extreme Right in Western Europe is rooted in Catholic fundamentalism and Counter-Revolutionary ideas. However, the Extreme Right, like all other political families, has had to adjust to an increasingly secular society. The old link between religion and the Extreme Right has thus been broken and in fact already was when Fascism overtook Europe: Fascism was secular, sometimes even anti-religious, in its essence. Although Catholic fundamentalists still retain strong positions within the apparatus of several Extreme Right parties (Front National, the vote for the Extreme Right is generally weak among regular churchgoers and strong among non-believers. In several countries, the vote for the Extreme Right is stronger among Protestant voters than among Catholics, since while Catholics may support Christian-Democratic parties, there are very few political parties linked to Protestant churches. Presently, it also seems that Paganism is becoming the dominant religious creed within the Extreme Right. In a multicultural Europe, non-Christian forms of religious fundamentalism such as Islamism also exist with ideological similarities to the Extreme Right, but this is not sufficient to categorize Islamism as a form of Fascism. Some Islamist groups seek alliances with the Extreme Right on the basis of their common dislike for Israel and the West, globalization and individual freedom of thought.

  10. The Now-or-Never bottleneck: A fundamental constraint on language.

    Science.gov (United States)

    Christiansen, Morten H; Chater, Nick

    2016-01-01

    Memory is fleeting. New material rapidly obliterates previous material. How, then, can the brain deal successfully with the continual deluge of linguistic input? We argue that, to deal with this "Now-or-Never" bottleneck, the brain must compress and recode linguistic input as rapidly as possible. This observation has strong implications for the nature of language processing: (1) the language system must "eagerly" recode and compress linguistic input; (2) as the bottleneck recurs at each new representational level, the language system must build a multilevel linguistic representation; and (3) the language system must deploy all available information predictively to ensure that local linguistic ambiguities are dealt with "Right-First-Time"; once the original input is lost, there is no way for the language system to recover. This is "Chunk-and-Pass" processing. Similarly, language learning must also occur in the here and now, which implies that language acquisition is learning to process, rather than inducing, a grammar. Moreover, this perspective provides a cognitive foundation for grammaticalization and other aspects of language change. Chunk-and-Pass processing also helps explain a variety of core properties of language, including its multilevel representational structure and duality of patterning. This approach promises to create a direct relationship between psycholinguistics and linguistic theory. More generally, we outline a framework within which to integrate often disconnected inquiries into language processing, language acquisition, and language change and evolution.

  11. 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.

  12. 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

  13. 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.

  14. Science or Art? How Aesthetic Standards Grease the Way Through the Publication Bottleneck but Undermine Science.

    Science.gov (United States)

    Giner-Sorolla, Roger

    2012-11-01

    The current crisis in psychological research involves issues of fraud, replication, publication bias, and false positive results. I argue that this crisis follows the failure of widely adopted solutions to psychology's similar crisis of the 1970s. The untouched root cause is an information-economic one: Too many studies divided by too few publication outlets equals a bottleneck. Articles cannot pass through just by showing theoretical meaning and methodological rigor; their results must appear to support the hypothesis perfectly. Consequently, psychologists must master the art of presenting perfect-looking results just to survive in the profession. This favors aesthetic criteria of presentation in a way that harms science's search for truth. Shallow standards of statistical perfection distort analyses and undermine the accuracy of cumulative data; narrative expectations encourage dishonesty about the relationship between results and hypotheses; criteria of novelty suppress replication attempts. Concerns about truth in research are emerging in other sciences and may eventually descend on our heads in the form of difficult and insensitive regulations. I suggest a more palatable solution: to open the bottleneck, putting structures in place to reward broader forms of information sharing beyond the exquisite art of present-day journal publication. © The Author(s) 2012.

  15. [Bottlenecks in the provision of inpatient care--caused by the Hospital Funding Act].

    Science.gov (United States)

    Jansen, Christoph

    2010-01-01

    The responsibility of the state for ensuring the provision of hospital care services to its citizens derives from the welfare state principle laid down in Sect. 20 para. 1 GG (Grundgesetz, i.e., the German constitutional law). The state fulfils this responsibility by means of planning and funding regulations in the Hospital Funding Act (KHG), the Hospital Remuneration Act (KHEntG), the National Ordinance on Hospital Rates (BPflV), the Hospital Laws of the German federal states and other supplementary legislation. The funding of hospitals is based on a dual funding system, meaning that hospital investment costs generally need to be borne by the German federal states as required, while operating costs will have to be funded through the remuneration for hospital treatments. Because of the tight budget situation of the German federal states a considerable backlog of investment has built up. After a transition period (between 2005 and 2009) operating costs are now funded on the basis of the so-called DRG system (DRG=Diagnosis Related Groups)--irrespective of the actual costs incurred by each individual hospital, which has led to a commodification of hospital care services. Whether this commodification avoids bottlenecks in the provision of health services to hospital patients or creates additional bottlenecks, is a controversial issue.

  16. Topological-based bottleneck analysis and improvement strategies for traffic networks

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    A method is proposed to find key components of traffic networks with homogenous and heterogeneous topologies, in which heavier traffic flow is transported. One component, called the skeleton, is the minimum spanning tree (MST) based on the zero flow cost (ZCMST). The other component is the infinite incipient percolation cluster (IIC) which represents the spine of the traffic network. Then, a new method to analysis the property of the bottleneck in a large scale traffic network is given from a macroscopic and statistical viewpoint. Moreover, three effective strategies are proposed to alleviate traffic congestion. The significance of the findings is that one can significantly improve the global transport by enhancing the capacity in the ZCMST with a few links, while for improving the local traffic property, improving a tiny fraction of the traffic network in the IIC is effective. The result can be used to help traffic managers prevent and alleviate traffic congestion in time, guard against the formation of congestion bottleneck, and make appropriate policies for traffic demand management. Meanwhile, the method has very important theoretical significance and practical worthiness in optimizing traffic organization, traffic control, and disposal of emergency.

  17. A Based-Bottleneck Multiple Vehicle Type Dynamic Marginal Cost Model and Algorithm

    Directory of Open Access Journals (Sweden)

    Shuguang Li

    2012-09-01

    Full Text Available Single vehicle type dynamic marginal cost model is extended to multiple vehicle type dynamic one based on time-dependent multiple vehicle type queue analysis at a bottleneck. A dynamic link model is presented to model interactions between cars and trucks, given the link consists of two distinct segments. The first segment is the running segment on which cars (trucks run at their free-flow speeds and the second segment is the exit queue segment. A car or a truck is assumed to be a point without length. The class-specific pi parameter is used to transform the effect of truck into passenger car equivalents, so the exit flow of cars and trucks can be calculated according to the exit capacity of a bottleneck. The analytic expression of multiple vehicle type dynamic marginal cost function is deduced under congested and uncongested conditions. Then a heuristic algorithm is presented in solving multiple vehicle type dynamic queues, tolls under system optimum and user equilibrium conditions. The numerical example illustrates the simplicity and applicability of the proposed approach.

  18. The physics of empirical nuclei for spontaneous traffic breakdown in free flow at highway bottlenecks

    Science.gov (United States)

    Kerner, Boris S.; Koller, Micha; Klenov, Sergey L.; Rehborn, Hubert; Leibel, Michael

    2015-11-01

    Based on an empirical study of real field traffic data measured in 1996-2014 through road detectors installed on German freeways, we reveal physical features of empirical nuclei for spontaneous traffic breakdown in free flow at highway bottlenecks. A microscopic stochastic three-phase traffic model of the nucleation of spontaneous traffic breakdown presented in the article explains the empirical findings. It turns out that in the most cases a nucleus for the breakdown occurs through an interaction of one of waves in free flow with an empirical permanent speed disturbance localized at a highway bottleneck. The wave is a localized structure in free flow, in which the total flow rate is larger and the speed averaged across the highway is smaller than outside the wave. The waves in free flow appear due to oscillations in the percentage of slow vehicles; these waves propagate with the average speed of slow vehicles in free flow. Any of the empirical waves exhibits a two-dimensional asymmetric spatiotemporal structure: Wave's characteristics are different in different highway lanes.

  19. Identification and Validation of Ifit1 as an Important Innate Immune Bottleneck

    Energy Technology Data Exchange (ETDEWEB)

    McDermott, Jason E.; Vartanian, Keri B.; Mitchell, Hugh D.; Stevens, S.L.; Sanfilippo, Antonio P.; Stenzel-Poore, Mary

    2012-06-20

    The innate immune system plays important roles in a number of disparate processes. Foremost, innate immunity is a first responder to invasion by pathogens and triggers early defensive responses and recruits the adaptive immune system. The innate immune system also responds to endogenous damage signals that arise from tissue injury. Recently it has been found that innate immunity plays an important role in neuroprotection against ischemic stroke through the activation of the primary innate immune receptors, Toll-like receptors (TLRs). Using several large-scale transcriptomic data sets from mouse and mouse macrophage studies we identified targets predicted to be important in controlling innate immune processes initiated by TLR activation. Targets were identified as genes with high betweenness centrality, so-called bottlenecks, in networks inferred from statistical associations between gene expression patterns. A small set of putative bottlenecks were identified in each of the data sets investigated including interferon-stimulated genes (Ifit1, Ifi47, Tgtp and Oasl2) as well as genes uncharacterized in immune responses (Axud1 and Ppp1r15a). We further validated one of these targets, Ifit1, in mouse macrophages by showing that silencing it suppresses induction of predicted downstream genes by lipopolysaccharide (LPS)-mediated TLR4 activation through an unknown direct or indirect mechanism. Our study demonstrates the utility of network analysis for identification of interesting targets related to innate immune function, and highlights that Ifit1 can exert a positive regulatory effect on downstream genes.

