Comparing the accuracy and precision of three techniques used for estimating missing landmarks when reconstructing fossil hominin crania.

PubMed

Neeser, Rudolph; Ackermann, Rebecca Rogers; Gain, James

2009-09-01

Various methodological approaches have been used for reconstructing fossil hominin remains in order to increase sample sizes and to better understand morphological variation. Among these, morphometric quantitative techniques for reconstruction are increasingly common. Here we compare the accuracy of three approaches--mean substitution, thin plate splines, and multiple linear regression--for estimating missing landmarks of damaged fossil specimens. Comparisons are made varying the number of missing landmarks, sample sizes, and the reference species of the population used to perform the estimation. The testing is performed on landmark data from individuals of Homo sapiens, Pan troglodytes and Gorilla gorilla, and nine hominin fossil specimens. Results suggest that when a small, same-species fossil reference sample is available to guide reconstructions, thin plate spline approaches perform best. However, if no such sample is available (or if the species of the damaged individual is uncertain), estimates of missing morphology based on a single individual (or even a small sample) of close taxonomic affinity are less accurate than those based on a large sample of individuals drawn from more distantly related extant populations using a technique (such as a regression method) able to leverage the information (e.g., variation/covariation patterning) contained in this large sample. Thin plate splines also show an unexpectedly large amount of error in estimating landmarks, especially over large areas. Recommendations are made for estimating missing landmarks under various scenarios. Copyright 2009 Wiley-Liss, Inc.

Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data.

PubMed

Bhaskar, Anand; Wang, Y X Rachel; Song, Yun S

2015-02-01

With the recent increase in study sample sizes in human genetics, there has been growing interest in inferring historical population demography from genomic variation data. Here, we present an efficient inference method that can scale up to very large samples, with tens or hundreds of thousands of individuals. Specifically, by utilizing analytic results on the expected frequency spectrum under the coalescent and by leveraging the technique of automatic differentiation, which allows us to compute gradients exactly, we develop a very efficient algorithm to infer piecewise-exponential models of the historical effective population size from the distribution of sample allele frequencies. Our method is orders of magnitude faster than previous demographic inference methods based on the frequency spectrum. In addition to inferring demography, our method can also accurately estimate locus-specific mutation rates. We perform extensive validation of our method on simulated data and show that it can accurately infer multiple recent epochs of rapid exponential growth, a signal that is difficult to pick up with small sample sizes. Lastly, we use our method to analyze data from recent sequencing studies, including a large-sample exome-sequencing data set of tens of thousands of individuals assayed at a few hundred genic regions. © 2015 Bhaskar et al.; Published by Cold Spring Harbor Laboratory Press.

Sample allocation balancing overall representativeness and stratum precision.

PubMed

Diaz-Quijano, Fredi Alexander

2018-05-07

In large-scale surveys, it is often necessary to distribute a preset sample size among a number of strata. Researchers must make a decision between prioritizing overall representativeness or precision of stratum estimates. Hence, I evaluated different sample allocation strategies based on stratum size. The strategies evaluated herein included allocation proportional to stratum population; equal sample for all strata; and proportional to the natural logarithm, cubic root, and square root of the stratum population. This study considered the fact that, from a preset sample size, the dispersion index of stratum sampling fractions is correlated with the population estimator error and the dispersion index of stratum-specific sampling errors would measure the inequality in precision distribution. Identification of a balanced and efficient strategy was based on comparing those both dispersion indices. Balance and efficiency of the strategies changed depending on overall sample size. As the sample to be distributed increased, the most efficient allocation strategies were equal sample for each stratum; proportional to the logarithm, to the cubic root, to square root; and that proportional to the stratum population, respectively. Depending on sample size, each of the strategies evaluated could be considered in optimizing the sample to keep both overall representativeness and stratum-specific precision. Copyright © 2018 Elsevier Inc. All rights reserved.

A high-throughput robotic sample preparation system and HPLC-MS/MS for measuring urinary anatabine, anabasine, nicotine and major nicotine metabolites.

PubMed

Wei, Binnian; Feng, June; Rehmani, Imran J; Miller, Sharyn; McGuffey, James E; Blount, Benjamin C; Wang, Lanqing

2014-09-25

Most sample preparation methods characteristically involve intensive and repetitive labor, which is inefficient when preparing large numbers of samples from population-scale studies. This study presents a robotic system designed to meet the sampling requirements for large population-scale studies. Using this robotic system, we developed and validated a method to simultaneously measure urinary anatabine, anabasine, nicotine and seven major nicotine metabolites: 4-Hydroxy-4-(3-pyridyl)butanoic acid, cotinine-N-oxide, nicotine-N-oxide, trans-3'-hydroxycotinine, norcotinine, cotinine and nornicotine. We analyzed robotically prepared samples using high-performance liquid chromatography (HPLC) coupled with triple quadrupole mass spectrometry in positive electrospray ionization mode using scheduled multiple reaction monitoring (sMRM) with a total runtime of 8.5 min. The optimized procedure was able to deliver linear analyte responses over a broad range of concentrations. Responses of urine-based calibrators delivered coefficients of determination (R(2)) of >0.995. Sample preparation recovery was generally higher than 80%. The robotic system was able to prepare four 96-well plate (384 urine samples) per day, and the overall method afforded an accuracy range of 92-115%, and an imprecision of <15.0% on average. The validation results demonstrate that the method is accurate, precise, sensitive, robust, and most significantly labor-saving for sample preparation, making it efficient and practical for routine measurements in large population-scale studies such as the National Health and Nutrition Examination Survey (NHANES) and the Population Assessment of Tobacco and Health (PATH) study. Published by Elsevier B.V.

Heritability of Autism Spectrum Disorder in a UK Population-Based Twin Sample

PubMed Central

Colvert, Emma; Tick, Beata; McEwen, Fiona; Stewart, Catherine; Curran, Sarah R.; Woodhouse, Emma; Gillan, Nicola; Hallett, Victoria; Lietz, Stephanie; Garnett, Tracy; Ronald, Angelica; Plomin, Robert; Rijsdijk, Frühling; Happé, Francesca; Bolton, Patrick

2016-01-01

IMPORTANCE Most evidence to date highlights the importance of genetic influences on the liability to autism and related traits. However, most of these findings are derived from clinically ascertained samples, possibly missing individuals with subtler manifestations, and obtained estimates may not be representative of the population. OBJECTIVES To establish the relative contributions of genetic and environmental factors in liability to autism spectrum disorder (ASD) and a broader autism phenotype in a large population-based twin sample and to ascertain the genetic/environmental relationship between dimensional trait measures and categorical diagnostic constructs of ASD. DESIGN, SETTING, AND PARTICIPANTS We used data from the population-based cohort Twins Early Development Study, which included all twin pairs born in England and Wales from January 1, 1994, through December 31, 1996. We performed joint continuous-ordinal liability threshold model fitting using the full information maximum likelihood method to estimate genetic and environmental parameters of covariance. Twin pairs underwent the following assessments: the Childhood Autism Spectrum Test (CAST) (6423 pairs; mean age, 7.9 years), the Development and Well-being Assessment (DAWBA) (359 pairs; mean age, 10.3 years), the Autism Diagnostic Observation Schedule (ADOS) (203 pairs; mean age, 13.2 years), the Autism Diagnostic Interview–Revised (ADI-R) (205 pairs; mean age, 13.2 years), and a best-estimate diagnosis (207 pairs). MAIN OUTCOMES AND MEASURES Participants underwent screening using a population-based measure of autistic traits (CAST assessment), structured diagnostic assessments (DAWBA, ADI-R, and ADOS), and a best-estimate diagnosis. RESULTS On all ASD measures, correlations among monozygotic twins (range, 0.77-0.99) were significantly higher than those for dizygotic twins (range, 0.22-0.65), giving heritability estimates of 56% to 95%. The covariance of CAST and ASD diagnostic status (DAWBA, ADOS and best-estimate diagnosis) was largely explained by additive genetic factors (76%-95%). For the ADI-R only, shared environmental influences were significant (30% [95% CI, 8%-47%]) but smaller than genetic influences (56% [95% CI, 37%-82%]). CONCLUSIONS AND RELEVANCE The liability to ASD and a more broadly defined high-level autism trait phenotype in this large population-based twin sample derives primarily from additive genetic and, to a lesser extent, nonshared environmental effects. The largely consistent results across different diagnostic tools suggest that the results are generalizable across multiple measures and assessment methods. Genetic factors underpinning individual differences in autismlike traits show considerable overlap with genetic influences on diagnosed ASD. PMID:25738232

Identifying currents in the gene pool for bacterial populations using an integrative approach.

PubMed

Tang, Jing; Hanage, William P; Fraser, Christophe; Corander, Jukka

2009-08-01

The evolution of bacterial populations has recently become considerably better understood due to large-scale sequencing of population samples. It has become clear that DNA sequences from a multitude of genes, as well as a broad sample coverage of a target population, are needed to obtain a relatively unbiased view of its genetic structure and the patterns of ancestry connected to the strains. However, the traditional statistical methods for evolutionary inference, such as phylogenetic analysis, are associated with several difficulties under such an extensive sampling scenario, in particular when a considerable amount of recombination is anticipated to have taken place. To meet the needs of large-scale analyses of population structure for bacteria, we introduce here several statistical tools for the detection and representation of recombination between populations. Also, we introduce a model-based description of the shape of a population in sequence space, in terms of its molecular variability and affinity towards other populations. Extensive real data from the genus Neisseria are utilized to demonstrate the potential of an approach where these population genetic tools are combined with an phylogenetic analysis. The statistical tools introduced here are freely available in BAPS 5.2 software, which can be downloaded from http://web.abo.fi/fak/mnf/mate/jc/software/baps.html.

Is urbanisation scrambling the genetic structure of human populations? A case study

PubMed Central

Ashrafian-Bonab, Maziar; Handley, Lori Lawson; Balloux, François

2007-01-01

Recent population expansion and increased migration linked to urbanisation are assumed to be eroding the genetic structure of human populations. We investigated change in population structure over three generations by analysing both demographic and mitochondrial DNA (mtDNA) data from a random sample of 2351 men from twenty-two Iranian populations. Potential changes in genetic diversity (θ) and genetic distance (FST) over the last three generations were analysed by assigning mtDNA sequences to populations based on the individual's place of birth or that of their mother or grandmother. Despite the fact that several areas included cities of over one million inhabitants, we detected no change in genetic diversity, and only a small decrease in population structure, except in the capital city (Tehran), which was characterised by massive immigration, increased θ and a large decrease in FST over time. Our results suggest that recent erosion of human population structure might not be as important as previously thought, except in some large conurbations, and this clearly has important implications for future sampling strategies. PMID:17106453

Recruiting and retaining youth and young adults: challenges and opportunities in survey research for tobacco control.

PubMed

Cantrell, Jennifer; Hair, Elizabeth C; Smith, Alexandria; Bennett, Morgane; Rath, Jessica Miller; Thomas, Randall K; Fahimi, Mansour; Dennis, J Michael; Vallone, Donna

2018-03-01

Evaluation studies of population-based tobacco control interventions often rely on large-scale survey data from numerous respondents across many geographic areas to provide evidence of their effectiveness. Significant challenges for survey research have emerged with the evolving communications landscape, particularly for surveying hard-to-reach populations such as youth and young adults. This study combines the comprehensive coverage of an address-based sampling (ABS) frame with the timeliness of online data collection to develop a nationally representative longitudinal cohort of young people aged 15-21. We constructed an ABS frame, partially supplemented with auxiliary data, to recruit this hard-to-reach sample. Branded and tested mail-based recruitment materials were designed to bring respondents online for screening, consent and surveying. Once enrolled, respondents completed online surveys every 6 months via computer, tablet or smartphone. Numerous strategies were utilized to enhance retention and representativeness RESULTS: Results detail sample performance, representativeness and retention rates as well as device utilization trends for survey completion among youth and young adult respondents. Panel development efforts resulted in a large, nationally representative sample with high retention rates. This study is among the first to employ this hybrid ABS-to-online methodology to recruit and retain youth and young adults in a probability-based online cohort panel. The approach is particularly valuable for conducting research among younger populations as it capitalizes on their increasing access to and comfort with digital communication. We discuss challenges and opportunities of panel recruitment and retention methods in an effort to provide valuable information for tobacco control researchers seeking to obtain representative, population-based samples of youth and young adults in the U.S. as well as across the globe. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Spreadsheet Simulation of the Law of Large Numbers

ERIC Educational Resources Information Center

Boger, George

2005-01-01

If larger and larger samples are successively drawn from a population and a running average calculated after each sample has been drawn, the sequence of averages will converge to the mean, [mu], of the population. This remarkable fact, known as the law of large numbers, holds true if samples are drawn from a population of discrete or continuous…

Estimating the probability that the sample mean is within a desired fraction of the standard deviation of the true mean.

PubMed

Schillaci, Michael A; Schillaci, Mario E

2009-02-01

The use of small sample sizes in human and primate evolutionary research is commonplace. Estimating how well small samples represent the underlying population, however, is not commonplace. Because the accuracy of determinations of taxonomy, phylogeny, and evolutionary process are dependant upon how well the study sample represents the population of interest, characterizing the uncertainty, or potential error, associated with analyses of small sample sizes is essential. We present a method for estimating the probability that the sample mean is within a desired fraction of the standard deviation of the true mean using small (n<10) or very small (n < or = 5) sample sizes. This method can be used by researchers to determine post hoc the probability that their sample is a meaningful approximation of the population parameter. We tested the method using a large craniometric data set commonly used by researchers in the field. Given our results, we suggest that sample estimates of the population mean can be reasonable and meaningful even when based on small, and perhaps even very small, sample sizes.

The Factor Structure of ADHD in a General Population of Primary School Children

ERIC Educational Resources Information Center

Ullebo, Anne Karin; Breivik, Kyrre; Gillberg, Christopher; Lundervold, Astri J.; Posserud, Maj-Britt

2012-01-01

Objective: To examine whether a bifactor model with a general ADHD factor and domain specific factors of inattention, hyperactivity and impulsivity was supported in a large general population sample of children. We also explored the utility of forming subscales based on the domain-specific factors. Methods: Child mental health questionnaires were…

The factor structures and correlates of PTSD in post-conflict Timor-Leste: an analysis of the Harvard Trauma Questionnaire.

PubMed

Tay, Alvin Kuowei; Mohsin, Mohammed; Rees, Susan; Steel, Zachary; Tam, Natalino; Soares, Zelia; Baker, Jessica; Silove, Derrick

2017-05-22

Post-traumatic stress disorder (PTSD) is the most widely assessed form of mental distress in cross-cultural studies conducted amongst populations exposed to mass conflict and displacement. Nevertheless, there have been longstanding concerns about the universality of PTSD as a diagnostic category when applied across cultures. One approach to examining this question is to assess whether the same factor structure can be identified in culturally diverse populations as has been described in populations of western societies. We examine this issue based on an analysis of the Harvard Trauma Questionnaire (HTQ) completed by a large community sample in conflict-affected Timor-Leste. Culturally adapted measures were applied to assess exposure to conflict-related traumatic events (TEs), ongoing adversities, symptoms of PTSD and psychological distress, and functional impairment amongst a large population sample (n = 2964, response rate: 82.4%) in post-conflict Timor-Leste. Confirmatory factor analyses of the ICD-10, ICD-11, DSM-IV, four-factor Emotional Numbing and five-factor Dysphoric-Arousal PTSD structures, found considerable support for all these models. Based on these classifications, concurrent validity was indicated by logistic regression analyses which showed that being a woman, trauma exposure, ongoing adversity, severe distress, and functional impairment were all associated with PTSD. Although symptom prevalence estimates varied widely based on different classifications, our study found a general agreement in PTSD assignments across contemporary diagnostic systems in a large conflict-affected population in Timor-Leste. Further studies are needed, however, to establish the construct and concurrent validity of PTSD in other cultures.

The functional spectrum of low-frequency coding variation.

PubMed

Marth, Gabor T; Yu, Fuli; Indap, Amit R; Garimella, Kiran; Gravel, Simon; Leong, Wen Fung; Tyler-Smith, Chris; Bainbridge, Matthew; Blackwell, Tom; Zheng-Bradley, Xiangqun; Chen, Yuan; Challis, Danny; Clarke, Laura; Ball, Edward V; Cibulskis, Kristian; Cooper, David N; Fulton, Bob; Hartl, Chris; Koboldt, Dan; Muzny, Donna; Smith, Richard; Sougnez, Carrie; Stewart, Chip; Ward, Alistair; Yu, Jin; Xue, Yali; Altshuler, David; Bustamante, Carlos D; Clark, Andrew G; Daly, Mark; DePristo, Mark; Flicek, Paul; Gabriel, Stacey; Mardis, Elaine; Palotie, Aarno; Gibbs, Richard

2011-09-14

Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, but because of insufficient sample size it is not clear if the same trend holds for rare variants below 1% allele frequency. The 1000 Genomes Exon Pilot Project has collected deep-coverage exon-capture data in roughly 1,000 human genes, for nearly 700 samples. Although medical whole-exome projects are currently afoot, this is still the deepest reported sampling of a large number of human genes with next-generation technologies. According to the goals of the 1000 Genomes Project, we created effective informatics pipelines to process and analyze the data, and discovered 12,758 exonic SNPs, 70% of them novel, and 74% below 1% allele frequency in the seven population samples we examined. Our analysis confirms that coding variants below 1% allele frequency show increased population-specificity and are enriched for functional variants. This study represents a large step toward detecting and interpreting low frequency coding variation, clearly lays out technical steps for effective analysis of DNA capture data, and articulates functional and population properties of this important class of genetic variation.

A general unified framework to assess the sampling variance of heritability estimates using pedigree or marker-based relationships.

PubMed

Visscher, Peter M; Goddard, Michael E

2015-01-01

Heritability is a population parameter of importance in evolution, plant and animal breeding, and human medical genetics. It can be estimated using pedigree designs and, more recently, using relationships estimated from markers. We derive the sampling variance of the estimate of heritability for a wide range of experimental designs, assuming that estimation is by maximum likelihood and that the resemblance between relatives is solely due to additive genetic variation. We show that well-known results for balanced designs are special cases of a more general unified framework. For pedigree designs, the sampling variance is inversely proportional to the variance of relationship in the pedigree and it is proportional to 1/N, whereas for population samples it is approximately proportional to 1/N(2), where N is the sample size. Variation in relatedness is a key parameter in the quantification of the sampling variance of heritability. Consequently, the sampling variance is high for populations with large recent effective population size (e.g., humans) because this causes low variation in relationship. However, even using human population samples, low sampling variance is possible with high N. Copyright © 2015 by the Genetics Society of America.

An integrated modeling approach to estimating Gunnison Sage-Grouse population dynamics: combining index and demographic data.

USGS Publications Warehouse

Davis, Amy J.; Hooten, Mevin B.; Phillips, Michael L.; Doherty, Paul F.

2014-01-01

Evaluation of population dynamics for rare and declining species is often limited to data that are sparse and/or of poor quality. Frequently, the best data available for rare bird species are based on large-scale, population count data. These data are commonly based on sampling methods that lack consistent sampling effort, do not account for detectability, and are complicated by observer bias. For some species, short-term studies of demographic rates have been conducted as well, but the data from such studies are typically analyzed separately. To utilize the strengths and minimize the weaknesses of these two data types, we developed a novel Bayesian integrated model that links population count data and population demographic data through population growth rate (λ) for Gunnison sage-grouse (Centrocercus minimus). The long-term population index data available for Gunnison sage-grouse are annual (years 1953–2012) male lek counts. An intensive demographic study was also conducted from years 2005 to 2010. We were able to reduce the variability in expected population growth rates across time, while correcting for potential small sample size bias in the demographic data. We found the population of Gunnison sage-grouse to be variable and slightly declining over the past 16 years.

Bounce Back Now! Protocol of a population-based randomized controlled trial to examine the efficacy of a Web-based intervention with disaster-affected families.

PubMed

Ruggiero, Kenneth J; Davidson, Tatiana M; McCauley, Jenna; Gros, Kirstin Stauffacher; Welsh, Kyleen; Price, Matthew; Resnick, Heidi S; Danielson, Carla Kmett; Soltis, Kathryn; Galea, Sandro; Kilpatrick, Dean G; Saunders, Benjamin E; Nissenboim, Josh; Muzzy, Wendy; Fleeman, Anna; Amstadter, Ananda B

2015-01-01

Disasters have far-reaching and potentially long-lasting effects on youth and families. Research has consistently shown a clear increase in the prevalence of several mental health disorders after disasters, including depression and posttraumatic stress disorder. Widely accessible evidence-based interventions are needed to address this unmet need for youth and families, who are underrepresented in disaster research. Rapid growth in Internet and Smartphone access, as well as several Web based evaluation studies with various adult populations has shown that Web-based interventions are likely to be feasible in this context and can improve clinical outcomes. Such interventions also are generally cost-effective, can be targeted or personalized, and can easily be integrated in a stepped care approach to screening and intervention delivery. This is a protocol paper that describes an innovative study design in which we evaluate a self-help Web-based resource, Bounce Back Now, with a population-based sample of disaster affected adolescents and families. The paper includes description and justification for sampling selection and procedures, selection of assessment measures and methods, design of the intervention, and statistical evaluation of critical outcomes. Unique features of this study design include the use of address-based sampling to recruit a population-based sample of disaster-affected adolescents and parents, telephone and Web-based assessments, and development and evaluation of a highly individualized Web intervention for adolescents. Challenges related to large-scale evaluation of technology-delivered interventions with high-risk samples in time-sensitive research are discussed, as well as implications for future research and practice. Published by Elsevier Inc.

Bounce Back Now! Protocol of a Population-Based Randomized Controlled Trial to Examine the Efficacy of a Web-based Intervention with Disaster-Affected Families

PubMed Central

Ruggiero, Kenneth J.; Davidson, Tatiana M.; McCauley, Jenna; Gros, Kirstin Stauffacher; Welsh, Kyleen; Price, Matthew; Resnick, Heidi S.; Danielson, Carla Kmett; Soltis, Kathryn; Galea, Sandro; Kilpatrick, Dean G.; Saunders, Benjamin E.; Nissenboim, Josh; Muzzy, Wendy; Fleeman, Anna; Amstadter, Ananda B.

2014-01-01

Disasters have far-reaching and potentially long-lasting effects on youth and families. Research has consistently shown a clear increase in the prevalence of several mental health disorders after disasters, including depression and posttraumatic stress disorder. Widely accessible evidence-based interventions are needed to address this unmet need for youth and families, who are underrepresented in disaster research. Rapid growth in Internet and Smartphone access, as well as several web based evaluation studies with various adult populations has shown that web-based interventions are likely to be feasible in this context and can improve clinical outcomes. Such interventions also are generally cost-effective, can be targeted or personalized, and can easily be integrated in a stepped care approach to screening and intervention delivery. This is a protocol paper that describes an innovative study design in which we evaluate a self-help web-based resource, Bounce Back Now, with a population-based sample of disaster affected adolescents and families. The paper includes description and justification for sampling selection and procedures, selection of assessment measures and methods, design of the intervention, and statistical evaluation of critical outcomes. Unique features of this study design include the use of address-based sampling to recruit a population-based sample of disaster-affected adolescents and parents, telephone and web-based assessments, and development and evaluation of a highly individualized web intervention for adolescents. Challenges related to large-scale evaluation of technology-delivered interventions with high-risk samples in time-sensitive research are discussed, as well as implications for future research and practice. PMID:25478956

Coalescence computations for large samples drawn from populations of time-varying sizes

PubMed Central

Polanski, Andrzej; Szczesna, Agnieszka; Garbulowski, Mateusz; Kimmel, Marek

2017-01-01

We present new results concerning probability distributions of times in the coalescence tree and expected allele frequencies for coalescent with large sample size. The obtained results are based on computational methodologies, which involve combining coalescence time scale changes with techniques of integral transformations and using analytical formulae for infinite products. We show applications of the proposed methodologies for computing probability distributions of times in the coalescence tree and their limits, for evaluation of accuracy of approximate expressions for times in the coalescence tree and expected allele frequencies, and for analysis of large human mitochondrial DNA dataset. PMID:28170404

Gone with the currents: lack of genetic differentiation at the circum-continental scale in the Antarctic krill Euphausia superba

PubMed Central

2011-01-01

Background Southern Ocean fauna represent a significant amount of global biodiversity, whose origin may be linked to glacial cycles determining local extinction/eradication with ice advance, survival of refugee populations and post-glacial re-colonization. This pattern implies high potential for differentiation in benthic shelf species with limited dispersal, yet consequences for pelagic organisms are less clear. The present study investigates levels of genetic variation and population structure of the Antarctic krill Euphausia superba using mitochondrial DNA and EST-linked microsatellite markers for an unprecedentedly comprehensive sampling of its populations over a circum-Antarctic range. Results MtDNA (ND1) sequences and EST-linked microsatellite markers indicated no clear sign of genetic structure among populations over large geographic scales, despite considerable power to detect differences inferred from forward-time simulations. Based on ND1, few instances of genetic heterogeneity, not significant after correction for multiple tests, were detected between geographic or temporal samples. Neutrality tests and mismatch distribution based on mtDNA sequences revealed strong evidence of past population expansion. Significant positive values of the parameter g (a measure of population growth) were obtained from microsatellite markers using a coalescent-based genealogical method and suggested a recent start (60 000 - 40 000 years ago) for the expansion. Conclusions The results provide evidence of lack of genetic heterogeneity of Antarctic krill at large geographic scales and unequivocal support for recent population expansion. Lack of genetic structuring likely reflects the tight link between krill and circum-Antarctic ocean currents and is consistent with the hypothesis that differentiation processes in Antarctic species are largely influenced by dispersal potential, whereas small-scale spatial and temporal differentiation might be due to local conditions leading to genetic patchiness. The signal of recent population growth suggests differential impact of glacial cycles on pelagic Antarctic species, which experienced population expansion during glaciations with increased available habitat, versus sedentary benthic shelf species. EST-linked microsatellites provide new perspectives to complement the results based on mtDNA and suggest that data-mining of EST libraries will be a useful approach to facilitate use of microsatellites for additional species. PMID:21486439

Minimal-assumption inference from population-genomic data

NASA Astrophysics Data System (ADS)

Weissman, Daniel; Hallatschek, Oskar

Samples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. Current methods that take advantage of this linkage information rely on models of recombination and coalescence, limiting the sample sizes and populations that they can analyze. We introduce a method, Minimal-Assumption Genomic Inference of Coalescence (MAGIC), that reconstructs key features of the evolutionary history, including the distribution of coalescence times, by integrating information across genomic length scales without using an explicit model of recombination, demography or selection. Using simulated data, we show that MAGIC's performance is comparable to PSMC' on single diploid samples generated with standard coalescent and recombination models. More importantly, MAGIC can also analyze arbitrarily large samples and is robust to changes in the coalescent and recombination processes. Using MAGIC, we show that the inferred coalescence time histories of samples of multiple human genomes exhibit inconsistencies with a description in terms of an effective population size based on single-genome data.

Aetiology for the covariation between combined type ADHD and reading difficulties in a family study: the role of IQ

PubMed Central

Cheung, Celeste H.M.; Wood, Alexis C.; Paloyelis, Yannis; Arias-Vasquez, Alejandro; Buitelaar, Jan K.; Franke, Barbara; Miranda, Ana; Mulas, Fernando; Rommelse, Nanda; Sergeant, Joseph A.; Sonuga-Barke, Edmund J.; Faraone, Stephen V.; Asherson, Philip; Kuntsi, Jonna

2012-01-01

Background Twin studies using both clinical and population-based samples suggest that the frequent co-occurrence of attention deficit hyperactivity disorder (ADHD) and reading ability/disability (RD) is largely driven by shared genetic influences. While both disorders are associated with lower IQ, recent twin data suggest that the shared genetic variability between reading difficulties and ADHD inattention symptoms is largely independent from genetic influences contributing to general cognitive ability. The current study aimed to extend the previous findings that were based on rating scale measures in a population sample by examining the generalizability of the findings to a clinical population, and by measuring reading difficulties both with a rating scale and with an objective task. We therefore investigated the familial relationships between ADHD, reading difficulties and IQ in a sample of individuals diagnosed with ADHD combined type, their siblings and control sibling pairs. Methods We ran multivariate familial models on data from 1789 individuals at ages 6 to 19. Reading difficulties were measured with both rating scale and an objective task. IQ was obtained using the Wechsler Intelligence Scales (WISC-III / WAIS-III). Results Significant phenotypic (0.2–0.4) and familial (0.3–0.5) correlations were observed among ADHD, reading difficulties and IQ. Yet 53% to 72% of the overlapping familial influences between ADHD and reading difficulties were not shared with IQ. Conclusions Our finding that familial influences shared with general cognitive ability, though present, do not account for the majority of the overlapping familial influences on ADHD and reading difficulties extends previous findings from a population-based study to a clinically-ascertained sample with combined type ADHD. PMID:22324316

Genetic analysis of floating Enteromorpha prolifera in the Yellow Sea with AFLP marker

NASA Astrophysics Data System (ADS)

Liu, Cui; Zhang, Jing; Sun, Xiaoyu; Li, Jian; Zhang, Xi; Liu, Tao

2011-09-01

Extremely large accumulation of green algae Enteromorpha prolifera floated along China' coastal region of the Yellow Sea ever since the summer of 2008. Amplified Fragment Length Polymorphism (AFLP) analysis was applied to assess the genetic diversity and relationships among E. prolifera samples collected from 9 affected areas of the Yellow Sea. Two hundred reproducible fragments were generated with 8 AFLP primer combinations, of which 194 (97%) were polymorphic. The average Nei's genetic diversity, the coefficiency of genetic differentiation (Gst), and the average gene flow estimated from Gst in the 9 populations were 0.4018, 0.6404 and 0.2807 respectively. Cluster analysis based on the unweighed pair group method with arithmetic averages (UPGMA) showed that the genetic relationships within one population or among different populations were all related to their collecting locations and sampling time. Large genetic differentiation was detected among the populations. The E. prolifera originated from different areas and were undergoing a course of mixing.

