WorldWideScience

Sample records for linkage groups covering

  1. Clifford algebras, spinors, spin groups and covering groups

    International Nuclear Information System (INIS)

    Magneville, C.; Pansart, J.P.

    1991-03-01

    The Dirac equation uses matrices named Υ matrices which are representations of general algebraic structures associated with a metric space. These algebras are the Clifford algebras. In the first past, these algebras are studied. Then the notion of spinor is developed. It is shown that Majorana and Weyl spinors only exist for some particular metric space. In the second part, Clifford and spinor groups are studied. They may be interpreted as the extension of the notion of orthogonal group for Clifford algebras and their spaces for representation. The rotation of a spinor is computed. In the last part, the connexion between the spinor groups and the Universal Covering Groups is presented [fr

  2. Infinity-Norm Permutation Covering Codes from Cyclic Groups

    OpenAIRE

    Karni, Ronen; Schwartz, Moshe

    2017-01-01

    We study covering codes of permutations with the $\\ell_\\infty$-metric. We provide a general code construction, which uses smaller building-block codes. We study cyclic transitive groups as building blocks, determining their exact covering radius, and showing linear-time algorithms for finding a covering codeword. We also bound the covering radius of relabeled cyclic transitive groups under conjugation.

  3. Complex group algebras of the double covers of the symmetric and alternating group

    DEFF Research Database (Denmark)

    Bessenrodt, Christine; Nguyen, Hung Ngoc; Olsson, Jørn Børling

    2015-01-01

    We prove that the double covers of the alternating and symmetric groups are determined by their complex group algebras......We prove that the double covers of the alternating and symmetric groups are determined by their complex group algebras...

  4. Cytogenetical anchoring of sheep linkage map and syntenic groups using a sheep BAC library

    Directory of Open Access Journals (Sweden)

    Cribiu Edmond-Paul

    2000-07-01

    Full Text Available Abstract In order to simultaneously integrate linkage and syntenic groups to the ovine chromosomal map, a sheep bacterial artificial chromosome (BAC library was screened with previously assigned microsatellites using a sheep-hamster hybrid panel and genetic linkage. Thirty-three BACs were obtained, fluorescently labelled and hybridised on sheep-goat hybrid metaphases (2n = 57. This study allowed us, (i, to anchor all linkage groups on sheep chromosomes, (ii, to give information on the probable position of the centromere on the linkage map for the centromeric chromosomes, (iii, to contradict the previous orientation of the ovine × linkage group by the mapping of BMS1008 on OARXq38. Concerning our somatic cell hybrid panel, this study resulted in the assignment of all the previously unassigned groups to ovine chromosomes and a complete characterisation of the hybrid panel. In addition, since hybridisations were performed on a sheep-goat hybrid, new marker/anchoring points were added to the caprine cytogenetic map.

  5. Cytogenetic characterization and AFLP-based genetic linkage mapping for the butterfly Bicyclus anynana, covering all 28 karyotyped chromosomes.

    Directory of Open Access Journals (Sweden)

    Arjen E Van't Hof

    Full Text Available BACKGROUND: The chromosome characteristics of the butterfly Bicyclus anynana, have received little attention, despite the scientific importance of this species. This study presents the characterization of chromosomes in this species by means of cytogenetic analysis and linkage mapping. METHODOLOGY/PRINCIPAL FINDINGS: Physical genomic features in the butterfly B. anynana were examined by karyotype analysis and construction of a linkage map. Lepidoptera possess a female heterogametic W-Z sex chromosome system. The WZ-bivalent in pachytene oocytes of B. anynana consists of an abnormally small, heterochromatic W-chromosome with the Z-chromosome wrapped around it. Accordingly, the W-body in interphase nuclei is much smaller than usual in Lepidoptera. This suggests an intermediate stage in the process of secondary loss of the W-chromosome to a ZZ/Z sex determination system. Two nucleoli are present in the pachytene stage associated with an autosome and the WZ-bivalent respectively. Chromosome counts confirmed a haploid number of n = 28. Linkage mapping had to take account of absence of crossing-over in females, and of our use of a full-sib crossing design. We developed a new method to determine and exclude the non-recombinant uninformative female inherited component in offspring. The linkage map was constructed using a novel approach that uses exclusively JOINMAP-software for Lepidoptera linkage mapping. This approach simplifies the mapping procedure, avoids over-estimation of mapping distance and increases the reliability of relative marker positions. A total of 347 AFLP markers, 9 microsatellites and one single-copy nuclear gene covered all 28 chromosomes, with a mapping distance of 1354 cM. Conserved synteny of Tpi on the Z-chromosome in Lepidoptera was confirmed for B. anynana. The results are discussed in relation to other mapping studies in Lepidoptera. CONCLUSIONS/SIGNIFICANCE: This study adds to the knowledge of chromosome structure and

  6. Microseismic Event Grouping Based on PageRank Linkage at the Newberry Volcano Geothermal Site

    Science.gov (United States)

    Aguiar, A. C.; Myers, S. C.

    2016-12-01

    The Newberry Volcano DOE FORGE site in Central Oregon has been stimulated two times using high-pressure fluid injection to study the Enhanced Geothermal Systems (EGS) technology. Several hundred microseismic events were generated during the first stimulation in the fall of 2012. Initial locations of this microseismicity do not show well defined subsurface structure in part because event location uncertainties are large (Foulger and Julian, 2013). We focus on this stimulation to explore the spatial and temporal development of microseismicity, which is key to understanding how subsurface stimulation modifies stress, fractures rock, and increases permeability. We use PageRank, Google's initial search algorithm, to determine connectivity within the events (Aguiar and Beroza, 2014) and assess signal-correlation topology for the micro-earthquakes. We then use this information to create signal families and compare these to the spatial and temporal proximity of associated earthquakes. We relocate events within families (identified by PageRank linkage) using the Bayesloc approach (Myers et al., 2007). Preliminary relocations show tight spatial clustering of event families as well as evidence of events relocating to a different cluster than originally reported. We also find that signal similarity (linkage) at several stations, not just one or two, is needed in order to determine that events are in close proximity to one another. We show that indirect linkage of signals using PageRank is a reliable way to increase the number of events that are confidently determined to be similar to one another, which may lead to efficient and effective grouping of earthquakes with similar physical characteristics, such as focal mechanisms and stress drop. Our ultimate goal is to determine whether changes in the state of stress and/or changes in the generation of subsurface fracture networks can be detected using PageRank topology as well as aid in the event relocation to obtain more accurate

  7. The Linkages between Mindfulness and Social Information Processing Theory on the Usage of Whatsapp Media Groups

    Directory of Open Access Journals (Sweden)

    Dina Sekar Vusparatih

    2018-03-01

    Full Text Available The objective of the research was to find the linkages between mindfulness and social information processing theory on the use of WhatsApp group of Elementary school Principals in District Cilandak Region III for the distribution of various information and instructions. Through the concept of mindfulness and Social Information Processing theory approach (SIP, this research would explore the causes of the frequent emergence of noise, misunderstanding, and even tangency to the WA group that was carried on the meeting of headmaster meetings and relationships between members. The research problem was why WA group still causing issues among the Principals. By using the qualitative approach, data collection techniques used in this research were the interview, observation, and literature study. It is found that technological sophistication does not go parallel with maturity in communicating using media technologies. Lack of mindfulness in the WA group is a form of organizational communication that is simply transferred into the form of text communication on mobile phones that is being the main cause. Also, the organizational structure is still inherent in it and only serves as a bridge/form of interim communication because the main form of communication is still in the form of correspondence and face-to-face meetings.

  8. Cytogenetic characterization and AFLP-based genetic linkage mapping for the butterfly Bicyclus anynana, covering all 28 karyotyped chromosomes

    Czech Academy of Sciences Publication Activity Database

    Van´t Hof, A. E.; Marec, František; Saccheri, I. J.; Brakefield, P. M.; Zwaan, B. J.

    2008-01-01

    Roč. 3, č. 12 (2008), e3882 E-ISSN 1932-6203 R&D Projects: GA ČR GA206/06/1860 Institutional research plan: CEZ:AV0Z50070508 Keywords : Bicyclus anynana * cytogenetic characterization * AFLP-based genetic linkage mapping Subject RIV: EB - Genetics ; Molecular Biology

  9. Coverings and the fundamental group for partial differential equations

    NARCIS (Netherlands)

    Igonin, S.

    2003-01-01

    Following I. S. Krasilshchik and A. M. Vinogradov, we regard systems of PDEs as manifolds with involutive distributions and consider their special morphisms called differential coverings, which include constructions like Lax pairs and B\\"acklund transformations in soliton theory. We show that,

  10. Detection of Duchenne/Becker Muscular Dystrophy Carriers in a Group of Iranian Families by Linkage Analysis

    Directory of Open Access Journals (Sweden)

    Fardeen Ali Malayeri

    2011-03-01

    Full Text Available This study determines the value of linkage analysis using six RFLP markers for carrier detection and prenatal diagnosis in familial DMD/BMD cases and their family members for the first time in the Iranian population. We studied the dystrophin gene in 33 unrelated patients with clinical diagnosis of DMD or BMD. Subsequently, we determined the rate of heterozygosity for six intragenic RFLP markers in the mothers of patients with dystrophin gene deletions. Finally, we studied the efficiency of linkage analysis by using RFLP markers for carrier status detection of DMD/BMD. In 63.6% of the patients we found one or more deletions. The most common heterozygous RFLP marker with 57.1% heterozygosity was pERT87.15Taq1. More than 80% of mothers in two groups of familial or non-familial cases had at least two heterozygous markers. Family linkage analysis was informative in more than 80% of the cases, allowing for accurate carrier detection. We found that linkage analysis using these six RFLP markers for carrier detection and prenatal diagnosis is a rapid, easy, reliable, and inexpensive method, suitable for most routine diagnostic services. The heterozygosity frequency of these markers is high enough in the Iranian population to allow carrier detection and prenatal diagnosis of DMD/BMD in more than 80% of familial cases in Iran.

  11. EnviroAtlas - Austin, TX - Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, green space, and agriculture. Forest is defined as...

  12. EnviroAtlas - Memphis, TN - Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, green space, agriculture, and wetlands. Forest is...

  13. EnviroAtlas - Portland, OR - Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, and green space. Forest is combination of trees and...

  14. EnviroAtlas - Fresno, CA - Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, and green space. Forest is combination of trees and...

  15. EnviroAtlas - Tampa, FL - Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, green space, wetland, and agriculture. Impervious is...

  16. EnviroAtlas - Portland, ME - Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, green space, wetland, and agriculture. Impervious is...

  17. EnviroAtlas - Woodbine, IA - Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, and green space. Forest is combination of trees and...

  18. EnviroAtlas - Cleveland, OH - Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, green space, and wetlands. In this community, forest...

  19. EnviroAtlas - Paterson, NJ - Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, and green space. Forest is just trees and forest....

  20. EnviroAtlas - Phoenix, AZ - Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, agriculture, and green space. Forest is combination...

  1. EnviroAtlas - Pittsburgh, PA - Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, and green space. Forest is combination of trees and...

  2. On the structure of finite-sheeted coverings of compact connected groups

    OpenAIRE

    Grigorian, S. A.; Gumerov, R. N.

    2004-01-01

    Finite-sheeted covering mappings onto compact connected groups are studied. It is shown that a finite-sheeted covering mapping from a connected Hausdorff topological space onto a compact connected abelian group G must be a homeomorphism provided that the character group of G admits division by the degree of given covering mapping. Using this result, we obtain criteria of triviality for finite coverings of G in terms of its character group and means on G. In order to establish these facts, for...

  3. ON THE FORMATION OF AMIDE POLYMERS VIA CARBONYL–AMINO GROUP LINKAGES IN ENERGETICALLY PROCESSED ICES OF ASTROPHYSICAL RELEVANCE

    Energy Technology Data Exchange (ETDEWEB)

    Förstel, Marko; Maksyutenko, Pavlo; Jones, Brant M.; Kaiser, Ralf I. [Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, 96822 HI (United States); Sun, Bing J.; Lee, Huan C.; Chang, Agnes H. H., E-mail: ralfk@hawaii.edu, E-mail: hhchang@mail.ndhu.edu.tw [Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 974, Taiwan (China)

    2016-04-01

    We report on the formation of organic amide polymers via carbonyl–amino group linkages in carbon monoxide and ammonia bearing energetically processed ices of astrophysical relevance. The first group comprises molecules with one carboxyl group and an increasing number of amine moieties starting with formamide (45 u), urea (60 u), and hydrazine carboxamide (75 u). The second group consists of species with two carboxyl (58 u) and up to three amine groups (73 u, 88 u, and 103 u). The formation and polymerization of these linkages from simple inorganic molecules via formamide und urea toward amide polymers is discussed in an astrophysical and astrobiological context. Our results show that long chain molecules, which are closely related to polypeptides, easily form by energetically processing simple, inorganic ices at very low temperatures and can be released into the gas phase by sublimation of the ices in star-forming regions. Our experimental results were obtained by employing reflectron time-of-flight mass spectroscopy, coupled with soft, single photon vacuum ultraviolet photoionization; they are complemented by theoretical calculations.

  4. ON THE FORMATION OF AMIDE POLYMERS VIA CARBONYL–AMINO GROUP LINKAGES IN ENERGETICALLY PROCESSED ICES OF ASTROPHYSICAL RELEVANCE

    International Nuclear Information System (INIS)

    Förstel, Marko; Maksyutenko, Pavlo; Jones, Brant M.; Kaiser, Ralf I.; Sun, Bing J.; Lee, Huan C.; Chang, Agnes H. H.

    2016-01-01

    We report on the formation of organic amide polymers via carbonyl–amino group linkages in carbon monoxide and ammonia bearing energetically processed ices of astrophysical relevance. The first group comprises molecules with one carboxyl group and an increasing number of amine moieties starting with formamide (45 u), urea (60 u), and hydrazine carboxamide (75 u). The second group consists of species with two carboxyl (58 u) and up to three amine groups (73 u, 88 u, and 103 u). The formation and polymerization of these linkages from simple inorganic molecules via formamide und urea toward amide polymers is discussed in an astrophysical and astrobiological context. Our results show that long chain molecules, which are closely related to polypeptides, easily form by energetically processing simple, inorganic ices at very low temperatures and can be released into the gas phase by sublimation of the ices in star-forming regions. Our experimental results were obtained by employing reflectron time-of-flight mass spectroscopy, coupled with soft, single photon vacuum ultraviolet photoionization; they are complemented by theoretical calculations

  5. On the Linkage between Springtime Eurasian Snow Cover Retreat due to the Global Warming and Changes in Summertime Atmospheric Circulation over Japan and East Asia

    Science.gov (United States)

    Nozawa, T.; Fujiwara, S.

    2017-12-01

    According to the 5th Assessment Report of the Intergovernmental Panel on Climate Change (IPCC AR5), snow cover extent (SCE) over the northern hemisphere is greatly decreasing in spring. This change is expected to affect atmospheric circulation change via land-atmosphere interactions. In this study, we investigated relationships between spring SCE anomaly over the Eurasia and changes in atmospheric circulations, mainly analyzing the Japanese 55-year Reanalysis (JRA-55). Differences in composites of zonal winds at upper and middle levels between large and small SCE years over Western Siberia in spring show that, around Japan and East Asia, jet stream in small SCE years is shifted southward in April and June. We also analyzed surface temperature and soil moisture and find that, in small SCE years, surface temperature in Western Siberia and Central Asia is increased and soil moisture reduced significantly in June. The air temperature in the middle and low level atmosphere also significantly increased and have wave-like pattern in May. These results suggest that there are some linkages between the springtime Eurasian SCE reduction and changes in summertime jet stream over Japan and East Asia through land-atmosphere interactions.

  6. COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge.

    Science.gov (United States)

    Lu, Yang Young; Chen, Ting; Fuhrman, Jed A; Sun, Fengzhu

    2017-03-15

    The advent of next-generation sequencing technologies enables researchers to sequence complex microbial communities directly from the environment. Because assembly typically produces only genome fragments, also known as contigs, instead of an entire genome, it is crucial to group them into operational taxonomic units (OTUs) for further taxonomic profiling and down-streaming functional analysis. OTU clustering is also referred to as binning. We present COCACOLA, a general framework automatically bin contigs into OTUs based on sequence composition and coverage across multiple samples. The effectiveness of COCACOLA is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, GroopM, MaxBin and MetaBAT. The superior performance of COCACOLA relies on two aspects. One is using L 1 distance instead of Euclidean distance for better taxonomic identification during initialization. More importantly, COCACOLA takes advantage of both hard clustering and soft clustering by sparsity regularization. In addition, the COCACOLA framework seamlessly embraces customized knowledge to facilitate binning accuracy. In our study, we have investigated two types of additional knowledge, the co-alignment to reference genomes and linkage of contigs provided by paired-end reads, as well as the ensemble of both. We find that both co-alignment and linkage information further improve binning in the majority of cases. COCACOLA is scalable and faster than CONCOCT, GroopM, MaxBin and MetaBAT. The software is available at https://github.com/younglululu/COCACOLA . fsun@usc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  7. Linkage group-chromosome correlations in Sordaria macrospora: Chromosome identification by three dimensional reconstruction of their synaptonemal complex.

    Science.gov (United States)

    Zickler, D; Leblon, G; Haedens, V; Collard, A; Thuriaux, P

    1984-01-01

    Reconstruction of serially sectioned zygotene and pachytene nuclei has allowed, by measuring the lengths of synaptonemal complexes, an assignment of the 7 linkage (LG) groups to the 7 chromosomes in the fungus Sordaria macrospora. The 7 LG have been established using 19 mutants showing low second division segregation frequencies. Eight chromosomal rearrangements mapped on the 7 LG were used to identify the chromosomes involved. The following one to one assignment of the 7 LG to specific chromosomes was obtained: LG a: chromosome (chr) 1, LG b: chr5, LG c: chr6, LG d: chr7, LG e: chr4, LG f: chr3 and LG g: chr2 (the chromosome carrying the nucleolus organizer region).

  8. Empowering rural women's groups for strengthening economic linkages: some Indian experiments.

    Science.gov (United States)

    Rajagopal

    1999-05-01

    Through organizing informal self-help groups (SHGs), rural women in India are provided credit and extension support for various production-oriented income-generating activities. These activities usually include garment-making, embroidery, food processing, bee-keeping, basketry, gem cutting, weaving, and knitting. SHGs are self-governed, with decisions about production and marketing taken collectively, although the group leader is responsible for identifying potential marketing centers and consumers. These groups represent a new culture in rural development, breaking with traditional bureaucracy and top-down management. Informal groups empower rural women to manage rural industries and make decisions collectively for their common economic interests. Experience with SHGs in Orissa, lessons from nongovernmental organization intervention, and a model for empowering poor people in a small town in Kerala are discussed.

  9. ABO Blood Group and Dementia Risk--A Scandinavian Record-Linkage Study

    DEFF Research Database (Denmark)

    Vasan, Senthil K; Rostgaard, Klaus; Ullum, Henrik

    2015-01-01

    ,615 cases of Alzheimer's disease, 1,842 cases of vascular dementia, and 9,091 cases of unspecified dementia. Overall, our study showed no association between ABO blood group and risk of Alzheimer's disease, vascular dementia or unspecified dementia. This was also true when analyses were restricted to donors......BACKGROUND: Dementia includes a group of neuro-degenerative disorders characterized by varying degrees of cognitive impairment. Recent data indicates that blood group AB is associated with impaired cognition in elderly patients. To date there are no large-scale studies that have examined...... the relationship between ABO blood group and dementia-related disorders in detail. METHODS: We used data from the SCANDAT2 database that contains information on over 1.6 million blood donors from 1968 in Sweden and 1981 from Denmark. The database was linked with health outcomes data from nationwide patient...

  10. ABO Blood Group and Dementia Risk--A Scandinavian Record-Linkage Study.

    Directory of Open Access Journals (Sweden)

    Senthil K Vasan

    Full Text Available Dementia includes a group of neuro-degenerative disorders characterized by varying degrees of cognitive impairment. Recent data indicates that blood group AB is associated with impaired cognition in elderly patients. To date there are no large-scale studies that have examined the relationship between ABO blood group and dementia-related disorders in detail.We used data from the SCANDAT2 database that contains information on over 1.6 million blood donors from 1968 in Sweden and 1981 from Denmark. The database was linked with health outcomes data from nationwide patient and cause of death registers to investigate the relationship between blood groups and risk of different types of dementia. The incident rate ratios were estimated using log-linear Poisson regression models.Among 1,598,294 donors followed over 24 million person-years of observation we ascertained 3,615 cases of Alzheimer's disease, 1,842 cases of vascular dementia, and 9,091 cases of unspecified dementia. Overall, our study showed no association between ABO blood group and risk of Alzheimer's disease, vascular dementia or unspecified dementia. This was also true when analyses were restricted to donors aged 70 years or older except for a slight, but significantly decreased risk of all dementia combined in subjects with blood group A (IRR, 0.93; 95% confidence interval [CI], 0.88-0.98, compared to those with blood group O.Our results provide no evidence that ABO blood group influences the risk of dementia.

  11. Myocardial infarction incidence and survival by ethnic group: Scottish Health and Ethnicity Linkage retrospective cohort study.

    Science.gov (United States)

    Bansal, Narinder; Fischbacher, Colin M; Bhopal, Raj S; Brown, Helen; Steiner, Markus Fc; Capewell, Simon

    2013-09-13

    Inequalities in coronary heart disease mortality by country of birth are large and poorly understood. However, these data misclassify UK-born minority ethnic groups and provide little detail on whether excess risk is due to increased incidence, poorer survival or both. Retrospective cohort study. General resident population of Scotland. All those residing in Scotland during the 2001 Census were eligible for inclusion: 2 972 120 people were included in the analysis. The number still residing in Scotland at the end of the study in 2008 is not known. As specified in the analysis plan, the primary outcome measures were first occurrence of admission or death due to myocardial infarction and time to event. There were no secondary outcome measures. Acute myocardial infarction (AMI) incidence risk ratios (95% CIs) relative to white Scottish populations (100) were highest among Pakistani men (164.1 (142.2 to 189.2)) and women (153.7 (120.5, 196.1)) and lowest for men and women of Chinese (39.5 (27.1 to 57.6) and 59.1 (38.6 to 90.7)), other white British (77 (74.2 to 79.8) and 72.2 (69.0 to 75.5)) and other white (83.1 (75.9 to 91.0) and 79.9 (71.5 to 89.3)) ethnic groups. Adjustment for educational qualification did not eliminate these differences. Cardiac intervention uptake was similar across most ethnic groups. Compared to white Scottish, 28-day survival did not differ by ethnicity, except in Pakistanis where it was better, particularly in women (0.44 (0.25 to 0.78)), a difference not removed by adjustment for education, travel time to hospital or cardiac intervention uptake. Pakistanis have the highest incidence of AMI in Scotland, a country renowned for internationally high cardiovascular disease rates. In contrast, survival is similar or better in minority ethnic groups. Clinical care and policy should focus on reducing incidence among Pakistanis through more aggressive prevention.

  12. A genetic linkage map of hexaploid naked oat constructed with SSR markers

    Directory of Open Access Journals (Sweden)

    Gaoyuan Song

    2015-08-01

    Full Text Available Naked oat is a unique health food crop in China. Using 202 F2 individuals derived from a hybrid between the variety 578 and the landrace Sanfensan, we constructed a genetic linkage map consisting of 22 linkage groups covering 2070.50 cM and including 208 simple sequence repeat (SSR markers. The minimum distance between adjacent markers was 0.01 cM and the average was 9.95 cM. Each linkage group contained 2–22 markers. The largest linkage group covered 174.40 cM and the shortest one covered 36.80 cM, with an average of 94.11 cM. Thirty-six markers (17.3% showing distorted segregation were distributed across linkage groups LG5 to LG22. This map complements published oat genetic maps and is applicable for quantitative trait locus analysis, gene cloning and molecular marker-assisted selection.

  13. Baryonic sources using irreducible representations of the double-covered octahedral group

    International Nuclear Information System (INIS)

    Basak, S.; Edwards, R.; Fiebig, R.; Fleming, G.T.; Heller, U.M.; Morningstar, C.; Richards, D.; Sato, I.; Wallace, S.

    2005-01-01

    Irreducible representations (IRs) of the double-covered octahedral group are used to construct lattice source and sink operators for three-quark baryons. The goal is to achieve a good coupling to higher spin states as well as ground states. Complete sets of local and nonlocal straight-link operators are explicitly shown for isospin 1/2 and 3/2 baryons. The orthogonality relations of the IR operators are confirmed in a quenched lattice simulation

  14. Baryonic sources using irreducible representations of the double-covered octahedral group

    International Nuclear Information System (INIS)

    Basak, S.; Edwards, R.; Fiebig, R.; Fleming, G. T.; Heller, U. M.; Morningstar, C.; Richards, D.; Sato, I.; Wallace, S.

    2004-01-01

    Irreducible representations (IRs) of the double-covered octahedral group are used to construct lattice source and sink operators for three-quark baryons. The goal is to achieve a good coupling to higher spin states as well as ground states. Complete sets of local and nonlocal straight-link operators are explicitly shown for isospin 1/2 and 3/2 baryons. The orthogonality relations of the IR operators are confirmed in a quenched lattice simulation

  15. Exploitation of linkage learning in evolutionary algorithms

    CERN Document Server

    Chen, Ying-ping

    2010-01-01

    The exploitation of linkage learning is enhancing the performance of evolutionary algorithms. This monograph examines recent progress in linkage learning, with a series of focused technical chapters that cover developments and trends in the field.

  16. Establishment of a molecular genetic map of distal mouse chromosome 1: further definition of a conserved linkage group syntenic with human chromosome 1q.

    Science.gov (United States)

    Seldin, M F; Morse, H C; LeBoeuf, R C; Steinberg, A D

    1988-01-01

    A linkage map of distal mouse chromosome 1 was constructed by restriction fragment length polymorphism analysis of DNAs from seven sets of recombinant inbred (RI) strains. The data obtained with seven probes on Southern hybridization combined with data from previous studies suggest the gene order Cfh, Pep-3/Ren-1,2, Ly-5, Lamb-2, At-3, Apoa-2/Ly-17,Spna-1. These results confirm and extend analyses of a large linkage group which includes genes present on a 20-30 cM span of mouse chromosome 1 and those localized to human chromosome 1q21-32. Moreover, the data indicate similar relative positions of human and mouse complement receptor-related genes REN, CD45, LAMB2, AT3, APOA2, and SPTA. These results suggest that mouse gene analyses may help in detailed mapping of human genes within such a syntenic group.

  17. Some AFLP amplicons are highly conserved DNA sequences mapping to the same linkage groups in two F2 populations of carrot

    Directory of Open Access Journals (Sweden)

    Santos Carlos A.F.

    2002-01-01

    Full Text Available Amplified fragment length polymorphism (AFLP is a fast and reliable tool to generate a large number of DNA markers. In two unrelated F2 populations of carrot (Daucus carota L., Brasilia x HCM and B493 x QAL (wild carrot, it was hypothesized that DNA 1 digested with the same restriction endonuclease enzymes and amplified with the same primer combination and 2 sharing the same position in polyacrylamide gels should be conserved sequences. To test this hypothesis AFLP fragments from polyacrylamide gels were eluted, reamplified, separated in agarose gels, purified, cloned and sequenced. Among thirty-one paired fragments from each F2 population, twenty-six had identity greater than 91% and five presented identity of 24% to 44%. Among the twenty-six conserved AFLPs only one mapped to different linkage groups in the two populations while four of the five less-conserved bands mapped to different linkage groups. Of eight SCAR (sequence characterized amplified regions primers tested, one conserved AFLP resulted in co-dominant markers in both populations. Screening among 14 carrot inbreds or cultivars with three AFLP-SCAR primers revealed clear and polymorphic PCR products, with similar molecular sizes on agarose gels. The development of co-dominant markers based on conserved AFLP fragments will be useful to detect seed mixtures among hybrids, to improve and to merge linkage maps and to study diversity and phylogenetic relationships.

  18. Exploring the linkage between spontaneous grass cover biodiversity and soil degradation in two olive orchard microcatchments with contrasting environmental and management conditions

    Science.gov (United States)

    Taguas, E. V.; Arroyo, C.; Lora, A.; Guzmán, G.; Vanderlinden, K.; Gómez, J. A.

    2015-11-01

    Spontaneous grass covers are an inexpensive soil erosion control measure in olive orchards. Olive farmers allow grass to grow on sloping terrain to comply with the basic environmental standards derived from the Common Agricultural Policy (CAP, European Commission). However, to date there are few studies assessing the environmental quality considering such covers. In this study, we measured biodiversity indices for spontaneous grass cover in two olive orchards with contrasting site conditions and management regimes in order to evaluate the potential for biodiversity metrics to serve as an indicator of soil degradation. In addition, the differences and temporal variability of biodiversity indicators and their relationships with environmental factors such as soil type and properties, precipitation, topography and soil management were analysed. Different grass cover biodiversity indices were evaluated in two olive orchard catchments under conventional tillage and no tillage with grass cover, during 3 hydrological years (2011-2013). Seasonal samples of vegetal material and photographs in a permanent grid (4 samples ha-1) were taken to characterize the temporal variations of the number of species, frequency of life forms, diversity and modified Shannon and Pielou indices. Sorensen's index showed strong differences in species composition for the grass covers in the two olive orchard catchments, which are probably linked to the different site conditions. The catchment (CN) with the best site conditions (deeper soil and higher precipitation) and most intense management presented the highest biodiversity indices as well as the highest soil losses (over 10 t ha-1). In absolute terms, the diversity indices of vegetation were reasonably high for agricultural systems in both catchments, despite the fact that management activities usually severely limit the landscape and the variety of species. Finally, a significantly higher content of organic matter in the first 10 cm of soil

  19. EnviroAtlas - Green Bay, WI - Riparian Buffer Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of different land cover types within 15- and 50-meters of hydrologically connected streams, rivers, and other water...

  20. EnviroAtlas - New Bedford, MA - Riparian Buffer Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of different land cover types within 15- and 50-meters of hydrologically connected streams, rivers, and other water...

  1. Impact of northern Eurasian snow cover in autumn on the warm Arctic-cold Eurasia pattern during the following January and its linkage to stationary planetary waves

    Science.gov (United States)

    Xu, Xinping; He, Shengping; Li, Fei; Wang, Huijun

    2018-03-01

    The connection between Eurasian snow cover (SC) in autumn and Eurasian winter mean surface air temperature (SAT) has been identified by many studies. However, some recent observations indicate that early and late winter climate sometimes shows an out-of-phase relationship, suggesting that the winter mean situation might obscure the important relationships that are relevant for scientific research and applications. This study investigates the relationship between October northern Eurasian SC (NESC; 58°-68°N, 30°-90°E) and Eurasian SAT during the winter months and finds a significant relationship only exists in January. Generally, following reduced October NESC, the East Asian trough and Ural high are intensified in January, and anomalous northeasterly winds prevail in mid-latitudes, causing cold anomalies over Eurasia. Meanwhile, anomalous southwesterly winds along the northern fringe of the Ural high favor warm anomalies in the Arctic. The dynamical mechanism for the connection between NESC in October and the warm Arctic-cold Eurasia (WACE) anomaly in January is further investigated from the perspective of quasi-stationary planetary wave activity. It is found that planetary waves with zonal wavenumber-1 (ZWN1) play a dominant role in this process. Specifically, the ZWN1 pattern of planetary-scale waves concurrent with October NESC anomaly extends from the surface to the upper-stratosphere. It persists in the stratosphere through November-December and propagates downward to the surface by the following January, making the connection between October NESC and January climate possible. Additionally, the influence of October NESC on the January WACE pattern has intensified since the early-2000s.

  2. Neuropeptide Y receptor genes on human chromosome 4q31-q32 map to conserved linkage groups on mouse chromosomes 3 and 8

    Energy Technology Data Exchange (ETDEWEB)

    Lutz, C.M.; Frankel, W.N. [Jackson Lab., Bar Harbor, ME (United States); Richards, J.E. [Univ. of Michigan Medical School, Ann Arbor, MI (United States)] [and others

    1997-05-01

    Npy1r and Npy2r, the genes encoding mouse type 1 and type 2 neuropeptide Y receptors, have been mapped by interspecific backcross analysis. Previous studies have localized the human genes encoding these receptors to chromosome 4q31-q32. We have now assigned Npy1r and Npy2r to conserved linkage groups on mouse Chr 8 and Chr 3, respectively, which correspond to the distal region of human chromosome 4q. Using yeast artificial chromosomes, we have estimated the distance between the human genes to be approximately 6 cM. Although ancient tandem duplication events may account for some closely spaced G-protein-coupled receptor genes, the large genetic distance between the human type 1 and type 2 neuropeptide Y receptor genes raises questions about whether this mechanism accounts for their proximity. 20 refs., 1 fig.

  3. Collective action in culturally similar and dissimilar groups: An axperiment on parochialism, conditional cooperation, and their linkages

    NARCIS (Netherlands)

    Koopmans, R.; Rebers, S.

    2009-01-01

    This study examines the effects of ingroup favoritism and outgroup hostility ("parochialism"), as well as of conditionally cooperative strategies, in explaining contributions to experimental public goods games. The experimental conditions vary group composition along two culturally inheritable

  4. Linkage of biomolecules to solid phases for immunoassay

    International Nuclear Information System (INIS)

    Chapman, R.S.

    1998-01-01

    Topics covered by this lecture include a brief review of the principal methods of linkage of biomolecules to solid phase matrices. Copies of the key self explanatory slides are presented as figures together with reprints of two publications by the author dealing with a preferred chemistry for the covalent linkage of antibodies to hydroxyl and amino functional groups and the effects of changes in solid phase matrix and antibody coupling chemistry on the performance of a typical excess reagent immunoassay for thyroid stimulating hormone

  5. Resistance to the tetracyclines and macrolide-lincosamide-streptogramin group of antibiotics and its genetic linkage – a review

    Directory of Open Access Journals (Sweden)

    Durdica Marosevic

    2017-06-01

    Full Text Available An excessive use of antimicrobial agents poses a risk for the selection of resistant bacteria. Of particular interest are antibiotics that have large consumption rates in both veterinary and human medicine, such as the tetracyclines and macrolide-lincosamide-streptogramin (MLS group of antibiotics. A high load of these agents increases the risk of transmission of resistant bacteria and/or resistance determinants to humans, leading to a subsequent therapeutic failure. An increasing incidence of bacteria resistant to both tetracyclines and MLS antibiotics has been recently observed. This review summarizes the current knowledge on different tetracycline and MLS resistance genes that can be linked together on transposable elements.

  6. Haplotype diversity and linkage disequilibrium at DRD2 locus--a study on four population groups of Andhra Pradesh, India.

    Science.gov (United States)

    Saraswathy, Kallur Nava; Mukhopadhyay, Rupak; Shukla, Deepti; Kaur, Harpreet; Sachdeva, Mohinder Pal; Rao, A P; Saksena, Deepti; Kalla, Aloke Kumar

    2009-02-01

    Dopamine receptor D2 (DRD2) is expressed in the central nervous system and has a high affinity for many antipsychotic drugs. Besides several epidemiological investigations on association of DRD2 locus polymorphism(s) with neuropsychiatric problems and addictive behavior, a few polymorphisms in this locus have also been used to understand genomic diversity and population migratory histories globally. The present study attempts to understand the genomic diversity/affinity among four endogamous groups of Andhra Pradesh (India) against the backdrop of diversity studies from other parts of India and the rest of the world, with special reference to DRD2 locus. The four population groups from Adilabad District of Andhra Pradesh, namely, Brahmin (n=50), Nayakpod (n=49), Thoti (n=52), and Kolam (n=53), were included in the study. The DRD2 markers typed for the present study are three biallelic restriction fragments, that is, TaqI A (rs1800497), TaqI B (rs1079597), and TaqI D (rs1800498). Scoring of DRD2 haplotypes with respect to the three TaqI sites shows that five out of eight possible haplotypes are shared by the four populations. Ancestral haplotype B2D2A1 is most frequent among Thotis (0.359). The results of the present study indicate a differential gene flow into South India followed by certain important demographic events resulting in diversified peopling of India.

  7. EnviroAtlas - New Bedford, MA - Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, green space, and wetlands. Forest is a combination of...

  8. EnviroAtlas - Durham, NC - Land Cover Summaries by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, green space, wetland, and agriculture. Impervious is...

  9. EnviroAtlas - Green Bay, WI - Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, and green space. Forest is combination of trees and...

  10. EnviroAtlas - New York, NY - Land Cover by Block Group

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset describes the percentage of each block group that is classified as impervious, forest, and green space. In this community, forest is defined...

  11. Conjectures on the normal covering number of finite symmetric and alternating groups

    Directory of Open Access Journals (Sweden)

    Daniela Bubboloni

    2014-06-01

    Full Text Available Let gamma(Sn be the minimum number of proper subgroups Hi, i = 1,...,ell, of the symmetric group Sn such that each element in Sn lies in some conjugate of one of the Hi. In this paper we conjecture that gamma(Sn =(n/2(1-1/p_1 (1-1/p_2 + 2, where p1, p2 are the two smallest primes in the factorization of n and n is neither a prime power nor a product of two primes. Support for the conjecture is given by a previous result for the case where n has at most two distinct prime divisors. We give further evidence by confirming the conjecture for certain integers of the form n = 15q, for an infinite set of primes q, and by reporting on a Magma computation. We make a similar conjecture for gamma(An, when n is even, and provide a similar amount of evidence.

  12. Zaire program expands to cover high-risk groups in two cities.

    Science.gov (United States)

    1989-01-01

    This article announces the expansion of Zaire's social marketing program for condoms to high-risk groups in the cities of Goma and Matadi. The program will use proven marketing techniques from Kinshasha, printed materials, and direct marketing to retail outlets, emphasizing hotels, bars, and other areas frequented by prostitutes, migrants, and other travelers. In addition to retail outlets such as pharmacies, 50 taxis will be tested as additional retail sources for Prudence condoms. Once under way, this effort could reach as many as 96,000 people/day. 5 new AIDS information spots are being televised, and an anti-AIDS song and jingle are on the air. Condom social marketing representatives report a 357% increase in condom sales through March, 1989, over 1988, and that products are now available in 85% of Kinshasha pharmacies. Medical center coverage has increased to 14 from 9 zones, while products reach 11 additional cities and 5 interior provinces.

  13. VT Wildlife Linkage Habitat

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) The Wildlife Linkage Habitat Analysis uses landscape scale data to identify or predict the location of potentially significant wildlife linkage...

  14. Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.).

    Science.gov (United States)

    Yagi, Masafumi; Yamamoto, Toshiya; Isobe, Sachiko; Hirakawa, Hideki; Tabata, Satoshi; Tanase, Koji; Yamaguchi, Hiroyasu; Onozaki, Takashi

    2013-10-26

    Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F2 populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research. We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data. The improved genetic linkage maps and SSR markers developed

  15. Genetic analysis of autoimmune gld mice. I. Identification of a restriction fragment length polymorphism closely linked to the gld mutation within a conserved linkage group

    Science.gov (United States)

    1988-01-01

    A linkage map of distal mouse chromosome 1 was generated using restriction fragment length polymorphism (RFLP) analysis of DNA prepared from 95 [C3H-gld/gld X Mus spretus)F1 X C3H-gld/gld] backcross mice. The gene order was: (centromere) C4bp, Ren-1,2, Ly-5, [At-3/gld], Apoa-2/Ly-17, Spna-1 (telomere). All mice expressing the phenotype of gld homozygotes were homozygous for the At-3 RFLP characteristic of C3H mice and none of the mice heterozygous for At-3 RFLPs had characteristics of gld homozygotes, demonstrating close linkage between these genes. The identification of an RFLP closely linked to the gld gene provides a starting point for the identification of a genetic defect that results in abnormal T cells and autoimmune disease. PMID:2894402

  16. Subsidiary Linkage Patterns

    DEFF Research Database (Denmark)

    Andersson, Ulf; Perri, Alessandra; Nell, Phillip C.

    2012-01-01

    channels for spillovers to competitors. We find a curvilinear relationship between the extent of competitive pressure and the quality of a subsidiary's set of local linkages. Furthermore, the extent to which a subsidiary possesses capabilities moderates this relationship: Very capable subsidiaries...... in strongly competitive environments tend to shy away from high quality linkages. We discuss our findings in light of the literature on spillovers and inter-organizational linkages.......This paper investigates the pattern of subsidiaries' local vertical linkages under varying levels of competition and subsidiary capabilities. Contrary to most previous literature, we explicitly account for the double role of such linkages as conduits of learning prospects as well as potential...

  17. An estimating function approach to linkage heterogeneity

    Indian Academy of Sciences (India)

    Testing linkage heterogeneity between two loci is an important issue in genetics. Currently, there are ... on linkage heterogeneity can help people to better understand complex .... χ2(F − 2) + cχ2 (1), where c is a constant (see Appendix). Here, it can be ..... gin, ancestry, gender, age, etc., for purpose of dividing sub- groups to ...

  18. The Royan Public Umbilical Cord Blood Bank: Does It Cover All Ethnic Groups in Iran Based on HLA Diversity?

    Science.gov (United States)

    Ebrahimkhani, Saeideh; Farjadian, Shirin; Ebrahimi, Marzieh

    2014-04-01

    Umbilical cord blood (UCB) stem cells allow the transplantation of partially human leukocyte antigen (HLA)-matched grafts and are a valuable resource for the treatment of hematologic malignancies and heritable hematologic, immunologic and metabolic diseases, especially when a compatible bone marrow donor is unavailable. The aim of this study was to determine how many ethnic groups in Iran are covered by the available UCB units based on HLA diversity. From 2009 until mid-2013, 4,981 (30.3%) of the 16,437 UCB samples collected met the storage criteria and were cryopreserved at a public cord blood bank (CBB) in Tehran, Iran. HLA-A, -B and -DRB1 were typed in 1,793 samples. The mean volume of the cryopreserved samples was 81.25 ± 20.3 ml. The range of total nucleated cells per unit was 51 × 10(7)-107 × 10(7). The most common HLA alleles were HLA-A*2 (17%) and HLA-A*24 (15.6%), HLA-B*35 (16.8%) and HLA-B*51 (13.9%), and HLA-DRB1*11 (20%) and HLA-DRB1*15 (14%). The predominant haplotypes were HLA-A*24-B*35-DRB1*11 (2%), HLA-A*02-B*50-DR*07 (1.8%), and HLA-A*02-B*51-DRB1*11 (1.5%). Based on the HLA-DRB1 profiles, the UCB units available at the Royan public UCB bank are a potentially adequate resource for hematopoietic stem cell transplantation for Iranian recipients belonging to particular ethnic groups. Regular educational programs to improve the public knowledge of UCB for transplantation can enhance the public CBB stocks for all Iranian ethnic groups in the future.

  19. Probabilistic record linkage.

    Science.gov (United States)

    Sayers, Adrian; Ben-Shlomo, Yoav; Blom, Ashley W; Steele, Fiona

    2016-06-01

    Studies involving the use of probabilistic record linkage are becoming increasingly common. However, the methods underpinning probabilistic record linkage are not widely taught or understood, and therefore these studies can appear to be a 'black box' research tool. In this article, we aim to describe the process of probabilistic record linkage through a simple exemplar. We first introduce the concept of deterministic linkage and contrast this with probabilistic linkage. We illustrate each step of the process using a simple exemplar and describe the data structure required to perform a probabilistic linkage. We describe the process of calculating and interpreting matched weights and how to convert matched weights into posterior probabilities of a match using Bayes theorem. We conclude this article with a brief discussion of some of the computational demands of record linkage, how you might assess the quality of your linkage algorithm, and how epidemiologists can maximize the value of their record-linked research using robust record linkage methods. © The Author 2015; Published by Oxford University Press on behalf of the International Epidemiological Association.

  20. Identification of the linkage group of the Z sex chromosomes of the sand lizard (Lacerta agilis, Lacertidae) and elucidation of karyotype evolution in lacertid lizards.

    Science.gov (United States)

    Srikulnath, Kornsorn; Matsubara, Kazumi; Uno, Yoshinobu; Nishida, Chizuko; Olsson, Mats; Matsuda, Yoichi

    2014-12-01

    The sand lizard (Lacerta agilis, Lacertidae) has a chromosome number of 2n = 38, with 17 pairs of acrocentric chromosomes, one pair of microchromosomes, a large acrocentric Z chromosome, and a micro-W chromosome. To investigate the process of karyotype evolution in L. agilis, we performed chromosome banding and fluorescent in situ hybridization for gene mapping and constructed a cytogenetic map with 86 functional genes. Chromosome banding revealed that the Z chromosome is the fifth largest chromosome. The cytogenetic map revealed homology of the L. agilis Z chromosome with chicken chromosomes 6 and 9. Comparison of the L. agilis cytogenetic map with those of four Toxicofera species with many microchromosomes (Elaphe quadrivirgata, Varanus salvator macromaculatus, Leiolepis reevesii rubritaeniata, and Anolis carolinensis) showed highly conserved linkage homology of L. agilis chromosomes (LAG) 1, 2, 3, 4, 5(Z), 7, 8, 9, and 10 with macrochromosomes and/or macrochromosome segments of the four Toxicofera species. Most of the genes located on the microchromosomes of Toxicofera were localized to LAG6, small acrocentric chromosomes (LAG11-18), and a microchromosome (LAG19) in L. agilis. These results suggest that the L. agilis karyotype resulted from frequent fusions of microchromosomes, which occurred in the ancestral karyotype of Toxicofera and led to the disappearance of microchromosomes and the appearance of many small macrochromosomes.

  1. A pantograph linkage

    International Nuclear Information System (INIS)

    Cole, G.V.

    1982-01-01

    A pantograph linkage is actuated by two linear actuators, pivotally connected together at the linkage. The displacement of the actuators is monitored by rectilinear potentiometers to provide feedback signals to a microprocessor which also receives input signals related to a required movement of a slave end of the linkage. In response to these signals, the microprocessor provides signals to control the displacement of the linear actuators to effect the required movement of the slave end. The movement of the slave end might be straightline in a substantially horizontal or vertical direction. (author)

  2. Short Communication: Genetic linkage map of Cucurbita maxima with molecular and morphological markers.

    Science.gov (United States)

    Ge, Y; Li, X; Yang, X X; Cui, C S; Qu, S P

    2015-05-22

    Cucurbita maxima is one of the most widely cultivated vegetables in China and exhibits distinct morphological characteristics. In this study, genetic linkage analysis with 57 simple-sequence repeats, 21 amplified fragment length polymorphisms, 3 random-amplified polymorphic DNA, and one morphological marker revealed 20 genetic linkage groups of C. maxima covering a genetic distance of 991.5 cM with an average of 12.1 cM between adjacent markers. Genetic linkage analysis identified the simple-sequence repeat marker 'PU078072' 5.9 cM away from the locus 'Rc', which controls rind color. The genetic map in the present study will be useful for better mapping, tagging, and cloning of quantitative trait loci/gene(s) affecting economically important traits and for breeding new varieties of C. maxima through marker-assisted selection.

  3. Determination of Germination Response to Temperature and Water Potential for a Wide Range of Cover Crop Species and Related Functional Groups.

    Science.gov (United States)

    Tribouillois, Hélène; Dürr, Carolyne; Demilly, Didier; Wagner, Marie-Hélène; Justes, Eric

    2016-01-01

    A wide range of species can be sown as cover crops during fallow periods to provide various ecosystem services. Plant establishment is a key stage, especially when sowing occurs in summer with high soil temperatures and low water availability. The aim of this study was to determine the response of germination to temperature and water potential for diverse cover crop species. Based on these characteristics, we developed contrasting functional groups that group species with the same germination ability, which may be useful to adapt species choice to climatic sowing conditions. Germination of 36 different species from six botanical families was measured in the laboratory at eight temperatures ranging from 4.5-43°C and at four water potentials. Final germination percentages, germination rate, cardinal temperatures, base temperature and base water potential were calculated for each species. Optimal temperatures varied from 21.3-37.2°C, maximum temperatures at which the species could germinate varied from 27.7-43.0°C and base water potentials varied from -0.1 to -2.6 MPa. Most cover crops were adapted to summer sowing with a relatively high mean optimal temperature for germination, but some Fabaceae species were more sensitive to high temperatures. Species mainly from Poaceae and Brassicaceae were the most resistant to water deficit and germinated under a low base water potential. Species were classified, independent of family, according to their ability to germinate under a range of temperatures and according to their base water potential in order to group species by functional germination groups. These groups may help in choosing the most adapted cover crop species to sow based on climatic conditions in order to favor plant establishment and the services provided by cover crops during fallow periods. Our data can also be useful as germination parameters in crop models to simulate the emergence of cover crops under different pedoclimatic conditions and crop

  4. Reference Genome-Directed Resolution of Homologous and Homeologous Relationships within and between Different Oat Linkage Maps

    Directory of Open Access Journals (Sweden)

    Juan J. Gutierrez-Gonzalez

    2011-11-01

    Full Text Available Genome research on oat ( L. has received less attention than wheat ( L. and barley ( L. because it is a less prominent component of the human food system. To assess the potential of the model grass (L P. Beauv. as a surrogate for oat genome research, the whole genome sequence (WGS of was employed for comparative analysis with oat genetic linkage maps. Sequences of mapped molecular markers from one diploid spp. and two hexaploid oat maps were aligned to the WGS to infer syntenic relationships. Diploid and exhibit a high degree of synteny with 18 syntenic blocks covering 87% of the oat genome, which permitted postulation of an ancestral spp. chromosome structure. Synteny between oat and was also prevalent, with 50 syntenic blocks covering 76.6% of the ‘Kanota’ × ‘Ogle’ linkage map. Coalignment of diploid and hexaploid maps to helped resolve homeologous relationships between different oat linkage groups but also revealed many major rearrangements in oat subgenomes. Extending the analysis to a second oat linkage map (Ogle × ‘TAM O-301’ allowed identification of several putative homologous linkage groups across the two oat populations. These results indicate that the genome sequence will be a useful resource to assist genetics and genomics research in oat. The analytical strategy employed here should be applicable for genome research in other temperate grass crops with modest amounts of genomic data.

  5. Intragroup emotions: physiological linkage and social presence

    Directory of Open Access Journals (Sweden)

    Simo eJärvelä

    2016-02-01

    Full Text Available We investigated how technologically mediating two different components of emotion – communicative expression and physiological state – to group members affects physiological linkage and self-reported feelings in a small group during video viewing. In different conditions the availability of second screen text chat (communicative expression and visualization of group level physiological heart rates and their dyadic linkage (physiology was varied. Within this four person group two participants formed a physically co-located dyad and the other two were individually situated in two separate rooms. We found that text chat always increased heart rate synchrony but HR visualization only with non-co-located dyads. We also found that physiological linkage was strongly connected to self-reported social presence. The results encourage further exploration of the possibilities of sharing group member’s physiological components of emotion by technological means to enhance mediated communication and strengthen social presence.

  6. Intragroup Emotions: Physiological Linkage and Social Presence.

    Science.gov (United States)

    Järvelä, Simo; Kätsyri, Jari; Ravaja, Niklas; Chanel, Guillaume; Henttonen, Pentti

    2016-01-01

    We investigated how technologically mediating two different components of emotion-communicative expression and physiological state-to group members affects physiological linkage and self-reported feelings in a small group during video viewing. In different conditions the availability of second screen text chat (communicative expression) and visualization of group level physiological heart rates and their dyadic linkage (physiology) was varied. Within this four person group two participants formed a physically co-located dyad and the other two were individually situated in two separate rooms. We found that text chat always increased heart rate synchrony but HR visualization only with non-co-located dyads. We also found that physiological linkage was strongly connected to self-reported social presence. The results encourage further exploration of the possibilities of sharing group member's physiological components of emotion by technological means to enhance mediated communication and strengthen social presence.

  7. Intragroup Emotions: Physiological Linkage and Social Presence

    Science.gov (United States)

    Järvelä, Simo; Kätsyri, Jari; Ravaja, Niklas; Chanel, Guillaume; Henttonen, Pentti

    2016-01-01

    We investigated how technologically mediating two different components of emotion—communicative expression and physiological state—to group members affects physiological linkage and self-reported feelings in a small group during video viewing. In different conditions the availability of second screen text chat (communicative expression) and visualization of group level physiological heart rates and their dyadic linkage (physiology) was varied. Within this four person group two participants formed a physically co-located dyad and the other two were individually situated in two separate rooms. We found that text chat always increased heart rate synchrony but HR visualization only with non-co-located dyads. We also found that physiological linkage was strongly connected to self-reported social presence. The results encourage further exploration of the possibilities of sharing group member's physiological components of emotion by technological means to enhance mediated communication and strengthen social presence. PMID:26903913

  8. Thermally actuated linkage arrangement

    International Nuclear Information System (INIS)

    Anderson, P.M.

    1981-01-01

    A reusable thermally actuated linkage arrangement includes a first link member having a longitudinal bore therein adapted to receive at least a portion of a second link member therein, the first and second members being sized to effect an interference fit preventing relative movement there-between at a temperature below a predetermined temperature. The link members have different coefficients of thermal expansion so that when the linkage is selectively heated by heating element to a temperature above the predetermined temperature, relative longitudinal and/or rotational movement between the first and second link members is enabled. Two embodiments of a thermally activated linkage are disclosed which find particular application in actuators for a grapple head positioning arm in a nuclear reactor fuel handling mechanism to facilitate back-up safety retraction of the grapple head independently from the primary fuel handling mechanism drive system. (author)

  9. Does the 'Scottish effect' apply to all ethnic groups? All-cancer, lung, colorectal, breast and prostate cancer in the Scottish Health and Ethnicity Linkage Cohort Study.

    Science.gov (United States)

    Bhopal, Raj S; Bansal, Narinder; Steiner, Markus; Brewster, David H

    2012-01-01

    Although ethnic group variations in cancer exist, no multiethnic, population-based, longitudinal studies are available in Europe. Our objectives were to examine ethnic variation in all-cancer, and lung, colorectal, breast and prostate cancers. DESIGN, SETTING, POPULATION, MEASURES AND ANALYSIS: This retrospective cohort study of 4.65 million people linked the 2001 Scottish Census (providing ethnic group) to cancer databases. With the White Scottish population as reference (value 100), directly age standardised rates and ratios (DASR and DASRR), and risk ratios, by sex and ethnic group with 95% CI were calculated for first cancers. In the results below, 95% CI around the DASRR excludes 100. Eight indicators of socio-economic position were assessed as potential confounders across all groups. For all cancers the White Scottish population (100) had the highest DASRRs, Indians the lowest (men 45.9 and women 41.2) and White British (men 87.6 and women 87.3) and other groups were intermediate (eg, Chinese men 57.6). For lung cancer the DASRRs for Pakistani men (45.0), and women (53.5), were low and for any mixed background men high (174.5). For colorectal cancer the DASRRs were lowest in Pakistanis (men 32.9 and women 68.9), White British (men 82.4 and women 83.7), other White (men 77.2 and women 74.9) and Chinese men (42.6). Breast cancer in women was low in Pakistanis (62.2), Chinese (63.0) and White Irish (84.0). Prostate cancer was lowest in Pakistanis (38.7), Indian (62.6) and White Irish (85.4). No socio-economic indicator was a valid confounding variable across ethnic groups. The 'Scottish effect' does not apply across ethnic groups for cancer. The findings have implications for clinical care, prevention and screening, for example, responding appropriately to the known low uptake among South Asian populations of bowel screening might benefit from modelling of cost-effectiveness of screening, given comparatively low cancer rates.

  10. The alternative site selection procedure as covered in the report by the Repository Site Selection Procedures Working Group

    International Nuclear Information System (INIS)

    Brenner, M.

    2005-01-01

    The 2002 Act on the Regulated Termination of the Use of Nuclear Power for Industrial Electricity Generation declared Germany's opting out of the peaceful uses of nuclear power. The problem of the permanent management of radioactive residues is becoming more and more important also in the light of that political decision. At the present time, there are no repositories offering the waste management capacities required. Such facilities need to be created. At the present stage, eligible repository sites are the Konrad mine, a former iron ore mine near Salzgitter, and the Gorleben salt dome. While the fate of the Konrad mine as a repository for waste generating negligible amounts of heat continues to be uncertain, despite a plan approval decision of June 2002, the Gorleben repository is still in the planning phase, at present in a dormant state, so to speak. The federal government expressed doubt about the suitability of the Gorleben site. Against this backdrop, the Federal Ministry for the Environment, Nature Conservation, and Nuclear Safety in February 1999 established AkEnd, the Working Group on Repository Site Selection Procedures. The Group was charged with developing, based on sound scientific criteria, a transparent site selection procedure in order to facilitate the search for repository sites. The Working Group presented its final report in December 2002 after approximately four years of work. The Group's proposals about alternative site selection procedures are explained in detail and, above all, reviewed critically. (orig.)

  11. Clause linkage in Ket

    NARCIS (Netherlands)

    Nefedov, Andrey

    2015-01-01

    This work provides a typologically oriented description of clause linkage strategies in Ket, a highly endangered language spoken in Central Siberia. It is now the only surviving member of the Yeniseian language family with the last remaining speakers residing in the north of Russia’s Krasnoyarsk

  12. Probing adenine rings and backbone linkages using base specific isotope-edited Raman spectroscopy: application to group II intron ribozyme domain V.

    Science.gov (United States)

    Chen, Yuanyuan; Eldho, Nadukkudy V; Dayie, T Kwaku; Carey, Paul R

    2010-04-27

    Raman difference spectroscopy is used to probe the properties of a 36-nt RNA molecule, "D5", which lies at the heart of the catalytic apparatus in group II introns. For D5 that has all of its adenine residues labeled with (13)C and (15)N and utilizing Raman difference spectroscopy, we identify the conformationally sensitive -C-O-P-O-C- stretching modes of the unlabeled bonds adjacent to adenine bases, as well as the adenine ring modes themselves. The phosphodiester modes can be assigned to individual adenine residues based on earlier NMR data. The effect of Mg(2+) binding was explored by analyzing the Raman difference spectra for [D5 + Mg(2+)] minus [D5 no Mg(2+)], for D5 unlabeled, or D5 labeled with (13)C/(15)N-enriched adenine. In both sets of data we assign differential features to G ring modes perturbed by Mg(2+) binding at the N7 position. In the A-labeled spectra we attribute a Raman differential near 1450 cm(-1) and changes of intensity at 1296 cm(-1) to Mg binding at the N7 position of adenine bases. The A and G bases involved in Mg(2+) binding again can be identified using earlier NMR results. For the unlabeled D5, a change in the C-O-P-O-C stretch profile at 811 cm(-1) upon magnesium binding is due to a "tightening up" (in the sense of a more rigid molecule with less dynamic interchange among competing ribose conformers) of the D5 structure. For adenine-labeled D5, small changes in the adenine backbone bond signatures in the 810-830 cm(-1) region suggest that small conformational changes occur in the tetraloop and bulge regions upon binding of Mg(2+). The PO(2)(-) stretching vibration, near 1100 cm(-1), from the nonbridging phosphate groups, probes the effect of Mg(2+)-hydrate inner-sphere interactions that cause an upshift. In turn, the upshift is modulated by the presence of monovalent cations since in the presence of Na(+) and Li(+) the upshift is 23 +/- 2 cm(-1) while in the presence of K(+) and Cs(+) it is 13 +/- 3 cm(-1), a finding that correlates

  13. The Barley Chromosome 5 Linkage Map

    DEFF Research Database (Denmark)

    Jensen, J.; Jørgensen, Jørgen Helms

    1975-01-01

    The distances between nine loci on barley chromosome 5 have been studied in five two-point tests, three three-point tests, and one four-point test. Our previous chromosome 5 linkage map, which contained eleven loci mapped from literature data (Jensen and Jørgensen 1975), is extended with four loci......-position is fixed on the map by a locus (necl), which has a good marker gene located centrally in the linkage group. The positions of the other loci are their distances in centimorgans from the 0-position; loci in the direction of the short chromosome arm are assigned positive values and those...