  20. Identification and validation of Ifit1 as an important innate immune bottleneck.

    Directory of Open Access Journals (Sweden)

    Jason E McDermott

    Full Text Available The innate immune system plays important roles in a number of disparate processes. Foremost, innate immunity is a first responder to invasion by pathogens and triggers early defensive responses and recruits the adaptive immune system. The innate immune system also responds to endogenous damage signals that arise from tissue injury. Recently it has been found that innate immunity plays an important role in neuroprotection against ischemic stroke through the activation of the primary innate immune receptors, Toll-like receptors (TLRs. Using several large-scale transcriptomic data sets from mouse and mouse macrophage studies we identified targets predicted to be important in controlling innate immune processes initiated by TLR activation. Targets were identified as genes with high betweenness centrality, so-called bottlenecks, in networks inferred from statistical associations between gene expression patterns. A small set of putative bottlenecks were identified in each of the data sets investigated including interferon-stimulated genes (Ifit1, Ifi47, Tgtp and Oasl2 as well as genes uncharacterized in immune responses (Axud1 and Ppp1r15a. We further validated one of these targets, Ifit1, in mouse macrophages by showing that silencing it suppresses induction of predicted downstream genes by lipopolysaccharide (LPS-mediated TLR4 activation through an unknown direct or indirect mechanism. Our study demonstrates the utility of network analysis for identification of interesting targets related to innate immune function, and highlights that Ifit1 can exert a positive regulatory effect on downstream genes.

  1. Interference of two codirectional exclusion processes in the presence of a static bottleneck: A biologically motivated model

    Science.gov (United States)

    Mishra, Bhavya; Chowdhury, Debashish

    2017-06-01

    We develop a two-species exclusion process with a distinct pair of entry and exit sites for each species of rigid rods. The relatively slower forward stepping of the rods in an extended bottleneck region, located in between the two entry sites, controls the extent of interference of the codirectional flow of the two species of rods. The relative positions of the sites of entry of the two species of rods with respect to the location of the bottleneck are motivated by a biological phenomenon. However, the primary focus of the study here is to explore the effects of the interference of the flow of the two species of rods on their spatiotemporal organization and the regulations of this interference by the extended bottleneck. By a combination of mean-field theory and computer simulation, we calculate the flux of both species of rods and their density profiles as well as the composite phase diagrams of the system. If the bottleneck is sufficiently stringent, then some of the phases become practically unrealizable, although not ruled out on the basis of any fundamental physical principle. Moreover, the extent of suppression of flow of the downstream entrants by the flow of the upstream entrants can also be regulated by the strength of the bottleneck. We speculate on the possible implications of the results in the context of the biological phenomenon that motivated the formulation of the theoretical model.

  2. Population status and population genetics of northern leopard frogs in Arizona

    Science.gov (United States)

    Theimer, Tad C.; Drost, Charles A.; O'Donnell, Ryan P.; Mock, Karen E.

    2011-01-01

    not native to the region. We found a high level of genetic divergence among the population centers (Lyman Lake, Stoneman Lake, Truxton Wash), and low genetic diversity in the small populations at Lyman Lake and Truxton. The extensive population in the Stoneman Lake area had high genetic diversity and relatively high gene flow among ponds and tanks across the entire extent of the area. However, this population also contained a mitochondrial haplotype from northern leopard frogs from the northeastern United States or southeastern Canada, probably representing the introduction of released pets or laboratory animals. These eastern frogs were extensively distributed through this population, and probably contributed to its high genetic diversity. Genetic diversity in the outlying populations such as Truxton Wash, East Buckskin Tank, and Hess Tank was low and showed signs of recent bottlenecks. However, supplementing genetic diversity in these native populations with artificial gene flow from the Stoneman Lake area may only be advisable in extreme situations for which there are no other alternatives. Until the nature and effects of genetic mixing of eastern and western genetic stocks of northern leopard frogs are better understood, the long-term persistence of the species in the Southwest may be best served by retaining as much genetic integrity of remaining native populations as possible.

  3. Inbreeding and loss of genetic variation in a reintroduced population of Mauritius Kestrel.

    Science.gov (United States)

    Ewing, Steven R; Nager, Ruedi G; Nicoll, Malcolm A C; Aumjaud, Aurelien; Jones, Carl G; Keller, Lukas F

    2008-04-01

    Many populations have recovered from severe bottlenecks either naturally or through intensive conservation management. In the past, however, few conservation programs have monitored the genetic health of recovering populations. We conducted a conservation genetic assessment of a small, reintroduced population of Mauritius Kestrel (Falco punctatus) to determine whether genetic deterioration has occurred since its reintroduction. We used pedigree analysis that partially accounted for individuals of unknown origin to document that (1) inbreeding occurred frequently (2.6% increase per generation; N(eI)= 18.9), (2) 25% of breeding pairs were composed of either closely or moderately related individuals, (3) genetic diversity has been lost from the population (1.6% loss per generation; N(eV)= 32.1) less rapidly than the corresponding increase in inbreeding, and (4) ignoring the contribution of unknown individuals to a pedigree will bias the metrics derived from that pedigree, ultimately obscuring the prevailing genetic dynamics. The rates of inbreeding and loss of genetic variation in the subpopulation of Mauritius Kestrel we examined were extreme and among the highest yet documented in a wild vertebrate population. Thus, genetic deterioration may affect this population's long-term viability. Remedial conservation strategies are needed to reduce the impact of inbreeding and loss of genetic variation in this species. We suggest that schemes to monitor genetic variation after reintroduction should be an integral component of endangered species recovery programs.

  4. Homopolymeric tract heteroplasmy in mtDNA from tissues and single oocytes: Support for a genetic bottleneck

    Energy Technology Data Exchange (ETDEWEB)

    Marchington, D.R.; Hartshorne, G.M.; Barlow, D.; Poulton, J. [Univ. of Oxford (United Kingdom)

    1997-02-01

    While mtDNA polymorphisms at single base positions are common, the overwhelming majority of the mitochondrial genomes within a single individual are usually identical. When there is a point-mutation difference between a mother and her offspring, there may be a complete switching of mtDNA type within a single generation. It is generally assumed that there is a genetic bottleneck whereby a single or small number of founder mtDNA(s) populate the organism, but it is not known at which stages the restriction/amplification of mtDNA subtype(s) occur, and this uncertainty impedes antenatal diagnosis for mtDNA disorders. Length polymorphisms in homopolymeric tracts have been demonstrated in the large noncoding region of mtDNA. We have developed a new method, T-PCR (trimmed PCR), to quantitate heteroplasmy for two of these tracts (D310 and D16189). D310 variation is sufficient to indicate clonal origins of tissues and single oocytes. Tissues from normal individuals often possessed more than one length variant (heteroplasmy). However, there was no difference in the pattern of the length variants between somatic tissues in any control individual when bulk samples were taken. Oocytes from normal women undergoing in vitro fertilization were frequently heteroplasmic for length variants, and in two cases the modal length of the D310 tract differed in individual oocytes from the same woman. These data suggest that a restriction/amplification event, which we attribute to clonal expansion of founder mtDNA(s), has occurred by the time oocytes are mature, although further segregation may occur at a later stage. In contrast to controls, the length distribution of the D310 tract varied between tissues in a patient with heteroplasmic mtDNA rearrangements, suggesting that these mutants influence segregation. These findings have important implications for the genetic counselling of patients with pathogenic mtDNA mutations. 21 refs., 5 figs., 1 tab.

  5. Venous Thrombosis Risk after Cast Immobilization of the Lower Extremity: Derivation and Validation of a Clinical Prediction Score, L-TRiP(cast), in Three Population-Based Case–Control Studies

    Science.gov (United States)

    Nemeth, Banne; van Adrichem, Raymond A.; van Hylckama Vlieg, Astrid; Bucciarelli, Paolo; Martinelli, Ida; Baglin, Trevor; Rosendaal, Frits R.; le Cessie, Saskia; Cannegieter, Suzanne C.

    2015-01-01

    Background Guidelines and clinical practice vary considerably with respect to thrombosis prophylaxis during plaster cast immobilization of the lower extremity. Identifying patients at high risk for the development of venous thromboembolism (VTE) would provide a basis for considering individual thromboprophylaxis use and planning treatment studies. The aims of this study were (1) to investigate the predictive value of genetic and environmental risk factors, levels of coagulation factors, and other biomarkers for the occurrence of VTE after cast immobilization of the lower extremity and (2) to develop a clinical prediction tool for the prediction of VTE in plaster cast patients. Methods and Findings We used data from a large population-based case–control study (MEGA study, 4,446 cases with VTE, 6,118 controls without) designed to identify risk factors for a first VTE. Cases were recruited from six anticoagulation clinics in the Netherlands between 1999 and 2004; controls were their partners or individuals identified via random digit dialing. Identification of predictor variables to be included in the model was based on reported associations in the literature or on a relative risk (odds ratio) > 1.2 and p ≤ 0.25 in the univariate analysis of all participants. Using multivariate logistic regression, a full prediction model was created. In addition to the full model (all variables), a restricted model (minimum number of predictors with a maximum predictive value) and a clinical model (environmental risk factors only, no blood draw or assays required) were created. To determine the discriminatory power in patients with cast immobilization (n = 230), the area under the curve (AUC) was calculated by means of a receiver operating characteristic. Validation was performed in two other case–control studies of the etiology of VTE: (1) the THE-VTE study, a two-center, population-based case–control study (conducted in Leiden, the Netherlands, and Cambridge, United Kingdom

  6. Venous Thrombosis Risk after Cast Immobilization of the Lower Extremity: Derivation and Validation of a Clinical Prediction Score, L-TRiP(cast, in Three Population-Based Case-Control Studies.