Automated array assembly, phase 2

NASA Technical Reports Server (NTRS)

Carbajal, B. G.

1979-01-01

Tasks of scaling up the tandem junction cell (TJC) from 2 cm x 2 cm to 6.2 cm and the assembly of several modules using these large area TJC's are described. The scale-up of the TJC was based on using the existing process and doing the necessary design activities to increase the cell area to an acceptably large area. The design was carried out using available device models. The design was verified and sample large area TJCs were fabricated. Mechanical and process problems occurred causing a schedule slippage that resulted in contract expiration before enough large-area TJCs were fabricated to populate the sample tandem junction modules (TJM). A TJM design was carried out in which the module interconnects served to augment the current collecting buses on the cell. No sample TJMs were assembled due to a shortage of large-area TJCs.

Exploring Anxiety Symptoms in a Large-Scale Twin Study of Children with Autism Spectrum Disorders, Their Co-Twins and Controls

ERIC Educational Resources Information Center

Hallett, Victoria; Ronald, Angelica; Colvert, Emma; Ames, Catherine; Woodhouse, Emma; Lietz, Stephanie; Garnett, Tracy; Gillan, Nicola; Rijsdijk, Fruhling; Scahill, Lawrence; Bolton, Patrick; Happé, Francesca

2013-01-01

Background: Although many children with autism spectrum disorders (ASDs) experience difficulties with anxiety, the manifestation of these difficulties remains unresolved. The current study assessed anxiety in a large population-based twin sample, aged 10-15 years. Phenotypic analyses were used to explore anxiety symptoms in children with ASDs,…

Evaluating information content of SNPs for sample-tagging in re-sequencing projects.

PubMed

Hu, Hao; Liu, Xiang; Jin, Wenfei; Hilger Ropers, H; Wienker, Thomas F

2015-05-15

Sample-tagging is designed for identification of accidental sample mix-up, which is a major issue in re-sequencing studies. In this work, we develop a model to measure the information content of SNPs, so that we can optimize a panel of SNPs that approach the maximal information for discrimination. The analysis shows that as low as 60 optimized SNPs can differentiate the individuals in a population as large as the present world, and only 30 optimized SNPs are in practice sufficient in labeling up to 100 thousand individuals. In the simulated populations of 100 thousand individuals, the average Hamming distances, generated by the optimized set of 30 SNPs are larger than 18, and the duality frequency, is lower than 1 in 10 thousand. This strategy of sample discrimination is proved robust in large sample size and different datasets. The optimized sets of SNPs are designed for Whole Exome Sequencing, and a program is provided for SNP selection, allowing for customized SNP numbers and interested genes. The sample-tagging plan based on this framework will improve re-sequencing projects in terms of reliability and cost-effectiveness.

Long-Term Physical and Mental Health Consequences of Childhood Physical Abuse: Results from a Large Population-Based Sample of Men and Women

ERIC Educational Resources Information Center

Springer, Kristen W.; Sheridan, Jennifer; Kuo, Daphne; Carnes, Molly

2007-01-01

Objective: Child maltreatment has been linked to negative adult health outcomes; however, much past research includes only clinical samples of women, focuses exclusively on sexual abuse and/or fails to control for family background and childhood characteristics, both potential confounders. Further research is needed to obtain accurate,…

Inexpensive and Highly Reproducible Cloud-Based Variant Calling of 2,535 Human Genomes

PubMed Central

Shringarpure, Suyash S.; Carroll, Andrew; De La Vega, Francisco M.; Bustamante, Carlos D.

2015-01-01

Population scale sequencing of whole human genomes is becoming economically feasible; however, data management and analysis remains a formidable challenge for many research groups. Large sequencing studies, like the 1000 Genomes Project, have improved our understanding of human demography and the effect of rare genetic variation in disease. Variant calling on datasets of hundreds or thousands of genomes is time-consuming, expensive, and not easily reproducible given the myriad components of a variant calling pipeline. Here, we describe a cloud-based pipeline for joint variant calling in large samples using the Real Time Genomics population caller. We deployed the population caller on the Amazon cloud with the DNAnexus platform in order to achieve low-cost variant calling. Using our pipeline, we were able to identify 68.3 million variants in 2,535 samples from Phase 3 of the 1000 Genomes Project. By performing the variant calling in a parallel manner, the data was processed within 5 days at a compute cost of $7.33 per sample (a total cost of $18,590 for completed jobs and $21,805 for all jobs). Analysis of cost dependence and running time on the data size suggests that, given near linear scalability, cloud computing can be a cheap and efficient platform for analyzing even larger sequencing studies in the future. PMID:26110529

Immunophenotype Discovery, Hierarchical Organization, and Template-Based Classification of Flow Cytometry Samples

DOE PAGES

Azad, Ariful; Rajwa, Bartek; Pothen, Alex

2016-08-31

We describe algorithms for discovering immunophenotypes from large collections of flow cytometry samples and using them to organize the samples into a hierarchy based on phenotypic similarity. The hierarchical organization is helpful for effective and robust cytometry data mining, including the creation of collections of cell populations’ characteristic of different classes of samples, robust classification, and anomaly detection. We summarize a set of samples belonging to a biological class or category with a statistically derived template for the class. Whereas individual samples are represented in terms of their cell populations (clusters), a template consists of generic meta-populations (a group ofmore » homogeneous cell populations obtained from the samples in a class) that describe key phenotypes shared among all those samples. We organize an FC data collection in a hierarchical data structure that supports the identification of immunophenotypes relevant to clinical diagnosis. A robust template-based classification scheme is also developed, but our primary focus is in the discovery of phenotypic signatures and inter-sample relationships in an FC data collection. This collective analysis approach is more efficient and robust since templates describe phenotypic signatures common to cell populations in several samples while ignoring noise and small sample-specific variations. We have applied the template-based scheme to analyze several datasets, including one representing a healthy immune system and one of acute myeloid leukemia (AML) samples. The last task is challenging due to the phenotypic heterogeneity of the several subtypes of AML. However, we identified thirteen immunophenotypes corresponding to subtypes of AML and were able to distinguish acute promyelocytic leukemia (APL) samples with the markers provided. Clinically, this is helpful since APL has a different treatment regimen from other subtypes of AML. Core algorithms used in our data analysis are available in the flowMatch package at www.bioconductor.org. It has been downloaded nearly 6,000 times since 2014.« less

Immunophenotype Discovery, Hierarchical Organization, and Template-Based Classification of Flow Cytometry Samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Azad, Ariful; Rajwa, Bartek; Pothen, Alex

We describe algorithms for discovering immunophenotypes from large collections of flow cytometry samples and using them to organize the samples into a hierarchy based on phenotypic similarity. The hierarchical organization is helpful for effective and robust cytometry data mining, including the creation of collections of cell populations’ characteristic of different classes of samples, robust classification, and anomaly detection. We summarize a set of samples belonging to a biological class or category with a statistically derived template for the class. Whereas individual samples are represented in terms of their cell populations (clusters), a template consists of generic meta-populations (a group ofmore » homogeneous cell populations obtained from the samples in a class) that describe key phenotypes shared among all those samples. We organize an FC data collection in a hierarchical data structure that supports the identification of immunophenotypes relevant to clinical diagnosis. A robust template-based classification scheme is also developed, but our primary focus is in the discovery of phenotypic signatures and inter-sample relationships in an FC data collection. This collective analysis approach is more efficient and robust since templates describe phenotypic signatures common to cell populations in several samples while ignoring noise and small sample-specific variations. We have applied the template-based scheme to analyze several datasets, including one representing a healthy immune system and one of acute myeloid leukemia (AML) samples. The last task is challenging due to the phenotypic heterogeneity of the several subtypes of AML. However, we identified thirteen immunophenotypes corresponding to subtypes of AML and were able to distinguish acute promyelocytic leukemia (APL) samples with the markers provided. Clinically, this is helpful since APL has a different treatment regimen from other subtypes of AML. Core algorithms used in our data analysis are available in the flowMatch package at www.bioconductor.org. It has been downloaded nearly 6,000 times since 2014.« less

Heritability of metabolic syndrome traits in a large population-based sample[S

PubMed Central

van Dongen, Jenny; Willemsen, Gonneke; Chen, Wei-Min; de Geus, Eco J. C.; Boomsma, Dorret I.

2013-01-01

Heritability estimates of metabolic syndrome traits vary widely across studies. Some studies have suggested that the contribution of genes may vary with age or sex. We estimated the heritability of 11 metabolic syndrome-related traits and height as a function of age and sex in a large population-based sample of twin families (N = 2,792–27,021, for different traits). A moderate-to-high heritability was found for all traits [from H2 = 0.47 (insulin) to H2 = 0.78 (BMI)]. The broad-sense heritability (H2) showed little variation between age groups in women; it differed somewhat more in men (e.g., for glucose, H2 = 0.61 in young females, H2 = 0.56 in older females, H2 = 0.64 in young males, and H2= 0.27 in older males). While nonadditive genetic effects explained little variation in the younger subjects, nonadditive genetic effects became more important at a greater age. Our findings show that in an unselected sample (age range, ∼18–98 years), the genetic contribution to individual differences in metabolic syndrome traits is moderate to large in both sexes and across age. Although the prevalence of the metabolic syndrome has greatly increased in the past decades due to lifestyle changes, our study indicates that most of the variation in metabolic syndrome traits between individuals is due to genetic differences. PMID:23918046

Adaptive sampling in behavioral surveys.

PubMed

Thompson, S K

1997-01-01

Studies of populations such as drug users encounter difficulties because the members of the populations are rare, hidden, or hard to reach. Conventionally designed large-scale surveys detect relatively few members of the populations so that estimates of population characteristics have high uncertainty. Ethnographic studies, on the other hand, reach suitable numbers of individuals only through the use of link-tracing, chain referral, or snowball sampling procedures that often leave the investigators unable to make inferences from their sample to the hidden population as a whole. In adaptive sampling, the procedure for selecting people or other units to be in the sample depends on variables of interest observed during the survey, so the design adapts to the population as encountered. For example, when self-reported drug use is found among members of the sample, sampling effort may be increased in nearby areas. Types of adaptive sampling designs include ordinary sequential sampling, adaptive allocation in stratified sampling, adaptive cluster sampling, and optimal model-based designs. Graph sampling refers to situations with nodes (for example, people) connected by edges (such as social links or geographic proximity). An initial sample of nodes or edges is selected and edges are subsequently followed to bring other nodes into the sample. Graph sampling designs include network sampling, snowball sampling, link-tracing, chain referral, and adaptive cluster sampling. A graph sampling design is adaptive if the decision to include linked nodes depends on variables of interest observed on nodes already in the sample. Adjustment methods for nonsampling errors such as imperfect detection of drug users in the sample apply to adaptive as well as conventional designs.

Observational studies of patients in the emergency department: a comparison of 4 sampling methods.

PubMed

Valley, Morgan A; Heard, Kennon J; Ginde, Adit A; Lezotte, Dennis C; Lowenstein, Steven R

2012-08-01

We evaluate the ability of 4 sampling methods to generate representative samples of the emergency department (ED) population. We analyzed the electronic records of 21,662 consecutive patient visits at an urban, academic ED. From this population, we simulated different models of study recruitment in the ED by using 2 sample sizes (n=200 and n=400) and 4 sampling methods: true random, random 4-hour time blocks by exact sample size, random 4-hour time blocks by a predetermined number of blocks, and convenience or "business hours." For each method and sample size, we obtained 1,000 samples from the population. Using χ(2) tests, we measured the number of statistically significant differences between the sample and the population for 8 variables (age, sex, race/ethnicity, language, triage acuity, arrival mode, disposition, and payer source). Then, for each variable, method, and sample size, we compared the proportion of the 1,000 samples that differed from the overall ED population to the expected proportion (5%). Only the true random samples represented the population with respect to sex, race/ethnicity, triage acuity, mode of arrival, language, and payer source in at least 95% of the samples. Patient samples obtained using random 4-hour time blocks and business hours sampling systematically differed from the overall ED patient population for several important demographic and clinical variables. However, the magnitude of these differences was not large. Common sampling strategies selected for ED-based studies may affect parameter estimates for several representative population variables. However, the potential for bias for these variables appears small. Copyright © 2012. Published by Mosby, Inc.

Problems with sampling desert tortoises: A simulation analysis based on field data

USGS Publications Warehouse

Freilich, J.E.; Camp, R.J.; Duda, J.J.; Karl, A.E.

2005-01-01

The desert tortoise (Gopherus agassizii) was listed as a U.S. threatened species in 1990 based largely on population declines inferred from mark-recapture surveys of 2.59-km2 (1-mi2) plots. Since then, several census methods have been proposed and tested, but all methods still pose logistical or statistical difficulties. We conducted computer simulations using actual tortoise location data from 2 1-mi2 plot surveys in southern California, USA, to identify strengths and weaknesses of current sampling strategies. We considered tortoise population estimates based on these plots as "truth" and then tested various sampling methods based on sampling smaller plots or transect lines passing through the mile squares. Data were analyzed using Schnabel's mark-recapture estimate and program CAPTURE. Experimental subsampling with replacement of the 1-mi2 data using 1-km2 and 0.25-km2 plot boundaries produced data sets of smaller plot sizes, which we compared to estimates from the 1-mi 2 plots. We also tested distance sampling by saturating a 1-mi 2 site with computer simulated transect lines, once again evaluating bias in density estimates. Subsampling estimates from 1-km2 plots did not differ significantly from the estimates derived at 1-mi2. The 0.25-km2 subsamples significantly overestimated population sizes, chiefly because too few recaptures were made. Distance sampling simulations were biased 80% of the time and had high coefficient of variation to density ratios. Furthermore, a prospective power analysis suggested limited ability to detect population declines as high as 50%. We concluded that poor performance and bias of both sampling procedures was driven by insufficient sample size, suggesting that all efforts must be directed to increasing numbers found in order to produce reliable results. Our results suggest that present methods may not be capable of accurately estimating desert tortoise populations.

Correction of Population Stratification in Large Multi-Ethnic Association Studies

PubMed Central

Serre, David; Montpetit, Alexandre; Paré, Guillaume; Engert, James C.; Yusuf, Salim; Keavney, Bernard; Hudson, Thomas J.; Anand, Sonia

2008-01-01

Background The vast majority of genetic risk factors for complex diseases have, taken individually, a small effect on the end phenotype. Population-based association studies therefore need very large sample sizes to detect significant differences between affected and non-affected individuals. Including thousands of affected individuals in a study requires recruitment in numerous centers, possibly from different geographic regions. Unfortunately such a recruitment strategy is likely to complicate the study design and to generate concerns regarding population stratification. Methodology/Principal Findings We analyzed 9,751 individuals representing three main ethnic groups - Europeans, Arabs and South Asians - that had been enrolled from 154 centers involving 52 countries for a global case/control study of acute myocardial infarction. All individuals were genotyped at 103 candidate genes using 1,536 SNPs selected with a tagging strategy that captures most of the genetic diversity in different populations. We show that relying solely on self-reported ethnicity is not sufficient to exclude population stratification and we present additional methods to identify and correct for stratification. Conclusions/Significance Our results highlight the importance of carefully addressing population stratification and of carefully “cleaning” the sample prior to analyses to obtain stronger signals of association and to avoid spurious results. PMID:18196181

Serum markers for type II diabetes mellitus

DOEpatents

Metz, Thomas O; Qian, Wei-Jun; Jacobs, Jon M; Polpitiya, Ashoka D; Camp, II, David G; Smith, Richard D

2014-03-18

A method for identifying persons with increased risk of developing type 2 diabetes mellitus utilizing selected biomarkers described hereafter either alone or in combination. The present invention allows for broad based, reliable, screening of large population bases and provides other advantages, including the formulation of effective strategies for characterizing, archiving, and contrasting data from multiple sample types under varying conditions.

Validity of LIDAS (LIfetime Depression Assessment Self-report): a self-report online assessment of lifetime major depressive disorder.

PubMed

Bot, M; Middeldorp, C M; de Geus, E J C; Lau, H M; Sinke, M; van Nieuwenhuizen, B; Smit, J H; Boomsma, D I; Penninx, B W J H

2017-01-01

There is a paucity of valid, brief instruments for the assessment of lifetime major depressive disorder (MDD) that can be used in, for example, large-scale genomics, imaging or biomarker studies on depression. We developed the LIfetime Depression Assessment Self-report (LIDAS), which assesses lifetime MDD diagnosis according to DSM criteria, and is largely based on the widely used Composite International Diagnostic Interview (CIDI). Here, we tested the feasibility and determined the sensitivity and specificity for measuring lifetime MDD with this new questionnaire, with a regular CIDI as reference. Sensitivity and specificity analyses of the online lifetime MDD questionnaire were performed in adults with (n = 177) and without (n = 87) lifetime MDD according to regular index CIDIs, selected from the Netherlands Study of Depression and Anxiety (NESDA) and Netherlands Twin Register (NTR). Feasibility was tested in an additional non-selective, population-based sample of NTR participants (n = 245). Of the 753 invited persons, 509 (68%) completed the LIDAS, of which 419 (82%) did this online. User-friendliness of the instrument was rated high. Median completion time was 6.2 min. Sensitivity and specificity for lifetime MDD were 85% [95% confidence interval (CI) 80-91%] and 80% (95% CI 72-89%), respectively. This LIDAS instrument gave a lifetime MDD prevalence of 20.8% in the population-based sample. Measuring lifetime MDD with an online instrument was feasible. Sensitivity and specificity were adequate. The instrument gave a prevalence of lifetime MDD in line with reported population prevalences. LIDAS is a promising tool for rapid determination of lifetime MDD status in large samples, such as needed for genomics studies.

Effects of Sample Selection Bias on the Accuracy of Population Structure and Ancestry Inference

PubMed Central

Shringarpure, Suyash; Xing, Eric P.

2014-01-01

Population stratification is an important task in genetic analyses. It provides information about the ancestry of individuals and can be an important confounder in genome-wide association studies. Public genotyping projects have made a large number of datasets available for study. However, practical constraints dictate that of a geographical/ethnic population, only a small number of individuals are genotyped. The resulting data are a sample from the entire population. If the distribution of sample sizes is not representative of the populations being sampled, the accuracy of population stratification analyses of the data could be affected. We attempt to understand the effect of biased sampling on the accuracy of population structure analysis and individual ancestry recovery. We examined two commonly used methods for analyses of such datasets, ADMIXTURE and EIGENSOFT, and found that the accuracy of recovery of population structure is affected to a large extent by the sample used for analysis and how representative it is of the underlying populations. Using simulated data and real genotype data from cattle, we show that sample selection bias can affect the results of population structure analyses. We develop a mathematical framework for sample selection bias in models for population structure and also proposed a correction for sample selection bias using auxiliary information about the sample. We demonstrate that such a correction is effective in practice using simulated and real data. PMID:24637351

Tissues from population-based cancer registries: a novel approach to increasing research potential.

PubMed

Goodman, Marc T; Hernandez, Brenda Y; Hewitt, Stephen; Lynch, Charles F; Coté, Timothy R; Frierson, Henry F; Moskaluk, Christopher A; Killeen, Jeffrey L; Cozen, Wendy; Key, Charles R; Clegg, Limin; Reichman, Marsha; Hankey, Benjamin F; Edwards, Brenda

2005-07-01

Population-based cancer registries, such as those included in the Surveillance, Epidemiology, and End-Results (SEER) Program, offer tremendous research potential beyond traditional surveillance activities. We describe the expansion of SEER registries to gather formalin-fixed, paraffin-embedded tissue from cancer patients on a population basis. Population-based tissue banks have the advantage of providing an unbiased sampling frame for evaluating the public health impact of genes or protein targets that may be used for therapeutic or diagnostic purposes in defined communities. Such repositories provide a unique resource for testing new molecular classification schemes for cancer, validating new biologic markers of malignancy, prognosis and progression, assessing therapeutic targets, and measuring allele frequencies of cancer-associated genetic polymorphisms or germline mutations in representative samples. The assembly of tissue microarrays will allow for the use of rapid, large-scale protein-expression profiling of tumor samples while limiting depletion of this valuable resource. Access to biologic specimens through SEER registries will provide researchers with demographic, clinical, and risk factor information on cancer patients with assured data quality and completeness. Clinical outcome data, such as disease-free survival, can be correlated with previously validated prognostic markers. Furthermore, the anonymity of the study subject can be protected through rigorous standards of confidentiality. SEER-based tissue resources represent a step forward in true, population-based tissue repositories of tumors from US patients and may serve as a foundation for molecular epidemiology studies of cancer in this country.

[Effect of data missing on population based viral load survey in HIV infected men who have sex with men sampled in 16 large cities, China].

PubMed

Jiang, Z; Dou, Z; Yan, Z H; Song, W L; Chen, Y; Ren, X L; Chen, J; Cao, W; Xu, J; Wu, Z Y

2017-09-10

Objective: To analyze the effect of missing data in population based viral load (PVL) survey in HIV infected men who have sex with men (MSM) sampled in 16 cities in China. Methods: The database of 3 virus load sampling survey conducted consecutively in HIV infected MSM population in 16 large cities (Beijing, Shanghai, Nanjing, Hangzhou, Wuhan, Chongqing, Kunming, Xi'an, Guangzhou, Shenzhen, Nanning, Urumuqi, Harbin, Changchun, Chengdu and Tianjin) during 2013-2015 was used. SPSS 17.0 software was used to describe distribution of the missing data and analyze associated factors. Results: A total of 12 150 HIV infected MSM were randomly selected for the surveys, in whom, 9 141 (75.2 % ) received virus load tests, while 3 009 (24.8 % ) received no virus load tests, whose virus load data missed. The virus load data missing rates in MSM with or without access to antiretroviral therapy (ART) were 11.5 % (765/6 675) and 39.4 % (2 060/5 223) respectively, and the virus load data missing rates were 21.9 % (1 866/8 523) and 28.4 % (959/3 374), respectively, in local residents and non-local residents (migrants). Conclusions: The analysis indicated that the data missing occurred in the virus load survey in HIV infected MSM population. ART status and census registering status were the main influencing factors. Data missing could influence the accurate evaluation of community viral load (CVL) and population viral load(PVL) levels in HIV infected MSM in China.

Large-scale assessment of myxomatosis prevalence in European wild rabbits (Oryctolagus cuniculus) 60years after first outbreak in Spain.

PubMed

Villafuerte, Rafael; Castro, Francisca; Ramírez, Esther; Cotilla, Irene; Parra, Francisco; Delibes-Mateos, Miguel; Recuerda, Pilar; Rouco, Carlos

2017-10-01

Myxomatosis is a viral disease that affects European rabbits (Oryctolagus cuniculus) worldwide. In Spain, populations of wild rabbits drastically decreased in the 1950s after the first outbreak of myxomatosis. Since that first appearance, it seems to be an annual epizootic in Spain with periodic outbreaks, predominantly in summer and autumn. Taking into account rabbit population structure, abundance, and genetic lineage, this paper attempts to make a large-scale characterization of myxomatosis seroprevalence based on the immune status of 29 rabbit populations distributed throughout Spain, where O. cuniculus cuniculus and O. c. algirus, the two known rabbit subspecies, naturally inhabit. A total of 654 samples were collected between 2003 and 2009, and seroprevalence of antibodies against Myxoma virus (MYXV) was determined. Overall, our results revealed that 53% of the rabbit samples were positive to antibodies against MYXV. Newborn and juvenile rabbits were the most susceptible animals to the virus, with 19% and 16% seropositivity for newborn and juveniles, respectively, while adult rabbits were the most protected, with 65% of seropositive samples. This suggests that prevalence is negatively related to the proportion of newborn and juvenile rabbits in a population. Our results also showed that seroprevalence against MYXV tended to be higher in high-abundance populations. In contrast, no differences were detected in seroprevalence between rabbit subspecies. This study confirms that >60years since first outbreak, myxomatosis is an endemic disease in Spain. Based on the results, the establishment of a myxomatosis surveillance protocol is proposed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Stratification of American hearing aid users by age and audiometric characteristics: a method for representative sampling.

PubMed

Aronoff, Justin M; Yoon, Yang-soo; Soli, Sigfrid D

2010-06-01

Stratified sampling plans can increase the accuracy and facilitate the interpretation of a dataset characterizing a large population. However, such sampling plans have found minimal use in hearing aid (HA) research, in part because of a paucity of quantitative data on the characteristics of HA users. The goal of this study was to devise a quantitatively derived stratified sampling plan for HA research, so that such studies will be more representative and generalizable, and the results obtained using this method are more easily reinterpreted as the population changes. Pure-tone average (PTA) and age information were collected for 84,200 HAs acquired in 2006 and 2007. The distribution of PTA and age was quantified for each HA type and for a composite of all HA users. Based on their respective distributions, PTA and age were each divided into three groups, the combination of which defined the stratification plan. The most populous PTA and age group was also subdivided, allowing greater homogeneity within strata. Finally, the percentage of users in each stratum was calculated. This article provides a stratified sampling plan for HA research, based on a quantitative analysis of the distribution of PTA and age for HA users. Adopting such a sampling plan will make HA research results more representative and generalizable. In addition, data acquired using such plans can be reinterpreted as the HA population changes.

Pre-Whaling Genetic Diversity and Population Ecology in Eastern Pacific Gray Whales: Insights from Ancient DNA and Stable Isotopes

PubMed Central

Alter, S. Elizabeth; Newsome, Seth D.; Palumbi, Stephen R.

2012-01-01

Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ∼5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region) and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size. PMID:22590499

MaCH-Admix: Genotype Imputation for Admixed Populations

PubMed Central

Liu, Eric Yi; Li, Mingyao; Wang, Wei; Li, Yun

2012-01-01

Imputation in admixed populations is an important problem but challenging due to the complex linkage disequilibrium (LD) pattern. The emergence of large reference panels such as that from the 1,000 Genomes Project enables more accurate imputation in general, and in particular for admixed populations and for uncommon variants. To efficiently benefit from these large reference panels, one key issue to consider in modern genotype imputation framework is the selection of effective reference panels. In this work, we consider a number of methods for effective reference panel construction inside a hidden Markov model and specific to each target individual. These methods fall into two categories: identity-by-state (IBS) based and ancestry-weighted approach. We evaluated the performance on individuals from recently admixed populations. Our target samples include 8,421 African Americans and 3,587 Hispanic Americans from the Women’s Health Initiative, which allow assessment of imputation quality for uncommon variants. Our experiments include both large and small reference panels; large, medium, and small target samples; and in genome regions of varying levels of LD. We also include BEAGLE and IMPUTE2 for comparison. Experiment results with large reference panel suggest that our novel piecewise IBS method yields consistently higher imputation quality than other methods/software. The advantage is particularly noteworthy among uncommon variants where we observe up to 5.1% information gain with the difference being highly significant (Wilcoxon signed rank test P-value < 0.0001). Our work is the first that considers various sensible approaches for imputation in admixed populations and presents a comprehensive comparison. PMID:23074066

Zoonoses research in the German National Cohort : feasibility of parallel sampling of pets and owners.