  14. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas

    Directory of Open Access Journals (Sweden)

    Matsumoto Takashi

    2010-04-01

    Full Text Available Abstract Background The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents. Results An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin. Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7% deviated (p Conclusions We propose a synthetic map with 11 linkage groups containing 489 markers (167 SSRs and 322 DArTs covering 1197 cM. This first saturated map is proposed as a "reference Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker

  15. A microsatellite linkage map of Drosophila mojavensis

    Directory of Open Access Journals (Sweden)

    Schully Sheri

    2004-05-01

    Full Text Available Abstract Background Drosophila mojavensis has been a model system for genetic studies of ecological adaptation and speciation. However, despite its use for over half a century, no linkage map has been produced for this species or its close relatives. Results We have developed and mapped 90 microsatellites in D. mojavensis, and we present a detailed recombinational linkage map of 34 of these microsatellites. A slight excess of repetitive sequence was observed on the X-chromosome relative to the autosomes, and the linkage groups have a greater recombinational length than the homologous D. melanogaster chromosome arms. We also confirmed the conservation of Muller's elements in 23 sequences between D. melanogaster and D. mojavensis. Conclusions The microsatellite primer sequences and localizations are presented here and made available to the public. This map will facilitate future quantitative trait locus mapping studies of phenotypes involved in adaptation or reproductive isolation using this species.

  16. Convergent modulation of singlet and triplet excited states of phosphine-oxide hosts through the management of molecular structure and functional-group linkages for low-voltage-driven electrophosphorescence.

    Science.gov (United States)

    Han, Chunmiao; Zhang, Zhensong; Xu, Hui; Xie, Guohua; Li, Jing; Zhao, Yi; Deng, Zhaopeng; Liu, Shiyong; Yan, Pengfei

    2013-01-02

    The controllable tuning of the excited states in a series of phosphine-oxide hosts (DPExPOCzn) was realized through introducing carbazolyl and diphenylphosphine-oxide (DPPO) moieties to adjust the frontier molecular orbitals, molecular rigidity, and the location of the triplet excited states by suppressing the intramolecular interplay of the combined multi-insulating and meso linkage. On increasing the number of substituents, simultaneous lowering of the first singlet energy levels (S(1)) and raising of the first triplet energy levels (T(1), about 3.0 eV) were achieved. The former change was mainly due to the contribution of the carbazolyl group to the HOMOs and the extended conjugation. The latter change was due to an enhanced molecular rigidity and the shift of the T(1) states from the diphenylether group to the carbazolyl moieties. This kind of convergent modulation of excited states not only facilitates the exothermic energy transfer to the dopants in phosphorescent organic light-emitting diodes (PHOLEDs), but also realizes the fine-tuning of electrical properties to achieve the balanced carrier injection and transportation in the emitting layers. As the result, the favorable performance of blue-light-emitting PHOLEDs was demonstrated, including much-lower driving voltages of 2.6 V for onset and 3.0 V at 100 cd m(-2), as well as a remarkably improved E.Q.E. of 12.6%. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Land Cover

    Data.gov (United States)

    Kansas Data Access and Support Center — The Land Cover database depicts 10 general land cover classes for the State of Kansas. The database was compiled from a digital classification of Landsat Thematic...

  18. Design of special planar linkages

    CERN Document Server

    Zhao, Jing-Shan; Ma, Ning; Chu, Fulei

    2013-01-01

    Planar linkages play a very important role in mechanical engineering. As the simplest closed chain mechanisms, planar four-bar linkages are widely used in mechanical engineering, civil engineering and aerospace engineering.Design of Special Planar Linkages proposes a uniform design theory for planar four-bar linkages. The merit of the method proposed in this book is that it allows engineers to directly obtain accurate results when there are such solutions for the specified n precise positions; otherwise, the best approximate solutions will be found. This book discusses the kinematics and reach

  19. An ecology of prestige in New York City: examining the relationships among population density, socio-economic status, group identity, and residential canopy cover.

    Science.gov (United States)

    Grove, J Morgan; Locke, Dexter H; O'Neil-Dunne, Jarlath P M

    2014-09-01

    Several social theories have been proposed to explain the uneven distribution of vegetation in urban residential areas: population density, social stratification, luxury effect, and ecology of prestige. We evaluate these theories using a combination of demographic and socio-economic predictors of vegetative cover on all residential lands in New York City. We use diverse data sources including the City's property database, time-series demographic and socio-economic data from the US Census, and land cover data from the University of Vermont's Spatial Analysis Lab (SAL). These data are analyzed using a multi-model inferential, spatial econometrics approach. We also examine the distribution of vegetation within distinct market categories using Claritas' Potential Rating Index for Zipcode Markets (PRIZM™) database. These categories can be disaggregated, corresponding to the four social theories. We compare the econometric and categorical results for validation. Models associated with ecology of prestige theory are more effective for predicting the distribution of vegetation. This suggests that private, residential patterns of vegetation, reflecting the consumption of environmentally relevant goods and services, are associated with different lifestyles and lifestages. Further, our spatial and temporal analyses suggest that there are significant spatial and temporal dependencies that have theoretical and methodological implications for understanding urban ecological systems. These findings may have policy implications. Decision makers may need to consider how to most effectively reach different social groups in terms of messages and messengers in order to advance land management practices and achieve urban sustainability.

  20. An Ecology of Prestige in New York City: Examining the Relationships Among Population Density, Socio-economic Status, Group Identity, and Residential Canopy Cover

    Science.gov (United States)

    Grove, J. Morgan; Locke, Dexter H.; O'Neil-Dunne, Jarlath P. M.

    2014-09-01

    Several social theories have been proposed to explain the uneven distribution of vegetation in urban residential areas: population density, social stratification, luxury effect, and ecology of prestige. We evaluate these theories using a combination of demographic and socio-economic predictors of vegetative cover on all residential lands in New York City. We use diverse data sources including the City's property database, time-series demographic and socio-economic data from the US Census, and land cover data from the University of Vermont's Spatial Analysis Lab (SAL). These data are analyzed using a multi-model inferential, spatial econometrics approach. We also examine the distribution of vegetation within distinct market categories using Claritas' Potential Rating Index for Zipcode Markets (PRIZM™) database. These categories can be disaggregated, corresponding to the four social theories. We compare the econometric and categorical results for validation. Models associated with ecology of prestige theory are more effective for predicting the distribution of vegetation. This suggests that private, residential patterns of vegetation, reflecting the consumption of environmentally relevant goods and services, are associated with different lifestyles and lifestages. Further, our spatial and temporal analyses suggest that there are significant spatial and temporal dependencies that have theoretical and methodological implications for understanding urban ecological systems. These findings may have policy implications. Decision makers may need to consider how to most effectively reach different social groups in terms of messages and messengers in order to advance land management practices and achieve urban sustainability.

  1. Prevalence of Types of Cancers in the Elderly Covered by Insurance of the Islamic Republic of Iran Broadcasting Company in 2015 - Comparison with Younger Groups.

    Science.gov (United States)

    Roshani, Zahra; Akbari Kamrani, Ahmad Ali; Shati, Mohsen; Sahaf, Robab

    2016-01-01

    Presently, the world population of the elderly is growing. By improving health hygiene and welfare indicators, mortality and birth rates decrease and life expectancy increases, making the present century the century of elderly. Aging is one of the main risk factors for development of cancer, which itself is the second cause of death in old people. This study was conducted to assess the prevalence of cancer in the elderly covered by the Islamic Republic of Iran Broadcasting (IRIB) insurance program and to obtain suitable programs for cancer screening and early detection, increase patient survival, improve elderly care and to reclaim the cost of treatment in comparison to the national and international statistics. This is a cross-sectional study conducted on all elderly patients diagnosed with malignancy based on their pathology reports. In this study, of the total 75,500 patients covered by IRIB insurance, 17.2% belonged to the elderly group, males accounting for 53.3%. The most common cancers in old men were prostatic cancer (61.3%), colon cancer (10.3%) cancer of the hematologic system, bladder cancer (9.6%), lung cancer (9.1%), thyroid cancer (3.9%) and brain tumors (1.3%). In the elderly women, the most common cancers were breast cancer (80.1%), colon cancer (5.1%), thyroid cancers (4.4%), bladder and hematologic system malignancies (3.6), lung cancer (2.9%) and brain tumors (0.7%). In addition, the prevalence of cancer was almost the same as national and international statistics. With the exception of non-melanoma skin cancer no difference was shown in prevalence of cancer between IRIB elderly patients and the other groups of cancer patients in Iran.

  2. Car Covers | Outdoor Covers Canada

    OpenAIRE

    Covers, Outdoor

    2018-01-01

    Protect your car from the elements with Ultimate Touch Car Cover. The multi-layer non-woven fabric is soft on the finish and offers 4 seasons all weather protection.https://outdoorcovers.ca/car-covers/

  3. Dense genetic linkage maps of three Populus species (Populus deltoides, P. nigra and P. trichocarpa) based on AFLP and microsatellite markers.

    Science.gov (United States)

    Cervera, M T; Storme, V; Ivens, B; Gusmão, J; Liu, B H; Hostyn, V; Van Slycken, J; Van Montagu, M; Boerjan, W

    2001-06-01

    Populus deltoides, P. nigra, and P. trichocarpa are the most important species for poplar breeding programs worldwide. In addition, Populus has become a model for fundamental research on trees. Linkage maps were constructed for these three species by analyzing progeny of two controlled crosses sharing the same female parent, Populus deltoides cv. S9-2 x P. nigra cv. Ghoy and P. deltoides cv. S9-2 x P. trichocarpa cv. V24. The two-way pseudotestcross mapping strategy was used to construct the maps. Amplified fragment length polymorphism (AFLP) markers that segregated 1:1 were used to form the four parental maps. Microsatellites and sequence-tagged sites were used to align homoeologous groups between the maps and to merge linkage groups within the individual maps. Linkage analysis and alignment of the homoeologous groups resulted in 566 markers distributed over 19 groups for P. deltoides covering 86% of the genome, 339 markers distributed over 19 groups for P. trichocarpa covering 73%, and 369 markers distributed over 28 groups for P. nigra covering 61%. Several tests for randomness showed that the AFLP markers were randomly distributed over the genome.

  4. A Formalization of Linkage Analysis

    DEFF Research Database (Denmark)

    Ingolfsdottir, Anna; Christensen, A.I.; Hansen, Jens A.

    In this report a formalization of genetic linkage analysis is introduced. Linkage analysis is a computationally hard biomathematical method, which purpose is to locate genes on the human genome. It is rooted in the new area of bioinformatics and no formalization of the method has previously been ...

  5. Probabilistic linkage to enhance deterministic algorithms and reduce data linkage errors in hospital administrative data.

    Science.gov (United States)

    Hagger-Johnson, Gareth; Harron, Katie; Goldstein, Harvey; Aldridge, Robert; Gilbert, Ruth

    2017-06-30

     BACKGROUND: The pseudonymisation algorithm used to link together episodes of care belonging to the same patients in England (HESID) has never undergone any formal evaluation, to determine the extent of data linkage error. To quantify improvements in linkage accuracy from adding probabilistic linkage to existing deterministic HESID algorithms. Inpatient admissions to NHS hospitals in England (Hospital Episode Statistics, HES) over 17 years (1998 to 2015) for a sample of patients (born 13/28th of months in 1992/1998/2005/2012). We compared the existing deterministic algorithm with one that included an additional probabilistic step, in relation to a reference standard created using enhanced probabilistic matching with additional clinical and demographic information. Missed and false matches were quantified and the impact on estimates of hospital readmission within one year were determined. HESID produced a high missed match rate, improving over time (8.6% in 1998 to 0.4% in 2015). Missed matches were more common for ethnic minorities, those living in areas of high socio-economic deprivation, foreign patients and those with 'no fixed abode'. Estimates of the readmission rate were biased for several patient groups owing to missed matches, which was reduced for nearly all groups. CONCLUSION: Probabilistic linkage of HES reduced missed matches and bias in estimated readmission rates, with clear implications for commissioning, service evaluation and performance monitoring of hospitals. The existing algorithm should be modified to address data linkage error, and a retrospective update of the existing data would address existing linkage errors and their implications.

  6. North-South Business Linkages

    DEFF Research Database (Denmark)

    Sørensen, Olav Jull; Kuada, John

    2006-01-01

    Based on empirical studies of linkages between TNCs and local firms in India, Malaysia, Vietnam, Ghana and South Africa, five themes are discussed and related to present theoretical perspectives. The themes are (1) Linakge Governance; (2) Globalisation and the dynamics in developing countries (the...... TNC-driven markets in developing countries); (3) The upgrading impact of FDI; (4) Non-equity linkages as a platform for business development, and (5) The learning perspective on international business linakges. The chapter offers at the end a three-dimanional model for impacts of business linkages....

  7. [Economic impact of etanercept and adalimumab biosimilars on hospitals scale covered by PharmAlp'Ain, a hospitals grouping of orders for health products].

    Science.gov (United States)

    Berreur, B; Guerin, F; Christophe, B; Limido, G; Paubel, P

    2018-01-01

    To evaluate the economic impact of future prescriptions of etanercept and adalimumab biosimilars at the territorial scale covered by PharmAlp'Ain, a hospitals grouping of orders for health products. Determination of the number and status of patients (naive or in continuation of treatment) from the National Database "Datamart de Consommation Inter-Régimes" of health insurance, concerned by a dispensation in a pharmacy of etanercept or adalimumab in 2015. Calculation of potential savings in case of biosimilar requirements according to 3 hypotheses: 63% (rate observed in a previous study) of initiations are treated with biosimiliaries and the others by princeps (H 1 ); all initiations under biosimilars and continuation therapy with the princeps (H 2 ) or all patients are treated with biosimilars (H 3 ). The annual savings are estimated at 237,000 € with the H 1 hypothesis. In the case of H 2 , the expected savings would be 376,200 € per year. In the case of H 3 , savings for the community could reach almost 1,282,800 € per year. The arrival of biosimilars allows significant savings for medicines market. According to the French recommendations in 2016, the expected savings are between the H 1 and H 2 hypothesis. The rate of penetration of biosimilars depends on many factors such as the involvement of health professionals, patient adherence, or health authority recommendations. Copyright © 2017 Académie Nationale de Pharmacie. Published by Elsevier Masson SAS. All rights reserved.

  8. Ethnicity and the ethics of data linkage

    Directory of Open Access Journals (Sweden)

    Boyd Kenneth M

    2007-11-01

    Full Text Available Abstract Linking health data with census data on ethnicity has potential benefits for the health of ethnic minority groups. Ethical objections to linking these data however include concerns about informed consent and the possibility of the findings being misused against the interests of ethnic minority groups. While consent concerns may be allayed by procedures to safeguard anonymity and respect privacy, robust procedures to demonstrate public approval of data linkage also need to be devised. The possibility of findings being misused against the interests of ethnic minority groups may be diminished by informed and open public discussion in mature democracies, but remain a concern in the international context.

  9. Construction of an ultrahigh-density genetic linkage map for Jatropha curcas L. and identification of QTL for fruit yield.

    Science.gov (United States)

    Xia, Zhiqiang; Zhang, Shengkui; Wen, Mingfu; Lu, Cheng; Sun, Yufang; Zou, Meiling; Wang, Wenquan

    2018-01-01

    As an important biofuel plant, the demand for higher yield Jatropha curcas L. is rapidly increasing. However, genetic analysis of Jatropha and molecular breeding for higher yield have been hampered by the limited number of molecular markers available. An ultrahigh-density linkage map for a Jatropha mapping population of 153 individuals was constructed and covered 1380.58 cM of the Jatropha genome, with average marker density of 0.403 cM. The genetic linkage map consisted of 3422 SNP and indel markers, which clustered into 11 linkage groups. With this map, 13 repeatable QTLs (reQTLs) for fruit yield traits were identified. Ten reQTLs, qNF - 1 , qNF - 2a , qNF - 2b , qNF - 2c , qNF - 3 , qNF - 4 , qNF - 6 , qNF - 7a , qNF - 7b and qNF - 8, that control the number of fruits (NF) mapped to LGs 1, 2, 3, 4, 6, 7 and 8, whereas three reQTLs, qTWF - 1 , qTWF - 2 and qTWF - 3, that control the total weight of fruits (TWF) mapped to LGs 1, 2 and 3, respectively. It is interesting that there are two candidate critical genes, which may regulate Jatropha fruit yield. We also identified three pleiotropic reQTL pairs associated with both the NF and TWF traits. This study is the first to report an ultrahigh-density Jatropha genetic linkage map construction, and the markers used in this study showed great potential for QTL mapping. Thirteen fruit-yield reQTLs and two important candidate genes were identified based on this linkage map. This genetic linkage map will be a useful tool for the localization of other economically important QTLs and candidate genes for Jatropha .

  10. Benthic Cover

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Benthic cover (habitat) maps are derived from aerial imagery, underwater photos, acoustic surveys, and data gathered from sediment samples. Shallow to moderate-depth...

  11. From Enclave to Linkage Economies?

    DEFF Research Database (Denmark)

    Hansen, Michael W.

    as the enclave economy par excellence, moving in with fully integrated value chains, extracting resources and exporting them as commodities having virtually no linkages to the local economy. However, new opportunities for promoting linkages are offered by changing business strategies of local African enterprises...... as well as foreign multinational corporations (MNCs). MNCs in extractives are increasingly seeking local linkages as part of their efficiency, risk, and asset-seeking strategies, and linkage programmes are becoming integral elements in many MNCs’ corporate social responsibility (CSR) activities....... At the same time, local African enterprises are eager to, and increasingly capable of, linking up to the foreign investors in order to expand their activities and acquire technology, skills and market access. The changing strategies of MNCs and the improving capabilities of African enterprises offer new...

  12. A saturated SSR/DArT linkage map of Musa acuminata addressing genome rearrangements among bananas.

    Science.gov (United States)

    Hippolyte, Isabelle; Bakry, Frederic; Seguin, Marc; Gardes, Laetitia; Rivallan, Ronan; Risterucci, Ange-Marie; Jenny, Christophe; Perrier, Xavier; Carreel, Françoise; Argout, Xavier; Piffanelli, Pietro; Khan, Imtiaz A; Miller, Robert N G; Pappas, Georgios J; Mbéguié-A-Mbéguié, Didier; Matsumoto, Takashi; De Bernardinis, Veronique; Huttner, Eric; Kilian, Andrzej; Baurens, Franc-Christophe; D'Hont, Angélique; Cote, François; Courtois, Brigitte; Glaszmann, Jean-Christophe

    2010-04-13

    The genus Musa is a large species complex which includes cultivars at diploid and triploid levels. These sterile and vegetatively propagated cultivars are based on the A genome from Musa acuminata, exclusively for sweet bananas such as Cavendish, or associated with the B genome (Musa balbisiana) in cooking bananas such as Plantain varieties. In M. acuminata cultivars, structural heterozygosity is thought to be one of the main causes of sterility, which is essential for obtaining seedless fruits but hampers breeding. Only partial genetic maps are presently available due to chromosomal rearrangements within the parents of the mapping populations. This causes large segregation distortions inducing pseudo-linkages and difficulties in ordering markers in the linkage groups. The present study aims at producing a saturated linkage map of M. acuminata, taking into account hypotheses on the structural heterozygosity of the parents. An F1 progeny of 180 individuals was obtained from a cross between two genetically distant accessions of M. acuminata, 'Borneo' and 'Pisang Lilin' (P. Lilin). Based on the gametic recombination of each parent, two parental maps composed of SSR and DArT markers were established. A significant proportion of the markers (21.7%) deviated (p DArTs) covering 1197 cM. This first saturated map is proposed as a "reference Musa map" for further analyses. We also propose two complete parental maps with interpretations of structural rearrangements localized on the linkage groups. The structural heterozygosity in P. Lilin is hypothesized to result from a duplication likely accompanied by an inversion on another chromosome. This paper also illustrates a methodological approach, transferable to other species, to investigate the mapping of structural rearrangements and determine their consequences on marker segregation.

  13. Integrated genetic linkage map of cultivated peanut by three RIL populations

    Institute of Scientific and Technical Information of China (English)

    Yanbin Song; Huifang Jiang; Huaiyong Luo; Li Huang; Yuning Chen; Weigang Chen; Nian Liu; Xiaoping Ren; Bolun Yu; Jianbin Guo

    2017-01-01

    High-density and precise genetic linkage map is fundamental to detect quanti-tative trait locus (QTL) of agronomic and quality related traits in cultivated peanut (Arachis hypogaea L.). In this study, three linkage maps from three RIL (recombinant inbred line) populations were used to construct an integrated map. A total of 2,069 SSR and transposon markers were anchored on the high-density integrated map which covered 2,231.53 cM with 20 linkage groups. Totally, 92 QTLs correlating with pod length (PL), pod width (PW), hun-dred pods weight (HPW) and plant height (PH) from above RIL populations were mapped on it. Seven intervals were found to harbor QTLs controlling the same traits in different pop-ulations, including one for PL, three for PW, two for HPW, and one for PH. Besides, QTLs controlling different traits in different populations were found to be overlapped in four inter-vals. Interval on A05 contains 17 QTLs for different traits from two RIL populations. New markers were added to these intervals to detect QTLs with narrow confidential intervals. Results obtained in this study may facilitate future genomic researches such as QTL study, fine mapping, positional cloning and marker-assisted selection (MAS) in peanut.

  14. In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut

    Directory of Open Access Journals (Sweden)

    Shirasawa Kenta

    2012-06-01

    Full Text Available Abstract Background Peanut (Arachis hypogaea is an autogamous allotetraploid legume (2n = 4x = 40 that is widely cultivated as a food and oil crop. More than 6,000 DNA markers have been developed in Arachis spp., but high-density linkage maps useful for genetics, genomics, and breeding have not been constructed due to extremely low genetic diversity. Polymorphic marker loci are useful for the construction of such high-density linkage maps. The present study used in silico analysis to develop simple sequence repeat-based and transposon-based markers. Results The use of in silico analysis increased the efficiency of polymorphic marker development by more than 3-fold. In total, 926 (34.2% of 2,702 markers showed polymorphisms between parental lines of the mapping population. Linkage analysis of the 926 markers along with 253 polymorphic markers selected from 4,449 published markers generated 21 linkage groups covering 2,166.4 cM with 1,114 loci. Based on the map thus produced, 23 quantitative trait loci (QTLs for 15 agronomical traits were detected. Another linkage map with 326 loci was also constructed and revealed a relationship between the genotypes of the FAD2 genes and the ratio of oleic/linoleic acid in peanut seed. Conclusions In silico analysis of polymorphisms increased the efficiency of polymorphic marker development, and contributed to the construction of high-density linkage maps in cultivated peanut. The resultant maps were applicable to QTL analysis. Marker subsets and linkage maps developed in this study should be useful for genetics, genomics, and breeding in Arachis. The data are available at the Kazusa DNA Marker Database (http://marker.kazusa.or.jp.

  15. Identification of QTLs Associated with Callogenesis and Embryogenesis in Oil Palm Using Genetic Linkage Maps Improved with SSR Markers

    Science.gov (United States)

    Ting, Ngoot-Chin; Jansen, Johannes; Nagappan, Jayanthi; Ishak, Zamzuri; Chin, Cheuk-Weng; Tan, Soon-Guan; Cheah, Suan-Choo; Singh, Rajinder

    2013-01-01

    Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR) markers were developed for dura (ENL48) and pisifera (ML161), the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs) in 23 linkage groups (LGs), covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs) in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs) associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm. PMID:23382832

  16. Identification of QTLs associated with callogenesis and embryogenesis in oil palm using genetic linkage maps improved with SSR markers.

    Directory of Open Access Journals (Sweden)

    Ngoot-Chin Ting

    Full Text Available Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR markers were developed for dura (ENL48 and pisifera (ML161, the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP and restriction fragment length polymorphism (RFLP markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs in 23 linkage groups (LGs, covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm.

  17. An ecology of prestige in New York City: Examining the relationships among population density, socio-economic status, group identity, and residential canopy cover

    Science.gov (United States)

    J. Morgan Grove; Dexter H. Locke; Jarlath P.M. O' Neil-Dunne

    2014-01-01

    Several social theories have been proposed to explain the uneven distribution of vegetation in urban residential areas: population density, social stratification, luxury effect, and ecology of prestige. We evaluate these theories using a combination of demographic and socio-economic predictors of vegetative cover on all residential lands in New York City. We use...

  18. Data Linkage: A powerful research tool with potential problems

    Directory of Open Access Journals (Sweden)

    Scott Ian

    2010-12-01

    Full Text Available Abstract Background Policy makers, clinicians and researchers are demonstrating increasing interest in using data linked from multiple sources to support measurement of clinical performance and patient health outcomes. However, the utility of data linkage may be compromised by sub-optimal or incomplete linkage, leading to systematic bias. In this study, we synthesize the evidence identifying participant or population characteristics that can influence the validity and completeness of data linkage and may be associated with systematic bias in reported outcomes. Methods A narrative review, using structured search methods was undertaken. Key words "data linkage" and Mesh term "medical record linkage" were applied to Medline, EMBASE and CINAHL databases between 1991 and 2007. Abstract inclusion criteria were; the article attempted an empirical evaluation of methodological issues relating to data linkage and reported on patient characteristics, the study design included analysis of matched versus unmatched records, and the report was in English. Included articles were grouped thematically according to patient characteristics that were compared between matched and unmatched records. Results The search identified 1810 articles of which 33 (1.8% met inclusion criteria. There was marked heterogeneity in study methods and factors investigated. Characteristics that were unevenly distributed among matched and unmatched records were; age (72% of studies, sex (50% of studies, race (64% of studies, geographical/hospital site (93% of studies, socio-economic status (82% of studies and health status (72% of studies. Conclusion A number of relevant patient or population factors may be associated with incomplete data linkage resulting in systematic bias in reported clinical outcomes. Readers should consider these factors in interpreting the reported results of data linkage studies.

  19. A prospective group sequential study evaluating a new type of fully covered self-expandable metal stent for the treatment of benign biliary strictures (with video).

    Science.gov (United States)

    Poley, Jan-Werner; Cahen, Djuna L; Metselaar, Herold J; van Buuren, Henk R; Kazemier, Geert; van Eijck, Casper H J; Haringsma, Jelle; Kuipers, Ernst J; Bruno, Marco J

    2012-04-01

    Fully-covered self expandable metal stents (fcSEMSs) are an alternative to progressive plastic stenting for the treatment of benign biliary strictures (BBS) with the prospect of a higher treatment efficacy and the need for fewer ERCPs, thereby reducing the burden for patients and possibly costs. Key to this novel treatment is safe stent removal. To investigate the feasibility and safety of stent removal of a fcSEMS with a proximal retrieval lasso: a long wire thread integrated in the proximal ends of the wire mesh that hangs freely in the stent lumen. Pulling it enables gradual removal of the stent inside-out. A secondary aim was success of stricture resolution. Non-randomized, prospective follow-up study with 3 sequential cohorts of 8 patients with BBS. Academic tertiary referral center. Eligible patients had strictures either postsurgical (post-cholecystectomy (LCx) or liver transplantation (OLT)), due to chronic pancreatitis (CP), or papillary stenosis (PF). Strictures had to be located at least 2 cm below the liver hilum. All patients had one plastic stent in situ across the stricture and had not undergone previous treatment with either multiple plastic stents or fcSEMS. The first cohort of patients underwent stent placement for 2 months, followed by 3 months if the stricture had not resolved. The second and third cohort started with 3 months and 4 months, respectively, both followed by another 4 months if indicated. Treatment success was defined by stricture resolution at cholangiography, the ability to pass an inflated extraction balloon and clinical follow-up (at least 6 months). safety of stent removal. Secondary outcomes were complications and successful stricture resolution. A total of 23 patients (11 female; 20-67 yrs) were eligible for final analysis. One patient developed a malignant neuroendocrine tumor in the setting of CP. Strictures were caused by CP (13), OLT (6), LCx (3) and PF (1). In total 39 fcSEMS were placed and removed. Removals were easy

  20. STAKEHOLDER LINKAGES FOR SUSTAINABLE LAND ...

    African Journals Online (AJOL)

    Osondu

    Key words: Stakeholders; farmer-expert linkages; resource management; Ethiopia. Introduction ... decentralized democratic decision making processes and thus ..... district offices within the given time limits. They were often .... -less willing and less ready to hearing weaker performance reports (expect more success with ...

  1. Poverty nutrition linkages.

    Science.gov (United States)

    Ramachandran, Prema

    2007-10-01

    cent and about half the children are undernourished. While poverty and mortality rates came down by 50 per cent, fertility rate by 40 per cent, the reduction in undernutrition in children is only 20 per cent. National surveys indicate that a third of the children from high income group who have not experienced any deprivations are undernourished. The high undernutrition rates among children appears to be mainly due to high low birthweight rates, poor infant and young child feeding and caring practices. At the other end of the spectrum, surveys in school children from high income groups indicate that between 10-20 per cent are overnourished; the major factor responsible appears to be reduction in physical activity. Some aspects of the rapidly changing, complex relationship between economic status, poverty, dietary intake, nutritional and health status are explored in this review.

  2. Efficient Record Linkage Algorithms Using Complete Linkage Clustering.

    Science.gov (United States)

    Mamun, Abdullah-Al; Aseltine, Robert; Rajasekaran, Sanguthevar

    2016-01-01

    Data from different agencies share data of the same individuals. Linking these datasets to identify all the records belonging to the same individuals is a crucial and challenging problem, especially given the large volumes of data. A large number of available algorithms for record linkage are prone to either time inefficiency or low-accuracy in finding matches and non-matches among the records. In this paper we propose efficient as well as reliable sequential and parallel algorithms for the record linkage problem employing hierarchical clustering methods. We employ complete linkage hierarchical clustering algorithms to address this problem. In addition to hierarchical clustering, we also use two other techniques: elimination of duplicate records and blocking. Our algorithms use sorting as a sub-routine to identify identical copies of records. We have tested our algorithms on datasets with millions of synthetic records. Experimental results show that our algorithms achieve nearly 100% accuracy. Parallel implementations achieve almost linear speedups. Time complexities of these algorithms do not exceed those of previous best-known algorithms. Our proposed algorithms outperform previous best-known algorithms in terms of accuracy consuming reasonable run times.

  3. Preliminary genetic linkage map of the abalone Haliotis diversicolor Reeve

    Science.gov (United States)

    Shi, Yaohua; Guo, Ximing; Gu, Zhifeng; Wang, Aimin; Wang, Yan

    2010-05-01

    Haliotis diversicolor Reeve is one of the most important mollusks cultured in South China. Preliminary genetic linkage maps were constructed with amplified fragment length polymorphism (AFLP) markers. A total of 2 596 AFLP markers were obtained from 28 primer combinations in two parents and 78 offsprings. Among them, 412 markers (15.9%) were polymorphic and segregated in the mapping family. Chi-square tests showed that 151 (84.4%) markers segregated according to the expected 1:1 Mendelian ratio ( P<0.05) in the female parent, and 200 (85.8%) in the male parent. For the female map, 179 markers were used for linkage analysis and 90 markers were assigned to 17 linkage groups with an average interval length of 25.7 cm. For the male map, 233 markers were used and 94 were mapped into 18 linkage groups, with an average interval of 25.0 cm. The estimated genome length was 2 773.0 cm for the female and 2 817.1 cm for the male map. The observed length of the linkage map was 1 875.2 cm and 1 896.5 cm for the female and male maps, respectively. When doublets were considered, the map length increased to 2 152.8 cm for the female and 2 032.7 cm for the male map, corresponding to genome coverage of 77.6% and 72.2%, respectively.

  4. Sganzerla Cover

    Directory of Open Access Journals (Sweden)

    Victor da Rosa

    2014-06-01

    Full Text Available Neste artigo, realizo uma leitura do cinema de Rogério Sganzerla, desde o clássico O bandido da luz vermelha até os documentários filmados na década de oitenta, a partir de duas noções centrais: cover e over. Para isso, parto de uma controvérsia com o ensaio de Ismail Xavier, Alegorias do subdesenvolvimento, em que o crítico realiza uma leitura do cinema brasileiro da década de sessenta através do conceito de alegoria; depois releio uma série de textos críticos do próprio Sganzerla, publicados em Edifício Sganzerla, procurando repensar as ideias de “herói vazio” ou “cinema impuro” e sugerindo assim uma nova relação do seu cinema com o tempo e a representação; então busco articular tais ideias com certos procedimentos de vanguarda, como a falsificação, a cópia, o clichê e a colagem; e finalmente procuro mostrar que, no cinema de Sganzerla, a partir principalmente de suas reflexões sobre Orson Welles, a voz é usada de maneira a deformar a interpretação naturalista.

  5. A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: a valuable resource for gene localisation and marker-assisted selection.

    Science.gov (United States)

    Jones, David B; Jerry, Dean R; Khatkar, Mehar S; Raadsma, Herman W; Zenger, Kyall R

    2013-11-20

    The silver-lipped pearl oyster, Pinctada maxima, is an important tropical aquaculture species extensively farmed for the highly sought "South Sea" pearls. Traditional breeding programs have been initiated for this species in order to select for improved pearl quality, but many economic traits under selection are complex, polygenic and confounded with environmental factors, limiting the accuracy of selection. The incorporation of a marker-assisted selection (MAS) breeding approach would greatly benefit pearl breeding programs by allowing the direct selection of genes responsible for pearl quality. However, before MAS can be incorporated, substantial genomic resources such as genetic linkage maps need to be generated. The construction of a high-density genetic linkage map for P. maxima is not only essential for unravelling the genomic architecture of complex pearl quality traits, but also provides indispensable information on the genome structure of pearl oysters. A total of 1,189 informative genome-wide single nucleotide polymorphisms (SNPs) were incorporated into linkage map construction. The final linkage map consisted of 887 SNPs in 14 linkage groups, spans a total genetic distance of 831.7 centimorgans (cM), and covers an estimated 96% of the P. maxima genome. Assessment of sex-specific recombination across all linkage groups revealed limited overall heterochiasmy between the sexes (i.e. 1.15:1 F/M map length ratio). However, there were pronounced localised differences throughout the linkage groups, whereby male recombination was suppressed near the centromeres compared to female recombination, but inflated towards telomeric regions. Mean values of LD for adjacent SNP pairs suggest that a higher density of markers will be required for powerful genome-wide association studies. Finally, numerous nacre biomineralization genes were localised providing novel positional information for these genes. This high-density SNP genetic map is the first comprehensive linkage

  6. A new genetic linkage map of the zygomycete fungus Phycomyces blakesleeanus.

    Directory of Open Access Journals (Sweden)

    Suman Chaudhary

    Full Text Available Phycomyces blakesleeanus is a member of the subphylum Mucoromycotina. A genetic map was constructed from 121 progeny of a cross between two wild type isolates of P. blakesleeanus with 134 markers. The markers were mostly PCR-RFLPs. Markers were located on 46 scaffolds of the genome sequence, covering more than 97% of the genome. Analysis of the alleles in the progeny revealed nine or 12 linkage groups, depending on the log of the odds (LOD score, across 1583.4 cM at LOD 5. The linkage groups were overlaid on previous mapping data from crosses between mutants, aided by new identification of the mutations in primary metabolism mutant strains. The molecular marker map, the phenotype map and the genome sequence are overall congruent, with some exceptions. The new genetic map provides a genome-wide estimate for recombination, with the average of 33.2 kb per cM. This frequency is one piece of evidence for meiosis during zygospore development in Mucoromycotina species. At the same time as meiosis, transmission of non-recombinant chromosomes is also evident in the mating process in Phycomyces. The new map provides scaffold ordering for the genome sequence and a platform upon which to identify the genes in mutants that are affected in traits of interest, such as carotene biosynthesis, phototropism or gravitropism, using positional cloning.

  7. Broad scan linkage analysis in a large Tourette family pedigree

    Energy Technology Data Exchange (ETDEWEB)

    Peiffer, A.; Leppert, M. [Univ. of Utah Health Sciences Center, Salt Lake City, UT (United States); Wetering, B.J.M. van der [Univ. Hospital Rotterdam (Netherlands)

    1994-09-01

    Attempts to find a gene causing Tourette syndrome (TS) using linkage analysis have been unsuccessful even though as much as 65% of the autosomal genetic map has been excluded by the pooled results from several laboratories collaborating worldwide. One reason for this failure may be the misclassification of affection status of marry-in spouses. Specifically, we have found that six unrelated spouses in our Utah TS pedigree suffer from TS, obsessive-compulsive disorder or chronic motor tics. In light of these findings we decided to conduct a complete genomic scan from this Utah kindred with polymorphic markers in three related sibships in which there was no assortative mating. A linkage study assuming autosomal dominant inheritance was done using tetranucleotide repeat markers developed at the University of Utah. We selected markers that were less than 300 bp in size and that gave a heterozygosity of over 70% upon analysis in 4 CEPH families. Results to date with 95 markers run at an interval of 30 cM (covering 61% of the genome) show no evidence of linkage. We intend to extend the coverage to 100% of the genome. Pending completion of this scan, failure to provide evidence of linkage in our TS pedigree might then be attributed to phenotypic misclassification or erroneous assumptions regarding the genetic model of transmission.

  8. Recombination patterns reveal information about centromere location on linkage maps

    DEFF Research Database (Denmark)

    Limborg, Morten T.; McKinney, Garrett J.; Seeb, Lisa W.

    2016-01-01

    . mykiss) characterized by low and unevenly distributed recombination – a general feature of male meiosis in many species. Further, a high frequency of double crossovers along chromosome arms in barley reduced resolution for locating centromeric regions on most linkage groups. Despite these limitations...

  9. Linkage Mechanisms among key Actors in Rice Innovation System ...

    African Journals Online (AJOL)

    In assessment of linkage mechanisms among key actors in rice innovation system in southeast Nigeria, actors were classified into six major groups according to their main activity in the system namely research agency, policy personnel, technology transfer agencies, farmers, marketers and consumers. These constituted the ...

  10. Health problems in childhood cancer survivors: Linkage studies and guideline development

    NARCIS (Netherlands)

    Font-Gonzalez, A.

    2016-01-01

    This thesis comprises two parts. The first part of this thesis aims to increase the evidence on the burden of disease in childhood cancer survivors and to define high-risk groups of survivors by using medical record linkage studies. A two-step record linkage methodology between Dutch national

  11. Privacy preserving interactive record linkage (PPIRL).

    Science.gov (United States)

    Kum, Hye-Chung; Krishnamurthy, Ashok; Machanavajjhala, Ashwin; Reiter, Michael K; Ahalt, Stanley

    2014-01-01

    Record linkage to integrate uncoordinated databases is critical in biomedical research using Big Data. Balancing privacy protection against the need for high quality record linkage requires a human-machine hybrid system to safely manage uncertainty in the ever changing streams of chaotic Big Data. In the computer science literature, private record linkage is the most published area. It investigates how to apply a known linkage function safely when linking two tables. However, in practice, the linkage function is rarely known. Thus, there are many data linkage centers whose main role is to be the trusted third party to determine the linkage function manually and link data for research via a master population list for a designated region. Recently, a more flexible computerized third-party linkage platform, Secure Decoupled Linkage (SDLink), has been proposed based on: (1) decoupling data via encryption, (2) obfuscation via chaffing (adding fake data) and universe manipulation; and (3) minimum information disclosure via recoding. We synthesize this literature to formalize a new framework for privacy preserving interactive record linkage (PPIRL) with tractable privacy and utility properties and then analyze the literature using this framework. Human-based third-party linkage centers for privacy preserving record linkage are the accepted norm internationally. We find that a computer-based third-party platform that can precisely control the information disclosed at the micro level and allow frequent human interaction during the linkage process, is an effective human-machine hybrid system that significantly improves on the linkage center model both in terms of privacy and utility.

  12. Prevalence and sequence variations of the genes encoding the five antigens included in the novel 5CVMB vaccine covering group B meningococcal disease.

    Science.gov (United States)

    Jacobsson, Susanne; Hedberg, Sara Thulin; Mölling, Paula; Unemo, Magnus; Comanducci, Maurizio; Rappuoli, Rino; Olcén, Per

    2009-03-04

    During the recent years, projects are in progress for designing broad-range non-capsular-based meningococcal vaccines, covering also serogroup B isolates. We have examined three genes encoding antigens (NadA, GNA1030 and GNA2091) included in a novel vaccine, i.e. the 5 Component Vaccine against Meningococcus B (5CVMB), in terms of gene prevalence and sequence variations. These data were combined with the results from a similar study, examining the two additional antigens included in the 5CVMB (fHbp and GNA2132). nadA and fHbp v. 1 were present in 38% (n=36), respectively 71% (n=67) of the isolates, whereas gna2132, gna1030 and gna2091 were present in all the Neisseria meningitidis isolates tested (n=95). The level of amino acid conservation was relatively high in GNA1030 (93%), GNA2091 (92%), and within the main variants of NadA and fHbp. GNA2132 (54% of the amino acids conserved) appeared to be the most diversified antigen. Consequently, the theoretical coverage of the 5CVMB antigens and the feasibility to use these in a broad-range meningococcal vaccine is appealing.

  13. When to conduct probabilistic linkage vs. deterministic linkage? A simulation study.

    Science.gov (United States)

    Zhu, Ying; Matsuyama, Yutaka; Ohashi, Yasuo; Setoguchi, Soko

    2015-08-01

    When unique identifiers are unavailable, successful record linkage depends greatly on data quality and types of variables available. While probabilistic linkage theoretically captures more true matches than deterministic linkage by allowing imperfection in identifiers, studies have shown inconclusive results likely due to variations in data quality, implementation of linkage methodology and validation method. The simulation study aimed to understand data characteristics that affect the performance of probabilistic vs. deterministic linkage. We created ninety-six scenarios that represent real-life situations using non-unique identifiers. We systematically introduced a range of discriminative power, rate of missing and error, and file size to increase linkage patterns and difficulties. We assessed the performance difference of linkage methods using standard validity measures and computation time. Across scenarios, deterministic linkage showed advantage in PPV while probabilistic linkage showed advantage in sensitivity. Probabilistic linkage uniformly outperformed deterministic linkage as the former generated linkages with better trade-off between sensitivity and PPV regardless of data quality. However, with low rate of missing and error in data, deterministic linkage performed not significantly worse. The implementation of deterministic linkage in SAS took less than 1min, and probabilistic linkage took 2min to 2h depending on file size. Our simulation study demonstrated that the intrinsic rate of missing and error of linkage variables was key to choosing between linkage methods. In general, probabilistic linkage was a better choice, but for exceptionally good quality data (<5% error), deterministic linkage was a more resource efficient choice. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. History of the Rochester Epidemiology Project: half a century of medical records linkage in a US population.

    Science.gov (United States)

    Rocca, Walter A; Yawn, Barbara P; St Sauver, Jennifer L; Grossardt, Brandon R; Melton, L Joseph

    2012-12-01

    The Rochester Epidemiology Project (REP) has maintained a comprehensive medical records linkage system for nearly half a century for almost all persons residing in Olmsted County, Minnesota. Herein, we provide a brief history of the REP before and after 1966, the year in which the REP was officially established. The key protagonists before 1966 were Henry Plummer, Mabel Root, and Joseph Berkson, who developed a medical records linkage system at Mayo Clinic. In 1966, Leonard Kurland established collaborative agreements with other local health care providers (hospitals, physician groups, and clinics [primarily Olmsted Medical Center]) to develop a medical records linkage system that covered the entire population of Olmsted County, and he obtained funding from the National Institutes of Health to support the new system. In 1997, L. Joseph Melton III addressed emerging concerns about the confidentiality of medical record information by introducing a broad patient research authorization as per Minnesota state law. We describe how the key protagonists of the REP have responded to challenges posed by evolving medical knowledge, information technology, and public expectation and policy. In addition, we provide a general description of the system; discuss issues of data quality, reliability, and validity; describe the research team structure; provide information about funding; and compare the REP with other medical information systems. The REP can serve as a model for the development of similar research infrastructures in the United States and worldwide. Copyright © 2012 Mayo Foundation for Medical Education and Research. Published by Elsevier Inc. All rights reserved.

  15. Preparation of Water-soluble Polyion Complex (PIC Micelles Covered with Amphoteric Random Copolymer Shells with Pendant Sulfonate and Quaternary Amino Groups

    Directory of Open Access Journals (Sweden)

    Rina Nakahata

    2018-02-01

    Full Text Available An amphoteric random copolymer (P(SA91 composed of anionic sodium 2-acrylamido-2-methylpropanesulfonate (AMPS, S and cationic 3-acrylamidopropyl trimethylammonium chloride (APTAC, A was prepared via reversible addition-fragmentation chain transfer (RAFT radical polymerization. The subscripts in the abbreviations indicate the degree of polymerization (DP. Furthermore, AMPS and APTAC were polymerized using a P(SA91 macro-chain transfer agent to prepare an anionic diblock copolymer (P(SA91S67 and a cationic diblock copolymer (P(SA91A88, respectively. The DP was estimated from quantitative 13C NMR measurements. A stoichiometrically charge neutralized mixture of the aqueous P(SA91S67 and P(SA91A88 formed water-soluble polyion complex (PIC micelles comprising PIC cores and amphoteric random copolymer shells. The PIC micelles were in a dynamic equilibrium state between PIC micelles and charge neutralized small aggregates composed of a P(SA91S67/P(SA91A88 pair. Interactions between PIC micelles and fetal bovine serum (FBS in phosphate buffered saline (PBS were evaluated by changing the hydrodynamic radius (Rh and light scattering intensity (LSI. Increases in Rh and LSI were not observed for the mixture of PIC micelles and FBS in PBS for one day. This observation suggests that there is no interaction between PIC micelles and proteins, because the PIC micelle surfaces were covered with amphoteric random copolymer shells. However, with increasing time, the diblock copolymer chains that were dissociated from PIC micelles interacted with proteins.

  16. Construction of an almond linkage map in an Australian population Nonpareil × Lauranne

    Science.gov (United States)

    2010-01-01

    Background Despite a high genetic similarity to peach, almonds (Prunus dulcis) have a fleshless fruit and edible kernel, produced as a crop for human consumption. While the release of peach genome v1.0 provides an excellent opportunity for almond genetic and genomic studies, well-assessed segregating populations and the respective saturated genetic linkage maps lay the foundation for such studies to be completed in almond. Results Using an almond intraspecific cross between 'Nonpareil' and 'Lauranne' (N × L), we constructed a moderately saturated map with SSRs, SNPs, ISSRs and RAPDs. The N × L map covered 591.4 cM of the genome with 157 loci. The average marker distance of the map was 4.0 cM. The map displayed high synteny and colinearity with the Prunus T × E reference map in all eight linkage groups (G1-G8). The positions of 14 mapped gene-anchored SNPs corresponded approximately with the positions of homologous sequences in the peach genome v1.0. Analysis of Mendelian segregation ratios showed that 17.9% of markers had significantly skewed genotype ratios at the level of P almond map, which is highly syntenic and collinear with the Prunus reference map and peach genome V1.0. Therefore, the well-assessed almond population reported here can be used to investigate the traits of interest under Australian growing conditions, and provides more information on the almond genome for the international community. PMID:20932335

  17. Linkage of PRA models. Phase 1, Results

    Energy Technology Data Exchange (ETDEWEB)

    Smith, C.L.; Knudsen, J.K.; Kelly, D.L.

    1995-12-01

    The goal of the Phase I work of the ``Linkage of PRA Models`` project was to postulate methods of providing guidance for US Nuclear Regulator Commission (NRC) personnel on the selection and usage of probabilistic risk assessment (PRA) models that are best suited to the analysis they are performing. In particular, methods and associated features are provided for (a) the selection of an appropriate PRA model for a particular analysis, (b) complementary evaluation tools for the analysis, and (c) a PRA model cross-referencing method. As part of this work, three areas adjoining ``linking`` analyses to PRA models were investigated: (a) the PRA models that are currently available, (b) the various types of analyses that are performed within the NRC, and (c) the difficulty in trying to provide a ``generic`` classification scheme to groups plants based upon a particular plant attribute.

  18. Linkage of PRA models. Phase 1, Results

    International Nuclear Information System (INIS)

    Smith, C.L.; Knudsen, J.K.; Kelly, D.L.

    1995-12-01

    The goal of the Phase I work of the ''Linkage of PRA Models'' project was to postulate methods of providing guidance for US Nuclear Regulator Commission (NRC) personnel on the selection and usage of probabilistic risk assessment (PRA) models that are best suited to the analysis they are performing. In particular, methods and associated features are provided for (a) the selection of an appropriate PRA model for a particular analysis, (b) complementary evaluation tools for the analysis, and (c) a PRA model cross-referencing method. As part of this work, three areas adjoining ''linking'' analyses to PRA models were investigated: (a) the PRA models that are currently available, (b) the various types of analyses that are performed within the NRC, and (c) the difficulty in trying to provide a ''generic'' classification scheme to groups plants based upon a particular plant attribute

  19. Bayesian estimates of linkage disequilibrium

    Directory of Open Access Journals (Sweden)

    Abad-Grau María M

    2007-06-01

    Full Text Available Abstract Background The maximum likelihood estimator of D' – a standard measure of linkage disequilibrium – is biased toward disequilibrium, and the bias is particularly evident in small samples and rare haplotypes. Results This paper proposes a Bayesian estimation of D' to address this problem. The reduction of the bias is achieved by using a prior distribution on the pair-wise associations between single nucleotide polymorphisms (SNPs that increases the likelihood of equilibrium with increasing physical distances between pairs of SNPs. We show how to compute the Bayesian estimate using a stochastic estimation based on MCMC methods, and also propose a numerical approximation to the Bayesian estimates that can be used to estimate patterns of LD in large datasets of SNPs. Conclusion Our Bayesian estimator of D' corrects the bias toward disequilibrium that affects the maximum likelihood estimator. A consequence of this feature is a more objective view about the extent of linkage disequilibrium in the human genome, and a more realistic number of tagging SNPs to fully exploit the power of genome wide association studies.

  20. Using Linkage Maps as a Tool To Determine Patterns of Chromosome Synteny in the Genus Salvelinus

    Directory of Open Access Journals (Sweden)

    Matthew C. Hale

    2017-11-01

    Full Text Available Next generation sequencing techniques have revolutionized the collection of genome and transcriptome data from nonmodel organisms. This manuscript details the application of restriction site-associated DNA sequencing (RADseq to generate a marker-dense genetic map for Brook Trout (Salvelinus fontinalis. The consensus map was constructed from three full-sib families totaling 176 F1 individuals. The map consisted of 42 linkage groups with a total female map size of 2502.5 cM, and a total male map size of 1863.8 cM. Synteny was confirmed with Atlantic Salmon for 38 linkage groups, with Rainbow Trout for 37 linkage groups, Arctic Char for 36 linkage groups, and with a previously published Brook Trout linkage map for 39 linkage groups. Comparative mapping confirmed the presence of 8 metacentric and 34 acrocentric chromosomes in Brook Trout. Six metacentric chromosomes seem to be conserved with Arctic Char suggesting there have been at least two species-specific fusion and fission events within the genus Salvelinus. In addition, the sex marker (sdY; sexually dimorphic on the Y chromosome was mapped to Brook Trout BC35, which is homologous with Atlantic Salmon Ssa09qa, Rainbow Trout Omy25, and Arctic Char AC04q. Ultimately, this linkage map will be a useful resource for studies on the genome organization of Salvelinus, and facilitates comparisons of the Salvelinus genome with Salmo and Oncorhynchus.

  1. Single Nucleotide Polymorphism Identification, Characterization, and Linkage Mapping in Quinoa

    Directory of Open Access Journals (Sweden)

    P. J. Maughan

    2012-11-01

    Full Text Available Quinoa ( Willd. is an important seed crop throughout the Andean region of South America. It is important as a regional food security crop for millions of impoverished rural inhabitants of the Andean Altiplano (high plains. Efforts to improve the crop have led to an increased focus on genetic research. We report the identification of 14,178 putative single nucleotide polymorphisms (SNPs using a genomic reduction protocol as well as the development of 511 functional SNP assays. The SNP assays are based on KASPar genotyping chemistry and were detected using the Fluidigm dynamic array platform. A diversity screen of 113 quinoa accessions showed that the minor allele frequency (MAF of the SNPs ranged from 0.02 to 0.50, with an average MAF of 0.28. Structure analysis of the quinoa diversity panel uncovered the two major subgroups corresponding to the Andean and coastal quinoa ecotypes. Linkage mapping of the SNPs in two recombinant inbred line populations produced an integrated linkage map consisting of 29 linkage groups with 20 large linkage groups, spanning 1404 cM with a marker density of 3.1 cM per SNP marker. The SNPs identified here represent important genomic tools needed in emerging plant breeding programs for advanced genetic analysis of agronomic traits in quinoa.

  2. Policy for home or hospice as the preferred place of death from cancer: Scottish Health and Ethnicity Linkage Study population cohort shows challenges across all ethnic groups in Scotland.

    Science.gov (United States)

    Sharpe, Katharine H; Cezard, Genevieve; Bansal, Narinder; Bhopal, Raj S; Brewster, David H

    2015-12-01

    Place of cancer death varies ethnically and internationally. Palliative care reviews highlight limited ability to demonstrate equal access due to incomplete or unreliable ethnicity data. To establish place of cancer death by ethnicity and describe patient characteristics. We linked census, hospital episode and mortality data for 117 467 persons dying of cancer, 2001-2009. With White Scottish population as reference, prevalence ratios (PR), 95% CIs and p values of death in hospital, home or hospice adjusted for sex and age were calculated by ethnic group. White Scottish group and minority ethnic groups combined constituted 91% and 0.4% of cancer deaths, respectively. South Asian, Chinese and African Origin patients were youngest at death (66, 66 and 65.9 years). Compared with the Scottish White reference, the White Irish (1.15 (1.10 to 1.22), pScottish White patients were less likely to die in hospital and more likely to die at home or in a hospice regardless of socioeconomic indicator used. Cancer deaths occur most often in hospital (52.3%) for all ethnic groups. Regardless of the socioeconomic indicator used, more affluent Scottish White patients were less likely to die in hospital; existing socioeconomic indicators detected no clear trend for the non-White population. Regardless of ethnic group, significant work is required to achieve more people dying at home or the setting of their choice. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  3. Challenges in administrative data linkage for research

    Directory of Open Access Journals (Sweden)

    Katie Harron

    2017-12-01

    Full Text Available Linkage of population-based administrative data is a valuable tool for combining detailed individual-level information from different sources for research. While not a substitute for classical studies based on primary data collection, analyses of linked administrative data can answer questions that require large sample sizes or detailed data on hard-to-reach populations, and generate evidence with a high level of external validity and applicability for policy making. There are unique challenges in the appropriate research use of linked administrative data, for example with respect to bias from linkage errors where records cannot be linked or are linked together incorrectly. For confidentiality and other reasons, the separation of data linkage processes and analysis of linked data is generally regarded as best practice. However, the ‘black box’ of data linkage can make it difficult for researchers to judge the reliability of the resulting linked data for their required purposes. This article aims to provide an overview of challenges in linking administrative data for research. We aim to increase understanding of the implications of (i the data linkage environment and privacy preservation; (ii the linkage process itself (including data preparation, and deterministic and probabilistic linkage methods and (iii linkage quality and potential bias in linked data. We draw on examples from a number of countries to illustrate a range of approaches for data linkage in different contexts.

  4. Does the ‘Scottish effect’ apply to all ethnic groups? All-cancer, lung, colorectal, breast and prostate cancer in the Scottish Health and Ethnicity Linkage Cohort Study

    Science.gov (United States)

    Bhopal, Raj S; Bansal, Narinder; Steiner, Markus; Brewster, David H

    2012-01-01

    Background and objectives Although ethnic group variations in cancer exist, no multiethnic, population-based, longitudinal studies are available in Europe. Our objectives were to examine ethnic variation in all-cancer, and lung, colorectal, breast and prostate cancers. Design, setting, population, measures and analysis This retrospective cohort study of 4.65 million people linked the 2001 Scottish Census (providing ethnic group) to cancer databases. With the White Scottish population as reference (value 100), directly age standardised rates and ratios (DASR and DASRR), and risk ratios, by sex and ethnic group with 95% CI were calculated for first cancers. In the results below, 95% CI around the DASRR excludes 100. Eight indicators of socio-economic position were assessed as potential confounders across all groups. Results For all cancers the White Scottish population (100) had the highest DASRRs, Indians the lowest (men 45.9 and women 41.2) and White British (men 87.6 and women 87.3) and other groups were intermediate (eg, Chinese men 57.6). For lung cancer the DASRRs for Pakistani men (45.0), and women (53.5), were low and for any mixed background men high (174.5). For colorectal cancer the DASRRs were lowest in Pakistanis (men 32.9 and women 68.9), White British (men 82.4 and women 83.7), other White (men 77.2 and women 74.9) and Chinese men (42.6). Breast cancer in women was low in Pakistanis (62.2), Chinese (63.0) and White Irish (84.0). Prostate cancer was lowest in Pakistanis (38.7), Indian (62.6) and White Irish (85.4). No socio-economic indicator was a valid confounding variable across ethnic groups. Conclusions The ‘Scottish effect’ does not apply across ethnic groups for cancer. The findings have implications for clinical care, prevention and screening, for example, responding appropriately to the known low uptake among South Asian populations of bowel screening might benefit from modelling of cost-effectiveness of screening, given comparatively low

  5. Linkage disequilibrium and association mapping.

    Science.gov (United States)

    Weir, B S

    2008-01-01

    Linkage disequilibrium refers to the association between alleles at different loci. The standard definition applies to two alleles in the same gamete, and it can be regarded as the covariance of indicator variables for the states of those two alleles. The corresponding correlation coefficient rho is the parameter that arises naturally in discussions of tests of association between markers and genetic diseases. A general treatment of association tests makes use of the additive and nonadditive components of variance for the disease gene. In almost all expressions that describe the behavior of association tests, additive variance components are modified by the squared correlation coefficient rho2 and the nonadditive variance components by rho4, suggesting that nonadditive components have less influence than additive components on association tests.

  6. Linkage and mapping analyses of the no glue egg gene Ng in the ...

    African Journals Online (AJOL)

    Jane

    2011-08-24

    Aug 24, 2011 ... The Ng gene was mapped at 28.0 of the silkworm classical genetic linkage group 12. (Xiang, 1995). In recent years, molecular biology has made consider- able progress ..... project (08080703017), China agriculture research.

  7. Above- and belowground linkages in Sphagnum peatland: climate warming affects plant-microbial interactions.

    Science.gov (United States)

    Jassey, Vincent E J; Chiapusio, Geneviève; Binet, Philippe; Buttler, Alexandre; Laggoun-Défarge, Fatima; Delarue, Frédéric; Bernard, Nadine; Mitchell, Edward A D; Toussaint, Marie-Laure; Francez, André-Jean; Gilbert, Daniel

    2013-03-01

    Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above- and belowground linkages that regulate soil organic carbon dynamics and C-balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top-predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum-polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above- and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands. © 2012 Blackwell Publishing Ltd.

  8. Construction of microsatellite-based linkage map and mapping of nectarilessness and hairiness genes in Gossypium tomentosum.

    Science.gov (United States)

    Hou, Meiying; Cai, Caiping; Zhang, Shuwen; Guo, Wangzhen; Zhang, Tianzhen; Zhou, Baoliang

    2013-12-01

    Gossypium tomentosum, a wild tetraploid cotton species with AD genomes, possesses genes conferring strong fibers and high heat tolerance. To effectively transfer these genes into Gossypium hirsutum, an entire microsatellite (simple sequence repeat, SSR)-based genetic map was constructed using the interspecific cross of G. hirsutum x G. tomentosum (HT). We detected 1800 loci from 1347 pairs of polymorphic primers. Of these, 1204 loci were grouped into 35 linkage groups at LOD ≥ 4. The map covers 3320.8 cM, with a mean density of 2.76 cM per locus. We detected 420 common loci (186 in the At subgenome and 234 in Dt) between the HT map and the map of TM-1 (G. hirsutum) and Hai 7124 (G. barbadense; HB map). The linkage groups were assigned chromosome numbers based on location of common loci and the HB map as reference. A comparison of common markers revealed that no significant chromosomal rearrangement exist between G. tomentosum and G. barbadense. Interestingly, however, we detected numerous (33.7%) segregation loci deviating from 3:1 ratio (P constructed in this study will be useful for further genetic studies on cotton breeding, including mapping loci controlling quantitative traits associated with fiber quality, stress tolerance and developing chromosome segment specific introgression lines from G. tomentosum into G. hirsutum using marker-assisted selection.