    Directory of Open Access Journals (Sweden)

    Banne Nemeth

    2015-11-01

    Full Text Available Guidelines and clinical practice vary considerably with respect to thrombosis prophylaxis during plaster cast immobilization of the lower extremity. Identifying patients at high risk for the development of venous thromboembolism (VTE would provide a basis for considering individual thromboprophylaxis use and planning treatment studies. The aims of this study were (1 to investigate the predictive value of genetic and environmental risk factors, levels of coagulation factors, and other biomarkers for the occurrence of VTE after cast immobilization of the lower extremity and (2 to develop a clinical prediction tool for the prediction of VTE in plaster cast patients.We used data from a large population-based case-control study (MEGA study, 4,446 cases with VTE, 6,118 controls without designed to identify risk factors for a first VTE. Cases were recruited from six anticoagulation clinics in the Netherlands between 1999 and 2004; controls were their partners or individuals identified via random digit dialing. Identification of predictor variables to be included in the model was based on reported associations in the literature or on a relative risk (odds ratio > 1.2 and p ≤ 0.25 in the univariate analysis of all participants. Using multivariate logistic regression, a full prediction model was created. In addition to the full model (all variables, a restricted model (minimum number of predictors with a maximum predictive value and a clinical model (environmental risk factors only, no blood draw or assays required were created. To determine the discriminatory power in patients with cast immobilization (n = 230, the area under the curve (AUC was calculated by means of a receiver operating characteristic. Validation was performed in two other case-control studies of the etiology of VTE: (1 the THE-VTE study, a two-center, population-based case-control study (conducted in Leiden, the Netherlands, and Cambridge, United Kingdom with 784 cases and 523

  7. Pedestrian Flow at Bottlenecks - Validation and Calibration of Vissim's Social Force Model of Pedestrian Traffic and its Empirical Foundations

    CERN Document Server

    Kretz, Tobias; Vortisch, Peter

    2008-01-01

    In this contribution first results of experiments on pedestrian flow through bottlenecks are presented and then compared to simulation results obtained with the Social Force Model in the Vissim simulation framework. Concerning the experiments it is argued that the basic dependence between flow and bottleneck width is not a step function but that it is linear and modified by the effect of a psychological phenomenon. The simulation results as well show a linear dependence and the parameters can be calibrated such that the absolute values for flow and time fit to range of experimental results.

  8. Basic newborn care and neonatal resuscitation: a multi-country analysis of health system bottlenecks and potential solutions.

    Science.gov (United States)

    Enweronu-Laryea, Christabel; Dickson, Kim E; Moxon, Sarah G; Simen-Kapeu, Aline; Nyange, Christabel; Niermeyer, Susan; Bégin, France; Sobel, Howard L; Lee, Anne C C; von Xylander, Severin; Lawn, Joy E

    2015-01-01

    An estimated two-thirds of the world's 2.7 million newborn deaths could be prevented with quality care at birth and during the postnatal period. Basic Newborn Care (BNC) is part of the solution and includes hygienic birth and newborn care practices including cord care, thermal care, and early and exclusive breastfeeding. Timely provision of resuscitation if needed is also critical to newborn survival. This paper describes health system barriers to BNC and neonatal resuscitation and proposes solutions to scale up evidence-based strategies. The maternal and newborn bottleneck analysis tool was applied by 12 countries in Africa and Asia as part of the Every Newborn Action Plan process. Country workshops engaged technical experts to complete the survey tool, which is designed to synthesise and grade health system "bottlenecks" 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 BNC and neonatal resuscitation. Eleven of the 12 countries provided grading data. Overall, bottlenecks were graded more severely for resuscitation. The most severely graded bottlenecks for BNC were health workforce (8 of 11 countries), health financing (9 out of 11) and service delivery (7 out of 9); and for neonatal resuscitation, workforce (9 out of 10), essential commodities (9 out of 10) and service delivery (8 out of 10). Country teams from Africa graded bottlenecks overall more severely. Improving workforce performance, availability of essential commodities, and well-integrated health service delivery were the key solutions proposed. BNC was perceived to have the least health system challenges among the seven maternal and newborn intervention packages assessed. Although neonatal resuscitation bottlenecks were graded more severe than for BNC, similarities particularly

  9. Bottlenecks, burstiness, and fat tails regulate mixing times of non-Poissonian random walks

    CERN Document Server

    Delvenne, Jean-Charles; Rocha, Luis E C

    2013-01-01

    We focus on general continuous-time random walks on networks and find that the mixing time, i.e. the relaxation time for the random process to reach stationarity, is determined by a combination of three factors: the spectral gap, associated to bottlenecks in the underlying topology, burstiness, related to the second moment of the waiting time distribution, and the characteristic time of its exponential tail, which is an indicator of the tail `fatness'. We show theoretically that a strong modular structure dampens the importance of burstiness, and empirically that either of the three factors may be dominant in real-life data. These results provide a theoretical framework for the modeling of diffusion on temporal networks representing human interactions, often characterized by non-Poissonian contact patterns.

  10. 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.

  11. 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....

  12. 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.

  13. Phonon bottleneck in p-type Ge/Si quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Yakimov, A. I., E-mail: yakimov@isp.nsc.ru [Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk (Russian Federation); Tomsk State University, 634050 Tomsk (Russian Federation); Kirienko, V. V.; Armbrister, V. A. [Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk (Russian Federation); Bloshkin, A. A.; Dvurechenskii, A. V. [Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk (Russian Federation); Novosibirsk State University, 630090 Novosibirsk (Russian Federation)

    2015-11-23

    We study the effect of quantum dot size on the mid-infrared photo- and dark current, photoconductive gain, and hole capture probability in ten-period p-type Ge/Si quantum dot heterostructures. The dot dimensions are varied by changing the Ge coverage and the growth temperature during molecular beam epitaxy of Ge/Si(001) system in the Stranski-Krastanov growth mode. In all samples, we observed the general tendency: with decreasing the size of the dots, the dark current and hole capture probability are reduced, while the photoconductive gain and photoresponse are enhanced. Suppression of the hole capture probability in small-sized quantum dots is attributed to a quenched electron-phonon scattering due to phonon bottleneck.

  14. Fast electronic relaxation in metal nanoclusters via excitation of coherent shape deformations: Circumventing a bottleneck

    CERN Document Server

    Kresin, V V; Kresin, Vitaly V.; Ovchinnikov, Yu. N.

    2006-01-01

    Electron-phonon relaxation in size-quantized systems may become inhibited when the spacing of discrete electron energy levels exceeds the magnitude of the phonon frequency. We show, however, that nanoclusters can support a fast nonradiative relaxation channel which derives from their distinctive ability to undergo Jahn-Teller shape deformations. Such a deformation represents a collective and coherent vibrational excitation and enables electronic transitions to occur without a multiphonon bottleneck. We analyze this mechanism for a metal cluster within the analytical framework of a three-dimensional potential well undergoing a spheroidal distortion. An expression for the time evolution of the distortion parameter is derived, the electronic level crossing condition formulated, and the probability of electronic transition at a level crossing is evaluated. An application to electron-hole recombination in a closed-shell aluminum cluster with 40 electrons shows that the short (~250 fs) excitation lifetime observed ...

  15. Experimental Analysis of Two-Dimensional Pedestrian Flow in front of the Bottleneck

    CERN Document Server

    cek, Marek Buká\\v; Krbálek, Milan

    2014-01-01

    This contribution presents experimental study of two-dimensional pedestrian flow with the aim to capture the pedestrian behaviour within the cluster formed in front of the bottleneck. Two experiments of passing through a room with one entrance and one exit were arranged according to phase transition study in Ezaki et al. (2012), the inflow rate was regulated to obtain different walking modes. By means of automatic image processing, pedestrians' paths are extracted from camera records to get actual velocity and local density. Macroscopic information is extracted by means of virtual detector and leaving times of pedestrians. The pedestrian's behaviour is evaluated by means of density and velocity. Different approaches of measurement are compared using several fundamental diagrams. Two phases of crowd behaviour have been recognized and the phase transition was described.

  16. Algorithm Based on Taboo Search and Shifting Bottleneck for Job Shop Scheduling

    Institute of Scientific and Technical Information of China (English)

    Wen-Qi Huang; Zhi Huang

    2004-01-01

    In this paper, a computational effective heuristic method for solving the minimum makespan problem of job shop scheduling is presented. It is based on taboo search procedure and on the shifting bottleneck procedure used to jump out of the trap of the taboo search procedure. A key point of the algorithm is that in the taboo search procedure two taboo lists are used to forbid two kinds of reversals of arcs, which is a new and effective way in taboo search methods for job shop scheduling. Computational experiments on a set of benchmark problem instances show that, in several cases, the approach, in reasonable time, yields better solutions than the other heuristic procedures discussed in the literature.

  17. 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.

  18. Quality of service estimation based on maximum bottleneck algorithm for domain aggregation in backbone networks

    Institute of Scientific and Technical Information of China (English)

    WANG Yang; ZHAN Yi-chun; YU Shao-hua

    2007-01-01

    This paper investigates the routing among autonomous systems (ASs) with quality of service (QoS) requirements. To avoid the intractability of the problem, abstract QoS capability must be informed among ASs, because the routhing which constrained QoS has been proved to be nondeterministic polynomial-time (NP) hard even inside an AS. This paper employs the modified Dijkstra algorithm to compute the maximum bottleneck bandwidth inside an AS. This approach lays a basis for the AS-level switching capability on which interdomain advertisement can be performed. Furthermore, the paper models the aggregated traffic in backbone network with fractional Brownian motion (FBM), and by integrating along the time axis in short intervals, a good estimation of the distribution of queue length in the next short intervals can be obtained. The proposed advertisement mechanism can be easily implemented with the current interdomain routing protocols. Numerical study indicates that the presented scheme is effective and feasible.