PubMed

Hille, Katja; Möbius, Nadine; Akmatov, Manas K; Verspohl, Jutta; Rabold, Denise; Hartmann, Maria; Günther, Kathrin; Obi, Nadia; Kreienbrock, Lothar

2014-11-01

Cats and dogs live in more than 20 % of German households and the contact between these pets and their owners can be very close. Therefore, a transmission of zoonotic pathogens may occur. To investigate whether zoonotic research questions can be examined in the context of population-based studies like the German National Cohort (GNC), two studies on different study populations were conducted as part of the feasibility tests of the GNC. The aim of the first study was to quantify the actual exposure of participants of the GNC to cats and dogs. In the second study summarised here the feasibility of the sampling of cats and dogs by their owners was tested. To quantify the exposure of participants of the GNC to cats and dogs 744 study participants of the Pretests of the GNC were asked whether they had contact with animals. Currently 10 % have a dog and 14 % have a cat in their household. These figures confirm that a large proportion of the German population has contact with pets and that there is a need for further zoonoses research. To establish the collection of biological samples from cats and dogs in the context of large-scale population-based studies feasible methods are needed. Therefore, a study was conducted to test whether pet owners can take samples from their cats and dogs and whether the quality of these samples is comparable to samples taken by a qualified veterinarian. A total of 82 dog and 18 cat owners were recruited in two veterinary practices in Hannover and the Clinic for Small Animals at the University of Veterinary Medicine in Hannover. Sampling instructions and sample material for nasal and buccal swabs, faecal samples and, in the case of cat owners, a brush for fur samples, were given to the pet owners. The pet owners were asked to take the samples from their pets at home and to send the samples by surface mail. Swab samples were cultured and bacterial growth was quantified independent of bacterial species. The growth of Gram-positive and Gram-negative bacteria from samples taken by the veterinarian and the pet owners were compared. For Gram-positive bacteria the agreement of laboratory results was 71 % for nasal swabs and 78 % for oral swabs while for Gram-negative bacteria the agreement of laboratory results was 55 % for nasal swabs and 87 % for oral swabs. In conclusion it has been shown that participants of the GNC are exposed to cats and dogs and that the sampling of cats and dogs by their owners is a feasible method which can be a useful tool for zoonoses research in population-based studies.

Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management.

PubMed

Grossmann, Sebastian; Nowak, Piotr; Neogi, Ujjwal

2015-01-01

HIV-1 near full-length genome (HIV-NFLG) sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT) for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Plasma samples (n=30) were obtained from HIV-1B (n=10), HIV-1C (n=10), CRF01_AE (n=5) and CRF01_AG (n=5) infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeq™ HIV-1 Genotyping System. After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92%) samples with the lowest viral load being 3000 copies/ml. High (>99%) concordance was observed between HIV-NFLG and ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples. Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay.

An ELISA method to compute endpoint titers to Epstein-Barr virus and cytomegalovirus: application to population-based studies.

PubMed

Stowe, Raymond P; Ruiz, R Jeanne; Fagundes, Christopher P; Stowe, Robin H; Chen, Min; Glaser, Ronald

2014-06-01

Indirect fluorescence analysis (IFA), the gold standard for determining herpesvirus antibody titers, is labor-intensive and poorly suited for large population-based studies. The enzyme-linked immunosorbent assay (ELISA) is used widely for measuring antiviral antibodies but also suffers drawbacks such as reduced specificity and the qualitative nature of the results due to limited interpretation of the optical density (OD) units. This paper describes a method to titer herpesvirus antibodies using microplates coated with virally-infected cells in which a standard curve, derived from IFA-scored samples, allowed OD units to be converted into titers. A LOOKUP function was created in order to report the data as traditional IFA-based (i.e., 2-fold) titers. The modified ELISA correlated significantly with IFA and was subsequently used to compute endpoint antibody titers to Epstein-Barr virus (EBV)-virus capsid antigen (VCA) and cytomegalovirus (CMV) in blood samples taken from 398 pregnant Hispanic women. Four women were EBV negative (1%), while 58 women were CMV negative (14.6%). EBV VCA antibody titers were significantly higher than CMV antibody titers (p<0.001). This method allows titering of herpesvirus antibodies by ELISA suitable for large population-based studies. In addition, the LOOKUP table enables conversion from OD-derived titers into 2-fold titers for comparison of results with other studies. Copyright © 2014 Elsevier B.V. All rights reserved.

Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error

PubMed Central

Liu, Xiaoming; Fu, Yun-Xin; Maxwell, Taylor J.; Boerwinkle, Eric

2010-01-01

It is known that sequencing error can bias estimation of evolutionary or population genetic parameters. This problem is more prominent in deep resequencing studies because of their large sample size n, and a higher probability of error at each nucleotide site. We propose a new method based on the composite likelihood of the observed SNP configurations to infer population mutation rate θ = 4Neμ, population exponential growth rate R, and error rate ɛ, simultaneously. Using simulation, we show the combined effects of the parameters, θ, n, ɛ, and R on the accuracy of parameter estimation. We compared our maximum composite likelihood estimator (MCLE) of θ with other θ estimators that take into account the error. The results show the MCLE performs well when the sample size is large or the error rate is high. Using parametric bootstrap, composite likelihood can also be used as a statistic for testing the model goodness-of-fit of the observed DNA sequences. The MCLE method is applied to sequence data on the ANGPTL4 gene in 1832 African American and 1045 European American individuals. PMID:19952140

Multi-Genetic Marker Approach and Spatio-Temporal Analysis Suggest There Is a Single Panmictic Population of Swordfish Xiphias gladius in the Indian Ocean

PubMed Central

Muths, Delphine; Le Couls, Sarah; Evano, Hugues; Grewe, Peter; Bourjea, Jerome

2013-01-01

Genetic population structure of swordfish Xiphias gladius was examined based on 2231 individual samples, collected mainly between 2009 and 2010, among three major sampling areas within the Indian Ocean (IO; twelve distinct sites), Atlantic (two sites) and Pacific (one site) Oceans using analysis of nineteen microsatellite loci (n = 2146) and mitochondrial ND2 sequences (n = 2001) data. Sample collection was stratified in time and space in order to investigate the stability of the genetic structure observed with a special focus on the South West Indian Ocean. Significant AMOVA variance was observed for both markers indicating genetic population subdivision was present between oceans. Overall value of F-statistics for ND2 sequences confirmed that Atlantic and Indian Oceans swordfish represent two distinct genetic stocks. Indo-Pacific differentiation was also significant but lower than that observed between Atlantic and Indian Oceans. However, microsatellite F-statistics failed to reveal structure even at the inter-oceanic scale, indicating that resolving power of our microsatellite loci was insufficient for detecting population subdivision. At the scale of the Indian Ocean, results obtained from both markers are consistent with swordfish belonging to a single unique panmictic population. Analyses partitioned by sampling area, season, or sex also failed to identify any clear structure within this ocean. Such large spatial and temporal homogeneity of genetic structure, observed for such a large highly mobile pelagic species, suggests as satisfactory to consider swordfish as a single panmictic population in the Indian Ocean. PMID:23717447

Exploitation of immunofluorescence for the quantification and characterization of small numbers of Pasteuria endospores.

PubMed

Costa, Sofia R; Kerry, Brian R; Bardgett, Richard D; Davies, Keith G

2006-12-01

The Pasteuria group of endospore-forming bacteria has been studied as a biocontrol agent of plant-parasitic nematodes. Techniques have been developed for its detection and quantification in soil samples, and these mainly focus on observations of endospore attachment to nematodes. Characterization of Pasteuria populations has recently been performed with DNA-based techniques, which usually require the extraction of large numbers of spores. We describe a simple immunological method for the quantification and characterization of Pasteuria populations. Bayesian statistics were used to determine an extraction efficiency of 43% and a threshold of detection of 210 endospores g(-1) sand. This provided a robust means of estimating numbers of endospores in small-volume samples from a natural system. Based on visual assessment of endospore fluorescence, a quantitative method was developed to characterize endospore populations, which were shown to vary according to their host.

Clinical prediction and the idea of a population.

PubMed

Armstrong, David

2017-04-01

Using an analysis of the British Medical Journal over the past 170 years, this article describes how changes in the idea of a population have informed new technologies of medical prediction. These approaches have largely replaced older ideas of clinical prognosis based on understanding the natural histories of the underlying pathologies. The 19 th -century idea of a population, which provided a denominator for medical events such as births and deaths, was constrained in its predictive power by its method of enumerating individual bodies. During the 20 th century, populations were increasingly constructed through inferential techniques based on patient groups and samples seen to possess variable characteristics. The emergence of these new virtual populations created the conditions for the emergence of predictive algorithms that are used to foretell our medical futures.

Integration of silicon-based neural probes and micro-drive arrays for chronic recording of large populations of neurons in behaving animals

NASA Astrophysics Data System (ADS)

Michon, Frédéric; Aarts, Arno; Holzhammer, Tobias; Ruther, Patrick; Borghs, Gustaaf; McNaughton, Bruce; Kloosterman, Fabian

2016-08-01

Objective. Understanding how neuronal assemblies underlie cognitive function is a fundamental question in system neuroscience. It poses the technical challenge to monitor the activity of populations of neurons, potentially widely separated, in relation to behaviour. In this paper, we present a new system which aims at simultaneously recording from a large population of neurons from multiple separated brain regions in freely behaving animals. Approach. The concept of the new device is to combine the benefits of two existing electrophysiological techniques, i.e. the flexibility and modularity of micro-drive arrays and the high sampling ability of electrode-dense silicon probes. Main results. Newly engineered long bendable silicon probes were integrated into a micro-drive array. The resulting device can carry up to 16 independently movable silicon probes, each carrying 16 recording sites. Populations of neurons were recorded simultaneously in multiple cortical and/or hippocampal sites in two freely behaving implanted rats. Significance. Current approaches to monitor neuronal activity either allow to flexibly record from multiple widely separated brain regions (micro-drive arrays) but with a limited sampling density or to provide denser sampling at the expense of a flexible placement in multiple brain regions (neural probes). By combining these two approaches and their benefits, we present an alternative solution for flexible and simultaneous recordings from widely distributed populations of neurons in freely behaving rats.

Association of serum homocysteine with major depressive disorder: results from a large population-based study.

PubMed

Nabi, Hermann; Bochud, Murielle; Glaus, Jennifer; Lasserre, Aurélie M; Waeber, Gérard; Vollenweider, Peter; Preisig, Martin

2013-10-01

Studies on the association between homocysteine levels and depression have shown conflicting results. To examine the association between serum total homocysteine (tHcy) levels and major depressive disorder (MDD) in a large community sample with an extended age range. A total of 3392 men and women aged 35-66 years participating in the CoLaus study and its psychiatric arm (PsyCoLaus) were included in the analyses. High tHcy measured from fasting blood samples was defined as a concentration ≥15μmol/L. MDD was assessed using the semi-structured Diagnostic Interview for Genetics Studies. In multivariate analyses, elevated tHcy levels were associated with greater odds of meeting the diagnostic criteria for lifetime MDD among men (OR=1.71; 95% CI, 1.18-2.50). This was particularly the case for remitted MDD. Among women, there was no significant association between tHcy levels and MDD and the association tended to be in the opposite direction (OR=0.61; 95% CI, 0.34-1.08). In this large population-based study, elevated tHcy concentrations are associated with lifetime MDD and particularly with remitted MDD among men. Copyright © 2013 Elsevier Ltd. All rights reserved.

Predictive equations for total lung capacity and residual volume calculated from radiographs in a random sample of the Michigan population.

PubMed Central

Kilburn, K H; Warshaw, R H; Thornton, J C; Thornton, K; Miller, A

1992-01-01

BACKGROUND: Published predicted values for total lung capacity and residual volume are often based on a small number of subjects and derive from different populations from predicted spirometric values. Equations from the only two large studies gave smaller predicted values for total lung capacity than the smaller studies. A large number of subjects have been studied from a population which has already provided predicted values for spirometry and transfer factor for carbon monoxide. METHODS: Total lung capacity was measured from standard posteroanterior and lateral chest radiographs and forced vital capacity by spirometry in a population sample of 771 subjects. Prediction equations were developed for total lung capacity (TLC), residual volume (RV) and RV/TLC in two groups--normal and total. Subjects with signs or symptoms of cardiopulmonary disease were combined with the normal subjects and equations for all subjects were also modelled. RESULTS: Prediction equations for TLC and RV in non-smoking normal men and women were square root transformations which included height and weight but not age. They included a coefficient for duration of smoking in current smokers. The predictive equation for RV/TLC included weight, age, age and duration of smoking for current smokers and ex-smokers of both sexes. For the total population the equations took the same form but the height coefficients and constants were slightly different. CONCLUSION: These population based prediction equations for TLC, RV and RV/TLC provide reference standards in a population that has provided reference standards for spirometry and single breath transfer factor for carbon monoxide. PMID:1412094

Complex Population Dynamics and the Coalescent Under Neutrality

PubMed Central

Volz, Erik M.

2012-01-01

Estimates of the coalescent effective population size Ne can be poorly correlated with the true population size. The relationship between Ne and the population size is sensitive to the way in which birth and death rates vary over time. The problem of inference is exacerbated when the mechanisms underlying population dynamics are complex and depend on many parameters. In instances where nonparametric estimators of Ne such as the skyline struggle to reproduce the correct demographic history, model-based estimators that can draw on prior information about population size and growth rates may be more efficient. A coalescent model is developed for a large class of populations such that the demographic history is described by a deterministic nonlinear dynamical system of arbitrary dimension. This class of demographic model differs from those typically used in population genetics. Birth and death rates are not fixed, and no assumptions are made regarding the fraction of the population sampled. Furthermore, the population may be structured in such a way that gene copies reproduce both within and across demes. For this large class of models, it is shown how to derive the rate of coalescence, as well as the likelihood of a gene genealogy with heterochronous sampling and labeled taxa, and how to simulate a coalescent tree conditional on a complex demographic history. This theoretical framework encapsulates many of the models used by ecologists and epidemiologists and should facilitate the integration of population genetics with the study of mathematical population dynamics. PMID:22042576

Taxonomic structure and stability of the bacterial community in belgian sourdough ecosystems as assessed by culture and population fingerprinting.

PubMed

Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert

2008-04-01

A total of 39 traditional sourdoughs were sampled at 11 bakeries located throughout Belgium which were visited twice with a 1-year interval. The taxonomic structure and stability of the bacterial communities occurring in these traditional sourdoughs were assessed using both culture-dependent and culture-independent methods. A total of 1,194 potential lactic acid bacterium (LAB) isolates were tentatively grouped and identified by repetitive element sequence-based PCR, followed by sequence-based identification using 16S rRNA and pheS genes from a selection of genotypically unique LAB isolates. In parallel, all samples were analyzed by denaturing gradient gel electrophoresis (DGGE) of V3-16S rRNA gene amplicons. In addition, extensive metabolite target analysis of more than 100 different compounds was performed. Both culturing and DGGE analysis showed that the species Lactobacillus sanfranciscensis, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus pontis dominated the LAB population of Belgian type I sourdoughs. In addition, DGGE band sequence analysis demonstrated the presence of Acetobacter sp. and a member of the Erwinia/Enterobacter/Pantoea group in some samples. Overall, the culture-dependent and culture-independent approaches each exhibited intrinsic limitations in assessing bacterial LAB diversity in Belgian sourdoughs. Irrespective of the LAB biodiversity, a large majority of the sugar and amino acid metabolites were detected in all sourdough samples. Principal component-based analysis of biodiversity and metabolic data revealed only little variation among the two samples of the sourdoughs produced at the same bakery. The rare cases of instability observed could generally be linked with variations in technological parameters or differences in detection capacity between culture-dependent and culture-independent approaches. Within a sampling interval of 1 year, this study reinforces previous observations that the bakery environment rather than the type or batch of flour largely determines the development of a stable LAB population in sourdoughs.

Taxonomic Structure and Stability of the Bacterial Community in Belgian Sourdough Ecosystems as Assessed by Culture and Population Fingerprinting▿ †

PubMed Central

Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert

2008-01-01

A total of 39 traditional sourdoughs were sampled at 11 bakeries located throughout Belgium which were visited twice with a 1-year interval. The taxonomic structure and stability of the bacterial communities occurring in these traditional sourdoughs were assessed using both culture-dependent and culture-independent methods. A total of 1,194 potential lactic acid bacterium (LAB) isolates were tentatively grouped and identified by repetitive element sequence-based PCR, followed by sequence-based identification using 16S rRNA and pheS genes from a selection of genotypically unique LAB isolates. In parallel, all samples were analyzed by denaturing gradient gel electrophoresis (DGGE) of V3-16S rRNA gene amplicons. In addition, extensive metabolite target analysis of more than 100 different compounds was performed. Both culturing and DGGE analysis showed that the species Lactobacillus sanfranciscensis, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus pontis dominated the LAB population of Belgian type I sourdoughs. In addition, DGGE band sequence analysis demonstrated the presence of Acetobacter sp. and a member of the Erwinia/Enterobacter/Pantoea group in some samples. Overall, the culture-dependent and culture-independent approaches each exhibited intrinsic limitations in assessing bacterial LAB diversity in Belgian sourdoughs. Irrespective of the LAB biodiversity, a large majority of the sugar and amino acid metabolites were detected in all sourdough samples. Principal component-based analysis of biodiversity and metabolic data revealed only little variation among the two samples of the sourdoughs produced at the same bakery. The rare cases of instability observed could generally be linked with variations in technological parameters or differences in detection capacity between culture-dependent and culture-independent approaches. Within a sampling interval of 1 year, this study reinforces previous observations that the bakery environment rather than the type or batch of flour largely determines the development of a stable LAB population in sourdoughs. PMID:18310426

Advancing Methods for U.S. Transgender Health Research

PubMed Central

Reisner, Sari L.; Deutsch, Madeline B.; Bhasin, Shalender; Bockting, Walter; Brown, George R.; Feldman, Jamie; Garofalo, Rob; Kreukels, Baudewijntje; Radix, Asa; Safer, Joshua D.; Tangpricha, Vin; T’Sjoen, Guy; Goodman, Michael

2016-01-01

Purpose of Review To describe methodological challenges, gaps, and opportunities in U.S. transgender health research. Recent Findings Lack of large prospective observational studies and intervention trials, limited data on risks and benefits of gender affirmation (e.g., hormones and surgical interventions), and inconsistent use of definitions across studies hinder evidence-based care for transgender people. Systematic high-quality observational and intervention-testing studies may be carried out using several approaches, including general population-based, health systems-based, clinic-based, venue-based, and hybrid designs. Each of these approaches has its strength and limitations; however, harmonization of research efforts is needed. Ongoing development of evidence-based clinical recommendations will benefit from a series of observational and intervention studies aimed at identification, recruitment, and follow-up of transgender people of different ages, from different racial, ethnic, and socioeconomic backgrounds and with diverse gender identities. Summary Transgender health research faces challenges that include standardization of lexicon, agreed-upon population definitions, study design, sampling, measurement, outcome ascertainment, and sample size. Application of existing and new methods is needed to fill existing gaps, increase the scientific rigor and reach of transgender health research, and inform evidence-based prevention and care for this underserved population. PMID:26845331

Effect of separate sampling on classification accuracy.

PubMed

Shahrokh Esfahani, Mohammad; Dougherty, Edward R

2014-01-15

Measurements are commonly taken from two phenotypes to build a classifier, where the number of data points from each class is predetermined, not random. In this 'separate sampling' scenario, the data cannot be used to estimate the class prior probabilities. Moreover, predetermined class sizes can severely degrade classifier performance, even for large samples. We employ simulations using both synthetic and real data to show the detrimental effect of separate sampling on a variety of classification rules. We establish propositions related to the effect on the expected classifier error owing to a sampling ratio different from the population class ratio. From these we derive a sample-based minimax sampling ratio and provide an algorithm for approximating it from the data. We also extend to arbitrary distributions the classical population-based Anderson linear discriminant analysis minimax sampling ratio derived from the discriminant form of the Bayes classifier. All the codes for synthetic data and real data examples are written in MATLAB. A function called mmratio, whose output is an approximation of the minimax sampling ratio of a given dataset, is also written in MATLAB. All the codes are available at: http://gsp.tamu.edu/Publications/supplementary/shahrokh13b.

33 CFR Appendix A to Part 279 - Sample Resource Use Objectives

Code of Federal Regulations, 2011 CFR

2011-07-01

... technical advice. Resource use objective: To establish an ecological study area at Wakulla Wash for the protection and study of its unique vegetative associations. (Discussion) The analysis of pertinent factors... educational purposes; there is a large population base within two hours drive of the project; two local...

Addressing Participant Validity in a Small Internet Health Survey (The Restore Study): Protocol and Recommendations for Survey Response Validation

PubMed Central

Dewitt, James; Capistrant, Benjamin; Kohli, Nidhi; Mitteldorf, Darryl; Merengwa, Enyinnaya; West, William

2018-01-01

Background While deduplication and cross-validation protocols have been recommended for large Web-based studies, protocols for survey response validation of smaller studies have not been published. Objective This paper reports the challenges of survey validation inherent in a small Web-based health survey research. Methods The subject population was North American, gay and bisexual, prostate cancer survivors, who represent an under-researched, hidden, difficult-to-recruit, minority-within-a-minority population. In 2015-2016, advertising on a large Web-based cancer survivor support network, using email and social media, yielded 478 completed surveys. Results Our manual deduplication and cross-validation protocol identified 289 survey submissions (289/478, 60.4%) as likely spam, most stemming from advertising on social media. The basic components of this deduplication and validation protocol are detailed. An unexpected challenge encountered was invalid survey responses evolving across the study period. This necessitated the static detection protocol be augmented with a dynamic one. Conclusions Five recommendations for validation of Web-based samples, especially with smaller difficult-to-recruit populations, are detailed. PMID:29691203

Utilizing the ultrasensitive Schistosoma up-converting phosphor lateral flow circulating anodic antigen (UCP-LF CAA) assay for sample pooling-strategies.

PubMed

Corstjens, Paul L A M; Hoekstra, Pytsje T; de Dood, Claudia J; van Dam, Govert J

2017-11-01

Methodological applications of the high sensitivity genus-specific Schistosoma CAA strip test, allowing detection of single worm active infections (ultimate sensitivity), are discussed for efficient utilization in sample pooling strategies. Besides relevant cost reduction, pooling of samples rather than individual testing can provide valuable data for large scale mapping, surveillance, and monitoring. The laboratory-based CAA strip test utilizes luminescent quantitative up-converting phosphor (UCP) reporter particles and a rapid user-friendly lateral flow (LF) assay format. The test includes a sample preparation step that permits virtually unlimited sample concentration with urine, reaching ultimate sensitivity (single worm detection) at 100% specificity. This facilitates testing large urine pools from many individuals with minimal loss of sensitivity and specificity. The test determines the average CAA level of the individuals in the pool thus indicating overall worm burden and prevalence. When requiring test results at the individual level, smaller pools need to be analysed with the pool-size based on expected prevalence or when unknown, on the average CAA level of a larger group; CAA negative pools do not require individual test results and thus reduce the number of tests. Straightforward pooling strategies indicate that at sub-population level the CAA strip test is an efficient assay for general mapping, identification of hotspots, determination of stratified infection levels, and accurate monitoring of mass drug administrations (MDA). At the individual level, the number of tests can be reduced i.e. in low endemic settings as the pool size can be increased as opposed to prevalence decrease. At the sub-population level, average CAA concentrations determined in urine pools can be an appropriate measure indicating worm burden. Pooling strategies allowing this type of large scale testing are feasible with the various CAA strip test formats and do not affect sensitivity and specificity. It allows cost efficient stratified testing and monitoring of worm burden at the sub-population level, ideally for large-scale surveillance generating hard data for performance of MDA programs and strategic planning when moving towards transmission-stop and elimination.

An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people

PubMed Central

Nelson, Matthew R.; Wegmann, Daniel; Ehm, Margaret G.; Kessner, Darren; St. Jean, Pamela; Verzilli, Claudio; Shen, Judong; Tang, Zhengzheng; Bacanu, Silviu-Alin; Fraser, Dana; Warren, Liling; Aponte, Jennifer; Zawistowski, Matthew; Liu, Xiao; Zhang, Hao; Zhang, Yong; Li, Jun; Li, Yun; Li, Li; Woollard, Peter; Topp, Simon; Hall, Matthew D.; Nangle, Keith; Wang, Jun; Abecasis, Gonçalo; Cardon, Lon R.; Zöllner, Sebastian; Whittaker, John C.; Chissoe, Stephanie L.; Novembre, John; Mooser, Vincent

2015-01-01

Rare genetic variants contribute to complex disease risk; however, the abundance of rare variants in human populations remains unknown. We explored this spectrum of variation by sequencing 202 genes encoding drug targets in 14,002 individuals. We find rare variants are abundant (one every 17 bases) and geographically localized, such that even with large sample sizes, rare variant catalogs will be largely incomplete. We used the observed patterns of variation to estimate population growth parameters, the proportion of variants in a given frequency class that are putatively deleterious, and mutation rates for each gene. Overall we conclude that, due to rapid population growth and weak purifying selection, human populations harbor an abundance of rare variants, many of which are deleterious and have relevance to understanding disease risk. PMID:22604722

Investigation of real tissue water equivalent path lengths using an efficient dose extinction method

NASA Astrophysics Data System (ADS)

Zhang, Rongxiao; Baer, Esther; Jee, Kyung-Wook; Sharp, Gregory C.; Flanz, Jay; Lu, Hsiao-Ming

2017-07-01

For proton therapy, an accurate conversion of CT HU to relative stopping power (RSP) is essential. Validation of the conversion based on real tissue samples is more direct than the current practice solely based on tissue substitutes and can potentially address variations over the population. Based on a novel dose extinction method, we measured water equivalent path lengths (WEPL) on animal tissue samples to evaluate the accuracy of CT HU to RSP conversion and potential variations over a population. A broad proton beam delivered a spread out Bragg peak to the samples sandwiched between a water tank and a 2D ion-chamber detector. WEPLs of the samples were determined from the transmission dose profiles measured as a function of the water level in the tank. Tissue substitute inserts and Lucite blocks with known WEPLs were used to validate the accuracy. A large number of real tissue samples were measured. Variations of WEPL over different batches of tissue samples were also investigated. The measured WEPLs were compared with those computed from CT scans with the Stoichiometric calibration method. WEPLs were determined within  ±0.5% percentage deviation (% std/mean) and  ±0.5% error for most of the tissue surrogate inserts and the calibration blocks. For biological tissue samples, percentage deviations were within  ±0.3%. No considerable difference (<1%) in WEPL was observed for the same type of tissue from different sources. The differences between measured WEPLs and those calculated from CT were within 1%, except for some bony tissues. Depending on the sample size, each dose extinction measurement took around 5 min to produce ~1000 WEPL values to be compared with calculations. This dose extinction system measures WEPL efficiently and accurately, which allows the validation of CT HU to RSP conversions based on the WEPL measured for a large number of samples and real tissues.

Tobacco, Marijuana, and Alcohol Use in University Students: A Cluster Analysis

PubMed Central

Primack, Brian A.; Kim, Kevin H.; Shensa, Ariel; Sidani, Jaime E.; Barnett, Tracey E.; Switzer, Galen E.

2012-01-01

Objective Segmentation of populations may facilitate development of targeted substance abuse prevention programs. We aimed to partition a national sample of university students according to profiles based on substance use. Participants We used 2008–2009 data from the National College Health Assessment from the American College Health Association. Our sample consisted of 111,245 individuals from 158 institutions. Method We partitioned the sample using cluster analysis according to current substance use behaviors. We examined the association of cluster membership with individual and institutional characteristics. Results Cluster analysis yielded six distinct clusters. Three individual factors—gender, year in school, and fraternity/sorority membership—were the most strongly associated with cluster membership. Conclusions In a large sample of university students, we were able to identify six distinct patterns of substance abuse. It may be valuable to target specific populations of college-aged substance users based on individual factors. However, comprehensive intervention will require a multifaceted approach. PMID:22686360

A panel of microsatellites to individually identify leopards and its application to leopard monitoring in human dominated landscapes.

PubMed

Mondol, Samrat; Navya, R; Athreya, Vidya; Sunagar, Kartik; Selvaraj, Velu Mani; Ramakrishnan, Uma

2009-12-04

Leopards are the most widely distributed of the large cats, ranging from Africa to the Russian Far East. Because of habitat fragmentation, high human population densities and the inherent adaptability of this species, they now occupy landscapes close to human settlements. As a result, they are the most common species involved in human wildlife conflict in India, necessitating their monitoring. However, their elusive nature makes such monitoring difficult. Recent advances in DNA methods along with non-invasive sampling techniques can be used to monitor populations and individuals across large landscapes including human dominated ones. In this paper, we describe a DNA-based method for leopard individual identification where we used fecal DNA samples to obtain genetic material. Further, we apply our methods to non-invasive samples collected in a human-dominated landscape to estimate the minimum number of leopards in this human-leopard conflict area in Western India. In this study, 25 of the 29 tested cross-specific microsatellite markers showed positive amplification in 37 wild-caught leopards. These loci revealed varied levels of polymorphism (four-12 alleles) and heterozygosity (0.05-0.79). Combining data on amplification success (including non-invasive samples) and locus specific polymorphisms, we showed that eight loci provide a sibling probability of identity of 0.0005, suggesting that this panel can be used to discriminate individuals in the wild. When this microsatellite panel was applied to fecal samples collected from a human-dominated landscape, we identified 7 individuals, with a sibling probability of identity of 0.001. Amplification success of field collected scats was up to 72%, and genotype error ranged from 0-7.4%. Our results demonstrated that the selected panel of eight microsatellite loci can conclusively identify leopards from various kinds of biological samples. Our methods can be used to monitor leopards over small and large landscapes to assess population trends, as well as could be tested for population assignment in forensic applications.