  9. Land Cover - Minnesota Land Cover Classification System

    Data.gov (United States)

    Minnesota Department of Natural Resources — Land cover data set based on the Minnesota Land Cover Classification System (MLCCS) coding scheme. This data was produced using a combination of aerial photograph...

  10. Linkage Behavior and Practices of Agencies in the Agricultural ...

    African Journals Online (AJOL)

    The study examined the linkage behaviour and practices of agencies in the ... institutes; while (61.5%,65.5%and 50.0%) indicated that linkages with universities of ... Existing institutional framework for linkages between research and extension ...

  11. PRESENTATION ON--LAND-COVER CHANGE DETECTION USING MULTI-TEMPORAL MODIS NDVI DATA

    Science.gov (United States)

    Monitoring the locations and distributions of land-cover changes is important for establishing linkages between policy decisions, regulatory actions and subsequent landuse activities. Past efforts incorporating two-date change detection using moderate resolution data (e.g., Lands...

  12. INDONESIAN COUNTRY PAPER MECHANISMS USED TO STRENGTHEN INFORMATION LINKAGES

    Directory of Open Access Journals (Sweden)

    Achmad Djuhamsa

    2011-12-01

    Full Text Available ENSICNET-Indonesia provides dissemination of information on the field of water supply and sanitation to potential users by using different methods which depend on their own function and duty. Linkage mechanisms are developed to make users aware of the sources, to identify and define user n~eds and to make the contact 'between the user need and the information sources. Several forms of communication which can link information resources to an individual or groups are disscussed.

  13. Linkage for Education and Research in Nursing (LEARN), une ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Linkage for Education and Research in Nursing (LEARN), une initiative de TIC-D dans les Caraïbes. Les infirmières représentent le plus important groupe de professionnels de la santé pouvant influer sur la qualité des soins dans les services de santé. Les efforts pour faire en sorte que les infirmières des Caraïbes soient ...

  14. The acceptability of conducting data linkage research without obtaining consent: lay people's views and justifications.

    Science.gov (United States)

    Xafis, Vicki

    2015-11-17

    A key ethical issue arising in data linkage research relates to consent requirements. Patients' consent preferences in the context of health research have been explored but their consent preferences regarding data linkage specifically have been under-explored. In addition, the views on data linkage are often those of patient groups. As a result, little is known about lay people's views and their preferences about consent requirements in the context of data linkage. This study explores lay people's views and justifications regarding the acceptability of conducting data linkage research without obtaining consent. A qualitative study explored lay people's views regarding consent requirements in data linkage via four hypothetical data linkage scenarios of increasing complexity. Prior to considering the scenarios, participants were provided with information regarding best practice data linkage processes via discussion and a diagrammatic representation of the process. Lay people were able to understand the intricate processes involved in data linkage and the key protections afforded within a short amount of time. They were supportive of data linkage research and, on the whole, believed it should be conducted without consent provided a data linkage organization de-identifies the data used so that researchers do not handle identifiable data. Many thought that de-identified data holds a different status to identifiable data and should be used without specific consent in research that aims to benefit society. In weighing up conflicting values and interests, participants shifted consent preferences before arriving at their final consent preference for each scenario and provided justifications for their choices. They considered the protection of people's information, societal benefits, and the nature and constraints of research and recognized that these need to be balanced. With some exposure to the features of data linkage, lay people have the capacity to understand the

  15. Linkage disequilibrium in wild mice.

    Directory of Open Access Journals (Sweden)

    Cathy C Laurie

    2007-08-01

    Full Text Available Crosses between laboratory strains of mice provide a powerful way of detecting quantitative trait loci for complex traits related to human disease. Hundreds of these loci have been detected, but only a small number of the underlying causative genes have been identified. The main difficulty is the extensive linkage disequilibrium (LD in intercross progeny and the slow process of fine-scale mapping by traditional methods. Recently, new approaches have been introduced, such as association studies with inbred lines and multigenerational crosses. These approaches are very useful for interval reduction, but generally do not provide single-gene resolution because of strong LD extending over one to several megabases. Here, we investigate the genetic structure of a natural population of mice in Arizona to determine its suitability for fine-scale LD mapping and association studies. There are three main findings: (1 Arizona mice have a high level of genetic variation, which includes a large fraction of the sequence variation present in classical strains of laboratory mice; (2 they show clear evidence of local inbreeding but appear to lack stable population structure across the study area; and (3 LD decays with distance at a rate similar to human populations, which is considerably more rapid than in laboratory populations of mice. Strong associations in Arizona mice are limited primarily to markers less than 100 kb apart, which provides the possibility of fine-scale association mapping at the level of one or a few genes. Although other considerations, such as sample size requirements and marker discovery, are serious issues in the implementation of association studies, the genetic variation and LD results indicate that wild mice could provide a useful tool for identifying genes that cause variation in complex traits.

  16. Resource linkages and sustainable development

    Science.gov (United States)

    Anouti, Yahya

    Historically, fossil fuel consumers in most developing hydrocarbon-rich countries have enjoyed retail prices at a discount from international benchmarks. Governments of these countries consider the subsidy transfer to be a means for sharing the wealth from their resource endowment. These subsidies create negative economic, environmental, and social distortions, which can only increase over time with a fast growing, young, and rich population. The pressure to phase out these subsidies has been mounting over the last years. At the same time, policy makers in resource-rich developing countries are keen to obtain the greatest benefits for their economies from the extraction of their exhaustible resources. To this end, they are deploying local content policies with the aim of increasing the economic linkages from extracting their resources. Against this background, this dissertation's three essays evaluate (1) the global impact of rationalizing transport fuel prices, (2) how resource-rich countries can achieve the objectives behind fuel subsidies more efficiently through direct cash transfers, and (3) the economic tradeoffs from deploying local content policies and the presence of an optimal path. We begin by reviewing the literature and building the case for rationalizing transport fuel prices to reflect their direct costs (production), indirect costs (road maintenance) and negative externalities (climate change, local pollutants, traffic accidents and congestion). To do so, we increase the scope of the economic literature by presenting an algorithm to evaluate the rationalized prices in different countries. Then, we apply this algorithm to quantify the rationalized prices across 123 countries in a partial equilibrium setting. Finally, we present the first comprehensive measure of the impact of rationalizing fuel prices on the global demand for gasoline and diesel, environmental emissions, government revenues, and consumers' welfare. By rationalizing transport fuel

  17. A genetic linkage map for the saltwater crocodile (Crocodylus porosus

    Directory of Open Access Journals (Sweden)

    Lance Stacey L

    2009-07-01

    Full Text Available Abstract Background Genome elucidation is now in high gear for many organisms, and whilst genetic maps have been developed for a broad array of species, surprisingly, no such maps exist for a crocodilian, or indeed any other non-avian member of the Class Reptilia. Genetic linkage maps are essential tools for the mapping and dissection of complex quantitative trait loci (QTL, and in order to permit systematic genome scans for the identification of genes affecting economically important traits in farmed crocodilians, a comprehensive genetic linage map will be necessary. Results A first-generation genetic linkage map for the saltwater crocodile (Crocodylus porosus was constructed using 203 microsatellite markers amplified across a two-generation pedigree comprising ten full-sib families from a commercial population at Darwin Crocodile Farm, Northern Territory, Australia. Linkage analyses identified fourteen linkage groups comprising a total of 180 loci, with 23 loci remaining unlinked. Markers were ordered within linkage groups employing a heuristic approach using CRIMAP v3.0 software. The estimated female and male recombination map lengths were 1824.1 and 319.0 centimorgans (cM respectively, revealing an uncommonly large disparity in recombination map lengths between sexes (ratio of 5.7:1. Conclusion We have generated the first genetic linkage map for a crocodilian, or indeed any other non-avian reptile. The uncommonly large disparity in recombination map lengths confirms previous preliminary evidence of major differences in sex-specific recombination rates in a species that exhibits temperature-dependent sex determination (TSD. However, at this point the reason for this disparity in saltwater crocodiles remains unclear. This map will be a valuable resource for crocodilian researchers, facilitating the systematic genome scans necessary for identifying genes affecting complex traits of economic importance in the crocodile industry. In addition

  18. Missing Linkages in California's Landscape [ds420

    Data.gov (United States)

    California Natural Resource Agency — The critical need for conserving landscape linkages first came to the forefront of conservation thinking in California in November 2000, when a statewide interagency...

  19. Multiobjective optimization of a steering linkage

    Energy Technology Data Exchange (ETDEWEB)

    Sleesonsom, S.; Bureerat, S. [Sustainable and Infrastructure Research and Development Center, Dept. of Mechanical Engineering, Faculty of Engineering, Khon Kaen University, Khon Kaen (Thailand)

    2016-08-15

    In this paper, multi-objective optimization of a rack-and-pinion steering linkage is proposed. This steering linkage is a common mechanism used in small cars with three advantages as it is simple to construct, economical to manufacture, and compact and easy to operate. In the previous works, many researchers tried to minimize a steering error but minimization of a turning radius is somewhat ignored. As a result, a multi-objective optimization problem is assigned to simultaneously minimize a steering error and a turning radius. The design variables are linkage dimensions. The design problem is solved by the hybrid of multi-objective population-based incremental learning and differential evolution with various constraint handling schemes. The new design strategy leads to effective design of rack-and-pinion steering linkages satisfying both steering error and turning radius criteria.

  20. EDITORIAL Development Linkages between Tree Breeding ...

    African Journals Online (AJOL)

    EDITORIAL Development Linkages between Tree Breeding Programmes and National/Regional Tree Seed Centres in Africa. ... Discovery and Innovation. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives.

  1. Missing Linkages in California's Landscape [ds420

    Data.gov (United States)

    California Department of Resources — The critical need for conserving landscape linkages first came to the forefront of conservation thinking in California in November 2000, when a statewide interagency...

  2. Multiobjective optimization of a steering linkage

    International Nuclear Information System (INIS)

    Sleesonsom, S.; Bureerat, S.

    2016-01-01

    In this paper, multi-objective optimization of a rack-and-pinion steering linkage is proposed. This steering linkage is a common mechanism used in small cars with three advantages as it is simple to construct, economical to manufacture, and compact and easy to operate. In the previous works, many researchers tried to minimize a steering error but minimization of a turning radius is somewhat ignored. As a result, a multi-objective optimization problem is assigned to simultaneously minimize a steering error and a turning radius. The design variables are linkage dimensions. The design problem is solved by the hybrid of multi-objective population-based incremental learning and differential evolution with various constraint handling schemes. The new design strategy leads to effective design of rack-and-pinion steering linkages satisfying both steering error and turning radius criteria

  3. Asian Financial Linkages: The Case of Japan

    OpenAIRE

    Fialová, Anežka

    2014-01-01

    This work reviews the topic of international financial linkages, including theoretical definitions and the main methodological approaches of the empirical measurement based on vector autoregressive models. One of the approaches, the Spillover Index methodology based on Diebold & Yilmaz (2009), is then used to analyze the developments of financial linkages of the Japanese stock market in the period from 1995 to 2012. The attention is paid both to the relations with western developed economies ...

  4. Effect of Linkage Disequilibrium on the Identification of Functional Variants

    Science.gov (United States)

    Thomas, Alun; Abel, Haley J; Di, Yanming; Faye, Laura L; Jin, Jing; Liu, Jin; Wu, Zheyan; Paterson, Andrew D

    2011-01-01

    We summarize the contributions of Group 9 of Genetic Analysis Workshop 17. This group addressed the problems of linkage disequilibrium and other longer range forms of allelic association when evaluating the effects of genotypes on phenotypes. Issues raised by long-range associations, whether a result of selection, stratification, possible technical errors, or chance, were less expected but proved to be important. Most contributors focused on regression methods of various types to illustrate problematic issues or to develop adaptations for dealing with high-density genotype assays. Study design was also considered, as was graphical modeling. Although no method emerged as uniformly successful, most succeeded in reducing false-positive results either by considering clusters of loci within genes or by applying smoothing metrics that required results from adjacent loci to be similar. Two unexpected results that questioned our assumptions of what is required to model linkage disequilibrium were observed. The first was that correlations between loci separated by large genetic distances can greatly inflate single-locus test statistics, and, whether the result of selection, stratification, possible technical errors, or chance, these correlations seem overabundant. The second unexpected result was that applying principal components analysis to genome-wide genotype data can apparently control not only for population structure but also for linkage disequilibrium. PMID:22128051

  5. Heritability and linkage analysis of personality in bipolar disorder.

    Science.gov (United States)

    Greenwood, Tiffany A; Badner, Judith A; Byerley, William; Keck, Paul E; McElroy, Susan L; Remick, Ronald A; Dessa Sadovnick, A; Kelsoe, John R

    2013-11-01

    The many attempts that have been made to identify genes for bipolar disorder (BD) have met with limited success, which may reflect an inadequacy of diagnosis as an informative and biologically relevant phenotype for genetic studies. Here we have explored aspects of personality as quantitative phenotypes for bipolar disorder through the use of the Temperament and Character Inventory (TCI), which assesses personality in seven dimensions. Four temperament dimensions are assessed: novelty seeking (NS), harm avoidance (HA), reward dependence (RD), and persistence (PS). Three character dimensions are also included: self-directedness (SD), cooperativeness (CO), and self-transcendence (ST). We compared personality scores between diagnostic groups and assessed heritability in a sample of 101 families collected for genetic studies of BD. A genome-wide SNP linkage analysis was then performed in the subset of 51 families for which genetic data was available. Significant group differences were observed between BD subjects, their first-degree relatives, and independent controls for all but RD and PS, and all but HA and RD were found to be significantly heritable in this sample. Linkage analysis of the heritable dimensions produced several suggestive linkage peaks for NS (chromosomes 7q21 and 10p15), PS (chromosomes 6q16, 12p13, and 19p13), and SD (chromosomes 4q35, 8q24, and 18q12). The relatively small size of our linkage sample likely limited our ability to reach genome-wide significance in this study. While not genome-wide significant, these results suggest that aspects of personality may prove useful in the identification of genes underlying BD susceptibility. © 2013 Elsevier B.V. All rights reserved.

  6. Linkage analysis by genotyping of sibling populations: a genetic map for the potato cyst nematode constructed using a "pseudo-F2" mapping strategy.

    Science.gov (United States)

    Rouppe van der Voort, J N; van Eck, H J; van Zandvoort, P M; Overmars, H; Helder, J; Bakker, J

    1999-07-01

    A mapping strategy is described for the construction of a linkage map of a non-inbred species in which individual offspring genotypes are not amenable to marker analysis. After one extra generation of random mating, the segregating progeny was propagated, and bulked populations of offspring were analyzed. Although the resulting population structure is different from that of commonly used mapping populations, we show that the maximum likelihood formula for a normal F2 is applicable for the estimation of recombination. This "pseudo-F2" mapping strategy, in combination with the development of an AFLP assay for single cysts, facilitated the construction of a linkage map for the potato cyst nematode Globodera rostochiensis. Using 12 pre-selected AFLP primer combinations, a total of 66 segregating markers were identified, 62 of which were mapped to nine linkage groups. These 62 AFLP markers are randomly distributed and cover about 65% of the genome. An estimate of the physical size of the Globodera genome was obtained from comparisons of the number of AFLP fragments obtained with the values for Caenorhabditis elegans. The methodology presented here resulted in the first genomic map for a cyst nematode. The low value of the kilobase/centimorgan (kb/cM) ratio for the Globodera genome will facilitate map-based cloning of genes that mediate the interaction between the nematode and its host plant.

  7. A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.

    Directory of Open Access Journals (Sweden)

    Duygu Ates

    Full Text Available Lentil (Lens culinaris ssp. culinaris Medikus is a diploid (2n = 2x = 14, self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes.A consensus map of lentil (Lens culinaris ssp. culinaris Medikus was constructed using three different lentils recombinant inbred line (RIL populations, including "CDC Redberry" x "ILL7502" (LR8, "ILL8006" x "CDC Milestone" (LR11 and "PI320937" x "Eston" (LR39.The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4. The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps.This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.

  8. A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.

    Science.gov (United States)

    Ates, Duygu; Aldemir, Secil; Alsaleh, Ahmad; Erdogmus, Semih; Nemli, Seda; Kahriman, Abdullah; Ozkan, Hakan; Vandenberg, Albert; Tanyolac, Bahattin

    2018-01-01

    Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39). The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.

  9. A SNP based high-density linkage map of Apis cerana reveals a high recombination rate similar to Apis mellifera.

    Directory of Open Access Journals (Sweden)

    Yuan Yuan Shi

    Full Text Available BACKGROUND: The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee. RESULTS: F2 workers (N = 103 were genotyped for 126,990 single nucleotide polymorphisms (SNPs. After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM with the largest linkage group (180 loci measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM. CONCLUSION: We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera.

  10. Construction of an almond linkage map in an Australian population Nonpareil × Lauranne

    Directory of Open Access Journals (Sweden)

    Gibson John P

    2010-10-01

    Full Text Available Abstract Background Despite a high genetic similarity to peach, almonds (Prunus dulcis have a fleshless fruit and edible kernel, produced as a crop for human consumption. While the release of peach genome v1.0 provides an excellent opportunity for almond genetic and genomic studies, well-assessed segregating populations and the respective saturated genetic linkage maps lay the foundation for such studies to be completed in almond. Results Using an almond intraspecific cross between 'Nonpareil' and 'Lauranne' (N × L, we constructed a moderately saturated map with SSRs, SNPs, ISSRs and RAPDs. The N × L map covered 591.4 cM of the genome with 157 loci. The average marker distance of the map was 4.0 cM. The map displayed high synteny and colinearity with the Prunus T × E reference map in all eight linkage groups (G1-G8. The positions of 14 mapped gene-anchored SNPs corresponded approximately with the positions of homologous sequences in the peach genome v1.0. Analysis of Mendelian segregation ratios showed that 17.9% of markers had significantly skewed genotype ratios at the level of P ® 3 were compared, and their high degree of similarity was evident despite the positional inconsistency of a few markers. Conclusions We presented a moderately saturated Australian almond map, which is highly syntenic and collinear with the Prunus reference map and peach genome V1.0. Therefore, the well-assessed almond population reported here can be used to investigate the traits of interest under Australian growing conditions, and provides more information on the almond genome for the international community.

  11. Construction of 2 intraspecific linkage maps and identification of resistance QTLs for Phytophthora capsici root-rot and foliar-blight diseases of pepper (Capsicum annuum L.).

    Science.gov (United States)

    Ogundiwin, Ebenezer A; Berke, Terry F; Massoudi, Mark; Black, Lowell L; Huestis, Gordon; Choi, Doil; Lee, Sanghyeob; Prince, James P

    2005-08-01

    Two linkage maps of pepper were constructed and used to identify quantitative trait loci (QTLs) conferring resistance to Phytophthora capsici. Inoculations were done with 7 isolates: 3 from Taiwan, 3 from California, and 1 from New Mexico. The first map was constructed from a set of recombinant inbred lines (RILs) of the PSP-11 (susceptible) x PI201234 (resistant) cross; and the second map was from a set of F(2) lines of the Joe E. Parker' (susceptible) x 'Criollo de Morelos 334' (resistant) cross. The RIL map covered 1466.1 cM of the pepper genome, and it consisted of 144 markers -- 91 amplified fragment length polymorphisms (AFLPs), 34 random amplified polymorphic DNA (RAPDs), 15 simple sequence repeats (SSRs), 1 sequence characterized amplified region (SCAR), and 3 morphological markers -- distributed over 17 linkage groups. The morphological markers mapped on this population were erect fruit habit (up), elongated fruit shape (fs(e)), and fasciculate fruit clusters (fa). The F(2) map consisted of 113 markers (51 AFLPs, 45 RAPDs, 14 SSRs, and 3 SCARs) distributed in 16 linkage groups, covering a total of 1089.2 cM of the pepper genome. Resistance to both root rot and foliar blight were evaluated in the RIL population using the 3 Taiwan isolates; the remaining isolates were used for the root-rot test only. Sixteen chromosomal regions of the RIL map contained single QTLs or clusters of resistance QTLs that had an effect on root rot and (or) foliar blight, revealing a complex set of genetics involved in resistance to P. capsici. Five QTLs were detected in the F(2) map that had an effect on resistance to root rot.

  12. Quantitative linkage genome scan for atopy in a large collection of Caucasian families

    DEFF Research Database (Denmark)

    Webb, BT; van den Oord, E; Akkari, A

    2007-01-01

    adulthood, asthma is frequently associated also with quantitative measures of atopy. Genome wide quantitative multipoint linkage analysis was conducted for serum IgE levels and percentage of positive skin prick test (SPT(per)) using three large groups of families originally ascertained for asthma....... In this report, 438 and 429 asthma families were informative for linkage using IgE and SPT(per) which represents 690 independent families. Suggestive linkage (LOD >/= 2) was found on chromosomes 1, 3, and 8q with maximum LODs of 2.34 (IgE), 2.03 (SPT(per)), and 2.25 (IgE) near markers D1S1653, D3S2322-D3S1764...... represents one of the biggest genome scans so far reported for asthma related phenotypes. This study also demonstrates the utility of increased sample sizes and quantitative phenotypes in linkage analysis of complex disorders....

  13. Quantitative linkage genome scan for atopy in a large collection of Caucasian families

    DEFF Research Database (Denmark)

    Webb, BT; van den Oord, E; Akkari, A

    2007-01-01

    Quantitative phenotypes correlated with a complex disorder offer increased power to detect linkage in comparison to affected-unaffected classifications. Asthma is a complex disorder characterized by periods of bronchial obstruction and increased bronchial hyper reactivity. In childhood and early...... adulthood, asthma is frequently associated also with quantitative measures of atopy. Genome wide quantitative multipoint linkage analysis was conducted for serum IgE levels and percentage of positive skin prick test (SPT(per)) using three large groups of families originally ascertained for asthma....... In this report, 438 and 429 asthma families were informative for linkage using IgE and SPT(per) which represents 690 independent families. Suggestive linkage (LOD >/= 2) was found on chromosomes 1, 3, and 8q with maximum LODs of 2.34 (IgE), 2.03 (SPT(per)), and 2.25 (IgE) near markers D1S1653, D3S2322-D3S1764...

  14. Dimensional threshold for fracture linkage and hooking

    Science.gov (United States)

    Lamarche, Juliette; Chabani, Arezki; Gauthier, Bertrand D. M.

    2018-03-01

    Fracture connectivity in rocks depends on spatial properties of the pattern including length, abundance and orientation. When fractures form a single-strike set, they hardly cross-cut each other and the connectivity is limited. Linkage probability increases with increasing fracture abundance and length as small fractures connect to each other to form longer ones. A process for parallel fracture linkage is the "hooking", where two converging fracture tips mutually deviate and then converge to connect due to the interaction of their crack-tip stresses. Quantifying the processes and conditions for fracture linkage in single-strike fracture sets is crucial to better predicting fluid flow in Naturally Fractured Reservoirs. For 1734 fractures in Permian shales of the Lodève Basin, SE France, we measured geometrical parameters in 2D, characterizing three stages of the hooking process: underlapping, overlapping and linkage. We deciphered the threshold values, shape ratios and limiting conditions to switch from one stage to another one. The hook set up depends on the spacing (S) and fracture length (Lh) with the relation S ≈ 0.15 Lh. Once the hooking is initiated, with the fracture deviation length (L) L ≈ 0.4 Lh, the fractures reaches the linkage stage only when the spacing is reduced to S ≈ 0.02 Lh and the convergence (C) is < 0.1 L. These conditions apply to multi-scale fractures with a shape ratio L/S = 10 and for fracture curvature of 10°-20°.

  15. Genome scan for linkage to asthma using a linkage disequilibrium-lod score test.

    Science.gov (United States)

    Jiang, Y; Slager, S L; Huang, J

    2001-01-01

    We report a genome-wide linkage study of asthma on the German and Collaborative Study on the Genetics of Asthma (CSGA) data. Using a combined linkage and linkage disequilibrium test and the nonparametric linkage score, we identified 13 markers from the German data, 1 marker from the African American (CSGA) data, and 7 markers from the Caucasian (CSGA) data in which the p-values ranged between 0.0001 and 0.0100. From our analysis and taking into account previous published linkage studies of asthma, we suggest that three regions in chromosome 5 (around D5S418, D5S644, and D5S422), one region in chromosome 6 (around three neighboring markers D6S1281, D6S291, and D6S1019), one region in chromosome 11 (around D11S2362), and two regions in chromosome 12 (around D12S351 and D12S324) especially merit further investigation.

  16. HLA region excluded by linkage analyses of early onset periodontitis

    Energy Technology Data Exchange (ETDEWEB)

    Sun, C.; Wang, S.; Lopez, N.

    1994-09-01

    Previous studies suggested that HLA genes may influence susceptibility to early-onset periodontitis (EOP). Segregation analyses indicate that EOP may be due to a single major gene. We conducted linkage analyses to assess possible HLA effects on EOP. Fifty families with two or more close relatives affected by EOP were ascertained in Virginia and Chile. A microsatellite polymorphism within the HLA region (at the tumor necrosis factor beta locus) was typed using PCR. Linkage analyses used a donimant model most strongly supported by previous studies. Assuming locus homogeneity, our results exclude a susceptibility gene within 10 cM on either side of our marker locus. This encompasses all of the HLA region. Analyses assuming alternative models gave qualitatively similar results. Allowing for locus heterogeneity, our data still provide no support for HLA-region involvement. However, our data do not statistically exclude (LOD <-2.0) hypotheses of disease-locus heterogeneity, including models where up to half of our families could contain an EOP disease gene located in the HLA region. This is due to the limited power of even our relatively large collection of families and the inherent difficulties of mapping genes for disorders that have complex and heterogeneous etiologies. Additional statistical analyses, recruitment of families, and typing of flanking DNA markers are planned to more conclusively address these issues with respect to the HLA region and other candidate locations in the human genome. Additional results for markers covering most of the human genome will also be presented.

  17. Irish study of high-density Schizophrenia families: Field methods and power to detect linkage

    Energy Technology Data Exchange (ETDEWEB)

    Kendler, K.S.; Straub, R.E.; MacLean, C.J. [Virginia Commonwealth Univ., Richmond, VA (United States)] [and others

    1996-04-09

    Large samples of multiplex pedigrees will probably be needed to detect susceptibility loci for schizophrenia by linkage analysis. Standardized ascertainment of such pedigrees from culturally and ethnically homogeneous populations may improve the probability of detection and replication of linkage. The Irish Study of High-Density Schizophrenia Families (ISHDSF) was formed from standardized ascertainment of multiplex schizophrenia families in 39 psychiatric facilities covering over 90% of the population in Ireland and Northern Ireland. We here describe a phenotypic sample and a subset thereof, the linkage sample. Individuals were included in the phenotypic sample if adequate diagnostic information, based on personal interview and/or hospital record, was available. Only individuals with available DNA were included in the linkage sample. Inclusion of a pedigree into the phenotypic sample required at least two first, second, or third degree relatives with non-affective psychosis (NAP), one of whom had schizophrenia (S) or poor-outcome schizoaffective disorder (PO-SAD). Entry into the linkage sample required DNA samples on at least two individuals with NAP, of whom at least one had S or PO-SAD. Affection was defined by narrow, intermediate, and broad criteria. 75 refs., 6 tabs.

  18. Some methods for blindfolded record linkage

    Directory of Open Access Journals (Sweden)

    Christen Peter

    2004-06-01

    Full Text Available Abstract Background The linkage of records which refer to the same entity in separate data collections is a common requirement in public health and biomedical research. Traditionally, record linkage techniques have required that all the identifying data in which links are sought be revealed to at least one party, often a third party. This necessarily invades personal privacy and requires complete trust in the intentions of that party and their ability to maintain security and confidentiality. Dusserre, Quantin, Bouzelat and colleagues have demonstrated that it is possible to use secure one-way hash transformations to carry out follow-up epidemiological studies without any party having to reveal identifying information about any of the subjects – a technique which we refer to as "blindfolded record linkage". A limitation of their method is that only exact comparisons of values are possible, although phonetic encoding of names and other strings can be used to allow for some types of typographical variation and data errors. Methods A method is described which permits the calculation of a general similarity measure, the n-gram score, without having to reveal the data being compared, albeit at some cost in computation and data communication. This method can be combined with public key cryptography and automatic estimation of linkage model parameters to create an overall system for blindfolded record linkage. Results The system described offers good protection against misdeeds or security failures by any one party, but remains vulnerable to collusion between or simultaneous compromise of two or more parties involved in the linkage operation. In order to reduce the likelihood of this, the use of last-minute allocation of tasks to substitutable servers is proposed. Proof-of-concept computer programmes written in the Python programming language are provided to illustrate the similarity comparison protocol. Conclusion Although the protocols described in

  19. The ties that bind: interorganizational linkages and physician-system alignment.

    Science.gov (United States)

    Alexander, J A; Waters, T M; Burns, L R; Shortell, S M; Gillies, R R; Budetti, P P; Zuckerman, H S

    2001-07-01

    To examine the association between the degree of alignment between physicians and health care systems, and interorganizational linkages between physician groups and health care systems. The study used a cross sectional, comparative analysis using a sample of 1,279 physicians practicing in loosely affiliated arrangements and 1,781 physicians in 61 groups closely affiliated with 14 vertically integrated health systems. Measures of physician alignment were based on multiitem scales validated in previous studies and derived from surveys sent to individual physicians. Measures of interorganizational linkages were specified at the institutional, administrative, and technical core levels of the physician group and were developed from surveys sent to the administrator of each of the 61 physician groups in the sample. Two stage Heckman models with fixed effects adjustments in the second stage were used to correct for sample selection and clustering respectively. After accounting for sample selection, fixed effects, and group and individual controls, physicians in groups with more valued practice service linkages display consistently higher alignment with systems than physicians in groups that have fewer such linkages. Results also suggest that centralized administrative control lowers physician-system alignment for selected measures of alignment. Governance interlocks exhibited only weak associations with alignment. Our findings suggest that alignment generally follows resource exchanges that promote value-added contributions to physicians and physician groups while preserving control and authority within the group.

  20. Branched polynomial covering maps

    DEFF Research Database (Denmark)

    Hansen, Vagn Lundsgaard

    1999-01-01

    A Weierstrass polynomial with multiple roots in certain points leads to a branched covering map. With this as the guiding example, we formally define and study the notion of a branched polynomial covering map. We shall prove that many finite covering maps are polynomial outside a discrete branch...... set. Particular studies are made of branched polynomial covering maps arising from Riemann surfaces and from knots in the 3-sphere....

  1. A Targeted Capture Linkage Map Anchors the Genome of the Schistosomiasis Vector Snail, Biomphalaria glabrata.

    Science.gov (United States)

    Tennessen, Jacob A; Bollmann, Stephanie R; Blouin, Michael S

    2017-07-05

    The aquatic planorbid snail Biomphalaria glabrata is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here, we used targeted capture markers to map over 10,000 B. glabrata scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups (LGs). We added additional scaffolds to these LGs based on linkage disequilibrium (LD) analysis of targeted capture and whole-genome sequences of 96 unrelated snails. Our final linkage map consists of 18,613 scaffolds comprising 515 Mb, representing 56% of the genome and 75% of genic and nonrepetitive regions. There are 18 large (> 10 Mb) LGs, likely representing the expected 18 haploid chromosomes, and > 50% of the genome has been assigned to LGs of at least 17 Mb. Comparisons with other gastropod genomes reveal patterns of synteny and chromosomal rearrangements. Linkage relationships of key immune-relevant genes may help clarify snail-schistosome interactions. By focusing on linkage among genic and nonrepetitive regions, we have generated a useful resource for associating snail phenotypes with causal genes, even in the absence of a complete genome assembly. A similar approach could potentially improve numerous poorly-assembled genomes in other taxa. This map will facilitate future work on this host of a serious human parasite. Copyright © 2017 Tennessen et al.

  2. Linkage Maps of a Mediterranean × Continental Tall Fescue Population and their Comparative Analysis with Other Poaceae Species

    Directory of Open Access Journals (Sweden)

    Ryan Dierking

    2015-03-01

    Full Text Available Temperate grasses belonging to the complex are important throughout the world in pasture and grassland agriculture. Tall fescue ( Schreb. is the predominant species in the United States, covering approximately 15 million ha. Tall fescue has distinctive morphotypes, two of which are Continental (summer active and Mediterranean (summer semidormant. This is the first report of a linkage map created for Mediterranean tall fescue, while updating the Continental map with additional simple sequence repeat and sequence-tagged site markers. Additionally, this is the first time that diversity arrays technology (DArT markers were used in the construction of a tall fescue map. The male parent (Continental, R43-64, map consisted of 594 markers arranged in 22 linkage groups (LGs and covered a total of 1577 cM. The female parent (Mediterranean, 103-2, map was shorter (1258 cM and consisted of only 208 markers arranged in 29 LGs. Marker densities for R43-64 and 103-2 were 2.65 and 6.08 cM per marker, respectively. When compared with the other Poaceae species, meadow fescue ( Huds., annual ryegrass ( Lam., perennial ryegrass ( L., (L. Beauv., and barley ( L., a total of 171 and 98 orthologous or homologous sequences, identified by DArT analysis, were identified in R43-64 and 103-2, respectively. By using genomic in situ hybridization, we aimed to identify potential progenitors of both morphotypes. However, no clear conclusion on genomic constitution was reached. These maps will aid in the search for quantitative trait loci of various traits as well as help define and distinguish genetic differences between the two morphotypes.

  3. Linkage disequilibrium and association mapping of drought ...

    African Journals Online (AJOL)

    Drought stress is a major abiotic stress that limits crop production. Molecular association mapping techniques through linkage disequilibrium (LD) can be effectively used to tag genomic regions involved in drought stress tolerance. With the association mapping approach, 90 genotypes of cotton Gossypium hirsutum, from ...

  4. principles, realities and challenges regarding institutional linkages ...

    African Journals Online (AJOL)

    p2333147

    (2) Compromise between proximity to community and effective coordination. If organisational linkage structures are to facilitate effective participation and ownership, it stands to reason that they should be as close to the grassroots community as possible. Unless community members regard such organisational structures as.

  5. Branched polynomial covering maps

    DEFF Research Database (Denmark)

    Hansen, Vagn Lundsgaard

    2002-01-01

    A Weierstrass polynomial with multiple roots in certain points leads to a branched covering map. With this as the guiding example, we formally define and study the notion of a branched polynomial covering map. We shall prove that many finite covering maps are polynomial outside a discrete branch ...... set. Particular studies are made of branched polynomial covering maps arising from Riemann surfaces and from knots in the 3-sphere. (C) 2001 Elsevier Science B.V. All rights reserved.......A Weierstrass polynomial with multiple roots in certain points leads to a branched covering map. With this as the guiding example, we formally define and study the notion of a branched polynomial covering map. We shall prove that many finite covering maps are polynomial outside a discrete branch...

  6. Landfill Top Covers

    DEFF Research Database (Denmark)

    Scheutz, Charlotte; Kjeldsen, Peter

    2011-01-01

    The purpose of the final cover of a landfill is to contain the waste and to provide for a physical separation between the waste and the environment for protection of public health. Most landfill covers are designed with the primary goal to reduce or prevent infiltration of precipitation...... into the landfill in order to minimize leachate generation. In addition the cover also has to control the release of gases produced in the landfill so the gas can be ventilated, collected and utilized, or oxidized in situ. The landfill cover should also minimize erosion and support vegetation. Finally the cover...... is landscaped in order to fit into the surrounding area/environment or meet specific plans for the final use of the landfill. To fulfill the above listed requirements landfill covers are often multicomponent systems which are placed directly on top of the waste. The top cover may be placed immediately after...

  7. Construction of a reference molecular linkage map of globe artichoke (Cynara cardunculus var. scolymus).

    Science.gov (United States)

    Portis, E; Mauromicale, G; Mauro, R; Acquadro, A; Scaglione, D; Lanteri, S

    2009-12-01

    The genome organization of globe artichoke (Cynara cardunculus var. scolymus), unlike other species belonging to Asteraceae (=Compositae) family (i.e. sunflower, lettuce and chicory), remains largely unexplored. The species is highly heterozygous and suffers marked inbreeding depression when forced to self-fertilize. Thus a two-way pseudo-testcross represents the optimal strategy for linkage analysis. Here, we report linkage maps based on the progeny of a cross between globe artichoke (C. cardunculus var. scolymus) and cultivated cardoon (C. cardunculus var. altilis). The population was genotyped using a variety of PCR-based marker platforms, resulting in the identification of 708 testcross markers suitable for map construction. The male map consisted of 177 loci arranged in 17 major linkage groups, spanning 1,015.5 cM, while female map was built with 326 loci arranged into 20 major linkage groups, spanning 1,486.8 cM. The presence of 84 loci shared between these maps and those previously developed from a cross within globe artichoke allowed for map alignment and the definition of 17 homologous linkage groups, corresponding to the haploid number of the species. This will provide a favourable property for QTL scanning; furthermore, as 25 mapped markers (8%) correspond to coding regions, it has an additional value as functional map and might represent an important genetic tool for candidate gene studies in globe artichoke.

  8. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers.

    Science.gov (United States)

    de Miguel, Marina; de Maria, Nuria; Guevara, M Angeles; Diaz, Luis; Sáez-Laguna, Enrique; Sánchez-Gómez, David; Chancerel, Emilie; Aranda, Ismael; Collada, Carmen; Plomion, Christophe; Cabezas, José-Antonio; Cervera, María-Teresa

    2012-10-04

    Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

  9. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

    Directory of Open Access Journals (Sweden)

    de Miguel Marina

    2012-10-01

    Full Text Available Abstract Background Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15 belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. Results We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. Conclusions This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

  10. Quantization of noncompact coverings and its physical applications

    Science.gov (United States)

    Ivankov, Petr

    2018-02-01

    A rigorous algebraic definition of noncommutative coverings is developed. In the case of commutative algebras this definition is equivalent to the classical definition of topological coverings of locally compact spaces. The theory has following nontrivial applications: • Coverings of continuous trace algebras, • Coverings of noncommutative tori, • Coverings of the quantum SU(2) group, • Coverings of foliations, • Coverings of isospectral deformations of Spin - manifolds. The theory supplies the rigorous definition of noncommutative Wilson lines.

  11. Armored Geomembrane Cover Engineering

    Directory of Open Access Journals (Sweden)

    Kevin Foye

    2011-06-01

    Full Text Available Geomembranes are an important component of modern engineered barriers to prevent the infiltration of stormwater and runoff into contaminated soil and rock as well as waste containment facilities—a function generally described as a geomembrane cover. This paper presents a case history involving a novel implementation of a geomembrane cover system. Due to this novelty, the design engineers needed to assemble from disparate sources the design criteria for the engineering of the cover. This paper discusses the design methodologies assembled by the engineering team. This information will aid engineers designing similar cover systems as well as environmental and public health professionals selecting site improvements that involve infiltration barriers.

  12. Percent Forest Cover (Future)

    Data.gov (United States)

    U.S. Environmental Protection Agency — Forests provide economic and ecological value. High percentages of forest cover (FORPCTFuture) generally indicate healthier ecosystems and cleaner surface water....

  13. Percent Forest Cover

    Data.gov (United States)

    U.S. Environmental Protection Agency — Forests provide economic and ecological value. High percentages of forest cover (FORPCT) generally indicate healthier ecosystems and cleaner surface water. More...

  14. Linkages from DOE’s Vehicle Technologies R&D in Advanced Combustion to More Efficient, Cleaner-Burning Engines

    Energy Technology Data Exchange (ETDEWEB)

    Ruegg, Rosalie [TIA Consulting Inc., Emerald Isle, NC (United States); Thomas, Patrick [1790 Analytics LLC., Haddonfield, NC (United States)

    2011-06-01

    This report uses bibliometric analysis, supported by interview and review of documents and databases, to trace linkages from knowledge outputs resulting from DOE's advances in vehicle engine combustion to downstream innovations in commercial diesel engines and other areas. This analysis covers the period from 1974 through 2008 (and in some cases to early 2009).

  15. Availability of Insurance Linkage Programs in U.S. Emergency Departments

    Directory of Open Access Journals (Sweden)

    Mia Kanak

    2014-07-01

    Full Text Available Introduction: As millions of uninsured citizens who use emergency department (ED services are now eligible for health insurance under the Affordable Care Act, the ED is ideally situated to facilitate linkage to insurance. Forty percent of U.S. EDs report having an insurance linkage program. This is the first national study to examine the characteristics of EDs that offer or do not offer these programs. Methods: This was a secondary analysis of data from the National Survey for Preventive Health Services in U.S. EDs conducted in 2008-09. We compared EDs with and without insurance programs across demographic and operational factors using univariate analysis. We then tested our hypotheses using multivariable logistic regression. We also further examined program capacity and priority among the sub-group of EDs with no insurance linkage program. Results: After adjustment, ED-insurance linkage programs were more likely to be located in the West (RR= 2.06, 95% CI = 1.33 – 2.72. The proportion of uninsured patients in an ED, teaching hospital status, and public ownership status were not associated with insurance linkage availability. EDs with linkage programs also offer more preventive services (RR = 1.87, 95% CI = 1.37–2.35 and have greater social worker availability (RR = 1.71, 95% CI = 1.12–2.33 than those who do not. Four of five EDs with a patient mix of ≥25% uninsured and no insurance linkage program reported that they could not offer a program with existing staff and funding. Conclusion: Availability of insurance linkage programs in the ED is not associated with the proportion of uninsured patients served by an ED. Policy or hospital-based interventions to increase insurance linkage should first target the 27% of EDs with high rates of uninsured patients that lack adequate program capacity. Further research on barriers to implementation and cost effectiveness may help to facilitate increased adoption of insurance linkage programs. [West J

  16. Braids and coverings selected topics

    CERN Document Server

    Hansen, Vagn Lundsgaard

    1989-01-01

    This book is based on a graduate course taught by the author at the University of Maryland, USA. The lecture notes have been revised and augmented by examples. The work falls into two strands. The first two chapters develop the elementary theory of Artin Braid groups both geometrically and via homotopy theory, and discuss the link between knot theory and the combinatorics of braid groups through Markov's Theorem. The final two chapters give a detailed investigation of polynomial covering maps, which may be viewed as a homomorphism of the fundamental group of the base space into the Artin braid

  17. Silicone covered vs. Non- covered endotracheal self expandable metallic stent: An experimental study

    Energy Technology Data Exchange (ETDEWEB)

    Do, Young Soo; Lee, Byung Hee; Kim, Soo Ah; Kim, Kie Hwan; Chin, Soo Yil; Cho, Kyung Ja; Cho, Dae Soon [Korea Cancer Center Hospital, Seoul (Korea, Republic of)

    1994-10-15

    To evaluate pathologic changes of the trachea and the lung after insertion of silicone covered and non covered Gianturco stent in the trachea of dog. Silicone covered(covered) and non covered(bare) Gianturco stent, six in each, were inserted into the tracheal lumen of six consecutive dogs. After 1-10 weeks observation, the dogs were sacrificed and their tracheas and lungs were examined grossly and histopathologically. Serial chest radiographs were performed to evaluate pneumonia and stent migration every 3-5 days. Pneumonia was observed in one of bare stent group and five of covered stent group. Stent migration was noted in three of covered stent group. In bare stent group, the epithelium of the trachea was markedly thickened by hyperplasia and stent was covered by granulation tissue from 6 weeks after stent insertion. Inflammation was focal at contact site between the stent and the trachea. In covered stent group, the epithelium was denuded at multiple areas and there were multifocal squamous metaplasia of the mucosa. Inflammatory reaction of the trachea was diffuse. Inflammatory reaction was more severe and stent migration was more frequent in covered stent group. The use of covered stent in the trachea should be studied further.

  18. Covered Bridge Security Manual

    Science.gov (United States)

    Brett Phares; Terry Wipf; Ryan Sievers; Travis Hosteng

    2013-01-01

    The design, construction, and use of covered timber bridges is all but a lost art in these days of pre-stressed concrete, high-performance steel, and the significant growth both in the volume and size of vehicles. Furthermore, many of the existing covered timber bridges are preserved only because of their status on the National Registry of Historic Places or the...

  19. Kempe's Linkages and the Universality Theorem

    Indian Academy of Sciences (India)

    sriranga

    that between BO and OA (i.e., \\BOA). Let these two angles be denoted by µ. Thus, if link OA makes an angle. µ with link OB, OE makes the same angle on the other side of OB. Kempe therefore referred to this linkage as the (angle) reversor. This is true irrespective of how OA and OB are placed relative to each other. Also ...

  20. Methods for genetic linkage analysis using trisomies.

    OpenAIRE

    Feingold, E; Lamb, N E; Sherman, S L

    1995-01-01

    Certain genetic disorders are rare in the general population, but more common in individuals with specific trisomies. Examples of this include leukemia and duodenal atresia in trisomy 21. This paper presents a linkage analysis method for using trisomic individuals to map genes for such traits. It is based on a very general gene-specific dosage model that posits that the trait is caused by specific effects of different alleles at one or a few loci and that duplicate copies of "susceptibility" ...

  1. Hidden linkages between urbanization and food systems.

    Science.gov (United States)

    Seto, Karen C; Ramankutty, Navin

    2016-05-20

    Global societies are becoming increasingly urban. This shift toward urban living is changing our relationship with food, including how we shop and what we buy, as well as ideas about sanitation and freshness. Achieving food security in an era of rapid urbanization will require considerably more understanding about how urban and food systems are intertwined. Here we discuss some potential understudied linkages that are ripe for further examination. Copyright © 2016, American Association for the Advancement of Science.

  2. 'Linkage' pharmaceutical evergreening in Canada and Australia

    Science.gov (United States)

    Faunce, Thomas A; Lexchin, Joel

    2007-01-01

    'Evergreening' is not a formal concept of patent law. It is best understood as a social idea used to refer to the myriad ways in which pharmaceutical patent owners utilise the law and related regulatory processes to extend their high rent-earning intellectual monopoly privileges, particularly over highly profitable (either in total sales volume or price per unit) 'blockbuster' drugs. Thus, while the courts are an instrument frequently used by pharmaceutical brand name manufacturers to prolong their patent royalties, 'evergreening' is rarely mentioned explicitly by judges in patent protection cases. The term usually refers to threats made to competitors about a brand-name manufacturer's tactical use of pharmaceutical patents (including over uses, delivery systems and even packaging), not to extension of any particular patent over an active product ingredient. This article focuses in particular on the 'evergreening' potential of so-called 'linkage' provisions, imposed on the regulatory (safety, quality and efficacy) approval systems for generic pharmaceuticals of Canada and Australia, by specific articles in trade agreements with the US. These 'linkage' provisions have also recently appeared in the Korea-US Free Trade Agreement (KORUSFTA). They require such drug regulators to facilitate notification of, or even prevent, any potential patent infringement by a generic pharmaceutical manufacturer. This article explores the regulatory lessons to be learnt from Canada's and Australia's shared experience in terms of minimizing potential adverse impacts of such 'linkage evergreening' provisions on drug costs and thereby potentially on citizen's access to affordable, essential medicines. PMID:17543113

  3. Production Cells in Construction: Considering Time, Space and Information Linkages to Seek Broader Implementations

    Directory of Open Access Journals (Sweden)

    Renato Nunes Mariz

    2013-01-01

    Full Text Available The use of production cells in manufacturing has achieved many benefits, motivating researchers to apply them in the construction environment. The aim of this research is to identify time, space, and information linkages in construction’s production cells applications, seeking opportunities for broader implementations. We adopted a literature review approach focusing on cases in the Brazilian construction sector that addressed cell applications. Subsequently, comparative tables of these publications were prepared, analyzing the consideration of time, space, and information linkages, as well as identified results. The article pointed out that there is a gap in publications that address the application of a production cell in almost all construction flows, except the job site flow, reflecting the tendency of most companies of applying lean concepts firstly in physical flows. By analyzing these aspects (group of features that enhance the use of the cell, it was found that “material flow and pull systems” and “operators interaction” were the aspects most often considered, but mostly partially. Few cases reported the use of “flexibility” and “equipment maintenance”. No case reported comprehensive considerations of the three important linkages of time, space, and information. Space was the linkage better considered compared to time and information linkages. Lead time reduction, cost savings and increased productivity were among the greatest benefits reported from the applications of production cells. There is also a positive correlation between the linkages coverage and the number of benefits obtained. Further research is suggested in order to investigate the results of a more comprehensive application considering all linkages.

  4. Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage Maps

    Science.gov (United States)

    Gosselin, Thierry; Normandeau, Eric; Lamothe, Manuel; Isabel, Nathalie; Audet, Céline; Bernatchez, Louis

    2016-01-01

    Whole genome duplication (WGD) can provide material for evolutionary innovation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, ∼65 Ma, then rediploidized and diversified. Extensive synteny between homologous chromosome arms occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for nonmodel species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Here, we generate a high-density linkage map (3,826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify corresponding chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus, and one species for each of Salmo, Coregonus, and the nonduplicated sister group for the salmonids, Northern Pike Esox lucius for identifying post-duplicated homeologs. To facilitate this process, we developed MapComp to identify identical and proximate (i.e. nearby) markers between linkage maps using a reference genome of a related species as an intermediate, increasing the number of comparable markers between linkage maps by 5-fold. This enabled a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/ PMID:28173098

  5. A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae

    Directory of Open Access Journals (Sweden)

    Kakioka Ryo

    2013-01-01

    Full Text Available Abstract Background The construction of linkage maps is a first step in exploring the genetic basis for adaptive phenotypic divergence in closely related species by quantitative trait locus (QTL analysis. Linkage maps are also useful for comparative genomics in non-model organisms. Advances in genomics technologies make it more feasible than ever to study the genetics of adaptation in natural populations. Restriction-site associated DNA (RAD sequencing in next-generation sequencers facilitates the development of many genetic markers and genotyping. We aimed to construct a linkage map of the gudgeons of the genus Gnathopogon (Cyprinidae for comparative genomics with the zebrafish Danio rerio (a member of the same family as gudgeons and for the future QTL analysis of the genetic architecture underlying adaptive phenotypic evolution of Gnathopogon. Results We constructed the first genetic linkage map of Gnathopogon using a 198 F2 interspecific cross between two closely related species in Japan: river-dwelling Gnathopogon elongatus and lake-dwelling Gnathopogon caerulescens. Based on 1,622 RAD-tag markers, a linkage map spanning 1,390.9 cM with 25 linkage groups and an average marker interval of 0.87 cM was constructed. We also identified a region involving female-specific transmission ratio distortion (TRD. Synteny and collinearity were extensively conserved between Gnathopogon and zebrafish. Conclusions The dense SNP-based linkage map presented here provides a basis for future QTL analysis. It will also be useful for transferring genomic information from a “traditional” model fish species, zebrafish, to screen candidate genes underlying ecologically important traits of the gudgeons.

  6. Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean.

    Science.gov (United States)

    Galeano, Carlos H; Fernandez, Andrea C; Franco-Herrera, Natalia; Cichy, Karen A; McClean, Phillip E; Vanderleyden, Jos; Blair, Matthew W

    2011-01-01

    Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364 × BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364 × G19833 (DG) and BAT93 × JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning.

  7. Extreme drought decouples silicon and carbon geochemical linkages in lakes.

    Science.gov (United States)

    Li, Tianyang; Li, Siyue; Bush, Richard T; Liang, Chuan

    2018-09-01

    Silicon and carbon geochemical linkages were usually regulated by chemical weathering and organism activity, but had not been investigated under the drought condition, and the magnitude and extent of drought effects remain poorly understood. We collected a comprehensive data set from a total of 13 sampling sites covering the main water body of the largest freshwater lake system in Australia, the Lower Lakes. Changes to water quality during drought (April 2008-September 2010) and post-drought (October 2010-October 2013) were compared to reveal the effects of drought on dissolved silica (DSi) and bicarbonate (HCO 3 - ) and other environmental factors, including sodium (Na + ), pH, electrical conductivity (EC), chlorophyll a (Chl-a), total dissolved solids (TDS), dissolved inorganic nitrogen (DIN), total nitrogen (TN), total phosphorus (TP) and water levels. Among the key observations, concentrations of DSi and DIN were markedly lower in drought than in post-drought period while pH, EC and concentrations of HCO 3 - , Na + , Chl-a, TDS, TN, TP and the ratio TN:TP had inverse trends. Stoichiometric ratios of DSi:HCO 3 - , DSi:Na + and HCO 3 - :Na + were significantly lower in the drought period. DSi exhibited significantly negative relationships with HCO 3 - , and DSi:Na + was strongly correlated with HCO 3 - :Na + in both drought and post-drought periods. The backward stepwise regression analysis that could avoid multicollinearity suggested that DSi:HCO 3 - ratio in drought period had significant relationships with fewer variables when compared to the post-drought, and was better predictable using nutrient variables during post-drought. Our results highlight the drought effects on variations of water constituents and point to the decoupling of silicon and carbon geochemical linkages in the Lower Lakes under drought conditions. Copyright © 2018 Elsevier B.V. All rights reserved.

  8. The score statistic of the LD-lod analysis: detecting linkage adaptive to linkage disequilibrium.

    Science.gov (United States)

    Huang, J; Jiang, Y

    2001-01-01

    We study the properties of a modified lod score method for testing linkage that incorporates linkage disequilibrium (LD-lod). By examination of its score statistic, we show that the LD-lod score method adaptively combines two sources of information: (a) the IBD sharing score which is informative for linkage regardless of the existence of LD and (b) the contrast between allele-specific IBD sharing scores which is informative for linkage only in the presence of LD. We also consider the connection between the LD-lod score method and the transmission-disequilibrium test (TDT) for triad data and the mean test for affected sib pair (ASP) data. We show that, for triad data, the recessive LD-lod test is asymptotically equivalent to the TDT; and for ASP data, it is an adaptive combination of the TDT and the ASP mean test. We demonstrate that the LD-lod score method has relatively good statistical efficiency in comparison with the ASP mean test and the TDT for a broad range of LD and the genetic models considered in this report. Therefore, the LD-lod score method is an interesting approach for detecting linkage when the extent of LD is unknown, such as in a genome-wide screen with a dense set of genetic markers. Copyright 2001 S. Karger AG, Basel

  9. Covering folded shapes

    Directory of Open Access Journals (Sweden)

    Oswin Aichholzer

    2014-05-01

    Full Text Available Can folding a piece of paper flat make it larger? We explore whether a shape S must be scaled to cover a flat-folded copy of itself. We consider both single folds and arbitrary folds (continuous piecewise isometries \\(S\\to\\mathbb{R}^2\\. The underlying problem is motivated by computational origami, and is related to other covering and fixturing problems, such as Lebesgue's universal cover problem and force closure grasps. In addition to considering special shapes (squares, equilateral triangles, polygons and disks, we give upper and lower bounds on scale factors for single folds of convex objects and arbitrary folds of simply connected objects.

  10. Condition of the centers of linkage of serum albumin in cancer gynecological patients at beam therapy

    International Nuclear Information System (INIS)

    Malenchenko, A.F.; Belyakovskij, V.N.; Lukovskaya, N.D.; Prigozhaya, T.I.; Stasenkova, S.V.

    2009-01-01

    With the use of the method of fluorescent probes the condition of the centers of linkage of serum albumin in healthy women and in the cancer patients, passing a course of beam therapy, is analyzed at different modes. It is shown that general concentration of albumin in healthy persons and cancer patients are in the limits of normal values, however parameters of effective concentration of albumin, reserve of albumin linkage and toxicity index of patients statistically, for certain, differ in comparison with those in the control group. Carrying out the beam therapy course both split and not split promotes an increase of values of toxicity index. (authors)

  11. Evapotranspiration (ET) covers.

    Science.gov (United States)

    Rock, Steve; Myers, Bill; Fiedler, Linda

    2012-01-01

    Evapotranspiration (ET) cover systems are increasingly being used at municipal solid waste (MSW) landfills, hazardous waste landfills, at industrial monofills, and at mine sites. Conventional cover systems use materials with low hydraulic permeability (barrier layers) to minimize the downward migration of water from the surface to the waste (percolation), ET cover systems use water balance components to minimize percolation. These cover systems rely on soil to capture and store precipitation until it is either transpired through vegetation or evaporated from the soil surface. Compared to conventional membrane or compacted clay cover systems, ET cover systems are expected to cost less to construct. They are often aesthetic because they employ naturalized vegetation, require less maintenance once the vegetative system is established, including eliminating mowing, and may require fewer repairs than a barrier system. All cover systems should consider the goals of the cover in terms of protectiveness, including the pathways of risk from contained material, the lifecycle of the containment system. The containment system needs to be protective of direct contact of people and animals with the waste, prevent surface and groundwater water pollution, and minimize release of airborne contaminants. While most containment strategies have been based on the dry tomb strategy of keeping waste dry, there are some sites where adding or allowing moisture to help decompose organic waste is the current plan. ET covers may work well in places where complete exclusion of precipitation is not needed. The U.S. EPA Alternative Cover Assessment Program (ACAP), USDOE, the Nuclear Regulatory Commission, and others have researched ET cover design and efficacy, including the history of their use, general considerations in their design, performance, monitoring, cost, current status, limitations on their use, and project specific examples. An on-line database has been developed with information

  12. Linkage isomerism in trimeric and polymeric 2,3-cis-procyanindins

    Science.gov (United States)

    Richard W. Hemingway; Lai Yeap Foo; Lawrence J. Porter

    1982-01-01

    Procyanindins polymers consist of chains of 5,7,3',4'-tetrahydroxyflavan-3-ol units linked by C(4)-C(6) or C(4)-C(8) bonds.1 Whereas the procyanidin-B group of dimers are known to exist as pairs of isomers with common flavan-3-ol units, but different interflavanoid linkages,2,3 the extent of such isomerism in...

  13. African American church-based HIV testing and linkage to care: assets, challenges and needs.

    Science.gov (United States)

    Stewart, Jennifer M; Thompson, Keitra; Rogers, Christopher

    2016-01-01

    The US National HIV AIDS strategy promotes the use of faith communities to lessen the burden of HIV in African American communities. One specific strategy presented is the use of these non-traditional venues for HIV testing and co-location of services. African American churches can be at the forefront of this endeavour through the provision of HIV testing and linkage to care. However, there are few interventions to promote the churches' involvement in both HIV testing and linkage to care. We conducted 4 focus groups (n = 39 participants), 4 interviews and 116 surveys in a mixed-methods study to examine the feasibility of a church-based HIV testing and linkage to care intervention in Philadelphia, PA, USA. Our objectives were to examine: (1) available assets, (2) challenges and barriers and (3) needs associated with church-based HIV testing and linkage to care. Analyses revealed several factors of importance, including the role of the church as an access point for testing in low-income neighbourhoods, challenges in openly discussing the relationship between sexuality and HIV, and buy-in among church leadership. These findings can support intervention development and necessitate situating African American church-based HIV testing and linkage to care interventions within a multi-level framework.

  14. Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.).