  19. Approximation Algorithm for Bottleneck Steiner Tree Problem in the Euclidean Plane

    Institute of Scientific and Technical Information of China (English)

    Zi-Mao Li; Da-Ming Zhu; Shao-Han Ma

    2004-01-01

    A special case of the bottleneck Steiner tree problem in the Euclidean plane was considered in this paper. The problem has applications in the design of wireless communication networks, multifacility location, VLSI routing and network routing. For the special case which requires that there should be no edge connecting any two Steiner points in the optimal solution, a 3-restricted Steiner tree can be found indicating the existence of the performance ratio √2. In this paper, the special case of the problem is proved to be NP-hard and cannot be approximated within ratio √2. First a simple polynomial time approximation algorithm with performance ratio √3 is presented. Then based on this algorithm and the existence of the 3-restricted Steiner tree, a polynomial time approximation algorithm with performance ratio-√2 + ε is proposed, for any ε>0.

  20. Legacy to the extreme

    NARCIS (Netherlands)

    A. van Deursen (Arie); T. Kuipers (Tobias); L.M.F. Moonen (Leon)

    2000-01-01

    textabstractWe explore the differences between developing a system using extreme programming techniques, and maintaining a legacy system. We investigate whether applying extreme programming techniques to legacy maintenance is useful and feasible.

  1. Legacy to the extreme

    NARCIS (Netherlands)

    Deursen, A. van; Kuipers, T.; Moonen, L.M.F.

    2000-01-01

    We explore the differences between developing a system using extreme programming techniques, and maintaining a legacy system. We investigate whether applying extreme programming techniques to legacy maintenance is useful and feasible.

  2. Reducing the Disk IO Bandwidth Bottleneck through Fast Floating Point Compression using Accelerators

    Directory of Open Access Journals (Sweden)

    Ajith Padyana

    2014-03-01

    Full Text Available Compute-intensive tasks in high-end high performance computing (HPC systems often generate large amounts of data, especially floating-point data that need to be transmitted over the network. Although computation speeds are very high, the overall performance of these applications is affected by the data transfer overhead. Moreover, as data sets are growing in size rapidly, bandwidth limitations pose a serious bottleneck in several scientific applications. Fast floating point compression can ameliorate the bandwidth limitations. If data is compressed well, then the amount of data transfer is reduced. This reduction in data transfer time comes at the expense of the increased computation required by compression and decompression. It is important for compression and decompression rates to be greater than the network bandwidth; otherwise, it will be faster to transmit uncompressed data directly [1]. Accelerators such as Graphics Processing Units (GPU provide much computational power. In this paper, we show that the computational power of GPUs and CellBE processor can be harnessed to provide sufficiently fast compression and decompression for this approach to be effective for data produced by many practical applications. In particularly, we use Holt`s Exponential smoothing algorithm from time series analysis, and encode the difference between its predictions and the actual data. This yields a lossless compression scheme. We show that it can be implemented efficiently on GPUs and CellBE to provide an effective compression scheme for the purpose of saving on data transfer overheads The primary contribution of this work lies in demonstrating the potential of floating point compression in reducing the I/O bandwidth bottleneck on modern hardware for important classes of scientific applications.

  3. 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.

  4. Extreme environment electronics

    CERN Document Server

    Cressler, John D

    2012-01-01

    Unfriendly to conventional electronic devices, circuits, and systems, extreme environments represent a serious challenge to designers and mission architects. The first truly comprehensive guide to this specialized field, Extreme Environment Electronics explains the essential aspects of designing and using devices, circuits, and electronic systems intended to operate in extreme environments, including across wide temperature ranges and in radiation-intense scenarios such as space. The Definitive Guide to Extreme Environment Electronics Featuring contributions by some of the world's foremost exp

  5. Deficiently Extremal Gorenstein Algebras

    Indian Academy of Sciences (India)

    Pavinder Singh

    2011-08-01

    The aim of this article is to study the homological properties of deficiently extremal Gorenstein algebras. We prove that if / is an odd deficiently extremal Gorenstein algebra with pure minimal free resolution, then the codimension of / must be odd. As an application, the structure of pure minimal free resolution of a nearly extremal Gorenstein algebra is obtained.

  6. The frankincense tree of Ethiopia : ecology, productivity and population dynamics

    NARCIS (Netherlands)

    Eshete Wassie, A.

    2011-01-01

    Keywords: Boswellian papyrifera, Frankincense tree, matrix model, population dynamics,
    population bottleneck, tapping. Combretum – Terminalia woodlands and Acacia – Commiphora woodlands are the two
    dominant vegetation types that cover large parts of the dry land areas in Eth

  7. Fine scale population genetic structure of Varroa destructor, an ectoparasitic mite of the honey bee (Apis mellifera)

    Science.gov (United States)

    Dynes, Travis L.; De Roode, Jacobus C.; Lyons, Justine I.; Berry, Jennifer A.; Delaplane, Keith S.; Brosi, Berry J.

    2016-01-01

    Varroa destructor is an obligate ectoparasitic mite and the most important biotic threat currently facing honey bees (Apis mellifera). We used neutral microsatellites to analyze previously unreported fine scale population structure of V. destructor, a species characterized by extreme lack of genetic diversity owing to multiple bottleneck events, haplodiploidy, and primarily brother-sister matings. Our results surprisingly indicate that detectable hierarchical genetic variation exists between apiaries, between colonies within an apiary, and even within colonies. This finding of within-colony parasite diversity provides empirical evidence that the spread of V. destructor is not accomplished solely by vertical transmission but that horizontal transmission (natural or human-mediated) must occur regularly. PMID:27812229

  8. Rising Precipitation Extremes across Nepal

    Directory of Open Access Journals (Sweden)

    Ramchandra Karki

    2017-01-01

    only over the WM region. Both high-intensity precipitation extremes and annual precipitation trends feature east−west contrast, suggesting significant increase over the WM and CH region but decrease over the EM and CM regions. Further, a significant positive trend in the number of consecutive dry days but significant negative trend in the number of wet (rainy days are observed over the whole of Nepal, implying the prolongation of the dry spell across the country. Overall, the intensification of different precipitation indices over distinct parts of the country indicates region-specific risks of floods, landslides and droughts. The presented findings, in combination with population and environmental pressures, can support in devising the adequate region-specific adaptation strategies for different sectors and in improving the livelihood of the rural communities in Nepal.

  9. Extreme value distributions

    CERN Document Server

    Ahsanullah, Mohammad

    2016-01-01

    The aim of the book is to give a through account of the basic theory of extreme value distributions. The book cover a wide range of materials available to date. The central ideas and results of extreme value distributions are presented. The book rwill be useful o applied statisticians as well statisticians interrested to work in the area of extreme value distributions.vmonograph presents the central ideas and results of extreme value distributions.The monograph gives self-contained of theory and applications of extreme value distributions.

  10. Agroecosystems shape population genetic structure of the greenhouse whitefly in Northern and Southern Europe.

    Science.gov (United States)

    Ovčarenko, Irina; Kapantaidaki, Despoina Evripidis; Lindström, Leena; Gauthier, Nathalie; Tsagkarakou, Anastasia; Knott, Karelyn Emily; Vänninen, Irene

    2014-07-29

    To predict further invasions of pests it is important to understand what factors contribute to the genetic structure of their populations. Cosmopolitan pest species are ideal for studying how different agroecosystems affect population genetic structure within a species at different climatic extremes. We undertook the first population genetic study of the greenhouse whitefly (Trialeurodes vaporariorum), a cosmopolitan invasive herbivore, and examined the genetic structure of this species in Northern and Southern Europe. In Finland, cold temperatures limit whiteflies to greenhouses and prevent them from overwintering in nature, and in Greece, milder temperatures allow whiteflies to inhabit both fields and greenhouses year round, providing a greater potential for connectivity among populations. Using nine microsatellite markers, we genotyped 1274 T. vaporariorum females collected from 18 greenhouses in Finland and eight greenhouses as well as eight fields in Greece. Populations from Finland were less diverse than those from Greece, suggesting that Greek populations are larger and subjected to fewer bottlenecks. Moreover, there was significant population genetic structure in both countries that was explained by different factors. Habitat (field vs. greenhouse) together with longitude explained genetic structure in Greece, whereas in Finland, genetic structure was explained by host plant species. Furthermore, there was no temporal genetic structure among populations in Finland, suggesting that year-round populations are able to persist in greenhouses. Taken together our results show that greenhouse agroecosystems can limit gene flow among populations in both climate zones. Fragmented populations in greenhouses could allow for efficient pest management. However, pest persistence in both climate zones, coupled with increasing opportunities for naturalization in temperate latitudes due to climate change, highlight challenges for the management of cosmopolitan pests in

  11. 一种城市交通瓶颈的计算方法%Method for calculating urban traffic bottlenecks

    Institute of Scientific and Technical Information of China (English)

    邱淳风; 温晓岳; 靳明豪; 李建元

    2015-01-01

    城市交通瓶颈指的是常发性拥堵路段或位置。以往基于交警的巡查经验来确定交通瓶颈,虽可以部分地反映实际情况,但成本太高且无法做到动态跟踪。运用交通传感数据提出了一个简单的交通瓶颈计算方法,通过计算统计周期内的路段拥堵概率来反映交通瓶颈的严重程度。实验表明该方法是有效的。%Traffic bottlenecks refer to road segments or locations with frequent traffic jams. Traditional methods for evaluating traffic bottlenecks are mainly based on patrol experience, which could partly work but is costly and cannot dynamically track the change of bottlenecks. This paper proposed a simple method that evaluates bottlenecks by using the congestion probabilities of road segments obtained from the analysis of traffic sensing data. The experimental results show the effectiveness of the proposed method.