A panel of microsatellites to individually identify leopards and its application to leopard monitoring in human dominated landscapes

PubMed Central

2009-01-01

Background Leopards are the most widely distributed of the large cats, ranging from Africa to the Russian Far East. Because of habitat fragmentation, high human population densities and the inherent adaptability of this species, they now occupy landscapes close to human settlements. As a result, they are the most common species involved in human wildlife conflict in India, necessitating their monitoring. However, their elusive nature makes such monitoring difficult. Recent advances in DNA methods along with non-invasive sampling techniques can be used to monitor populations and individuals across large landscapes including human dominated ones. In this paper, we describe a DNA-based method for leopard individual identification where we used fecal DNA samples to obtain genetic material. Further, we apply our methods to non-invasive samples collected in a human-dominated landscape to estimate the minimum number of leopards in this human-leopard conflict area in Western India. Results In this study, 25 of the 29 tested cross-specific microsatellite markers showed positive amplification in 37 wild-caught leopards. These loci revealed varied levels of polymorphism (four-12 alleles) and heterozygosity (0.05-0.79). Combining data on amplification success (including non-invasive samples) and locus specific polymorphisms, we showed that eight loci provide a sibling probability of identity of 0.0005, suggesting that this panel can be used to discriminate individuals in the wild. When this microsatellite panel was applied to fecal samples collected from a human-dominated landscape, we identified 7 individuals, with a sibling probability of identity of 0.001. Amplification success of field collected scats was up to 72%, and genotype error ranged from 0-7.4%. Conclusion Our results demonstrated that the selected panel of eight microsatellite loci can conclusively identify leopards from various kinds of biological samples. Our methods can be used to monitor leopards over small and large landscapes to assess population trends, as well as could be tested for population assignment in forensic applications. PMID:19961605

Life-History Traits of the Miocene Hipparion concudense (Spain) Inferred from Bone Histological Structure

PubMed Central

Martinez-Maza, Cayetana; Alberdi, Maria Teresa; Nieto-Diaz, Manuel; Prado, José Luis

2014-01-01

Histological analyses of fossil bones have provided clues on the growth patterns and life history traits of several extinct vertebrates that would be unavailable for classical morphological studies. We analyzed the bone histology of Hipparion to infer features of its life history traits and growth pattern. Microscope analysis of thin sections of a large sample of humeri, femora, tibiae and metapodials of Hipparion concudense from the upper Miocene site of Los Valles de Fuentidueña (Segovia, Spain) has shown that the number of growth marks is similar among the different limb bones, suggesting that equivalent skeletochronological inferences for this Hipparion population might be achieved by means of any of the elements studied. Considering their abundance, we conducted a skeletechronological study based on the large sample of third metapodials from Los Valles de Fuentidueña together with another large sample from the Upper Miocene locality of Concud (Teruel, Spain). The data obtained enabled us to distinguish four age groups in both samples and to determine that Hipparion concudense tended to reach skeletal maturity during its third year of life. Integration of bone microstructure and skeletochronological data allowed us to identify ontogenetic changes in bone structure and growth rate and to distinguish three histologic ontogenetic stages corresponding to immature, subadult and adult individuals. Data on secondary osteon density revealed an increase in bone remodeling throughout the ontogenetic stages and a lesser degree thereof in the Concud population, which indicates different biomechanical stresses in the two populations, likely due to environmental differences. Several individuals showed atypical growth patterns in the Concud sample, which may also reflect environmental differences between the two localities. Finally, classification of the specimens’ age within groups enabled us to characterize the age structure of both samples, which is typical of attritional assemblages. PMID:25098950

Is family size related to adolescence mental hospitalization?

PubMed

Kylmänen, Paula; Hakko, Helinä; Räsänen, Pirkko; Riala, Kaisa

2010-05-15

The aim of this study was to investigate the association between family size and psychiatric disorders of underage adolescent psychiatric inpatients. The study sample consisted of 508 adolescents (age 12-17) admitted to psychiatric impatient care between April 2001 and March 2006. Diagnostic and Statistical Manual of Mental Disorders, fourth edition-based psychiatric diagnoses and variables measuring family size were obtained from the Schedule for Affective Disorder and Schizophrenia for School-Age Children Present and Lifetime (K-SADS-PL). The family size of the general Finnish population was used as a reference population. There was a significant difference between the family size of the inpatient adolescents and the general population: 17.0% of adolescents came from large families (with 6 or more children) while the percentage in the general population was 3.3. A girl from a large family had an about 4-fold risk of psychosis other than schizophrenia. However, large family size was not associated with a risk for schizophrenia. Large family size was overrepresented among underage adolescents admitted for psychiatric hospitalization in Northern Finland. Copyright 2009 Elsevier Ltd. All rights reserved.

Exposure to childhood adversity and deficits in emotion recognition: results from a large, population-based sample.

PubMed

Dunn, Erin C; Crawford, Katherine M; Soare, Thomas W; Button, Katherine S; Raffeld, Miriam R; Smith, Andrew D A C; Penton-Voak, Ian S; Munafò, Marcus R

2018-03-07

Emotion recognition skills are essential for social communication. Deficits in these skills have been implicated in mental disorders. Prior studies of clinical and high-risk samples have consistently shown that children exposed to adversity are more likely than their unexposed peers to have emotion recognition skills deficits. However, only one population-based study has examined this association. We analyzed data from children participating in the Avon Longitudinal Study of Parents and Children, a prospective birth cohort (n = 6,506). We examined the association between eight adversities, assessed repeatedly from birth to age 8 (caregiver physical or emotional abuse; sexual or physical abuse; maternal psychopathology; one adult in the household; family instability; financial stress; parent legal problems; neighborhood disadvantage) and the ability to recognize facial displays of emotion measured using the faces subtest of the Diagnostic Assessment of Non-Verbal Accuracy (DANVA) at age 8.5 years. In addition to examining the role of exposure (vs. nonexposure) to each type of adversity, we also evaluated the role of the timing, duration, and recency of each adversity using a Least Angle Regression variable selection procedure. Over three-quarters of the sample experienced at least one adversity. We found no evidence to support an association between emotion recognition deficits and previous exposure to adversity, either in terms of total lifetime exposure, timing, duration, or recency, or when stratifying by sex. Results from the largest population-based sample suggest that even extreme forms of adversity are unrelated to emotion recognition deficits as measured by the DANVA, suggesting the possible immutability of emotion recognition in the general population. These findings emphasize the importance of population-based studies to generate generalizable results. © 2018 Association for Child and Adolescent Mental Health.

Using the Johns Hopkins' Aggregated Diagnosis Groups (ADGs) to predict 1-year mortality in population-based cohorts of patients with diabetes in Ontario, Canada.

PubMed

Austin, P C; Shah, B R; Newman, A; Anderson, G M

2012-09-01

There are limited validated methods to ascertain comorbidities for risk adjustment in ambulatory populations of patients with diabetes using administrative health-care databases. The objective was to examine the ability of the Johns Hopkins' Aggregated Diagnosis Groups to predict mortality in population-based ambulatory samples of both incident and prevalent subjects with diabetes. Retrospective cohorts constructed using population-based administrative data. The incident cohort consisted of all 346,297 subjects diagnosed with diabetes between 1 April 2004 and 31 March 2008. The prevalent cohort consisted of all 879,849 subjects with pre-existing diabetes on 1 January, 2007. The outcome was death within 1 year of the subject's index date. A logistic regression model consisting of age, sex and indicator variables for 22 of the 32 Johns Hopkins' Aggregated Diagnosis Group categories had excellent discrimination for predicting mortality in incident diabetes patients: the c-statistic was 0.87 in an independent validation sample. A similar model had excellent discrimination for predicting mortality in prevalent diabetes patients: the c-statistic was 0.84 in an independent validation sample. Both models demonstrated very good calibration, denoting good agreement between observed and predicted mortality across the range of predicted mortality in which the large majority of subjects lay. For comparative purposes, regression models incorporating the Charlson comorbidity index, age and sex, age and sex, and age alone had poorer discrimination than the model that incorporated the Johns Hopkins' Aggregated Diagnosis Groups. Logistical regression models using age, sex and the John Hopkins' Aggregated Diagnosis Groups were able to accurately predict 1-year mortality in population-based samples of patients with diabetes. © 2011 The Authors. Diabetic Medicine © 2011 Diabetes UK.

Regional surnames and genetic structure in Great Britain.

PubMed

Kandt, Jens; Cheshire, James A; Longley, Paul A

2016-10-01

Following the increasing availability of DNA-sequenced data, the genetic structure of populations can now be inferred and studied in unprecedented detail. Across social science, this innovation is shaping new bio-social research agendas, attracting substantial investment in the collection of genetic, biological and social data for large population samples. Yet genetic samples are special because the precise populations that they represent are uncertain and ill-defined. Unlike most social surveys, a genetic sample's representativeness of the population cannot be established by conventional procedures of statistical inference, and the implications for population-wide generalisations about bio-social phenomena are little understood. In this paper, we seek to address these problems by linking surname data to a censored and geographically uneven sample of DNA scans, collected for the People of the British Isles study. Based on a combination of global and local spatial correspondence measures, we identify eight regions in Great Britain that are most likely to represent the geography of genetic structure of Great Britain's long-settled population. We discuss the implications of this regionalisation for bio-social investigations. We conclude that, as the often highly selective collection of DNA and biomarkers becomes a more common practice, geography is crucial to understanding variation in genetic information within diverse populations.

Origin of magnetization in lunar breccias - An example of thermal overprinting

NASA Technical Reports Server (NTRS)

Gose, W. A.; Strangway, D. W.; Pearce, G. W.

1978-01-01

Twenty six samples from seven hand specimens, collected from the station 6 boulder at the Apollo 17 landing site, were studied magnetically. The boulder is a breccia consisting of three lithologic units distinguished by their clast population. The direction of magnetization of samples from unit B which is almost devoid of large clasts cluster fairly well after alternating field demagnetization. Samples from unit C which is characterized by abundant large clasts up to 1 m in size do not contain a uniform direction of magnetization but the distribution is not random. Based on these data we propose that the natural remanent magnetization (NRM) in these breccias is the vector sum of two magnetizations, a pre-impact magnetization and a partial thermoremanence acquired during breccia formation. The relative contribution of the two components is controlled by the thermal history of the ejecta, which in turn is determined by its clast population. Depending on the clast population, the NRM can be a total thermoremanence, a partial thermoremanence plus a pre-impact magnetization, or a pre-impact magnetization. This model of thermal overprinting might be applicable to all lunar breccias of medium and higher metamorphic grade.

Surveillance Among Men Who have Sex with Men in the United States: A Comparison of Web-Based and Venue-Based Samples.

PubMed

Chen, Yen-Tyng; Bowles, Kristina; An, Qian; DiNenno, Elizabeth; Finlayson, Teresa; Hoots, Brooke; Paz-Bailey, Gabriela; Wejnert, Cyprian

2018-07-01

Although men who have sex with men (MSM) recruited through web-based and venue-based sampling methods have been compared, no large web-based and venue-based samples using similar survey instruments have been examined in the U.S. This study describes the differences in sociodemographic characteristics and risk behaviors between the 2012 Web-based HIV Behavioral Survey (n = 3221) and 2011 National HIV Behavioral Surveillance (n = 9256). Compared with participants in the venue-based sample, participants in the web-based sample were older, less likely to be black or Hispanic, more likely to have higher socioeconomic status, and more likely to have anal sex without a condom with their last male sex partner. Web-based participants were less likely to have multiple male sex partners, ever injected drugs, been tested for HIV in the past 12 months, and received free condoms than venue-based participants. The method for sampling MSM into a behavioral survey should consider the sub-population of MSM to be reached.

Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster

PubMed Central

Turner, Thomas L.; Stewart, Andrew D.; Fields, Andrew T.; Rice, William R.; Tarone, Aaron M.

2011-01-01

Body size is a classic quantitative trait with evolutionarily significant variation within many species. Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular, as well as quantitative traits in general. However, successful genome-wide association of genotype and phenotype may require very large sample sizes if alleles have low population frequencies or modest effects. As a complementary approach, we propose that population-based resequencing of experimentally evolved populations allows for considerable power to map functional variation. Here, we use this technique to investigate the genetic basis of natural variation in body size in Drosophila melanogaster. Significant differentiation of hundreds of loci in replicate selection populations supports the hypothesis that the genetic basis of body size variation is very polygenic in D. melanogaster. Significantly differentiated variants are limited to single genes at some loci, allowing precise hypotheses to be formed regarding causal polymorphisms, while other significant regions are large and contain many genes. By using significantly associated polymorphisms as a priori candidates in follow-up studies, these data are expected to provide considerable power to determine the genetic basis of natural variation in body size. PMID:21437274

[New population curves in spanish extremely preterm neonates].

PubMed

García-Muñoz Rodrigo, F; García-Alix Pérez, A; Figueras Aloy, J; Saavedra Santana, P

2014-08-01

Most anthropometric reference data for extremely preterm infants used in Spain are outdated and based on non-Spanish populations, or are derived from small hospital-based samples that failed to include neonates of borderline viability. To develop gender-specific, population-based curves for birth weight, length, and head circumference in extremely preterm Caucasian infants, using a large contemporary sample size of Spanish singletons. Anthropometric data from neonates ≤ 28 weeks of gestational age were collected between January 2002 and December 2010 using the Spanish database SEN1500. Gestational age was estimated according to obstetric data (early pregnancy ultrasound). The data were analyzed with the SPSS.20 package, and centile tables were created for males and females using the Cole and Green LMS method. This study presents the first population-based growth curves for extremely preterm infants, including those of borderline viability, in Spain. A sexual dimorphism is evident for all of the studied parameters, starting at early gestation. These new gender-specific and population-based data could be useful for the improvement of growth assessments of extremely preterm infants in our country, for the development of epidemiological studies, for the evaluation of temporal trends, and for clinical or public health interventions seeking to optimize fetal growth. Copyright © 2013 Asociación Española de Pediatría. Published by Elsevier Espana. All rights reserved.

Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct.

PubMed

Peacock, Mary M; Hekkala, Evon R; Kirchoff, Veronica S; Heki, Lisa G

2017-11-01

Currently one small, native population of the culturally and ecologically important Lahontan cutthroat trout ( Oncorhynchus clarkii henshawi , LCT, Federally listed) remains in the Truckee River watershed of northwestern Nevada and northeastern California. The majority of populations in this watershed were extirpated in the 1940s due to invasive species, overharvest, anthropogenic water consumption and changing precipitation regimes. In 1977, a population of cutthroat trout discovered in the Pilot Peak Mountains in the Bonneville basin of Utah, was putatively identified as the extirpated LCT lacustrine lineage native to Pyramid Lake in the Truckee River basin based on morphological and meristic characters. Our phylogenetic and Bayesian genotype clustering analyses of museum specimens collected from the large lakes (1872-1913) and contemporary samples collected from populations throughout the extant range provide evidence in support of a genetically distinct Truckee River basin origin for this population. Analysis of museum samples alone identified three distinct genotype clusters and historical connectivity among water bodies within the Truckee River basin. Baseline data from museum collections indicate that the extant Pilot Peak strain represents a remnant of the extirpated lacustrine lineage. Given the limitations on high-quality data when working with a sparse number of preserved museum samples, we acknowledge that, in the end, this may be a more complicated story. However, the paucity of remnant populations in the Truckee River watershed, in combination with data on the distribution of morphological, meristic and genetic data for Lahontan cutthroat trout, suggests that recovery strategies, particularly in the large lacustrine habitats should consider this lineage as an important part of the genetic legacy of this species.

Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct

PubMed Central

Hekkala, Evon R.; Kirchoff, Veronica S.; Heki, Lisa G.

2017-01-01

Currently one small, native population of the culturally and ecologically important Lahontan cutthroat trout (Oncorhynchus clarkii henshawi, LCT, Federally listed) remains in the Truckee River watershed of northwestern Nevada and northeastern California. The majority of populations in this watershed were extirpated in the 1940s due to invasive species, overharvest, anthropogenic water consumption and changing precipitation regimes. In 1977, a population of cutthroat trout discovered in the Pilot Peak Mountains in the Bonneville basin of Utah, was putatively identified as the extirpated LCT lacustrine lineage native to Pyramid Lake in the Truckee River basin based on morphological and meristic characters. Our phylogenetic and Bayesian genotype clustering analyses of museum specimens collected from the large lakes (1872–1913) and contemporary samples collected from populations throughout the extant range provide evidence in support of a genetically distinct Truckee River basin origin for this population. Analysis of museum samples alone identified three distinct genotype clusters and historical connectivity among water bodies within the Truckee River basin. Baseline data from museum collections indicate that the extant Pilot Peak strain represents a remnant of the extirpated lacustrine lineage. Given the limitations on high-quality data when working with a sparse number of preserved museum samples, we acknowledge that, in the end, this may be a more complicated story. However, the paucity of remnant populations in the Truckee River watershed, in combination with data on the distribution of morphological, meristic and genetic data for Lahontan cutthroat trout, suggests that recovery strategies, particularly in the large lacustrine habitats should consider this lineage as an important part of the genetic legacy of this species. PMID:29291110

Large-scale mapping and predictive modeling of submerged aquatic vegetation in a shallow eutrophic lake.

PubMed

Havens, Karl E; Harwell, Matthew C; Brady, Mark A; Sharfstein, Bruce; East, Therese L; Rodusky, Andrew J; Anson, Daniel; Maki, Ryan P

2002-04-09

A spatially intensive sampling program was developed for mapping the submerged aquatic vegetation (SAV) over an area of approximately 20,000 ha in a large, shallow lake in Florida, U.S. The sampling program integrates Geographic Information System (GIS) technology with traditional field sampling of SAV and has the capability of producing robust vegetation maps under a wide range of conditions, including high turbidity, variable depth (0 to 2 m), and variable sediment types. Based on sampling carried out in August-September 2000, we measured 1,050 to 4,300 ha of vascular SAV species and approximately 14,000 ha of the macroalga Chara spp. The results were similar to those reported in the early 1990s, when the last large-scale SAV sampling occurred. Occurrence of Chara was strongly associated with peat sediments, and maximal depths of occurrence varied between sediment types (mud, sand, rock, and peat). A simple model of Chara occurrence, based only on water depth, had an accuracy of 55%. It predicted occurrence of Chara over large areas where the plant actually was not found. A model based on sediment type and depth had an accuracy of 75% and produced a spatial map very similar to that based on observations. While this approach needs to be validated with independent data in order to test its general utility, we believe it may have application elsewhere. The simple modeling approach could serve as a coarse-scale tool for evaluating effects of water level management on Chara populations.

Estimation of stream salamander (Plethodontidae, Desmognathinae and Plethodontinae) populations in Shenandoah National Park, Virginia, USA

USGS Publications Warehouse

Jung, R.E.; Royle, J. Andrew; Sauer, J.R.; Addison, C.; Rau, R.D.; Shirk, J.L.; Whissel, J.C.

2005-01-01

Stream salamanders in the family Plethodontidae constitute a large biomass in and near headwater streams in the eastern United States and are promising indicators of stream ecosystem health. Many studies of stream salamanders have relied on population indices based on counts rather than population estimates based on techniques such as capture-recapture and removal. Application of estimation procedures allows the calculation of detection probabilities (the proportion of total animals present that are detected during a survey) and their associated sampling error, and may be essential for determining salamander population sizes and trends. In 1999, we conducted capture-recapture and removal population estimation methods for Desmognathus salamanders at six streams in Shenandoah National Park, Virginia, USA. Removal sampling appeared more efficient and detection probabilities from removal data were higher than those from capture-recapture. During 2001-2004, we used removal estimation at eight streams in the park to assess the usefulness of this technique for long-term monitoring of stream salamanders. Removal detection probabilities ranged from 0.39 to 0.96 for Desmognathus, 0.27 to 0.89 for Eurycea and 0.27 to 0.75 for northern spring (Gyrinophilus porphyriticus) and northern red (Pseudotriton ruber) salamanders across stream transects. Detection probabilities did not differ across years for Desmognathus and Eurycea, but did differ among streams for Desmognathus. Population estimates of Desmognathus decreased between 2001-2002 and 2003-2004 which may be related to changes in stream flow conditions. Removal-based procedures may be a feasible approach for population estimation of salamanders, but field methods should be designed to meet the assumptions of the sampling procedures. New approaches to estimating stream salamander populations are discussed.

Navigating complex sample analysis using national survey data.

PubMed

Saylor, Jennifer; Friedmann, Erika; Lee, Hyeon Joo

2012-01-01

The National Center for Health Statistics conducts the National Health and Nutrition Examination Survey and other national surveys with probability-based complex sample designs. Goals of national surveys are to provide valid data for the population of the United States. Analyses of data from population surveys present unique challenges in the research process but are valuable avenues to study the health of the United States population. The aim of this study was to demonstrate the importance of using complex data analysis techniques for data obtained with complex multistage sampling design and provide an example of analysis using the SPSS Complex Samples procedure. Illustration of challenges and solutions specific to secondary data analysis of national databases are described using the National Health and Nutrition Examination Survey as the exemplar. Oversampling of small or sensitive groups provides necessary estimates of variability within small groups. Use of weights without complex samples accurately estimates population means and frequency from the sample after accounting for over- or undersampling of specific groups. Weighting alone leads to inappropriate population estimates of variability, because they are computed as if the measures were from the entire population rather than a sample in the data set. The SPSS Complex Samples procedure allows inclusion of all sampling design elements, stratification, clusters, and weights. Use of national data sets allows use of extensive, expensive, and well-documented survey data for exploratory questions but limits analysis to those variables included in the data set. The large sample permits examination of multiple predictors and interactive relationships. Merging data files, availability of data in several waves of surveys, and complex sampling are techniques used to provide a representative sample but present unique challenges. In sophisticated data analysis techniques, use of these data is optimized.

One-step estimation of networked population size: Respondent-driven capture-recapture with anonymity.

PubMed

Khan, Bilal; Lee, Hsuan-Wei; Fellows, Ian; Dombrowski, Kirk

2018-01-01

Size estimation is particularly important for populations whose members experience disproportionate health issues or pose elevated health risks to the ambient social structures in which they are embedded. Efforts to derive size estimates are often frustrated when the population is hidden or hard-to-reach in ways that preclude conventional survey strategies, as is the case when social stigma is associated with group membership or when group members are involved in illegal activities. This paper extends prior research on the problem of network population size estimation, building on established survey/sampling methodologies commonly used with hard-to-reach groups. Three novel one-step, network-based population size estimators are presented, for use in the context of uniform random sampling, respondent-driven sampling, and when networks exhibit significant clustering effects. We give provably sufficient conditions for the consistency of these estimators in large configuration networks. Simulation experiments across a wide range of synthetic network topologies validate the performance of the estimators, which also perform well on a real-world location-based social networking data set with significant clustering. Finally, the proposed schemes are extended to allow them to be used in settings where participant anonymity is required. Systematic experiments show favorable tradeoffs between anonymity guarantees and estimator performance. Taken together, we demonstrate that reasonable population size estimates are derived from anonymous respondent driven samples of 250-750 individuals, within ambient populations of 5,000-40,000. The method thus represents a novel and cost-effective means for health planners and those agencies concerned with health and disease surveillance to estimate the size of hidden populations. We discuss limitations and future work in the concluding section.

An adaptive two-stage sequential design for sampling rare and clustered populations

USGS Publications Warehouse

Brown, J.A.; Salehi, M.M.; Moradi, M.; Bell, G.; Smith, D.R.

2008-01-01

How to design an efficient large-area survey continues to be an interesting question for ecologists. In sampling large areas, as is common in environmental studies, adaptive sampling can be efficient because it ensures survey effort is targeted to subareas of high interest. In two-stage sampling, higher density primary sample units are usually of more interest than lower density primary units when populations are rare and clustered. Two-stage sequential sampling has been suggested as a method for allocating second stage sample effort among primary units. Here, we suggest a modification: adaptive two-stage sequential sampling. In this method, the adaptive part of the allocation process means the design is more flexible in how much extra effort can be directed to higher-abundance primary units. We discuss how best to design an adaptive two-stage sequential sample. ?? 2008 The Society of Population Ecology and Springer.

Protection motivation theory and physical activity: a longitudinal test among a representative population sample of Canadian adults.

PubMed

Plotnikoff, Ronald C; Rhodes, Ryan E; Trinh, Linda

2009-11-01

The purpose of this study was to examine the Protection Motivation Theory (PMT) to predict physical activity (PA) behaviour in a large, population-based sample of adults. One thousand six hundred and two randomly selected individuals completed two telephone interviews over two consecutive six-month periods assessing PMT constructs. PMT explained 35 per cent and 20 per cent of the variance in intention and behaviour respectively. Coping cognitions as moderators of threat explained 1 per cent of the variance in intention and behaviour. Age and gender as moderators of threat did not provide additional variance in the models. We conclude that salient PMT predictors (e.g. self-efficacy) may guide the development of effective PA interventions in the general population.

Effect of aircraft noise on the equilibrium of airport residents: Longitudinal study around Roissy, phase 3

NASA Technical Reports Server (NTRS)

Francois, J.

1981-01-01

The effects of airplane noise on the mental equilibrium of residents living near airports are discussed, and based on population sample surveys involving health questionnaires and self-administered personality tests. Progressive changes were observed on the part of residents living near a large airport.

Overeating and Binge Eating in Emerging Adulthood: 10-Year Stability and Risk Factors

ERIC Educational Resources Information Center

Goldschmidt, Andrea B.; Wall, Melanie M.; Zhang, Jun; Loth, Katie A.; Neumark-Sztainer, Dianne

2016-01-01

Overeating (eating an unusually large amount of food) and binge eating (overeating with loss of control [LOC]) predict adverse health consequences in adolescence. We aimed to characterize the stability of and risk factors for these distinct but interrelated constructs during critical developmental transitions. We used a population-based sample (n…

The Population Reference Sample, POPRES: A Resource for Population, Disease, and Pharmacological Genetics Research

PubMed Central

Nelson, Matthew R.; Bryc, Katarzyna; King, Karen S.; Indap, Amit; Boyko, Adam R.; Novembre, John; Briley, Linda P.; Maruyama, Yuka; Waterworth, Dawn M.; Waeber, Gérard; Vollenweider, Peter; Oksenberg, Jorge R.; Hauser, Stephen L.; Stirnadel, Heide A.; Kooner, Jaspal S.; Chambers, John C.; Jones, Brendan; Mooser, Vincent; Bustamante, Carlos D.; Roses, Allen D.; Burns, Daniel K.; Ehm, Margaret G.; Lai, Eric H.

2008-01-01

Technological and scientific advances, stemming in large part from the Human Genome and HapMap projects, have made large-scale, genome-wide investigations feasible and cost effective. These advances have the potential to dramatically impact drug discovery and development by identifying genetic factors that contribute to variation in disease risk as well as drug pharmacokinetics, treatment efficacy, and adverse drug reactions. In spite of the technological advancements, successful application in biomedical research would be limited without access to suitable sample collections. To facilitate exploratory genetics research, we have assembled a DNA resource from a large number of subjects participating in multiple studies throughout the world. This growing resource was initially genotyped with a commercially available genome-wide 500,000 single-nucleotide polymorphism panel. This project includes nearly 6,000 subjects of African-American, East Asian, South Asian, Mexican, and European origin. Seven informative axes of variation identified via principal-component analysis (PCA) of these data confirm the overall integrity of the data and highlight important features of the genetic structure of diverse populations. The potential value of such extensively genotyped collections is illustrated by selection of genetically matched population controls in a genome-wide analysis of abacavir-associated hypersensitivity reaction. We find that matching based on country of origin, identity-by-state distance, and multidimensional PCA do similarly well to control the type I error rate. The genotype and demographic data from this reference sample are freely available through the NCBI database of Genotypes and Phenotypes (dbGaP). PMID:18760391

Multimethod, multistate Bayesian hierarchical modeling approach for use in regional monitoring of wolves.

PubMed

Jiménez, José; García, Emilio J; Llaneza, Luis; Palacios, Vicente; González, Luis Mariano; García-Domínguez, Francisco; Múñoz-Igualada, Jaime; López-Bao, José Vicente

2016-08-01

In many cases, the first step in large-carnivore management is to obtain objective, reliable, and cost-effective estimates of population parameters through procedures that are reproducible over time. However, monitoring predators over large areas is difficult, and the data have a high level of uncertainty. We devised a practical multimethod and multistate modeling approach based on Bayesian hierarchical-site-occupancy models that combined multiple survey methods to estimate different population states for use in monitoring large predators at a regional scale. We used wolves (Canis lupus) as our model species and generated reliable estimates of the number of sites with wolf reproduction (presence of pups). We used 2 wolf data sets from Spain (Western Galicia in 2013 and Asturias in 2004) to test the approach. Based on howling surveys, the naïve estimation (i.e., estimate based only on observations) of the number of sites with reproduction was 9 and 25 sites in Western Galicia and Asturias, respectively. Our model showed 33.4 (SD 9.6) and 34.4 (3.9) sites with wolf reproduction, respectively. The number of occupied sites with wolf reproduction was 0.67 (SD 0.19) and 0.76 (0.11), respectively. This approach can be used to design more cost-effective monitoring programs (i.e., to define the sampling effort needed per site). Our approach should inspire well-coordinated surveys across multiple administrative borders and populations and lead to improved decision making for management of large carnivores on a landscape level. The use of this Bayesian framework provides a simple way to visualize the degree of uncertainty around population-parameter estimates and thus provides managers and stakeholders an intuitive approach to interpreting monitoring results. Our approach can be widely applied to large spatial scales in wildlife monitoring where detection probabilities differ between population states and where several methods are being used to estimate different population parameters. © 2016 Society for Conservation Biology.