    Science.gov (United States)

    Cadic, Elena; Coque, Marie; Vear, Felicity; Grezes-Besset, Bruno; Pauquet, Jerôme; Piquemal, Joël; Lippi, Yannick; Blanchard, Philippe; Romestant, Michel; Pouilly, Nicolas; Rengel, David; Gouzy, Jerôme; Langlade, Nicolas; Mangin, Brigitte; Vincourt, Patrick

    2013-05-01

    Association mapping and linkage mapping were used to identify quantitative trait loci (QTL) and/or causative mutations involved in the control of flowering time in cultivated sunflower Helianthus annuus. A panel of 384 inbred lines was phenotyped through testcrosses with two tester inbred lines across 15 location × year combinations. A recombinant inbred line (RIL) population comprising 273 lines was phenotyped both per se and through testcrosses with one or two testers in 16 location × year combinations. In the association mapping approach, kinship estimation using 5,923 single nucleotide polymorphisms was found to be the best covariate to correct for effects of panel structure. Linkage disequilibrium decay ranged from 0.08 to 0.26 cM for a threshold of 0.20, after correcting for structure effects, depending on the linkage group (LG) and the ancestry of inbred lines. A possible hitchhiking effect is hypothesized for LG10 and LG08. A total of 11 regions across 10 LGs were found to be associated with flowering time, and QTLs were mapped on 11 LGs in the RIL population. Whereas eight regions were demonstrated to be common between the two approaches, the linkage disequilibrium approach did not detect a documented QTL that was confirmed using the linkage mapping approach.

  15. Linkage Map of Lissotriton Newts Provides Insight into the Genetic Basis of Reproductive Isolation

    Directory of Open Access Journals (Sweden)

    Marta Niedzicka

    2017-07-01

    Full Text Available Linkage maps are widely used to investigate structure, function, and evolution of genomes. In speciation research, maps facilitate the study of the genetic architecture of reproductive isolation by allowing identification of genomic regions underlying reduced fitness of hybrids. Here we present a linkage map for European newts of the Lissotriton vulgaris species complex, constructed using two families of F2 L. montandoni × L. vulgaris hybrids. The map consists of 1146 protein-coding genes on 12 linkage groups, equal to the haploid chromosome number, with a total length of 1484 cM (1.29 cM per marker. It is notably shorter than two other maps available for salamanders, but the differences in map length are consistent with cytogenetic estimates of the number of chiasmata per chromosomal arm. Thus, large salamander genomes do not necessarily translate into long linkage maps, as previously suggested. Consequently, salamanders are an excellent model to study evolutionary consequences of recombination rate variation in taxa with large genomes and a similar number of chromosomes. A complex pattern of transmission ratio distortion (TRD was detected: TRD occurred mostly in one family, in one breeding season, and was clustered in two genomic segments. This is consistent with environment-dependent mortality of individuals carrying L. montandoni alleles in these two segments and suggests a role of TRD blocks in reproductive isolation. The reported linkage map will empower studies on the genomic architecture of divergence and interactions between the genomes of hybridizing newts.

  16. Mekong Land Cover Dasboard: Regional Land Cover Mointoring Systems

    Science.gov (United States)

    Saah, D. S.; Towashiraporn, P.; Aekakkararungroj, A.; Phongsapan, K.; Triepke, J.; Maus, P.; Tenneson, K.; Cutter, P. G.; Ganz, D.; Anderson, E.

    2016-12-01

    SERVIR-Mekong, a USAID-NASA partnership, helps decision makers in the Lower Mekong Region utilize GIS and Remote Sensing information to inform climate related activities. In 2015, SERVIR-Mekong conducted a geospatial needs assessment for the Lower Mekong countries which included individual country consultations. The team found that many countries were dependent on land cover and land use maps for land resource planning, quantifying ecosystem services, including resilience to climate change, biodiversity conservation, and other critical social issues. Many of the Lower Mekong countries have developed national scale land cover maps derived in part from remote sensing products and geospatial technologies. However, updates are infrequent and classification systems do not always meet the needs of key user groups. In addition, data products stop at political boundaries and are often not accessible making the data unusable across country boundaries and with resource management partners. Many of these countries rely on global land cover products to fill the gaps of their national efforts, compromising consistency between data and policies. These gaps in national efforts can be filled by a flexible regional land cover monitoring system that is co-developed by regional partners with the specific intention of meeting national transboundary needs, for example including consistent forest definitions in transboundary watersheds. Based on these facts, key regional stakeholders identified a need for a land cover monitoring system that will produce frequent, high quality land cover maps using a consistent regional classification scheme that is compatible with national country needs. SERVIR-Mekong is currently developing a solution that leverages recent developments in remote sensing science and technology, such as Google Earth Engine (GEE), and working together with production partners to develop a system that will use a common set of input data sources to generate high

  17. Fine mapping quantitative trait loci under selective phenotyping strategies based on linkage and linkage disequilibrium criteria

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P; Lund, M S

    2009-01-01

    disequilibrium-based sampling criteria (LDC) for selecting individuals to phenotype are compared to random phenotyping in a quantitative trait loci (QTL) verification experiment using stochastic simulation. Several strategies based on LAC and LDC for selecting the most informative 30%, 40% or 50% of individuals...... for phenotyping to extract maximum power and precision in a QTL fine mapping experiment were developed and assessed. Linkage analyses for the mapping was performed for individuals sampled on LAC within families and combined linkage disequilibrium and linkage analyses was performed for individuals sampled across...... the whole population based on LDC. The results showed that selecting individuals with similar haplotypes to the paternal haplotypes (minimum recombination criterion) using LAC compared to random phenotyping gave at least the same power to detect a QTL but decreased the accuracy of the QTL position. However...

  18. Percent of Impervious Cover

    Data.gov (United States)

    U.S. Environmental Protection Agency — High amounts of impervious cover (parking lots, rooftops, roads, etc.) can increase water runoff, which may directly enter surface water. Runoff from roads often...

  19. GAP Land Cover - Image

    Data.gov (United States)

    Minnesota Department of Natural Resources — This raster dataset is a simple image of the original detailed (1-acre minimum), hierarchically organized vegetation cover map produced by computer classification of...

  20. GAP Land Cover - Vector

    Data.gov (United States)

    Minnesota Department of Natural Resources — This vector dataset is a detailed (1-acre minimum), hierarchically organized vegetation cover map produced by computer classification of combined two-season pairs of...

  1. Percent Wetland Cover

    Data.gov (United States)

    U.S. Environmental Protection Agency — Wetlands act as filters, removing or diminishing the amount of pollutants that enter surface water. Higher values for percent of wetland cover (WETLNDSPCT) may be...

  2. Percent Wetland Cover (Future)

    Data.gov (United States)

    U.S. Environmental Protection Agency — Wetlands act as filters, removing or diminishing the amount of pollutants that enter surface water. Higher values for percent of wetland cover (WETLNDSPCT) may be...

  3. A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii

    Directory of Open Access Journals (Sweden)

    Patel Hardip R

    2011-08-01

    Full Text Available Abstract Background The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species. Results A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH, (b End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers to all seven autosomes and the X chromosome. The sex-pooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map. Conclusions Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby

  4. A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii).

    Science.gov (United States)

    Wang, Chenwei; Webley, Lee; Wei, Ke-jun; Wakefield, Matthew J; Patel, Hardip R; Deakin, Janine E; Alsop, Amber; Marshall Graves, Jennifer A; Cooper, Desmond W; Nicholas, Frank W; Zenger, Kyall R

    2011-08-19

    The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species. A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a) sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH), (b) End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c) tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers) to all seven autosomes and the X chromosome. The sex-pooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map. Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby genome and considerably extends that of the first

  5. Theory of Lie groups

    CERN Document Server

    Chevalley, Claude

    2018-01-01

    The standard text on the subject for many years, this introductory treatment covers classical linear groups, topological groups, manifolds, analytic groups, differential calculus of Cartan, and compact Lie groups and their representations. 1946 edition.

  6. Climate under cover

    CERN Document Server

    Takakura, Tadashi

    2002-01-01

    1.1. INTRODUCTION Plastic covering, either framed or floating, is now used worldwide to protect crops from unfavorable growing conditions, such as severe weather and insects and birds. Protected cultivation in the broad sense, including mulching, has been widely spread by the innovation of plastic films. Paper, straw, and glass were the main materials used before the era of plastics. Utilization of plastics in agriculture started in the developed countries and is now spreading to the developing countries. Early utilization of plastic was in cold regions, and plastic was mainly used for protection from the cold. Now plastic is used also for protection from wind, insects and diseases. The use of covering techniques started with a simple system such as mulching, then row covers and small tunnels were developed, and finally plastic houses. Floating mulch was an exception to this sequence: it was introduced rather recently, although it is a simple structure. New development of functional and inexpensive films trig...

  7. A gene-based SNP resource and linkage map for the copepod Tigriopus californicus

    Directory of Open Access Journals (Sweden)

    Foley Brad R

    2011-11-01

    Full Text Available Abstract Background As yet, few genomic resources have been developed in crustaceans. This lack is particularly evident in Copepoda, given the extraordinary numerical abundance, and taxonomic and ecological diversity of this group. Tigriopus californicus is ideally suited to serve as a genetic model copepod and has been the subject of extensive work in environmental stress and reproductive isolation. Accordingly, we set out to develop a broadly-useful panel of genetic markers and to construct a linkage map dense enough for quantitative trait locus detection in an interval mapping framework for T. californicus--a first for copepods. Results One hundred and ninety Single Nucleotide Polymorphisms (SNPs were used to genotype our mapping population of 250 F2 larvae. We were able to construct a linkage map with an average intermarker distance of 1.8 cM, and a maximum intermarker distance of 10.3 cM. All markers were assembled into linkage groups, and the 12 linkage groups corresponded to the 12 known chromosomes of T. californicus. We estimate a total genome size of 401.0 cM, and a total coverage of 73.7%. Seventy five percent of the mapped markers were detected in 9 additional populations of T. californicus. Of available model arthropod genomes, we were able to show more colocalized pairs of homologues between T. californicus and the honeybee Apis mellifera, than expected by chance, suggesting preserved macrosynteny between Hymenoptera and Copepoda. Conclusions Our study provides an abundance of linked markers spanning all chromosomes. Many of these markers are also found in multiple populations of T. californicus, and in two other species in the genus. The genomic resource we have developed will enable mapping throughout the geographical range of this species and in closely related species. This linkage map will facilitate genome sequencing, mapping and assembly in an ecologically and taxonomically interesting group for which genomic resources are

  8. A gene-based SNP resource and linkage map for the copepod Tigriopus californicus

    Science.gov (United States)

    2011-01-01

    Background As yet, few genomic resources have been developed in crustaceans. This lack is particularly evident in Copepoda, given the extraordinary numerical abundance, and taxonomic and ecological diversity of this group. Tigriopus californicus is ideally suited to serve as a genetic model copepod and has been the subject of extensive work in environmental stress and reproductive isolation. Accordingly, we set out to develop a broadly-useful panel of genetic markers and to construct a linkage map dense enough for quantitative trait locus detection in an interval mapping framework for T. californicus--a first for copepods. Results One hundred and ninety Single Nucleotide Polymorphisms (SNPs) were used to genotype our mapping population of 250 F2 larvae. We were able to construct a linkage map with an average intermarker distance of 1.8 cM, and a maximum intermarker distance of 10.3 cM. All markers were assembled into linkage groups, and the 12 linkage groups corresponded to the 12 known chromosomes of T. californicus. We estimate a total genome size of 401.0 cM, and a total coverage of 73.7%. Seventy five percent of the mapped markers were detected in 9 additional populations of T. californicus. Of available model arthropod genomes, we were able to show more colocalized pairs of homologues between T. californicus and the honeybee Apis mellifera, than expected by chance, suggesting preserved macrosynteny between Hymenoptera and Copepoda. Conclusions Our study provides an abundance of linked markers spanning all chromosomes. Many of these markers are also found in multiple populations of T. californicus, and in two other species in the genus. The genomic resource we have developed will enable mapping throughout the geographical range of this species and in closely related species. This linkage map will facilitate genome sequencing, mapping and assembly in an ecologically and taxonomically interesting group for which genomic resources are currently under development

  9. Strike-slip tectonics during rift linkage

    Science.gov (United States)

    Pagli, C.; Yun, S. H.; Ebinger, C.; Keir, D.; Wang, H.

    2017-12-01

    The kinematics of triple junction linkage and the initiation of transforms in magmatic rifts remain debated. Strain patterns from the Afar triple junction provide tests of current models of how rifts grow to link in area of incipient oceanic spreading. Here we present a combined analysis of seismicity, InSAR and GPS derived strain rate maps to reveal that the plate boundary deformation in Afar is accommodated primarily by extensional tectonics in the Red Sea and Gulf of Aden rifts, and does not require large rotations about vertical axes (bookshelf faulting). Additionally, models of stress changes and seismicity induced by recent dykes in one sector of the Afar triple junction provide poor fit to the observed strike-slip earthquakes. Instead we explain these patterns as rift-perpendicular shearing at the tips of spreading rifts where extensional strains terminate against less stretched lithosphere. Our results demonstrate that rift-perpendicular strike-slip faulting between rift segments achieves plate boundary linkage during incipient seafloor spreading.

  10. On Covering Approximation Subspaces

    Directory of Open Access Journals (Sweden)

    Xun Ge

    2009-06-01

    Full Text Available Let (U';C' be a subspace of a covering approximation space (U;C and X⊂U'. In this paper, we show that and B'(X⊂B(X∩U'. Also, iff (U;C has Property Multiplication. Furthermore, some connections between outer (resp. inner definable subsets in (U;C and outer (resp. inner definable subsets in (U';C' are established. These results answer a question on covering approximation subspace posed by J. Li, and are helpful to obtain further applications of Pawlak rough set theory in pattern recognition and artificial intelligence.

  11. Effects of Worldwide Population Subdivision on ALDH2 Linkage Disequilibrium

    OpenAIRE

    Peterson, Raymond J.; Goldman, David; Long, Jeffrey C.

    1999-01-01

    The effect of human population subdivision on linkage disequilibrium has previously been studied for unlinked genes. However, no study has focused on closely linked polymorphisms or formally partitioned linkage disequilibrium within and among worldwide populations. With an emphasis on population subdivision, the goal of this paper is to investigate the causes of linkage disequilibrium in ALDH2, the gene that encodes aldehyde dehydrogenase 2. Haplotypes for 756 people from 17 populations acros...

  12. Amides are excellent mimics of phosphate internucleoside linkages and are well tolerated in short interfering RNAs.

    Science.gov (United States)

    Mutisya, Daniel; Selvam, Chelliah; Lunstad, Benjamin D; Pallan, Pradeep S; Haas, Amanda; Leake, Devin; Egli, Martin; Rozners, Eriks

    2014-06-01

    RNA interference (RNAi) has become an important tool in functional genomics and has an intriguing therapeutic potential. However, the current design of short interfering RNAs (siRNAs) is not optimal for in vivo applications. Non-ionic phosphate backbone modifications may have the potential to improve the properties of siRNAs, but are little explored in RNAi technologies. Using X-ray crystallography and RNAi activity assays, the present study demonstrates that 3'-CH2-CO-NH-5' amides are excellent replacements for phosphodiester internucleoside linkages in RNA. The crystal structure shows that amide-modified RNA forms a typical A-form duplex. The amide carbonyl group points into the major groove and assumes an orientation that is similar to the P-OP2 bond in the phosphate linkage. Amide linkages are well hydrated by tandem waters linking the carbonyl group and adjacent phosphate oxygens. Amides are tolerated at internal positions of both the guide and passenger strand of siRNAs and may increase the silencing activity when placed near the 5'-end of the passenger strand. As a result, an siRNA containing eight amide linkages is more active than the unmodified control. The results suggest that RNAi may tolerate even more extensive amide modification, which may be useful for optimization of siRNAs for in vivo applications. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Amides are excellent mimics of phosphate internucleoside linkages and are well tolerated in short interfering RNAs

    Science.gov (United States)

    Mutisya, Daniel; Selvam, Chelliah; Lunstad, Benjamin D.; Pallan, Pradeep S.; Haas, Amanda; Leake, Devin; Egli, Martin; Rozners, Eriks

    2014-01-01

    RNA interference (RNAi) has become an important tool in functional genomics and has an intriguing therapeutic potential. However, the current design of short interfering RNAs (siRNAs) is not optimal for in vivo applications. Non-ionic phosphate backbone modifications may have the potential to improve the properties of siRNAs, but are little explored in RNAi technologies. Using X-ray crystallography and RNAi activity assays, the present study demonstrates that 3′-CH2-CO-NH-5′ amides are excellent replacements for phosphodiester internucleoside linkages in RNA. The crystal structure shows that amide-modified RNA forms a typical A-form duplex. The amide carbonyl group points into the major groove and assumes an orientation that is similar to the P–OP2 bond in the phosphate linkage. Amide linkages are well hydrated by tandem waters linking the carbonyl group and adjacent phosphate oxygens. Amides are tolerated at internal positions of both the guide and passenger strand of siRNAs and may increase the silencing activity when placed near the 5′-end of the passenger strand. As a result, an siRNA containing eight amide linkages is more active than the unmodified control. The results suggest that RNAi may tolerate even more extensive amide modification, which may be useful for optimization of siRNAs for in vivo applications. PMID:24813446

  14. Covering tree with stars

    DEFF Research Database (Denmark)

    Baumbach, Jan; Guo, Jian-Ying; Ibragimov, Rashid

    2013-01-01

    We study the tree edit distance problem with edge deletions and edge insertions as edit operations. We reformulate a special case of this problem as Covering Tree with Stars (CTS): given a tree T and a set of stars, can we connect the stars in by adding edges between them such that the resulting ...

  15. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich.

    Science.gov (United States)

    Marubodee, Rusama; Ogiso-Tanaka, Eri; Isemura, Takehisa; Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

    2015-01-01

    Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits.

  16. A genetic linkage map of the chromosome 4 short arm

    Energy Technology Data Exchange (ETDEWEB)

    Locke, P.A.; MacDonald, M.E.; Srinidhi, J.; Tanzi, R.E.; Haines, J.L. (Massachusetts General Hospital, Boston (United States)); Gilliam, T.C. (Columbia Univ., New York, NY (United States)); Conneally, P.M. (Indiana Univ. Medical Center, Indianapolis (United States)); Wexler, N.S. (Columbia Univ., New York, NY (United States) Hereditary Disease Foundation, Santa Monica, CA (United States)); Gusella, J.F. (Massachusetts General Hospital, Boston (United States) Harvard Univ., Boston, MA (United States))

    1993-01-01

    The authors have generated an 18-interval contiguous genetic linkage map of human chromosome 4 spanning the entire short arm and proximal long arm. Fifty-seven polymorphisms, representing 42 loci, were analyzed in the Venezuelan reference pedigree. The markers included seven genes (ADRA2C, ALB, GABRB1, GC, HOX7, IDUA, QDPR), one pseudogene (RAF1P1), and 34 anonymous DNA loci. Four loci were represented by microsatellite polymorphisms and one (GC) was expressed as a protein polymorphism. The remainder were genotyped based on restriction fragment length polymorphism. The sex-averaged map covered 123 cM. Significant differences in sex-specific rates of recombination were observed only in the pericentromeric and proximal long arm regions, but these contributed to different overall map lengths of 115 cM in males and 138 cM in females. This map provides 19 reference points along chromosome 4 that will be particularly useful in anchoring and seeding physical mapping studies and in aiding in disease studies. 26 refs., 1 fig., 1 tab.

  17. Novel fluorescent sequence-related amplified polymorphism(FSRAP markers for the construction of a genetic linkage map of wheat(Triticum aestivum L.

    Directory of Open Access Journals (Sweden)

    Zhao Lingbo

    2017-01-01

    Full Text Available Novel fluorescent sequence-related amplified polymorphism (FSRAP markers were developed based on the SRAP molecular marker. Then, the FSRAP markers were used to construct the genetic map of a wheat (Triticum aestivumL. recombinant inbred line population derived from a Chuanmai 42×Chuannong 16 cross. Reproducibility and polymorphism tests indicated that the FSRAP markers have repeatability and better reflect the polymorphism of wheat varieties compared with SRAP markers. A total of 430 polymorphic loci between Chuanmai 42 and Chuannong 16 were detected with 189 FSRAP primer combinations. A total of 281 FSARP markers and 39 SSR markers re classified into 20 linkage groups. The maps spanned a total length of 2499.3cM with an average distance of 7.81cM between markers. A total of 201 markers were mapped on the B genome and covered a distance of 1013cM. On the A genome, 84 markers were mapped and covered a distance of 849.6cM. On the D genome, however, only 35 markers were mapped and covered a distance of 636.7cM. No FSRAP markers were distributed on the 7D chromosome. The results of the present study revealed that the novel FSRAP markers can be used to generate dense, uniform genetic maps of wheat.

  18. Alternative cover design

    International Nuclear Information System (INIS)

    1988-11-01

    The special study on Alternative Cover Designs is one of several studies initiated by the US Department of Energy (DOE) in response to the proposed US Environmental Protection Agency (EPA) groundwater standards. The objective of this study is to investigate the possibility of minimizing the infiltration of precipitation through stabilized tailings piles by altering the standard design of covers currently used on the Uranium Mill Tailings Remedial Action (UMTRA) Project. Prior. to the issuance of the proposed standards, UMTRA Project piles had common design elements to meet the required criteria, the most important of which were for radon diffusion, long-term stability, erosion protection, and groundwater protection. The standard pile covers consisted of three distinct layers. From top to bottom they were: rock for erosion protection; a sand bedding layer; and the radon barrier, usually consisting of a clayey sand material, which also functioned to limit infiltration into the tailings. The piles generally had topslopes from 2 to 4 percent and sideslopes of 20 percent

  19. Genome-wide linkage scan for colorectal cancer susceptibility genes supports linkage to chromosome 3q

    Directory of Open Access Journals (Sweden)

    Velculescu Victor E

    2008-04-01

    Full Text Available Abstract Background Colorectal cancer is one of the most common causes of cancer-related mortality. The disease is clinically and genetically heterogeneous though a strong hereditary component has been identified. However, only a small proportion of the inherited susceptibility can be ascribed to dominant syndromes, such as Hereditary Non-Polyposis Colorectal Cancer (HNPCC or Familial Adenomatous Polyposis (FAP. In an attempt to identify novel colorectal cancer predisposing genes, we have performed a genome-wide linkage analysis in 30 Swedish non-FAP/non-HNPCC families with a strong family history of colorectal cancer. Methods Statistical analysis was performed using multipoint parametric and nonparametric linkage. Results Parametric analysis under the assumption of locus homogeneity excluded any common susceptibility regions harbouring a predisposing gene for colorectal cancer. However, several loci on chromosomes 2q, 3q, 6q, and 7q with suggestive linkage were detected in the parametric analysis under the assumption of locus heterogeneity as well as in the nonparametric analysis. Among these loci, the locus on chromosome 3q21.1-q26.2 was the most consistent finding providing positive results in both parametric and nonparametric analyses Heterogeneity LOD score (HLOD = 1.90, alpha = 0.45, Non-Parametric LOD score (NPL = 2.1. Conclusion The strongest evidence of linkage was seen for the region on chromosome 3. Interestingly, the same region has recently been reported as the most significant finding in a genome-wide analysis performed with SNP arrays; thus our results independently support the finding on chromosome 3q.

  20. Land-Cover Change Detection Using Multi-Temporal MODIS NDVI Imagery

    Science.gov (United States)

    Monitoring the locations and distributions of land-cover change is important for establishing linkages between policy decisions, regulatory actions and subsequent land-use activities. Past studies incorporating two-date change detection using Landsat data have tended to be perfor...

  1. Genome-wide linkage analysis for human longevity

    DEFF Research Database (Denmark)

    Beekman, Marian; Blanché, Hélène; Perola, Markus

    2013-01-01

    Clear evidence exists for heritability of human longevity, and much interest is focused on identifying genes associated with longer lives. To identify such longevity alleles, we performed the largest genome-wide linkage scan thus far reported. Linkage analyses included 2118 nonagenarian Caucasian...

  2. Effects of aquaculture researchers' job characteristics on linkage ...

    African Journals Online (AJOL)

    The study examined the effects of researchers' job characteristics on linkage activities in Nigeria due to the fact that many fish farmers have not been properly reached with technologies and the problem of poor fish production has been attributed to the weak linkages existing between research, extension and fish farmers.

  3. Electrostatic microactuators with integrated gear linkages for mechanical power transmission

    NARCIS (Netherlands)

    Legtenberg, R.; Legtenberg, Rob; Berenschot, Johan W.; Elwenspoek, Michael Curt; Fluitman, J.H.J.

    1996-01-01

    In this paper a surface micromachining process is presented which has been used to fabricate electrostatic microactuators that are interconnected with each other and linked to other movable microstructures by integrated gear linkages. The gear linkages consist of rotational and linear gear

  4. Privacy-preserving record linkage on large real world datasets.

    Science.gov (United States)

    Randall, Sean M; Ferrante, Anna M; Boyd, James H; Bauer, Jacqueline K; Semmens, James B

    2014-08-01

    Record linkage typically involves the use of dedicated linkage units who are supplied with personally identifying information to determine individuals from within and across datasets. The personally identifying information supplied to linkage units is separated from clinical information prior to release by data custodians. While this substantially reduces the risk of disclosure of sensitive information, some residual risks still exist and remain a concern for some custodians. In this paper we trial a method of record linkage which reduces privacy risk still further on large real world administrative data. The method uses encrypted personal identifying information (bloom filters) in a probability-based linkage framework. The privacy preserving linkage method was tested on ten years of New South Wales (NSW) and Western Australian (WA) hospital admissions data, comprising in total over 26 million records. No difference in linkage quality was found when the results were compared to traditional probabilistic methods using full unencrypted personal identifiers. This presents as a possible means of reducing privacy risks related to record linkage in population level research studies. It is hoped that through adaptations of this method or similar privacy preserving methods, risks related to information disclosure can be reduced so that the benefits of linked research taking place can be fully realised. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. Identifying and Mapping Linkages between Actors in the Climate ...

    African Journals Online (AJOL)

    Promoting innovations in climate change requires innovation partnerships and linkages and also creating an enabling environment for actors. The paper reviewed available information on the identification and mapping of linkages between actors in the climate change innovation system. The findings showed different ...

  6. Agriculture–Tourism Linkages in Botswana: Evidence from the ...

    African Journals Online (AJOL)

    Tourism researchers are increasingly recognising that strengthened linkages between the sectors of tourism and agriculture are significant for maximising local multipliers and especially for pro-poor impacts. This article examines the linkages between the tourism and agriculture sectors in Botswana using evidence ...

  7. High-density Integrated Linkage Map Based on SSR Markers in Soybean

    Science.gov (United States)

    Hwang, Tae-Young; Sayama, Takashi; Takahashi, Masakazu; Takada, Yoshitake; Nakamoto, Yumi; Funatsuki, Hideyuki; Hisano, Hiroshi; Sasamoto, Shigemi; Sato, Shusei; Tabata, Satoshi; Kono, Izumi; Hoshi, Masako; Hanawa, Masayoshi; Yano, Chizuru; Xia, Zhengjun; Harada, Kyuya; Kitamura, Keisuke; Ishimoto, Masao

    2009-01-01

    A well-saturated molecular linkage map is a prerequisite for modern plant breeding. Several genetic maps have been developed for soybean with various types of molecular markers. Simple sequence repeats (SSRs) are single-locus markers with high allelic variation and are widely applicable to different genotypes. We have now mapped 1810 SSR or sequence-tagged site markers in one or more of three recombinant inbred populations of soybean (the US cultivar ‘Jack’ × the Japanese cultivar ‘Fukuyutaka’, the Chinese cultivar ‘Peking’ × the Japanese cultivar ‘Akita’, and the Japanese cultivar ‘Misuzudaizu’ × the Chinese breeding line ‘Moshidou Gong 503’) and have aligned these markers with the 20 consensus linkage groups (LGs). The total length of the integrated linkage map was 2442.9 cM, and the average number of molecular markers was 90.5 (range of 70–114) for the 20 LGs. We examined allelic diversity for 1238 of the SSR markers among 23 soybean cultivars or lines and a wild accession. The number of alleles per locus ranged from 2 to 7, with an average of 2.8. Our high-density linkage map should facilitate ongoing and future genomic research such as analysis of quantitative trait loci and positional cloning in addition to marker-assisted selection in soybean breeding. PMID:19531560

  8. SNP identification from RNA sequencing and linkage map construction of rubber tree for anchoring the draft genome.

    Science.gov (United States)

    Shearman, Jeremy R; Sangsrakru, Duangjai; Jomchai, Nukoon; Ruang-Areerate, Panthita; Sonthirod, Chutima; Naktang, Chaiwat; Theerawattanasuk, Kanikar; Tragoonrung, Somvong; Tangphatsornruang, Sithichoke

    2015-01-01

    Hevea brasiliensis, or rubber tree, is an important crop species that accounts for the majority of natural latex production. The rubber tree nuclear genome consists of 18 chromosomes and is roughly 2.15 Gb. The current rubber tree reference genome assembly consists of 1,150,326 scaffolds ranging from 200 to 531,465 bp and totalling 1.1 Gb. Only 143 scaffolds, totalling 7.6 Mb, have been placed into linkage groups. We have performed RNA-seq on 6 varieties of rubber tree to identify SNPs and InDels and used this information to perform target sequence enrichment and high throughput sequencing to genotype a set of SNPs in 149 rubber tree offspring from a cross between RRIM 600 and RRII 105 rubber tree varieties. We used this information to generate a linkage map allowing for the anchoring of 24,424 contigs from 3,009 scaffolds, totalling 115 Mb or 10.4% of the published sequence, into 18 linkage groups. Each linkage group contains between 319 and 1367 SNPs, or 60 to 194 non-redundant marker positions, and ranges from 156 to 336 cM in length. This linkage map includes 20,143 of the 69,300 predicted genes from rubber tree and will be useful for mapping studies and improving the reference genome assembly.

  9. Construction of a genetic linkage map in Lilium using a RIL mapping population based on SRAP marker

    Directory of Open Access Journals (Sweden)

    Chen Li-Jing

    2015-01-01

    Full Text Available A genetic linkage map of lily was constructed using RILs (recombinant inbred lines population of 180 individuals. This mapping population was developed by crossing Raizan No.1 (Formolongo and Gelria (Longiflomm cultivars through single-seed descent (SSD. SRAPs were generated by using restriction enzymes EcoRI in combination with either MseI. The resulting products were separated by electrophoresis on 6% denaturing polyacrylamide gel and visualized by silver staining. The segregation of each marker and linkage analysis was done using the program Mapmaker3.0. With 50 primer pairs, a total of 189 parental polymorphic bands were detected and 78 were used for mapping. The total map length was 2,135.5 cM consisted of 16 linkage groups. The number of markers in the linkage groups varied from 1 to 12. The length of linkage groups was range from 11.2 cM to 425.9 cM and mean marker interval distance range from 9.4 cM to 345.4 cM individually. The mean marker interval distance between markers was 27.4 cM. The map developed in the present study was the first sequence-related amplified polymorphism markers map of lily constructed with recombinant inbred lines, it could be used for genetic mapping and molecular marker assisted breeding and quantitative trait locus mapping of Lilium.

  10. Inducing Water Productivity from Snow Cover for Sustainable Water Management in Ibrahim River Basin, Lebanon

    OpenAIRE

    Darwish , Talal; SHABAN , Amin; Portoghese , Ivan; Vurro , Michele; Khadra , Roula; Saqallah , Sagedah; Drapeau , Laurent; Gascoin , Simon; Amacha , Nabil

    2015-01-01

    International audience; The aim of this paper is to explore the effects and linkages between snow cover areas, distribution, probability and measured water discharge along east Mediterranean coastal watershed using moderate-resolution satellite images (MODIS-Terra). The Nahr Ibrahim River is a typical Lebanese watershed with an area of 326 km2 stretching between the sea and mountainous terrain to the east. The largest snow cover often exists in January-February with snow-free conditions betwe...

  11. The alternative site selection procedure as covered in the report by the Repository Site Selection Procedures Working Group; Das Verfahren der alternativen Standortsuche im Bericht des Arbeitskreises Auswahlverfahren Endlagerstandorte

    Energy Technology Data Exchange (ETDEWEB)

    Brenner, M. [Jena Univ. (Germany). Juristische Fakultaet

    2005-01-01

    The 2002 Act on the Regulated Termination of the Use of Nuclear Power for Industrial Electricity Generation declared Germany's opting out of the peaceful uses of nuclear power. The problem of the permanent management of radioactive residues is becoming more and more important also in the light of that political decision. At the present time, there are no repositories offering the waste management capacities required. Such facilities need to be created. At the present stage, eligible repository sites are the Konrad mine, a former iron ore mine near Salzgitter, and the Gorleben salt dome. While the fate of the Konrad mine as a repository for waste generating negligible amounts of heat continues to be uncertain, despite a plan approval decision of June 2002, the Gorleben repository is still in the planning phase, at present in a dormant state, so to speak. The federal government expressed doubt about the suitability of the Gorleben site. Against this backdrop, the Federal Ministry for the Environment, Nature Conservation, and Nuclear Safety in February 1999 established AkEnd, the Working Group on Repository Site Selection Procedures. The Group was charged with developing, based on sound scientific criteria, a transparent site selection procedure in order to facilitate the search for repository sites. The Working Group presented its final report in December 2002 after approximately four years of work. The Group's proposals about alternative site selection procedures are explained in detail and, above all, reviewed critically. (orig.)

  12. Linkage analysis: Inadequate for detecting susceptibility loci in complex disorders?

    Energy Technology Data Exchange (ETDEWEB)

    Field, L.L.; Nagatomi, J. [Univ. of Calgary, Alberta (Canada)

    1994-09-01

    Insulin-dependent diabetes mellitus (IDDM) may provide valuable clues about approaches to detecting susceptibility loci in other oligogenic disorders. Numerous studies have demonstrated significant association between IDDM and a VNTR in the 5{prime} flanking region of the insulin (INS) gene. Paradoxically, all attempts to demonstrate linkage of IDDM to this VNTR have failed. Lack of linkage has been attributed to insufficient marker locus information, genetic heterogeneity, or high frequency of the IDDM-predisposing allele in the general population. Tyrosine hydroxylase (TH) is located 2.7 kb from INS on the 5` side of the VNTR and shows linkage disequilibrium with INS region loci. We typed a highly polymorphic microsatellite within TH in 176 multiplex families, and performed parametric (lod score) linkage analysis using various intermediate reduced penetrance models for IDDM (including rare and common disease allele frequencies), as well as non-parametric (affected sib pair) linkage analysis. The scores significantly reject linkage for recombination values of .05 or less, excluding the entire 19 kb region containing TH, the 5{prime} VNTR, the INS gene, and IGF2 on the 3{prime} side of INS. Non-parametric linkage analysis also provided no significant evidence for linkage (mean TH allele sharing 52.5%, P=.12). These results have important implications for efforts to locate genes predisposing to complex disorders, strongly suggesting that regions which are significantly excluded by linkage methods may nevertheless contain predisposing genes readily detectable by association methods. We advocate that investigators routinely perform association analyses in addition to linkage analyses.

  13. Covering tree with stars

    DEFF Research Database (Denmark)

    Baumbach, Jan; Guo, Jiong; Ibragimov, Rashid

    2015-01-01

    We study the tree edit distance problem with edge deletions and edge insertions as edit operations. We reformulate a special case of this problem as Covering Tree with Stars (CTS): given a tree T and a set of stars, can we connect the stars in by adding edges between them such that the resulting...... tree is isomorphic to T? We prove that in the general setting, CST is NP-complete, which implies that the tree edit distance considered here is also NP-hard, even when both input trees having diameters bounded by 10. We also show that, when the number of distinct stars is bounded by a constant k, CTS...

  14. Alternate cover materials

    International Nuclear Information System (INIS)

    1988-09-01

    As an effort to enhance compliance with the proposed US Environmental Protection Agency (EPA) groundwater standards, several special studies are being performed by the Technical Assistance Contractor (TAC) to identify and evaluate various design features that may reduce groundwater-related releases from tailings piles. The objective of this special study is to assess the suitability of using alternate cover materials (other than geomembranes) as infiltration barriers in Uranium Mill Tailings Remedial Action (UMTRA) Project piles to minimize leachate generation. The materials evaluated in this study include various types of asphalts, concretes, and a sodium bentonite clay/polypropylene liner system

  15. Mapping of yield, yield stability, yield adaptability and other traits in barley using linkage disequilibrium mapping and linkage analysis

    NARCIS (Netherlands)

    Kraakman, A.T.W.

    2005-01-01

    Plants is mostly done through linkage analysis. A segregating mapping population Identification and mappping of Quantitative Trait Loci (QTLs) in is created from a bi-parental cross and linkages between trait values and mapped markers reveal the positions ofQTLs. In

  16. Mapping of yield, yield stability, yield adaptability and other traits in barley using linkage disequilibrium mapping and linkage analysis

    OpenAIRE

    Kraakman, A.T.W.

    2005-01-01

    Plants is mostly done through linkage analysis. A segregating mapping population Identification and mappping of Quantitative Trait Loci (QTLs) in is created from a bi-parental cross and linkages between trait values and mapped markers reveal the positions ofQTLs. Inthisstudyweexploredlinkagedisequilibrium(LD)mappingof traits in a set of modernbarleycultivars. LDbetweenmolecularmarkerswasfoundup to a distance of 10 centimorgan,whichislargecomparedtootherspecies.Thelarge distancemightbeinducedb...

  17. [MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data].

    Science.gov (United States)

    Liu, Ren-Hu; Meng, Jin-Ling

    2003-05-01

    MAPMAKER is one of the most widely used computer software package for constructing genetic linkage maps.However, the PC version, MAPMAKER 3.0 for PC, could not draw the genetic linkage maps that its Macintosh version, MAPMAKER 3.0 for Macintosh,was able to do. Especially in recent years, Macintosh computer is much less popular than PC. Most of the geneticists use PC to analyze their genetic linkage data. So a new computer software to draw the same genetic linkage maps on PC as the MAPMAKER for Macintosh to do on Macintosh has been crying for. Microsoft Excel,one component of Microsoft Office package, is one of the most popular software in laboratory data processing. Microsoft Visual Basic for Applications (VBA) is one of the most powerful functions of Microsoft Excel. Using this program language, we can take creative control of Excel, including genetic linkage map construction, automatic data processing and more. In this paper, a Microsoft Excel macro called MapDraw is constructed to draw genetic linkage maps on PC computer based on given genetic linkage data. Use this software,you can freely construct beautiful genetic linkage map in Excel and freely edit and copy it to Word or other application. This software is just an Excel format file. You can freely copy it from ftp://211.69.140.177 or ftp://brassica.hzau.edu.cn and the source code can be found in Excel's Visual Basic Editor.

  18. High resolution linkage maps of the model organism Petunia reveal substantial synteny decay with the related genome of tomato

    OpenAIRE

    Bossolini, Eligio; Klahre, Ulrich; Brandenburg, Anna; Reinhardt, Didier; Kuhlemeier, Cris

    2011-01-01

    Two linkage maps were constructed for the model plant Petunia. Mapping populations were obtained by crossing the wild species Petunia axillaris subsp. axillaris with Petunia inflata, and Petunia axillaris subsp. parodii with Petunia exserta. Both maps cover the seven chromosomes of Petunia, and span 970 centimorgans (cM) and 700 cM of the genomes, respectively. In total, 207 markers were mapped. Of these, 28 are multilocus amplified fragment length polymorphism (AFLP) markers and 179 are gene...

  19. Large-scale development of SSR markers in tobacco and construction of a linkage map in flue-cured tobacco.

    Science.gov (United States)

    Tong, Zhijun; Xiao, Bingguang; Jiao, Fangchan; Fang, Dunhuang; Zeng, Jianmin; Wu, Xingfu; Chen, Xuejun; Yang, Jiankang; Li, Yongping

    2016-06-01

    Tobacco (Nicotiana tabacum L.), particularly flue-cured tobacco, is one of the most economically important nonfood crops and is also an important model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available for genome analysis, genetic mapping, and breeding. Simple sequence repeats (SSR) are one of the most widely-used molecular markers, having significant advantages including that they are generally co-dominant, easy to use, abundant in eukaryotic organisms, and produce highly reproducible results. In this study, based on the genome sequence data of flue-cured tobacco (K326), we developed a total of 13,645 mostly novel SSR markers, which were working in a set of eighteen tobacco varieties of four different types. A mapping population of 213 backcross (BC1) individuals, which were derived from an intra-type cross between two flue-cured tobacco varieties, Y3 and K326, was selected for mapping. Based on the newly developed SSR markers as well as published SSR markers, we constructed a genetic map consisting of 626 SSR loci distributed across 24 linkage groups and covering a total length of 1120.45 cM with an average distance of 1.79 cM between adjacent markers, which is the highest density map of flue-cured tobacco till date.

  20. A consensus linkage map of the grass carp (Ctenopharyngodon idella based on microsatellites and SNPs

    Directory of Open Access Journals (Sweden)

    Li Jiale

    2010-02-01

    Full Text Available Abstract Background Grass carp (Ctenopharyngodon idella belongs to the family Cyprinidae which includes more than 2000 fish species. It is one of the most important freshwater food fish species in world aquaculture. A linkage map is an essential framework for mapping traits of interest and is often the first step towards understanding genome evolution. The aim of this study is to construct a first generation genetic map of grass carp using microsatellites and SNPs to generate a new resource for mapping QTL for economically important traits and to conduct a comparative mapping analysis to shed new insights into the evolution of fish genomes. Results We constructed a first generation linkage map of grass carp with a mapping panel containing two F1 families including 192 progenies. Sixteen SNPs in genes and 263 microsatellite markers were mapped to twenty-four linkage groups (LGs. The number of LGs was corresponding to the haploid chromosome number of grass carp. The sex-specific map was 1149.4 and 888.8 cM long in females and males respectively whereas the sex-averaged map spanned 1176.1 cM. The average resolution of the map was 4.2 cM/locus. BLAST searches of sequences of mapped markers of grass carp against the whole genome sequence of zebrafish revealed substantial macrosynteny relationship and extensive colinearity of markers between grass carp and zebrafish. Conclusions The linkage map of grass carp presented here is the first linkage map of a food fish species based on co-dominant markers in the family Cyprinidae. This map provides a valuable resource for mapping phenotypic variations and serves as a reference to approach comparative genomics and understand the evolution of fish genomes and could be complementary to grass carp genome sequencing project.

  1. Accuracy of Probabilistic Linkage Using the Enhanced Matching System for Public Health and Epidemiological Studies.

    Science.gov (United States)

    Aldridge, Robert W; Shaji, Kunju; Hayward, Andrew C; Abubakar, Ibrahim

    2015-01-01

    The Enhanced Matching System (EMS) is a probabilistic record linkage program developed by the tuberculosis section at Public Health England to match data for individuals across two datasets. This paper outlines how EMS works and investigates its accuracy for linkage across public health datasets. EMS is a configurable Microsoft SQL Server database program. To examine the accuracy of EMS, two public health databases were matched using National Health Service (NHS) numbers as a gold standard unique identifier. Probabilistic linkage was then performed on the same two datasets without inclusion of NHS number. Sensitivity analyses were carried out to examine the effect of varying matching process parameters. Exact matching using NHS number between two datasets (containing 5931 and 1759 records) identified 1071 matched pairs. EMS probabilistic linkage identified 1068 record pairs. The sensitivity of probabilistic linkage was calculated as 99.5% (95%CI: 98.9, 99.8), specificity 100.0% (95%CI: 99.9, 100.0), positive predictive value 99.8% (95%CI: 99.3, 100.0), and negative predictive value 99.9% (95%CI: 99.8, 100.0). Probabilistic matching was most accurate when including address variables and using the automatically generated threshold for determining links with manual review. With the establishment of national electronic datasets across health and social care, EMS enables previously unanswerable research questions to be tackled with confidence in the accuracy of the linkage process. In scenarios where a small sample is being matched into a very large database (such as national records of hospital attendance) then, compared to results presented in this analysis, the positive predictive value or sensitivity may drop according to the prevalence of matches between databases. Despite this possible limitation, probabilistic linkage has great potential to be used where exact matching using a common identifier is not possible, including in low-income settings, and for vulnerable

  2. The Structure-Function Linkage Database.

    Science.gov (United States)

    Akiva, Eyal; Brown, Shoshana; Almonacid, Daniel E; Barber, Alan E; Custer, Ashley F; Hicks, Michael A; Huang, Conrad C; Lauck, Florian; Mashiyama, Susan T; Meng, Elaine C; Mischel, David; Morris, John H; Ojha, Sunil; Schnoes, Alexandra M; Stryke, Doug; Yunes, Jeffrey M; Ferrin, Thomas E; Holliday, Gemma L; Babbitt, Patricia C

    2014-01-01

    The Structure-Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure-function relationships for functionally diverse enzyme superfamilies. Members of such superfamilies are diverse in their overall reactions yet share a common ancestor and some conserved active site features associated with conserved functional attributes such as a partial reaction. Thus, despite their different functions, members of these superfamilies 'look alike', making them easy to misannotate. To address this complexity and enable rational transfer of functional features to unknowns only for those members for which we have sufficient functional information, we subdivide superfamily members into subgroups using sequence information, and lastly into families, sets of enzymes known to catalyze the same reaction using the same mechanistic strategy. Browsing and searching options in the SFLD provide access to all of these levels. The SFLD offers manually curated as well as automatically classified superfamily sets, both accompanied by search and download options for all hierarchical levels. Additional information includes multiple sequence alignments, tab-separated files of functional and other attributes, and sequence similarity networks. The latter provide a new and intuitively powerful way to visualize functional trends mapped to the context of sequence similarity.

  3. The Structure–Function Linkage Database

    Science.gov (United States)

    Akiva, Eyal; Brown, Shoshana; Almonacid, Daniel E.; Barber, Alan E.; Custer, Ashley F.; Hicks, Michael A.; Huang, Conrad C.; Lauck, Florian; Mashiyama, Susan T.; Meng, Elaine C.; Mischel, David; Morris, John H.; Ojha, Sunil; Schnoes, Alexandra M.; Stryke, Doug; Yunes, Jeffrey M.; Ferrin, Thomas E.; Holliday, Gemma L.; Babbitt, Patricia C.

    2014-01-01

    The Structure–Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure–function relationships for functionally diverse enzyme superfamilies. Members of such superfamilies are diverse in their overall reactions yet share a common ancestor and some conserved active site features associated with conserved functional attributes such as a partial reaction. Thus, despite their different functions, members of these superfamilies ‘look alike’, making them easy to misannotate. To address this complexity and enable rational transfer of functional features to unknowns only for those members for which we have sufficient functional information, we subdivide superfamily members into subgroups using sequence information, and lastly into families, sets of enzymes known to catalyze the same reaction using the same mechanistic strategy. Browsing and searching options in the SFLD provide access to all of these levels. The SFLD offers manually curated as well as automatically classified superfamily sets, both accompanied by search and download options for all hierarchical levels. Additional information includes multiple sequence alignments, tab-separated files of functional and other attributes, and sequence similarity networks. The latter provide a new and intuitively powerful way to visualize functional trends mapped to the context of sequence similarity. PMID:24271399

  4. Linkages at Tourism Destinations: Challenges in Zanzibar

    Directory of Open Access Journals (Sweden)

    Wineaster Anderson

    2011-06-01

    Full Text Available This study explores challenges facing the linkages between the tourism industry and local suppliers at the destinations. During 2010 surveys involving hotel and restaurant operators, local suppliers and tourists were conducted in Zanzibar. Qualitative analysis of the perspectives of the respondents reveals the multitude of constraints. From operators, the main constraints include poor quality of the locally supplied products, business informalities, high transaction costs and violation of agreements by local suppliers. Low production levels, low prices offered by hotels and restaurants coupled with late payments for the products delivered were the most serious problems cited by local suppliers. There is also a certain degree of mistrust between the local suppliers and the operators. However, the source of the tourism products consumed in the hotels or restaurants was not a point of concern, at least from the tourists’ perspective. Strategies to bridge the demandsupply gaps in order to maximize the benefits of tourism, among the tools for fighting the rampant poverty, have been recommended.

  5. Impact analysis of coal-electricity pricing linkage scheme in China based on stochastic frontier cost function

    International Nuclear Information System (INIS)

    Li, Hong-Zhou; Tian, Xian-Liang; Zou, Tao

    2015-01-01

    Highlights: • This study evaluates the coal-electricity pricing linkage policy in China. • Six stochastic frontier cost models are used to estimate efficiency measures. • The coal-electricity pricing linkage scheme is a double-edged sword. • We suggest the threshold value of 5% or group specific. - Abstract: This study evaluates the feasibility and fairness of 2012 amendment to coal-electricity pricing linkage policy in China. Our empirical design is based on several stochastic frontier cost functions and the results show that the amended pricing linkage scheme is a double-edged sword as follows. On the one hand, it provides incentives for less-efficient (with efficiency less than 90%) power plants to increase their efficiency. One the other hand, it imposes a penalty to highly-efficient power plants (with efficiency more than 90%). And even worse, the higher the efficiency is, the bigger the penalty will be. To make the current coal-electricity pricing linkage scheme more feasible, we suggest the threshold value of 5 instead of 10%, and a group specific threshold value instead of the current one-size-for-all practice

  6. ANALYSIS OF INTER SECTORAL LINKAGES IN SEMARANG REGENCY

    Directory of Open Access Journals (Sweden)

    Fafurida

    2014-03-01

    Full Text Available This research aims to analyze inter economic sectoral linkages and to arrange the Klassen typology of economic sectors in Semarang Regency. The Klassen typology is composed from the result of the linkage analysis. To construct the analysis, this paper also utulizes the input-output analysis. It finds that service sector has the highest backward linkage while farming sector has the highest forward linkage. Based on the Klassen typology analysis, sectors with the highest backward and forward linkages and potential to be the leading sector are farming sector, dan trade, hotel and restaurant sector.Keywords: Backward linkage,forward linkage, Klassen typologyJEL classification number: R15, O21AbstrakPenelitian ini bertujuan untuk mengkaji seberapa besar keterkaitan antar sektor ekonomi di Kabupaten Semarang dan memetakan tipologi Klassennya. Tipologi Klasen disusun berdasarkan hasil perhitungan analisis keterkaitannya. Untuk menyusun analisis tersebut, paper ini juga menggunakan analisis input-output. Hasil penelitian menunjukkan bahwa sektor jasa memiliki keterkaitan ke belakang tertinggi dibandingkan dengan sektor lainnya. Sementara itu, sektor pertanian merupakan sektor yang memiliki keterkaitan ke depan tertinggi. Berdasarkan hasil analisis tipologi Klassen, sektor yang memiliki keterkaitan ke depan dan ke belakang yang tinggi dan dapat menjadi sektor unggulan adalah sektor perdagangan, hotel dan sektor restoran.Kata kunci: Keterkaitan ke belakang, keterkaitan ke depan, tipologi KlassenJEL classification numbers: R15, O21

  7. Posterior probability of linkage and maximal lod score.

    Science.gov (United States)

    Génin, E; Martinez, M; Clerget-Darpoux, F

    1995-01-01

    To detect linkage between a trait and a marker, Morton (1955) proposed to calculate the lod score z(theta 1) at a given value theta 1 of the recombination fraction. If z(theta 1) reaches +3 then linkage is concluded. However, in practice, lod scores are calculated for different values of the recombination fraction between 0 and 0.5 and the test is based on the maximum value of the lod score Zmax. The impact of this deviation of the test on the probability that in fact linkage does not exist, when linkage was concluded, is documented here. This posterior probability of no linkage can be derived by using Bayes' theorem. It is less than 5% when the lod score at a predetermined theta 1 is used for the test. But, for a Zmax of +3, we showed that it can reach 16.4%. Thus, considering a composite alternative hypothesis instead of a single one decreases the reliability of the test. The reliability decreases rapidly when Zmax is less than +3. Given a Zmax of +2.5, there is a 33% chance that linkage does not exist. Moreover, the posterior probability depends not only on the value of Zmax but also jointly on the family structures and on the genetic model. For a given Zmax, the chance that linkage exists may then vary.

  8. Interrelationships between soil cover and plant cover depending on land use

    Directory of Open Access Journals (Sweden)

    Tiina Köster

    2013-05-01

    Full Text Available Interrelationships between soil cover and plant cover of normally developed (or postlithogenic mineral soils are analysed on the basis of four sampling soil groups. The four-link pedo-ecological sequence of analysed soils, rendzinas → brown soils → pseudopodzolic soils → gley-podzols, forms a representative cross section in relation to the normal mineral soils of Estonia. All groups differ substantially from each other in terms of soil properties (calcareousness, acidity, nutrition conditions, profile fabric and humus cover. The primary tasks of the research were (1 to elucidate the main pedo-ecological characteristics of the four soil groups and their suitability for plant cover, (2 to evaluate comparatively soils in terms of productivity, sustainability, biodiversity and environmental protection ability and (3 to analyse possibilities for ecologically sound matching of soil cover with suitable plant cover. On the basis of the same material, the influence of land-use change on humus cover (epipedon fabric, properties of the entire soil cover and soil–plant interrelationship were also analysed. An ecosystem approach enables us to observe particularities caused by specific properties of a soil type (species, variety in biological turnover and in the formation of biodiversity.

  9. Distribution of lod scores in oligogenic linkage analysis.

    Science.gov (United States)

    Williams, J T; North, K E; Martin, L J; Comuzzie, A G; Göring, H H; Blangero, J

    2001-01-01

    In variance component oligogenic linkage analysis it can happen that the residual additive genetic variance bounds to zero when estimating the effect of the ith quantitative trait locus. Using quantitative trait Q1 from the Genetic Analysis Workshop 12 simulated general population data, we compare the observed lod scores from oligogenic linkage analysis with the empirical lod score distribution under a null model of no linkage. We find that zero residual additive genetic variance in the null model alters the usual distribution of the likelihood-ratio statistic.

  10. Bayesian linkage and segregation analysis: factoring the problem.

    Science.gov (United States)

    Matthysse, S

    2000-01-01

    Complex segregation analysis and linkage methods are mathematical techniques for the genetic dissection of complex diseases. They are used to delineate complex modes of familial transmission and to localize putative disease susceptibility loci to specific chromosomal locations. The computational problem of Bayesian linkage and segregation analysis is one of integration in high-dimensional spaces. In this paper, three available techniques for Bayesian linkage and segregation analysis are discussed: Markov Chain Monte Carlo (MCMC), importance sampling, and exact calculation. The contribution of each to the overall integration will be explicitly discussed.

  11. National Land Cover Database (NLCD) Land Cover Collection

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The National Land Cover Database (NLCD) Land Cover Collection is produced through a cooperative project conducted by the Multi-Resolution Land Characteristics (MRLC)...

  12. Group representations

    CERN Document Server

    Karpilovsky, G

    1994-01-01

    This third volume can be roughly divided into two parts. The first part is devoted to the investigation of various properties of projective characters. Special attention is drawn to spin representations and their character tables and to various correspondences for projective characters. Among other topics, projective Schur index and projective representations of abelian groups are covered. The last topic is investigated by introducing a symplectic geometry on finite abelian groups. The second part is devoted to Clifford theory for graded algebras and its application to the corresponding theory

  13. Relative linkages of peatland methane and carbon dioxide fluxes with climatic, environmental and ecological parameters and their inter-comparison

    Science.gov (United States)

    Banerjee, Tirtha; Hommeltenberg, Janina; Roy, Avipsa; De Roo, Frederik; Mauder, Matthias

    2016-04-01

    Although methane (CH4) is the second most important greenhouse gas (GHG) after CO2, about 80% of its global production is biogenic (wetlands, enteric fermentation and water disposal from animals) contrary to major anthropogenic sources of most other GHGs. Although on a shorter time scale, global emissions of methane are greater (10 year time frame) or about 80% (20 year time frame) of those of carbon dioxide in terms of their influence on global warming, methane emissions have been studied much less than CO2 emissions. Lakes, reservoirs and wetlands are estimated to contribute about 15-40% to the global methane source budget, which is higher than total oceanic CH4 emission. Half of the world's wetlands are represented by peatlands which cover 3% of the global total land area. Peatlands have a thick water-logged organic soil layer (peat) made up of dead and decaying plant material. Moreover, they are carbon rich, containing twice as much stock as the entire forest biomass of the world (550 Gt carbon). When disturbed, they can become significant sources of greenhouse gas emissions. The organic carbon exposed to air due to various mechanisms can release CH4 or CO2 in the atmosphere. Thus the nature of vegetation cover, radiation environment, wind turbulence, soil characteristics, water table depth etc. are expected to be important forcings that influence the emission of CH4 or CO2 in the shorter time scale. However, long term climate change can also influence these governing factors themselves over a larger time scale, which in turn can influence the wetland GHG emissions. Thus developing a predictive framework and long term source appropriation for wetland CH4 or CO2 warrants an identification of the major environmental forcings on the CH4 or CO2 flux. In the present work, we use a simple and systematic data-analytics approach to determine the relative linkages of different climate and environmental variables with the canopy level half-hourly CH4 or CO2 fluxes over a

  14. Markov chain Monte Carlo linkage analysis: effect of bin width on the probability of linkage.

    Science.gov (United States)

    Slager, S L; Juo, S H; Durner, M; Hodge, S E

    2001-01-01

    We analyzed part of the Genetic Analysis Workshop (GAW) 12 simulated data using Monte Carlo Markov chain (MCMC) methods that are implemented in the computer program Loki. The MCMC method reports the "probability of linkage" (PL) across the chromosomal regions of interest. The point of maximum PL can then be taken as a "location estimate" for the location of the quantitative trait locus (QTL). However, Loki does not provide a formal statistical test of linkage. In this paper, we explore how the bin width used in the calculations affects the max PL and the location estimate. We analyzed age at onset (AO) and quantitative trait number 5, Q5, from 26 replicates of the general simulated data in one region where we knew a major gene, MG5, is located. For each trait, we found the max PL and the corresponding location estimate, using four different bin widths. We found that bin width, as expected, does affect the max PL and the location estimate, and we recommend that users of Loki explore how their results vary with different bin widths.

  15. Introduction to topological groups

    CERN Document Server

    Husain, Taqdir

    2018-01-01

    Concise treatment covers semitopological groups, locally compact groups, Harr measure, and duality theory and some of its applications. The volume concludes with a chapter that introduces Banach algebras. 1966 edition.

  16. Review of the Linkages between Gender Equity and Climate ...

    African Journals Online (AJOL)

    Review of the Linkages between Gender Equity and Climate Change Issues in ... thereby exacerbating inequalities in health status and access to adequate food, clean ... Again, in traditional societies, women are even more vulnerable to the ...

  17. Solid-Phase Synthesis of RNA Analogs Containing Phosphorodithioate Linkages.

    Science.gov (United States)

    Yang, Xianbin

    2017-09-18

    The oligoribonucleotide phosphorodithioate (PS2-RNA) modification uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphorodiester backbone linkage. Like a natural phosphodiester RNA backbone linkage, a PS2-modified backbone linkage is achiral at phosphorus. PS2-RNAs are highly stable to nucleases and several in vitro assays have demonstrated their biological activity. For example, PS2-RNAs silenced mRNA in vitro and bound to protein targets in the form of PS2-aptamers (thioaptamers). Thus, the interest in and promise of PS2-RNAs has drawn attention to synthesizing, isolating, and characterizing these compounds. RNA-thiophosphoramidite monomers are commercially available from AM Biotechnologies and this unit describes an effective methodology for solid-phase synthesis, deprotection, and purification of RNAs having PS2 internucleotide linkages. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  18. Mapping organizational linkages in the agricultural innovation system of Azerbaijan

    NARCIS (Netherlands)

    Temel, T.

    2004-01-01

    This study describes the evolving context and organisational linkages in the agricultural innovation system of Azerbaijan and suggests ways to promote effective organisational ties for the development, distribution and use of new or improved information and knowledge related to agriculture.

  19. Strengthening industry-research linkage for small scale industrial ...

    African Journals Online (AJOL)

    Strengthening industry-research linkage for small scale industrial development in Ghana - the relevance of scientific and technological information. ... Journal of Applied Science and Technology. Journal Home · ABOUT · Advanced Search ...

  20. Underreporting of maternal mortality in Taiwan: A data linkage study

    Directory of Open Access Journals (Sweden)

    Tung-Pi Wu

    2015-12-01

    Conclusion: Approximately two-thirds of the maternal deaths in Taiwan were unreported in the officially published mortality data. Hence, routine nationwide data linkage is essential to monitor maternal mortality in Taiwan accurately.