  12. Capacity drop: A comparison between stop-and-go wave and standing queue at lane-drop bottleneck

    NARCIS (Netherlands)

    Yuan, K.; Knoop, V.L.; Leclercq, L.; Hoogendoorn, S.P.

    2014-01-01

    In freeways, the maximum traffic flow through a bottleneck is usually higher than the outflow of congestion there. This phenomenon is called the capacity drop. In literature, there are considerable debates about the mechanism causing this phenomenon. This paper studies the mechanism by analyzing rea

  13. 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

  14. Moderate and extreme maternal obesity.

    LENUS (Irish Health Repository)

    Abdelmaboud, M O

    2012-05-01

    The aim of this study was to investigate the prevalence of moderate and extreme obesity among an Irish obstetric population over a 10-year period, and to evaluate the obstetric features of such pregnancies. Of 31,869 women delivered during the years 2000-2009, there were 306 women in the study group, including 173 in the moderate or Class 2 obese category (BMI 35-39.9) and 133 in the extreme or Class 3 obese category (BMI > or = 40).The prevalence of obese women with BMI > or = 35 was 9.6 per 1000 (0.96%), with an upward trend observed from 2.1 per 1000 in the year 2000, to 11.8 per 1000 in the year 2009 (P = 0.001). There was an increase in emergency caesarean section (EMCS) risk for primigravida versus multigravid women, within both obese categories (P < 0.001). However, there was no significant difference in EMCS rates observed between Class 2 and Class 3 obese women, when matched for parity. The prevalence of moderate and extreme obesity reported in this population is high, and appears to be increasing. The increased rates of abdominal delivery, and the levels of associated morbidity observed, have serious implications for such women embarking on pregnancy.

  15. 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

  16. Multiple excitons and the electron phonon bottleneck in semiconductor quantum dots: An ab initio perspective

    Science.gov (United States)

    Prezhdo, Oleg V.

    2008-07-01

    regarding the phonon bottleneck and the generation of multiple excitons in semiconductor QDs. Both the electron-hole and charge-phonon interactions are strong and, therefore, optical excitations can directly generate multiple excitons, while the electron-phonon relaxation exhibits no bottlenecks, except at low excitation energies and in very small QDs.

  17. Genetic structuring among silverside fish (Atherinella brasiliensis) populations from different Brazilian regions

    Science.gov (United States)

    da Silva Cortinhas, Maria Cristina; Kersanach, Ralf; Proietti, Maíra; Dumont, Luiz Felipe Cestari; D'Incao, Fernando; Lacerda, Ana Luzia F.; Prata, Pedro Sanmartin; Matoso, Daniele Aparecida; Noleto, Rafael Bueno; Ramsdorf, Wanessa; Boni, Talge Aiex; Prioli, Alberto José; Cestari, Marta Margarete

    2016-09-01

    Estuaries are dynamic environments, key for the survival of innumerous ecologically or economically important fish species. Among these species are Neotropical silversides (Atherinella brasiliensis), which are resident and abundant in Brazilian estuaries and used as a complementary source of income and food for local communities. To better understand silverside populations in Brazil, we evaluated the genetic diversity, structure and demography of fish sampled at six estuaries from the northeastern to the southern coast, using Random Amplified Polymorphic DNA and mitochondrial DNA (D-loop) markers. High haplotype diversities (h ranging from 0.75 to 0.99) were found in all populations except Carapebus, located in Southeast Brazil (h = 0.54). A total of 69 mtDNA haplotypes were found, with Itaparica (Northeast Brazil) and Carapebus presenting only exclusive haplotypes, while some were shared among populations in the South. Strong regional structure was observed, with very high differentiation between Itaparica and Carapebus, as well as among these two populations and the ones from the Southern region (Paranaguá, Conceição, Camacho and Patos). Among southern areas, low/moderate structure was detected. Most populations showed unimodal mismatch distributions indicating recent demographic expansion, while Carapebus presented a multimodal distribution characteristic of a stable or bottlenecked population. Times since possible population expansion were highest in Itaparica (32,500 ya) and Carapebus (29,540 ya), while in the Southern region longest time was observed at Conceição (25,540 ya) and shortest at Patos (9720 ya). In a general manner, haplotype diversities were directly related to times since population expansions; again, Carapebus was the exception, displaying long time since expansion but low diversity, possibly due to a recent bottleneck caused by the isolation and human impacts this lagoon is subject to. Isolation by Distance was significant for Itaparica

  18. Extreme Velocity Wind Sensor

    Science.gov (United States)

    Perotti, Jose; Voska, Ned (Technical Monitor)

    2002-01-01

    This presentation provides an overview of the development of new hurricane wind sensor (Extreme Velocity Wind Sensor) for the Kennedy Space Center (KSC) which is designed to withstand winds of up to three hundred miles an hour. The proposed Extreme Velocity Wind Sensor contains no moveable components that would be exposed to extreme wind conditions. Topics covered include: need for new hurricane wind sensor, conceptual design, software applications, computational fluid dynamic simulations of design concept, preliminary performance tests, and project status.

  19. Women in extreme poverty.

    Science.gov (United States)

    1994-01-01

    Population is estimated to increase from 5.5 billion in 1990 to 10 billion by 2050; the poverty level is expected to increase from 1 billion to 2-3 billion people. Women in development has been promoted throughout the UN and development system, but women in poverty who perform work in the informal sector are still uncounted, and solutions are elusive. The issue of extreme poverty can not be approached as just another natural disaster with immediate emergency relief. Many people live in precarious economic circumstances throughout their lives. Recent research reveals a greater understanding of the underlying causes and the need for inclusion of poor women in sustainable development. Sanitation, water, housing, health facilities need to be improved. Women must have access to education, opportunities for trading, and loans on reasonable terms. UNESCO makes available a book on survival strategies for poor women in the informal sector. The profile shows common problems of illiteracy, broken marriages, and full time involvement in provision of subsistence level existence. Existence is a fragile balance. Jeanne Vickers' "Women and the World" offers simple, low cost interventions for aiding extremely poor women. The 1992 Commission on the Status of Women was held in Vienna. Excerpts from several speeches are provided. The emphasis is on some global responses and an analysis of solutions. The recommendation is for attention to the gender dimension of poverty. Women's dual role contributes to greater disadvantages. Women are affected differently by macroeconomic factors, and that there is intergenerational transfer of poverty. Social services should be viewed as investments and directed to easing the burdens on time and energy. Public programs must be equipped to deal with poverty and to bring about social and economic change. Programs must be aware of the different distribution of resources within households. Women must be recognized as principal economic providers within

  20. How extreme is extreme hourly precipitation?

    Science.gov (United States)

    Papalexiou, Simon Michael; Dialynas, Yannis G.; Pappas, Christoforos

    2016-04-01

    The importance of accurate representation of precipitation at fine time scales (e.g., hourly), directly associated with flash flood events, is crucial in hydrological design and prediction. The upper part of a probability distribution, known as the distribution tail, determines the behavior of extreme events. In general, and loosely speaking, tails can be categorized in two families: the subexponential and the hyperexponential family, with the first generating more intense and more frequent extremes compared to the latter. In past studies, the focus has been mainly on daily precipitation, with the Gamma distribution being the most popular model. Here, we investigate the behaviour of tails of hourly precipitation by comparing the upper part of empirical distributions of thousands of records with three general types of tails corresponding to the Pareto, Lognormal, and Weibull distributions. Specifically, we use thousands of hourly rainfall records from all over the USA. The analysis indicates that heavier-tailed distributions describe better the observed hourly rainfall extremes in comparison to lighter tails. Traditional representations of the marginal distribution of hourly rainfall may significantly deviate from observed behaviours of extremes, with direct implications on hydroclimatic variables modelling and engineering design.

  1. Calculation of the mean circle size does not circumvent the bottleneck of crowding.

    Science.gov (United States)

    Banno, Hayaki; Saiki, Jun

    2012-10-22

    Visually, we can extract a statistical summary of sets of elements efficiently. However, our visual system has a severe limitation in that the ability to recognize an object is remarkably impaired when it is surrounded by other objects. The goal of this study was to investigate whether the crowding effect obstructs the calculation of the mean size of objects. First, we verified that the crowding effect occurs when comparing the sizes of circles (Experiment 1). Next, we manipulated the distances between circles and measured the sensitivity when circles were on or off the limitation of crowding (Experiment 2). Participants were asked to compare the mean sizes of the circles in the left and right visual fields and to judge which was larger. Participants' sensitivity to mean size difference was lower when the circles were located in the nearer distance. Finally, we confirmed that crowding is responsible for the observed results by showing that displays without a crowded object eliminated the effects (Experiment 3). Our results indicate that the statistical information of size does not circumvent the bottleneck of crowding.

  2. 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.

  3. Circum-planetary discs as bottlenecks for gas accretion onto giant planets

    CERN Document Server

    Rivier, Guillaume; Morbidelli, Alessandro; Brouet, Yann

    2012-01-01

    With hundreds of exoplanets detected, it is necessary to revisit giant planets accretion models to explain their mass distribution. In particular, formation of sub-jovian planets remains unclear, given the short timescale for the runaway accretion of massive atmospheres. However, gas needs to pass through a circum-planetary disc. If the latter has a low viscosity (as expected if planets form in "dead zones"), it might act as a bottleneck for gas accretion. We investigate what the minimum accretion rate is for a planet under the limit assumption that the circum-planetary disc is totally inviscid, and the transport of angular momentum occurs solely because of the gravitational perturbations from the star. To estimate the accretion rate, we present a steady-state model of an inviscid circum-planetary disc, with vertical gas inflow and external torque from the star. Hydrodynamical simulations of a circum-planetary disc were conducted in 2D, in a planetocentric frame, with the star as an external perturber in orde...