Population clustering based on copy number variations detected from next generation sequencing data.

PubMed

Duan, Junbo; Zhang, Ji-Gang; Wan, Mingxi; Deng, Hong-Wen; Wang, Yu-Ping

2014-08-01

Copy number variations (CNVs) can be used as significant bio-markers and next generation sequencing (NGS) provides a high resolution detection of these CNVs. But how to extract features from CNVs and further apply them to genomic studies such as population clustering have become a big challenge. In this paper, we propose a novel method for population clustering based on CNVs from NGS. First, CNVs are extracted from each sample to form a feature matrix. Then, this feature matrix is decomposed into the source matrix and weight matrix with non-negative matrix factorization (NMF). The source matrix consists of common CNVs that are shared by all the samples from the same group, and the weight matrix indicates the corresponding level of CNVs from each sample. Therefore, using NMF of CNVs one can differentiate samples from different ethnic groups, i.e. population clustering. To validate the approach, we applied it to the analysis of both simulation data and two real data set from the 1000 Genomes Project. The results on simulation data demonstrate that the proposed method can recover the true common CNVs with high quality. The results on the first real data analysis show that the proposed method can cluster two family trio with different ancestries into two ethnic groups and the results on the second real data analysis show that the proposed method can be applied to the whole-genome with large sample size consisting of multiple groups. Both results demonstrate the potential of the proposed method for population clustering.

Men, women…who cares? A population-based study on sex differences and gender roles in empathy and moral cognition.

PubMed

Baez, Sandra; Flichtentrei, Daniel; Prats, María; Mastandueno, Ricardo; García, Adolfo M; Cetkovich, Marcelo; Ibáñez, Agustín

2017-01-01

Research on sex differences in empathy has revealed mixed findings. Whereas experimental and neuropsychological measures show no consistent sex effect, self-report data consistently indicates greater empathy in women. However, available results mainly come from separate populations with relatively small samples, which may inflate effect sizes and hinder comparability between both empirical corpora. To elucidate the issue, we conducted two large-scale studies. First, we examined whether sex differences emerge in a large population-based sample (n = 10,802) when empathy is measured with an experimental empathy-for-pain paradigm. Moreover, we investigated the relationship between empathy and moral judgment. In the second study, a subsample (n = 334) completed a self-report empathy questionnaire. Results showed some sex differences in the experimental paradigm, but with minuscule effect sizes. Conversely, women did portray themselves as more empathic through self-reports. In addition, utilitarian responses to moral dilemmas were less frequent in women, although these differences also had small effect sizes. These findings suggest that sex differences in empathy are highly driven by the assessment measure. In particular, self-reports may induce biases leading individuals to assume gender-role stereotypes. Awareness of the role of measurement instruments in this field may hone our understanding of the links between empathy, sex differences, and gender roles.

Multiple data sources improve DNA-based mark-recapture population estimates of grizzly bears.

PubMed

Boulanger, John; Kendall, Katherine C; Stetz, Jeffrey B; Roon, David A; Waits, Lisette P; Paetkau, David

2008-04-01

A fundamental challenge to estimating population size with mark-recapture methods is heterogeneous capture probabilities and subsequent bias of population estimates. Confronting this problem usually requires substantial sampling effort that can be difficult to achieve for some species, such as carnivores. We developed a methodology that uses two data sources to deal with heterogeneity and applied this to DNA mark-recapture data from grizzly bears (Ursus arctos). We improved population estimates by incorporating additional DNA "captures" of grizzly bears obtained by collecting hair from unbaited bear rub trees concurrently with baited, grid-based, hair snag sampling. We consider a Lincoln-Petersen estimator with hair snag captures as the initial session and rub tree captures as the recapture session and develop an estimator in program MARK that treats hair snag and rub tree samples as successive sessions. Using empirical data from a large-scale project in the greater Glacier National Park, Montana, USA, area and simulation modeling we evaluate these methods and compare the results to hair-snag-only estimates. Empirical results indicate that, compared with hair-snag-only data, the joint hair-snag-rub-tree methods produce similar but more precise estimates if capture and recapture rates are reasonably high for both methods. Simulation results suggest that estimators are potentially affected by correlation of capture probabilities between sample types in the presence of heterogeneity. Overall, closed population Huggins-Pledger estimators showed the highest precision and were most robust to sparse data, heterogeneity, and capture probability correlation among sampling types. Results also indicate that these estimators can be used when a segment of the population has zero capture probability for one of the methods. We propose that this general methodology may be useful for other species in which mark-recapture data are available from multiple sources.

The effects of isolation on the demography and genetic diversity of long-lived species: Implications for conservation and management of the gopher tortoise (Gopherus polyphemus)

USGS Publications Warehouse

Ennen, J.R.; Birkhead, R.D.; Kreiser, B.R.; Gaillard, D.L.; Qualls, C.P.; Lovich, J.E.

2011-01-01

In the southeastern United States, habitat loss has fragmented the landscape and isolated many populations of this region's flora and fauna, which has presumably resulted in smaller population sizes and reduced levels of genetic diversity. For example, forestry practices and anthropogenic disturbances are both cited as factors fragmenting the once extensive range of Gopherus polyphemus. One localized, but extreme, source of fragmentation was the impoundment of the Chattahoochee River in 1963 to form Walter F. George Reservoir along the border of Georgia and Alabama. The formation of this reservoir isolated populations of G. polyphemus on two newly created islands providing a natural laboratory to explore the demographics and genetic effects of fragmentation on a long-lived species. These populations were first surveyed in 1984 and, 21 years later, we revisited them to collect demographic data and tissue samples for genetic analysis. We genotyped all individuals for 10 microsatellite loci, and we tested these data for bottlenecks and compared them to levels of genetic diversity for populations from other portions of the range. We found 45 and two individuals on the larger and smaller islands, respectively. On the large island, however, the population size was identical to the 1984 survey. Only the population structure based on estimated age differed between the 1984 and 2004 surveys, while population size structure based on carapace length, sex ratio, and sex-specific growth rates did not differ. The population of the large island showed genetic evidence of a past bottleneck. The genetic diversity indices from the population of the large island, however, were comparable to or greater than those found at mainland sites, in particular from western populations.

Phylogeography of Y-chromosome haplogroup O3a2b2-N6 reveals patrilineal traces of Austronesian populations on the eastern coastal regions of Asia

PubMed Central

Teo, Yik-Ying; Huang, Yun-Zhi; Wang, Ling-Xiang; Yu, Ge; Saw, Woei-Yuh; Ong, Rick Twee-Hee; Lu, Yan; Zhang, Chao; Xu, Shu-Hua; Jin, Li; Li, Hui

2017-01-01

Austronesian diffusion is considered one of the greatest dispersals in human history; it led to the peopling of an extremely vast region, ranging from Madagascar in the Indian Ocean to Easter Island in Remote Oceania. The Y-chromosome haplogroup O3a2b*-P164(xM134), a predominant paternal lineage of Austronesian populations, is found at high frequencies in Polynesian populations. However, the internal phylogeny of this haplogroup remains poorly investigated. In this study, we analyzed -seventeen Y-chromosome sequences of haplogroup O3a2b*-P164(xM134) and generated a revised phylogenetic tree of this lineage based on 310 non-private Y-chromosome polymorphisms. We discovered that all available O3a2b*-P164(xM134) samples belong to the newly defined haplogroup O3a2b2-N6 and samples from Austronesian populations belong to the sublineage O3a2b2a2-F706. Additionally, we genotyped a series of Y-chromosome polymorphisms in a large collection of samples from China. We confirmed that the sublineage O3a2b2a2b-B451 is unique to Austronesian populations. We found that O3a2b2-N6 samples are widely distributed on the eastern coastal regions of Asia, from Korea to Vietnam. Furthermore, we propose- that the O3a2b2a2b-B451 lineage represents a genetic connection between ancestors of Austronesian populations and ancient populations in North China, where foxtail millet was domesticated about 11,000 years ago. The large number of newly defined Y-chromosome polymorphisms and the revised phylogenetic tree of O3a2b2-N6 will be helpful to explore the origin of proto-Austronesians and the early diffusion process of Austronesian populations. PMID:28380021

The Queensland study of Melanoma: Environmental and Genetic Associations (Q-MEGA). Study design, baseline characteristics, and repeatability of phenotype and sun exposure measures

PubMed Central

Baxter, Amanda J.; Hughes, Maria Celia; Kvaskoff, Marina; Siskind, Victor; Shekar, Sri; Aitken, Joanne F.; Green, Adele C.; Duffy, David L.; Hayward, Nicholas K.; Martin, Nicholas G.; Whiteman, David C.

2013-01-01

Cutaneous malignant melanoma (CMM) is a major health issue in Queensland, Australia which has the world’s highest incidence. Recent molecular and epidemiologic studies suggest that CMM arises through multiple etiological pathways involving gene-environment interactions. Understanding the potential mechanisms leading to CMM requires larger studies than those previously conducted. This article describes the design and baseline characteristics of Q-MEGA, the Queensland study of Melanoma: Environmental and Genetic Associations, which followed-up four population-based samples of CMM patients in Queensland, including children, adolescents, men aged over 50, and a large sample of adult cases and their families, including twins. Q-MEGA aims to investigate the roles of genetic and environmental factors, and their interaction, in the etiology of melanoma. 3,471 participants took part in the follow-up study and were administered a computer-assisted telephone interview in 2002–2005. Updated data on environmental and phenotypic risk factors, and 2,777 blood samples were collected from interviewed participants as well as a subset of relatives. This study provides a large and well-described population-based sample of CMM cases with follow-up data. Characteristics of the cases and repeatability of sun exposure and phenotype measures between the baseline and the follow-up surveys, from six to 17 years later, are also described. PMID:18361720

Estimating population trends with a linear model

USGS Publications Warehouse

Bart, Jonathan; Collins, Brian D.; Morrison, R.I.G.

2003-01-01

We describe a simple and robust method for estimating trends in population size. The method may be used with Breeding Bird Survey data, aerial surveys, point counts, or any other program of repeated surveys at permanent locations. Surveys need not be made at each location during each survey period. The method differs from most existing methods in being design based, rather than model based. The only assumptions are that the nominal sampling plan is followed and that sample size is large enough for use of the t-distribution. Simulations based on two bird data sets from natural populations showed that the point estimate produced by the linear model was essentially unbiased even when counts varied substantially and 25% of the complete data set was missing. The estimating-equation approach, often used to analyze Breeding Bird Survey data, performed similarly on one data set but had substantial bias on the second data set, in which counts were highly variable. The advantages of the linear model are its simplicity, flexibility, and that it is self-weighting. A user-friendly computer program to carry out the calculations is available from the senior author.

Horvitz-Thompson survey sample methods for estimating large-scale animal abundance

USGS Publications Warehouse

Samuel, M.D.; Garton, E.O.

1994-01-01

Large-scale surveys to estimate animal abundance can be useful for monitoring population status and trends, for measuring responses to management or environmental alterations, and for testing ecological hypotheses about abundance. However, large-scale surveys may be expensive and logistically complex. To ensure resources are not wasted on unattainable targets, the goals and uses of each survey should be specified carefully and alternative methods for addressing these objectives always should be considered. During survey design, the impoflance of each survey error component (spatial design, propofiion of detected animals, precision in detection) should be considered carefully to produce a complete statistically based survey. Failure to address these three survey components may produce population estimates that are inaccurate (biased low), have unrealistic precision (too precise) and do not satisfactorily meet the survey objectives. Optimum survey design requires trade-offs in these sources of error relative to the costs of sampling plots and detecting animals on plots, considerations that are specific to the spatial logistics and survey methods. The Horvitz-Thompson estimators provide a comprehensive framework for considering all three survey components during the design and analysis of large-scale wildlife surveys. Problems of spatial and temporal (especially survey to survey) heterogeneity in detection probabilities have received little consideration, but failure to account for heterogeneity produces biased population estimates. The goal of producing unbiased population estimates is in conflict with the increased variation from heterogeneous detection in the population estimate. One solution to this conflict is to use an MSE-based approach to achieve a balance between bias reduction and increased variation. Further research is needed to develop methods that address spatial heterogeneity in detection, evaluate the effects of temporal heterogeneity on survey objectives and optimize decisions related to survey bias and variance. Finally, managers and researchers involved in the survey design process must realize that obtaining the best survey results requires an interactive and recursive process of survey design, execution, analysis and redesign. Survey refinements will be possible as further knowledge is gained on the actual abundance and distribution of the population and on the most efficient techniques for detection animals.

The Association of Hot Red Chili Pepper Consumption and Mortality: A Large Population-Based Cohort Study

PubMed Central

Chopan, Mustafa

2017-01-01

The evidence base for the health effects of spice consumption is insufficient, with only one large population-based study and no reports from Europe or North America. Our objective was to analyze the association between consumption of hot red chili peppers and mortality, using a population-based prospective cohort from the National Health and Nutritional Examination Survey (NHANES) III, a representative sample of US noninstitutionalized adults, in which participants were surveyed from 1988 to 1994. The frequency of hot red chili pepper consumption was measured in 16,179 participants at least 18 years of age. Total and cause-specific mortality were the main outcome measures. During 273,877 person-years of follow-up (median 18.9 years), a total of 4,946 deaths were observed. Total mortality for participants who consumed hot red chili peppers was 21.6% compared to 33.6% for those who did not (absolute risk reduction of 12%; relative risk of 0.64). Adjusted for demographic, lifestyle, and clinical characteristics, the hazard ratio was 0.87 (P = 0.01; 95% Confidence Interval 0.77, 0.97). Consumption of hot red chili peppers was associated with a 13% reduction in the instantaneous hazard of death. Similar, but statistically nonsignificant trends were seen for deaths from vascular disease, but not from other causes. In this large population-based prospective study, the consumption of hot red chili pepper was associated with reduced mortality. Hot red chili peppers may be a beneficial component of the diet. PMID:28068423

IMa2p - Parallel MCMC and inference of ancient demography under the Isolation with Migration (IM) model

PubMed Central

Sethuraman, Arun; Hey, Jody

2015-01-01

IMa2 and related programs are used to study the divergence of closely related species and of populations within species. These methods are based on the sampling of genealogies using MCMC, and they can proceed quite slowly for larger data sets. We describe a parallel implementation, called IMa2p, that provides a nearly linear increase in genealogy sampling rate with the number of processors in use. IMa2p is written in OpenMPI and C++, and scales well for demographic analyses of a large number of loci and populations, which are difficult to study using the serial version of the program. PMID:26059786

SNP-VISTA: An interactive SNP visualization tool

PubMed Central

Shah, Nameeta; Teplitsky, Michael V; Minovitsky, Simon; Pennacchio, Len A; Hugenholtz, Philip; Hamann, Bernd; Dubchak, Inna L

2005-01-01

Background Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide Polymorphisms (SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of eukaryotic species. With today's technological capabilities, it has become possible to re-sequence a large set of appropriate candidate genes in individuals with a given disease in an attempt to identify causative mutations. In addition, SNPs have been used extensively in efforts to study the evolution of microbial populations, and the recent application of random shotgun sequencing to environmental samples enables more extensive SNP analysis of co-occurring and co-evolving microbial populations. The program is available at [1]. Results We have developed and present two modifications of an interactive visualization tool, SNP-VISTA, to aid in the analyses of the following types of data: A. Large-scale re-sequence data of disease-related genes for discovery of associated and/or causative alleles (GeneSNP-VISTA). B. Massive amounts of ecogenomics data for studying homologous recombination in microbial populations (EcoSNP-VISTA). The main features and capabilities of SNP-VISTA are: 1) mapping of SNPs to gene structure; 2) classification of SNPs, based on their location in the gene, frequency of occurrence in samples and allele composition; 3) clustering, based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences; 4) integration of protein evolutionary conservation visualization; and 5) display of automatically calculated recombination points that are user-editable. Conclusion The main strength of SNP-VISTA is its graphical interface and use of visual representations, which support interactive exploration and hence better understanding of large-scale SNP data by the user. PMID:16336665

Evaluating sample allocation and effort in detecting population differentiation for discrete and continuously distributed individuals

Treesearch

Erin L. Landguth; Michael K. Schwartz

2014-01-01

One of the most pressing issues in spatial genetics concerns sampling. Traditionally, substructure and gene flow are estimated for individuals sampled within discrete populations. Because many species may be continuously distributed across a landscape without discrete boundaries, understanding sampling issues becomes paramount. Given large-scale, geographically broad...

The Impact of Accelerating Faster than Exponential Population Growth on Genetic Variation

PubMed Central

Reppell, Mark; Boehnke, Michael; Zöllner, Sebastian

2014-01-01

Current human sequencing projects observe an abundance of extremely rare genetic variation, suggesting recent acceleration of population growth. To better understand the impact of such accelerating growth on the quantity and nature of genetic variation, we present a new class of models capable of incorporating faster than exponential growth in a coalescent framework. Our work shows that such accelerated growth affects only the population size in the recent past and thus large samples are required to detect the models’ effects on patterns of variation. When we compare models with fixed initial growth rate, models with accelerating growth achieve very large current population sizes and large samples from these populations contain more variation than samples from populations with constant growth. This increase is driven almost entirely by an increase in singleton variation. Moreover, linkage disequilibrium decays faster in populations with accelerating growth. When we instead condition on current population size, models with accelerating growth result in less overall variation and slower linkage disequilibrium decay compared to models with exponential growth. We also find that pairwise linkage disequilibrium of very rare variants contains information about growth rates in the recent past. Finally, we demonstrate that models of accelerating growth may substantially change estimates of present-day effective population sizes and growth times. PMID:24381333

The impact of accelerating faster than exponential population growth on genetic variation.

PubMed

Reppell, Mark; Boehnke, Michael; Zöllner, Sebastian

2014-03-01

Current human sequencing projects observe an abundance of extremely rare genetic variation, suggesting recent acceleration of population growth. To better understand the impact of such accelerating growth on the quantity and nature of genetic variation, we present a new class of models capable of incorporating faster than exponential growth in a coalescent framework. Our work shows that such accelerated growth affects only the population size in the recent past and thus large samples are required to detect the models' effects on patterns of variation. When we compare models with fixed initial growth rate, models with accelerating growth achieve very large current population sizes and large samples from these populations contain more variation than samples from populations with constant growth. This increase is driven almost entirely by an increase in singleton variation. Moreover, linkage disequilibrium decays faster in populations with accelerating growth. When we instead condition on current population size, models with accelerating growth result in less overall variation and slower linkage disequilibrium decay compared to models with exponential growth. We also find that pairwise linkage disequilibrium of very rare variants contains information about growth rates in the recent past. Finally, we demonstrate that models of accelerating growth may substantially change estimates of present-day effective population sizes and growth times.

DESCARTES' RULE OF SIGNS AND THE IDENTIFIABILITY OF POPULATION DEMOGRAPHIC MODELS FROM GENOMIC VARIATION DATA.

PubMed

Bhaskar, Anand; Song, Yun S

2014-01-01

The sample frequency spectrum (SFS) is a widely-used summary statistic of genomic variation in a sample of homologous DNA sequences. It provides a highly efficient dimensional reduction of large-scale population genomic data and its mathematical dependence on the underlying population demography is well understood, thus enabling the development of efficient inference algorithms. However, it has been recently shown that very different population demographies can actually generate the same SFS for arbitrarily large sample sizes. Although in principle this nonidentifiability issue poses a thorny challenge to statistical inference, the population size functions involved in the counterexamples are arguably not so biologically realistic. Here, we revisit this problem and examine the identifiability of demographic models under the restriction that the population sizes are piecewise-defined where each piece belongs to some family of biologically-motivated functions. Under this assumption, we prove that the expected SFS of a sample uniquely determines the underlying demographic model, provided that the sample is sufficiently large. We obtain a general bound on the sample size sufficient for identifiability; the bound depends on the number of pieces in the demographic model and also on the type of population size function in each piece. In the cases of piecewise-constant, piecewise-exponential and piecewise-generalized-exponential models, which are often assumed in population genomic inferences, we provide explicit formulas for the bounds as simple functions of the number of pieces. Lastly, we obtain analogous results for the "folded" SFS, which is often used when there is ambiguity as to which allelic type is ancestral. Our results are proved using a generalization of Descartes' rule of signs for polynomials to the Laplace transform of piecewise continuous functions.

DESCARTES’ RULE OF SIGNS AND THE IDENTIFIABILITY OF POPULATION DEMOGRAPHIC MODELS FROM GENOMIC VARIATION DATA1

PubMed Central

Bhaskar, Anand; Song, Yun S.

2016-01-01

The sample frequency spectrum (SFS) is a widely-used summary statistic of genomic variation in a sample of homologous DNA sequences. It provides a highly efficient dimensional reduction of large-scale population genomic data and its mathematical dependence on the underlying population demography is well understood, thus enabling the development of efficient inference algorithms. However, it has been recently shown that very different population demographies can actually generate the same SFS for arbitrarily large sample sizes. Although in principle this nonidentifiability issue poses a thorny challenge to statistical inference, the population size functions involved in the counterexamples are arguably not so biologically realistic. Here, we revisit this problem and examine the identifiability of demographic models under the restriction that the population sizes are piecewise-defined where each piece belongs to some family of biologically-motivated functions. Under this assumption, we prove that the expected SFS of a sample uniquely determines the underlying demographic model, provided that the sample is sufficiently large. We obtain a general bound on the sample size sufficient for identifiability; the bound depends on the number of pieces in the demographic model and also on the type of population size function in each piece. In the cases of piecewise-constant, piecewise-exponential and piecewise-generalized-exponential models, which are often assumed in population genomic inferences, we provide explicit formulas for the bounds as simple functions of the number of pieces. Lastly, we obtain analogous results for the “folded” SFS, which is often used when there is ambiguity as to which allelic type is ancestral. Our results are proved using a generalization of Descartes’ rule of signs for polynomials to the Laplace transform of piecewise continuous functions. PMID:28018011

Categorizing Cells on the Basis of their Chemical Profiles: Progress in Single-Cell Mass Spectrometry.

PubMed

Comi, Troy J; Do, Thanh D; Rubakhin, Stanislav S; Sweedler, Jonathan V

2017-03-22

The chemical differences between individual cells within large cellular populations provide unique information on organisms' homeostasis and the development of diseased states. Even genetically identical cell lineages diverge due to local microenvironments and stochastic processes. The minute sample volumes and low abundance of some constituents in cells hinder our understanding of cellular heterogeneity. Although amplification methods facilitate single-cell genomics and transcriptomics, the characterization of metabolites and proteins remains challenging both because of the lack of effective amplification approaches and the wide diversity in cellular constituents. Mass spectrometry has become an enabling technology for the investigation of individual cellular metabolite profiles with its exquisite sensitivity, large dynamic range, and ability to characterize hundreds to thousands of compounds. While advances in instrumentation have improved figures of merit, acquiring measurements at high throughput and sampling from large populations of cells are still not routine. In this Perspective, we highlight the current trends and progress in mass-spectrometry-based analysis of single cells, with a focus on the technologies that will enable the next generation of single-cell measurements.

Inferring microevolution from museum collections and resampling: lessons learned from Cepaea.

PubMed

Ożgo, Małgorzata; Liew, Thor-Seng; Webster, Nicole B; Schilthuizen, Menno

2017-01-01

Natural history collections are an important and largely untapped source of long-term data on evolutionary changes in wild populations. Here, we utilize three large geo-referenced sets of samples of the common European land-snail Cepaea nemoralis stored in the collection of Naturalis Biodiversity Center in Leiden, the Netherlands. Resampling of these populations allowed us to gain insight into changes occurring over 95, 69, and 50 years. Cepaea nemoralis is polymorphic for the colour and banding of the shell; the mode of inheritance of these patterns is known, and the polymorphism is under both thermal and predatory selection. At two sites the general direction of changes was towards lighter shells (yellow and less heavily banded), which is consistent with predictions based on on-going climatic change. At one site no directional changes were detected. At all sites there were significant shifts in morph frequencies between years, and our study contributes to the recognition that short-term changes in the states of populations often exceed long-term trends. Our interpretation was limited by the few time points available in the studied collections. We therefore stress the need for natural history collections to routinely collect large samples of common species, to allow much more reliable hind-casting of evolutionary responses to environmental change.

Relationship between Special Abilities and Autistic-Like Traits in a Large Population-Based Sample of 8-Year-Olds

ERIC Educational Resources Information Center

Vital, Pedro M.; Ronald, Angelica; Wallace, Gregory L.; Happe, Francesca

2009-01-01

Background: The raised incidence of special abilities or "savant skills" among individuals with autism spectrum disorders (ASD) relative to other developmental disorders suggests an association between the traits characteristic of ASD and special abilities. The purpose of this study was to investigate the association between special abilities and…

Childhood Mental Disorders in Great Britain: An Epidemiological Perspective

ERIC Educational Resources Information Center

Meltzer, Howard

2007-01-01

The objective of this article is to describe the prevalence of childhood disorders and examine the factors associated with higher rates of disorder by combining the data from two large population-based samples of British children and young people aged 5-15. Just over 18,000 children were assessed in 1999 and 2004 using the Development and…

Diversity of Participation in Children with Cerebral Palsy

ERIC Educational Resources Information Center

Imms, Christine; Reilly, Sheena; Carlin, John; Dodd, Karen

2008-01-01

The aim of this study was to investigate the participation of children with cerebral palsy (CP) in activities outside school and to compare their participation with a large representative sample of children. A population-based survey was conducted of children with CP born in Victoria, Australia in 1994 and 1995. Of 219 living children identified,…

Risk Factors for Learning-Related Behavior Problems at 24 Months of Age: Population-Based Estimates

ERIC Educational Resources Information Center

Morgan, Paul L.; Farkas, George; Hillemeier, Marianne M.; Maczuga, Steven

2009-01-01

We used a large sample of singleton children to estimate the effects of socioeconomic status (SES), race/ethnicity, gender, additional socio-demographics, gestational and birth factors, and parenting on children's risk for learning-related behavior problems at 24 months of age. We investigated to what extent these factors increased a child's risk…

Cortical morphology as a shared neurobiological substrate of attention-deficit/hyperactivity symptoms and executive functioning: a population-based pediatric neuroimaging study

PubMed Central

Mous, Sabine E.; White, Tonya; Muetzel, Ryan L.; El Marroun, Hanan; Rijlaarsdam, Jolien; Polderman, Tinca J.C.; Jaddoe, Vincent W.; Verhulst, Frank C.; Posthuma, Danielle; Tiemeier, Henning

2017-01-01

Background Attention-deficit/hyperactivity symptoms have repeatedly been associated with poor cognitive functioning. Genetic studies have demonstrated a shared etiology of attention-deficit/hyperactivity disorder (ADHD) and cognitive ability, suggesting a common underlying neurobiology of ADHD and cognition. Further, neuroimaging studies suggest that altered cortical development is related to ADHD. In a large population-based sample we investigated whether cortical morphology, as a potential neurobiological substrate, underlies the association between attention-deficit/hyperactivity symptoms and cognitive problems. Methods The sample consisted of school-aged children with data on attention-deficit/hyperactivity symptoms, cognitive functioning and structural imaging. First, we investigated the association between attention-deficit/hyperactivity symptoms and different domains of cognition. Next, we identified cortical correlates of attention-deficit/hyperactivity symptoms and related cognitive domains. Finally, we studied the role of cortical thickness and gyrification in the behaviour–cognition associations. Results We included 776 children in our analyses. We found that attention-deficit/hyperactivity symptoms were associated specifically with problems in attention and executive functioning (EF; b = −0.041, 95% confidence interval [CI] −0.07 to −0.01, p = 0.004). Cortical thickness and gyrification were associated with both attention-deficit/hyperactivity symptoms and EF in brain regions that have been previously implicated in ADHD. This partly explained the association between attention-deficit/hyperactivity symptoms and EF (bindirect = −0.008, bias-corrected 95% CI −0.018 to −0.001). Limitations The nature of our study did not allow us to draw inferences regarding temporal associations; longitudinal studies are needed for clarification. Conclusion In a large, population-based sample of children, we identified a shared cortical morphology underlying attention-deficit/hyperactivity symptoms and EF. PMID:27673503

Cortical morphology as a shared neurobiological substrate of attention-deficit/hyperactivity symptoms and executive functioning: a population-based pediatric neuroimaging study.