  1. Estimating parameters for probabilistic linkage of privacy-preserved datasets.

    Science.gov (United States)

    Brown, Adrian P; Randall, Sean M; Ferrante, Anna M; Semmens, James B; Boyd, James H

    2017-07-10

    Probabilistic record linkage is a process used to bring together person-based records from within the same dataset (de-duplication) or from disparate datasets using pairwise comparisons and matching probabilities. The linkage strategy and associated match probabilities are often estimated through investigations into data quality and manual inspection. However, as privacy-preserved datasets comprise encrypted data, such methods are not possible. In this paper, we present a method for estimating the probabilities and threshold values for probabilistic privacy-preserved record linkage using Bloom filters. Our method was tested through a simulation study using synthetic data, followed by an application using real-world administrative data. Synthetic datasets were generated with error rates from zero to 20% error. Our method was used to estimate parameters (probabilities and thresholds) for de-duplication linkages. Linkage quality was determined by F-measure. Each dataset was privacy-preserved using separate Bloom filters for each field. Match probabilities were estimated using the expectation-maximisation (EM) algorithm on the privacy-preserved data. Threshold cut-off values were determined by an extension to the EM algorithm allowing linkage quality to be estimated for each possible threshold. De-duplication linkages of each privacy-preserved dataset were performed using both estimated and calculated probabilities. Linkage quality using the F-measure at the estimated threshold values was also compared to the highest F-measure. Three large administrative datasets were used to demonstrate the applicability of the probability and threshold estimation technique on real-world data. Linkage of the synthetic datasets using the estimated probabilities produced an F-measure that was comparable to the F-measure using calculated probabilities, even with up to 20% error. Linkage of the administrative datasets using estimated probabilities produced an F-measure that was higher

  2. Learning Expressive Linkage Rules for Entity Matching using Genetic Programming

    OpenAIRE

    Isele, Robert

    2013-01-01

    A central problem in data integration and data cleansing is to identify pairs of entities in data sets that describe the same real-world object. Many existing methods for matching entities rely on explicit linkage rules, which specify how two entities are compared for equivalence. Unfortunately, writing accurate linkage rules by hand is a non-trivial problem that requires detailed knowledge of the involved data sets. Another important issue is the efficient execution of link...

  3. Climate change and its linkages with development, equity and sustainability

    International Nuclear Information System (INIS)

    Munasinghe, M.; Swart, R.

    2000-01-01

    The IPCC Working Groups 2 and 3 (on impacts and adaptation, and on mitigation, respectively) have taken the initiative to organise a number of expert meetings. The main goals of the meetings are: (a) to increase co-ordination among, and inform lead authors about development, equity and sustainability (DES) issues and climate change; and (b) to better place the IPCC Third Assessment Report in the context of DES, through enhanced access to the best available scientific, technical economic and social information from across the world. The rapidly growing economies of Asia will play a key role in determining future climate change policy. Thus, the organisation of the first expert meeting in Colombo, Sri Lanka, under the able guidance of Professor Mohan Munasinghe, is very appropriate. The conference has provided a crucial first step towards broadening the scope of the IPCC reports, by integrating DES issues into climate change response strategies. This Proceedings volume is also important as a key policy-relevant (but not policy-prescriptive) vehicle that will better inform worldwide networks of scientists from different regional, cultural and disciplinary backgrounds, in their pursuit of the best scientific information on the linkages between climate change and sustainable development. refs

  4. Linkage disequilibrium in HLA cannot be explained by selective recombination.

    Science.gov (United States)

    Termijtelen, A; D'Amaro, J; van Rood, J J; Schreuder, G M

    1995-11-01

    Some combinations of HLA-A, -B and -DR antigens occur more frequently than would be expected from their gene frequencies in the population. This phenomenon, referred to as Linkage Disequilibrium (LD) has been the origin of many speculations. One hypothesis to explain LD is that some haplotypes are protected from recombination. A second hypothesis is that these HLA antigens preferentially recombine after cross-over to create an LD haplotype. We tested these 2 hypotheses: from a pool of over 10,000 families typed in our department, we analyzed 126 families in which HLA-A:B or B:DR recombinant offspring was documented. To overcome a possible bias in our material, we used the non-recombined haplotypes from the same 126 families as a control group. Our results show that the number of cross-overs through LD haplotypes is not significantly lower then would be expected if recombination occurred randomly. Also the number of LD haplotypes created upon recombination was not significantly increased.

  5. Allegheny County Land Cover Areas

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — The Land Cover dataset demarcates 14 land cover types by area; such as Residential, Commercial, Industrial, Forest, Agriculture, etc. If viewing this description on...

  6. Selective cleavage of the C(α)-C(β) linkage in lignin model compounds via Baeyer-Villiger oxidation.

    Science.gov (United States)

    Patil, Nikhil D; Yao, Soledad G; Meier, Mark S; Mobley, Justin K; Crocker, Mark

    2015-03-21

    Lignin is an amorphous aromatic polymer derived from plants and is a potential source of fuels and bulk chemicals. Herein, we present a survey of reagents for selective stepwise oxidation of lignin model compounds. Specifically, we have targeted the oxidative cleavage of Cα-Cβ bonds as a means to depolymerize lignin and obtain useful aromatic compounds. In this work, we prepared several lignin model compounds that possess structures, characteristic reactivity, and linkages closely related to the parent lignin polymer. We observed that selective oxidation of benzylic hydroxyl groups, followed by Baeyer-Villiger oxidation of the resulting ketones, successfully cleaves the Cα-Cβ linkage in these model compounds.

  7. Building an Entrepreneurial University in Brazil: The Role and Potential of University-Industry Linkages in Promoting Regional Economic Development

    Science.gov (United States)

    Amaral, Marcelo; Ferreira, Andre; Teodoro, Pitias

    2011-01-01

    This study is part of a broader research project, conducted by the Triple Helix Research Group--Brazil, focusing on university-industry-government linkages in the state of Rio de Janeiro. The case study reported here is that of the Regional University of Volta Redonda: the aim was to develop an understanding of how a regional university can be…

  8. On approximating restricted cycle covers

    NARCIS (Netherlands)

    Manthey, Bodo

    2008-01-01

    A cycle cover of a graph is a set of cycles such that every vertex is part of exactly one cycle. An $L$-cycle cover is a cycle cover in which the length of every cycle is in the set $L$. The weight of a cycle cover of an edge-weighted graph is the sum of the weights of its edges. We come close to

  9. Gainesville's urban forest canopy cover

    Science.gov (United States)

    Francisco Escobedo; Jennifer A. Seitz; Wayne Zipperer

    2009-01-01

    Ecosystem benefits from trees are linked directly to the amount of healthy urban forest canopy cover. Urban forest cover is dynamic and changes over time due to factors such as urban development, windstorms, tree removals, and growth. The amount of a city's canopy cover depends on its land use, climate, and people's preferences. This fact sheet examines how...

  10. A genetic linkage map of sole (Solea solea: a tool for evolutionary and comparative analyses of exploited (flatfishes.

    Directory of Open Access Journals (Sweden)

    Eveline Diopere

    Full Text Available Linkage maps based on markers derived from genes are essential evolutionary tools for commercial marine fish to help identify genomic regions associated with complex traits and subject to selective forces at play during exploitation or selective breeding. Additionally, they allow the use of genomic information from other related species for which more detailed information is available. Sole (solea solea L. is a commercially important flatfish species in the North Sea, subject to overexploitation and showing evidence of fisheries-induced evolutionary changes in growth- and maturation-related traits. Sole would definitely benefit from a linkage map to better understand how evolution has shaped its genome structure. This study presents a linkage map of sole based on 423 single nucleotide polymorphisms derived from expressed sequence tags and 8 neutral microsatellite markers. The total map length is 1233.8 cM and consists of 38 linkage groups with a size varying between 0 to 92.1 cM. Being derived from expressed sequence tags allowed us to align the map with the genome of four model fish species, namely medaka (Oryzias latipes, Nile tilapia (Oreochromis niloticus, three-spined stickleback (Gasterosteus aculeatus and green spotted pufferfish (Tetraodon nigroviridis. This comparison revealed multiple conserved syntenic regions with all four species, and suggested that the linkage groups represent 21 putative sole chromosomes. The map was also compared to the linkage map of turbot (Scophthalmus maximus, another commercially important flatfish species and closely related to sole. For all putative sole chromosomes (except one a turbot homolog was detected, confirming the even higher degree of synteny between these two flatfish species.

  11. A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

    Directory of Open Access Journals (Sweden)

    Palhares Alessandra C

    2012-06-01

    Full Text Available Abstract Background The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results The mapping population parents (‘IAC66-6’ and ‘TUC71-7’ contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs. Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56 were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. Conclusions Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60

  12. Focusing on Concepts by Covering Them Simultaneously

    Science.gov (United States)

    Shwartz, Pete

    2017-01-01

    "Parallel" pedagogy covers the four mechanics concepts of momentum, energy, forces, and kinematics simultaneously instead of building each concept on an understanding of the previous one. Course content is delivered through interactive videos, allowing class time for group work and student-centered activities. We start with simple…

  13. Using Bureaucratic and Cultural Linkages to Improve Instruction: The Principal's Contribution.

    Science.gov (United States)

    Firestone, William A.; Wilson, Bruce L.

    1985-01-01

    Principals can influence teachers and instructional behavior by working through linkage mechanisms within the organizational structure of the school. Two types of linkages are identified: bureaucratic and cultural. Principals have access to linkages of both kinds; using linkages effectively, they can generate a common purpose in their schools. (MD)

  14. Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information

    Science.gov (United States)

    2012-01-01

    Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. Conclusion This study will serve as a valuable genomic resource

  15. The Model For Linking Savings And Credit Groups With Banks In ...

    African Journals Online (AJOL)

    The linkage program will greatly be enhanced if the design of the linkage encourages joint liability in loan repayment and if the savings instrument is adequately flexible such that groups can use part of the mandatory savings to repay loans when group income falls short of the group's financial obligations. Key Words: ...

  16. RLT-S: A Web System for Record Linkage.

    Directory of Open Access Journals (Sweden)

    Abdullah-Al Mamun

    Full Text Available Record linkage integrates records across multiple related data sources identifying duplicates and accounting for possible errors. Real life applications require efficient algorithms to merge these voluminous data sources to find out all records belonging to same individuals. Our recently devised highly efficient record linkage algorithms provide best-known solutions to this challenging problem.We have developed RLT-S, a freely available web tool, which implements our single linkage clustering algorithm for record linkage. This tool requires input data sets and a small set of configuration settings about these files to work efficiently. RLT-S employs exact match clustering, blocking on a specified attribute and single linkage based hierarchical clustering among these blocks.RLT-S is an implementation package of our sequential record linkage algorithm. It outperforms previous best-known implementations by a large margin. The tool is at least two times faster for any dataset than the previous best-known tools.RLT-S tool implements our record linkage algorithm that outperforms previous best-known algorithms in this area. This website also contains necessary information such as instructions, submission history, feedback, publications and some other sections to facilitate the usage of the tool.RLT-S is integrated into http://www.rlatools.com, which is currently serving this tool only. The tool is freely available and can be used without login. All data files used in this paper have been stored in https://github.com/abdullah009/DataRLATools. For copies of the relevant programs please see https://github.com/abdullah009/RLATools.

  17. Genetic mapping of the gene for Usher syndrome: Linkage analysis in a large Samaritan kindred

    Energy Technology Data Exchange (ETDEWEB)

    Bonne-Tamir, B.; Korostishevsky, M.; Kalinsky, H.; Seroussi, E.; Beker, R.; Weiss, S. (Sackler Faculty of Medicine, Ramat-Aviv (Israel)); Godel, V. (Ichilov Hospital, Tel-Aviv (Israel))

    1994-03-01

    Usher syndrome is a group of autosomal recessive disorders associated with congenital sensorineural deafness and progressive visual loss due to retinitis pigmentosa. Sixteen members of the small inbred Samaritan isolate with autosomal recessive deafness from 59 individuals including parents and affected and nonaffected sibs were typed for markers on chromosomes 1q and 11q for which linkage has recently been established for Usher syndrome types II and I. Statistically significant linkage was observed with four markers on 11q (D11S533, D11S527, OMP, and INT2) with a maximum six-point location score of 11.61 at the D11S533 locus. Analysis of haplotypes supports the notion that the mutation arose only once in an ancestral chromosome carrying a specific haplotype. The availability of markers closely linked to the disease locus allows indirect genotype analysis and identifies all carriers of the gene within the community. Furthermore, the detection of complete linkage disequilibrium between the D11S533 marker and the Usher gene suggests that these loci are either identical or adjacent and narrows the critical region to which physical mapping efforts are currently directed. 35 refs., 2 figs., 6 tabs.

  18. Constructing linkage maps in the genomics era with MapDisto 2.0.

    Science.gov (United States)

    Heffelfinger, Christopher; Fragoso, Christopher A; Lorieux, Mathias

    2017-07-15

    Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user-friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation efficiency, both in terms of speed and use of random-access memory (RAM). MapDisto v.2.0 is a user-friendly computer program for construction of genetic linkage maps. It includes several new major features: (i) handling of very large genotyping datasets like the ones generated by GBS; (ii) direct importation and conversion of Variant Call Format (VCF) files; (iii) detection of linkage, i.e. construction of linkage groups in case of segregation distortion; (iv) data imputation on VCF files using a new approach, called LB-Impute. Features i to iv operate through inclusion of new Java modules that are used transparently by MapDisto; (v) QTL detection via a new R/qtl graphical interface. The program is available free of charge at mapdisto.free.fr. mapdisto@gmail.com. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  19. Genetic mapping of the gene for Usher syndrome: linkage analysis in a large Samaritan kindred.

    Science.gov (United States)

    Bonné-Tamir, B; Korostishevsky, M; Kalinsky, H; Seroussi, E; Beker, R; Weiss, S; Godel, V

    1994-03-01

    Usher syndrome is a group of autosomal recessive disorders associated with congenital sensorineural deafness and progressive visual loss due to retinitis pigmentosa. Sixteen members of the small inbred Samaritan isolate with autosomal recessive deafness were studied in 10 related sibships. DNA samples from 59 individuals including parents and affected and nonaffected sibs were typed for markers on chromosomes 1q and 11q for which linkage has recently been established for Usher syndrome types II and I. Statistically significant linkage was observed with four markers on 11q (D11S533, D11S527, OMP, and INT2) with a maximum six-point location score of 11.61 at the D11S533 locus. Analysis of haplotypes supports the notion that the mutation arose only once in an ancestral chromosome carrying a specific haplotype. The availability of markers closely linked to the disease locus allows indirect genotype analysis and identifies all carriers of the gene within the community. Furthermore, the detection of complete linkage disequilibrium between the D11S533 marker and the Usher gene suggests that these loci are either identical or adjacent and narrows the critical region to which physical mapping efforts are currently directed.

  20. Construction of the first genetic linkage map of Japanese gentian (Gentianaceae

    Directory of Open Access Journals (Sweden)

    Nakatsuka Takashi

    2012-11-01

    Full Text Available Abstract Background Japanese gentians (Gentiana triflora and Gentiana scabra are amongst the most popular floricultural plants in Japan. However, genomic resources for Japanese gentians have not yet been developed, mainly because of the heterozygous genome structure conserved by outcrossing, the long juvenile period, and limited knowledge about the inheritance of important traits. In this study, we developed a genetic linkage map to improve breeding programs of Japanese gentians. Results Enriched simple sequence repeat (SSR libraries from a G. triflora double haploid line yielded almost 20,000 clones using 454 pyrosequencing technology, 6.7% of which could be used to design SSR markers. To increase the number of molecular markers, we identified three putative long terminal repeat (LTR sequences using the recently developed inter-primer binding site (iPBS method. We also developed retrotransposon microsatellite amplified polymorphism (REMAP markers combining retrotransposon and inter-simple sequence repeat (ISSR markers. In addition to SSR and REMAP markers, modified amplified fragment length polymorphism (AFLP and random amplification polymorphic DNA (RAPD markers were developed. Using 93 BC1 progeny from G. scabra backcrossed with a G. triflora double haploid line, 19 linkage groups were constructed with a total of 263 markers (97 SSR, 97 AFLP, 39 RAPD, and 30 REMAP markers. One phenotypic trait (stem color and 10 functional markers related to genes controlling flower color, flowering time and cold tolerance were assigned to the linkage map, confirming its utility. Conclusions This is the first reported genetic linkage map for Japanese gentians and for any species belonging to the family Gentianaceae. As demonstrated by mapping of functional markers and the stem color trait, our results will help to explain the genetic basis of agronomic important traits, and will be useful for marker-assisted selection in gentian breeding programs. Our map

  1. Hybrid scaffold bearing polymer-siloxane Schiff base linkage for bone tissue engineering

    Energy Technology Data Exchange (ETDEWEB)

    Nair, Bindu P., E-mail: bindumelekkuttu@gmail.com; Gangadharan, Dhanya; Mohan, Neethu; Sumathi, Babitha; Nair, Prabha D., E-mail: pdnair49@gmail.com

    2015-07-01

    Scaffolds that can provide the requisite biological cues for the fast regeneration of bone are highly relevant to the advances in tissue engineering and regenerative medicine. In the present article, we report the fabrication of a chitosan–gelatin–siloxane scaffold bearing interpolymer-siloxane Schiff base linkage, through a single-step dialdehyde cross-linking and freeze-drying method using 3-aminopropyltriethoxysilane as the siloxane precursor. Swelling of the scaffolds in phosphate buffered saline indicates enhancement with increase in siloxane concentration, whereas compressive moduli of the wet scaffolds reveal inverse dependence, owing to the presence of siloxane, rich in silanol groups. It is suggested that through the strategy of dialdehyde cross-linking, a limiting siloxane loading of 20 wt.% into a chitosan-gelatin matrix should be considered ideal for bone tissue engineering, because the scaffold made with 30 wt.% siloxane loading degrades by 48 wt.%, in 21 days. The hybrid scaffolds bearing Schiff base linkage between the polymer and siloxane, unlike the stable linkages in earlier reports, are expected to give a faster release of siloxanes and enhancement in osteogenesis. This is verified by the in vitro evaluation of the hybrid scaffolds using rabbit adipose mesenchymal stem cells, which revealed osteogenic cell-clusters on a polymer-siloxane scaffold, enhanced alkaline phosphatase activity and the expression of bone-specific genes, whereas the control scaffold without siloxane supported more of cell-proliferation than differentiation. A siloxane concentration dependent enhancement in osteogenic differentiation is also observed. - Highlights: • A hybrid scaffold bearing interpolymer-siloxane Schiff base linkage • A limiting siloxane loading of 20 wt.% into chitosan–gelatin matrix • A siloxane concentration dependent enhancement in osteogenic differentiation.

  2. Multiple Linkage Disequilibrium Mapping Methods to Validate Additive Quantitative Trait Loci in Korean Native Cattle (Hanwoo

    Directory of Open Access Journals (Sweden)

    Yi Li

    2015-07-01

    Full Text Available The efficiency of genome-wide association analysis (GWAS depends on power of detection for quantitative trait loci (QTL and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM, a combined linkage and linkage disequilibrium analysis (LDLA and a BayesCπ approach. The phenotypes of 486 steers were collected for weaning weight (WWT, yearling weight (YWT, carcass weight (CWT, backfat thickness (BFT, longissimus dorsi muscle area, and marbling score (Marb. Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX] may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.

  3. Nature–society linkages in the Aral Sea region

    Directory of Open Access Journals (Sweden)

    Kristopher D. White

    2013-01-01

    Full Text Available Central Asia's Aral Sea crisis represents a disaster of monumental proportions, a tragedy for both the region's ecology and its human inhabitants. While the human and natural environments had operated in a sustainable co-joined system for millennia, Tsarist Russian expansion into Central Asia, followed by Soviet expansion of both the cotton industry and unsustainable irrigation practices to anchor it spelled doom for the Aral Sea. Today, many of the political and economic stimuli for such misguided practices continue, as do the continued retreat of the Sea and the proliferation of poor human health. The Aral Sea crisis has received ample scholarly attention, though somewhat surprising is a relative dearth of research explicitly investigating the nature, variety, and directionality of nature–society linkages today within the region. The purpose of this paper is to elucidate the contemporary nature–society linkages operating within the Aral Sea region of Central Asia. Historical nexuses will provide necessary background, and the linkages operating currently within the spheres of regional economy, human health, and political considerations will be detailed. Couching the current crisis within the framework of coupled human–environment system contexts reveals a region in which these linkages are largely inextricable. This paper concludes with a call for a reconsideration of the nature-society linkages and a greater emphasis placed on the local region's ecological and social sustainability.

  4. Autosomal dominant distal myopathy: Linkage to chromosome 14

    Energy Technology Data Exchange (ETDEWEB)

    Laing, N.G.; Laing, B.A.; Wilton, S.D.; Dorosz, S.; Mastaglia, F.L.; Kakulas, B.A. [Australian Neuromuscular Research Institute, Perth (Australia); Robbins, P.; Meredith, C.; Honeyman, K.; Kozman, H.

    1995-02-01

    We have studied a family segregating a form of autosomal dominant distal myopathy (MIM 160500) and containing nine living affected individuals. The myopathy in this family is closest in clinical phenotype to that first described by Gowers in 1902. A search for linkage was conducted using microsatellite, VNTR, and RFLP markers. In total, 92 markers on all 22 autosomes were run. Positive linkage was obtained with 14 of 15 markers tested on chromosome 14, with little indication of linkage elsewhere in the genome. Maximum two-point LOD scores of 2.60 at recombination fraction .00 were obtained for the markers MYH7 and D14S64 - the family structure precludes a two-point LOD score {ge} 3. Recombinations with D14S72 and D14S49 indicate that this distal myopathy locus, MPD1, should lie between these markers. A multipoint analysis assuming 100% penetrance and using the markers D14S72, D14S50, MYH7, D14S64, D14S54, and D14S49 gave a LOD score of exactly 3 at MYH7. Analysis at a penetrance of 80% gave a LOD score of 2.8 at this marker. This probable localization of a gene for distal myopathy, MPD1, on chromosome 14 should allow other investigators studying distal myopathy families to test this region for linkage in other types of the disease, to confirm linkage or to demonstrate the likely genetic heterogeneity. 24 refs., 3 figs., 1 tab.

  5. Two-locus linkage analysis in multiple sclerosis (MS)

    Energy Technology Data Exchange (ETDEWEB)

    Tienari, P.J. (National Public Health Institute, Helsinki (Finland) Univ. of Helsinki (Finland)); Terwilliger, J.D.; Ott, J. (Columbia Univ., New York (United States)); Palo, J. (Univ. of Helsinki (Finland)); Peltonen, L. (National Public Health Institute, Helsinki (Finland))

    1994-01-15

    One of the major challenges in genetic linkage analyses is the study of complex diseases. The authors demonstrate here the use of two-locus linkage analysis in multiple sclerosis (MS), a multifactorial disease with a complex mode of inheritance. In a set of Finnish multiplex families, they have previously found evidence for linkage between MS susceptibility and two independent loci, the myelin basic protein gene (MBP) on chromosome 18 and the HLA complex on chromosome 6. This set of families provides a unique opportunity to perform linkage analysis conditional on two loci contributing to the disease. In the two-trait-locus/two-marker-locus analysis, the presence of another disease locus is parametrized and the analysis more appropriately treats information from the unaffected family member than single-disease-locus analysis. As exemplified here in MS, the two-locus analysis can be a powerful method for investigating susceptibility loci in complex traits, best suited for analysis of specific candidate genes, or for situations in which preliminary evidence for linkage already exists or is suggested. 41 refs., 6 tabs.

  6. A meiotic linkage map of the silver fox, aligned and compared to the canine genome.

    Science.gov (United States)

    Kukekova, Anna V; Trut, Lyudmila N; Oskina, Irina N; Johnson, Jennifer L; Temnykh, Svetlana V; Kharlamova, Anastasiya V; Shepeleva, Darya V; Gulievich, Rimma G; Shikhevich, Svetlana G; Graphodatsky, Alexander S; Aguirre, Gustavo D; Acland, Gregory M

    2007-03-01

    A meiotic linkage map is essential for mapping traits of interest and is often the first step toward understanding a cryptic genome. Specific strains of silver fox (a variant of the red fox, Vulpes vulpes), which segregate behavioral and morphological phenotypes, create a need for such a map. One such strain, selected for docility, exhibits friendly dog-like responses to humans, in contrast to another strain selected for aggression. Development of a fox map is facilitated by the known cytogenetic homologies between the dog and fox, and by the availability of high resolution canine genome maps and sequence data. Furthermore, the high genomic sequence identity between dog and fox allows adaptation of canine microsatellites for genotyping and meiotic mapping in foxes. Using 320 such markers, we have constructed the first meiotic linkage map of the fox genome. The resulting sex-averaged map covers 16 fox autosomes and the X chromosome with an average inter-marker distance of 7.5 cM. The total map length corresponds to 1480.2 cM. From comparison of sex-averaged meiotic linkage maps of the fox and dog genomes, suppression of recombination in pericentromeric regions of the metacentric fox chromosomes was apparent, relative to the corresponding segments of acrocentric dog chromosomes. Alignment of the fox meiotic map against the 7.6x canine genome sequence revealed high conservation of marker order between homologous regions of the two species. The fox meiotic map provides a critical tool for genetic studies in foxes and identification of genetic loci and genes implicated in fox domestication.

  7. Combinatorial aspects of covering arrays

    Directory of Open Access Journals (Sweden)

    Charles J. Colbourn

    2004-11-01

    Full Text Available Covering arrays generalize orthogonal arrays by requiring that t -tuples be covered, but not requiring that the appearance of t -tuples be balanced.Their uses in screening experiments has found application in software testing, hardware testing, and a variety of fields in which interactions among factors are to be identified. Here a combinatorial view of covering arrays is adopted, encompassing basic bounds, direct constructions, recursive constructions, algorithmic methods, and applications.

  8. Factors associated with linkage to HIV care and TB treatment at community-based HIV testing services in Cape Town, South Africa.

    Science.gov (United States)

    Meehan, Sue-Ann; Sloot, Rosa; Draper, Heather R; Naidoo, Pren; Burger, Ronelle; Beyers, Nulda

    2018-01-01

    Diagnosing HIV and/or TB is not sufficient; linkage to care and treatment is conditional to reduce the burden of disease. This study aimed to determine factors associated with linkage to HIV care and TB treatment at community-based services in Cape Town, South Africa. This retrospective cohort study utilized routinely collected data from clients who utilized stand-alone (fixed site not attached to a health facility) and mobile HIV testing services in eight communities in the City of Cape Town Metropolitan district, between January 2008 and June 2012. Clients were included in the analysis if they were ≥12 years and had a known HIV status. Generalized estimating equations (GEE) logistic regression models were used to assess the association between determinants (sex, age, HIV testing service and co-infection status) and self-reported linkage to HIV care and/or TB treatment. Linkage to HIV care was 3 738/5 929 (63.1%). Linkage to HIV care was associated with the type of HIV testing service. Clients diagnosed with HIV at mobile services had a significantly reduced odds of linking to HIV care (aOR 0.7 (CI 95%: 0.6-0.8), p<0.001. Linkage to TB treatment was 210/275 (76.4%). Linkage to TB treatment was not associated with sex and service type, but was associated with age. Clients in older age groups were less likely to link to TB treatment compared to clients in the age group 12-24 years (all, p-value<0.05). A large proportion of clients diagnosed with HIV at mobile services did not link to care. Almost a quarter of clients diagnosed with TB did not link to treatment. Integrated community-based HIV and TB testing services are efficient in diagnosing HIV and TB, but strategies to improve linkage to care are required to control these epidemics.

  9. Effective interventions to improve young adults' linkage to HIV care in Sub-Saharan Africa: a systematic review.

    Science.gov (United States)

    Mavegam, Bertille Octavie; Pharr, Jennifer R; Cruz, Patricia; Ezeanolue, Echezona E

    2017-10-01

    HIV/AIDS remains a major public health problem despite the efforts to prevent and decrease its spread. Sub-Saharan Africa (SSA) represents 70% of the global number of people living with HIV and 73% of all HIV/AIDS-related deaths. Young adults age 15-24 years are disproportionately impacted by HIV/AIDS in SSA with 34% of people living with HIV (PLWHIV) and 37% of newly diagnosed individuals being in this age group. It is important that PLWHIV be linked to care to facilitate antiretroviral therapy (ART) initiation and limit the spread of infection. We conducted a systematic literature review to identify effective interventions designed to improve linkage to care among HIV-infected young adults in SSA. One hundred and forty-six titles and abstracts were screened, 28 full-texts were reviewed, and 6 articles met the inclusion and exclusion criteria. Home-based HIV counseling and testing, home-based HIV self-testing, and mobile HIV counseling and testing followed by proper referral of HIV-positive patients to HIV care were effective for improving linkage of young adults to care. Other factors such as referral forms, transportation allowance, home initiation of HIV care, and volunteer escort to the HIV treatment clinic were effective in reducing time to linkage to care. There is a vast need for research and interventions that target HIV-positive young adults in SSA which aim to improve their linkage and access to HIV care. The results of this study illustrate effective interventions in improving linkage to care and reducing time to linkage to care of young adults in SSA.

  10. GLCF: Landsat GeoCover

    Science.gov (United States)

    satellite imagery provided in a standardized, orthorectified format, covering the entire land surface of the * Orthorectification * Distribution Status * Hard Media Orders * Letters Delivered Quick Links * Create True Color

  11. Robust LOD scores for variance component-based linkage analysis.

    Science.gov (United States)

    Blangero, J; Williams, J T; Almasy, L

    2000-01-01

    The variance component method is now widely used for linkage analysis of quantitative traits. Although this approach offers many advantages, the importance of the underlying assumption of multivariate normality of the trait distribution within pedigrees has not been studied extensively. Simulation studies have shown that traits with leptokurtic distributions yield linkage test statistics that exhibit excessive Type I error when analyzed naively. We derive analytical formulae relating the deviation from the expected asymptotic distribution of the lod score to the kurtosis and total heritability of the quantitative trait. A simple correction constant yields a robust lod score for any deviation from normality and for any pedigree structure, and effectively eliminates the problem of inflated Type I error due to misspecification of the underlying probability model in variance component-based linkage analysis.

  12. Parametric and nonparametric Granger causality testing: Linkages between international stock markets

    Science.gov (United States)

    De Gooijer, Jan G.; Sivarajasingham, Selliah

    2008-04-01

    This study investigates long-term linear and nonlinear causal linkages among eleven stock markets, six industrialized markets and five emerging markets of South-East Asia. We cover the period 1987-2006, taking into account the on-set of the Asian financial crisis of 1997. We first apply a test for the presence of general nonlinearity in vector time series. Substantial differences exist between the pre- and post-crisis period in terms of the total number of significant nonlinear relationships. We then examine both periods, using a new nonparametric test for Granger noncausality and the conventional parametric Granger noncausality test. One major finding is that the Asian stock markets have become more internationally integrated after the Asian financial crisis. An exception is the Sri Lankan market with almost no significant long-term linear and nonlinear causal linkages with other markets. To ensure that any causality is strictly nonlinear in nature, we also examine the nonlinear causal relationships of VAR filtered residuals and VAR filtered squared residuals for the post-crisis sample. We find quite a few remaining significant bi- and uni-directional causal nonlinear relationships in these series. Finally, after filtering the VAR-residuals with GARCH-BEKK models, we show that the nonparametric test statistics are substantially smaller in both magnitude and statistical significance than those before filtering. This indicates that nonlinear causality can, to a large extent, be explained by simple volatility effects.

  13. The millennium development goals and road traffic injuries: exploring the linkages in South Asia.

    Science.gov (United States)

    Hyder, Adnan A; Ghaffar, Abdul

    2004-12-01

    In a major summit of the members of the United Nations (UN) in 2000, a Millennium Declaration was adopted which called for making the elimination of poverty and promotion of sustainable development a global priority. A road map was agreed upon to operationalize the declaration, and the Millennium Development Goals (MDG) were integrated within the document. The MDGs are now increasingly being used to assess the performance of countries, institutions and the global community. WHO declares that the MDGs provide "a set of outcomes that are relevant to the development of national health policy frameworks". It also states that although MDGs do not cover all the components of public health, when broadly interpreted "the goals provide an opportunity to address important cross-cutting issues and key constraints to health". Consistent with WHO's call for a broad interpretation of the MDGs, and building on the health linkages identified by WHO, this paper explores the linkages between the MDGs and the impact of road traffic injuries (RTI). This is done in the context of South Asia, one of the poorest and populated regions of the developing world.

  14. Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton

    Directory of Open Access Journals (Sweden)

    Michael A. Gore

    2014-03-01

    Full Text Available The superior fiber properties of L. serve as a source of novel variation for improving fiber quality in Upland cotton ( L., but introgression from has been largely unsuccessful due to hybrid breakdown and a lack of genetic and genomic resources. In an effort to overcome these limitations, we constructed a linkage map and conducted a quantitative trait locus (QTL analysis of 10 agronomic and fiber quality traits in a recombinant inbred mapping population derived from a cross between TM-1, an Upland cotton line, and NM24016, an elite line with stabilized introgression from . The linkage map consisted of 429 simple-sequence repeat (SSR and 412 genotyping-by-sequencing (GBS-based single-nucleotide polymorphism (SNP marker loci that covered half of the tetraploid cotton genome. Notably, the 841 marker loci were unevenly distributed among the 26 chromosomes of tetraploid cotton. The 10 traits evaluated on the TM-1 × NM24016 population in a multienvironment trial were highly heritable, and most of the fiber traits showed considerable transgressive variation. Through the QTL analysis, we identified a total of 28 QTLs associated with the 10 traits. Our study provides a novel resource that can be used by breeders and geneticists for the genetic improvement of agronomic and fiber quality traits in Upland cotton.

  15. A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations.

    Science.gov (United States)

    Kling, Daniel; Tillmar, Andreas; Egeland, Thore; Mostad, Petter

    2015-09-01

    Several applications necessitate an unbiased determination of relatedness, be it in linkage or association studies or in a forensic setting. An appropriate model to compute the joint probability of some genetic data for a set of persons given some hypothesis about the pedigree structure is then required. The increasing number of markers available through high-density SNP microarray typing and NGS technologies intensifies the demand, where using a large number of markers may lead to biased results due to strong dependencies between closely located loci, both within pedigrees (linkage) and in the population (allelic association or linkage disequilibrium (LD)). We present a new general model, based on a Markov chain for inheritance patterns and another Markov chain for founder allele patterns, the latter allowing us to account for LD. We also demonstrate a specific implementation for X chromosomal markers that allows for computation of likelihoods based on hypotheses of alleged relationships and genetic marker data. The algorithm can simultaneously account for linkage, LD, and mutations. We demonstrate its feasibility using simulated examples. The algorithm is implemented in the software FamLinkX, providing a user-friendly GUI for Windows systems (FamLinkX, as well as further usage instructions, is freely available at www.famlink.se ). Our software provides the necessary means to solve cases where no previous implementation exists. In addition, the software has the possibility to perform simulations in order to further study the impact of linkage and LD on computed likelihoods for an arbitrary set of markers.

  16. Climate Impacts of Cover Crops

    Science.gov (United States)

    Lombardozzi, D.; Wieder, W. R.; Bonan, G. B.; Morris, C. K.; Grandy, S.

    2016-12-01

    Cover crops are planted in agricultural rotation with the intention of protecting soil rather than harvest. Cover crops have numerous environmental benefits that include preventing soil erosion, increasing soil fertility, and providing weed and pest control- among others. In addition to localized environmental benefits, cover crops can have important regional or global biogeochemical impacts by increasing soil organic carbon, changing emissions of greenhouse trace gases like nitrous oxide and methane, and reducing hydrologic nitrogen losses. Cover crops may additionally affect climate by changing biogeophysical processes, like albedo and latent heat flux, though these potential changes have not yet been evaluated. Here we use the coupled Community Atmosphere Model (CAM5) - Community Land Model (CLM4.5) to test how planting cover crops in the United States may change biogeophysical fluxes and climate. We present seasonal changes in albedo, heat fluxes, evaporative partitioning, radiation, and the resulting changes in temperature. Preliminary analyses show that during seasons when cover crops are planted, latent heat flux increases and albedo decreases, changing the evaporative fraction and surface temperatures. Understanding both the biogeophysical changes caused by planting cover crops in this study and the biogeochemical changes found in other studies will give a clearer picture of the overall impacts of cover crops on climate and atmospheric chemistry, informing how this land use strategy will impact climate in the future.

  17. Landfill covers for dry environments

    International Nuclear Information System (INIS)

    Dwyer, S.F.

    1996-01-01

    A large-scale landfill cover field test is currently underway at Sandia National Laboratories in Albuquerque, New Mexico. It is intended to compare and document the performance of alternative landfill cover technologies of various costs and complexities for interim stabilization and/or final closure of landfills in arid and semi-arid environments. Test plots of traditional designs recommended by the US Environmental Protection Agency for both RCRA Subtitle open-quote C close-quote and open-quote D close-quote regulated facilities have been constructed side-by-side with the alternative covers and will serve as baselines for comparison to these alternative covers. The alternative covers were designed specifically for dry environments. The covers will be tested under both ambient and stressed conditions. All covers have been instrumented to measure water balance variables and soil temperature. An on-site weather station records all pertinent climatological data. A key to acceptance of an alternative environmental technology is seeking regulatory acceptance and eventual permitting. The lack of acceptance by regulatory agencies is a significant barrier to development and implementation of innovative cover technologies. Much of the effort on this demonstration has been toward gaining regulatory and public acceptance

  18. An improved recommendation algorithm via weakening indirect linkage effect

    International Nuclear Information System (INIS)

    Chen Guang; Qiu Tian; Shen Xiao-Quan

    2015-01-01

    We propose an indirect-link-weakened mass diffusion method (IMD), by considering the indirect linkage and the source object heterogeneity effect in the mass diffusion (MD) recommendation method. Experimental results on the MovieLens, Netflix, and RYM datasets show that, the IMD method greatly improves both the recommendation accuracy and diversity, compared with a heterogeneity-weakened MD method (HMD), which only considers the source object heterogeneity. Moreover, the recommendation accuracy of the cold objects is also better elevated in the IMD than the HMD method. It suggests that eliminating the redundancy induced by the indirect linkages could have a prominent effect on the recommendation efficiency in the MD method. (paper)

  19. Mapping autism risk loci using genetic linkage and chromosomal rearrangements

    Science.gov (United States)

    Szatmari, Peter; Paterson, Andrew; Zwaigenbaum, Lonnie; Roberts, Wendy; Brian, Jessica; Liu, Xiao-Qing; Vincent, John; Skaug, Jennifer; Thompson, Ann; Senman, Lili; Feuk, Lars; Qian, Cheng; Bryson, Susan; Jones, Marshall; Marshall, Christian; Scherer, Stephen; Vieland, Veronica; Bartlett, Christopher; Mangin, La Vonne; Goedken, Rhinda; Segre, Alberto; Pericak-Vance, Margaret; Cuccaro, Michael; Gilbert, John; Wright, Harry; Abramson, Ruth; Betancur, Catalina; Bourgeron, Thomas; Gillberg, Christopher; Leboyer, Marion; Buxbaum, Joseph; Davis, Kenneth; Hollander, Eric; Silverman, Jeremy; Hallmayer, Joachim; Lotspeich, Linda; Sutcliffe, James; Haines, Jonathan; Folstein, Susan; Piven, Joseph; Wassink, Thomas; Sheffield, Val; Geschwind, Daniel; Bucan, Maja; Brown, Ted; Cantor, Rita; Constantino, John; Gilliam, Conrad; Herbert, Martha; Lajonchere, Clara; Ledbetter, David; Lese-Martin, Christa; Miller, Janet; Nelson, Stan; Samango-Sprouse, Carol; Spence, Sarah; State, Matthew; Tanzi, Rudolph; Coon, Hilary; Dawson, Geraldine; Devlin, Bernie; Estes, Annette; Flodman, Pamela; Klei, Lambertus; Mcmahon, William; Minshew, Nancy; Munson, Jeff; Korvatska, Elena; Rodier, Patricia; Schellenberg, Gerard; Smith, Moyra; Spence, Anne; Stodgell, Chris; Tepper, Ping Guo; Wijsman, Ellen; Yu, Chang-En; Rogé, Bernadette; Mantoulan, Carine; Wittemeyer, Kerstin; Poustka, Annemarie; Felder, Bärbel; Klauck, Sabine; Schuster, Claudia; Poustka, Fritz; Bölte, Sven; Feineis-Matthews, Sabine; Herbrecht, Evelyn; Schmötzer, Gabi; Tsiantis, John; Papanikolaou, Katerina; Maestrini, Elena; Bacchelli, Elena; Blasi, Francesca; Carone, Simona; Toma, Claudio; Van Engeland, Herman; De Jonge, Maretha; Kemner, Chantal; Koop, Frederieke; Langemeijer, Marjolein; Hijmans, Channa; Staal, Wouter; Baird, Gillian; Bolton, Patrick; Rutter, Michael; Weisblatt, Emma; Green, Jonathan; Aldred, Catherine; Wilkinson, Julie-Anne; Pickles, Andrew; Le Couteur, Ann; Berney, Tom; Mcconachie, Helen; Bailey, Anthony; Francis, Kostas; Honeyman, Gemma; Hutchinson, Aislinn; Parr, Jeremy; Wallace, Simon; Monaco, Anthony; Barnby, Gabrielle; Kobayashi, Kazuhiro; Lamb, Janine; Sousa, Ines; Sykes, Nuala; Cook, Edwin; Guter, Stephen; Leventhal, Bennett; Salt, Jeff; Lord, Catherine; Corsello, Christina; Hus, Vanessa; Weeks, Daniel; Volkmar, Fred; Tauber, Maïté; Fombonne, Eric; Shih, Andy; Meyer, Kacie

    2007-01-01

    Autism spectrum disorders (ASD) are common, heritable neurodevelopmental conditions. The genetic architecture of ASD is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASD by using Affymetrix 10K single nucleotide polymorphism (SNP) arrays and 1168 families with ≥ 2 affected individuals to perform the largest linkage scan to date, while also analyzing copy number variation (CNV) in these families. Linkage and CNV analyses implicate chromosome 11p12-p13 and neurexins, respectively, amongst other candidate loci. Neurexins team with previously-implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for ASD. PMID:17322880

  20. Allele-sharing models: LOD scores and accurate linkage tests.

    Science.gov (United States)

    Kong, A; Cox, N J

    1997-11-01

    Starting with a test statistic for linkage analysis based on allele sharing, we propose an associated one-parameter model. Under general missing-data patterns, this model allows exact calculation of likelihood ratios and LOD scores and has been implemented by a simple modification of existing software. Most important, accurate linkage tests can be performed. Using an example, we show that some previously suggested approaches to handling less than perfectly informative data can be unacceptably conservative. Situations in which this model may not perform well are discussed, and an alternative model that requires additional computations is suggested.

  1. Record linkage for pharmacoepidemiological studies in cancer patients.

    Science.gov (United States)

    Herk-Sukel, Myrthe P P van; Lemmens, Valery E P P; Poll-Franse, Lonneke V van de; Herings, Ron M C; Coebergh, Jan Willem W

    2012-01-01

    An increasing need has developed for the post-approval surveillance of (new) anti-cancer drugs by means of pharmacoepidemiology and outcomes research in the area of oncology. To create an overview that makes researchers aware of the available database linkages in Northern America and Europe which facilitate pharmacoepidemiology and outcomes research in cancer patients. In addition to our own database, i.e. the Eindhoven Cancer Registry (ECR) linked to the PHARMO Record Linkage System, we considered database linkages between a population-based cancer registry and an administrative healthcare database that at least contains information on drug use and offers a longitudinal perspective on healthcare utilization. Eligible database linkages were limited to those that had been used in multiple published articles in English language included in Pubmed. The HMO Cancer Research Network (CRN) in the US was excluded from this review, as an overview of the linked databases participating in the CRN is already provided elsewhere. Researchers who had worked with the data resources included in our review were contacted for additional information and verification of the data presented in the overview. The following database linkages were included: the Surveillance, Epidemiology, and End-Results-Medicare; cancer registry data linked to Medicaid; Canadian cancer registries linked to population-based drug databases; the Scottish cancer registry linked to the Tayside drug dispensing data; linked databases in the Nordic Countries of Europe: Norway, Sweden, Finland and Denmark; and the ECR-PHARMO linkage in the Netherlands. Descriptives of the included database linkages comprise population size, generalizability of the population, year of first data availability, contents of the cancer registry, contents of the administrative healthcare database, the possibility to select a cancer-free control cohort, and linkage to other healthcare databases. The linked databases offer a longitudinal

  2. Determinants of woody cover in African savannas

    Science.gov (United States)

    Sankaran, M.; Hanan, N.P.; Scholes, Robert J.; Ratnam, J.; Augustine, D.J.; Cade, B.S.; Gignoux, J.; Higgins, S.I.; Le, Roux X.; Ludwig, F.; Ardo, J.; Banyikwa, F.; Bronn, A.; Bucini, G.; Caylor, K.K.; Coughenour, M.B.; Diouf, A.; Ekaya, W.; Feral, C.J.; February, E.C.; Frost, P.G.H.; Hiernaux, P.; Hrabar, H.; Metzger, K.L.; Prins, H.H.T.; Ringrose, S.; Sea, W.; Tews, J.; Worden, J.; Zambatis, N.

    2005-01-01

    Savannas are globally important ecosystems of great significance to human economies. In these biomes, which are characterized by the co-dominance of trees and grasses, woody cover is a chief determinant of ecosystem properties 1-3. The availability of resources (water, nutrients) and disturbance regimes (fire, herbivory) are thought to be important in regulating woody cover1,2,4,5, but perceptions differ on which of these are the primary drivers of savanna structure. Here we show, using data from 854 sites across Africa, that maximum woody cover in savannas receiving a mean annual precipitation (MAP) of less than ???650 mm is constrained by, and increases linearly with, MAP. These arid and semi-arid savannas may be considered 'stable' systems in which water constrains woody cover and permits grasses to coexist, while fire, herbivory and soil properties interact to reduce woody cover below the MAP-controlled upper bound. Above a MAP of ???650 mm, savannas are 'unstable' systems in which MAP is sufficient for woody canopy closure, and disturbances (fire, herbivory) are required for the coexistence of trees and grass. These results provide insights into the nature of African savannas and suggest that future changes in precipitation 6 may considerably affect their distribution and dynamics. ?? 2005 Nature Publishing Group.

  3. Automatic design of magazine covers

    Science.gov (United States)

    Jahanian, Ali; Liu, Jerry; Tretter, Daniel R.; Lin, Qian; Damera-Venkata, Niranjan; O'Brien-Strain, Eamonn; Lee, Seungyon; Fan, Jian; Allebach, Jan P.

    2012-03-01

    In this paper, we propose a system for automatic design of magazine covers that quantifies a number of concepts from art and aesthetics. Our solution to automatic design of this type of media has been shaped by input from professional designers, magazine art directors and editorial boards, and journalists. Consequently, a number of principles in design and rules in designing magazine covers are delineated. Several techniques are derived and employed in order to quantify and implement these principles and rules in the format of a software framework. At this stage, our framework divides the task of design into three main modules: layout of magazine cover elements, choice of color for masthead and cover lines, and typography of cover lines. Feedback from professional designers on our designs suggests that our results are congruent with their intuition.

  4. A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity

    Science.gov (United States)

    Leitwein, Maeva; Guinand, Bruno; Pouzadoux, Juliette; Desmarais, Erick; Berrebi, Patrick; Gagnaire, Pierre-Alexandre

    2017-01-01

    High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout. PMID:28235829

  5. A Dense Brown Trout (Salmo trutta Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity

    Directory of Open Access Journals (Sweden)

    Maeva Leitwein

    2017-04-01

    Full Text Available High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta, a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout.

  6. A saturated genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using genotyping-by-sequencing is highly syntenous with the Medicago truncatula genome.

    Science.gov (United States)

    Li, Xuehui; Wei, Yanling; Acharya, Ananta; Jiang, Qingzhen; Kang, Junmei; Brummer, E Charles

    2014-08-21

    A genetic linkage map is a valuable tool for quantitative trait locus mapping, map-based gene cloning, comparative mapping, and whole-genome assembly. Alfalfa, one of the most important forage crops in the world, is autotetraploid, allogamous, and highly heterozygous, characteristics that have impeded the construction of a high-density linkage map using traditional genetic marker systems. Using genotyping-by-sequencing (GBS), we constructed low-cost, reasonably high-density linkage maps for both maternal and paternal parental genomes of an autotetraploid alfalfa F1 population. The resulting maps contain 3591 single-nucleotide polymorphism markers on 64 linkage groups across both parents, with an average density of one marker per 1.5 and 1.0 cM for the maternal and paternal haplotype maps, respectively. Chromosome assignments were made based on homology of markers to the M. truncatula genome. Four linkage groups representing the four haplotypes of each alfalfa chromosome were assigned to each of the eight Medicago chromosomes in both the maternal and paternal parents. The alfalfa linkage groups were highly syntenous with M. truncatula, and clearly identified the known translocation between Chromosomes 4 and 8. In addition, a small inversion on Chromosome 1 was identified between M. truncatula and M. sativa. GBS enabled us to develop a saturated linkage map for alfalfa that greatly improved genome coverage relative to previous maps and that will facilitate investigation of genome structure. GBS could be used in breeding populations to accelerate molecular breeding in alfalfa. Copyright © 2014 Li et al.

  7. Mangrove macrobenthos: Assemblages, services, and linkages

    Science.gov (United States)

    Lee, S. Y.

    2008-02-01

    Macrobenthic assemblages are relatively poorly known compared to other components of the mangrove ecosystem. Tropical mangroves support macrobenthic biodiversity resources yet to be properly documented and interpreted. Some methodological challenges, such as the generally high spatial heterogeneity and complexity of the habitat, evidently reduce sampling efficiency and accuracy, while also leaving some microhabitats under-sampled. Macrobenthic assemblage structure seems to be influenced by local environmental conditions, such as hydroperiod, organic matter availability and sediment characteristics. Brachyurans, gastropods and oligochaetes dominate in the sediment, with the former two groups also common on hard surfaces provided by tree trunks, while insects and arachnids inhabit the canopy. Traditionally, studies of mangrove macrobenthos have focused on assemblage structure or the biology of individual species, but more complex inter-specific interactions and the inter-relationship between habitat and the biota are recently being addressed. Brachyuran crabs are the best-studied macrobenthos group, but many issues about their role in mangrove ecosystem dynamics are still controversial. Despite many species of mangrove macrobenthos being referred to as 'trophic dead ends', most serve as important links between recalcitrant mangrove organic matter and estuarine secondary production, through feeding excursion by mobile nekton during the high tide, and macrobenthos-mediated processing and exportation of organic matter. A significant difference in the standing crop biomass of forests between the Indo-west-Pacific (IWP)' and Atlantic-east-Pacific (AEP) mangroves may be related to the difference in species richness of mangrove as well as macrobenthos diversity in the two bioregions. Such differences in assemblage structure may also result in different ecosystem functioning, but the nature of the links is, however, yet to be explored. There is also a strong need for

  8. Groups – Additive Notation

    Directory of Open Access Journals (Sweden)

    Coghetto Roland

    2015-06-01

    Full Text Available We translate the articles covering group theory already available in the Mizar Mathematical Library from multiplicative into additive notation. We adapt the works of Wojciech A. Trybulec [41, 42, 43] and Artur Korniłowicz [25].

  9. Groups – Additive Notation

    OpenAIRE

    Coghetto Roland

    2015-01-01

    We translate the articles covering group theory already available in the Mizar Mathematical Library from multiplicative into additive notation. We adapt the works of Wojciech A. Trybulec [41, 42, 43] and Artur Korniłowicz [25].

  10. The art of the cover.

    Science.gov (United States)

    Porter, Nora

    2017-07-01

    Often, it's difficult to match up our cover artwork with the subjects of our lead articles and special reports. Of necessity, we sometimes turn to pure abstraction. How else to illustrate technical policy articles on subjects such as changing research protocols or informed consent, or abstract ideas like congruence, duality, imbalance, causality? At such times, we have to be pretty creative, and my search for cover art can be long and challenging. In the end, we hope that the reader will make the connection between cover and content. However, at other times, the subject of a lead article or special report overflows with artistic possibilities. © 2017 The Hastings Center.

  11. On numerically pluricanonical cyclic coverings

    International Nuclear Information System (INIS)

    Kulikov, V S; Kharlamov, V M

    2014-01-01

    We investigate some properties of cyclic coverings f:Y→X (where X is a complex surface of general type) branched along smooth curves B⊂X that are numerically equivalent to a multiple of the canonical class of X. Our main results concern coverings of surfaces of general type with p g =0 and Miyaoka-Yau surfaces. In particular, such coverings provide new examples of multi-component moduli spaces of surfaces with given Chern numbers and new examples of surfaces that are not deformation equivalent to their complex conjugates

  12. Inherently balanced 4R four-bar based linkages

    NARCIS (Netherlands)

    van der Wijk, V.; Herder, Justus Laurens; Lenarcis, J.; Husty, M.

    2012-01-01

    Synthesis of mechanisms with their center of mass (CoM) at an invariant point on one of the elements is useful for the design of statically balanced and shaking-force balanced mechanisms and manipulators. For this purpose, a kinematic architecture based on a general 4R four-bar linkage is found by

  13. Linkages between biodiversity attributes and ecosystem services: A systematic review

    NARCIS (Netherlands)

    Harrison, P.A.; Berry, P.M.; Simpson, G.; Haslett, J.R.; Blicharska, M.; Bucur, M.; Dunford, R.; Egoh, B.; Garcia-llorente, M.; Geamănă, N.; Geertsema, W.; Lommelen, E.; Meiresonne, L.; Turkelboom, F.

    2014-01-01

    A systematic literature review was undertaken to analyse the linkages between different biodiversity attributes and 11 ecosystem services. The majority of relationships between attributes and ecosystem services cited in the 530 studies were positive. For example, the services of water quality

  14. Genetic linkage map of cowpea ( Vigna unguiculata (L.) Walp) using ...

    African Journals Online (AJOL)

    Genetic linkage maps provide a genomic framework for quantitative trait loci identification applied in marker assisted selection breeding in crops with limited resources. It serves as a powerful tool to breeders for analysing the mode of inheritance of genes of interest and monitoring of the transmission of target genes from ...

  15. Linkages between aggregate formation, porosity and soil chemical properties

    NARCIS (Netherlands)

    Regelink, I.C.; Stoof, C.R.; Rousseva, S.; Weng, L.; Lair, G.J.; Kram, P.; Nikolaidis, N.P.; Kercheva, M.; Banwart, S.; Comans, R.N.J.

    2015-01-01

    Linkages between soil structure and physical–chemical soil properties are still poorly understood due to the wide size-range at which aggregation occurs and the variety of aggregation factors involved. To improve understanding of these processes, we collected data on aggregate fractions, soil

  16. Analysis of Linkage Effects among Currency Networks Using REER Data

    Directory of Open Access Journals (Sweden)

    Haishu Qiao

    2015-01-01

    Full Text Available We modeled the currency networks through the use of REER (real effective exchange rate instead of a bilateral exchange rate in order to overcome the confusion in selecting base currencies. Based on the MST (minimum spanning tree approach and the rolling-window method, we constructed time-varying and correlation-based networks with which we investigate the linkage effects among different currencies. In particular, and as the source of empirical data, we chose the monthly REER data for a set of 61 major currencies during the period from 1994 to 2014. The study demonstrated that obvious linkage effects existed among currency networks and the euro (EUR was confirmed as the predominant world currency. Additionally, we used the rolling-window method to investigate the stability of linkage effects, doing so by calculating the mean correlations and mean distances as well as the normalized tree length and degrees of those currencies. The results showed that financial crises during the study period had a great effect on the currency network’s topology structure and led to more clustered currency networks. Our results suggested that it is more appropriate to estimate the linkage effects among currency networks through the use of REER data.

  17. insights from a linkage map of the damselfly Ischnura elegans

    Indian Academy of Sciences (India)

    tion of achiasmiatic meiosis. Biochem. Genet. 19, 1237–. 1245. Cooper G., Miller P. L. and Holland P. W. H. 1994 Molecular genetic analysis of sperm competition in the damselfly Ischnura elegans (Vander Linden). Proc. R. Soc. London, Ser. B 263,. 1343–1349. Huxley J. S. 1928 Sexual differences in linkage in Gammar-.

  18. Changing rural urban linkages in Africa in a globalizing economy ...

    African Journals Online (AJOL)

    The role of rural-urban linkages is critically vital for Africa‟s development in this era of rapid socio-economic transformation. A better understanding of cities and how they relate both to the rural and urban development is needed in view of the continuous changes in development. This paper argues that many of Africa‟s ...

  19. Creative arts linkages, historiography: means to global aesthetics ...

    African Journals Online (AJOL)

    This paper surveys linkages and historiography in creative arts and globalization. The appreciation and possession of other nations' creative art objects/artifacts links different cultures and nations together as they share common aesthetic experiences, history and knowledge which was unique to a particular nation.

  20. A study of inter linkage effects on Candu feeder piping

    International Nuclear Information System (INIS)

    Li, M.; Aggarwal, M.L.; Meysner, A.

    2005-01-01

    A CANDU (Canadian Deuterium Uranium) reactor core consists of a large number of fuel channels where heat is generated. Two feeder pipes are connected to each fuel channel to transport D 2 O coolant into and out of the reactor core. The feeder piping is designed to the requirements of Class 1 piping of Section III NB of the ASME Boiler and Pressure Vessel and CSA Codes. Feeder piping stress analysis is being performed to demonstrate the code compliance check and the fitness for service of feeders. In the past, stress analyses were conducted for each individual feeder without including interaction effects among connected feeders. Interaction effects occur as a result of linkages that exist between feeders to prevent fretting and impacting damage during normal, abnormal and accident conditions. In this paper, a 'combined' approach is adopted to include all feeders connected by inter linkages into one feeder piping model. MSC/NASTRAN finite element software was used in the stress simulation, which contains up to 127 feeder pipes. The ASME Class 1 piping analysis was conducted to investigate the effects of the linkages between feeders. Both seismic time history and broadened response spectra methods were used in the seismic stress calculation. The results show that the effect of linkages is significant in dynamic stresses for all feeder configurations, as well as in static stresses for certain feeder configurations. The single feeder analysis could either underestimate or overestimate feeder stresses depending on the pipe geometry and bend wall thickness. (authors)

  1. Linkages among Key Actors in the Climate Change and Food ...

    African Journals Online (AJOL)

    Sierra Leone and Liberia, but a low linkage index of less than 2 between farmers and policy making bodies for all the countries. Poor generation of innovations over the past ten years and poor domestic support for climate change adaptation and food security in the West African sub-region were identified. The study points to ...

  2. Economic Growth, Structural Change and Productive Employment Linkages in India

    DEFF Research Database (Denmark)

    Aggarwal, Aradhna

    2018-01-01

    This article presents a quantitative analysis of growth, structural change and employment linkages at the aggregate level and by sector under the state- and market-led regimes in India. The underlying objectives are: (a) to understand how economic liberalization has affected the economic and labour...... intervention to broad base structural change for generating productive employment, which is at the core of poverty reduction....

  3. A consensus linkage map of the chicken genome

    NARCIS (Netherlands)

    Groenen, M.A.M.; Cheng, H.H.; Bumstead, N.; Benkel, B.; Briles, E.; Burt, D.W.; Burke, T.; Dodgson, J.; Hillel, J.; Lamont, S.; Ponce, de F.A.; Soller, M.