  4. 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.

  5. Identifying Processor Bottlenecks in Virtual Machine Based Execution of Java Bytecode

    Science.gov (United States)

    Rao, Pradeep; Murakami, Kazuaki

    Despite the prevalence of Java workloads across a variety of processor architectures, there is very little published data on the impact of the various processor design decisions on Java performance. We attribute the lack of data to the large design space resulting from the complexity of the modern superscalar processor and the additional complexities associated with executing Java bytecode using a virtual machine. To address this shortcoming, we use a statistically rigorous methodology to systematically quantify the the impact of the various processor microarchitecture parameters on Java execution performance. The adopted methodology enables efficient screening of significant factor effects in a large design space consisting of 35 factors (32-billion potential configurations) using merely 72 observations per benchmark application. We quantify and tabulate the significance of each of the 35 factors for 13 benchmark applications. While these tables provide various insights into Java performance, they consistently highlight the performance significance of the instruction delivery mechanism, especially the instruction cache and the ITLB design parameters. Furthermore, these tables enable the architect to identify processor bottlenecks for Java workloads by providing an estimate of the relative impact of various design decisions.

  6. Effect of density feedback on the two-route traffic scenario with bottleneck

    Science.gov (United States)

    Sun, Xiao-Yan; Ding, Zhong-Jun; Huang, Guo-Hua

    2016-12-01

    In this paper, we investigate the effect of density feedback on the two-route scenario with a bottleneck. The simulation and theory analysis shows that there exist two critical vehicle entry probabilities αc1 and αc2. When vehicle entry probability α≤αc1, four different states, i.e. free flow state, transition state, maximum current state and congestion state are identified in the system, which correspond to three critical reference densities. However, in the interval αc1congestion state when α≥αc2. According to the results, traffic control center can adjust the reference density so that the system is in maximum current state. In this case, the capacity of the traffic system reaches maximum so that drivers can make full use of the roads. We hope that the study results can provide good advice for alleviating traffic jam and be useful to traffic control center for designing advanced traveller information systems.

  7. 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...

  8. 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.

  9. Pressure-temperature dependence of growth bottlenecks and phenotypic transitions of Escherichia coli

    Science.gov (United States)

    Kumar, Pradeep; Libchaber, Albert J.

    2012-02-01

    A vast majority of bacteria and archaea can grow in diverse environmental conditions. The range of those conditions include high pressures, high temperature, low temperature, high salinity, low and high pH etc. We investigate the growth bottlenecks and phenotypic transitions of Escherichia coli (E. coli), a mesophilic bacterium, as a function of pressure and temperature. We find that E.coli can grow and proliferate in a wide range of pressures (1-400 atm) and temperatures (23-40 deg C). Moreover, we find that the division time of E. coli increases monotonically upon increasing pressure and exhibits a sharp increase in division time at pressures between 250-400 atm for all the temperatures investigated in our experiments. The sharp change in division time is followed by a sharp change in phenotypic transition of E. Coli at high pressures where bacterial cells switch to an elongating cell type. We propose that this phenotypics changes in bacteria at high pressures is an irreversible stochastic process whereas the switching probability to elongating cell type increases with increasing pressure. Furthermore, we propose an irreversible stochastic model of cell phenotype switching. We find that model fits well the experimental data. We discuss our experimental results in the light of structural and so the functional changes in proteins and structural changes in membranes at different pressure and temperature.

  10. Methods and Techniques for Conserving Wild Plant Species with Extremely Small Populations%极小种群野生植物保护的主要内容和技术要点*

    Institute of Scientific and Technical Information of China (English)

    杨文忠; 康洪梅; 向振勇; 张珊珊; 彭宗妮

    2014-01-01

    Saving wild plant species with extremely small populations (PSESP) is crucial in biodiversity conserva-tion since it is a way to save many other ecologically-linked species .The first inventory of national key protected wild plant resources in 1997~2003 revealed that there was an urgent need to strengthen the protection of species on the brink of extinction in China .Thereafter PSESP concept , name list , and relevant measures were proposed to protect those species .In this paper we reviewed the processes of formation of PSESP concept , identification of PSESP name list , and formulation of conservation plans , along with the research progresses in rare and endangered plant conservation .We summarized main methods and techniques to conserve PSESP based in particular on experi -ences learnt from conservation practices of Nyssa yunnanensis and other species .Technical measures for rescuing and saving PSESP covers not only germplasm resources preservation through in situ, ex situ and in vitro conserva-tion , but also population rehabilitation and reestablishment through regeneration promoting , seedling raising , qua-si in situ conservation , reintroduction , and reinforcement .Our summarization attempts to provide guidance for for-mulating and implementing action plans of PSESP conservation .%拯救与保护极小种群野生植物是生物多样性保护的重要内容。在完成第一次全国重点保护野生植物资源调查后,为适应珍稀濒危植物保护的迫切需要,提出了极小种群野生植物的概念、名录和相关的保护措施。本文在回顾我国极小种群野生植物相关概念形成、物种名录确定和拯救保护计划制定过程的基础上,结合开展云南蓝果树毛枝五针松等的种群调查分析及拯救保护行动实践,基于国内外珍稀濒危野生植物保护的研究和实践,提出了极小种群野生植物保护的主要内容和技术要点。极小种群野生植物的拯救保护,

  11. 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

  12. Classifying Returns as Extreme

    DEFF Research Database (Denmark)

    Christiansen, Charlotte

    2014-01-01

    I consider extreme returns for the stock and bond markets of 14 EU countries using two classification schemes: One, the univariate classification scheme from the previous literature that classifies extreme returns for each market separately, and two, a novel multivariate classification scheme tha...

  13. 城市轨道交通车站动态瓶颈识别方法研究%Identification of Dynamic Bottlenecks of Urban Rail Transit Stations

    Institute of Scientific and Technical Information of China (English)

    黄令海; 李海鹰; 许心越

    2015-01-01

    瓶颈识别是城市轨道交通车站规划设计和运营管理亟待解决的难题。本文在既有静态瓶颈和动态瓶颈的基础上,按动态瓶颈产生原因将其细化为原发性瓶颈及继发性瓶颈;研究瓶颈的动态传播特性,提出关联瓶颈与瓶颈簇理论,以此刻画瓶颈传播机理,并在此基础上构建车站动态瓶颈识别方法;以瓶颈簇理论为支撑,定量分析单个设备能力对车站集散能力的影响程度,提出基于灵敏度分析的瓶颈疏解策略。最后,对北京地铁某车站进行案例分析,验证该瓶颈识别方法的有效性与实用性。案例表明,该方法能够有效识别车站瓶颈,明确瓶颈之间的依附关系以及瓶颈的重要程度。与既有方法相比减少66.7%的仿真次数,可以明显提高识别效率。%Bottleneck identification is an urgent issue that needs to be addressed in the planning,design and op-eration management of urban rail transit stations.Based on the concepts of existing static bottlenecks and dy-namic bottlenecks,dynamic bottlenecks were classified into two categories,i.e.primary bottlenecks and sec-ondary bottlenecks,according to the causes of dynamic bottlenecks.The dynamic bottleneck transmission characteristics were studied,and the correlation bottleneck and bottleneck cluster concepts were proposed to describe the bottleneck transmission mechanism,whereby a new bottleneck identification method was pro-posed.Supported by bottleneck cluster concept,quantitative analysis was conducted on the effect of the capaci-ty of an individual facility on collection and distribution capacity of the station,and sensitivity analysis-based bottleneck relief strategy was proposed.Finally,a case study of a station in Beijing subway was implemented to verify the validity and practicability of the proposed method.The results showed that this method can identi-fy the bottlenecks of a station effectively,and define the dependence

  14. Addressing the current bottlenecks of metabolomics: Isotopic Ratio Outlier Analysis™, an isotopic-labeling technique for accurate biochemical profiling.

    Science.gov (United States)

    de Jong, Felice A; Beecher, Chris

    2012-09-01

    Metabolomics or biochemical profiling is a fast emerging science; however, there are still many associated bottlenecks to overcome before measurements will be considered robust. Advances in MS resolution and sensitivity, ultra pressure LC-MS, ESI, and isotopic approaches such as flux analysis and stable-isotope dilution, have made it easier to quantitate biochemicals. The digitization of mass spectrometers has simplified informatic aspects. However, issues of analytical variability, ion suppression and metabolite identification still plague metabolomics investigators. These hurdles need to be overcome for accurate metabolite quantitation not only for in vitro systems, but for complex matrices such as biofluids and tissues, before it is possible to routinely identify biomarkers that are associated with the early prediction and diagnosis of diseases. In this report, we describe a novel isotopic-labeling method that uses the creation of distinct biochemical signatures to eliminate current bottlenecks and enable accurate metabolic profiling.

  15. A New Wireless Packet Scheduling Algorithm Based on EDF and Its Application in Multi-bottleneck Networks

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Most of current wireless packet scheduling algorithms aim at resource allocation as fairly as possible or maximizing throughput. This paper proposed a new packet scheduling algorithm that aims at satisfying delay requirement and is the improvement of earliest due first (EDF) algorithm in wired networks. The main idea is to classify the packets based on their delay bound, scheduling the most "urgent" class of user and the users that have the best channel condition with higher priority. This algorithm can easily integrate with common buffer management algorithms, when buffer management algorithm cannot accept new arrival packets, try to modify scheduling policy. Packet scheduling algorithms in multiple bottleneck wireless networks were also discussed. A new variable multi-hop factor was defined to estimate the congestion situation (including channel condition) of future hops.Multi-hop factor can be integrated into packet scheduling algorithms as assistant and supplement to improve its performance in multi-bottleneck wireless networks.