PubMed

Mous, Sabine E; White, Tonya; Muetzel, Ryan L; El Marroun, Hanan; Rijlaarsdam, Jolien; Polderman, Tinca J C; Jaddoe, Vincent W; Verhulst, Frank C; Posthuma, Danielle; Tiemeier, Henning

2017-03-01

Attention-deficit/hyperactivity symptoms have repeatedly been associated with poor cognitive functioning. Genetic studies have demonstrated a shared etiology of attention-deficit/hyperactivity disorder (ADHD) and cognitive ability, suggesting a common underlying neurobiology of ADHD and cognition. Further, neuroimaging studies suggest that altered cortical development is related to ADHD. In a large population-based sample we investigated whether cortical morphology, as a potential neurobiological substrate, underlies the association between attention-deficit/hyperactivity symptoms and cognitive problems. The sample consisted of school-aged children with data on attention-deficit/hyperactivity symptoms, cognitive functioning and structural imaging. First, we investigated the association between attention-deficit/ hyperactivity symptoms and different domains of cognition. Next, we identified cortical correlates of attention-deficit/hyperactivity symptoms and related cognitive domains. Finally, we studied the role of cortical thickness and gyrification in the behaviour-cognition associations. We included 776 children in our analyses. We found that attention-deficit/hyperactivity symptoms were associated specifically with problems in attention and executive functioning (EF; b = -0.041, 95% confidence interval [CI] -0.07 to -0.01, p = 0.004). Cortical thickness and gyrification were associated with both attention-deficit/hyperactivity symptoms and EF in brain regions that have been previously implicated in ADHD. This partly explained the association between attention-deficit/hyperactivity symptoms and EF (b indirect = -0.008, bias-corrected 95% CI -0.018 to -0.001). The nature of our study did not allow us to draw inferences regarding temporal associations; longitudinal studies are needed for clarification. In a large, population-based sample of children, we identified a shared cortical morphology underlying attention-deficit/hyperactivity symptoms and EF.

Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding.

PubMed

Lan, Freeman; Demaree, Benjamin; Ahmed, Noorsher; Abate, Adam R

2017-07-01

The application of single-cell genome sequencing to large cell populations has been hindered by technical challenges in isolating single cells during genome preparation. Here we present single-cell genomic sequencing (SiC-seq), which uses droplet microfluidics to isolate, fragment, and barcode the genomes of single cells, followed by Illumina sequencing of pooled DNA. We demonstrate ultra-high-throughput sequencing of >50,000 cells per run in a synthetic community of Gram-negative and Gram-positive bacteria and fungi. The sequenced genomes can be sorted in silico based on characteristic sequences. We use this approach to analyze the distributions of antibiotic-resistance genes, virulence factors, and phage sequences in microbial communities from an environmental sample. The ability to routinely sequence large populations of single cells will enable the de-convolution of genetic heterogeneity in diverse cell populations.

Characterization of Aspergillus section Nigri species populations in vineyard soil using droplet digital PCR

USDA-ARS?s Scientific Manuscript database

Identification of populations of Aspergillus section Nigri species in environmental samples using traditional methods is laborious and impractical for large numbers of samples. We developed species-specific primers and probes for quantitative droplet digital PCR (ddPCR) to improve sample throughput ...

Multilocus nuclear DNA markers reveal population structure and demography of Anopheles minimus.

PubMed

Dixit, Jyotsana; Arunyawat, Uraiwan; Huong, Ngo Thi; Das, Aparup

2014-11-01

Utilization of multiple putatively neutral DNA markers for inferring evolutionary history of species population is considered to be the most robust approach. Molecular population genetic studies have been conducted in many species of Anopheles genus, but studies based on single nucleotide polymorphism (SNP) data are still very scarce. Anopheles minimus is one of the principal malaria vectors of Southeast (SE) Asia including the Northeastern (NE) India. Although population genetic studies with mitochondrial genetic variation data have been utilized to infer phylogeography of the SE Asian populations of this species, limited information on the population structure and demography of Indian An. minimus is available. We herewith have developed multilocus nuclear genetic approach with SNP markers located in X chromosome of An. minimus in eight Indian and two SE Asian population samples (121 individual mosquitoes in total) to infer population history and test several hypotheses on the phylogeography of this species. While the Thai population sample of An. minimus presented the highest nucleotide diversity, majority of the Indian samples were also fairly diverse. In general, An. minimus populations were moderately substructured in the distribution range covering SE Asia and NE India, largely falling under three distinct genetic clusters. Moreover, demographic expansion events could be detected in the majority of the presently studied populations of An. minimus. Additional DNA sequencing of the mitochondrial COII region in a subset of the samples (40 individual mosquitoes) corroborated the existing hypothesis of Indian An. minimus falling under the earlier reported mitochondrial lineage B. © 2014 John Wiley & Sons Ltd.

A new method for estimating the demographic history from DNA sequences: an importance sampling approach

PubMed Central

Ait Kaci Azzou, Sadoune; Larribe, Fabrice; Froda, Sorana

2015-01-01

The effective population size over time (demographic history) can be retraced from a sample of contemporary DNA sequences. In this paper, we propose a novel methodology based on importance sampling (IS) for exploring such demographic histories. Our starting point is the generalized skyline plot with the main difference being that our procedure, skywis plot, uses a large number of genealogies. The information provided by these genealogies is combined according to the IS weights. Thus, we compute a weighted average of the effective population sizes on specific time intervals (epochs), where the genealogies that agree more with the data are given more weight. We illustrate by a simulation study that the skywis plot correctly reconstructs the recent demographic history under the scenarios most commonly considered in the literature. In particular, our method can capture a change point in the effective population size, and its overall performance is comparable with the one of the bayesian skyline plot. We also introduce the case of serially sampled sequences and illustrate that it is possible to improve the performance of the skywis plot in the case of an exponential expansion of the effective population size. PMID:26300910

Colon Cancer Family Registry: an international resource for studies of the genetic epidemiology of colon cancer.

PubMed

Newcomb, Polly A; Baron, John; Cotterchio, Michelle; Gallinger, Steve; Grove, John; Haile, Robert; Hall, David; Hopper, John L; Jass, Jeremy; Le Marchand, Loïc; Limburg, Paul; Lindor, Noralane; Potter, John D; Templeton, Allyson S; Thibodeau, Steve; Seminara, Daniela

2007-11-01

Family studies have served as a cornerstone of genetic research on colorectal cancer. The Colorectal Cancer Family Registry (Colon CFR) is an international consortium of six centers in North America and Australia formed as a resource to support studies on the etiology, prevention, and clinical management of colorectal cancer. Differences in design and sampling schemes ensures a resource that covers the continuum of disease risk. Two separate recruitment strategies identified colorectal cancer cases: population-based (incident case probands identified by cancer registries; all six centers) and clinic-based (families with multiple cases of colorectal cancer presenting at cancer family clinics; three centers). At this time, the Colon CFR is in year 10 with the second phase of enrollment nearly complete. In phase I recruitment (1998-2002), population-based sampling ranged from all incident cases of colorectal cancer to a subsample based on age at diagnosis and/or family cancer history. During phase II (2002-2007), population-based recruitment targeted cases diagnosed before the age of 50 years are more likely attributable to genetic factors. Standardized protocols were used to collect information regarding family cancer history and colorectal cancer risk factors, and biospecimens were obtained to assess microsatellite instability (MSI) status, expression of mismatch repair proteins, and other molecular and genetic processes. Of the 8,369 case probands enrolled to date, 2,602 reported having one or more colorectal cancer-affected relatives and 799 met the Amsterdam I criteria for Lynch syndrome. A large number of affected (1,324) and unaffected (19,816) relatives were enrolled, as were population-based (4,108) and spouse (983) controls. To date, 91% of case probands provided blood (or, for a few, buccal cell) samples and 75% provided tumor tissue. For a selected sample of high-risk subjects, lymphocytes have been immortalized. Nearly 600 case probands had more than two affected colorectal cancer relatives, and 800 meeting the Amsterdam I criteria and 128, the Amsterdam II criteria. MSI testing for 10 markers was attempted on all obtained tumors. Of the 4,011 tumors collected in phase I that were successfully tested, 16% were MSI-high, 12% were MSI-low, and 72% were microsatellite stable. Tumor tissues from clinic-based cases were twice as likely as population-based cases to be MSI-high (34% versus 17%). Seventeen percent of phase I proband tumors and 24% of phase II proband tumors had some loss of mismatch repair protein, with the prevalence depending on sampling. Active follow-up to update personal and family histories, new neoplasms, and deaths in probands and relatives is nearly complete. The Colon CFR supports an evolving research program that is broad and interdisciplinary. The greater scientific community has access to this large and well-characterized resource for studies of colorectal cancer.

The 'number needed to sample' in primary care research. Comparison of two primary care sampling frames for chronic back pain.

PubMed

Smith, Blair H; Hannaford, Philip C; Elliott, Alison M; Smith, W Cairns; Chambers, W Alastair

2005-04-01

Sampling for primary care research must strike a balance between efficiency and external validity. For most conditions, even a large population sample will yield a small number of cases, yet other sampling techniques risk problems with extrapolation of findings. To compare the efficiency and external validity of two sampling methods for both an intervention study and epidemiological research in primary care--a convenience sample and a general population sample--comparing the response and follow-up rates, the demographic and clinical characteristics of each sample, and calculating the 'number needed to sample' (NNS) for a hypothetical randomized controlled trial. In 1996, we selected two random samples of adults from 29 general practices in Grampian, for an epidemiological study of chronic pain. One sample of 4175 was identified by an electronic questionnaire that listed patients receiving regular analgesic prescriptions--the 'repeat prescription sample'. The other sample of 5036 was identified from all patients on practice lists--the 'general population sample'. Questionnaires, including demographic, pain and general health measures, were sent to all. A similar follow-up questionnaire was sent in 2000 to all those agreeing to participate in further research. We identified a potential group of subjects for a hypothetical trial in primary care based on a recently published trial (those aged 25-64, with severe chronic back pain, willing to participate in further research). The repeat prescription sample produced better response rates than the general sample overall (86% compared with 82%, P < 0.001), from both genders and from the oldest and youngest age groups. The NNS using convenience sampling was 10 for each member of the final potential trial sample, compared with 55 using general population sampling. There were important differences between the samples in age, marital and employment status, social class and educational level. However, among the potential trial sample, there were no demographic differences. Those from the repeat prescription sample had poorer indices than the general population sample in all pain and health measures. The repeat prescription sampling method was approximately five times more efficient than the general population method. However demographic and clinical differences in the repeat prescription sample might hamper extrapolation of findings to the general population, particularly in an epidemiological study, and demonstrate that simple comparison with age and gender of the target population is insufficient.

The demand control model and circadian saliva cortisol variations in a Swedish population based sample (The PART study)

PubMed Central

Alderling, Magnus; Theorell, Töres; de la Torre, Bartolomé; Lundberg, Ingvar

2006-01-01

Background Previous studies of the relationship between job strain and blood or saliva cortisol levels have been small and based on selected occupational groups. Our aim was to examine the association between job strain and saliva cortisol levels in a population-based study in which a number of potential confounders could be adjusted for. Methods The material derives from a population-based study in Stockholm on mental health and its potential determinants. Two data collections were performed three years apart with more than 8500 subjects responding to a questionnaire in both waves. In this paper our analyses are based on 529 individuals who held a job, participated in both waves as well as in an interview linked to the second wave. They gave saliva samples at awakening, half an hour later, at lunchtime and before going to bed on a weekday in close connection with the interview. Job control and job demands were assessed from the questionnaire in the second wave. Mixed models were used to analyse the association between the demand control model and saliva cortisol. Results Women in low strain jobs (high control and low demands) had significantly lower cortisol levels half an hour after awakening than women in high strain (low control and high demands), active (high control and high demands) or passive jobs (low control and low demands). There were no significant differences between the groups during other parts of the day and furthermore there was no difference between the job strain, active and passive groups. For men, no differences were found between demand control groups. Conclusion This population-based study, on a relatively large sample, weakly support the hypothesis that the demand control model is associated with saliva cortisol concentrations. PMID:17129377

Shell productivity of the large benthic foraminifer Baculogypsina sphaerulata, based on the population dynamics in a tropical reef environment

NASA Astrophysics Data System (ADS)

Fujita, Kazuhiko; Otomaru, Maki; Lopati, Paeniu; Hosono, Takashi; Kayanne, Hajime

2016-03-01

Carbonate production by large benthic foraminifers is sometimes comparable to that of corals and coralline algae, and contributes to sedimentation on reef islands and beaches in the tropical Pacific. Population dynamic data, such as population density and size structure (size-frequency distribution), are vital for an accurate estimation of shell production of foraminifers. However, previous production estimates in tropical environments were based on a limited sampling period with no consideration of seasonality. In addition, no comparisons were made of various estimation methods to determine more accurate estimates. Here we present the annual gross shell production rate of Baculogypsina sphaerulata, estimated based on population dynamics studied over a 2-yr period on an ocean reef flat of Funafuti Atoll (Tuvalu, tropical South Pacific). The population density of B. sphaerulata increased from January to March, when northwest winds predominated and the study site was on the leeward side of reef islands, compared to other seasons when southeast trade winds predominated and the study site was on the windward side. This result suggested that wind-driven flows controlled the population density at the study site. The B. sphaerulata population had a relatively stationary size-frequency distribution throughout the study period, indicating no definite intensive reproductive period in the tropical population. Four methods were applied to estimate the annual gross shell production rates of B. sphaerulata. The production rates estimated by three of the four methods (using monthly biomass, life tables and growth increment rates) were in the order of hundreds of g CaCO3 m-2 yr-1 or cm-3 m-2 yr-1, and the simple method using turnover rates overestimated the values. This study suggests that seasonal surveys should be undertaken of population density and size structure as these can produce more accurate estimates of shell productivity of large benthic foraminifers.

Ischemic stroke subtypes: a population-based study of incidence rates among blacks and whites.

PubMed

Schneider, Alexander T; Kissela, Brett; Woo, Daniel; Kleindorfer, Dawn; Alwell, Kathleen; Miller, Rosemary; Szaflarski, Jerzy; Gebel, James; Khoury, Jane; Shukla, Rakesh; Moomaw, Charles; Pancioli, Arthur; Jauch, Edward; Broderick, Joseph

2004-07-01

Blacks have an excess burden of stroke compared with whites; however, data comparing ischemic stroke subtypes among the 2 groups are limited and typically involve relative frequencies. The objective of this study is to compare the incidence rates of ischemic stroke subtypes between blacks and whites within a large, representative, biracial population. The Greater Cincinnati/Northern Kentucky Stroke Study is designed to measure incidence rates and trends of all strokes within a well-defined, large, biracial population. Hospitalized cases were ascertained by International Classification of Disease (9th revision; ICD-9) discharge codes. Out-of-hospital events were ascertained by prospective screening of emergency department admission logs, review of coroners' cases, and monitoring all public health and hospital-based primary care clinics. A sampling scheme was used to ascertain events from nursing homes and all other primary care physician offices. All potential cases underwent detailed chart abstraction and confirmed by physician review. Based on all available clinical, laboratory, and radiographic information, ischemic stroke cases were subtyped into the following categories: cardioembolic, large-vessel, small-vessel, other, and stroke of undetermined cause. Race-specific incidence rates were calculated and compared after adjusting for age and gender, and standardizing to the 1990 US population. Between July 1, 1993, and June 30, 1994, 1956 first-ever ischemic strokes occurred among blacks and whites in the study population. Small-vessel strokes and strokes of undetermined cause were nearly twice as common among blacks. Large-vessel strokes were 40% more common among blacks than whites, and there was a trend toward cardioembolic strokes being more common among blacks. The excess burden of ischemic strokes among blacks compared with whites is not uniformly spread across the different subtypes. Large-vessel strokes are more common and cardioembolic stroke are as common among blacks, traditionally thought to be more common among whites.

A two-stage cluster sampling method using gridded population data, a GIS, and Google Earth(TM) imagery in a population-based mortality survey in Iraq.

PubMed

Galway, Lp; Bell, Nathaniel; Sae, Al Shatari; Hagopian, Amy; Burnham, Gilbert; Flaxman, Abraham; Weiss, Wiliam M; Rajaratnam, Julie; Takaro, Tim K

2012-04-27

Mortality estimates can measure and monitor the impacts of conflict on a population, guide humanitarian efforts, and help to better understand the public health impacts of conflict. Vital statistics registration and surveillance systems are rarely functional in conflict settings, posing a challenge of estimating mortality using retrospective population-based surveys. We present a two-stage cluster sampling method for application in population-based mortality surveys. The sampling method utilizes gridded population data and a geographic information system (GIS) to select clusters in the first sampling stage and Google Earth TM imagery and sampling grids to select households in the second sampling stage. The sampling method is implemented in a household mortality study in Iraq in 2011. Factors affecting feasibility and methodological quality are described. Sampling is a challenge in retrospective population-based mortality studies and alternatives that improve on the conventional approaches are needed. The sampling strategy presented here was designed to generate a representative sample of the Iraqi population while reducing the potential for bias and considering the context specific challenges of the study setting. This sampling strategy, or variations on it, are adaptable and should be considered and tested in other conflict settings.

A two-stage cluster sampling method using gridded population data, a GIS, and Google EarthTM imagery in a population-based mortality survey in Iraq

PubMed Central

2012-01-01

Background Mortality estimates can measure and monitor the impacts of conflict on a population, guide humanitarian efforts, and help to better understand the public health impacts of conflict. Vital statistics registration and surveillance systems are rarely functional in conflict settings, posing a challenge of estimating mortality using retrospective population-based surveys. Results We present a two-stage cluster sampling method for application in population-based mortality surveys. The sampling method utilizes gridded population data and a geographic information system (GIS) to select clusters in the first sampling stage and Google Earth TM imagery and sampling grids to select households in the second sampling stage. The sampling method is implemented in a household mortality study in Iraq in 2011. Factors affecting feasibility and methodological quality are described. Conclusion Sampling is a challenge in retrospective population-based mortality studies and alternatives that improve on the conventional approaches are needed. The sampling strategy presented here was designed to generate a representative sample of the Iraqi population while reducing the potential for bias and considering the context specific challenges of the study setting. This sampling strategy, or variations on it, are adaptable and should be considered and tested in other conflict settings. PMID:22540266

How Large Should a Statistical Sample Be?

ERIC Educational Resources Information Center

Menil, Violeta C.; Ye, Ruili

2012-01-01

This study serves as a teaching aid for teachers of introductory statistics. The aim of this study was limited to determining various sample sizes when estimating population proportion. Tables on sample sizes were generated using a C[superscript ++] program, which depends on population size, degree of precision or error level, and confidence…

SNPs and Haplotypes in Native American Populations

PubMed Central

Kidd, Judith R.; Friedlaender, Françoise; Pakstis, Andrew J.; Furtado, Manohar; Fang, Rixun; Wang, Xudong; Nievergelt, Caroline M.; Kidd, Kenneth K.

2013-01-01

Autosomal DNA polymorphisms can provide new information and understanding of both the origins of and relationships among modern Native American populations. At the same time that autosomal markers can be highly informative, they are also susceptible to ascertainment biases in the selection of the markers to use. Identifying markers that can be used for ancestry inference among Native American populations can be considered separate from identifying markers to further the quest for history. In the current study we are using data on nine Native American populations to compare the results based on a large haplotype-based dataset with relatively small independent sets of SNPs. We are interested in what types of limited datasets an individual laboratory might be able to collect are best for addressing two different questions of interest. First, how well can we differentiate the Native American populations and/or infer ancestry by assigning an individual to her population(s) of origin? Second, how well can we infer the historical/evolutionary relationships among Native American populations and their Eurasian origins. We conclude that only a large comprehensive dataset involving multiple autosomal markers on multiple populations will be able to answer both questions; different small sets of markers are able to answer only one or the other of these questions. Using our largest dataset we see a general increasing distance from Old World populations from North to South in the New World except for an unexplained close relationship between our Maya and Quechua samples. PMID:21913176

Pilot Test of a Novel Method for Assessing Community Response to Low-Amplitude Sonic Booms

NASA Technical Reports Server (NTRS)

Fidell, Sanford; Horonjeff, Richard D.; Harris, Michael

2012-01-01

A pilot test of a novel method for assessing residents annoyance to sonic booms was performed. During a two-week period, residents of the base housing area at Edwards Air Force Base provided data on their reactions to sonic booms using Smartphone-based interviews. Noise measurements were conducted at the same time. The report presents information about data collection methods and about test participants reactions to low-amplitude sonic booms. The latter information should not be viewed as definitive for several reasons. It may not be reliably generalized to the wider U.S. residential population (because it was not derived from a representative random sample) and the sample itself was not large.

A modified approach to estimating sample size for simple logistic regression with one continuous covariate.

PubMed

Novikov, I; Fund, N; Freedman, L S

2010-01-15

Different methods for the calculation of sample size for simple logistic regression (LR) with one normally distributed continuous covariate give different results. Sometimes the difference can be large. Furthermore, some methods require the user to specify the prevalence of cases when the covariate equals its population mean, rather than the more natural population prevalence. We focus on two commonly used methods and show through simulations that the power for a given sample size may differ substantially from the nominal value for one method, especially when the covariate effect is large, while the other method performs poorly if the user provides the population prevalence instead of the required parameter. We propose a modification of the method of Hsieh et al. that requires specification of the population prevalence and that employs Schouten's sample size formula for a t-test with unequal variances and group sizes. This approach appears to increase the accuracy of the sample size estimates for LR with one continuous covariate.

Core dimensions of personality broadly account for the link from perceived social support to symptoms of depression and anxiety.

PubMed

Lewis, Gary J; Bates, Timothy C; Posthuma, Danielle; Polderman, Tinca J C

2014-08-01

Specific personality traits and poor social support are risk factors for anxiety and depression. Little work, however, has considered the effects of social support and personality on these aspects of psychopathology simultaneously. We examined whether perceived social support mediates the effects of core personality domains on symptoms of anxiety and depression. Measures of personality (based on the Five-Factor Model [FFM]), perceived social support, and symptoms of depression and anxiety were collected in a large Dutch adult population-based sample (n = 555), and, except for depression symptoms, in an independent U.S. adult population-based sample (n = 511). Path modeling was used to test the effects of FFM traits on symptoms of depression and anxiety, with and without the mediation of perceived social support. Social support showed no link to symptoms of anxiety and only modest links to symptoms of depression when controlling for the FFM traits. Neuroticism had the strongest effect on symptoms of both depression and anxiety, with Extraversion also showing links to symptoms of depression. Social support has limited influence on symptoms of depression, and no effects on anxiety, over and above the effects of personality. Links between social support and anxiety/depression may largely reflect influences of Neuroticism and Extraversion. © 2013 Wiley Periodicals, Inc.

On incomplete sampling under birth-death models and connections to the sampling-based coalescent.

PubMed

Stadler, Tanja

2009-11-07

The constant rate birth-death process is used as a stochastic model for many biological systems, for example phylogenies or disease transmission. As the biological data are usually not fully available, it is crucial to understand the effect of incomplete sampling. In this paper, we analyze the constant rate birth-death process with incomplete sampling. We derive the density of the bifurcation events for trees on n leaves which evolved under this birth-death-sampling process. This density is used for calculating prior distributions in Bayesian inference programs and for efficiently simulating trees. We show that the birth-death-sampling process can be interpreted as a birth-death process with reduced rates and complete sampling. This shows that joint inference of birth rate, death rate and sampling probability is not possible. The birth-death-sampling process is compared to the sampling-based population genetics model, the coalescent. It is shown that despite many similarities between these two models, the distribution of bifurcation times remains different even in the case of very large population sizes. We illustrate these findings on an Hepatitis C virus dataset from Egypt. We show that the transmission times estimates are significantly different-the widely used Gamma statistic even changes its sign from negative to positive when switching from the coalescent to the birth-death process.

Age, maturation, and population structure of the Humboldt squid Dosidicus gigas off the Peruvian Exclusive Economic Zones

NASA Astrophysics Data System (ADS)

Liu, Bilin; Chen, Xinjun; Chen, Yong; Tian, Siquan; Li, Jianhua; Fang, Zhou; Yang, Mingxia

2013-01-01

Age, maturation and population structure of the Humboldt squid Dosidicus gigas were studied based on random sampling of the Chinese jigging fishery off the Peruvian Exclusive Economic Zones (EEZ) during 2008-2010. Estimated ages ranged from 144 to 633 days, confirming that the squid is a short-lived species with longevity no longer than 2 years. Occurrence of mature females and hatching in each month indicated that Humboldt squid spawned year-round. Back-calculated hatching dates for the samples were from January 22nd, 2008 to April 22nd, 2010 with a peak between January and March. Two size-based and two hatching date-based populations could be defined from mantle length (ML) at maturity and back-calculated hatching dates, respectively. Females matured at a larger size than males, and there was a significant difference in ML at maturity between the two hatching groups ( P <0.05). The waters adjacent to 11°S off the Peruvian EEZ may be a potential spawning ground. This study shows the complexity of the population structure and large variability in key life history parameters in the Humboldt squid off the Peruvian EEZ, which should be considered in the assessment and management of this important resource.

Size-based trends and management implications of microhabitat utilization by Brown Treesnakes, with an emphasis on juvenile snakes

USGS Publications Warehouse

Rodda, Gordon H.; Reed, Robert N.

2007-01-01

The brown treesnake (Boiga irregularis, or BTS), a costly invasive species, has been the subject of intensive research on Guam over the past two decades. The behavior and habitat use of hatchling and juvenile snakes, however, remain largely unknown. We used a long-term dataset of BTS captures (N = 2,415) and a dataset resulting from intensive sampling within and immediately around a 5-ha fenced population (N = 2,541) to examine habitat use of BTS. Small snakes were almost exclusively arboreal and that they appeared to prefer tangantangan (Leucaena leucocephala) habitats. In contrast, large snakes used arboreal and terrestrial habitats in roughly equal proportion, and were less frequently found in tangantangan. Among snakes found in trees, there were no clear size-based preferences for certain heights above ground, nor for size-based choice of perch diameters. We discuss these results as they relate to management and interdiction implications for brown treesnakes on Guam and in potential incipient populations on other islands.

Mammary tumor associated Hspb1 mutation and screening of eight cat populations of the world.

PubMed

Saif, R; Awan, A R; Lyons, L; Gandolfi, B; Tayyab, M; Ellahi Babar, M; Wasim, M

2016-01-01

Current research highlights the Hspb1 based screening of eight cat populations of the world to investigate the association of newly found locus within cat mammary tumors. Total 180 cats were screened on the basis of Hspb1 4 bp deletion locus (1514-1517del4) which was observed in six mammary tumor cases in Siamese cat breed. Case-control association study revealed the non-significance with P=0.201 and an overall mutant allele frequency of 0.30 ranging from 0.20-0.40 was observed in other cat populations. Similarly, HWE was also obeyed in combined population samples with P=0.860 and found non-significant with range of 0.429-0.708 in other non-Pakistani cat populations as well. These results might be helpful to understand the association of this novel locus in a better way with large sample size of cases and may also serve as a potential marker for mammary tumor diagnosis, particularly in cats and generally in all other animal populations in comparative genetics and genomics context.

Identifying personal microbiomes using metagenomic codes

PubMed Central

Franzosa, Eric A.; Huang, Katherine; Meadow, James F.; Gevers, Dirk; Lemon, Katherine P.; Bohannan, Brendan J. M.; Huttenhower, Curtis

2015-01-01

Community composition within the human microbiome varies across individuals, but it remains unknown if this variation is sufficient to uniquely identify individuals within large populations or stable enough to identify them over time. We investigated this by developing a hitting set-based coding algorithm and applying it to the Human Microbiome Project population. Our approach defined body site-specific metagenomic codes: sets of microbial taxa or genes prioritized to uniquely and stably identify individuals. Codes capturing strain variation in clade-specific marker genes were able to distinguish among 100s of individuals at an initial sampling time point. In comparisons with follow-up samples collected 30–300 d later, ∼30% of individuals could still be uniquely pinpointed using metagenomic codes from a typical body site; coincidental (false positive) matches were rare. Codes based on the gut microbiome were exceptionally stable and pinpointed >80% of individuals. The failure of a code to match its owner at a later time point was largely explained by the loss of specific microbial strains (at current limits of detection) and was only weakly associated with the length of the sampling interval. In addition to highlighting patterns of temporal variation in the ecology of the human microbiome, this work demonstrates the feasibility of microbiome-based identifiability—a result with important ethical implications for microbiome study design. The datasets and code used in this work are available for download from huttenhower.sph.harvard.edu/idability. PMID:25964341

Population structure of the large Japanese field mouse, Apodemus speciosus (Rodentia: Muridae), in suburban landscape, based on mitochondrial D-loop sequences.