    2000-01-01

    A consensus linkage map has been developed in the chicken that combines all of the genotyping data from the three available chicken mapping populations. Genotyping data were contributed by the laboratories that have been using the East Lansing and Compton reference populations and from the Animal

  4. The western arctic linkage experiment (WALE): overview and synthesis

    Science.gov (United States)

    A.D. McGuire; J. Walsh; J.S. Kimball; J.S. Clein; S.E. Euskirdhen; S. Drobot; U.C. Herzfeld; J. Maslanik; R.B. Lammers; M.A. Rawlins; C.J. Vorosmarty; T.S. Rupp; W. Wu; M. Calef

    2008-01-01

    The primary goal of the Western Arctic Linkage Experiment (WALE) was to better understand uncertainties of simulated hydrologic and ecosystem dynamics of the western Arctic in the context of 1) uncertainties in the data available to drive the models and 2) different approaches to simulating regional hydrology and ecosystem dynamics. Analyses of datasets on climate...

  5. Human Capital Linkages to Labour Productivity: Implications from Thai Manufacturers

    Science.gov (United States)

    Rukumnuaykit, Pungpond; Pholphirul, Piriya

    2016-01-01

    Human capital investment is a necessary condition for improving labour market outcomes in most countries. Empirical studies to investigate human capital and its linkages on the labour demand side are, however, relatively scarce due to limitations of firm-level data-sets. Using firm-level data from the Thai manufacturing sector, this paper aims to…

  6. The Dynamics of Linkages and Innovativeness in Publicly and ...

    African Journals Online (AJOL)

    The study examined how linkages among actors in the cocoa and pineapple value chains relate to the innovativeness of actors in the chains. The study showed that a policy environment that promoted public sector leadership in value chain functions and service provision, tended to offer less incentives for smallholder ...

  7. Patient and provider perspectives on improving the linkage of HIV ...

    African Journals Online (AJOL)

    This study examined barriers and facilitators to the linkage of HIV-positive pregnant women from antenatal care (ANC) to long-term HIV care from patient and provider perspectives, following the implementation of a collaborative quality improvement project in Eastern Uganda. It also solicited recommendations for improving ...

  8. Innovation and inter-firm linkages : new implications for policy

    NARCIS (Netherlands)

    Nooteboom, B

    This article discusses the implications for competition, innovation and learning of different forms of inter-firm linkage, ways to govern them, different 'generic systems' of innovation, and government policy. It employs a transformed theory of transactions that can deal with innovation and

  9. Localizing genes using linkage disequilibrium in plants: integrating ...

    African Journals Online (AJOL)

    GREGO

    2007-03-19

    Mar 19, 2007 ... Localizing genes using linkage disequilibrium in plants: integrating lessons ... reduce that association as a function of the marker distance from the QTL. ..... the gene locus enhanced the resolution power of asso- ciation tests .... agents, such as insects, birds, water and wind, so mating is determined by a ...

  10. Multiple operating models for data linkage: A privacy positive

    Directory of Open Access Journals (Sweden)

    Katrina Irvine

    2017-04-01

    Our data linkage centre will implement new operating models with cascading levels of data handling on behalf of custodians. Sharing or publication of empirical evidence on timeframes, efficiency and quality can provide useful inputs in the design of new operating models and assist with the development of stakeholder and public confidence.

  11. International Environmental Problems, Issue Linkage and the European Union

    NARCIS (Netherlands)

    Kroeze-Gil, J.

    2003-01-01

    This thesis explores the circumstances under which issue linkage can be applied to achieve cooperation on international environmental problems in general and on environmental problems in the European Union in particular. A major topic in this thesis is the development and analysis of cooperative and

  12. Linkages over Time between Adolescents' Relationships with Parents and Friends

    Science.gov (United States)

    De Goede, Irene H. A.; Branje, Susan J. T.; Delsing, Marc J. M. H.; Meeus, Wim H. J.

    2009-01-01

    This 5-wave longitudinal study examines linkages over time between adolescents' perceptions of relationships with parents and friends with respect to support, negative interaction, and power. A total of 575 early adolescents (54.1% boys) and 337 middle adolescents (43.3% boys) participated. Path analyses mainly showed bidirectional associations…

  13. Strengthening linkages of the financial services and real sectors of ...

    African Journals Online (AJOL)

    Strengthening linkages of the financial services and real sectors of the ... policy, financial sector credit and capital market activities have impacted on the real sector growth. ... sector as a result such financial crimes like misappropriation of funds. ... better results; more investment instruments such as derivatives, convertibles, ...

  14. The first genetic linkage map of Primulina eburnea (Gesneriaceae)

    Indian Academy of Sciences (India)

    Primulina eburneais a promising candidate for domestication and floriculture, since it is easy to culture and has beautiful flow-ers. An F2population of 189 individuals was established for the construction of first-generation linkage maps based onexpressed sequence tags-derived single-nucleotide polymorphism markers ...

  15. Evaluation of Price Linkages within the Supply Chain of Rice ...

    African Journals Online (AJOL)

    This paper evaluates price linkages within the supply chain of rice markets in Cross River State using weekly prices in three urban markets located in major rice producing areas of the State. The Johansen cointegration test indicated one cointegrating vector both at the 1% and 5% level of significance. The results of the ...

  16. Whole genome study of linkage disequilibrium in Sahiwal cattle

    African Journals Online (AJOL)

    Esnart Mukumbo

    2017-12-30

    Dec 30, 2017 ... 500,968 SNPs comprising 2518.1 Mb of the genome, were used for the LD estimation. The minior ..... on a high density SNP panel. BMC Genom. ... Linkage disequilibrium and the mapping of complex human traits. Trend.

  17. Linkages between landscapes and human well-being

    DEFF Research Database (Denmark)

    Bieling, Claudia; Plieninger, Tobias; Pirker, Heidemarie

    2014-01-01

    in Germany and Austria by performing open, single-question interviews with 262 respondents. Data reveal an outstanding relevance of nonmaterial values. Linkages between landscapes and human well-being are tied to specific features of the material environment but, likewise, practices and experiences play...

  18. Entrepreneurship And Business Management - Exploring Linkages For Sustainable Development

    Directory of Open Access Journals (Sweden)

    Dr Serah K Mbetwa

    2015-08-01

    Full Text Available Entrepreneurs have emerged as market leaders in todays business world amidst the numerous economic turmoil constantly affecting economies on a global scale. This research paper is on entrepreneurship and business management and its linkages to other business stakeholders. The research paper therefore discusses entrepreneurship and business management exploring the linkages to available financing and potential institutions for startup capital by linking entrepreneurs to the government financiers and the public clientele. It is believed that this can bring about achievement of sustainable development goals translating into sustainable development and hence economic growth. The idea of funding is echoed by Robert Rice 2016 An entrepreneur without funding is like a musician with no instruments. Sustainability and entrepreneurship sustainopreneurship is made possible with availability of information on linkages between entrepreneurs and financial lending institutions as well as government policy. It is hoped that the research will add to the existing knowledge and help entrepreneurs with funding options for their business ideas to come to life. Findings show that the government financial lending institutions and the public are the major linkages between entrepreneurship and business management and are critical for attaining sustainable development goals and achieving economic growth.

  19. Identification of Sex-determining Loci in Pacific White Shrimp Litopeneaus vannamei Using Linkage and Association Analysis.

    Science.gov (United States)

    Yu, Yang; Zhang, Xiaojun; Yuan, Jianbo; Wang, Quanchao; Li, Shihao; Huang, Hao; Li, Fuhua; Xiang, Jianhai

    2017-06-01

    The Pacific white shrimp Litopenaeus vannamei is a predominant aquaculture shrimp species in the world. Like other animals, the L. vannamei exhibited sexual dimorphism in growth trait. Mapping of the sex-determining locus will be very helpful to clarify the sex determination system and further benefit the shrimp aquaculture industry towards the production of mono-sex stocks. Based on the data used for high-density linkage map construction, linkage-mapping analysis was conducted. The sex determination region was mapped in linkage group (LG) 18. A large region from 0 to 21.205 cM in LG18 showed significant association with sex. However, none of the markers in this region showed complete association with sex in the other populations. So an association analysis was designed using the female parent, pool of female progenies, male parent, and pool of male progenies. Markers were de novo developed and those showing significant differences between female and male pools were identified. Among them, three sex-associated markers including one fully associated marker were identified. Integration of linkage and association analysis showed that the sex determination region was fine-mapped in a small region along LG18. The identified sex-associated marker can be used for the sex detection of this species at genetic level. The fine-mapped sex-determining region will contribute to the mapping of sex-determining gene and help to clarify sex determination system for L. vannamei.

  20. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers.

    Science.gov (United States)

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-08-04

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future.

  1. Special study on vegetative covers

    International Nuclear Information System (INIS)

    1988-11-01

    This report describes the findings of a special study on the use of vegetative covers to stabilize tailings piles for the Uranium Mill Tailings Remedial Action (UMTRA) Project. The principal rationale for using plants would be to establish a dynamic system for controlling water balance. Specifically, vegetation would be used to intercept and transpire precipitation to the atmosphere, rather than allowing water to drain into the tailings and mobilize contaminants. This would facilitate compliance with groundwater standards proposed for the UMTRA Project by the Environmental Protection Agency. The goals of the study were to evaluate the feasibility of using vegetative covers on UMTRA Project piles, define the advantages and disadvantages of vegetative covers, and develop general guidelines for their use when such use seems reasonable. The principal method for the study was to analyze and apply to the UMTRA Project the results of research programs on vegetative covers at other US Department of Energy (DOE) waste management facilities. The study also relied upon observations made of existing stabilized piles at UMTRA Project sites where natural vegetation is growing on the rock-covered surfaces. Water balance and erosion models were also used to quantify the long-term performance of vegetative covers planned for the topslopes of stabilized piles at Grand Junction and Durango, Colorado, two UMTRA Project sites where the decision was made during the course of this special study to use vegetative covers. Elements in the design and construction of the vegetative covers at these two sites are discussed in the report, with explanations of the differing features that reflect differing environmental conditions. 28 refs., 18 figs., 9 tabs

  2. Land-cover change detection

    Science.gov (United States)

    Chen, Xuexia; Giri, Chandra; Vogelmann, James

    2012-01-01

    Land cover is the biophysical material on the surface of the earth. Land-cover types include grass, shrubs, trees, barren, water, and man-made features. Land cover changes continuously.  The rate of change can be either dramatic and abrupt, such as the changes caused by logging, hurricanes and fire, or subtle and gradual, such as regeneration of forests and damage caused by insects (Verbesselt et al., 2001).  Previous studies have shown that land cover has changed dramatically during the past sevearal centuries and that these changes have severely affected our ecosystems (Foody, 2010; Lambin et al., 2001). Lambin and Strahlers (1994b) summarized five types of cause for land-cover changes: (1) long-term natural changes in climate conditions, (2) geomorphological and ecological processes, (3) human-induced alterations of vegetation cover and landscapes, (4) interannual climate variability, and (5) human-induced greenhouse effect.  Tools and techniques are needed to detect, describe, and predict these changes to facilitate sustainable management of natural resources.

  3. Transnational linkages in sustainability experiments : A typology and the case of solar photovoltaic energy in India

    NARCIS (Netherlands)

    Wieczorek, A.J.; Raven, R.; Berkhout, F.

    2015-01-01

    This paper explores transnational linkages in sustainability experiments. Transnational linkages refer to diverse cross-border relationships and interactions that can complement local, regional and national capabilities enabling sustainability experiments. The paper develops a typology of

  4. Detection of QTL for Carcass Quality on Chromosome 6 by Exploiting Linkage and Linkage Disequilibrium in Hanwoo

    Directory of Open Access Journals (Sweden)

    J.-H. Lee

    2012-01-01

    Full Text Available The purpose of this study was to improve mapping power and resolution for the QTL influencing carcass quality in Hanwoo, which was previously detected on the bovine chromosome (BTA 6. A sample of 427 steers were chosen, which were the progeny from 45 Korean proven sires in the Hanwoo Improvement Center, Seosan, Korea. The samples were genotyped with the set of 2,535 SNPs on BTA6 that were imbedded in the Illumina bovine 50 k chip. A linkage disequilibrium variance component mapping (LDVCM method, which exploited both linkage between sires and their steers and population-wide linkage disequilibrium, was applied to detect QTL for four carcass quality traits. Fifteen QTL were detected at 0.1% comparison-wise level, for which five, three, five, and two QTL were associated with carcass weight (CWT, backfat thickness (BFT, longissimus dorsi muscle area (LMA, and marbling score (Marb, respectively. The number of QTL was greater compared with our previous results, in which twelve QTL for carcass quality were detected on the BTA6 in the same population by applying other linkage disequilibrium mapping approaches. One QTL for LMA was detected on the distal region (110,285,672 to 110,633,096 bp with the most significant evidence for linkage (p<10−5. Another QTL that was detected on the proximal region (33,596,515 to 33,897,434 bp was pleiotrophic, i.e. influencing CWT, BFT, and LMA. Our results suggest that the LDVCM is a good alternative method for QTL fine-mapping in detection and characterization of QTL.

  5. Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping.

    Directory of Open Access Journals (Sweden)

    Bianca B Z Vigna

    Full Text Available The African species Urochloa humidicola (Rendle Morrone & Zuloaga (syn. Brachiaria humidicola (Rendle Schweick. is an important perennial forage grass found throughout the tropics. This species is polyploid, ranging from tetra to nonaploid, and apomictic, which makes genetic studies challenging; therefore, the number of currently available genetic resources is limited. The genomic architecture and evolution of U. humidicola and the molecular markers linked to apomixis were investigated in a full-sib F1 population obtained by crossing the sexual accession H031 and the apomictic cultivar U. humidicola cv. BRS Tupi, both of which are hexaploid. A simple sequence repeat (SSR-based linkage map was constructed for the species from 102 polymorphic and specific SSR markers based on simplex and double-simplex markers. The map consisted of 49 linkage groups (LGs and had a total length of 1702.82 cM, with 89 microsatellite loci and an average map density of 10.6 cM. Eight homology groups (HGs were formed, comprising 22 LGs, and the other LGs remained ungrouped. The locus that controls apospory (apo-locus was mapped in LG02 and was located 19.4 cM from the locus Bh027.c.D2. In the cytological analyses of some hybrids, bi- to hexavalents at diakinesis were observed, as well as two nucleoli in some meiocytes, smaller chromosomes with preferential allocation within the first metaphase plate and asynchronous chromosome migration to the poles during anaphase. The linkage map and the meiocyte analyses confirm previous reports of hybridization and suggest an allopolyploid origin of the hexaploid U. humidicola. This is the first linkage map of an Urochloa species, and it will be useful for future quantitative trait locus (QTL analysis after saturation of the map and for genome assembly and evolutionary studies in Urochloa spp. Moreover, the results of the apomixis mapping are consistent with previous reports and confirm the need for additional studies to search for

  6. Linkage mechanisms in the vertebrate skull: Structure and function of three-dimensional, parallel transmission systems.

    Science.gov (United States)

    Olsen, Aaron M; Westneat, Mark W

    2016-12-01

    Many musculoskeletal systems, including the skulls of birds, fishes, and some lizards consist of interconnected chains of mobile skeletal elements, analogous to linkage mechanisms used in engineering. Biomechanical studies have applied linkage models to a diversity of musculoskeletal systems, with previous applications primarily focusing on two-dimensional linkage geometries, bilaterally symmetrical pairs of planar linkages, or single four-bar linkages. Here, we present new, three-dimensional (3D), parallel linkage models of the skulls of birds and fishes and use these models (available as free kinematic simulation software), to investigate structure-function relationships in these systems. This new computational framework provides an accessible and integrated workflow for exploring the evolution of structure and function in complex musculoskeletal systems. Linkage simulations show that kinematic transmission, although a suitable functional metric for linkages with single rotating input and output links, can give misleading results when applied to linkages with substantial translational components or multiple output links. To take into account both linear and rotational displacement we define force mechanical advantage for a linkage (analogous to lever mechanical advantage) and apply this metric to measure transmission efficiency in the bird cranial mechanism. For linkages with multiple, expanding output points we propose a new functional metric, expansion advantage, to measure expansion amplification and apply this metric to the buccal expansion mechanism in fishes. Using the bird cranial linkage model, we quantify the inaccuracies that result from simplifying a 3D geometry into two dimensions. We also show that by combining single-chain linkages into parallel linkages, more links can be simulated while decreasing or maintaining the same number of input parameters. This generalized framework for linkage simulation and analysis can accommodate linkages of differing

  7. Linkage of the Canadian Study of Health and Aging to provincial administrative health care databases in Nova Scotia.

    Science.gov (United States)

    Yip, A M; Kephart, G; Rockwood, K

    2001-01-01

    The Canadian Study of Health and Aging (CSHA) was a cohort study that included 528 Nova Scotian community-dwelling participants. Linkage of CSHA and provincial Medical Services Insurance (MSI) data enabled examination of health care utilization in this subsample. This article discusses methodological and ethical issues of database linkage and explores variation in the use of health services by demographic variables and health status. Utilization over 24 months following baseline was extracted from MSI's physician claims, hospital discharge abstracts, and Pharmacare claims databases. Twenty-nine subjects refused consent for access to their MSI file; health card numbers for three others could not be retrieved. A significant difference in healthcare use by age and self-rated health was revealed. Linkage of population-based data with provincial administrative health care databases has the potential to guide health care planning and resource allocation. This process must include steps to ensure protection of confidentiality. Standard practices for linkage consent and routine follow-up should be adopted. The Canadian Study of Health and Aging (CSHA) began in 1991-92 to explore dementia, frailty, and adverse health outcomes (Canadian Study of Health and Aging Working Group, 1994). The original CSHA proposal included linkage to provincial administrative health care databases by the individual CSHA study centers to enhance information on health care utilization and outcomes of study participants. In Nova Scotia, the Medical Services Insurance (MSI) administration, which drew the sampling frame for the original CSHA, did not retain the list of corresponding health card numbers. Furthermore, consent for this access was not asked of participants at the time of the first interview. The objectives of this study reported here were to examine the feasibility and ethical considerations of linking data from the CSHA to MSI utilization data, and to explore variation in health

  8. Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench)

    Science.gov (United States)

    Yabe, Shiori; Hara, Takashi; Ueno, Mariko; Enoki, Hiroyuki; Kimura, Tatsuro; Nishimura, Satoru; Yasui, Yasuo; Ohsawa, Ryo; Iwata, Hiroyoshi

    2014-01-01

    For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information. PMID:25914583

  9. Nance-Horan syndrome: linkage analysis in a family from The Netherlands

    NARCIS (Netherlands)

    Bergen, A. A.; ten Brink, J.; Schuurman, E. J.; Bleeker-Wagemakers, E. M.

    1994-01-01

    Linkage analysis was carried out in a Dutch family with Nance-Horan (NH) syndrome. Close linkage without recombination between NH and the Xp loci DXS207, DXS43, and DXS365 (zmax = 3.23) was observed. Multipoint linkage analysis and the analysis of recombinations in multiple informative meioses

  10. Data Linkage in VET Research: Opportunities, Challenges and Principles. Discussion Paper

    Science.gov (United States)

    Osborne, Kristen; Fowler, Craig; Circelli, Michelle

    2018-01-01

    This discussion paper explores the possibilities and risks that data linkage presents for the vocational education and training (VET) sector. Along with a broad overview of the nature of data linkage, it highlights possible applications for data linkage in the VET sector and examines the key challenges associated with its use. A number of case…

  11. Symmetry and group theory in chemistry

    CERN Document Server

    Ladd, M

    1998-01-01

    A comprehensive discussion of group theory in the context of molecular and crystal symmetry, this book covers both point-group and space-group symmetries.Provides a comprehensive discussion of group theory in the context of molecular and crystal symmetryCovers both point-group and space-group symmetriesIncludes tutorial solutions

  12. The National Land Cover Database

    Science.gov (United States)

    Homer, Collin G.; Fry, Joyce A.; Barnes, Christopher A.

    2012-01-01

    The National Land Cover Database (NLCD) serves as the definitive Landsat-based, 30-meter resolution, land cover database for the Nation. NLCD provides spatial reference and descriptive data for characteristics of the land surface such as thematic class (for example, urban, agriculture, and forest), percent impervious surface, and percent tree canopy cover. NLCD supports a wide variety of Federal, State, local, and nongovernmental applications that seek to assess ecosystem status and health, understand the spatial patterns of biodiversity, predict effects of climate change, and develop land management policy. NLCD products are created by the Multi-Resolution Land Characteristics (MRLC) Consortium, a partnership of Federal agencies led by the U.S. Geological Survey. All NLCD data products are available for download at no charge to the public from the MRLC Web site: http://www.mrlc.gov.

  13. Design control and scientific investigations: Is there any linkage?

    International Nuclear Information System (INIS)

    Richards, R.R.

    1995-01-01

    The quality assurance requirements that apply to the effort to achieve safe transportation, storage, and disposal of high-level nuclear waste specify that ''design control'' be applied to design activities. That effort also involves extensive scientific investigation activities to, among other things, develop information that may be used in engineering design activities. Individuals who are charged with the implementation of such quality assurance requirements have come to a variety of conclusions about whether there is any firm linkage between design control and the conduct of scientific investigations. This paper contends that there is a reasonable and necessary linkage between ''design control'' and scientific activities, though not a connection that has traditionally been made and not one addressed in the QA standards for radioactive waste management programs

  14. Countering Islamic State Messaging Through “Linkage-Based” Analysis

    Directory of Open Access Journals (Sweden)

    J.M. Berger

    2017-08-01

    Full Text Available The Islamic State’s recent losses on the battlefield, including significant casualties within its media and propaganda division, offer a unique opportunity to inject competing and alternative messages into the information space. This paper proposes that the content of such messages should be guided by a linkage-based analysis of existing Islamic State messaging. A linkage-based analysis of a top-level 2017 audio message by Islamic State spokesperson Abu Hasan al Muhajir offers several potential insights into crafting effective content for competing and alternative messages. A comparison of the 2017 work to earlier Islamic State messaging also reveals specific opportunities to undermine the credibility of the organisation’s broader propaganda programme by highlighting the organisation’s repeated failure to follow through on its extravagantly promised commitment to achieving its stated goals.

  15. An improved recommendation algorithm via weakening indirect linkage effect

    Science.gov (United States)

    Chen, Guang; Qiu, Tian; Shen, Xiao-Quan

    2015-07-01

    We propose an indirect-link-weakened mass diffusion method (IMD), by considering the indirect linkage and the source object heterogeneity effect in the mass diffusion (MD) recommendation method. Experimental results on the MovieLens, Netflix, and RYM datasets show that, the IMD method greatly improves both the recommendation accuracy and diversity, compared with a heterogeneity-weakened MD method (HMD), which only considers the source object heterogeneity. Moreover, the recommendation accuracy of the cold objects is also better elevated in the IMD than the HMD method. It suggests that eliminating the redundancy induced by the indirect linkages could have a prominent effect on the recommendation efficiency in the MD method. Project supported by the National Natural Science Foundation of China (Grant No. 11175079) and the Young Scientist Training Project of Jiangxi Province, China (Grant No. 20133BCB23017).

  16. Nuclear hazard/fire hazard: an elusive and important linkage

    International Nuclear Information System (INIS)

    Mariani, L.P.

    1977-01-01

    The Brown's Ferry Fire signaled a yellow alert for nuclear safety related fire protection and showed that fire protection engineering must be regarded as a bona fide nuclear discipline. A single-failure design criteria violation resulted in fire damage to plant systems and plant instrumentation. Localized damage lead to significant consequences. Although the linkage between fire and nuclear hazard is termed subtle, effective standards and criteria development must be aimed to future plants. Combined fire protection and nuclear engineering inspections are planned

  17. The changing international linkages of Switzerland: An overview

    OpenAIRE

    Tille, Cédric

    2017-01-01

    Over the last decade, the economic linkages between Switzerland and the rest of the world have been transformed. First, merchanting and the chemical industry account for an increasing share of international trade, with chemicals exports expanding robustly in recent years despite the European crisis and the strong Swiss franc. Second, the nature of international financial integration has changed. While private investors drove Switzerland's financial flows and net foreign assets before the fina...

  18. Linear models for joint association and linkage QTL mapping

    Directory of Open Access Journals (Sweden)

    Fernando Rohan L

    2009-09-01

    Full Text Available Abstract Background Populational linkage disequilibrium and within-family linkage are commonly used for QTL mapping and marker assisted selection. The combination of both results in more robust and accurate locations of the QTL, but models proposed so far have been either single marker, complex in practice or well fit to a particular family structure. Results We herein present linear model theory to come up with additive effects of the QTL alleles in any member of a general pedigree, conditional to observed markers and pedigree, accounting for possible linkage disequilibrium among QTLs and markers. The model is based on association analysis in the founders; further, the additive effect of the QTLs transmitted to the descendants is a weighted (by the probabilities of transmission average of the substitution effects of founders' haplotypes. The model allows for non-complete linkage disequilibrium QTL-markers in the founders. Two submodels are presented: a simple and easy to implement Haley-Knott type regression for half-sib families, and a general mixed (variance component model for general pedigrees. The model can use information from all markers. The performance of the regression method is compared by simulation with a more complex IBD method by Meuwissen and Goddard. Numerical examples are provided. Conclusion The linear model theory provides a useful framework for QTL mapping with dense marker maps. Results show similar accuracies but a bias of the IBD method towards the center of the region. Computations for the linear regression model are extremely simple, in contrast with IBD methods. Extensions of the model to genomic selection and multi-QTL mapping are straightforward.

  19. Genome scan for linkage to Gilles de la Tourette syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Barr, C.L.; Livingston, J.; Williamson, R. [and others

    1994-09-01

    Gilles de la Tourette Syndrome (TS) is a familial, neuropsychiatric disorder characterized by chronic, intermittent motor and vocal tics. In addition to tics, affected individuals frequently display symptoms such as attention-deficit hyperactivity disorder and/or obsessive compulsive disorder. Genetic analyses of family data have suggested that susceptibility to the disorder is most likely due to a single genetic locus with a dominant mode of transmission and reduced penetrance. In the search for genetic linkage for TS, we have collected well-characterized pedigrees with multiple affected individuals on whom extensive diagnostic evaluations have been done. The first stage of our study is to scan the genome systematically using a panel of uniformly spaced (10 to 20 cM), highly polymorphic, microsatellite markers on 5 families segregating TS. To date, 290 markers have been typed and 3,660 non-overlapping cM of the genome have been excluded for possible linkage under the assumption of genetic homogeneity. Because of the possibility of locus heterogeneity overall summed exclusion is not considered tantamount to absolute exclusion of a disease locus in that region. The results from each family are carefully evaluated and a positive lod score in a single family is followed up by typing closely linked markers. Linkage to TS was examined by two-point analysis using the following genetic model: single autosomal dominant gene with gene frequency .003 and maximum penetrance of .99. An age-of-onset correction is included using a linear function increasing from age 2 years to 21 years. A small rate of phenocopies is also incorporated into the model. Only individuals with TS or CMT according to DSM III-R criteria were regarded as affected for the purposes of this summary. Additional markers are being tested to provide coverage at 5 cM intervals. Moreover, we are currently analyzing the data non-parametrically using the Affected-Pedigree-Member Method of linkage analysis.

  20. Backward linkages from foreign investors to domestic firms

    OpenAIRE

    Apostolov, Mico

    2016-01-01

    The analysis of how to design policies to promote backward linkages would not be complete without introducing sound discovery into the debate. Foreign investors would naturally prefer to avoid creating rivals to their market position, aiming at horizontal positioning. But workers and managers often leave foreign plants to start up their own; local firms learn from watching the operations of foreigners. In the vertical direction, in cont...

  1. Linkage Disequilibrium between STRPs and SNPs across the Human Genome

    OpenAIRE

    Payseur, Bret A.; Place, Michael; Weber, James L.

    2008-01-01

    Patterns of linkage disequilibrium (LD) reveal the action of evolutionary processes and provide crucial information for association mapping of disease genes. Although recent studies have described the landscape of LD among single nucleotide polymorphisms (SNPs) from across the human genome, associations involving other classes of molecular variation remain poorly understood. In addition to recombination and population history, mutation rate and process are expected to shape LD. To test this i...

  2. Identifying causal linkages between environmental variables and African conflicts

    Science.gov (United States)

    Nguy-Robertson, A. L.; Dartevelle, S.

    2017-12-01

    Environmental variables that contribute to droughts, flooding, and other natural hazards are often identified as factors contributing to conflict; however, few studies attempt to quantify these causal linkages. Recent research has demonstrated that the environment operates within a dynamical system framework and the influence of variables can be identified from convergent cross mapping (CCM) between shadow manifolds. We propose to use CCM to identify causal linkages between environmental variables and incidences of conflict. This study utilizes time series data from Climate Forecast System ver. 2 and MODIS satellite sensors processed using Google Earth Engine to aggregate country and regional trends. These variables are then compared to Armed Conflict Location & Event Data Project observations at similar scales. Results provide relative rankings of variables and their linkage to conflict. Being able to identify which factors contributed more strongly to a conflict can allow policy makers to prepare solutions to mitigate future crises. Knowledge of the primary environmental factors can lead to the identification of other variables to examine in the causal network influencing conflict.

  3. Evolution of zygotic linkage disequilibrium in a finite local population.

    Directory of Open Access Journals (Sweden)

    Xin-Sheng Hu

    Full Text Available One crucial feature of zygotic linkage disequilibrium (LD analysis is its direct use of diploid genotyping data, irrespective of the type of mating system. Previous theories from an evolutionary perspective mainly focus on gametic LD, but the equivalent development for zygotic LD is not available. Here I study the evolution of zygotic LD and the covariances between gametic and zygotic LDs or between distinct zygotic LDs in a finite local population under constant immigration from a continent population. I derive the analytical theory under genetic hitchhiking effects or in a neutral process. Results indicate that zygotic LDs (diploid level are more informative than gametic LD (haploid level in indicating the effects of different evolutionary forces. Zygotic LDs may be greater than or comparable to gametic LD under the epistatic selection process, but smaller than gametic LD under the non epistatic selection process. The covariances between gametic and zygotic LDs are strongly affected by the mating system, linkage distance, and genetic drift effects, but weakly affected by seed and pollen flow and natural selection. The covariances between different zygotic LDs are generally robust to the effects of gene flow, selection, and linkage distance, but sensitive to the effects of genetic drift and mating system. Consistent patterns exist for the covariances between the zygotic LDs for the two-locus genotypes with one common genotype at one locus or without any common genotype at each locus. The results highlight that zygotic LDs can be applied to detecting natural population history.

  4. Arctic-midlatitude weather linkages in North America

    Science.gov (United States)

    Overland, James E.; Wang, Muyin

    2018-06-01

    There is intense public interest in whether major Arctic changes can and will impact midlatitude weather such as cold air outbreaks on the central and east side of continents. Although there is progress in linkage research for eastern Asia, a clear gap is conformation for North America. We show two stationary temperature/geopotential height patterns where warmer Arctic temperatures have reinforced existing tropospheric jet stream wave amplitudes over North America: a Greenland/Baffin Block pattern during December 2010 and an Alaska Ridge pattern during December 2017. Even with continuing Arctic warming over the past decade, other recent eastern US winter months were less susceptible for an Arctic linkage: the jet stream was represented by either zonal flow, progressive weather systems, or unfavorable phasing of the long wave pattern. The present analysis lays the scientific controversy over the validity of linkages to the inherent intermittency of jet stream dynamics, which provides only an occasional bridge between Arctic thermodynamic forcing and extended midlatitude weather events.

  5. A dynamic birth-death model via Intrinsic Linkage

    Directory of Open Access Journals (Sweden)

    Robert Schoen

    2013-05-01

    Full Text Available BACKGROUND Dynamic population models, or models with changing vital rates, are only beginning to receive serious attention from mathematical demographers. Despite considerable progress, there is still no general analytical solution for the size or composition of a population generated by an arbitrary sequence of vital rates. OBJECTIVE The paper introduces a new approach, Intrinsic Linkage, that in many cases can analytically determine the birth trajectory of a dynamic birth-death population. METHODS Intrinsic Linkage assumes a weighted linear relationship between (i the time trajectory of proportional increases in births in a population and (ii the trajectory of the intrinsic rates of growth of the projection matrices that move the population forward in time. Flexibility is provided through choice of the weighting parameter, w, that links these two trajectories. RESULTS New relationships are found linking implied intrinsic and observed population patterns of growth. Past experience is "forgotten" through a process of simple exponential decay. When the intrinsic growth rate trajectory follows a polynomial, exponential, or cyclical pattern, the population birth trajectory can be expressed analytically in closed form. Numerical illustrations provide population values and relationships in metastable and cyclically stable models. Plausible projection matrices are typically found for a broad range of values of w, although w appears to vary greatly over time in actual populations. CONCLUSIONS The Intrinsic Linkage approach extends current techniques for dynamic modeling, revealing new relationships between population structures and the changing vital rates that generate them.

  6. Linkage and related analyses of Barrett's esophagus and its associated adenocarcinomas.

    Science.gov (United States)

    Sun, Xiangqing; Elston, Robert; Falk, Gary W; Grady, William M; Faulx, Ashley; Mittal, Sumeet K; Canto, Marcia I; Shaheen, Nicholas J; Wang, Jean S; Iyer, Prasad G; Abrams, Julian A; Willis, Joseph E; Guda, Kishore; Markowitz, Sanford; Barnholtz-Sloan, Jill S; Chandar, Apoorva; Brock, Wendy; Chak, Amitabh

    2016-07-01

    Familial aggregation and segregation analysis studies have provided evidence of a genetic basis for esophageal adenocarcinoma (EAC) and its premalignant precursor, Barrett's esophagus (BE). We aim to demonstrate the utility of linkage analysis to identify the genomic regions that might contain the genetic variants that predispose individuals to this complex trait (BE and EAC). We genotyped 144 individuals in 42 multiplex pedigrees chosen from 1000 singly ascertained BE/EAC pedigrees, and performed both model-based and model-free linkage analyses, using S.A.G.E. and other software. Segregation models were fitted, from the data on both the 42 pedigrees and the 1000 pedigrees, to determine parameters for performing model-based linkage analysis. Model-based and model-free linkage analyses were conducted in two sets of pedigrees: the 42 pedigrees and a subset of 18 pedigrees with female affected members that are expected to be more genetically homogeneous. Genome-wide associations were also tested in these families. Linkage analyses on the 42 pedigrees identified several regions consistently suggestive of linkage by different linkage analysis methods on chromosomes 2q31, 12q23, and 4p14. A linkage on 15q26 is the only consistent linkage region identified in the 18 female-affected pedigrees, in which the linkage signal is higher than in the 42 pedigrees. Other tentative linkage signals are also reported. Our linkage study of BE/EAC pedigrees identified linkage regions on chromosomes 2, 4, 12, and 15, with some reported associations located within our linkage peaks. Our linkage results can help prioritize association tests to delineate the genetic determinants underlying susceptibility to BE and EAC.

  7. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

    Directory of Open Access Journals (Sweden)

    King Graham J

    2010-10-01

    Full Text Available Abstract Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola. Results In this study, we identified over 23,000 simple sequence repeats (SSRs from 536 sequenced BACs. 890 SSR markers (designated as BrGMS were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH. Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs, 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus. Conclusion The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species.

  8. Emerging Infectious Diseases Cover Art

    Centers for Disease Control (CDC) Podcasts

    2017-07-26

    Byron Breedlove, managing editor of the EID Journal, discusses his approach to cover art.  Created: 7/26/2017 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 7/26/2017.

  9. Cover Crops in Hillside Agriculture

    International Development Research Centre (IDRC) Digital Library (Canada)

    Our study focuses on the wet tropical hillsides of northern Honduras (Figure 1). ..... The eastern extreme of the region (Jutiapa) is a dry spot, with less rainfall (2 000 mm a-1) as a result ...... Paper presented at the International Workshop on Green Manure–Cover Crops for Smallholders in ..... Lamaster, J.P.; Jones, I.R. 1923.

  10. Cover times of random searches

    Science.gov (United States)

    Chupeau, Marie; Bénichou, Olivier; Voituriez, Raphaël

    2015-10-01

    How long must one undertake a random search to visit all sites of a given domain? This time, known as the cover time, is a key observable to quantify the efficiency of exhaustive searches, which require a complete exploration of an area and not only the discovery of a single target. Examples range from immune-system cells chasing pathogens to animals harvesting resources, from robotic exploration for cleaning or demining to the task of improving search algorithms. Despite its broad relevance, the cover time has remained elusive and so far explicit results have been scarce and mostly limited to regular random walks. Here we determine the full distribution of the cover time for a broad range of random search processes, including Lévy strategies, intermittent strategies, persistent random walks and random walks on complex networks, and reveal its universal features. We show that for all these examples the mean cover time can be minimized, and that the corresponding optimal strategies also minimize the mean search time for a single target, unambiguously pointing towards their robustness.

  11. Genetic Linkage Map Construction and QTL Analysis of Two Interspecific Reproductive Isolation Traits in Sponge Gourd.

    Science.gov (United States)

    Wu, Haibin; He, Xiaoli; Gong, Hao; Luo, Shaobo; Li, Mingzhu; Chen, Junqiu; Zhang, Changyuan; Yu, Ting; Huang, Wangping; Luo, Jianning

    2016-01-01

    The hybrids between Luffa acutangula (L.) Roxb. and L.cylindrica (L.) Roem. have strong heterosis effects. However, some reproductive isolation traits hindered their normal hybridization and fructification, which was mainly caused by the flowering time and hybrid pollen sterility. In order to study the genetic basis of two interspecific reproductive isolation traits, we constructed a genetic linkage map using an F2 population derived from a cross between S1174 [L. acutangula (L.) Roxb.] and 93075 [L. cylindrica (L.) Roem.]. The map spans 1436.12 CentiMorgans (cM), with an average of 8.11 cM among markers, and consists of 177 EST-SSR markers distributed in 14 linkage groups (LG) with an average of 102.58 cM per LG. Meanwhile, we conducted colinearity analysis between the sequences of EST-SSR markers and the genomic sequences of cucumber, melon and watermelon. On the basis of genetic linkage map, we conducted QTL mapping of two reproductive isolation traits in sponge gourd, which were the flowering time and hybrid male sterility. Two putative QTLs associated with flowering time (FT) were both detected on LG 1. The accumulated contribution of these two QTLs explained 38.07% of the total phenotypic variance (PV), and each QTL explained 15.36 and 22.71% of the PV respectively. Four QTLs for pollen fertility (PF) were identified on LG 1 (qPF1.1 and qPF1.2), LG 3 (qPF3) and LG 7 (qPF7), respectively. The percentage of PF explained by these QTLs varied from 2.91 to 16.79%, and all together the four QTLs accounted for 39.98% of the total PV. Our newly developed EST-SSR markers and linkage map are very useful for gene mapping, comparative genomics and molecular marker-assisted breeding. These QTLs for interspecific reproductive isolation will also contribute to the cloning of genes relating to interspecific reproductive isolation and the utilization of interspecific heterosis in sponge gourd in further studies.

  12. Identifying common barriers and facilitators to linkage and retention in chronic disease care in western Kenya

    Directory of Open Access Journals (Sweden)

    Beth Rachlis

    2016-08-01

    Full Text Available Abstract Background Sub-Saharan Africa is increasingly being challenged in providing care and treatment for chronic diseases, both communicable and non-communicable. In order to address the challenges of linkage to and retention in chronic disease management, there is the need to understand the factors that can influence engagement in care. We conducted a qualitative study to identify barriers and facilitators to linkage and retention in chronic care for HIV, tuberculosis (TB and Hypertension (HTN as part of the Academic Model Providing Access to Healthcare (AMPATH program in western Kenya. Methods In-depth interviews and focus group discussions were conducted July 2012-August 2013. Study participants were purposively sampled from three AMPATH clinics and included patients within the AMPATH program receiving HIV, TB, and HTN care, as well as caregivers of children with HIV, community leaders, and healthcare providers. A set of interview guides were developed to explore perceived barriers and facilitators to chronic disease management, particularly related to linkage to and retention in HIV, TB and HTN care. Data were coded and various themes were identified. We organized the concepts and themes generated using the Andersen-Newman Framework of Health Services Utilization. Results A total of 235 participants including 110 individuals living with HIV (n = 50, TB (n = 39, or HTN (n = 21; 24 caregivers; 10 community leaders; and 62 healthcare providers participated. Barriers and facilitators were categorized as predisposing characteristics, enabling resources and need factors. Many of the facilitators and barriers reported in this study were consistently reported across disease categories including personal drive, patient-provider relationships and the need for social and peer support. Conclusions Our findings provide insight into the individual as well as broader structural factors that can deter or encourage linkage and retention that

  13. ANALISIS KEBIJAKAN LINKAGE PROGRAM LEMBAGA KEUANGAN SYARIAH DALAM RANGKA PEMBERDAYAAN UKM DI INDONESIA

    Directory of Open Access Journals (Sweden)

    Siti Hamidah

    2016-03-01

    Linkage program adalah program yang menghubungkan bank dengan pelaku usaha mikro kecil melalui lembaga keuangan mikro. Kelemahan dalam Linkage program adalah pada aspek peraturan yang tersebar dalam berbagai aturan, dan khusus bagi lembaga keuangan syariah terdapat pula kendala berkaitan dengan kesesuaian dengan ketentuan syariah. Dari penelitian dengan pendekatan perundang-undangan dan pendekatan konseptual ini diperoleh inventarisasi serta analisis kebijakan Linkage Program bagi Lembaga Keuangan Syariah dalam hukum positif Indonesia. Kebijakan terkait Linkage program, diklasifikasi dalam 2 kelompok, yaitu kebijakan substansi dan prosedural. Aturan inilah yang menjadi rujukan bagi lembaga keuangan syariah rangka pemberdayaan usaha kecil mikro di Indonesia. Kata kunci: Linkage program, lembaga keuangan syariah, usaha mikro kecil

  14. Family-Peer Linkages for Children with Intellectual Disability and Children with Learning Disabilities.

    Science.gov (United States)

    Floyd, Frank J; Olsen, Darren L

    2017-09-01

    Family interactions are potential contexts for children with intellectual and learning disabilities to develop skillful social behaviors needed to relate effectively with peers. This study examined problem solving interactions within families of elementary school-age children (7-11 years) with intellectual disability (n = 37), specific learning disabilities (n =48), and without disabilities (n = 22). After accounting for group differences in children's behaviors and peer acceptance, across all groups, mothers' behaviors that encouraged egalitarian problem solving predicted more engaged and skillful problem solving by the children. However, mothers' controlling, directive behaviors predicted fewer of these behaviors by the children. Fathers' behaviors had mixed associations with the children's actions, possibly because they were reactive to children's unengaged and negative behaviors. For the children, greater involvement, more facilitative behaviors, and less negativity with their families were associated with greater acceptance from their peers, supporting family-peer linkages for children at risk for peer rejection.

  15. Linkage of α-cyclodextrin-terminated poly(dimethylsiloxanes by inclusion of quasi bifunctional ferrocene

    Directory of Open Access Journals (Sweden)

    Helmut Ritter

    2013-07-01

    Full Text Available We report the noncovalent linkage of terminally substituted oligo(dimethylsiloxanes bearing α-cyclodextrins (α-CD as host end groups for the cyclopentadienyl rings of ferrocene. This double complexation of unsubstituted ferrocene leads to a supramolecuar formation of the siloxane strands. Structural characterization was performed by the use of 1H NMR and IR spectroscopy and by mass spectrometry. Electron microscopy studies and dynamic light scattering measurements show a significant decrease of the derivative size after the complexation with ferrocene. In addition, further evidence for the successful complexation of the end groups was verified by the shifts of the protons in the 1H NMR spectra and in the correlation signals of the 2D ROESY NMR spectra.

  16. A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)

    Institute of Scientific and Technical Information of China (English)

    ZHAI Hui-jie; FENG Zhi-yu; LIU Xin-ye; CHENG Xue-jiao; PENG Hui-ru; YAO Ying-yin; SUN Qi-xin; NI Zhong-fu

    2015-01-01

    The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci (QTLs) controlling agronomically important traits. In this study, simple sequence repeat (SSR) markers and Illumina 9K iSelect single nucleotide polymorphism (SNP) genechip were employed to construct one genetic linkage map of common wheat (Triticum aestivum L.) using 191 recombinant inbred lines (RILs) derived from cross Yu 8679xJing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 cM and 1 000 marker bins, with an average interval distance of 1.66 cM. A, B and D genomes covered 719.1,703.5 and 237.3 cM, with an average interval distance of 1.66, 1.45 and 2.9 cM, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754 (92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184 (97.4%) were located on one single chromosome, and the rest 31 (2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags (ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.

  17. Dissection of the major late blight resistance cluster on potato linkage group IV

    NARCIS (Netherlands)

    Lokossou, A.A.

    2010-01-01

    Potato is consumed worldwide and represents the fourth most important staple food crop after rice and wheat. Potato cultivars display a large variety of color, shape, taste, cooking properties and starch content but are all derived from the same species; Solanum tuberosum. Potato breeding is an

  18. A guide to evaluating linkage quality for the analysis of linked data.

    Science.gov (United States)

    Harron, Katie L; Doidge, James C; Knight, Hannah E; Gilbert, Ruth E; Goldstein, Harvey; Cromwell, David A; van der Meulen, Jan H

    2017-10-01

    Linked datasets are an important resource for epidemiological and clinical studies, but linkage error can lead to biased results. For data security reasons, linkage of personal identifiers is often performed by a third party, making it difficult for researchers to assess the quality of the linked dataset in the context of specific research questions. This is compounded by a lack of guidance on how to determine the potential impact of linkage error. We describe how linkage quality can be evaluated and provide widely applicable guidance for both data providers and researchers. Using an illustrative example of a linked dataset of maternal and baby hospital records, we demonstrate three approaches for evaluating linkage quality: applying the linkage algorithm to a subset of gold standard data to quantify linkage error; comparing characteristics of linked and unlinked data to identify potential sources of bias; and evaluating the sensitivity of results to changes in the linkage procedure. These approaches can inform our understanding of the potential impact of linkage error and provide an opportunity to select the most appropriate linkage procedure for a specific analysis. Evaluating linkage quality in this way will improve the quality and transparency of epidemiological and clinical research using linked data. © The Author 2017. Published by Oxford University Press on behalf of the International Epidemiological Association.

  19. Construction of the High-Density Genetic Linkage Map and Chromosome Map of Large Yellow Croaker (Larimichthys crocea

    Directory of Open Access Journals (Sweden)

    Jingqun Ao

    2015-11-01

    Full Text Available High-density genetic maps are essential for genome assembly, comparative genomic analysis and fine mapping of complex traits. In this study, 31,191 single nucleotide polymorphisms (SNPs evenly distributed across the large yellow croaker (Larimichthys crocea genome were identified using restriction-site associated DNA sequencing (RAD-seq. Among them, 10,150 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs. The total length of the genetic linkage map was 5451.3 cM with an average distance of 0.54 cM between loci. This represents the densest genetic map currently reported for large yellow croaker. Using 2889 SNPs to target specific scaffolds, we assigned 533 scaffolds, comprising 421.44 Mb (62.04% of the large yellow croaker assembled sequence, to the 24 linkage groups. The mapped assembly scaffolds in large yellow croaker were used for genome synteny analyses against the stickleback (Gasterosteus aculeatus and medaka (Oryzias latipes. Greater synteny was observed between large yellow croaker and stickleback. This supports the hypothesis that large yellow croaker is more closely related to stickleback than to medaka. Moreover, 1274 immunity-related genes and 195 hypoxia-related genes were mapped to the 24 chromosomes of large yellow croaker. The integration of the high-resolution genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits in large yellow croaker.

  20. Geometric group theory

    CERN Document Server

    Druţu, Cornelia

    2018-01-01

    The key idea in geometric group theory is to study infinite groups by endowing them with a metric and treating them as geometric spaces. This applies to many groups naturally appearing in topology, geometry, and algebra, such as fundamental groups of manifolds, groups of matrices with integer coefficients, etc. The primary focus of this book is to cover the foundations of geometric group theory, including coarse topology, ultralimits and asymptotic cones, hyperbolic groups, isoperimetric inequalities, growth of groups, amenability, Kazhdan's Property (T) and the Haagerup property, as well as their characterizations in terms of group actions on median spaces and spaces with walls. The book contains proofs of several fundamental results of geometric group theory, such as Gromov's theorem on groups of polynomial growth, Tits's alternative, Stallings's theorem on ends of groups, Dunwoody's accessibility theorem, the Mostow Rigidity Theorem, and quasiisometric rigidity theorems of Tukia and Schwartz. This is the f...

  1. Genetic linkage map and QTL identification for adventitious rooting traits in red gum eucalypts.

    Science.gov (United States)

    Sumathi, Murugan; Bachpai, Vijaya Kumar Waman; Mayavel, A; Dasgupta, Modhumita Ghosh; Nagarajan, Binai; Rajasugunasekar, D; Sivakumar, Veerasamy; Yasodha, Ramasamy

    2018-05-01

    The eucalypt species, Eucalyptus tereticornis and Eucalyptus camaldulensis , show tolerance to drought and salinity conditions, respectively, and are widely cultivated in arid and semiarid regions of tropical countries. In this study, genetic linkage map was developed for interspecific cross E. tereticornis  ×  E. camaldulensis using pseudo-testcross strategy with simple sequence repeats (SSRs), intersimple sequence repeats (ISSRs), and sequence-related amplified polymorphism (SRAP) markers. The consensus genetic map comprised totally 283 markers with 84 SSRs, 94 ISSRs, and 105 SRAP markers on 11 linkage groups spanning 1163.4 cM genetic distance. Blasting the SSR sequences against E. grandis sequences allowed an alignment of 64% and the average ratio of genetic-to-physical distance was 1.7 Mbp/cM, which strengths the evidence that high amount of synteny and colinearity exists among eucalypts genome. Blast searches also revealed that 37% of SSRs had homologies with genes, which could potentially be used in the variety of downstream applications including candidate gene polymorphism. Quantitative trait loci (QTL) analysis for adventitious rooting traits revealed six QTL for rooting percent and root length on five chromosomes with interval and composite interval mapping. All the QTL explained 12.0-14.7% of the phenotypic variance, showing the involvement of major effect QTL on adventitious rooting traits. Increasing the density of markers would facilitate the detection of more number of small-effect QTL and also underpinning the genes involved in rooting process.

  2. Allele-specific marker generation and linkage mapping on the Xiphophorus sex chromosomes.

    Science.gov (United States)

    Woolcock, B; Kazianis, S; Lucito, R; Walter, R B; Kallman, K D; Morizot, D C; Vielkind, J R

    2006-01-01

    There is great interest in the sex chromosomes of Xiphophorus fishes because both WY/YY and XX/XY sex-determining mechanisms function in these species, with at least one taxon possessing all three types of sex chromosomes, and because in certain interspecific hybrids melanoma arises as a consequence of inheritance of the sex-linked macromelanophore determining locus (MDL). Representational difference analysis (RDA) has been used to clone two sequences from the sex-determining region of X. maculatus, including a cholinergic receptor, nicotinic, delta polypeptide (CHRND) orthologue. Allele-specific assays for these sequences, as well as for the sex-linked XMRK1 and XMRK2 genes, were developed to distinguish W, X, and Y chromosomes derived from a X. maculatus (XX/XY) strain and a X. helleri (WY/YY) strain. Linkage mapping localized these markers to linkage group (LG) 24. No recombinants were observed between XMRK2 and MDL, confirming a role for XMRK2 in macromelanophore development. Although the master sex-determining (SD) locus certainly resides on Xiphophorus LG 24, autosomal loci are probably involved in sex determination as well, as indicated by the abnormal sex ratios in the backcross hybrids that contrast theoretical predictions based on LG 24 genotyping. Marker development and allelic discrimination on the Xiphophorus sex chromosomes should prove highly useful for studies that utilize this genus as an animal model.

  3. Development of a humanoid robot hand with coupling four-bar linkage

    Directory of Open Access Journals (Sweden)

    Xinhua Liu

    2017-01-01

    Full Text Available To improve the operating performance of robots’ end-effector, a humanoid robot hand based on coupling four-bar linkage was designed. An improved transmission system was proposed for the base joint of the thumb. Thus, a far greater motion range and more reasonable layout of the palm were obtained. Moreover, the mathematical model for kinematics simulation was presented based on the Assur linkage group theory to verify and optimize the proposed structure. To research the motion relationships between the fingers and the object in the process of grasping object, the grasping analysis of multi-finger manipulation was presented based on contact kinematics. Finally, a prototype of the humanoid robot hand was produced by a three-dimensional printer, and a kinematics simulation example and the workspace solving of the humanoid robot hand were carried out. The results showed that the velocities of finger joints approximately met the proportion relationship 1:1:1, which accorded with the grasping law of the human hand. In addition, the large workspace, reasonable layout, and good manipulability of the humanoid robot hand were verified.

  4. Search for linkage to schizophrenia on the X and Y chromosomes

    Energy Technology Data Exchange (ETDEWEB)

    Devoto, M.; Ott, J. [Columbia Univ., New York, NY (United States); Vita, A. [Univ. of Milan (Italy)] [and others

    1994-06-15

    Markers for X chromosome loci were used in linkage studies of a large group of small families (n = 126) with at least two schizophrenic members in one sibship. Based on the hypothesis that a gene for schizophrenia could be X-Y linked, with homologous loci on both X and Y, our analyses included all families regardless of the pattern of familial inheritance. Lod scores were computed with both standard X-linked and a novel X-Y model, and sib-pair analyses were performed for all markers examining the sharing of maternal alleles. Small positive lod scores were obtained for loci pericentromeric, from Xp11.4 to Xq12. Lod scores were also computed separately in families selected for evidence of maternal inheritance and absence of male to male transmission of psychosis. The lod scores for linkage to the locus DXS7 reached a maximum of 1.83 at 0.08% recombination, assuming dominant inheritance on the X chromosome in these families (n = 34). Further investigation of the X-Y homologous gene hypothesis focussing on this region is warranted. 39 refs. 1 fig., 6 tabs.

  5. The Influence of Local Ethnic Diversity on Group-Centric Crime Attitudes

    DEFF Research Database (Denmark)

    Hjorth, Frederik

    2017-01-01

    Several studies provide evidence of group-centric policy attitudes, that is, citizens evaluating policies based on linkages with visible social groups. The existing literature generally points to the role of media imagery, rhetoric and prominent political sponsors in driving group-centric attitudes......-down’ influence on group-centric attitudes by elite actors is complemented by ‘bottom-up’ local processes of experiential learning about group–policy linkages....

  6. An extended anchored linkage map and virtual mapping for the american mink genome based on homology to human and dog

    DEFF Research Database (Denmark)

    Anistoroaei, Razvan Marian; Ansari, S.; Farid, A.

    2009-01-01

    hybridization (FISH) and/or by means of human/dog/mink comparative homology. The average interval between markers is 8.5 cM and the linkage groups collectively span 1340 cM. In addition, 217 and 275 mink microsatellites have been placed on human and dog genomes, respectively. In conjunction with the existing...... comparative human/dog/mink data, these assignments represent useful virtual maps for the American mink genome. Comparison of the current human/dog assembled sequential map with the existing Zoo-FISH-based human/dog/mink maps helped to refine the human/dog/mink comparative map. Furthermore, comparison...... of the human and dog genome assemblies revealed a number of large synteny blocks, some of which are corroborated by data from the mink linkage map....

  7. First High-Density Linkage Map and Single Nucleotide Polymorphisms Significantly Associated With Traits of Economic Importance in Yellowtail Kingfish Seriola lalandi

    Directory of Open Access Journals (Sweden)

    Nguyen H. Nguyen

    2018-04-01

    Full Text Available The genetic resources available for the commercially important fish species Yellowtail kingfish (YTK (Seriola lalandi are relative sparse. To overcome this, we aimed (1 to develop a linkage map for this species, and (2 to identify markers/variants associated with economically important traits in kingfish (with an emphasis on body weight. Genetic and genomic analyses were conducted using 13,898 single nucleotide polymorphisms (SNPs generated from a new high-throughput genotyping by sequencing platform, Diversity Arrays Technology (DArTseqTM in a pedigreed population comprising 752 animals. The linkage analysis enabled to map about 4,000 markers to 24 linkage groups (LGs, with an average density of 3.4 SNPs per cM. The linkage map was integrated into a genome-wide association study (GWAS and identified six variants/SNPs associated with body weight (P < 5e-8 when a multi-locus mixed model was used. Two out of the six significant markers were mapped to LGs 17 and 23, and collectively they explained 5.8% of the total genetic variance. It is concluded that the newly developed linkage map and the significantly associated markers with body weight provide fundamental information to characterize genetic architecture of growth-related traits in this population of YTK S. lalandi.

  8. First High-Density Linkage Map and Single Nucleotide Polymorphisms Significantly Associated With Traits of Economic Importance in Yellowtail Kingfish Seriola lalandi.

    Science.gov (United States)

    Nguyen, Nguyen H; Rastas, Pasi M A; Premachandra, H K A; Knibb, Wayne

    2018-01-01

    The genetic resources available for the commercially important fish species Yellowtail kingfish (YTK) ( Seriola lalandi) are relative sparse. To overcome this, we aimed (1) to develop a linkage map for this species, and (2) to identify markers/variants associated with economically important traits in kingfish (with an emphasis on body weight). Genetic and genomic analyses were conducted using 13,898 single nucleotide polymorphisms (SNPs) generated from a new high-throughput genotyping by sequencing platform, Diversity Arrays Technology (DArTseq TM ) in a pedigreed population comprising 752 animals. The linkage analysis enabled to map about 4,000 markers to 24 linkage groups (LGs), with an average density of 3.4 SNPs per cM. The linkage map was integrated into a genome-wide association study (GWAS) and identified six variants/SNPs associated with body weight ( P 5e -8 ) when a multi-locus mixed model was used. Two out of the six significant markers were mapped to LGs 17 and 23, and collectively they explained 5.8% of the total genetic variance. It is concluded that the newly developed linkage map and the significantly associated markers with body weight provide fundamental information to characterize genetic architecture of growth-related traits in this population of YTK S. lalandi .

  9. Linkage of the gene that encodes the alpha 1 chain of type V collagen (COL5A1) to type II Ehlers-Danlos syndrome (EDS II).

    Science.gov (United States)

    Loughlin, J; Irven, C; Hardwick, L J; Butcher, S; Walsh, S; Wordsworth, P; Sykes, B

    1995-09-01

    Ehlers-Danlos syndrome (EDS) is a group of heritable disorders of connective tissue with skin, ligaments and blood vessels being the main sites affected. The commonest variant (EDS II) exhibits an autosomal dominant mode of inheritance and is characterized by joint hypermobility, cigarette paper scars, lax skin and excessive bruising. As yet no gene has been linked to EDS II, nor has linkage been established to a specific region of the genome. However, several candidate genes encoding proteins of the extracellular matrix have been excluded. Using an intragenic simple sequence repeat polymorphism, we report linkage of the COL5A1 gene, which encodes the alpha 1(V) chain of type V collagen, to EDS II. A maximum LOD score (Zmax) for linkage of 8.3 at theta = 0.00 was generated for a single large pedigree.

  10. Sky cover from MFRSR observations

    Directory of Open Access Journals (Sweden)

    E. Kassianov

    2011-07-01

    Full Text Available The diffuse all-sky surface irradiances measured at two nearby wavelengths in the visible spectral range and their modeled clear-sky counterparts are the main components of a new method for estimating the fractional sky cover of different cloud types, including cumuli. The performance of this method is illustrated using 1-min resolution data from a ground-based Multi-Filter Rotating Shadowband Radiometer (MFRSR. The MFRSR data are collected at the US Department of Energy Atmospheric Radiation Measurement (ARM Climate Research Facility (ACRF Southern Great Plains (SGP site during the summer of 2007 and represent 13 days with cumuli. Good agreement is obtained between estimated values of the fractional sky cover and those provided by a well-established independent method based on broadband observations.