  16. Identification of Bottlenecks and Capacity Constraints in F-14, F-15, F-16, and F/A-18 Aircraft Production.

    Science.gov (United States)

    1983-04-01

    TRENDS IN LEAD TIME One important indication of the existence of capaci+ constraints and bottlenecks is the amount of lead cime required to obtain an item...MAK11BUY PRODUCTIONi AV11,1TO11Y S,our c e Gene -..al Dyn~amics ?tG’!RE 13 56 inventory would provide a 33 percent reduction in F-16 lead time. Figure 14

  17. Oracle Database Common Bottleneck Issues Analysis%Oracle数据库常见的瓶颈问题分析

    Institute of Scientific and Technical Information of China (English)

    李文鹏

    2011-01-01

    Oracle database as the world's largest database companies at home and abroad has been applied widely.Article on the current Oracle database common bottleneck issues analyzed and discussed.%Oracle数据库作为全球第一大数据库厂商,在国内外获得了广泛应用。文章对目前Oracle数据库常见的瓶颈问题进行了分析探讨。

  18. Raptor mortality in wind farms of southern Spain: mitigation measures on a major migration bottleneck area

    Energy Technology Data Exchange (ETDEWEB)

    Gallego, Antonio-Roman Munoz; Lucas, Manuela De; Casado, Eva; Ferrer, Miguel

    2011-07-01

    Full text: To assess and monitor the impact of wind farms on fauna is crucial if we want to achieve ecologically sustainable development of this renewable energy resource. Today there are clear evidences that the probability of raptor collision depends critically on species behaviour and weather conditions, and the topographic factors related to each windmill. In our study area EIA were not able to predict this differential risk and in these circumstances mitigating the causes of bird mortality becomes a task of major importance, especially to those wind farms located in the Strait of Gibraltar, a water crossing of 14 km at its shortest distance acting as a major migration bottleneck for Paleo-African soaring migrants. We collected all available information on raptor collision from 1992, when the first wind farm was installed, and from 2005 until present a total of 262 turbines, grouped into 20 wind farms, were surveyed in a daily basis through a surveillance program with the main goal of register the actual mortality of birds. A total of 1291 raptors of 19 species were found of which 78.5% correspond to two species, the griffon vulture (Gyps fulvus) and the kestrel (Falco tinnunculus). In order to mitigate the impact on raptors, and particularly on the griffon vulture, in 2007 a program based on selective stopping of turbines was imposed, in collaboration with the environmental competent authority, on new approved projects. During 2008 there was a reduction in mortality by 48%, which remained in 2009 with a remarkably lower economic cost. An analysis of the temporal collision patterns will be presented and discussed, with special attention to those species suffering higher mortality rate, and to those who have some degree of threat. (Author)

  19. 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.

  20. Science Driven Supercomputing Architectures: AnalyzingArchitectural Bottlenecks with Applications and Benchmark Probes

    Energy Technology Data Exchange (ETDEWEB)

    Kamil, S.; Yelick, K.; Kramer, W.T.; Oliker, L.; Shalf, J.; Shan,H.; Strohmaier, E.

    2005-09-26

    There is a growing gap between the peak speed of parallel computing systems and the actual delivered performance for scientific applications. In general this gap is caused by inadequate architectural support for the requirements of modern scientific applications, as commercial applications and the much larger market they represent, have driven the evolution of computer architectures. This gap has raised the importance of developing better benchmarking methodologies to characterize and to understand the performance requirements of scientific applications, to communicate them efficiently to influence the design of future computer architectures. This improved understanding of the performance behavior of scientific applications will allow improved performance predictions, development of adequate benchmarks for identification of hardware and application features that work well or poorly together, and a more systematic performance evaluation in procurement situations. The Berkeley Institute for Performance Studies has developed a three-level approach to evaluating the design of high end machines and the software that runs on them: (1) A suite of representative applications; (2) A set of application kernels; and (3) Benchmarks to measure key system parameters. The three levels yield different type of information, all of which are useful in evaluating systems, and enable NSF and DOE centers to select computer architectures more suited for scientific applications. The analysis will further allow the centers to engage vendors in discussion of strategies to alleviate the present architectural bottlenecks using quantitative information. These may include small hardware changes or larger ones that may be out interest to non-scientific workloads. Providing quantitative models to the vendors allows them to assess the benefits of technology alternatives using their own internal cost-models in the broader marketplace, ideally facilitating the development of future computer

  1. Science Driven Supercomputing Architectures: AnalyzingArchitectural Bottlenecks with Applications and Benchmark Probes

    Energy Technology Data Exchange (ETDEWEB)

    Kamil, S.; Yelick, K.; Kramer, W.T.; Oliker, L.; Shalf, J.; Shan,H.; Strohmaier, E.

    2005-09-26

    There is a growing gap between the peak speed of parallelcomputing systems and the actual delivered performance for scientificapplications. In general this gap is caused by inadequate architecturalsupport for the requirements of modern scientific applications, ascommercial applications and the much larger market they represent, havedriven the evolution of computer architectures. This gap has raised theimportance of developing better benchmarking methodologies tocharacterize and to understand the performance requirements of scientificapplications, to communicate them efficiently to influence the design offuture computer architectures. This improved understanding of theperformance behavior of scientific applications will allow improvedperformance predictions, development of adequate benchmarks foridentification of hardware and application features that work well orpoorly together, and a more systematic performance evaluation inprocurement situations. The Berkeley Institute for Performance Studieshas developed a three-level approach to evaluating the design of high endmachines and the software that runs on them: 1) A suite of representativeapplications; 2) A set of application kernels; and 3) Benchmarks tomeasure key system parameters. The three levels yield different type ofinformation, all of which are useful in evaluating systems, and enableNSF and DOE centers to select computer architectures more suited forscientific applications. The analysis will further allow the centers toengage vendors in discussion of strategies to alleviate the presentarchitectural bottlenecks using quantitative information. These mayinclude small hardware changes or larger ones that may be out interest tonon-scientific workloads. Providing quantitative models to the vendorsallows them to assess the benefits of technology alternatives using theirown internal cost-models in the broader marketplace, ideally facilitatingthe development of future computer architectures more suited forscientific

  2. Acoustic-optical phonon up-conversion and hot-phonon bottleneck in lead-halide perovskites

    Science.gov (United States)

    Yang, Jianfeng; Wen, Xiaoming; Xia, Hongze; Sheng, Rui; Ma, Qingshan; Kim, Jincheol; Tapping, Patrick; Harada, Takaaki; Kee, Tak W.; Huang, Fuzhi; Cheng, Yi-Bing; Green, Martin; Ho-Baillie, Anita; Huang, Shujuan; Shrestha, Santosh; Patterson, Robert; Conibeer, Gavin

    2017-01-01

    The hot-phonon bottleneck effect in lead-halide perovskites (APbX3) prolongs the cooling period of hot charge carriers, an effect that could be used in the next-generation photovoltaics devices. Using ultrafast optical characterization and first-principle calculations, four kinds of lead-halide perovskites (A=FA+/MA+/Cs+, X=I−/Br−) are compared in this study to reveal the carrier-phonon dynamics within. Here we show a stronger phonon bottleneck effect in hybrid perovskites than in their inorganic counterparts. Compared with the caesium-based system, a 10 times slower carrier-phonon relaxation rate is observed in FAPbI3. The up-conversion of low-energy phonons is proposed to be responsible for the bottleneck effect. The presence of organic cations introduces overlapping phonon branches and facilitates the up-transition of low-energy modes. The blocking of phonon propagation associated with an ultralow thermal conductivity of the material also increases the overall up-conversion efficiency. This result also suggests a new and general method for achieving long-lived hot carriers in materials. PMID:28106061

  3. Childhood leukemia genetic bottleneck phenomenon related to TEL-AML1: the postulation by a mathematical model

    Institute of Scientific and Technical Information of China (English)

    Petar Ivanovski; Ivan Ivanovski; Dimitrije Nikoli(c); Ivana Jovanovi(c)

    2012-01-01

    Childhood leukemia bottleneck phenomenon is the most mysterious corollary of the prenatal origin discovery of leukemogenic chromosome translocations.The bottleneck is evidence that leukemia initiation,by in utero acquired chromosome translocations that generate functional fusion genes,is far more common than the incidence rate of corresponding leukemia.For childhood TEL-AML1+ acute lymphoblastic leukemia (ALL) this equates to approximately 100 times.Practically this means that among a hundred children born with TEL-AML1 fusion gene,only one child will later in its life develop ALL.The key data necessary for unraveling of this mystery were discovered in 2002.It was the level of TEL-AML1 + cells' frequency.The bottleneck is caused by the very low body TEL-AML1 + cell count.Only one out of a thousand B cells carries TEL-AML1 fusion gene.TEL-AML1+ body cell count is low because TEL-AML1 fusion is generated at cell level of 10a to 10-4 just during the late fetal lymphopoiesis i.e.after the 36th gestational week.