PubMed

Hirota, Tadao; Hirohata, Tetsuo; Mashima, Hiroshi; Satoh, Toshiyuki; Obara, Yoshiaki

2004-11-01

Genetic structure of the large Japanese field mouse populations in suburban landscape of West Tokyo, Japan was determined using mitochondrial DNA control region sequence. Samples were collected from six habitats linked by forests and green tract along the Tama River, and from two forests segregated by urban areas from those continuous habitats. Thirty-five haplotypes were detected in 221 animals. Four to eight haplotypes were found within each local population belonging to the continuous landscape. Some haplotypes were shared by two or three adjacent local populations. On the other hand, two isolated habitats were occupied by one or two indigenous haplotypes. Significant genetic differentiation between all pairs of local populations, except for one pair in the continuous habitats, was found by analysis of molecular variance (amova). The geographical distance between habitats did not explain the large variance of pairwise F(ST)-values among local populations. F(ST)-values between local populations segregated by urban areas were higher than those between local populations in the continuous habitat, regardless of geographical distance. The results of this study demonstrated quantitatively that urban areas inhibit the migration of Apodemus speciosus, whereas a linear green tract along a river functions as a corridor. Moreover, it preserves the metapopulation structure of A. speciosus as well as the corridors in suburban landscape.

Men, women…who cares? A population-based study on sex differences and gender roles in empathy and moral cognition

PubMed Central

Baez, Sandra; Flichtentrei, Daniel; Prats, María; Mastandueno, Ricardo; García, Adolfo M.; Cetkovich, Marcelo

2017-01-01

Research on sex differences in empathy has revealed mixed findings. Whereas experimental and neuropsychological measures show no consistent sex effect, self-report data consistently indicates greater empathy in women. However, available results mainly come from separate populations with relatively small samples, which may inflate effect sizes and hinder comparability between both empirical corpora. To elucidate the issue, we conducted two large-scale studies. First, we examined whether sex differences emerge in a large population-based sample (n = 10,802) when empathy is measured with an experimental empathy-for-pain paradigm. Moreover, we investigated the relationship between empathy and moral judgment. In the second study, a subsample (n = 334) completed a self-report empathy questionnaire. Results showed some sex differences in the experimental paradigm, but with minuscule effect sizes. Conversely, women did portray themselves as more empathic through self-reports. In addition, utilitarian responses to moral dilemmas were less frequent in women, although these differences also had small effect sizes. These findings suggest that sex differences in empathy are highly driven by the assessment measure. In particular, self-reports may induce biases leading individuals to assume gender-role stereotypes. Awareness of the role of measurement instruments in this field may hone our understanding of the links between empathy, sex differences, and gender roles. PMID:28632770

The population-based Barcelona-Asymptomatic Intracranial Atherosclerosis Study (ASIA): rationale and design.

PubMed

López-Cancio, Elena; Dorado, Laura; Millán, Mónica; Reverté, Silvia; Suñol, Anna; Massuet, Anna; Mataró, María; Galán, Amparo; Alzamora, Maite; Pera, Guillem; Torán, Pere; Dávalos, Antoni; Arenillas, Juan F

2011-02-17

Large-artery intracranial atherosclerosis may be the most frequent cause of ischemic stroke worldwide. Traditional approaches have attempted to target the disease when it is already symptomatic. However, early detection of intracranial atherosclerosis may allow therapeutic intervention while the disease is still asymptomatic. The prevalence and natural history of asymptomatic intracranial atherosclerosis in Caucasians remain unclear. The aims of the Barcelona-ASymptomatic Intracranial Atherosclerosis (ASIA) study are (1) to determine the prevalence of ASIA in a moderate-high vascular risk population, (2) to study its prognostic impact on the risk of suffering future major ischemic events, and (3) to identify predictors of the development, progression and clinical expression of this condition. Cross-over and cohort, population-based study. A randomly selected representative sample of 1,503 subjects with a mild-moderate-high vascular risk (as defined by a REGICOR score ≥ 5%) and with neither a history of cerebrovascular nor ischemic heart disease will be studied. At baseline, all individuals will undergo extracranial and transcranial Color-Coded Duplex (TCCD) ultrasound examinations to detect presence and severity of extra and intracranial atherosclerosis. Intracranial stenoses will be assessed by magnetic resonance angiography (MRA). Clinical and demographic variables will be recorded and blood samples will be drawn to investigate clinical, biological and genetic factors associated with the presence of ASIA. A long-term clinical and sonographic follow-up will be conducted thereafter to identify predictors of disease progression and of incident vascular events. The Barcelona-ASIA is a population-based study aiming to evaluate the prevalence and clinical importance of asymptomatic intracranial large-artery atherosclerosis in Caucasians. The ASIA project may provide a unique scientific resource to better understand the dynamics of intracranial atherosclerosis from its early stages and to identify new potential therapeutic targets for this condition.

The Disease Burden of Childhood Adversities in Adults: A Population-Based Study

ERIC Educational Resources Information Center

Cuijpers, Pim; Smit, Filip; Unger, Froukje; Stikkelbroek, Yvonne; ten Have, Margreet; de Graaf, Ron

2011-01-01

Objectives: There is much evidence showing that childhood adversities have considerable effects on the mental and physical health of adults. It could be assumed therefore, that the disease burden of childhood adversities is high. It has not yet been examined, however, whether this is true. Method: We used data of a large representative sample (N =…

Aetiology for the Covariation between Combined Type ADHD and Reading Difficulties in a Family Study: The Role of IQ

ERIC Educational Resources Information Center

Cheung, Celeste H. M.; Wood, Alexis C.; Paloyelis, Yannis; Arias-Vasquez, Alejandro; Buitelaar, Jan K.; Franke, Barbara; Miranda, Ana; Mulas, Fernando; Rommelse, Nanda; Sergeant, Joseph A.; Sonuga-Barke, Edmund J.; Faraone, Stephen V.; Asherson, Philip; Kuntsi, Jonna

2012-01-01

Background: Twin studies using both clinical and population-based samples suggest that the frequent co-occurrence of attention deficit hyperactivity disorder (ADHD) and reading ability/disability (RD) is largely driven by shared genetic influences. While both disorders are associated with lower IQ, recent twin data suggest that the shared genetic…

Distinct Trajectories of Separation Anxiety in the Preschool Years: Persistence at School Entry and Early-Life Associated Factors

ERIC Educational Resources Information Center

Battaglia, Marco; Touchette, Évelyne; Garon-Carrier, Gabrielle; Dionne, Ginette; Côté, Sylvana M.; Vitaro, Frank; Tremblay, Richard E.; Boivin, Michel

2016-01-01

Background: Little is known about how children differ in the onset and evolution of separation anxiety (SA) symptoms during the preschool years, and how SA develops into separation anxiety disorder. In a large, representative population-based sample, we investigated the developmental trajectories of SA symptoms from infancy to school entry, their…

Community Support for the Public Schools in a Large Metropolitan Area. Final Report.

ERIC Educational Resources Information Center

Smith, Ralph V.; And Others

An extensive survey was conducted in 1965 by a team of white and Negro interviewers in an application of ecological theory to a study of the support relationship between the community and its school system. Findings are based upon interview data from a probability sample of 931 respondents selected from the population of persons 21 years of age…

The Impact of Attention-Deficit/Hyperactivity Disorder on Preadolescent Adjustment May Be Greater for Girls than for Boys

ERIC Educational Resources Information Center

Elkins, Irene J.; Malone, Steve; Keyes, Margaret; Iacono, William G.; McGue, Matt

2011-01-01

Whether gender differences exist in the impairment associated with attention-deficit/hyperactivity disorder (ADHD) is still largely unknown, because most samples have few affected girls or include only one sex. The current study evaluated whether ADHD affects adjustment differently for girls than boys in a population-based cohort of 11-year-olds…

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

USGS Publications Warehouse

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

2006-01-01

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

The relationship between the Five-Factor Model personality traits and peptic ulcer disease in a large population-based adult sample.

PubMed

Realo, Anu; Teras, Andero; Kööts-Ausmees, Liisi; Esko, Tõnu; Metspalu, Andres; Allik, Jüri

2015-12-01

The current study examined the relationship between the Five-Factor Model personality traits and physician-confirmed peptic ulcer disease (PUD) diagnosis in a large population-based adult sample, controlling for the relevant behavioral and sociodemographic factors. Personality traits were assessed by participants themselves and by knowledgeable informants using the NEO Personality Inventory-3 (NEO PI-3). When controlling for age, sex, education, and cigarette smoking, only one of the five NEO PI-3 domain scales - higher Neuroticism - and two facet scales - lower A1: Trust and higher C1: Competence - made a small, yet significant contribution (p < 0.01) to predicting PUD in logistic regression analyses. In the light of these relatively modest associations, our findings imply that it is certain behavior (such as smoking) and sociodemographic variables (such as age, gender, and education) rather than personality traits that are associated with the diagnosis of PUD at a particular point in time. Further prospective studies with a longitudinal design and multiple assessments would be needed to fully understand if the FFM personality traits serve as risk factors for the development of PUD. © 2015 Scandinavian Psychological Associations and John Wiley & Sons Ltd.

MendeLIMS: a web-based laboratory information management system for clinical genome sequencing.

PubMed

Grimes, Susan M; Ji, Hanlee P

2014-08-27

Large clinical genomics studies using next generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate laboratory information management systems to manage the thousands of patient samples that are subject to this type of genetic analysis. To meet the needs of clinical population studies using genome sequencing, we developed a web-based laboratory information management system (LIMS) with a flexible configuration that is adaptable to continuously evolving experimental protocols of next generation DNA sequencing technologies. Our system is referred to as MendeLIMS, is easily implemented with open source tools and is also highly configurable and extensible. MendeLIMS has been invaluable in the management of our clinical genome sequencing studies. We maintain a publicly available demonstration version of the application for evaluation purposes at http://mendelims.stanford.edu. MendeLIMS is programmed in Ruby on Rails (RoR) and accesses data stored in SQL-compliant relational databases. Software is freely available for non-commercial use at http://dna-discovery.stanford.edu/software/mendelims/.

Intercoalescence time distribution of incomplete gene genealogies in temporally varying populations, and applications in population genetic inference.

PubMed

Chen, Hua

2013-03-01

Tracing back to a specific time T in the past, the genealogy of a sample of haplotypes may not have reached their common ancestor and may leave m lineages extant. For such an incomplete genealogy truncated at a specific time T in the past, the distribution and expectation of the intercoalescence times conditional on T are derived in an exact form in this paper for populations of deterministically time-varying sizes, specifically, for populations growing exponentially. The derived intercoalescence time distribution can be integrated to the coalescent-based joint allele frequency spectrum (JAFS) theory, and is useful for population genetic inference from large-scale genomic data, without relying on computationally intensive approaches, such as importance sampling and Markov Chain Monte Carlo (MCMC) methods. The inference of several important parameters relying on this derived conditional distribution is demonstrated: quantifying population growth rate and onset time, and estimating the number of ancestral lineages at a specific ancient time. Simulation studies confirm validity of the derivation and statistical efficiency of the methods using the derived intercoalescence time distribution. Two examples of real data are given to show the inference of the population growth rate of a European sample from the NIEHS Environmental Genome Project, and the number of ancient lineages of 31 mitochondrial genomes from Tibetan populations. © 2013 Blackwell Publishing Ltd/University College London.

Inference of the genetic architecture underlying BMI and height with the use of 20,240 sibling pairs.

PubMed

Hemani, Gibran; Yang, Jian; Vinkhuyzen, Anna; Powell, Joseph E; Willemsen, Gonneke; Hottenga, Jouke-Jan; Abdellaoui, Abdel; Mangino, Massimo; Valdes, Ana M; Medland, Sarah E; Madden, Pamela A; Heath, Andrew C; Henders, Anjali K; Nyholt, Dale R; de Geus, Eco J C; Magnusson, Patrik K E; Ingelsson, Erik; Montgomery, Grant W; Spector, Timothy D; Boomsma, Dorret I; Pedersen, Nancy L; Martin, Nicholas G; Visscher, Peter M

2013-11-07

Evidence that complex traits are highly polygenic has been presented by population-based genome-wide association studies (GWASs) through the identification of many significant variants, as well as by family-based de novo sequencing studies indicating that several traits have a large mutational target size. Here, using a third study design, we show results consistent with extreme polygenicity for body mass index (BMI) and height. On a sample of 20,240 siblings (from 9,570 nuclear families), we used a within-family method to obtain narrow-sense heritability estimates of 0.42 (SE = 0.17, p = 0.01) and 0.69 (SE = 0.14, p = 6 × 10(-)(7)) for BMI and height, respectively, after adjusting for covariates. The genomic inflation factors from locus-specific linkage analysis were 1.69 (SE = 0.21, p = 0.04) for BMI and 2.18 (SE = 0.21, p = 2 × 10(-10)) for height. This inflation is free of confounding and congruent with polygenicity, consistent with observations of ever-increasing genomic-inflation factors from GWASs with large sample sizes, implying that those signals are due to true genetic signals across the genome rather than population stratification. We also demonstrate that the distribution of the observed test statistics is consistent with both rare and common variants underlying a polygenic architecture and that previous reports of linkage signals in complex traits are probably a consequence of polygenic architecture rather than the segregation of variants with large effects. The convergent empirical evidence from GWASs, de novo studies, and within-family segregation implies that family-based sequencing studies for complex traits require very large sample sizes because the effects of causal variants are small on average. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

The 'Natural Laboratory', a tool for deciphering growth, lifetime and population dynamics in larger benthic foraminifera

NASA Astrophysics Data System (ADS)

Hohenegger, Johann

2015-04-01

The shells of symbiont-bearing larger benthic Foraminifera (LBF) represent the response to physiological requirements in dependence of environmental conditions. All compartments of the shell such as chambers and chamberlets accommodate the growth of the cell protoplasm and are adaptations for housing photosymbiotic algae. Investigations on the biology of LBF were predominantly based on laboratory studies. The lifetime of LBF under natural conditions is still unclear. LBF, which can build >100 chambers during their lifetime, are thought to live at least one year under natural conditions. This is supported by studies on population dynamics of eulittoral foraminifera. In species characterized by a time-restricted single reproduction period the mean size of specimens increases from small to large during lifetime simultaneously reducing individual number. This becomes more complex when two or more reproduction times are present within a one-year cycle leading to a mixture of abundant small individuals with few large specimens during the year, while keeping mean size more or less constant. This mixture is typical for most sublittoral megalospheric (gamonts or schizonts) LBF. Nothing is known on the lifetime of agamonts, the diploid asexually reproducing generation. In all hyaline LBF it is thought to be significantly longer than 1 year based on the large size and considering the mean chamber building rate of the gamont/schizonts. Observations on LBF under natural conditions have not been performed yet in the deeper sublittoral. This reflects the difficulties due to intense hydrodynamics that hinder deploying technical equipment for studies in the natural environment. Therefore, studying growth, lifetime and reproduction of sublittoral LBF under natural conditions can be performed using the so-called 'natural laboratory' in comparison with laboratory investigations. The best sampling method in the upper sublittoral from 5 to 70 m depth is by SCUBA diving. Irregular sampling intervals caused by differing weather conditions may range from weeks to one month, whereby the latter represents the upper limit: larger intervals could render the data set worthless. The number of sampling points at the location must be more than 4, randomly distributed and approximately 5m apart to smooth the effects of patchy distributions, which are typical for most LBF. Only three simple measurements are necessary to determine chamber building rate and population dynamics under natural conditions. These are the number of individuals, number of chambers and the largest diameter of the individual. The determination of a standardized sample surface area, which is necessary for population dynamic investigations, depends on the sampling method. Reproduction and longevity can be estimated based on shell size using the date where the mean abundance of specimens with minimum size (expected after a one month's growth) characterizes the reproduction period. Then the difference to the date with the mean abundance of specimens characterized by large size indicating readiness for reproduction marks the life time. Calculation of the chamber-building rate based on chamber number is more complex and depends on the reproduction period and longevity. This can be fitted with theoretical growth functions (e.g. Michaelis Menten Function). According to the above mentioned methods, chamber building rates, longevity and population dynamics can be obtained for the shallow sublittoral symbiont-bearing LBF using the 'natural laboratory'.

A comparison of respondent-driven and venue-based sampling of female sex workers in Liuzhou, China

PubMed Central

Weir, Sharon S; Merli, M Giovanna; Li, Jing; Gandhi, Anisha D; Neely, William W; Edwards, Jessie K; Suchindran, Chirayath M; Henderson, Gail E; Chen, Xiang-Sheng

2012-01-01

Objectives To compare two methods for sampling female sex workers (FSWs) for bio-behavioural surveillance. We compared the populations of sex workers recruited by the venue-based Priorities for Local AIDS Control Efforts (PLACE) method and a concurrently implemented network-based sampling method, respondent-driven sampling (RDS), in Liuzhou, China. Methods For the PLACE protocol, all female workers at a stratified random sample of venues identified as places where people meet new sexual partners were interviewed and tested for syphilis. Female workers who reported sex work in the past 4 weeks were categorised as FSWs. RDS used peer recruitment and chain referral to obtain a sample of FSWs. Data were collected between October 2009 and January 2010. We compared the socio-demographic characteristics and the percentage with a positive syphilis test of FSWs recruited by PLACE and RDS. Results The prevalence of a positive syphilis test was 24% among FSWs recruited by PLACE and 8.5% among those recruited by RDS and tested (prevalence ratio 3.3; 95% CI 1.5 to 7.2). Socio-demographic characteristics (age, residence and monthly income) also varied by sampling method. PLACE recruited fewer FSWs than RDS (161 vs 583), was more labour-intensive and had difficulty gaining access to some venues. RDS was more likely to recruit from areas near the RDS office and from large low prevalence entertainment venues. Conclusions Surveillance protocols using different sampling methods can obtain different estimates of prevalence and population characteristics. Venue-based and network-based methods each have strengths and limitations reflecting differences in design and assumptions. We recommend that more research be conducted on measuring bias in bio-behavioural surveillance. PMID:23172350

Assessment of sampling stability in ecological applications of discriminant analysis

USGS Publications Warehouse

Williams, B.K.; Titus, K.

1988-01-01

A simulation study was undertaken to assess the sampling stability of the variable loadings in linear discriminant function analysis. A factorial design was used for the factors of multivariate dimensionality, dispersion structure, configuration of group means, and sample size. A total of 32,400 discriminant analyses were conducted, based on data from simulated populations with appropriate underlying statistical distributions. A review of 60 published studies and 142 individual analyses indicated that sample sizes in ecological studies often have met that requirement. However, individual group sample sizes frequently were very unequal, and checks of assumptions usually were not reported. The authors recommend that ecologists obtain group sample sizes that are at least three times as large as the number of variables measured.

The impact of sample size on the reproducibility of voxel-based lesion-deficit mappings.

PubMed

Lorca-Puls, Diego L; Gajardo-Vidal, Andrea; White, Jitrachote; Seghier, Mohamed L; Leff, Alexander P; Green, David W; Crinion, Jenny T; Ludersdorfer, Philipp; Hope, Thomas M H; Bowman, Howard; Price, Cathy J

2018-07-01

This study investigated how sample size affects the reproducibility of findings from univariate voxel-based lesion-deficit analyses (e.g., voxel-based lesion-symptom mapping and voxel-based morphometry). Our effect of interest was the strength of the mapping between brain damage and speech articulation difficulties, as measured in terms of the proportion of variance explained. First, we identified a region of interest by searching on a voxel-by-voxel basis for brain areas where greater lesion load was associated with poorer speech articulation using a large sample of 360 right-handed English-speaking stroke survivors. We then randomly drew thousands of bootstrap samples from this data set that included either 30, 60, 90, 120, 180, or 360 patients. For each resample, we recorded effect size estimates and p values after conducting exactly the same lesion-deficit analysis within the previously identified region of interest and holding all procedures constant. The results show (1) how often small effect sizes in a heterogeneous population fail to be detected; (2) how effect size and its statistical significance varies with sample size; (3) how low-powered studies (due to small sample sizes) can greatly over-estimate as well as under-estimate effect sizes; and (4) how large sample sizes (N ≥ 90) can yield highly significant p values even when effect sizes are so small that they become trivial in practical terms. The implications of these findings for interpreting the results from univariate voxel-based lesion-deficit analyses are discussed. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Genetic assessment of the effects of streamscape succession on coho salmon Oncorhynchus kisutch colonization in recently deglaciated streams

USGS Publications Warehouse

Scribner, Kim T.; Soiseth, Chad; McGuire, Jeffrey J.; Sage, Kevin; Thorsteinson, Lyman K.; Nielsen, J. L.; Knudsen, E.

2017-01-01

Measures of genetic diversity within and among populations and historical geomorphological data on stream landscapes were used in model simulations based on approximate Bayesian computation (ABC) to examine hypotheses of the relative importance of stream features (geomorphology and age) associated with colonization events and gene flow for coho salmon Oncorhynchus kisutch breeding in recently deglaciated streams (50–240 years b.p.) in Glacier Bay National Park (GBNP), Alaska. Population estimates of genetic diversity including heterozygosity and allelic richness declined significantly and monotonically from the oldest and largest to youngest and smallest GBNP streams. Interpopulation variance in allele frequency increased with increasing distance between streams (r = 0·435, P < 0·01) and was inversely related to stream age (r = –0·281, P < 0·01). The most supported model of colonization involved ongoing or recent (<10 generations before sampling) colonization originating from large populations outside Glacier Bay proper into all other GBNP streams sampled. Results here show that sustained gene flow from large source populations is important to recently established O. kisutch metapopulations. Studies that document how genetic and demographic characteristics of newly founded populations vary associated with successional changes in stream habitat are of particular importance to and have significant implications for, restoration of declining or repatriation of extirpated populations in other regions of the species' native range.

Validation of the MOS Social Support Survey 6-item (MOS-SSS-6) measure with two large population-based samples of Australian women.

PubMed

Holden, Libby; Lee, Christina; Hockey, Richard; Ware, Robert S; Dobson, Annette J

2014-12-01

This study aimed to validate a 6-item 1-factor global measure of social support developed from the Medical Outcomes Study Social Support Survey (MOS-SSS) for use in large epidemiological studies. Data were obtained from two large population-based samples of participants in the Australian Longitudinal Study on Women's Health. The two cohorts were aged 53-58 and 28-33 years at data collection (N = 10,616 and 8,977, respectively). Items selected for the 6-item 1-factor measure were derived from the factor structure obtained from unpublished work using an earlier wave of data from one of these cohorts. Descriptive statistics, including polychoric correlations, were used to describe the abbreviated scale. Cronbach's alpha was used to assess internal consistency and confirmatory factor analysis to assess scale validity. Concurrent validity was assessed using correlations between the new 6-item version and established 19-item version, and other concurrent variables. In both cohorts, the new 6-item 1-factor measure showed strong internal consistency and scale reliability. It had excellent goodness-of-fit indices, similar to those of the established 19-item measure. Both versions correlated similarly with concurrent measures. The 6-item 1-factor MOS-SSS measures global functional social support with fewer items than the established 19-item measure.

Reliability and longitudinal change of detrital-zircon age spectra in the Snake River system, Idaho and Wyoming: An example of reproducing the bumpy barcode

NASA Astrophysics Data System (ADS)

Link, Paul Karl; Fanning, C. Mark; Beranek, Luke P.

2005-12-01

Detrital-zircon age-spectra effectively define provenance in Holocene and Neogene fluvial sands from the Snake River system of the northern Rockies, U.S.A. SHRIMP U-Pb dates have been measured for forty-six samples (about 2700 zircon grains) of fluvial and aeolian sediment. The detrital-zircon age distributions are repeatable and demonstrate predictable longitudinal variation. By lumping multiple samples to attain populations of several hundred grains, we recognize distinctive, provenance-defining zircon-age distributions or "barcodes," for fluvial sedimentary systems of several scales, within the upper and middle Snake River system. Our detrital-zircon studies effectively define the geochronology of the northern Rocky Mountains. The composite detrital-zircon grain distribution of the middle Snake River consists of major populations of Neogene, Eocene, and Cretaceous magmatic grains plus intermediate and small grain populations of multiply recycled Grenville (˜950 to 1300 Ma) grains and Yavapai-Mazatzal province grains (˜1600 to 1800 Ma) recycled through the upper Belt Supergroup and Cretaceous sandstones. A wide range of older Paleoproterozoic and Archean grains are also present. The best-case scenario for using detrital-zircon populations to isolate provenance is when there is a point-source pluton with known age, that is only found in one location or drainage. We find three such zircon age-populations in fluvial sediments downstream from the point-source plutons: Ordovician in the southern Beaverhead Mountains, Jurassic in northern Nevada, and Oligocene in the Albion Mountains core complex of southern Idaho. Large detrital-zircon age-populations derived from regionally well-defined, magmatic or recycled sedimentary, sources also serve to delimit the provenance of Neogene fluvial systems. In the Snake River system, defining populations include those derived from Cretaceous Atlanta lobe of the Idaho batholith (80 to 100 Ma), Eocene Challis Volcanic Group and associated plutons (˜45 to 52 Ma), and Neogene rhyolitic Yellowstone-Snake River Plain volcanics (˜0 to 17 Ma). For first-order drainage basins containing these zircon-rich source terranes, or containing a point-source pluton, a 60-grain random sample is sufficient to define the dominant provenance. The most difficult age-distributions to analyze are those that contain multiple small zircon age-populations and no defining large populations. Examples of these include streams draining the Proterozoic and Paleozoic Cordilleran miogeocline in eastern Idaho and Pleistocene loess on the Snake River Plain. For such systems, large sample bases of hundreds of grains, plus the use of statistical methods, may be necessary to distinguish detrital-zircon age-spectra.

Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts.

PubMed

Hakenberg, Jörg; Cheng, Wei-Yi; Thomas, Philippe; Wang, Ying-Chih; Uzilov, Andrew V; Chen, Rong

2016-01-08

Data from a plethora of high-throughput sequencing studies is readily available to researchers, providing genetic variants detected in a variety of healthy and disease populations. While each individual cohort helps gain insights into polymorphic and disease-associated variants, a joint perspective can be more powerful in identifying polymorphisms, rare variants, disease-associations, genetic burden, somatic variants, and disease mechanisms. We have set up a Reference Variant Store (RVS) containing variants observed in a number of large-scale sequencing efforts, such as 1000 Genomes, ExAC, Scripps Wellderly, UK10K; various genotyping studies; and disease association databases. RVS holds extensive annotations pertaining to affected genes, functional impacts, disease associations, and population frequencies. RVS currently stores 400 million distinct variants observed in more than 80,000 human samples. RVS facilitates cross-study analysis to discover novel genetic risk factors, gene-disease associations, potential disease mechanisms, and actionable variants. Due to its large reference populations, RVS can also be employed for variant filtration and gene prioritization. A web interface to public datasets and annotations in RVS is available at https://rvs.u.hpc.mssm.edu/.

Harnessing Data to Assess Equity of Care by Race, Ethnicity and Language

PubMed Central

Gracia, Amber; Cheirif, Jorge; Veliz, Juana; Reyna, Melissa; Vecchio, Mara; Aryal, Subhash

2015-01-01

Objective: Determine any disparities in care based on race, ethnicity and language (REaL) by utilizing inpatient (IP) core measures at Texas Health Resources, a large, faith-based, non-profit health care delivery system located in a large, ethnically diverse metropolitan area in Texas. These measures, which were established by the U.S. Centers for Medicare and Medicaid Services (CMS) and The Joint Commission (TJC), help to ensure better accountability for patient outcomes throughout the U.S. health care system. Methods: Sample analysis to understand the architecture of race, ethnicity and language (REaL) variables within the Texas Health clinical database, followed by development of the logic, method and framework for isolating populations and evaluating disparities by race (non-Hispanic White, non-Hispanic Black, Native American/Native Hawaiian/Pacific Islander, Asian and Other); ethnicity (Hispanic and non-Hispanic); and preferred language (English and Spanish). The study is based on use of existing clinical data for four inpatient (IP) core measures: Acute Myocardial Infarction (AMI), Congestive Heart Failure (CHF), Pneumonia (PN) and Surgical Care (SCIP), representing 100% of the sample population. These comprise a high number of cases presenting in our acute care facilities. Findings are based on a sample of clinical data (N = 19,873 cases) for the four inpatient (IP) core measures derived from 13 of Texas Health’s wholly-owned facilities, formulating a set of baseline data. Results: Based on applied method, Texas Health facilities consistently scored high with no discernable race, ethnicity and language (REaL) disparities as evidenced by a low percentage difference to the reference point (non-Hispanic White) on IP core measures, including: AMI (0.3%–1.2%), CHF (0.7%–3.0%), PN (0.5%–3.7%), and SCIP (0–0.7%). PMID:26703665

An unusual haplotype structure on human chromosome 8p23 derived from the inversion polymorphism.