  11. CORINE land cover and floristic variation in a Mediterranean wetland.

    Science.gov (United States)

    Giallonardo, Tommaso; Landi, Marco; Frignani, Flavio; Geri, Francesco; Lastrucci, Lorenzo; Angiolini, Claudia

    2011-11-01

    The aims of the present study were to: (1) investigate whether CORINE land cover classes reflect significant differences in floristic composition, using a very detailed CORINE land cover map (scale 1:5000); (2) decompose the relationships between floristic assemblages and three groups of explanatory variables (CORINE land cover classes, environmental characteristics and spatial structure) into unique and interactive components. Stratified sampling was used to select a set of 100-m(2) plots in each land cover class identified in the semi-natural wetland surrounding a lake in central Italy. The following six classes were considered: stable meadows, deciduous oak dominated woods, hygrophilous broadleaf dominated woods, heaths and shrublands, inland swamps, canals or watercourses. The relationship between land cover classes and floristic composition was tested using several statistical techniques in order to determine whether the results remained consistent with different procedures. The variation partitioning approach was applied to identify the relative importance of three groups of explanatory variables in relation to floristic variation. The most important predictor was land cover, which explained 20.7% of the variation in plant distribution, although the hypothesis that each land cover class could be associated with a particular floristic pattern was not verified. Multi Response Permutation Analysis did not indicate a strong floristic separability between land cover classes and only 9.5% of species showed a significant indicator value for a specific land cover class. We suggest that land cover classes linked with hygrophilous and herbaceous communities in a wetland may have floristic patterns that vary with fine scale and are not compatible with a land cover map.

  12. Covering and Reimbursing Telehealth Services.

    Science.gov (United States)

    Blackman, Kate

    2016-01-01

    Policymakers who are striving to achieve better health care, improved health outcomes and lower costs are considering new strategies and technologies. Telehealth is a tool that uses technology to provide health services remotely, and state leaders are looking to it now more than ever as a way to address workforce gaps and reach underserved patients. Among the challenges facing state lawmakers who are working to introduce or expand telehealth is how to handle covering patients and reimbursing providers.

  13. Complex land use and cover trajectories in the northern Choco bioregion of Colombia

    Science.gov (United States)

    Santos, Carolina

    The Choco bioregion in Northwestern Colombia is a lowland rain forest and hotspot of biodiversity. Significant land use and cover change (LUCC) is occurring throughout the region driven by global markets, illicit drug production, and civil unrest. The dominant land cover conversion is from primary forest to African Palm plantations, mediated and modified by complex combinations of social and biophysical drivers. This research combined a remote sensing based methodology to monitor LUCC in the region with an analytical approach for evaluating the possible trajectories of LUCC in a complex biological, socio-economical, and political environment. Synoptic LUCC models were developed using textural classification derived from Synthetic Aperture Radar (SAR) images for the period 1995 to 2010. LUCC models along with empirical social and spatial biophysical drivers were used to project historical land use trajectories. DINAMICA EGO a complex systems based spatial analytical framework was adopted as the platform to model land use change. The RADAR backscatter was able to capture areas were forest has been converted to African Oil Palm Plantations. However, an in depth characterization of the LUC dynamics was problematic given the spectral and spatial limitations of the sensor combined with the lack of ground data. The results of the LUC model suggest that under the current socio-political conditions African oil palm plantations will continue to expand toward forested areas into the territories traditionally inhabited by Afro-Colombians and Indigenous populations. Insecure land tenure appears as a main driver of the transformation in close association with the conditions created by the armed conflict, and the drug traffic. The rate of the transformation appears to slow down in the period after 2007. However, according to the model by 2020 most of the area inhabited by ethnic groups will be transform to AOP. This study contributes towards the understanding of land use change

  14. Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa).

    Science.gov (United States)

    Nagano, Soichiro; Shirasawa, Kenta; Hirakawa, Hideki; Maeda, Fumi; Ishikawa, Masami; Isobe, Sachiko N

    2017-05-12

    The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S 1 mapping population of the cultivar 'Reikou' with an IStraw90 Axiom® SNP array and previously published SSR markers. The 'Reikou' linkage map consisted of 11,574 loci (11,002 SNPs and 572 SSR loci) spanning 2816.5 cM of 31 linkage groups. The 11,574 loci were located on 4738 unique positions (bin) on the linkage map. Of the mapped loci, 8999 (8588 SNPs and 411 SSR loci) showed a 1:2:1 segregation ratio of AA:AB:BB allele, which suggested the possibility of deriving loci from candidate subgenome-specific sequences. In addition, 2575 loci (2414 SNPs and 161 SSR loci) showed a 3:1 segregation of AB:BB allele, indicating they were derived from homoeologous genomic sequences. Comparative analysis of the homoeologous linkage groups revealed differences in genome structure among the subgenomes. Our results suggest that candidate subgenome-specific loci are randomly located across the genomes, and that there are small- to large-scale structural variations among the subgenomes. The mapped SNPs and SSR loci on the linkage map are expected to be seed points for the construction of pseudomolecules in the octoploid strawberry.

  15. Multi-temporal Linkages of Net Ecosystem Exchanges (NEE) with the Climatic and Ecohydrologic Drivers in a Florida Everglades Short-hydroperiod Freshwater Marsh

    Science.gov (United States)

    Zaki, M. T.; Abdul-Aziz, O. I.; Ishtiaq, K. S.

    2017-12-01

    Wetlands are considered one of the most productive and ecologically valuable ecosystems on earth. We investigated the multi-temporal linkages of net ecosystem exchange (NEE) with the relevant climatic and ecohydrological drivers for a Florida Everglades short-hydroperiod freshwater wetland. Hourly NEE observations and the associated driving variables during 2008-12 were collected from the AmeriFlux and EDEN databases, and then averaged for the four temporal scales (1-day, 8-day, 15-day, and 30-day). Pearson correlation and factor analysis were employed to identify the interrelations and grouping patterns among the participatory variables for each time scale. The climatic and ecohydrological linkages of NEE were then reliably estimated using bootstrapped (1000 iterations) partial least squares regressions by resolving multicollinearity. The analytics identified four bio-physical components exhibiting relatively robust interrelations and grouping patterns with NEE across the temporal scales. In general, NEE was most strongly linked with the `radiation-energy (RE)' component, while having a moderate linkage with the `temperature-hydrology (TH)' and `aerodynamic (AD)' components. However, the `ambient atmospheric CO2 (AC)' component was very weakly linked to NEE. Further, RE and TH had a decreasing trend with the increasing time scales (1-30 days). In contrast, the linkages of AD and AC components increased from 1-day to 8-day scales, and then remained relatively invariable at the longer scales of aggregation. The estimated linkages provide insights into the dominant biophysical process components and drivers of ecosystem carbon in the Everglades. The invariant linking pattern and linkages would help to develop low-dimensional models to reliably predict CO2 fluxes from the tidal freshwater wetlands.

  16. A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus Genome Provides Insights into the Diploidization Process After Whole Genome Duplication

    Directory of Open Access Journals (Sweden)

    Cameron M. Nugent

    2017-02-01

    Full Text Available Diploidization, which follows whole genome duplication events, does not occur evenly across the genome. In salmonid fishes, certain pairs of homeologous chromosomes preserve tetraploid loci in higher frequencies toward the telomeres due to residual tetrasomic inheritance. Research suggests this occurs only in homeologous pairs where one chromosome arm has undergone a fusion event. We present a linkage map for Arctic charr (Salvelinus alpinus, a salmonid species with relatively fewer chromosome fusions. Genotype by sequencing identified 19,418 SNPs, and a linkage map consisting of 4508 markers was constructed from a subset of high quality SNPs and microsatellite markers that were used to anchor the new map to previous versions. Both male- and female-specific linkage maps contained the expected number of 39 linkage groups. The chromosome type associated with each linkage group was determined, and 10 stable metacentric chromosomes were identified, along with a chromosome polymorphism involving the sex chromosome AC04. Two instances of a weak form of pseudolinkage were detected in the telomeric regions of homeologous chromosome arms in both female and male linkage maps. Chromosome arm homologies within the Atlantic salmon (Salmo salar and rainbow trout (Oncorhynchus mykiss genomes were determined. Paralogous sequence variants (PSVs were identified, and their comparative BLASTn hit locations showed that duplicate markers exist in higher numbers on seven pairs of homeologous arms, previously identified as preserving tetrasomy in salmonid species. Homeologous arm pairs where neither arm has been part of a fusion event in Arctic charr had fewer PSVs, suggesting faster diploidization rates in these regions.

  17. Genome-wide linkage meta-analysis identifies susceptibility loci at 2q34 and 13q31.3 for genetic generalized epilepsies.

    Science.gov (United States)

    Leu, Costin; de Kovel, Carolien G F; Zara, Federico; Striano, Pasquale; Pezzella, Marianna; Robbiano, Angela; Bianchi, Amedeo; Bisulli, Francesca; Coppola, Antonietta; Giallonardo, Anna Teresa; Beccaria, Francesca; Trenité, Dorothée Kasteleijn-Nolst; Lindhout, Dick; Gaus, Verena; Schmitz, Bettina; Janz, Dieter; Weber, Yvonne G; Becker, Felicitas; Lerche, Holger; Kleefuss-Lie, Ailing A; Hallman, Kerstin; Kunz, Wolfram S; Elger, Christian E; Muhle, Hiltrud; Stephani, Ulrich; Møller, Rikke S; Hjalgrim, Helle; Mullen, Saul; Scheffer, Ingrid E; Berkovic, Samuel F; Everett, Kate V; Gardiner, Mark R; Marini, Carla; Guerrini, Renzo; Lehesjoki, Anna-Elina; Siren, Auli; Nabbout, Rima; Baulac, Stephanie; Leguern, Eric; Serratosa, Jose M; Rosenow, Felix; Feucht, Martha; Unterberger, Iris; Covanis, Athanasios; Suls, Arvid; Weckhuysen, Sarah; Kaneva, Radka; Caglayan, Hande; Turkdogan, Dilsad; Baykan, Betul; Bebek, Nerses; Ozbek, Ugur; Hempelmann, Anne; Schulz, Herbert; Rüschendorf, Franz; Trucks, Holger; Nürnberg, Peter; Avanzini, Giuliano; Koeleman, Bobby P C; Sander, Thomas

    2012-02-01

    Genetic generalized epilepsies (GGEs) have a lifetime prevalence of 0.3% with heritability estimates of 80%. A considerable proportion of families with siblings affected by GGEs presumably display an oligogenic inheritance. The present genome-wide linkage meta-analysis aimed to map: (1) susceptibility loci shared by a broad spectrum of GGEs, and (2) seizure type-related genetic factors preferentially predisposing to either typical absence or myoclonic seizures, respectively. Meta-analysis of three genome-wide linkage datasets was carried out in 379 GGE-multiplex families of European ancestry including 982 relatives with GGEs. To dissect out seizure type-related susceptibility genes, two family subgroups were stratified comprising 235 families with predominantly genetic absence epilepsies (GAEs) and 118 families with an aggregation of juvenile myoclonic epilepsy (JME). To map shared and seizure type-related susceptibility loci, both nonparametric loci (NPL) and parametric linkage analyses were performed for a broad trait model (GGEs) in the entire set of GGE-multiplex families and a narrow trait model (typical absence or myoclonic seizures) in the subgroups of JME and GAE families. For the entire set of 379 GGE-multiplex families, linkage analysis revealed six loci achieving suggestive evidence for linkage at 1p36.22, 3p14.2, 5q34, 13q12.12, 13q31.3, and 19q13.42. The linkage finding at 5q34 was consistently supported by both NPL and parametric linkage results across all three family groups. A genome-wide significant nonparametric logarithm of odds score of 3.43 was obtained at 2q34 in 118 JME families. Significant parametric linkage to 13q31.3 was found in 235 GAE families assuming recessive inheritance (heterogeneity logarithm of odds = 5.02). Our linkage results support an oligogenic predisposition of familial GGE syndromes. The genetic risk factor at 5q34 confers risk to a broad spectrum of familial GGE syndromes, whereas susceptibility loci at 2q34 and 13q31

  18. The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes

    Directory of Open Access Journals (Sweden)

    Ané Jean-Michel

    2002-01-01

    Full Text Available Abstract Background The legume Medicago truncatula has emerged as a model plant for the molecular and genetic dissection of various plant processes involved in rhizobial, mycorrhizal and pathogenic plant-microbe interactions. Aiming to develop essential tools for such genetic approaches, we have established the first genetic map of this species. Two parental homozygous lines were selected from the cultivar Jemalong and from the Algerian natural population (DZA315 on the basis of their molecular and phenotypic polymorphism. Results An F2 segregating population of 124 individuals between these two lines was obtained using an efficient manual crossing technique established for M. truncatula and was used to construct a genetic map. This map spans 1225 cM (average 470 kb/cM and comprises 289 markers including RAPD, AFLP, known genes and isoenzymes arranged in 8 linkage groups (2n = 16. Markers are uniformly distributed throughout the map and segregation distortion is limited to only 3 linkage groups. By mapping a number of common markers, the eight linkage groups are shown to be homologous to those of diploid alfalfa (M. sativa, implying a good level of macrosynteny between the two genomes. Using this M. truncatula map and the derived F3 populations, we were able to map the Mtsym6 symbiotic gene on linkage group 8 and the SPC gene, responsible for the direction of pod coiling, on linkage group 7. Conclusions These results demonstrate that Medicago truncatula is amenable to diploid genetic analysis and they open the way to map-based cloning of symbiotic or other agronomically-important genes using this model plant.

  19. Prioritizing tiger conservation through landscape genetics and habitat linkages.

    Science.gov (United States)

    Yumnam, Bibek; Jhala, Yadvendradev V; Qureshi, Qamar; Maldonado, Jesus E; Gopal, Rajesh; Saini, Swati; Srinivas, Y; Fleischer, Robert C

    2014-01-01

    Even with global support for tiger (Panthera tigris) conservation their survival is threatened by poaching, habitat loss and isolation. Currently about 3,000 wild tigers persist in small fragmented populations within seven percent of their historic range. Identifying and securing habitat linkages that connect source populations for maintaining landscape-level gene flow is an important long-term conservation strategy for endangered carnivores. However, habitat corridors that link regional tiger populations are often lost to development projects due to lack of objective evidence on their importance. Here, we use individual based genetic analysis in combination with landscape permeability models to identify and prioritize movement corridors across seven tiger populations within the Central Indian Landscape. By using a panel of 11 microsatellites we identified 169 individual tigers from 587 scat and 17 tissue samples. We detected four genetic clusters within Central India with limited gene flow among three of them. Bayesian and likelihood analyses identified 17 tigers as having recent immigrant ancestry. Spatially explicit tiger occupancy obtained from extensive landscape-scale surveys across 76,913 km(2) of forest habitat was found to be only 21,290 km(2). After accounting for detection bias, the covariates that best explained tiger occupancy were large, remote, dense forest patches; large ungulate abundance, and low human footprint. We used tiger occupancy probability to parameterize habitat permeability for modeling habitat linkages using least-cost and circuit theory pathway analyses. Pairwise genetic differences (FST) between populations were better explained by modeled linkage costs (r>0.5, p<0.05) compared to Euclidean distances, which was in consonance with observed habitat fragmentation. The results of our study highlight that many corridors may still be functional as there is evidence of contemporary migration. Conservation efforts should provide legal status

  20. Prioritizing tiger conservation through landscape genetics and habitat linkages.

    Directory of Open Access Journals (Sweden)

    Bibek Yumnam

    Full Text Available Even with global support for tiger (Panthera tigris conservation their survival is threatened by poaching, habitat loss and isolation. Currently about 3,000 wild tigers persist in small fragmented populations within seven percent of their historic range. Identifying and securing habitat linkages that connect source populations for maintaining landscape-level gene flow is an important long-term conservation strategy for endangered carnivores. However, habitat corridors that link regional tiger populations are often lost to development projects due to lack of objective evidence on their importance. Here, we use individual based genetic analysis in combination with landscape permeability models to identify and prioritize movement corridors across seven tiger populations within the Central Indian Landscape. By using a panel of 11 microsatellites we identified 169 individual tigers from 587 scat and 17 tissue samples. We detected four genetic clusters within Central India with limited gene flow among three of them. Bayesian and likelihood analyses identified 17 tigers as having recent immigrant ancestry. Spatially explicit tiger occupancy obtained from extensive landscape-scale surveys across 76,913 km(2 of forest habitat was found to be only 21,290 km(2. After accounting for detection bias, the covariates that best explained tiger occupancy were large, remote, dense forest patches; large ungulate abundance, and low human footprint. We used tiger occupancy probability to parameterize habitat permeability for modeling habitat linkages using least-cost and circuit theory pathway analyses. Pairwise genetic differences (FST between populations were better explained by modeled linkage costs (r>0.5, p<0.05 compared to Euclidean distances, which was in consonance with observed habitat fragmentation. The results of our study highlight that many corridors may still be functional as there is evidence of contemporary migration. Conservation efforts should

  1. Testing association and linkage using affected-sib-parent study designs.

    Science.gov (United States)

    Millstein, Joshua; Siegmund, Kimberly D; Conti, David V; Gauderman, W James

    2005-11-01

    We have developed a method for jointly testing linkage and association using data from affected sib pairs and their parents. We specify a conditional logistic regression model with two covariates, one that quantifies association (either direct association or indirect association via linkage disequilibrium), and a second that quantifies linkage. The latter covariate is computed based on expected identity-by-descend (ibd) sharing of marker alleles between siblings. In addition to a joint test of linkage and association, our general framework can be used to obtain a linkage test comparable to the mean test (Blackwelder and Elston [1985] Genet. Epidemiol. 2:85-97), and an association test comparable to the Family-Based Association Test (FBAT; Rabinowitz and Laird [2000] Hum. Hered. 50:211-223). We present simulation results demonstrating that our joint test can be more powerful than some standard tests of linkage or association. For example, with a relative risk of 2.7 per variant allele at a disease locus, the estimated power to detect a nearby marker with a modest level of LD was 58.1% by the mean test (linkage only), 69.8% by FBAT, and 82.5% by our joint test of linkage and association. Our model can also be used to obtain tests of linkage conditional on association and association conditional on linkage, which can be helpful in fine mapping. Copyright 2005 Wiley-Liss, Inc.

  2. Haplotype analysis and linkage disequilibrium for DGAT1

    OpenAIRE

    Strucken, Eva M.; Rahmatalla, Siham; De Koning, Dirk-Jan; Brockmann, Gudrun A.

    2010-01-01

    This study focused on haplotype effects and linkage disequilibrium (LD) for the K232A locus and the promoter VNTR in the DGAT1 gene. Analyses were carried out in three German Holstein Frisian populations (including 492, 305, and 518 animals) for milk yield, milk fat and protein yield, and milk fat and protein content. We found that effects of the promoter VNTR were not significant and explain only a small amount of the variation of the QTL on BTA14. Haplotype effects were less significant tha...

  3. Learning and Competence Building through Cross-cultural Linkages

    DEFF Research Database (Denmark)

    Sørensen, Olav Jull

    2006-01-01

    The aim of the chapter is to study upgrading of companies in developing countries in a learning perspective. Both formal and experiential and tacit knowledge is discussed. Learning effects of different management modes, expatriates, linkages to customers and suppliers are discussed as are learning...... thorugh actual production as well as through explicit transfer of knowledge. The chapter in this way makes an attempt to provide an overview of the multiplicity og learning interfaces. It is concluded that the learning perspective need to be adressed more both by managers and scholars....

  4. IFPE/GBGI, Grain-Bubble Gas Inter-linkage

    International Nuclear Information System (INIS)

    2007-01-01

    Description: The fuel microstructure examination at the thermocouple tips in the lower and upper part of a steady-state irradiated experimental fuel rod with different as fabricated fuel-to-clad gaps in these two regions revealed on-set of grain boundary gas bubble precipitation in the fuel center of the small-gap/low-temperature region (lower part) and developed inter-linkage in the fuel center of the large-gap/high-temperature region (upper part). By use of a diffusion model and the measured temperatures, corresponding grain boundary gas 'concentrations' were calculated

  5. Monetary Policy with Sectoral Linkages and Durable Goods

    DEFF Research Database (Denmark)

    Petrella, Ivan; Rossi, Raffaele; Santoro, Emiliano

    We study the normative implications of a New Keynesian model featuring intersectoral trade of intermediate goods between two sectors that produce durables and non-durables. The interplay between durability and sectoral production linkages fundamentally alters the intersectoral stabilization trade....... Aggregating durable and non-durable inflation depending on the relative degrees of sectoral price stickiness may induce a severe bias. Input materials attenuate the response of sectoral inflations to movements in the real marginal costs, so that the effective slopes of the sectoral supply schedules...

  6. Association between cancer and contact allergy: a linkage study

    DEFF Research Database (Denmark)

    Engkilde, Kaare; Thyssen, Jacob P; Menné, Torkil

    2011-01-01

    by logistic regression analysis. Results An inverse association between contact allergy and non-melanoma skin- and breast cancer, respectively, was identified in both sexes, and an inverse trend for brain cancer was found in women with contact allergy. Additionally, a positive association between contact...... and cancer, few have looked into the association between cancer and contact allergy, a type IV allergy. By linking two clinical databases, the authors investigate the possible association between contact allergy and cancer. Methods Record linkage of two different registers was performed: (1) a tertiary...

  7. Gear-shaft linkage, especially for nuclear reactor coolant pumps

    International Nuclear Information System (INIS)

    Delaunois, T.; Lefevre, R.

    1990-01-01

    The pump comprises: - inlet and outlet channels for the pumped fluid - a rotating shaft - a gear wheel mounted on the shaft by an axial locking nut which can support the axial hydraulic force - a thermal barrier above the gear wheel. A hydrostatic bearing fitted to the exterior surround of the gear wheel, the gear shaft linkage is made by at least a centering and locating device having a cylindrical span and an axial stop and another independent device which can take up the torque [fr

  8. COMMUNICATIONS GROUP

    CERN Multimedia

    L. Taylor

    2011-01-01

    Communications Infrastructure The 55 CMS Centres worldwide are well used by physicists working on remote CMS shifts, Computing operations, data quality monitoring, data analysis and outreach. The CMS Centre@CERN in Meyrin is particularly busy at the moment, hosting about 50 physicists taking part in the heavy-ion data-taking and analysis. Three new CMS meeting room will be equipped for videoconferencing in early 2012: 40/5B-08, 42/R-031, and 28/S-029. The CMS-TV service showing LHC Page 1, CMS Page 1, etc. (http://cmsdoc.cern.ch/cmscc/projector/index.jsp) is now also available for mobile devices: http://cern.ch/mcmstv. Figure 12: Screenshots of CMS-TV for mobile devices Information Systems CMS has a new web site: (http://cern.ch/cms) using a modern web Content Management System to ensure content and links are managed and updated easily and coherently. It covers all CMS sub-projects and groups, replacing the iCMS internal pages. It also incorporates the existing CMS public web site (http:/...

  9. COMMUNICATIONS GROUP

    CERN Multimedia

    L. Taylor

    2012-01-01

      Outreach and Education We are fortunate that our research has captured the public imagination, even though this inevitably puts us under the global media spotlight, as we saw with the Higgs seminar at CERN in December, which had 110,000 distinct webcast viewers. The media interest was huge with 71 media organisations registering to come to CERN to cover the Higgs seminar, which was followed by a press briefing with the DG and Spokespersons. This event resulted in about 2,000 generally positive stories in the global media. For this seminar, the CMS Communications Group prepared up-to-date news and public material, including links to the CMS results, animations and event displays [http://cern.ch/go/Ch8thttp://cern.ch/go/Ch8t]. There were 44,000 page-views on the CMS public website, with the Higgs news article being by far the most popular item. CMS event displays from iSpy are fast becoming the iconic media images, featuring on numerous major news outlets (BBC, CNN, MSN...) as well as in the sci...

  10. A reduction of the globalization and U(1)-covering

    International Nuclear Information System (INIS)

    Tran Dao Dong.

    1993-03-01

    We suggest a reduction of the globalization and multidimensional quantization to the case of reductive Lie groups by lifting to U(1)-covering. our construction is connected with M. Duflo's third method for algebraic groups. From a reductive datum of the given real algebraic Lie group we firstly construct geometric complexes with respect to U(1)-covering by using the unipotent positive distributions. Then we describe in terms of local cohomology the maximal globalization of Harish-Chandra modules which correspond to the geometric complexes. (author). 9 refs

  11. A microsatellite linkage map for Drosophila montana shows large variation in recombination rates, and a courtship song trait maps to an area of low recombination.

    Science.gov (United States)

    Schäfer, M A; Mazzi, D; Klappert, K; Kauranen, H; Vieira, J; Hoikkala, A; Ritchie, M G; Schlötterer, C

    2010-03-01

    Current advances in genetic analysis are opening up our knowledge of the genetics of species differences, but challenges remain, particularly for out-bred natural populations. We constructed a microsatellite-based linkage map for two out-bred lines of Drosophila montana derived from divergent populations by taking advantage of the Drosophila virilis genome and available cytological maps of both species. Although the placement of markers was quite consistent with cytological predictions, the map indicated large heterogeneity in recombination rates along chromosomes. We also performed a quantitative trait locus (QTL) analysis on a courtship song character (carrier frequency), which differs between populations and is subject to strong sexual selection. Linkage mapping yielded two significant QTLs, which explained 3% and 14% of the variation in carrier frequency, respectively. Interestingly, as in other recent studies of traits which can influence speciation, the strongest QTL mapped to a genomic region partly covered by an inversion polymorphism.

  12. A high-density linkage map and QTL mapping of fruit-related traits in pumpkin (Cucurbita moschata Duch.).

    Science.gov (United States)

    Zhong, Yu-Juan; Zhou, Yang-Yang; Li, Jun-Xing; Yu, Ting; Wu, Ting-Quan; Luo, Jian-Ning; Luo, Shao-Bo; Huang, He-Xun

    2017-10-06

    Pumpkin (Cucurbita moschata) is an economically worldwide crop. Few quantitative trait loci (QTLs) were reported previously due to the lack of genomic and genetic resources. In this study, a high-density linkage map of C. moschata was structured by double-digest restriction site-associated DNA sequencing, using 200 F2 individuals of CMO-1 × CMO-97. By filtering 74,899 SNPs, a total of 3,470 high quality SNP markers were assigned to the map spanning a total genetic distance of 3087.03 cM on 20 linkage groups (LGs) with an average genetic distance of 0.89 cM. Based on this map, both pericarp color and strip were fined mapped to a novel single locus on LG8 in the same region of 0.31 cM with phenotypic variance explained (PVE) of 93.6% and 90.2%, respectively. QTL analysis was also performed on carotenoids, sugars, tuberculate fruit, fruit diameter, thickness and chamber width with a total of 12 traits. 29 QTLs distributed in 9 LGs were detected with PVE from 9.6% to 28.6%. It was the first high-density linkage SNP map for C. moschata which was proved to be a valuable tool for gene or QTL mapping. This information will serve as significant basis for map-based gene cloning, draft genome assembling and molecular breeding.

  13. Inter-linkage between Hinterlands and Service Centers of Bima and Darbang VDCs in Myagdi District: A Rural Development Perspective

    Directory of Open Access Journals (Sweden)

    Beg Prasad Garbuja

    2015-12-01

    Full Text Available This study focuses on exploring the status and contribution of inter- linkage relationship between service center and rural hinterland. The study was conducted in Bima and Darbang Village Development Committees (VDCs of Myagdi district. This paper has used rural development perspective. The respondents were from 63 sample households including producers, consumers and service providers selected by using probability and non probability sampling methods. The primary data were collected through survey questionnaire, key informant interview, participant observation and focus group discussion whereas secondary data were generated from published and unpublished books, articles, journals, profile of VDCs and DDC. The study has revealed with various types of linkage between service center and rural hinterland i.e. service delivery, spatial or physical, administrative, economic, technological, financial and socio-cultural, educational and health service linkage. The study also highlighted productive role of remittance, international experience and adaptation of modern agriculture technology that has been positively affecting socio-economic life of the rural people. Further, joint efforts of public and private sectors’ and local stakeholders’ can be applied for developing and promoting service delivery opportunities and marketing facilities to the local people. The finding of the study has very strong implications to the local stakeholders for formulation of short run and long run local development plan in a similar situation.

  14. Construction and analysis of a high-density genetic linkage map in cabbage (Brassica oleracea L. var. capitata

    Directory of Open Access Journals (Sweden)

    Wang Wanxing

    2012-10-01

    Full Text Available Abstract Background Brassica oleracea encompass a family of vegetables and cabbage that are among the most widely cultivated crops. In 2009, the B. oleracea Genome Sequencing Project was launched using next generation sequencing technology. None of the available maps were detailed enough to anchor the sequence scaffolds for the Genome Sequencing Project. This report describes the development of a large number of SSR and SNP markers from the whole genome shotgun sequence data of B. oleracea, and the construction of a high-density genetic linkage map using a double haploid mapping population. Results The B. oleracea high-density genetic linkage map that was constructed includes 1,227 markers in nine linkage groups spanning a total of 1197.9 cM with an average of 0.98 cM between adjacent loci. There were 602 SSR markers and 625 SNP markers on the map. The chromosome with the highest number of markers (186 was C03, and the chromosome with smallest number of markers (99 was C09. Conclusions This first high-density map allowed the assembled scaffolds to be anchored to pseudochromosomes. The map also provides useful information for positional cloning, molecular breeding, and integration of information of genes and traits in B. oleracea. All the markers on the map will be transferable and could be used for the construction of other genetic maps.

  15. Biocompatibility of a new device of self-expandable covered and non-covered tracheal stent: comparative study in rats

    Directory of Open Access Journals (Sweden)

    Olavo Ribeiro Rodrigues

    2013-01-01

    Full Text Available PURPOSE: To investigate the compatibility of a new model of self-expandable tracheal stent in rats. METHODS: A new device of polyurethane covered and non - covered stent was placed in the trachea of Wistar rats. Animals were distributed in two groups: the polyurethane covered and non-covered group. Macroscopic parameters included position within the tracheal lumen, adherence to the mucosa, degree of dilatation, permeability and internal diameter. Microscopic findings evaluated were: incorporation, inflammatory activity, granulation tissue and epithelial revetment injuries. The observation follow-up was six weeks. All parameters were quantified based on determined score values. Incorporation of the stents was evaluated based on the observation if the stent was fixed into the trachea or if it could be removed. Degree of dilatation was performed by external diameter measurements. Granulation tissue was evaluated by measurements of height of the tissue growing into the tracheal lumen. RESULTS: 100% of non-covered stents had total attachment to mucosa and 100% of polyurethane covered type had adherence only. Regarding dilatation, granulation tissue, inflammatory activity and internal diameter measurements, there were no significant differences between the groups. Pathological tracheal wall injuries were present in both groups. CONCLUSION: Both models of stent demonstrated biocompatibility with the trachea. Rats are suitable for an experimental model of tracheal stent study.

  16. Group theory I essentials

    CERN Document Server

    Milewski, Emil G

    2012-01-01

    REA's Essentials provide quick and easy access to critical information in a variety of different fields, ranging from the most basic to the most advanced. As its name implies, these concise, comprehensive study guides summarize the essentials of the field covered. Essentials are helpful when preparing for exams, doing homework and will remain a lasting reference source for students, teachers, and professionals. Group Theory I includes sets and mapping, groupoids and semi-groups, groups, isomorphisms and homomorphisms, cyclic groups, the Sylow theorems, and finite p-groups.

  17. A genome-wide search for linkage of estimated glomerular filtration rate (eGFR in the Family Investigation of Nephropathy and Diabetes (FIND.

    Directory of Open Access Journals (Sweden)

    Farook Thameem

    Full Text Available Estimated glomerular filtration rate (eGFR, a measure of kidney function, is heritable, suggesting that genes influence renal function. Genes that influence eGFR have been identified through genome-wide association studies. However, family-based linkage approaches may identify loci that explain a larger proportion of the heritability. This study used genome-wide linkage and association scans to identify quantitative trait loci (QTL that influence eGFR.Genome-wide linkage and sparse association scans of eGFR were performed in families ascertained by probands with advanced diabetic nephropathy (DN from the multi-ethnic Family Investigation of Nephropathy and Diabetes (FIND study. This study included 954 African Americans (AA, 781 American Indians (AI, 614 European Americans (EA and 1,611 Mexican Americans (MA. A total of 3,960 FIND participants were genotyped for 6,000 single nucleotide polymorphisms (SNPs using the Illumina Linkage IVb panel. GFR was estimated by the Modification of Diet in Renal Disease (MDRD formula.The non-parametric linkage analysis, accounting for the effects of diabetes duration and BMI, identified the strongest evidence for linkage of eGFR on chromosome 20q11 (log of the odds [LOD] = 3.34; P = 4.4 × 10(-5 in MA and chromosome 15q12 (LOD = 2.84; P = 1.5 × 10(-4 in EA. In all subjects, the strongest linkage signal for eGFR was detected on chromosome 10p12 (P = 5.5 × 10(-4 at 44 cM near marker rs1339048. A subsequent association scan in both ancestry-specific groups and the entire population identified several SNPs significantly associated with eGFR across the genome.The present study describes the localization of QTL influencing eGFR on 20q11 in MA, 15q21 in EA and 10p12 in the combined ethnic groups participating in the FIND study. Identification of causal genes/variants influencing eGFR, within these linkage and association loci, will open new avenues for functional analyses and development of novel diagnostic markers

  18. A genome-wide search for linkage of estimated glomerular filtration rate (eGFR) in the Family Investigation of Nephropathy and Diabetes (FIND).

    Science.gov (United States)

    Thameem, Farook; Igo, Robert P; Freedman, Barry I; Langefeld, Carl; Hanson, Robert L; Schelling, Jeffrey R; Elston, Robert C; Duggirala, Ravindranath; Nicholas, Susanne B; Goddard, Katrina A B; Divers, Jasmin; Guo, Xiuqing; Ipp, Eli; Kimmel, Paul L; Meoni, Lucy A; Shah, Vallabh O; Smith, Michael W; Winkler, Cheryl A; Zager, Philip G; Knowler, William C; Nelson, Robert G; Pahl, Madeline V; Parekh, Rulan S; Kao, W H Linda; Rasooly, Rebekah S; Adler, Sharon G; Abboud, Hanna E; Iyengar, Sudha K; Sedor, John R

    2013-01-01

    Estimated glomerular filtration rate (eGFR), a measure of kidney function, is heritable, suggesting that genes influence renal function. Genes that influence eGFR have been identified through genome-wide association studies. However, family-based linkage approaches may identify loci that explain a larger proportion of the heritability. This study used genome-wide linkage and association scans to identify quantitative trait loci (QTL) that influence eGFR. Genome-wide linkage and sparse association scans of eGFR were performed in families ascertained by probands with advanced diabetic nephropathy (DN) from the multi-ethnic Family Investigation of Nephropathy and Diabetes (FIND) study. This study included 954 African Americans (AA), 781 American Indians (AI), 614 European Americans (EA) and 1,611 Mexican Americans (MA). A total of 3,960 FIND participants were genotyped for 6,000 single nucleotide polymorphisms (SNPs) using the Illumina Linkage IVb panel. GFR was estimated by the Modification of Diet in Renal Disease (MDRD) formula. The non-parametric linkage analysis, accounting for the effects of diabetes duration and BMI, identified the strongest evidence for linkage of eGFR on chromosome 20q11 (log of the odds [LOD] = 3.34; P = 4.4 × 10(-5)) in MA and chromosome 15q12 (LOD = 2.84; P = 1.5 × 10(-4)) in EA. In all subjects, the strongest linkage signal for eGFR was detected on chromosome 10p12 (P = 5.5 × 10(-4)) at 44 cM near marker rs1339048. A subsequent association scan in both ancestry-specific groups and the entire population identified several SNPs significantly associated with eGFR across the genome. The present study describes the localization of QTL influencing eGFR on 20q11 in MA, 15q21 in EA and 10p12 in the combined ethnic groups participating in the FIND study. Identification of causal genes/variants influencing eGFR, within these linkage and association loci, will open new avenues for functional analyses and development of novel diagnostic markers

  19. Non-commutative covering spaces and their symmetries

    DEFF Research Database (Denmark)

    Canlubo, Clarisson

    dened and its corresponding Galois theory. Using this and basic concepts from algebraic geometryand spectral theory, we will give a full description of the general structure of non-centralcoverings. Examples of coverings of the rational and irrational non-commutative tori will alsobe studied. Using...... will explain this and relate it to bi-Galois theory.Using the OZ-transform, we will show that non-commutative covering spaces come in pairs.Several categories of covering spaces will be dened and studied. Appealing to Tannaka duality,we will explain how this lead to a notion of an etale fundamental group...

  20. A node linkage approach for sequential pattern mining.

    Directory of Open Access Journals (Sweden)

    Osvaldo Navarro

    Full Text Available Sequential Pattern Mining is a widely addressed problem in data mining, with applications such as analyzing Web usage, examining purchase behavior, and text mining, among others. Nevertheless, with the dramatic increase in data volume, the current approaches prove inefficient when dealing with large input datasets, a large number of different symbols and low minimum supports. In this paper, we propose a new sequential pattern mining algorithm, which follows a pattern-growth scheme to discover sequential patterns. Unlike most pattern growth algorithms, our approach does not build a data structure to represent the input dataset, but instead accesses the required sequences through pseudo-projection databases, achieving better runtime and reducing memory requirements. Our algorithm traverses the search space in a depth-first fashion and only preserves in memory a pattern node linkage and the pseudo-projections required for the branch being explored at the time. Experimental results show that our new approach, the Node Linkage Depth-First Traversal algorithm (NLDFT, has better performance and scalability in comparison with state of the art algorithms.

  1. Optimizing Opt-Out Consent for Record Linkage

    Directory of Open Access Journals (Sweden)

    Das Marcel

    2014-09-01

    Full Text Available This article reports on a study testing the effects of different ways of administering an opt-out consent for record linkage in a probability-based Internet panel. First, we conducted cognitive interviews to explore reactions to a draft version of the opt-out consent text. Second, we conducted a two-factor experiment to test the effects of content manipulations and mode. The results indicate that the way in which respondents were informed did not have much effect on opting out. Results from a follow-up survey on attitudes regarding privacy, confidentiality, and trust, along with knowledge questions about the process of linking, showed no evidence that presenting the opt-out consent statement makes respondents more concerned about privacy. Knowledge about the aspects of record linkage is generally not high. When looking at long-term effects of sending an opt-out consent statement, we found no evidence that this leads to higher attrition or lower participation rates.

  2. A genetic linkage map for the apicomplexan protozoan parasite Eimeria maxima and comparison with Eimeria tenella.

    Science.gov (United States)

    Blake, Damer P; Oakes, Richard; Smith, Adrian L

    2011-02-01

    Eimeria maxima is one of the seven Eimeria spp. that infect the chicken and cause the disease coccidiosis. The well characterised immunogenicity and genetic diversity associated with E. maxima promote its use in genetics-led studies on avian coccidiosis. The development of a genetic map for E. maxima, presented here based upon 647 amplified fragment length polymorphism markers typed from 22 clonal hybrid lines and assembled into 13 major linkage groups, is a major new resource for work with this parasite. Comparison with genetic maps produced for other coccidial parasites indicates relatively high levels of genetic recombination. Conversion of ∼14% of the markers representing the major linkage groups to sequence characterised amplified region markers can provide a scaffold for the assembly of future genomic sequences as well as providing a foundation for more detailed genetic maps. Comparison with the Eimeria tenella genetic map produced 10years ago has revealed a less biased marker distribution, with no more than nine markers mapped within any unresolved heritable unit. Nonetheless, preliminary bioinformatic characterisation of the three largest publicly available genomic E. maxima sequences suggest that the feature-poor/feature-rich structure which has previously been found to define the first sequenced E. tenella chromosome also defines the E. maxima genome. The significance of such a segmented genome and the apparent potential for variation in genetic recombination will be relevant to haplotype stability and the longevity of future anticoccidial strategies based upon multiple loci targeted by novel chemotherapeutic drugs or recombinant subunit vaccines. Copyright © 2010 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

  3. Risk factors, barriers and facilitators for linkage to antiretroviral therapy care: a systematic review.

    Science.gov (United States)

    Govindasamy, Darshini; Ford, Nathan; Kranzer, Katharina

    2012-10-23

    To characterize patient and programmatic factors associated with retention in care during the pre-antiretroviral therapy (ART) period and linkage to ART care. Systematic literature review. An electronic search was conducted on MEDLINE, Global Health, Google Scholar and conference databases to identify studies reporting on predictors, barriers and facilitators of retention in care in the pre-ART period, and linkage to care at three steps: ART-eligibility assessment, pre-ART care and ART initiation. Factors associated with attrition were then divided into areas for intervention. Seven hundred and sixty-eight citations were identified. Forty-two studies from 12 countries were included for review, with the majority from South Africa (16). The most commonly cited category of factors was transport costs and distance. Stigma and fear of disclosure comprised the second most commonly cited category of factors followed by staff shortages, long waiting times, fear of drug side effects, male sex, younger age and the need to take time off work. This review highlights the importance of investigating interventions that could reduce transport difficulties. Decentralization, task-shifting and integration of services need to be expedited to alleviate health system barriers. Patient support groups and strategic posttest counselling are essential to assist patients deal with stigma and disclosure. Moreover, well tolerated first-line drugs and treatment literacy programmes are needed to improve acceptance of ART. This review suggests a combination of interventions to retain specific groups at risk for attrition such as workplace programmes for employed patients, dedicated clinic and support programmes for men and younger individuals.

  4. Linkage between pain sensitivity and empathic response in adolescents with autism spectrum conditions and conduct disorder symptoms.

    Science.gov (United States)

    Chen, Chenyi; Hung, An-Yi; Fan, Yang-Teng; Tan, Shuai; Hong, Hua; Cheng, Yawei

    2017-02-01

    Lack of empathy is one of the behavioral hallmarks in individuals with autism spectrum conditions (ASC) as well as youth with conduct disorder symptoms (CDS). Previous research has reliably documented considerable overlap between the perception of others' pain and first-hand experience of pain. However, the linkage between empathy for pain and sensitivity to physical pain needs to be empirically determined, particularly in individuals with empathy deficits. This study measured the pressure pain threshold, which indexes sensitization of peripheral nociceptors, and assessed subjective ratings of unpleasantness and pain intensity in response to empathy-eliciting stimuli depicting physical bodily injuries in three age- and sex-matched participant groups: ASC, CDS, and typically developing controls (TDC). The results indicated that the pain threshold was lowest in the ASC group and highest in the CDS group. The ASC group displayed lower ratings of unpleasantness and pain intensity than did the TDC and CDS groups. Within the ASC and CDS, pain intensity ratings were significantly correlated with unpleasantness ratings to others' pain. Moreover, the ASC significantly differed from the TDC in the correlation between pain threshold values and unpleasantness ratings. These findings may cast some light on the linkage between atypical low-level sensory functioning, for instance altered pain sensitivity, and high-level empathic processing. Autism Res 2017, 10: 267-275. © 2016 International Society for Autism Research, Wiley Periodicals, Inc. © 2016 International Society for Autism Research, Wiley Periodicals, Inc.

  5. 7 CFR 30.7 - Group.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Group. 30.7 Section 30.7 Agriculture Regulations of... AND STANDARDS Classification of Leaf Tobacco Covering Classes, Types and Groups of Grades § 30.7 Group. A group of grades, or a division of a type covering several closely related grades, based on the...

  6. A literature review of record linkage procedures focusing on infant health outcomes

    Directory of Open Access Journals (Sweden)

    Carla Jorge Machado

    Full Text Available Record linkage is a powerful tool in assembling information from different data sources and has been used by a number of public health researchers. In this review, we provide an overview of the record linkage methodologies, focusing particularly on probabilistic record linkage. We then stress the purposes and research applications of linking records by focusing on studies of infant health outcomes based on large data sets, and provide a critical review of the studies in Brazil.

  7. Heritability and whole genome linkage of pulse pressure in Chinese twin pairs

    DEFF Research Database (Denmark)

    Jiang, Wengjie; Zhang, Dongfeng; Pang, Zengchang

    2012-01-01

    with a heritability estimate of 0.45. Genome-wide non-parametric linkage analysis identified three significant linkage peaks on chromosome 11 (lod score 4.06 at 30.5 cM), chromosome 12 (lod score 3.97 at 100.7 cM), and chromosome 18 (lod score 4.01 at 70.7 cM) with the last two peaks closely overlapping with linkage...

  8. MICA diversity and linkage disequilibrium with HLA-B alleles in renal-transplant candidates in southern Brazil.

    Science.gov (United States)

    Yamakawa, Roger Haruki; Saito, Patrícia Keiko; Gelmini, Geórgia Fernanda; da Silva, José Samuel; Bicalho, Maria da Graça; Borelli, Sueli Donizete

    2017-01-01

    The major histocompatibility complex (MHC) class I chain-related gene A (MICA) is located centromerically to the human leukocyte antigen (HLA)-B. The short distance between these loci in the MHC indicates the presence of linkage disequilibrium (LD). Similarly to the HLA, the MICA is highly polymorphic, and this polymorphism has not been well documented in different populations. In this study, we estimated the allelic frequencies of MICA and the linkage disequilibrium with HLA-B alleles in 346 renal-transplant candidates in southern Brazil. MICA and HLA were typed using the polymerase chain reaction-sequence-specific primer method (PCR-SSO), combined with the Luminex technology. A total of 19 MICA allele groups were identified. The most frequent allele groups were MICA*008 (21.6%), MICA*002 (17.0%) and MICA*004 (14.8%). The most common haplotypes were MICA*009-B*51 (7.8%), MICA*004-B*44 (6.06%) and MICA*002-B*35 (5.63%). As expected from the proximity of the MICA and HLA-B loci, most haplotypes showed strong LD. Renal patients and healthy subjects in the same region of Brazil showed statistically significant differences in their MICA polymorphisms. The MICA*027 allele group was more frequent in renal patients (Pc = 0.018, OR: 3.421, 95% CI: 1.516-7.722), while the MICA*019 allele group was more frequent in healthy subjects (Pc = 0.001, OR: 0.027, 95% CI: 0.002-0.469). This study provided information on the distribution of MICA polymorphisms and linkage disequilibrium with HLA-B alleles in Brazilian renal-transplant candidates. This information should help to determine the mechanisms of susceptibility to different diseases in patients with chronic kidney disease, and to elucidate the mechanisms involved in allograft rejection associated with MICA polymorphisms in a Brazilian population.

  9. Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

    Science.gov (United States)

    2014-01-01

    Background The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Results Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. Conclusions These

  10. Monte Carlo simulations on marker grouping and ordering.

    Science.gov (United States)

    Wu, J; Jenkins, J; Zhu, J; McCarty, J; Watson, C

    2003-08-01

    Four global algorithms, maximum likelihood (ML), sum of adjacent LOD score (SALOD), sum of adjacent recombinant fractions (SARF) and product of adjacent recombinant fraction (PARF), and one approximation algorithm, seriation (SER), were used to compare the marker ordering efficiencies for correctly given linkage groups based on doubled haploid (DH) populations. The Monte Carlo simulation results indicated the marker ordering powers for the five methods were almost identical. High correlation coefficients were greater than 0.99 between grouping power and ordering power, indicating that all these methods for marker ordering were reliable. Therefore, the main problem for linkage analysis was how to improve the grouping power. Since the SER approach provided the advantage of speed without losing ordering power, this approach was used for detailed simulations. For more generality, multiple linkage groups were employed, and population size, linkage cutoff criterion, marker spacing pattern (even or uneven), and marker spacing distance (close or loose) were considered for obtaining acceptable grouping powers. Simulation results indicated that the grouping power was related to population size, marker spacing distance, and cutoff criterion. Generally, a large population size provided higher grouping power than small population size, and closely linked markers provided higher grouping power than loosely linked markers. The cutoff criterion range for achieving acceptable grouping power and ordering power differed for varying cases; however, combining all situations in this study, a cutoff criterion ranging from 50 cM to 60 cM was recommended for achieving acceptable grouping power and ordering power for different cases.

  11. Quantifying sources of bias in longitudinal data linkage studies of child abuse and neglect: measuring impact of outcome specification, linkage error, and partial cohort follow-up.

    Science.gov (United States)

    Parrish, Jared W; Shanahan, Meghan E; Schnitzer, Patricia G; Lanier, Paul; Daniels, Julie L; Marshall, Stephen W

    2017-12-01

    Health informatics projects combining statewide birth populations with child welfare records have emerged as a valuable approach to conducting longitudinal research of child maltreatment. The potential bias resulting from linkage misspecification, partial cohort follow-up, and outcome misclassification in these studies has been largely unexplored. This study integrated epidemiological survey and novel administrative data sources to establish the Alaska Longitudinal Child Abuse and Neglect Linkage (ALCANLink) project. Using these data we evaluated and quantified the impact of non-linkage misspecification and single source maltreatment ascertainment use on reported maltreatment risk and effect estimates. The ALCANLink project integrates the 2009-2011 Alaska Pregnancy Risk Assessment Monitoring System (PRAMS) sample with multiple administrative databases through 2014, including one novel administrative source to track out-of-state emigration. For this project we limited our analysis to the 2009 PRAMS sample. We report on the impact of linkage quality, cohort follow-up, and multisource outcome ascertainment on the incidence proportion of reported maltreatment before age 6 and hazard ratios of selected characteristics that are often available in birth cohort linkage studies of maltreatment. Failure to account for out-of-state emigration biased the incidence proportion by 12% (from 28.3% w to 25.2% w ), and the hazard ratio (HR) by as much as 33% for some risk factors. Overly restrictive linkage parameters biased the incidence proportion downwards by 43% and the HR by as much as 27% for some factors. Multi-source linkages, on the other hand, were of little benefit for improving reported maltreatment ascertainment. Using the ALCANLink data which included a novel administrative data source, we were able to observe and quantify bias to both the incidence proportion and HR in a birth cohort linkage study of reported child maltreatment. Failure to account for out

  12. Genomewide Linkage Screen for Waldenström Macroglobulinemia Susceptibility Loci in High-Risk Families

    Science.gov (United States)

    McMaster, Mary L.; Goldin, Lynn R.; Bai, Yan; Ter-Minassian, Monica; Boehringer, Stefan; Giambarresi, Therese R.; Vasquez, Linda G.; Tucker, Margaret A.

    2006-01-01

    Waldenström macroglobulinemia (WM), a distinctive subtype of non-Hodgkin lymphoma that features overproduction of immunoglobulin M (IgM), clearly has a familial component; however, no susceptibility genes have yet been identified. We performed a genomewide linkage analysis in 11 high-risk families with WM that were informative for linkage, for a total of 122 individuals with DNA samples, including 34 patients with WM and 10 patients with IgM monoclonal gammopathy of undetermined significance (IgM MGUS). We genotyped 1,058 microsatellite markers (average spacing 3.5 cM), performed both nonparametric and parametric linkage analysis, and computed both two-point and multipoint linkage statistics. The strongest evidence of linkage was found on chromosomes 1q and 4q when patients with WM and with IgM MGUS were both considered affected; nonparametric linkage scores were 2.5 (P=.0089) and 3.1 (P=.004), respectively. Other locations suggestive of linkage were found on chromosomes 3 and 6. Results of two-locus linkage analysis were consistent with independent effects. The findings from this first linkage analysis of families at high risk for WM represent important progress toward identifying gene(s) that modulate susceptibility to WM and toward understanding its complex etiology. PMID:16960805

  13. A Simple Sampling Method for Estimating the Accuracy of Large Scale Record Linkage Projects.

    Science.gov (United States)

    Boyd, James H; Guiver, Tenniel; Randall, Sean M; Ferrante, Anna M; Semmens, James B; Anderson, Phil; Dickinson, Teresa

    2016-05-17

    Record linkage techniques allow different data collections to be brought together to provide a wider picture of the health status of individuals. Ensuring high linkage quality is important to guarantee the quality and integrity of research. Current methods for measuring linkage quality typically focus on precision (the proportion of incorrect links), given the difficulty of measuring the proportion of false negatives. The aim of this work is to introduce and evaluate a sampling based method to estimate both precision and recall following record linkage. In the sampling based method, record-pairs from each threshold (including those below the identified cut-off for acceptance) are sampled and clerically reviewed. These results are then applied to the entire set of record-pairs, providing estimates of false positives and false negatives. This method was evaluated on a synthetically generated dataset, where the true match status (which records belonged to the same person) was known. The sampled estimates of linkage quality were relatively close to actual linkage quality metrics calculated for the whole synthetic dataset. The precision and recall measures for seven reviewers were very consistent with little variation in the clerical assessment results (overall agreement using the Fleiss Kappa statistics was 0.601). This method presents as a possible means of accurately estimating matching quality and refining linkages in population level linkage studies. The sampling approach is especially important for large project linkages where the number of record pairs produced may be very large often running into millions.

  14. The Importance of Geographical Proximity for New Product Development Activities within Inter-firm Linkages

    DEFF Research Database (Denmark)

    Dahlgren, Johan Henrich

    important as a resource and where collaboration partners are important. Hypotheses are tested by means of a quantitative analysis of a data set containing information about 4842 domestic and international inter-firm linkages of Danish firms in manufacturing industries. The findings in this analysis exhibit...... for international linkages. It is further suggested closer geographical distance for inter-firm linkages with medium and high level of interaction, suppliers or customers accounting for more than one third of total purchases or sales, and for linkages lasting for at least 10 years.Key words: capabilities, economics...

  15. Genetic linkage map and comparative genome analysis for the estuarine Atlantic killifish (Fundulus heteroclitus)

    Data.gov (United States)

    U.S. Environmental Protection Agency — Genetic linkage maps are valuable tools in evolutionary biology; however, their availability for wild populations is extremely limited. Fundulus heteroclitus...

  16. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

    DEFF Research Database (Denmark)

    Muller, J; Szklarczyk, D; Julien, P

    2010-01-01

    The identification of orthologous relationships forms the basis for most comparative genomics studies. Here, we present the second version of the eggNOG database, which contains orthologous groups (OGs) constructed through identification of reciprocal best BLAST matches and triangular linkage...... of the tree of life; in addition to the species groups included in our first release (i.e. fungi, metazoa, insects, vertebrates and mammals), we have now constructed OGs for archaea, fishes, rodents and primates. We automatically annotate the non-supervised orthologous groups (NOGs) with functional...... descriptions, protein domains, and functional categories as defined initially for the COG/KOG database. In-depth analysis is facilitated by precomputed high-quality multiple sequence alignments and maximum-likelihood trees for each of the available OGs. Altogether, eggNOG covers 2,242 035 proteins (built from...

  17. Water balance in the complex mountainous terrain of Bhutan and linkages to land use

    Directory of Open Access Journals (Sweden)

    Ugyen Dorji

    2016-09-01

    Study Focus: Located in the Himalayas with elevation ranging 100–7550 m and with an area equivalent to Switzerland, Bhutan has great biodiversity despite its small area. A monsoon-dominated climate causes generally wet summer and dry winter. Bhutan is highly dependent of climatic conditions for its developmental activities. Using multiple regression analysis we have established models to predict the evapotranspiration (ETo and water balance and test the linkage to vegetation and land cover using meteorological data from 70 weather stations across Bhutan. Temperature-based ETo equations were evaluated in reference to the Penman-Monteith (PM method and a calibrated Hargreaves (H equation was used for computing the ETo. New Hydrological Insights for the Region. The calibrated Hargreaves equation gave good estimates of average daily ETo comparable to the PM ETo. The spatial variation in PM ETo is linked to variation in sunshine hours in summer and temperature in other seasons. Seasonal and annual ETo was mainly affected by elevation and latitude, which is linked to temperature and sunshine duration. Precipitation and water balance correlated positively with the Southern Oscillation Index (SOI while ETo correlated negatively. Our models for predicting ETo and water balances performed clearly better than the global CRU gridded data for Bhutan. A positive water balance is found in broadleaf forest areas and small or negative water balance for coniferous forests.

  18. Planning for the Maintenance of Floristic Diversity in the Face of Land Cover and Climate Change

    Science.gov (United States)

    Jewitt, Debbie; Goodman, Peter S.; Erasmus, Barend F. N.; O'Connor, Timothy G.; Witkowski, Ed T. F.

    2017-05-01

    Habitat loss and climate change are primary drivers of global biodiversity loss. Species will need to track changing environmental conditions through fragmented and transformed landscapes such as KwaZulu-Natal, South Africa. Landscape connectivity is an important tool for maintaining resilience to global change. We develop a coarse-grained connectivity map between protected areas to aid decision-making for implementing corridors to maintain floristic diversity in the face of global change. The spatial location of corridors was prioritised using a biological underpinning of floristic composition that incorporated high beta diversity regions, important plant areas, climate refugia, and aligned to major climatic gradients driving floristic pattern. We used Linkage Mapper to develop the connectivity network. The resistance layer was based on land-cover categories with natural areas discounted according to their contribution towards meeting the biological objectives. Three corridor maps were developed; a conservative option for meeting minimum corridor requirements, an optimal option for meeting a target amount of 50% of the landscape and an option including linkages in highly transformed areas. The importance of various protected areas and critical linkages in maintaining landscape connectivity are discussed, disconnected protected areas and pinch points identified where the loss of small areas could compromise landscape connectivity. This framework is suggested as a way to conserve floristic diversity into the future and is recommended as an approach for other global connectivity initiatives. A lack of implementation of corridors will lead to further habitat loss and fragmentation, resulting in further risk to plant diversity.

  19. Conservation of gene linkage in dispersed vertebrate NK homeobox clusters.

    Science.gov (United States)

    Wotton, Karl R; Weierud, Frida K; Juárez-Morales, José L; Alvares, Lúcia E; Dietrich, Susanne; Lewis, Katharine E

    2009-10-01

    Nk homeobox genes are important regulators of many different developmental processes including muscle, heart, central nervous system and sensory organ development. They are thought to have arisen as part of the ANTP megacluster, which also gave rise to Hox and ParaHox genes, and at least some NK genes remain tightly linked in all animals examined so far. The protostome-deuterostome ancestor probably contained a cluster of nine Nk genes: (Msx)-(Nk4/tinman)-(Nk3/bagpipe)-(Lbx/ladybird)-(Tlx/c15)-(Nk7)-(Nk6/hgtx)-(Nk1/slouch)-(Nk5/Hmx). Of these genes, only NKX2.6-NKX3.1, LBX1-TLX1 and LBX2-TLX2 remain tightly linked in humans. However, it is currently unclear whether this is unique to the human genome as we do not know which of these Nk genes are clustered in other vertebrates. This makes it difficult to assess whether the remaining linkages are due to selective pressures or because chance rearrangements have "missed" certain genes. In this paper, we identify all of the paralogs of these ancestrally clustered NK genes in several distinct vertebrates. We demonstrate that tight linkages of Lbx1-Tlx1, Lbx2-Tlx2 and Nkx3.1-Nkx2.6 have been widely maintained in both the ray-finned and lobe-finned fish lineages. Moreover, the recently duplicated Hmx2-Hmx3 genes are also tightly linked. Finally, we show that Lbx1-Tlx1 and Hmx2-Hmx3 are flanked by highly conserved noncoding elements, suggesting that shared regulatory regions may have resulted in evolutionary pressure to maintain these linkages. Consistent with this, these pairs of genes have overlapping expression domains. In contrast, Lbx2-Tlx2 and Nkx3.1-Nkx2.6, which do not seem to be coexpressed, are also not associated with conserved noncoding sequences, suggesting that an alternative mechanism may be responsible for the continued clustering of these genes.