  4. Childhood leukemia genetic bottleneck phenomenon related to TEL-AML1: the postulation by a mathematical model.

    Science.gov (United States)

    Ivanovski, Petar; Ivanovski, Ivan; Nikolić, Dimitrije; Jovanović, Ivana

    2012-03-01

    Childhood leukemia bottleneck phenomenon is the most mysterious corollary of the prenatal origin discovery of leukemogenic chromosome translocations. The bottleneck is evidence that leukemia initiation, by in utero acquired chromosome translocations that generate functional fusion genes, is far more common than the incidence rate of corresponding leukemia. For childhood TEL-AML1(+) acute lymphoblastic leukemia (ALL) this equates to approximately 100 times. Practically this means that among a hundred children born with TEL-AML1 fusion gene, only one child will later in its life develop ALL. The key data necessary for unraveling of this mystery were discovered in 2002. It was the level of TEL-AML1(+) cells’ frequency. The bottleneck is caused by the very low body TEL-AML1(+) cell count. Only one out of a thousand B cells carries TEL-AML1 fusion gene. TEL-AML1(+) body cell count is low because TEL-AML1 fusion is generated at cell level of 10(-3) to 10(-4) just during the late fetal lymphopoiesis i.e. after the 36th gestational week.

  5. Acoustic-optical phonon up-conversion and hot-phonon bottleneck in lead-halide perovskites

    Science.gov (United States)

    Yang, Jianfeng; Wen, Xiaoming; Xia, Hongze; Sheng, Rui; Ma, Qingshan; Kim, Jincheol; Tapping, Patrick; Harada, Takaaki; Kee, Tak W.; Huang, Fuzhi; Cheng, Yi-Bing; Green, Martin; Ho-Baillie, Anita; Huang, Shujuan; Shrestha, Santosh; Patterson, Robert; Conibeer, Gavin

    2017-01-01

    The hot-phonon bottleneck effect in lead-halide perovskites (APbX3) prolongs the cooling period of hot charge carriers, an effect that could be used in the next-generation photovoltaics devices. Using ultrafast optical characterization and first-principle calculations, four kinds of lead-halide perovskites (A=FA+/MA+/Cs+, X=I-/Br-) are compared in this study to reveal the carrier-phonon dynamics within. Here we show a stronger phonon bottleneck effect in hybrid perovskites than in their inorganic counterparts. Compared with the caesium-based system, a 10 times slower carrier-phonon relaxation rate is observed in FAPbI3. The up-conversion of low-energy phonons is proposed to be responsible for the bottleneck effect. The presence of organic cations introduces overlapping phonon branches and facilitates the up-transition of low-energy modes. The blocking of phonon propagation associated with an ultralow thermal conductivity of the material also increases the overall up-conversion efficiency. This result also suggests a new and general method for achieving long-lived hot carriers in materials.

  6. Acoustic-optical phonon up-conversion and hot-phonon bottleneck in lead-halide perovskites.

    Science.gov (United States)

    Yang, Jianfeng; Wen, Xiaoming; Xia, Hongze; Sheng, Rui; Ma, Qingshan; Kim, Jincheol; Tapping, Patrick; Harada, Takaaki; Kee, Tak W; Huang, Fuzhi; Cheng, Yi-Bing; Green, Martin; Ho-Baillie, Anita; Huang, Shujuan; Shrestha, Santosh; Patterson, Robert; Conibeer, Gavin

    2017-01-20

    The hot-phonon bottleneck effect in lead-halide perovskites (APbX3) prolongs the cooling period of hot charge carriers, an effect that could be used in the next-generation photovoltaics devices. Using ultrafast optical characterization and first-principle calculations, four kinds of lead-halide perovskites (A=FA(+)/MA(+)/Cs(+), X=I(-)/Br(-)) are compared in this study to reveal the carrier-phonon dynamics within. Here we show a stronger phonon bottleneck effect in hybrid perovskites than in their inorganic counterparts. Compared with the caesium-based system, a 10 times slower carrier-phonon relaxation rate is observed in FAPbI3. The up-conversion of low-energy phonons is proposed to be responsible for the bottleneck effect. The presence of organic cations introduces overlapping phonon branches and facilitates the up-transition of low-energy modes. The blocking of phonon propagation associated with an ultralow thermal conductivity of the material also increases the overall up-conversion efficiency. This result also suggests a new and general method for achieving long-lived hot carriers in materials.

  7. A Qualitative Study of Bottlenecks and Causes of Fractions for Dedicated Incomes of Health Centers and Solutions for their Reduction

    Science.gov (United States)

    Tabrizi, Jafar Sadegh; Alidoost, Saeide; Abdolahi, Hossein Mashhadi

    2016-01-01

    Background: Primary health care is one of effective approaches for improving public health. Providing optimal cares requires supplication of various resources such as financial resources. “Fractions of incomes” in health centers is one of the remarkable problems for the domain of financial resources management in Iran. This study was aimed to identify bottlenecks and causes of fractions for incomes in health centers and solutions for their reduction. Methods: The current study was conducted in a qualitative phenomenology method in East Azerbaijan province of Iran in 2014. Data collection method was focus group discussion and semi-structured interview. Purposive sampling was used for selecting participants. Focus group discussions and interviews were conducted based on pre-prepared guidance and continued till data saturation. Validity of guidance was approved by qualitative studies experts. Data were analyzed using content analysis method. Results: Based on the opinions of participants, two and six themes were respectively extracted for bottlenecks of fractions and causes and solutions for their reduction. Themes for bottlenecks of fractions included cash (monetary) and non-cash (non-monetary) fractions and themes for causes and solutions included causes and solutions for fractions per capita, insurance deductions, fractions related to sending documents, registration fractions, discounts fractions, and incomplete deposit of cash incomes. Conclusion: All cash and non-cash incomes of health centers are subject to fractions. The causes of fractions are related to the whole process of converting services to incomes and insurance requirements. Identified solutions and interventions also focus on these areas.

  8. 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

  9. Moving in extreme environments

    DEFF Research Database (Denmark)

    Lucas, Samuel J E; Helge, Jørn W; Schütz, Uwe H W;

    2016-01-01

    This review addresses human capacity for movement in the context of extreme loading and with it the combined effects of metabolic, biomechanical and gravitational stress on the human body. This topic encompasses extreme duration, as occurs in ultra-endurance competitions (e.g. adventure racing...... and transcontinental races) and expeditions (e.g. polar crossings), to the more gravitationally limited load carriage (e.g. in the military context). Juxtaposed to these circumstances is the extreme metabolic and mechanical unloading associated with space travel, prolonged bedrest and sedentary lifestyle, which may...

  10. Extremal surface barriers

    Energy Technology Data Exchange (ETDEWEB)

    Engelhardt, Netta; Wall, Aron C. [Department of Physics, University of California,Santa Barbara, CA 93106 (United States)

    2014-03-13

    We present a generic condition for Lorentzian manifolds to have a barrier that limits the reach of boundary-anchored extremal surfaces of arbitrary dimension. We show that any surface with nonpositive extrinsic curvature is a barrier, in the sense that extremal surfaces cannot be continuously deformed past it. Furthermore, the outermost barrier surface has nonnegative extrinsic curvature. Under certain conditions, we show that the existence of trapped surfaces implies a barrier, and conversely. In the context of AdS/CFT, these barriers imply that it is impossible to reconstruct the entire bulk using extremal surfaces. We comment on the implications for the firewall controversy.

  11. Analysis of talent bottleneck of chain retailing business%连锁零售企业人才瓶颈问题浅析

    Institute of Scientific and Technical Information of China (English)

    赵根良

    2012-01-01

    In the chain retailing business operation and management, talent is the foundation of its success and continuous development. With the rapid expansion of chain retailing business, chain retailing business in China has relatively serious talent bottleneck problem. Based on the analysis of the situation and reasons of Chinese chain retailing business talent bottleneck, this article puts forward counter- measures and suggestions to solve Chinese chain retailing business talent bottleneck problem.%在分析了我国连锁零售企业人才瓶颈的现状和原因的基础上,提出了解决这一问题的对策和建议。

  12. Analysis of extreme events

    CSIR Research Space (South Africa)

    Khuluse, S

    2009-04-01

    Full Text Available ) determination of the distribution of the damage and (iii) preparation of products that enable prediction of future risk events. The methodology provided by extreme value theory can also be a powerful tool in risk analysis...

  13. Extreme environments and exobiology.

    Science.gov (United States)

    Friedmann, E I

    1993-01-01

    Ecological research on extreme environments can be applied to exobiological problems such as the question of life on Mars. If life forms (fossil or extant) are found on Mars, their study will help to solve fundamental questions about the nature of life on Earth. Extreme environments that are beyond the range of adaptability of their inhabitants are defined as "absolute extreme". Such environments can serve as terrestrial models for the last stages of life in the history of Mars, when the surface cooled down and atmosphere and water disappeared. The cryptoendolithic microbial community in porous rocks of the Ross Desert in Antarctica and the microbial mats at the bottom of frozen Antarctic lakes are such examples. The microbial communities of Siberian permafrost show that, in frozen but stable communities, long-term survival is possible. In the context of terraforming Mars, selected microorganisms isolated from absolute extreme environments are considered for use in creation of a biological carbon cycle.

  14. Venous Ultrasound (Extremities)

    Science.gov (United States)

    ... News Physician Resources Professions Site Index A-Z Ultrasound - Venous (Extremities) Venous ultrasound uses sound waves to ... limitations of Venous Ultrasound Imaging? What is Venous Ultrasound Imaging? Ultrasound is safe and painless, and produces ...

  15. Statistics of extremes

    CERN Document Server

    Gumbel, E J

    2012-01-01

    This classic text covers order statistics and their exceedances; exact distribution of extremes; the 1st asymptotic distribution; uses of the 1st, 2nd, and 3rd asymptotes; more. 1958 edition. Includes 44 tables and 97 graphs.

  16. Extreme weather events and infectious disease outbreaks.

    Science.gov (United States)

    McMichael, Anthony J

    2015-01-01

    Human-driven climatic changes will fundamentally influence patterns of human health, including infectious disease clusters and epidemics following extreme weather events. Extr