  20. Data linkage in an established longitudinal cohort: the Western Australian Pregnancy Cohort (Raine) Study.

    Science.gov (United States)

    Mountain, Jenny A; Nyaradi, Anett; Oddy, Wendy H; Glauert, Rebecca A; de Klerk, Nick H; Straker, Leon M; Stanley, Fiona J

    2016-07-15

    The Western Australian Data Linkage System is one of a few comprehensive, population-based data linkage systems worldwide, creating links between information from different sources relating to the same individual, family, place or event, while maintaining privacy. The Raine Study is an established cohort study with more than 2000 currently active participants. Individual consent was obtained from participants for information in publicly held databases to be linked to their study data. A waiver of consent was granted where it was impracticable to obtain consent. Approvals to link the datasets were obtained from relevant ethics committees and data custodians. The Raine Study dataset was subsequently linked to academic testing data collected by the Western Australian Department of Education. Examination of diet and academic performance showed that children who were predominantly breastfed for at least 6 months scored higher academically at age 10 than children who were breastfed for less than 6 months. A further study found that better diet quality at ages 1, 2 and 3 years was associated with higher academic scores at ages 10 and 12 years. Examination of nutritional intake at 14 years of age found that a better dietary pattern was associated with higher academic performance. The detailed longitudinal data collected in the Raine Study allowed for adjustment for multiple covariates and confounders. Data linkage reduces the burden on cohort participants by providing additional information without the need to contact participants. It can give information on participants who have been lost to follow-up; provide or complement missing data; give the opportunity for validation studies comparing recall of participants with administrative records; increase the population sample of studies by adding control participants from the general population; and allow for the adjustment of multiple covariates and confounders. The Raine Study dataset is extensive and detailed, and can be

  1. Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua

    Directory of Open Access Journals (Sweden)

    Higgins Brent

    2010-03-01

    Full Text Available Abstract Background Atlantic cod (Gadus morhua is a species with increasing economic significance for the aquaculture industry. The genetic improvement of cod will play a critical role in achieving successful large-scale aquaculture. While many microsatellite markers have been developed in cod, the number of single nucleotide polymorphisms (SNPs is currently limited. Here we report the identification of SNPs from sequence data generated by a large-scale expressed sequence tag (EST program, focusing on fish originating from Canadian waters. Results A total of 97976 ESTs were assembled to generate 13448 contigs. We detected 4753 SNPs that met our selection criteria (depth of coverage ≥ 4 reads; minor allele frequency > 25%. 3072 SNPs were selected for testing. The percentage of successful assays was 75%, with 2291 SNPs amplifying correctly. Of these, 607 (26% SNPs were monomorphic for all populations tested. In total, 64 (4% of SNPs are likely to represent duplicated genes or highly similar members of gene families, rather than alternative alleles of the same gene, since they showed a high frequency of heterozygosity. The remaining polymorphic SNPs (1620 were categorised as validated SNPs. The mean minor allele frequency of the validated loci was 0.258 (± 0.141. Of the 1514 contigs from which validated SNPs were selected, 31% have a significant blast hit. For the SNPs predicted to occur in coding regions (141, we determined that 36% (51 are non-synonymous. Many loci (1033 SNPs; 64% are polymorphic in all populations tested. However a small number of SNPs (184 that are polymorphic in the Western Atlantic were monomorphic in fish tested from three European populations. A preliminary linkage map has been constructed with 23 major linkage groups and 924 mapped SNPs. Conclusions These SNPs represent powerful tools to accelerate the genetic improvement of cod aquaculture. They have been used to build a genetic linkage map that can be applied to

  2. SNP-based linkage mapping for validation of QTLs for resistance to ascochyta blight in lentil

    Directory of Open Access Journals (Sweden)

    Shimna Sudheesh

    2016-11-01

    Full Text Available Lentil (Lens culinaris Medik. is a self-pollinating, diploid, annual, cool-season, food legume crop that is cultivated throughout the world. Ascochyta blight (AB, caused by Ascochyta lentis Vassilievsky, is an economically important and widespread disease of lentil. Development of cultivars with high levels of durable resistance provides an environmentally acceptable and economically feasible method for AB control. A detailed understanding of the genetic basis of AB resistance is hence highly desirable, in order to obtain insight into the number and influence of resistance genes. Genetic linkage maps based on single nucleotide polymorphisms (SNP and simple sequence repeat (SSR markers have been developed from three recombinant inbred line (RIL populations. The IH x NF map contained 460 loci across 1461.6 cM, while the IH x DIG map contained 329 loci across 1302.5 cM and the third map, NF x DIG contained 330 loci across 1914.1 cM. Data from these maps were combined with a map from a previously published study through use of bridging markers to generate a consensus linkage map containing 689 loci distributed across 7 linkage groups (LGs, with a cumulative length of 2429.61 cM at an average density of one marker per 3.5 cM. Trait dissection of AB resistance was performed for the RIL populations, identifying totals of two and three quantitative trait loci (QTLs explaining 52% and 69% of phenotypic variation for resistance to infection in the IH x DIG and IH x NF populations, respectively. Presence of common markers in the vicinity of the AB_IH1- and AB_IH2.1/AB_IH2.2-containing regions on both maps supports the inference that a common genomic region is responsible for conferring resistance and is associated with the resistant parent, Indianhead. The third QTL was derived from Northfield. Evaluation of markers associated with AB resistance across a diverse lentil germplasm panel revealed that the identity of alleles associated with AB_IH1 predicted

  3. How home HIV testing and counselling with follow-up support achieves high testing coverage and linkage to treatment and prevention: a qualitative analysis from Uganda.

    Science.gov (United States)

    Ware, Norma C; Wyatt, Monique A; Asiimwe, Stephen; Turyamureeba, Bosco; Tumwesigye, Elioda; van Rooyen, Heidi; Barnabas, Ruanne V; Celum, Connie L

    2016-01-01

    The successes of HIV treatment scale-up and the availability of new prevention tools have raised hopes that the epidemic can finally be controlled and ended. Reduction in HIV incidence and control of the epidemic requires high testing rates at population levels, followed by linkage to treatment or prevention. As effective linkage strategies are identified, it becomes important to understand how these strategies work. We use qualitative data from The Linkages Study, a recent community intervention trial of community-based testing with linkage interventions in sub-Saharan Africa, to show how lay counsellor home HIV testing and counselling (home HTC) with follow-up support leads to linkage to clinic-based HIV treatment and medical male circumcision services. We conducted 99 semi-structured individual interviews with study participants and three focus groups with 16 lay counsellors in Kabwohe, Sheema District, Uganda. The participant sample included both HIV+ men and women (N=47) and HIV-uncircumcised men (N=52). Interview and focus group audio-recordings were translated and transcribed. Each transcript was summarized. The summaries were analyzed inductively to identify emergent themes. Thematic concepts were grouped to develop general constructs and framing propositional statements. Trial participants expressed interest in linking to clinic-based services at testing, but faced obstacles that eroded their initial enthusiasm. Follow-up support by lay counsellors intervened to restore interest and inspire action. Together, home HTC and follow-up support improved morale, created a desire to reciprocate, and provided reassurance that services were trustworthy. In different ways, these functions built links to the health service system. They worked to strengthen individuals' general sense of capability, while making the idea of accessing services more manageable and familiar, thus reducing linkage barriers. Home HTC with follow-up support leads to linkage by building

  4. Environmental groups in politics

    International Nuclear Information System (INIS)

    Lowe, P.; Goyder, J.

    1983-01-01

    The subject is covered in chapters, entitled: introduction; (Part I) the environmental movement (environmental groups and the attentive public; the episodic development of the environmental movement; the underlying values of environmentalism; the roots of environmental concern; the social limits to growth; elite manipulation of values); the organisation of environmental groups; environmental groups in national politics; environmental groups in local politics; (Part II) the Henley Society; Friends of the Earth; the National Trust; the Royal Society for Nature Conservation; the European Environmental Bureau. (U.K.)

  5. Groups, rings, modules

    CERN Document Server

    Auslander, Maurice

    2014-01-01

    This classic monograph is geared toward advanced undergraduates and graduate students. The treatment presupposes some familiarity with sets, groups, rings, and vector spaces. The four-part approach begins with examinations of sets and maps, monoids and groups, categories, and rings. The second part explores unique factorization domains, general module theory, semisimple rings and modules, and Artinian rings. Part three's topics include localization and tensor products, principal ideal domains, and applications of fundamental theorem. The fourth and final part covers algebraic field extensions

  6. The value of snow cover

    Science.gov (United States)

    Sokratov, S. A.

    2009-04-01

    only and not even the main outcome from snow cover use. The value of snow cover for agriculture, water resources, industry and transportation is so naturally inside the activities that is not often quantified. However, any considerations of adaptation strategies for climate change with changing snow conditions need such quantification.

  7. Strategies for Sustainable Urban Development and Urban-Rural Linkages

    DEFF Research Database (Denmark)

    Nilsson, Kjell; Nielsen, Thomas Alexander Sick; Aalbers, Carmen

    2014-01-01

    , identified how land use conflicts and the pressure towards peri- urban areas can be strategically managed in different development and regulatory contexts. To summarise, the following strategies were identified as important steps towards more sustainable urban-rural futures: (i) better coordination...... of transport, land use and open space planning; (ii) urban containment and densification – development a green compact city; (iii) preservation of blue and green infrastructure; and (iv) preservation of agricultural land and the promotion of local production. The need also remains to strengthen governance...... at the regional level while at the pan-European level there is clearly a need for more policy attention to be given to urban-rural linkages....

  8. Exploiting linkage disequilibrium in statistical modelling in quantitative genomics

    DEFF Research Database (Denmark)

    Wang, Lei

    Alleles at two loci are said to be in linkage disequilibrium (LD) when they are correlated or statistically dependent. Genomic prediction and gene mapping rely on the existence of LD between gentic markers and causul variants of complex traits. In the first part of the thesis, a novel method...... to quantify and visualize local variation in LD along chromosomes in describet, and applied to characterize LD patters at the local and genome-wide scale in three Danish pig breeds. In the second part, different ways of taking LD into account in genomic prediction models are studied. One approach is to use...... the recently proposed antedependence models, which treat neighbouring marker effects as correlated; another approach involves use of haplotype block information derived using the program Beagle. The overall conclusion is that taking LD information into account in genomic prediction models potentially improves...

  9. Biosynthesis of riboflavin: mechanism of formation of the ribitylamino linkage

    International Nuclear Information System (INIS)

    Keller, P.J.; Van, Q.L.; Kim, S.U.; Bown, D.H.; Chen, H.C.; Kohnle, A.; Bacher, A.; Floss, H.G.

    1988-01-01

    Feeding experiments with Ashbya gossypii followed by NMR analysis of the resulting riboflavin showed incorporation of deuterium from D-[2- 2 H]ribose at C-2' and from D-[1- 2 H] ribose in the pro-R position at C-1' of the ribityl side chain. The results rule out an Amadori rearrangement mechanism for the reduction of the ribosylamino to the ribitylamino linkage and point to formation of a Schiff base that is reduced stereospecifically opposite to the face from which the oxygen has departed. As prerequisite for the analysis, the 1 H NMR signals for the pro-R and pro-S hydrogens at C-1' of 6,7-dimethyl-8-ribityllumazine and riboflavin and its tetraacetate were assigned with the aid of synthetic stereospecifically deuteriated samples

  10. X linked exudative vitreoretinopathy: clinical features and genetic linkage analysis.

    Science.gov (United States)

    Fullwood, P; Jones, J; Bundey, S; Dudgeon, J; Fielder, A R; Kilpatrick, M W

    1993-03-01

    A four generation family in which familial exudative vitreoretinopathy is inherited as an X linked condition is described. Essentially the condition is one of abnormal vascularisation and signs at birth are those of a retinopathy superficially resembling retinopathy of prematurity, retinal folds, or, in advanced cases, enophthalmos or even phthisis. Prognosis depends on the progression of the retinal changes. The family members, including seven affected males and five obligate carrier females, have been types for 20 DNA markers, and linkage analysis suggests a gene locus either at Xq21.3 or at Xp11. As the latter region includes the locus for the gene for Norrie disease, it is possible that this and X linked vitreoretinopathy are allelic. We can further speculate that the differences in severity of the clinical manifestations are dependent only upon the timing of the insult.

  11. Construction of functional linkage gene networks by data integration.

    Science.gov (United States)

    Linghu, Bolan; Franzosa, Eric A; Xia, Yu

    2013-01-01

    Networks of functional associations between genes have recently been successfully used for gene function and disease-related research. A typical approach for constructing such functional linkage gene networks (FLNs) is based on the integration of diverse high-throughput functional genomics datasets. Data integration is a nontrivial task due to the heterogeneous nature of the different data sources and their variable accuracy and completeness. The presence of correlations between data sources also adds another layer of complexity to the integration process. In this chapter we discuss an approach for constructing a human FLN from data integration and a subsequent application of the FLN to novel disease gene discovery. Similar approaches can be applied to nonhuman species and other discovery tasks.

  12. Linkage of management decision to shareholder's value: EVA concept

    Directory of Open Access Journals (Sweden)

    Shrikant Krupasindhu Panigrahi

    2014-02-01

    Full Text Available In this paper, the author investigated the influence of management decisions like capital structure, dividend policies, remunerations, credit policy decisions and investment decisions on shareholder wealth maximization. To achieve the objective, portfolio theory, capital asset pricing model and modern financial theory providing evidence on the linkage between management decisions to shareholder’s value. Shareholders are only concerned about the value of shares of the company and the amount of return in the form of dividend paid. Thus in order to meet the demands of the shareholders of the company, managers needs to increase their abilities and skills to overcome the organizational goals. Thus the main goal of this paper is to discuss on the role of management decisions towards increasing shareholder’s wealth and meet organizational goals.

  13. Spin Transfer in Polymer Degradation of Abnormal Linkage

    Science.gov (United States)

    Yu, Tianrong; Tian, Chuanjin; Liu, Xizhe; Wang, Jia; Gao, Yang; Wang, Zhigang

    2017-07-01

    The degradation of polymer materials plays an important role in production and life. In this work, the degradation mechanism of poly-α-methylstyrene (PAMS) tetramers with abnormal linkage was investigated by using density functional theory (DFT). Calculated results indicate that the head-to-head and the tail-to-tail reactions needed to overcome the energy barriers are about 0.15 eV and about 1.26 eV, respectively. The broken C-C bond at the unsaturated end of the chain leads to the dissociation of alpha-methylstyrene (AMS) monomers one by one. Furthermore, the analyses of bond characteristics are in good agreement with the results of energy barriers. In addition, the spin population analysis presents an interesting net spin transfer process in depolymerization reactions. We hope that the current theoretical results provide useful help to understand the degradation mechanism of polymers.

  14. Linkage of anthropogenic aerosol to clouds and climate

    International Nuclear Information System (INIS)

    Hudson, J.G.

    1992-01-01

    This progress report describes the monitoring being done to validate a linkage of anthropogenic aerosol to clouds and climate. Equipment and findings are reported. The equipment construction called for in the original proposal has now been competed. These instruments are the high temperature processor, the data acquisition system for the direct Royco optical particle counter (OPC), and modifications to the formvar replicator. The main field effort during the past year has been the shipboard experiment SEAHUNT (Shiptrail Evolution Above High Updraft Naval Targets). There were also some laboratory and local ambient particle measurements and a surface field program on and near the California coast. The shipboard project was not anticipated in the original proposal but the laboratory and surface measurements were along the lines suggested in the original proposal

  15. Validation of an instrument to measure inter-organisational linkages in general practice.

    Science.gov (United States)

    Amoroso, Cheryl; Proudfoot, Judith; Bubner, Tanya; Jayasinghe, Upali W; Holton, Christine; Winstanley, Julie; Beilby, Justin; Harris, Mark F

    2007-12-03

    Linkages between general medical practices and external services are important for high quality chronic disease care. The purpose of this research is to describe the development, evaluation and use of a brief tool that measures the comprehensiveness and quality of a general practice's linkages with external providers for the management of patients with chronic disease. In this study, clinical linkages are defined as the communication, support, and referral arrangements between services for the care and assistance of patients with chronic disease. An interview to measure surgery-level (rather than individual clinician-level) clinical linkages was developed, piloted, reviewed, and evaluated with 97 Australian general practices. Two validated survey instruments were posted to patients, and a survey of locally available services was developed and posted to participating Divisions of General Practice (support organisations). Hypotheses regarding internal validity, association with local services, and patient satisfaction were tested using factor analysis, logistic regression and multilevel regression models. The resulting General Practice Clinical Linkages Interview (GP-CLI) is a nine-item tool with three underlying factors: referral and advice linkages, shared care and care planning linkages, and community access and awareness linkages. Local availability of chronic disease services has no affect on the comprehensiveness of services with which practices link, however, comprehensiveness of clinical linkages has an association with patient assessment of access, receptionist services, and of continuity of care in their general practice. The GP-CLI may be useful to researchers examining comparable health care systems for measuring the comprehensiveness and quality of linkages at a general practice-level with related services, possessing both internal and external validity. The tool can be used with large samples exploring the impact, outcomes, and facilitators of high

  16. Validation of an instrument to measure inter-organisational linkages in general practice

    Directory of Open Access Journals (Sweden)

    Cheryl Amoroso

    2007-11-01

    Full Text Available Purpose: Linkages between general medical practices and external services are important for high quality chronic disease care. The purpose of this research is to describe the development, evaluation and use of a brief tool that measures the comprehensiveness and quality of a general practice’s linkages with external providers for the management of patients with chronic disease. In this study, clinical linkages are defined as the communication, support, and referral arrangements between services for the care and assistance of patients with chronic disease. Methods: An interview to measure surgery-level (rather than individual clinician-level clinical linkages was developed, piloted, reviewed, and evaluated with 97 Australian general practices. Two validated survey instruments were posted to patients, and a survey of locally available services was developed and posted to participating Divisions of General Practice (support organisations. Hypotheses regarding internal validity, association with local services, and patient satisfaction were tested using factor analysis, logistic regression and multilevel regression models. Results: The resulting General Practice Clinical Linkages Interview (GP-CLI is a nine-item tool with three underlying factors: referral and advice linkages, shared care and care planning linkages, and community access and awareness linkages. Local availability of chronic disease services has no affect on the comprehensiveness of services with which practices link, however comprehensiveness of clinical linkages has an association with patient assessment of access, receptionist services, and of continuity of care in their general practice. Conclusions: The GP-CLI may be useful to researchers examining comparable health care systems for measuring the comprehensiveness and quality of linkages at a general practice-level with related services, possessing both internal and external validity. The tool can be used with large samples

  17. Rethinking health sector procurement as developmental linkages in East Africa.

    Science.gov (United States)

    Mackintosh, Maureen; Tibandebage, Paula; Karimi Njeru, Mercy; Kariuki Kungu, Joan; Israel, Caroline; Mujinja, Phares G M

    2018-03-01

    Health care forms a large economic sector in all countries, and procurement of medicines and other essential commodities necessarily creates economic linkages between a country's health sector and local and international industrial development. These procurement processes may be positive or negative in their effects on populations' access to appropriate treatment and on local industrial development, yet procurement in low and middle income countries (LMICs) remains under-studied: generally analysed, when addressed at all, as a public sector technical and organisational challenge rather than a social and economic element of health system governance shaping its links to the wider economy. This article uses fieldwork in Tanzania and Kenya in 2012-15 to analyse procurement of essential medicines and supplies as a governance process for the health system and its industrial links, drawing on aspects of global value chain theory. We describe procurement work processes as experienced by front line staff in public, faith-based and private sectors, linking these experiences to wholesale funding sources and purchasing practices, and examining their implications for medicines access and for local industrial development within these East African countries. We show that in a context of poor access to reliable medicines, extensive reliance on private medicines purchase, and increasing globalisation of procurement systems, domestic linkages between health and industrial sectors have been weakened, especially in Tanzania. We argue in consequence for a more developmental perspective on health sector procurement design, including closer policy attention to strengthening vertical and horizontal relational working within local health-industry value chains, in the interests of both wider access to treatment and improved industrial development in Africa. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  18. Efficient sequential and parallel algorithms for record linkage.

    Science.gov (United States)

    Mamun, Abdullah-Al; Mi, Tian; Aseltine, Robert; Rajasekaran, Sanguthevar

    2014-01-01

    Integrating data from multiple sources is a crucial and challenging problem. Even though there exist numerous algorithms for record linkage or deduplication, they suffer from either large time needs or restrictions on the number of datasets that they can integrate. In this paper we report efficient sequential and parallel algorithms for record linkage which handle any number of datasets and outperform previous algorithms. Our algorithms employ hierarchical clustering algorithms as the basis. A key idea that we use is radix sorting on certain attributes to eliminate identical records before any further processing. Another novel idea is to form a graph that links similar records and find the connected components. Our sequential and parallel algorithms have been tested on a real dataset of 1,083,878 records and synthetic datasets ranging in size from 50,000 to 9,000,000 records. Our sequential algorithm runs at least two times faster, for any dataset, than the previous best-known algorithm, the two-phase algorithm using faster computation of the edit distance (TPA (FCED)). The speedups obtained by our parallel algorithm are almost linear. For example, we get a speedup of 7.5 with 8 cores (residing in a single node), 14.1 with 16 cores (residing in two nodes), and 26.4 with 32 cores (residing in four nodes). We have compared the performance of our sequential algorithm with TPA (FCED) and found that our algorithm outperforms the previous one. The accuracy is the same as that of this previous best-known algorithm.

  19. Association and linkage analysis of aluminum tolerance genes in maize.

    Directory of Open Access Journals (Sweden)

    Allison M Krill

    Full Text Available BACKGROUND: Aluminum (Al toxicity is a major worldwide constraint to crop productivity on acidic soils. Al becomes soluble at low pH, inhibiting root growth and severely reducing yields. Maize is an important staple food and commodity crop in acidic soil regions, especially in South America and Africa where these soils are very common. Al exclusion and intracellular tolerance have been suggested as two important mechanisms for Al tolerance in maize, but little is known about the underlying genetics. METHODOLOGY: An association panel of 282 diverse maize inbred lines and three F2 linkage populations with approximately 200 individuals each were used to study genetic variation in this complex trait. Al tolerance was measured as net root growth in nutrient solution under Al stress, which exhibited a wide range of variation between lines. Comparative and physiological genomics-based approaches were used to select 21 candidate genes for evaluation by association analysis. CONCLUSIONS: Six candidate genes had significant results from association analysis, but only four were confirmed by linkage analysis as putatively contributing to Al tolerance: Zea mays AltSB like (ZmASL, Zea mays aluminum-activated malate transporter2 (ALMT2, S-adenosyl-L-homocysteinase (SAHH, and Malic Enzyme (ME. These four candidate genes are high priority subjects for follow-up biochemical and physiological studies on the mechanisms of Al tolerance in maize. Immediately, elite haplotype-specific molecular markers can be developed for these four genes and used for efficient marker-assisted selection of superior alleles in Al tolerance maize breeding programs.

  20. The linkage between geopotential height and monthly precipitation in Iran

    Science.gov (United States)

    Shirvani, Amin; Fadaei, Amir Sabetan; Landman, Willem A.

    2018-04-01

    This paper investigates the linkage between large-scale atmospheric circulation and monthly precipitation during November to April over Iran. Canonical correlation analysis (CCA) is used to set up the statistical linkage between the 850 hPa geopotential height large-scale circulation and monthly precipitation over Iran for the period 1968-2010. The monthly precipitation dataset for 50 synoptic stations distributed in different climate regions of Iran is considered as the response variable in the CCA. The monthly geopotential height reanalysis dataset over an area between 10° N and 60° N and from 20° E to 80° E is utilized as the explanatory variable in the CCA. Principal component analysis (PCA) as a pre-filter is used for data reduction for both explanatory and response variables before applying CCA. The optimal number of principal components and canonical variables to be retained in the CCA equations is determined using the highest average cross-validated Kendall's tau value. The 850 hPa geopotential height pattern over the Red Sea, Saudi Arabia, and Persian Gulf is found to be the major pattern related to Iranian monthly precipitation. The Pearson correlation between the area averaged of the observed and predicted precipitation over the study area for Jan, Feb, March, April, November, and December months are statistically significant at the 5% significance level and are 0.78, 0.80, 0.82, 0.74, 0.79, and 0.61, respectively. The relative operating characteristic (ROC) indicates that the highest scores for the above- and below-normal precipitation categories are, respectively, for February and April and the lowest scores found for December.

  1. Exploiting semantic linkages among multiple sources for semantic information retrieval

    Science.gov (United States)

    Li, JianQiang; Yang, Ji-Jiang; Liu, Chunchen; Zhao, Yu; Liu, Bo; Shi, Yuliang

    2014-07-01

    The vision of the Semantic Web is to build a global Web of machine-readable data to be consumed by intelligent applications. As the first step to make this vision come true, the initiative of linked open data has fostered many novel applications aimed at improving data accessibility in the public Web. Comparably, the enterprise environment is so different from the public Web that most potentially usable business information originates in an unstructured form (typically in free text), which poses a challenge for the adoption of semantic technologies in the enterprise environment. Considering that the business information in a company is highly specific and centred around a set of commonly used concepts, this paper describes a pilot study to migrate the concept of linked data into the development of a domain-specific application, i.e. the vehicle repair support system. The set of commonly used concepts, including the part name of a car and the phenomenon term on the car repairing, are employed to build the linkage between data and documents distributed among different sources, leading to the fusion of documents and data across source boundaries. Then, we describe the approaches of semantic information retrieval to consume these linkages for value creation for companies. The experiments on two real-world data sets show that the proposed approaches outperform the best baseline 6.3-10.8% and 6.4-11.1% in terms of top five and top 10 precisions, respectively. We believe that our pilot study can serve as an important reference for the development of similar semantic applications in an enterprise environment.

  2. Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

    Directory of Open Access Journals (Sweden)

    Ward Judson A

    2013-01-01

    Full Text Available Abstract Background Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry. Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker density, but result in some genotype errors and a large number of missing genotype values. Imputation can reduce the number of missing values and can correct genotyping errors, but current methods of imputation require a reference genome and thus are not an option for most species. Results Genotyping by Sequencing (GBS was used to produce highly saturated maps for a R. idaeus pseudo-testcross progeny. While low coverage and high variance in sequencing resulted in a large number of missing values for some individuals, a novel method of imputation based on maximum likelihood marker ordering from initial marker segregation overcame the challenge of missing values, and made map construction computationally tractable. The two resulting parental maps contained 4521 and 2391 molecular markers spanning 462.7 and 376.6 cM respectively over seven linkage groups. Detection of precise genomic regions with segregation distortion was possible because of map saturation. Microsatellites (SSRs linked these results to published maps for cross-validation and map comparison. Conclusions GBS together with genome-independent imputation provides a rapid method for genetic map construction in any pseudo-testcross progeny. Our method of imputation estimates the correct genotype call of missing values and corrects genotyping errors that lead to inflated map size and reduced precision in marker placement. Comparison of SSRs to published R. idaeus maps showed that the linkage maps constructed with GBS and our method of imputation were robust, and marker positioning reliable. The high marker density allowed identification of genomic regions with segregation

  3. Linkage strategies for successful and sustainable partnerships: a practical framework for community engagement by palliative care services.

    Science.gov (United States)

    Rosenberg, John

    2018-01-01

    Partnerships are central to the success of linkages between palliative care services and the communities they support. The goal of partnership is to achieve more than individuals and groups can achieve on their own, yet the concept is often poorly understood. A clearly articulated understanding of partnership is a powerful step in transforming an organization's engagement with the community. The aim of this workshop is to enable participants to gain a clear understanding of partnership, understand the recognized evidence-based principles of establishing and maintaining partnerships, and identify practical approaches to partnering to take back to their organizations and communities.

  4. Colorectal cancer linkage on chromosomes 4q21, 8q13, 12q24, and 15q22.

    Directory of Open Access Journals (Sweden)

    Mine S Cicek

    Full Text Available A substantial proportion of familial colorectal cancer (CRC is not a consequence of known susceptibility loci, such as mismatch repair (MMR genes, supporting the existence of additional loci. To identify novel CRC loci, we conducted a genome-wide linkage scan in 356 white families with no evidence of defective MMR (i.e., no loss of tumor expression of MMR proteins, no microsatellite instability (MSI-high tumors, or no evidence of linkage to MMR genes. Families were ascertained via the Colon Cancer Family Registry multi-site NCI-supported consortium (Colon CFR, the City of Hope Comprehensive Cancer Center, and Memorial University of Newfoundland. A total of 1,612 individuals (average 5.0 per family including 2.2 affected were genotyped using genome-wide single nucleotide polymorphism linkage arrays; parametric and non-parametric linkage analysis used MERLIN in a priori-defined family groups. Five lod scores greater than 3.0 were observed assuming heterogeneity. The greatest were among families with mean age of diagnosis less than 50 years at 4q21.1 (dominant HLOD = 4.51, α = 0.84, 145.40 cM, rs10518142 and among all families at 12q24.32 (dominant HLOD = 3.60, α = 0.48, 285.15 cM, rs952093. Among families with four or more affected individuals and among clinic-based families, a common peak was observed at 15q22.31 (101.40 cM, rs1477798; dominant HLOD = 3.07, α = 0.29; dominant HLOD = 3.03, α = 0.32, respectively. Analysis of families with only two affected individuals yielded a peak at 8q13.2 (recessive HLOD = 3.02, α = 0.51, 132.52 cM, rs1319036. These previously unreported linkage peaks demonstrate the continued utility of family-based data in complex traits and suggest that new CRC risk alleles remain to be elucidated.

  5. New South Wales Child Development Study (NSW-CDS): an Australian multiagency, multigenerational, longitudinal record linkage study.

    Science.gov (United States)

    Carr, Vaughan J; Harris, Felicity; Raudino, Alessandra; Luo, Luming; Kariuki, Maina; Liu, Enwu; Tzoumakis, Stacy; Smith, Maxwell; Holbrook, Allyson; Bore, Miles; Brinkman, Sally; Lenroot, Rhoshel; Dix, Katherine; Dean, Kimberlie; Laurens, Kristin R; Green, Melissa J

    2016-02-11

    The initial aim of this multiagency, multigenerational record linkage study is to identify childhood profiles of developmental vulnerability and resilience, and to identify the determinants of these profiles. The eventual aim is to identify risk and protective factors for later childhood-onset and adolescent-onset mental health problems, and other adverse social outcomes, using subsequent waves of record linkage. The research will assist in informing the development of public policy and intervention guidelines to help prevent or mitigate adverse long-term health and social outcomes. The study comprises a population cohort of 87,026 children in the Australian State of New South Wales (NSW). The cohort was defined by entry into the first year of full-time schooling in NSW in 2009, at which time class teachers completed the Australian Early Development Census (AEDC) on each child (with 99.7% coverage in NSW). The AEDC data have been linked to the children's birth, health, school and child protection records for the period from birth to school entry, and to the health and criminal records of their parents, as well as mortality databases. Descriptive data summarising sex, geographic and socioeconomic distributions, and linkage rates for the various administrative databases are presented. Child data are summarised, and the mental health and criminal records data of the children's parents are provided. In 2015, at age 11 years, a self-report mental health survey was administered to the cohort in collaboration with government, independent and Catholic primary school sectors. A second record linkage, spanning birth to age 11 years, will be undertaken to link this survey data with the aforementioned administrative databases. This will enable a further identification of putative risk and protective factors for adverse mental health and other outcomes in adolescence, which can then be tested in subsequent record linkages. Published by the BMJ Publishing Group Limited. For

  6. Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.

    Directory of Open Access Journals (Sweden)

    Shokeen Bhumika

    2011-02-01

    Full Text Available Abstract Background Chickpea (Cicer arietinum L. is an economically important cool season grain legume crop that is valued for its nutritive seeds having high protein content. However, several biotic and abiotic stresses and the low genetic variability in the chickpea genome have continuously hindered the chickpea molecular breeding programs. STMS (Sequence Tagged Microsatellite Sites markers which are preferred for the construction of saturated linkage maps in several crop species, have also emerged as the most efficient and reliable source for detecting allelic diversity in chickpea. However, the number of STMS markers reported in chickpea is still limited and moreover exhibit low rates of both inter and intraspecific polymorphism, thereby limiting the positions of the SSR markers especially on the intraspecific linkage maps of chickpea. Hence, this study was undertaken with the aim of developing additional STMS markers and utilizing them for advancing the genetic linkage map of chickpea which would have applications in QTL identification, MAS and for de novo assembly of high throughput whole genome sequence data. Results A microsatellite enriched library of chickpea (enriched for (GT/CAn and (GA/CTn repeats was constructed from which 387 putative microsatellite containing clones were identified. From these, 254 STMS primers were designed of which 181 were developed as functional markers. An intraspecific mapping population of chickpea, [ICCV-2 (single podded × JG-62 (double podded] and comprising of 126 RILs, was genotyped for mapping. Of the 522 chickpea STMS markers (including the double-podding trait, screened for parental polymorphism, 226 (43.3% were polymorphic in the parents and were used to genotype the RILs. At a LOD score of 3.5, eight linkage groups defining the position of 138 markers were obtained that spanned 630.9 cM with an average marker density of 4.57 cM. Further, based on the common loci present between the current map

  7. Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Gaur, Rashmi; Sethy, Niroj K; Choudhary, Shalu; Shokeen, Bhumika; Gupta, Varsha; Bhatia, Sabhyata

    2011-02-17

    Chickpea (Cicer arietinum L.) is an economically important cool season grain legume crop that is valued for its nutritive seeds having high protein content. However, several biotic and abiotic stresses and the low genetic variability in the chickpea genome have continuously hindered the chickpea molecular breeding programs. STMS (Sequence Tagged Microsatellite Sites) markers which are preferred for the construction of saturated linkage maps in several crop species, have also emerged as the most efficient and reliable source for detecting allelic diversity in chickpea. However, the number of STMS markers reported in chickpea is still limited and moreover exhibit low rates of both inter and intraspecific polymorphism, thereby limiting the positions of the SSR markers especially on the intraspecific linkage maps of chickpea. Hence, this study was undertaken with the aim of developing additional STMS markers and utilizing them for advancing the genetic linkage map of chickpea which would have applications in QTL identification, MAS and for de novo assembly of high throughput whole genome sequence data. A microsatellite enriched library of chickpea (enriched for (GT/CA)n and (GA/CT)n repeats) was constructed from which 387 putative microsatellite containing clones were identified. From these, 254 STMS primers were designed of which 181 were developed as functional markers. An intraspecific mapping population of chickpea, [ICCV-2 (single podded) × JG-62 (double podded)] and comprising of 126 RILs, was genotyped for mapping. Of the 522 chickpea STMS markers (including the double-podding trait, screened for parental polymorphism, 226 (43.3%) were polymorphic in the parents and were used to genotype the RILs. At a LOD score of 3.5, eight linkage groups defining the position of 138 markers were obtained that spanned 630.9 cM with an average marker density of 4.57 cM. Further, based on the common loci present between the current map and the previously published chickpea

  8. Statistical Monitoring of Changes to Land Cover

    KAUST Repository

    Zerrouki, Nabil; Harrou, Fouzi; Sun, Ying

    2018-01-01

    Accurate detection of changes in land cover leads to better understanding of the dynamics of landscapes. This letter reports the development of a reliable approach to detecting changes in land cover based on remote sensing and radiometric data

  9. VT National Land Cover Dataset - 2001

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) The NLCD2001 layer available from VCGI is a subset of the the National Land Cover Database 2001 land cover layer for mapping zone 65 was produced...

  10. Watershed impervious cover relative to stream location

    Data.gov (United States)

    U.S. Environmental Protection Agency — Estimates of watershed (12-digit huc) impervious cover and impervious cover near streams and water body shorelines for three dates (2001, 2006, 2011) using NLCD...

  11. 1990 Kansas Land Cover Patterns Update

    Data.gov (United States)

    Kansas Data Access and Support Center — In 2008, an update of the 1990 Kansas Land Cover Patterns (KLCP) database was undertaken. The 1990 KLCP database depicts 10 general land cover classes for the State...

  12. Linkage mapping in the oilseed crop Jatropha curcas L. reveals a locus controlling the biosynthesis of phorbol esters which cause seed toxicity.

    Science.gov (United States)

    King, Andrew J; Montes, Luis R; Clarke, Jasper G; Affleck, Julie; Li, Yi; Witsenboer, Hanneke; van der Vossen, Edwin; van der Linde, Piet; Tripathi, Yogendra; Tavares, Evanilda; Shukla, Parul; Rajasekaran, Thirunavukkarasu; van Loo, Eibertus N; Graham, Ian A

    2013-10-01

    Current efforts to grow the tropical oilseed crop Jatropha curcas L. economically are hampered by the lack of cultivars and the presence of toxic phorbol esters (PE) within the seeds of most provenances. These PE restrict the conversion of seed cake into animal feed, although naturally occurring 'nontoxic' provenances exist which produce seed lacking PE. As an important step towards the development of genetically improved varieties of J. curcas, we constructed a linkage map from four F₂ mapping populations. The consensus linkage map contains 502 codominant markers, distributed over 11 linkage groups, with a mean marker density of 1.8 cM per unique locus. Analysis of the inheritance of PE biosynthesis indicated that this is a maternally controlled dominant monogenic trait. This maternal control is due to biosynthesis of the PE occurring only within maternal tissues. The trait segregated 3 : 1 within seeds collected from F₂ plants, and QTL analysis revealed that a locus on linkage group 8 was responsible for phorbol ester biosynthesis. By taking advantage of the draft genome assemblies of J. curcas and Ricinus communis (castor), a comparative mapping approach was used to develop additional markers to fine map this mutation within 2.3 cM. The linkage map provides a framework for the dissection of agronomic traits in J. curcas, and the development of improved varieties by marker-assisted breeding. The identification of the locus responsible for PE biosynthesis means that it is now possible to rapidly breed new nontoxic varieties. © 2013 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  13. Linear algebra and group theory

    CERN Document Server

    Smirnov, VI

    2011-01-01

    This accessible text by a Soviet mathematician features material not otherwise available to English-language readers. Its three-part treatment covers determinants and systems of equations, matrix theory, and group theory. 1961 edition.

  14. An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis

    NARCIS (Netherlands)

    Geest, van Geert; Bourke, Peter M.; Voorrips, Roeland E.; Marasek-Ciolakowska, Agnieszka; Liao, Yanlin; Post, Aike; Meeteren, van Uulke; Visser, Richard G.F.; Maliepaard, Chris; Arens, Paul

    2017-01-01

    Key message: We constructed the first integrated genetic linkage map in a polysomic hexaploid. This enabled us to estimate inheritance of parental haplotypes in the offspring and detect multi-allelic QTL.Abstract: Construction and use of linkage maps are challenging in hexaploids with polysomic

  15. Meta-analysis of genome-wide linkage scans of attention deficit hyperactivity disorder

    NARCIS (Netherlands)

    Zhou, K.; Dempfle, A.; Arcos-Burgos, M.; Bakker, S.C.; Banaschewski, T.; Biederman, J; Buitelaar, J.K.; Castellanos, F.X.; Doyle, A.; Ebstein, R.; Ekholm, J.; Forabosco, P.; Franke, F.; Freitag, C.; Friedel, S.; Gill, M.; Hebebrand, J.; Hinney, A.; Jacob, C.; Lesch, K.P.; Loo, S.K.; Lopera, F.; McCracken, J.T.; McGough, J.J.; Meyer, J.; Mick, E.; Miranda, A.; Muenkel, M.; Mulas, F.; Nelson, S.F.; Nguyen, T.T.; Oades, R.D.; Ogdie, M.N.; Palacio, J.D.; Pineda, D.; Reif, A.; Renner, T.J.; Roeyers, H.; Romanos, M.; Rothenberger, A.; Schäfer, H.; Sergeant, J.A.; Sinke, R.J.; Smalley, S.L.; Sonuga-Barke, E.; Steinhausen, H.C.; van der Meulen, E.; Walitza, S.; Warnke, A.; Lewis, C.M.; Faraone, S.V.; Asherson, P.

    2008-01-01

    Genetic contribution to the development of attention deficit hyperactivity disorder (ADHD) is well established. Seven independent genome-wide linkage scans have been performed to map loci that increase the risk for ADHD. Although significant linkage signals were identified in some of the studies,

  16. Meta-analysis of genome-wide linkage scans of attention deficit hyperactivity disorder.

    NARCIS (Netherlands)

    Zhou, K.; Dempfle, A.; Arcos-Burgos, M.; Bakker, S.C.; Banaschewski, T.; Biederman, J.; Buitelaar, J.K.; Castellanos, F.X.; Doyle, A.; Ebstein, R.P.; Ekholm, J.; Forabosco, P.; Franke, B.; Freitag, C.; Friedel, S.; Gill, M.; Hebebrand, J.; Hinney, A.; Jacob, C.; Lesch, K.P.; Loo, S.K.; Lopera, F.; McCracken, J.T.; McGough, J.J.; Meyer, J.; Mick, E.; Miranda, A.; Muenke, M.; Mulas, F.; Nelson, S.F.; Nguyen, T.T.; Oades, R.D.; Ogdie, M.N.; Palacio, J.D.; Pineda, D.; Reif, A.; Renner, T.J.; Roeyers, H.; Romanos, M.; Rothenberger, A.; Schafer, H.; Sergeant, J.A.; Sinke, R.J.; Smalley, S.L.; Sonuga-Barke, E.J.S.; Steinhausen, H.C.; Meulen, E. van der; Walitza, S.; Warnke, A.; Lewis, C.M.; Faraone, S.V.; Asherson, P.

    2008-01-01

    Genetic contribution to the development of attention deficit hyperactivity disorder (ADHD) is well established. Seven independent genome-wide linkage scans have been performed to map loci that increase the risk for ADHD. Although significant linkage signals were identified in some of the studies,

  17. Applying Topographic Classification, Based on the Hydrological Process, to Design Habitat Linkages for Climate Change

    Directory of Open Access Journals (Sweden)

    Yongwon Mo

    2017-11-01

    Full Text Available The use of biodiversity surrogates has been discussed in the context of designing habitat linkages to support the migration of species affected by climate change. Topography has been proposed as a useful surrogate in the coarse-filter approach, as the hydrological process caused by topography such as erosion and accumulation is the basis of ecological processes. However, some studies that have designed topographic linkages as habitat linkages, so far have focused much on the shape of the topography (morphometric topographic classification with little emphasis on the hydrological processes (generic topographic classification to find such topographic linkages. We aimed to understand whether generic classification was valid for designing these linkages. First, we evaluated whether topographic classification is more appropriate for describing actual (coniferous and deciduous and potential (mammals and amphibians habitat distributions. Second, we analyzed the difference in the linkages between the morphometric and generic topographic classifications. The results showed that the generic classification represented the actual distribution of the trees, but neither the morphometric nor the generic classification could represent the potential animal distributions adequately. Our study demonstrated that the topographic classes, according to the generic classification, were arranged successively according to the flow of water, nutrients, and sediment; therefore, it would be advantageous to secure linkages with a width of 1 km or more. In addition, the edge effect would be smaller than with the morphometric classification. Accordingly, we suggest that topographic characteristics, based on the hydrological process, are required to design topographic linkages for climate change.

  18. Multipoint linkage analysis and homogeneity tests in 15 Dutch X-linked retinitis pigmentosa families

    NARCIS (Netherlands)

    Bergen, A. A.; van den Born, L. I.; Schuurman, E. J.; Pinckers, A. J.; van Ommen, G. J.; Bleekers-Wagemakers, E. M.; Sandkuijl, L. A.

    1995-01-01

    Linkage analysis and homogeneity tests were carried out in 15 Dutch families segregating X-linked retinitis pigmentosa (X L R P). The study included segregation data for eight polymorphic DNA markers from the short arm of the human X chromosome. The results of both multipoint linkage analysis in

  19. Testing for linkage disequilibrium in the New Zealand radiata pine breeding population

    Science.gov (United States)

    S. Kumar; Craig Echt; P.L. Wilcox; T.E. Richardson

    2004-01-01

    Linkage analysis is commonly uscd to find marker-trait associations within the full-sib families of forest tree and other species. Study of marker-trait associations at the population level is termed linkage-disequilibrium (LD) mapping. A female-tester design comprising 200 full-sib families generated by crossing 40 pollen parents with five female parents was used to...

  20. Multipoint linkage analysis in X-linked ocular albinism of the Nettleship-Falls type

    NARCIS (Netherlands)

    Bergen, A. A.; Samanns, C.; Schuurman, E. J.; van Osch, L.; van Dorp, D. B.; Pinckers, A. J.; Bakker, E.; Gal, A.; van Ommen, G. J.; Bleeker-Wagemakers, E. M.

    1991-01-01

    An extensive linkage analysis was performed by studying ten Xp22 loci in ten families segregating for X-linked ocular albinism of the Nettleship-Falls type (XOA). Linkage was confirmed between the XOA locus (OA1) and both DXS16 (theta max = 0.10, zeta max = 4.09) and DXS237 (theta max = 0.12, zeta

  1. Sustaining innovations : schools, institutions and linkages in the Cuzco region, Peru

    NARCIS (Netherlands)

    ChavezTafur, J.

    1998-01-01

    This thesis is about linkages between the different institutions operating in the rural areas and the contributions these linkages provide. Numerous activities are found taking place in the rural areas of Peru. Many are the result of a specific intervention, designed and implemented towards

  2. Hereditary spastic paraplegia: LOD-score considerations for confirmation of linkage in a heterogeneous trait

    Energy Technology Data Exchange (ETDEWEB)

    Dube, M.P.; Kibar, Z.; Rouleau, G.A. [McGill Univ., Quebec (Canada)] [and others

    1997-03-01

    Hereditary spastic paraplegia (HSP) is a degenerative disorder of the motor system, defined by progressive weakness and spasticity of the lower limbs. HSP may be inherited as an autosomal dominant (AD), autosomal recessive, or an X-linked trait. AD HSP is genetically heterogeneous, and three loci have been identified so far: SPG3 maps to chromosome 14q, SPG4 to 2p, and SPG4a to 15q. We have undertaken linkage analysis with 21 uncomplicated AD families to the three AD HSP loci. We report significant linkage for three of our families to the SPG4 locus and exclude several families by multipoint linkage. We used linkage information from several different research teams to evaluate the statistical probability of linkage to the SPG4 locus for uncomplicated AD HSP families and established the critical LOD-score value necessary for confirmation of linkage to the SPG4 locus from Bayesian statistics. In addition, we calculated the empirical P-values for the LOD scores obtained with all families with computer simulation methods. Power to detect significant linkage, as well as type I error probabilities, were evaluated. This combined analytical approach permitted conclusive linkage analyses on small to medium-size families, under the restrictions of genetic heterogeneity. 19 refs., 1 fig., 1 tab.

  3. Hereditary spastic paraplegia: LOD-score considerations for confirmation of linkage in a heterogeneous trait.

    Science.gov (United States)

    Dubé, M P; Mlodzienski, M A; Kibar, Z; Farlow, M R; Ebers, G; Harper, P; Kolodny, E H; Rouleau, G A; Figlewicz, D A

    1997-03-01

    Hereditary spastic paraplegia (HSP) is a degenerative disorder of the motor system, defined by progressive weakness and spasticity of the lower limbs. HSP may be inherited as an autosomal dominant (AD), autosomal recessive, or an X-linked trait. AD HSP is genetically heterogeneous, and three loci have been identified so far: SPG3 maps to chromosome 14q, SPG4 to 2p, and SPG4a to 15q. We have undertaken linkage analysis with 21 uncomplicated AD families to the three AD HSP loci. We report significant linkage for three of our families to the SPG4 locus and exclude several families by multipoint linkage. We used linkage information from several different research teams to evaluate the statistical probability of linkage to the SPG4 locus for uncomplicated AD HSP families and established the critical LOD-score value necessary for confirmation of linkage to the SPG4 locus from Bayesian statistics. In addition, we calculated the empirical P-values for the LOD scores obtained with all families with computer simulation methods. Power to detect significant linkage, as well as type I error probabilities, were evaluated. This combined analytical approach permitted conclusive linkage analyses on small to medium-size families, under the restrictions of genetic heterogeneity.

  4. Point-of-Care HIV Testing and Linkage in an Urban Cohort in the Southern US

    Directory of Open Access Journals (Sweden)

    Anne Zinski

    2013-01-01

    Full Text Available The Southern states experience the highest rates of HIV and AIDS in the US, and point-of-care (POC testing outside of primary care may contribute to status awareness in medically underserved populations in this region. To evaluate POC screening and linkage to care at an urban south site, analyses were performed on a dataset of 3,651 individuals from an integrated rapid-result HIV testing and linkage program to describe this test-seeking cohort and determine trends associated with screening, results, and linkage to care. Four percent of the population had positive results. We observed significant differences by test result for age, race and gender, reported risk behaviors, test location, and motivation for screening. The overall linkage rate was 86%, and we found significant differences for clients who were linked to HIV care versus persons whose linkage could not be confirmed with respect to race and gender, location, and motivation. The linkage rate for POC testing that included a comprehensive intake visit and colocated primary care services for in-state residents was 97%. Additional research on integrated POC screening and linkage methodologies that provide intake services at time of testing is essential for increasing status awareness and improving linkage to HIV care in the US.

  5. Prospective Linkages between Peer Victimization and Externalizing Problems in Children: A Meta-Analysis

    NARCIS (Netherlands)

    Reijntjes, A.; Kamphuis, J.H.; Prinzie, P.; Boelen, P.A.; van der Schoot, M.; Telch, M.J.

    2011-01-01

    Previous meta-analytic research has shown both concurrent and prospective linkages between peer victimization and internalizing problems in youth. However, the linkages between peer victimization and externalizing problems over time have not been systematically examined, and it is therefore unknown

  6. Linkage disequilibrium and demographic history of the isolated population of the Faroe Islands

    DEFF Research Database (Denmark)

    Jorgensen, Tove H; Degn, Birte; Wang, August G

    2002-01-01

    The isolated population of the Faroe Islands has a history of recent expansion after being limited to a small size for centuries. Such an isolated population may be ideal for linkage disequilibrium mapping of disease genes if linkage disequilibrium (LD) extends over large regions. Analyses of 18 ...

  7. [Linkage to care among new human immunodeficiency virus diagnoses in Spain].

    Science.gov (United States)

    Oliva, Jesús; Malo, Carmen; Fernández, Ana; Izquierdo, Ana; Marcos, Henar; Cevallos, Carlos; Castilla, Jesús; García, Rocio; Díez, Mercedes

    2014-03-01

    To describe linkage to care among new HIV diagnoses in Spain; and to estimate factors associated to linkage to care within three months after diagnosis. The distribution of the time elapsing between the date of HIV diagnosis and the date of first determination of CD4 (considered to be the date of linkage to care) was calculated among new HIV diagnoses in 2010 in the seven Autonomous Regions participating, where data on date of CD4 count was available. Linkage to care was considered «correct» if done within three months after diagnosis. Factors associated to correct linkage to care were estimated using logistic regression. A total of 1769 new HIV diagnoses were included. Of them, 83.1% had evidence of linkage to care within a year, and 75.7% were linked within three months after diagnosis. Being an injectable drug user (IDU) was the only factor inversely associated with linkage to care within 3 months (OR = 0.3; 95% CI: 0.2-0.6). In Spain linkage to care after HIV diagnosis is good, but there is still room for improvement, especially among IDUs. Copyright © 2013 Elsevier España, S.L. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  8. Model reduction of detailed-balanced reaction networks by clustering linkage classes

    NARCIS (Netherlands)

    Rao, Shodhan; Jayawardhana, Bayu; van der Schaft, Abraham; Findeisen, Rolf; Bullinger, Eric; Balsa-Canto, Eva; Bernaerts, Kristel

    2016-01-01

    We propose a model reduction method that involves sequential application of clustering of linkage classes and Kron reduction. This approach is specifically useful for chemical reaction networks with each linkage class having less number of reactions. In case of detailed balanced chemical reaction

  9. Climatological determinants of woody cover in Africa

    OpenAIRE

    Good, Stephen P.; Caylor, Kelly K.

    2011-01-01

    Determining the factors that influence the distribution of woody vegetation cover and resolving the sensitivity of woody vegetation cover to shifts in environmental forcing are critical steps necessary to predict continental-scale responses of dryland ecosystems to climate change. We use a 6-year satellite data record of fractional woody vegetation cover and an 11-year daily precipitation record to investigate the climatological controls on woody vegetation cover across the African continent....

  10. [Snow cover pollution monitoring in Ufa].

    Science.gov (United States)

    Daukaev, R A; Suleĭmanov, R A

    2008-01-01

    The paper presents the results of examining the snow cover polluted with heavy metals in the large industrial town of Ufa. The level of man-caused burden on the snow cover of the conventional parts of the town was estimated and compared upon exposure to a wide range of snow cover pollutants. The priority snow cover pollutants were identified among the test heavy metals.

  11. E-groups training

    CERN Multimedia

    HR Department

    2012-01-01

    There will be an e-groups training course on 16 March 2012 which will cover the main e-groups functionalities i.e.: creating and managing e-groups, difference between static and dynamic e-groups, configuring posting restrictions and archives, examples of where e-groups can be used in daily work. Even if you have already worked with e-groups, this may be a good opportunity to learn about the best practices and security related recommendations when using e-groups. You can find more details as well as enrolment form for the training (it’s free) here. The number of places is limited, so enrolling early is recommended.   Technical Training Tel. 72844

  12. Chemical linkage to injected tissues is a distinctive property of oxidized avidin.

    Directory of Open Access Journals (Sweden)

    Rita De Santis

    Full Text Available We recently reported that the oxidized avidin, named AvidinOX®, resides for weeks within injected tissues as a consequence of the formation of Schiff's bases between its aldehyde groups and tissue protein amino groups. We also showed, in a mouse pre-clinical model, the usefulness of AvidinOX for the delivery of radiolabeled biotin to inoperable tumors. Taking into account that AvidinOX is the first oxidized glycoprotein known to chemically link to injected tissues, we tested in the mouse a panel of additional oxidized glycoproteins, with the aim of investigating the phenomenon. We produced oxidized ovalbumin and mannosylated streptavidin which share with avidin glycosylation pattern and tetrameric structure, respectively and found that neither of them linked significantly to cells in vitro nor to injected tissues in vivo, despite the presence of functional aldehyde groups. The study, extended to additional oxidized glycoproteins, showed that the in vivo chemical conjugation is a distinctive property of the oxidized avidin. Relevance of the high cationic charge of avidin into the stable linkage of AvidinOX to tissues is demonstrated as the oxidized acetylated avidin lost the property. Plasmon resonance on matrix proteins and cellular impedance analyses showed in vitro that avidin exhibits a peculiar interaction with proteins and cells that allows the formation of highly stable Schiff's bases, after oxidation.

  13. Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice.

    Science.gov (United States)

    Lou, Qiaojun; Chen, Liang; Mei, Hanwei; Wei, Haibin; Feng, Fangjun; Wang, Pei; Xia, Hui; Li, Tiemei; Luo, Lijun

    2015-08-01

    Deep rooting is a very important trait for plants' drought avoidance, and it is usually represented by the ratio of deep rooting (RDR). Three sets of rice populations were used to determine the genetic base for RDR. A linkage mapping population with 180 recombinant inbred lines and an association mapping population containing 237 rice varieties were used to identify genes linked to RDR. Six quantitative trait loci (QTLs) of RDR were identified as being located on chromosomes 1, 2, 4, 7, and 10. Using 1 019 883 single-nucleotide polymorphisms (SNPs), a genome-wide association study of the RDR was performed. Forty-eight significant SNPs of the RDR were identified and formed a clear peak on the short arm of chromosome 1 in a Manhattan plot. Compared with the shallow-rooting group and the whole collection, the deep-rooting group had selective sweep regions on chromosomes 1 and 2, especially in the major QTL region on chromosome 2. Seven of the nine candidate SNPs identified by association mapping were verified in two RDR extreme groups. The findings from this study will be beneficial to rice drought-resistance research and breeding. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  14. Linkage in the chain of care: a grounded theory of professional cooperation between antenatal care, postpartum care and child health care

    Directory of Open Access Journals (Sweden)

    Mia Barimani

    2008-12-01

    Full Text Available Purpose: The purpose of this article is to present a Swedish study exploring health care professionals’ cooperation in the chain of care for expectant and new parents between antenatal care (AC, postpartum care (PC and child health care (CHC. Furthermore, the rationale was to conceptualise barriers and facilitators of cooperation in order to generate a comprehensive theoretical model which may explain variations in the care providers’ experiences. Methods: Thirty-two midwives and CHC nurses were interviewed in five focus group – and two individual interviews in a suburb of a large Swedish city. Grounded Theory was applied as the research methodology. Results: One core category was discerned: linkage in the chain of care, including six categories with subcategories. Despite the fact that midwives as well as CHC nurses have common visions about linkage, cooperation is not achieved because of interacting barriers that have different influences on the three links in the chain. Conclusions: Barriers to linkage are lack of professional gain, link perspective and first or middle position in the chain, while facilitators are chain perspective, professional gain and last position in the chain. As the last link, CHC nurses promote a linkage most strongly and have the greatest gain from such linking.

  15. Measuring and analyzing urban tree cover

    Science.gov (United States)

    David J. Nowak; Rowan A. Rowntree; E. Gregory McPherson; Susan M. Sisinni; Esther R. Kirkmann; Jack C. Stevens

    1996-01-01

    Measurement of city tree cover can aid in urban vegetation planning, management, and research by revealing characteristics of vegetation across a city. Urban tree cover in the United States ranges from 0.4% in Lancaster, California, to 55% in Baton Rouge, Louisiana. Two important factors that affect the amount of urban tree cover are the natural environment and land...

  16. Land cover changes in central Sonora Mexico

    Science.gov (United States)

    Diego Valdez-Zamudio; Alejandro Castellanos-Villegas; Stuart Marsh

    2000-01-01

    Remote sensing techniques have been demonstrated to be very effective tools to help detect, analyze, and evaluate land cover changes in natural areas of the world. Changes in land cover can generally be attributed to either natural or anthropogenic forces. Multitemporal satellite imagery and airborne videography were used to detect, analyze, and evaluate land cover...

  17. Completion of the National Land Cover Database (NLCD) 1992-2001 Land Cover Change Retrofit Product

    Science.gov (United States)

    The Multi-Resolution Land Characteristics Consortium has supported the development of two national digital land cover products: the National Land Cover Dataset (NLCD) 1992 and National Land Cover Database (NLCD) 2001. Substantial differences in imagery, legends, and methods betwe...

  18. Uptake of HIV testing and counseling, risk perception and linkage to HIV care among Thai university students

    Directory of Open Access Journals (Sweden)

    Thana Khawcharoenporn

    2016-07-01

    Full Text Available Abstract Background HIV testing and counseling (HTC with linkage to care after known infection are key components for HIV transmission prevention. This study was conducted to assess HTC uptake, HIV risk perception and linkage to care among Thai university students. Methods An outreach HTC program was conducted in a large public university in Thailand from January 2013 to December 2014. The program consisted of brief HIV knowledge assessment, free HTC, HIV risk assessment and education provided by the healthcare personnel. Students were categorized into low, moderate and high-risk groups according to the pre-defined HIV risk characteristics. Results One-thousand-eight-hundred-one students participated in the program, 494 (27 % underwent HTC. Independent characteristics associated with no HTC uptake included female sex (P < 0.001, lower HIV knowledge score (P < 0.001, younger age (P < 0.001 and students from non-health science faculties (P = 0.02. Among the 494 students undergoing HTC, 141 (29 % were categorized into moderate or high-risk group, of whom 45/141 (32 % had false perception of low HIV risk. Being heterosexual was independently associated with false perception of low HIV risk (P = 0.04. The rate of new HIV infection diagnosis was 4/494 (0.8 %. Of these 4 HIV-infected students, 3 (75 % were men who have sex with men and only 2 of the 4 students (50 % showed up for HIV continuity care. Conclusions An outreach HIV prevention program with HTC was feasible and beneficial in detecting HIV risk and infection among the university students. However, interventions to improve HTC uptake, HIV risk perception and linkage to care are needed.

  19. Wave boundary layer over a stone-covered bed

    DEFF Research Database (Denmark)

    Dixen, Martin; Hatipoglu, Figen; Sumer, B. Mutlu

    2008-01-01

    This paper summarizes the results of an experimental investigation on wave boundary layers over a bed with large roughness, simulating stone/rock/armour block cover on the sea bottom. The roughness elements used in the experiments were stones the size of 1.4cm and 3.85cm in one group of experiments...

  20. 'COVER STORY': A STUDY IN lAND MANAGEMENT

    African Journals Online (AJOL)

    The group was concerned with soil ero- sion and the associated effect upon the vegetation cover. The first s~ge of the project was to est- ablish exactly which aspects of soil erosion should be studied. The following points were initially considered: soil types and characteristics different grasses and their carrying capacity.