PubMed

Deng, Libin; Zhang, Yuezheng; Kang, Jian; Liu, Tao; Zhao, Hongbin; Gao, Yang; Li, Chaohua; Pan, Hao; Tang, Xiaoli; Wang, Dunmei; Niu, Tianhua; Yang, Huanming; Zeng, Changqing

2008-10-01

Chromosomal inversion is an important type of genomic variations involved in both evolution and disease pathogenesis. Here, we describe the refined genetic structure of a 3.8-Mb inversion polymorphism at chromosome 8p23. Using HapMap data of 1,073 SNPs generated from 209 unrelated samples from CEPH-Utah residents with ancestry from northern and western Europe (CEU); Yoruba in Ibadan, Nigeria (YRI); and Asian (ASN) samples, which were comprised of Han Chinese from Beijing, China (CHB) and Japanese from Tokyo, Japan (JPT)-we successfully deduced the inversion orientations of all their 418 haplotypes. In particular, distinct haplotype subgroups were identified based on principal component analysis (PCA). Such genetic substructures were consistent with clustering patterns based on neighbor-joining tree reconstruction, which revealed a total of four haplotype clades across all samples. Metaphase fluorescence in situ hybridization (FISH) in a subset of 10 HapMap samples verified their inversion orientations predicted by PCA or phylogenetic tree reconstruction. Positioning of the outgroup haplotype within one of YRI clades suggested that Human NCBI Build 36-inverted order is most likely the ancestral orientation. Furthermore, the population differentiation test and the relative extended haplotype homozygosity (REHH) analysis in this region discovered multiple selection signals, also in a population-specific manner. A positive selection signal was detected at XKR6 in the ASN population. These results revealed the correlation of inversion polymorphisms to population-specific genetic structures, and various selection patterns as possible mechanisms for the maintenance of a large chromosomal rearrangement at 8p23 region during evolution. In addition, our study also showed that haplotype-based clustering methods, such as PCA, can be applied in scanning for cryptic inversion polymorphisms at a genome-wide scale.

Evaluating sampling designs by computer simulation: A case study with the Missouri bladderpod

USGS Publications Warehouse

Morrison, L.W.; Smith, D.R.; Young, C.; Nichols, D.W.

2008-01-01

To effectively manage rare populations, accurate monitoring data are critical. Yet many monitoring programs are initiated without careful consideration of whether chosen sampling designs will provide accurate estimates of population parameters. Obtaining accurate estimates is especially difficult when natural variability is high, or limited budgets determine that only a small fraction of the population can be sampled. The Missouri bladderpod, Lesquerella filiformis Rollins, is a federally threatened winter annual that has an aggregated distribution pattern and exhibits dramatic interannual population fluctuations. Using the simulation program SAMPLE, we evaluated five candidate sampling designs appropriate for rare populations, based on 4 years of field data: (1) simple random sampling, (2) adaptive simple random sampling, (3) grid-based systematic sampling, (4) adaptive grid-based systematic sampling, and (5) GIS-based adaptive sampling. We compared the designs based on the precision of density estimates for fixed sample size, cost, and distance traveled. Sampling fraction and cost were the most important factors determining precision of density estimates, and relative design performance changed across the range of sampling fractions. Adaptive designs did not provide uniformly more precise estimates than conventional designs, in part because the spatial distribution of L. filiformis was relatively widespread within the study site. Adaptive designs tended to perform better as sampling fraction increased and when sampling costs, particularly distance traveled, were taken into account. The rate that units occupied by L. filiformis were encountered was higher for adaptive than for conventional designs. Overall, grid-based systematic designs were more efficient and practically implemented than the others. ?? 2008 The Society of Population Ecology and Springer.

Three Decades of Farmed Escapees in the Wild: A Spatio-Temporal Analysis of Atlantic Salmon Population Genetic Structure throughout Norway

PubMed Central

Glover, Kevin A.; Quintela, María; Wennevik, Vidar; Besnier, François; Sørvik, Anne G. E.; Skaala, Øystein

2012-01-01

Each year, hundreds of thousands of domesticated farmed Atlantic salmon escape into the wild. In Norway, which is the world’s largest commercial producer, many native Atlantic salmon populations have experienced large numbers of escapees on the spawning grounds for the past 15–30 years. In order to study the potential genetic impact, we conducted a spatio-temporal analysis of 3049 fish from 21 populations throughout Norway, sampled in the period 1970–2010. Based upon the analysis of 22 microsatellites, individual admixture, FST and increased allelic richness revealed temporal genetic changes in six of the populations. These changes were highly significant in four of them. For example, 76% and 100% of the fish comprising the contemporary samples for the rivers Vosso and Opo were excluded from their respective historical samples at P = 0.001. Based upon several genetic parameters, including simulations, genetic drift was excluded as the primary cause of the observed genetic changes. In the remaining 15 populations, some of which had also been exposed to high numbers of escapees, clear genetic changes were not detected. Significant population genetic structuring was observed among the 21 populations in the historical (global FST = 0.038) and contemporary data sets (global FST = 0.030), although significantly reduced with time (P = 0.008). This reduction was especially distinct when looking at the six populations displaying temporal changes (global FST dropped from 0.058 to 0.039, P = 0.006). We draw two main conclusions: 1. The majority of the historical population genetic structure throughout Norway still appears to be retained, suggesting a low to modest overall success of farmed escapees in the wild; 2. Genetic introgression of farmed escapees in native salmon populations has been strongly population-dependent, and it appears to be linked with the density of the native population. PMID:22916215

Adaptively resizing populations: Algorithm, analysis, and first results

NASA Technical Reports Server (NTRS)

Smith, Robert E.; Smuda, Ellen

1993-01-01

Deciding on an appropriate population size for a given Genetic Algorithm (GA) application can often be critical to the algorithm's success. Too small, and the GA can fall victim to sampling error, affecting the efficacy of its search. Too large, and the GA wastes computational resources. Although advice exists for sizing GA populations, much of this advice involves theoretical aspects that are not accessible to the novice user. An algorithm for adaptively resizing GA populations is suggested. This algorithm is based on recent theoretical developments that relate population size to schema fitness variance. The suggested algorithm is developed theoretically, and simulated with expected value equations. The algorithm is then tested on a problem where population sizing can mislead the GA. The work presented suggests that the population sizing algorithm may be a viable way to eliminate the population sizing decision from the application of GA's.

Addressing Participant Validity in a Small Internet Health Survey (The Restore Study): Protocol and Recommendations for Survey Response Validation.

PubMed

Dewitt, James; Capistrant, Benjamin; Kohli, Nidhi; Rosser, B R Simon; Mitteldorf, Darryl; Merengwa, Enyinnaya; West, William

2018-04-24

While deduplication and cross-validation protocols have been recommended for large Web-based studies, protocols for survey response validation of smaller studies have not been published. This paper reports the challenges of survey validation inherent in a small Web-based health survey research. The subject population was North American, gay and bisexual, prostate cancer survivors, who represent an under-researched, hidden, difficult-to-recruit, minority-within-a-minority population. In 2015-2016, advertising on a large Web-based cancer survivor support network, using email and social media, yielded 478 completed surveys. Our manual deduplication and cross-validation protocol identified 289 survey submissions (289/478, 60.4%) as likely spam, most stemming from advertising on social media. The basic components of this deduplication and validation protocol are detailed. An unexpected challenge encountered was invalid survey responses evolving across the study period. This necessitated the static detection protocol be augmented with a dynamic one. Five recommendations for validation of Web-based samples, especially with smaller difficult-to-recruit populations, are detailed. ©James Dewitt, Benjamin Capistrant, Nidhi Kohli, B R Simon Rosser, Darryl Mitteldorf, Enyinnaya Merengwa, William West. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 24.04.2018.

Determination of the optimal sample size for a clinical trial accounting for the population size.

PubMed

Stallard, Nigel; Miller, Frank; Day, Simon; Hee, Siew Wan; Madan, Jason; Zohar, Sarah; Posch, Martin

2017-07-01

The problem of choosing a sample size for a clinical trial is a very common one. In some settings, such as rare diseases or other small populations, the large sample sizes usually associated with the standard frequentist approach may be infeasible, suggesting that the sample size chosen should reflect the size of the population under consideration. Incorporation of the population size is possible in a decision-theoretic approach either explicitly by assuming that the population size is fixed and known, or implicitly through geometric discounting of the gain from future patients reflecting the expected population size. This paper develops such approaches. Building on previous work, an asymptotic expression is derived for the sample size for single and two-arm clinical trials in the general case of a clinical trial with a primary endpoint with a distribution of one parameter exponential family form that optimizes a utility function that quantifies the cost and gain per patient as a continuous function of this parameter. It is shown that as the size of the population, N, or expected size, N∗ in the case of geometric discounting, becomes large, the optimal trial size is O(N1/2) or O(N∗1/2). The sample size obtained from the asymptotic expression is also compared with the exact optimal sample size in examples with responses with Bernoulli and Poisson distributions, showing that the asymptotic approximations can also be reasonable in relatively small sample sizes. © 2016 The Author. Biometrical Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Occupational self-coding and automatic recording (OSCAR): a novel web-based tool to collect and code lifetime job histories in large population-based studies.

PubMed

De Matteis, Sara; Jarvis, Deborah; Young, Heather; Young, Alan; Allen, Naomi; Potts, James; Darnton, Andrew; Rushton, Lesley; Cullinan, Paul

2017-03-01

Objectives The standard approach to the assessment of occupational exposures is through the manual collection and coding of job histories. This method is time-consuming and costly and makes it potentially unfeasible to perform high quality analyses on occupational exposures in large population-based studies. Our aim was to develop a novel, efficient web-based tool to collect and code lifetime job histories in the UK Biobank, a population-based cohort of over 500 000 participants. Methods We developed OSCAR (occupations self-coding automatic recording) based on the hierarchical structure of the UK Standard Occupational Classification (SOC) 2000, which allows individuals to collect and automatically code their lifetime job histories via a simple decision-tree model. Participants were asked to find each of their jobs by selecting appropriate job categories until they identified their job title, which was linked to a hidden 4-digit SOC code. For each occupation a job title in free text was also collected to estimate Cohen's kappa (κ) inter-rater agreement between SOC codes assigned by OSCAR and an expert manual coder. Results OSCAR was administered to 324 653 UK Biobank participants with an existing email address between June and September 2015. Complete 4-digit SOC-coded lifetime job histories were collected for 108 784 participants (response rate: 34%). Agreement between the 4-digit SOC codes assigned by OSCAR and the manual coder for a random sample of 400 job titles was moderately good [κ=0.45, 95% confidence interval (95% CI) 0.42-0.49], and improved when broader job categories were considered (κ=0.64, 95% CI 0.61-0.69 at a 1-digit SOC-code level). Conclusions OSCAR is a novel, efficient, and reasonably reliable web-based tool for collecting and automatically coding lifetime job histories in large population-based studies. Further application in other research projects for external validation purposes is warranted.

Lot quality assurance sampling (LQAS) for monitoring a leprosy elimination program.

PubMed

Gupte, M D; Narasimhamurthy, B

1999-06-01

In a statistical sense, prevalences of leprosy in different geographical areas can be called very low or rare. Conventional survey methods to monitor leprosy control programs, therefore, need large sample sizes, are expensive, and are time-consuming. Further, with the lowering of prevalence to the near-desired target level, 1 case per 10,000 population at national or subnational levels, the program administrator's concern will be shifted to smaller areas, e.g., districts, for assessment and, if needed, for necessary interventions. In this paper, Lot Quality Assurance Sampling (LQAS), a quality control tool in industry, is proposed to identify districts/regions having a prevalence of leprosy at or above a certain target level, e.g., 1 in 10,000. This technique can also be considered for identifying districts/regions at or below the target level of 1 per 10,000, i.e., areas where the elimination level is attained. For simulating various situations and strategies, a hypothetical computerized population of 10 million persons was created. This population mimics the actual population in terms of the empirical information on rural/urban distributions and the distribution of households by size for the state of Tamil Nadu, India. Various levels with respect to leprosy prevalence are created using this population. The distribution of the number of cases in the population was expected to follow the Poisson process, and this was also confirmed by examination. Sample sizes and corresponding critical values were computed using Poisson approximation. Initially, villages/towns are selected from the population and from each selected village/town households are selected using systematic sampling. Households instead of individuals are used as sampling units. This sampling procedure was simulated 1000 times in the computer from the base population. The results in four different prevalence situations meet the required limits of Type I error of 5% and 90% Power. It is concluded that after validation under field conditions, this method can be considered for a rapid assessment of the leprosy situation.

A model-based 'varimax' sampling strategy for a heterogeneous population.

PubMed

Akram, Nuzhat A; Farooqi, Shakeel R

2014-01-01

Sampling strategies are planned to enhance the homogeneity of a sample, hence to minimize confounding errors. A sampling strategy was developed to minimize the variation within population groups. Karachi, the largest urban agglomeration in Pakistan, was used as a model population. Blood groups ABO and Rh factor were determined for 3000 unrelated individuals selected through simple random sampling. Among them five population groups, namely Balochi, Muhajir, Pathan, Punjabi and Sindhi, based on paternal ethnicity were identified. An index was designed to measure the proportion of admixture at parental and grandparental levels. Population models based on index score were proposed. For validation, 175 individuals selected through stratified random sampling were genotyped for the three STR loci CSF1PO, TPOX and TH01. ANOVA showed significant differences across the population groups for blood groups and STR loci distribution. Gene diversity was higher across the sub-population model than in the agglomerated population. At parental level gene diversities are significantly higher across No admixture models than Admixture models. At grandparental level the difference was not significant. A sub-population model with no admixture at parental level was justified for sampling the heterogeneous population of Karachi.

Massively parallel digital transcriptional profiling of single cells

PubMed Central

Zheng, Grace X. Y.; Terry, Jessica M.; Belgrader, Phillip; Ryvkin, Paul; Bent, Zachary W.; Wilson, Ryan; Ziraldo, Solongo B.; Wheeler, Tobias D.; McDermott, Geoff P.; Zhu, Junjie; Gregory, Mark T.; Shuga, Joe; Montesclaros, Luz; Underwood, Jason G.; Masquelier, Donald A.; Nishimura, Stefanie Y.; Schnall-Levin, Michael; Wyatt, Paul W.; Hindson, Christopher M.; Bharadwaj, Rajiv; Wong, Alexander; Ness, Kevin D.; Beppu, Lan W.; Deeg, H. Joachim; McFarland, Christopher; Loeb, Keith R.; Valente, William J.; Ericson, Nolan G.; Stevens, Emily A.; Radich, Jerald P.; Mikkelsen, Tarjei S.; Hindson, Benjamin J.; Bielas, Jason H.

2017-01-01

Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3′ mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system's technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system's ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients. PMID:28091601

The role of stressful life events preceding death by suicide: Evidence from two samples of suicide decedents.

PubMed

Buchman-Schmitt, Jennifer M; Chu, Carol; Michaels, Matthew S; Hames, Jennifer L; Silva, Caroline; Hagan, Christopher R; Ribeiro, Jessica D; Selby, Edward A; Joiner, Thomas E

2017-10-01

Stressful life events (SLEs) are associated with increased risk for suicidal behavior. Less is known regarding the intensity of SLEs and how this may vary as a function of suicide attempt history. As a large percentage of suicide decedents do not have a history of suicidal behavior, SLEs precipitating suicide may help characterize suicidality in this understudied population. This paper examines the intensity, number, and accumulation of SLEs preceding death by suicide among decedents with varying suicide attempt histories. Suicide attempts, SLEs, and suicide methods were examined in two samples: 62 prison-based and 117 community-based suicide decedents. Regression was used to compare the level of stressor precipitating death by suicide in decedents who died on a first attempt versus multiple previous attempts. A non-significant trend was observed in the prison population which was supported by significant findings in the community-based sample. Decedents who died on a first attempt experienced a stressor of a lower magnitude when compared to decedents with multiple previous suicide attempts. We discuss the implications of these findings in relation to the stress-diathesis model for suicide. Copyright © 2017 Elsevier B.V. All rights reserved.

Mean population salt intake estimated from 24-h urine samples and spot urine samples: a systematic review and meta-analysis.

PubMed

Huang, Liping; Crino, Michelle; Wu, Jason H Y; Woodward, Mark; Barzi, Federica; Land, Mary-Anne; McLean, Rachael; Webster, Jacqui; Enkhtungalag, Batsaikhan; Neal, Bruce

2016-02-01

Estimating equations based on spot urine samples have been identified as a possible alternative approach to 24-h urine collections for determining mean population salt intake. This review compares estimates of mean population salt intake based upon spot and 24-h urine samples. We systematically searched for all studies that reported estimates of daily salt intake based upon both spot and 24-h urine samples for the same population. The associations between the two were quantified and compared overall and in subsets of studies. A total of 538 records were identified, 108 were assessed as full text and 29 were included. The included studies involved 10,414 participants from 34 countries and made 71 comparisons available for the primary analysis. Overall average population salt intake estimated from 24-h urine samples was 9.3 g/day compared with 9.0 g/day estimated from the spot urine samples. Estimates based upon spot urine samples had excellent sensitivity (97%) and specificity (100%) at classifying mean population salt intake as above or below the World Health Organization maximum target of 5 g/day. Compared with the 24-h samples, estimates based upon spot urine overestimated intake at lower levels of consumption and underestimated intake at higher levels of consumption. Estimates of mean population salt intake based upon spot urine samples can provide countries with a good indication of mean population salt intake and whether action on salt consumption is required. Published by Oxford University Press on behalf of the International Epidemiological Association 2015. This work is written by US Government employees and is in the public domain in the US.

Determining the fraction of reddened quasars in COSMOS with multiple selection techniques from X-ray to radio wavelengths

NASA Astrophysics Data System (ADS)

Heintz, K. E.; Fynbo, J. P. U.; Møller, P.; Milvang-Jensen, B.; Zabl, J.; Maddox, N.; Krogager, J.-K.; Geier, S.; Vestergaard, M.; Noterdaeme, P.; Ledoux, C.

2016-10-01

The sub-population of quasars reddened by intrinsic or intervening clouds of dust are known to be underrepresented in optical quasar surveys. By defining a complete parent sample of the brightest and spatially unresolved quasars in the COSMOS field, we quantify to which extent this sub-population is fundamental to our understanding of the true population of quasars. By using the available multiwavelength data of various surveys in the COSMOS field, we built a parent sample of 33 quasars brighter than J = 20 mag, identified by reliable X-ray to radio wavelength selection techniques. Spectroscopic follow-up with the NOT/ALFOSC was carried out for four candidate quasars that had not been targeted previously to obtain a 100% redshift completeness of the sample. The population of high AV quasars (HAQs), a specific sub-population of quasars selected from optical/near-infrared photometry, some of which were shown to be missed in large optical surveys such as SDSS, is found to contribute 21%+9-5 of the parent sample. The full population of bright spatially unresolved quasars represented by our parent sample consists of 39%+9-8 reddened quasars defined by having AV > 0.1, and 21%+9-5 of the sample having E(B-V) > 0.1 assuming the extinction curve of the Small Magellanic Cloud. We show that the HAQ selection works well for selecting reddened quasars, but some are missed because their optical spectra are too blue to pass the g-r color cut in the HAQ selection. This is either due to a low degree of dust reddening or anomalous spectra. We find that the fraction of quasars with contributing light from the host galaxy, causing observed extended spatial morphology, is most dominant at z ≲ 1. At higher redshifts the population of spatially unresolved quasars selected by our parent sample is found to be representative of the full population of bright active galactic nuclei at J< 20 mag. This work quantifies the bias against reddened quasars in studies that are based solely on optical surveys. Partly based on observations made with the Nordic Optical Telescope, operated by the Nordic Optical Telescope Scientific Association at the Observatorio del Roque de los Muchachos, La Palma, Spain, of the Instituto de Astrofisica de Canarias.

Estimating population abundance and mapping distribution of wintering sea ducks in coastal waters of the mid-Atlantic

USGS Publications Warehouse

Koneff, M.D.; Royle, J. Andrew; Forsell, D.J.; Wortham, J.S.; Boomer, G.S.; Perry, M.C.

2005-01-01

Survey design for wintering scoters (Melanitta sp.) and other sea ducks that occur in offshore waters is challenging because these species have large ranges, are subject to distributional shifts among years and within a season, and can occur in aggregations. Interest in winter sea duck population abundance surveys has grown in recent years. This interest stems from concern over the population status of some sea ducks, limitations of extant breeding waterfowl survey programs in North America and logistical challenges and costs of conducting surveys in northern breeding regions, high winter area philopatry in some species and potential conservation implications, and increasing concern over offshore development and other threats to sea duck wintering habitats. The efficiency and practicality of statistically-rigorous monitoring strategies for mobile, aggregated wintering sea duck populations have not been sufficiently investigated. This study evaluated a 2-phase adaptive stratified strip transect sampling plan to estimate wintering population size of scoters, long-tailed ducks (Clangua hyemalis), and other sea ducks and provide information on distribution. The sampling plan results in an optimal allocation of a fixed sampling effort among offshore strata in the U.S. mid-Atlantic coast region. Phase I transect selection probabilities were based on historic distribution and abundance data, while Phase 2 selection probabilities were based on observations made during Phase 1 flights. Distance sampling methods were used to estimate detection rates. Environmental variables thought to affect detection rates were recorded during the survey and post-stratification and covariate modeling were investigated to reduce the effect of heterogeneity on detection estimation. We assessed cost-precision tradeoffs under a number of fixed-cost sampling scenarios using Monte Carlo simulation. We discuss advantages and limitations of this sampling design for estimating wintering sea duck abundance and mapping distribution and suggest improvements for future surveys.

Evaluating mortality rates with a novel integrated framework for nonmonogamous species.

PubMed

Tenan, Simone; Iemma, Aaron; Bragalanti, Natalia; Pedrini, Paolo; De Barba, Marta; Randi, Ettore; Groff, Claudio; Genovart, Meritxell

2016-12-01

The conservation of wildlife requires management based on quantitative evidence, and especially for large carnivores, unraveling cause-specific mortalities and understanding their impact on population dynamics is crucial. Acquiring this knowledge is challenging because it is difficult to obtain robust long-term data sets on endangered populations and, usually, data are collected through diverse sampling strategies. Integrated population models (IPMs) offer a way to integrate data generated through different processes. However, IPMs are female-based models that cannot account for mate availability, and this feature limits their applicability to monogamous species only. We extended classical IPMs to a two-sex framework that allows investigation of population dynamics and quantification of cause-specific mortality rates in nonmonogamous species. We illustrated our approach by simultaneously modeling different types of data from a reintroduced, unhunted brown bear (Ursus arctos) population living in an area with a dense human population. In a population mainly driven by adult survival, we estimated that on average 11% of cubs and 61% of adults died from human-related causes. Although the population is currently not at risk, adult survival and thus population dynamics are driven by anthropogenic mortality. Given the recent increase of human-bear conflicts in the area, removal of individuals for management purposes and through poaching may increase, reversing the positive population growth rate. Our approach can be generalized to other species affected by cause-specific mortality and will be useful to inform conservation decisions for other nonmonogamous species, such as most large carnivores, for which data are scarce and diverse and thus data integration is highly desirable. © 2016 Society for Conservation Biology.

Potential effects of maternal contribution on egg and larva population dynamics of striped bass: Integrated individual-based model and directed field sampling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cowan, J.H., Jr.; Rose, K.A.

1991-01-01

We have used a bioenergetically-driven, individual-based model (IBM) of striped bass as a framework for synthesizing available information on population biology and quantifying, in a relative sense, factors that potentially affect year class success. The IBM has been configured to simulate environmental conditions experienced by several striped bass populations; i.e., in the Potomac River, MD; in Hudson River, NY; in the Santee-Cooper River System, SC, and; in the San Joaquin-Sacramento River System CA. These sites represent extremes in the geographic distribution and thus, environmental variability of striped bass spawning. At each location, data describing the physio-chemical and biological characteristics ofmore » the spawning population and nursery area are being collected and synthesized by means of a prioritized, directed field sampling program that is organized by the individual-based recruitment model. Here, we employ the striped bass IBM configured for the Potomac River, MD from spawning into the larval period to evaluate the potential for maternal contribution to affect larva survival and growth. Model simulations in which the size distribution and spawning day of females are altered indicate that larva survival is enhanced (3.3-fold increase) when a high fraction of females in the spawning population are large. Larva stage duration also is less ({bar X} = 18.4 d and 22.2 d) when large and small females, respectively, are mothers in simulations. Although inconclusive, these preliminary results for Potomac River striped bass suggest that the effects of female size, timing of spawning nad maternal contribution on recruitment dynamics potentially are important and illustrate our approach to the study of recruitment in striped bass. We hope to use the model, field collections and management alternatives that vary from site to site, in an iterative manner for some time to come. 54 refs., 4 figs., 1 tab.« less

How Much Can Remotely-Sensed Natural Resource Inventories Benefit from Finer Spatial Resolutions?

NASA Astrophysics Data System (ADS)

Hou, Z.; Xu, Q.; McRoberts, R. E.; Ståhl, G.; Greenberg, J. A.

2017-12-01

For remote sensing facilitated natural resource inventories, the effects of spatial resolution in the form of pixel size and the effects of subpixel information on estimates of population parameters were evaluated by comparing results obtained using Landsat 8 and RapidEye auxiliary imagery. The study area was in Burkina Faso, and the variable of interest was the stem volume (m3/ha) convertible to the woodland aboveground biomass. A sample consisting of 160 field plots was selected and measured from the population following a two-stage sampling design. Models were fit using weighted least squares; the population mean, mu, and the variance of the estimator of the population mean, Var(mu.hat), were estimated in two inferential frameworks, model-based and model-assisted, and compared; for each framework, Var(mu.hat) was estimated both analytically and empirically. Empirical variances were estimated with bootstrapping that for resampling takes clustering effects into account. The primary results were twofold. First, for the effects of spatial resolution and subpixel information, four conclusions are relevant: (1) finer spatial resolution imagery indeed contributes to greater precision for estimators of population parameter, but this increase is slight at a maximum rate of 20% considering that RapidEye data are 36 times finer resolution than Landsat 8 data; (2) subpixel information on texture is marginally beneficial when it comes to making inference for population of large areas; (3) cost-effectiveness is more favorable for the free of charge Landsat 8 imagery than RapidEye imagery; and (4) for a given plot size, candidate remote sensing auxiliary datasets are more cost-effective when their spatial resolutions are similar to the plot size than with much finer alternatives. Second, for the comparison between estimators, three conclusions are relevant: (1) model-based variance estimates are consistent with each other and about half as large as stabilized model-assisted estimates, suggesting superior effectiveness of model-based inference to model-assisted inference; (2) bootstrapping is an effective alternative to analytical variance estimators; and (3) prediction accuracy expressed by RMSE is useful for screening candidate models to be used for population inferences.

Findings from the First & Only National Data Base on Elemiddle & Middle Schools (Executive Summary)

ERIC Educational Resources Information Center

Hough, David L.

2009-01-01

The study presented here is the first large scale effort on a national level to examine the relationship between K-8 Elemiddle Schools and 6-8 Middle Schools. From a population of more than 2,000 middle grades schools in 49 public school districts across 26 states, a sample of 542 Elemiddle and 506 Middle Schools was drawn. Both regression and…

Population Structure, Diversity and Reproductive Mode of the Grape Phylloxera (Daktulosphaira vitifoliae) across Its Native Range

PubMed Central

Walker, M. Andrew

2017-01-01

Grape Phylloxera, Daktulosphaira vitifoliae, is a gall-forming insect that feeds on the leaves and roots of many Vitis species. The roots of the cultivated V. vinifera cultivars and hybrids are highly susceptible to grape phylloxera feeding damage. The native range of this insect covers most of North America, and it is particularly abundant in the eastern and central United States. Phylloxera was introduced from North America to almost all grape-growing regions across five of the temperate zone continents. It devastated vineyards in each of these regions causing large-scale disruptions to grape growers, wine makers and national economies. In order to understand the population diversity of grape phylloxera in its native range, more than 500 samples from 19 States and 34 samples from the introduced range (northern California, Europe and South America) were genotyped with 32 simple sequence repeat markers. STRUCTURE, a model based clustering method identified five populations within these samples. The five populations were confirmed by a neighbor-joining tree and principal coordinate analysis (PCoA). These populations were distinguished by their Vitis species hosts and their geographic locations. Samples collected from California, Europe and South America traced back to phylloxera sampled in the northeastern United States on V. riparia, with some influence from phylloxera collected along the Atlantic Coast and Central Plains on V. vulpina. Reproductive statistics conclusively confirmed that sexual reproduction is common in the native range and is combined with cyclical parthenogenesis. Native grape phylloxera populations were identified to be under Hardy-Weinberg equilibrium. The identification of admixed samples between many of these populations indicates that shared environments facilitate sexual reproduction between different host associated populations to create new genotypes of phylloxera. This study also found that assortative mating might occur across the sympatric range of the V. vulpina west and V. cinerea populations. PMID:28125736

Electrofishing effort required to estimate biotic condition in southern Idaho Rivers

USGS Publications Warehouse

Maret, Terry R.; Ott, Douglas S.; Herlihy, Alan T.

2007-01-01

An important issue surrounding biomonitoring in large rivers is the minimum sampling effort required to collect an adequate number of fish for accurate and precise determinations of biotic condition. During the summer of 2002, we sampled 15 randomly selected large-river sites in southern Idaho to evaluate the effects of sampling effort on an index of biotic integrity (IBI). Boat electrofishing was used to collect sample populations of fish in river reaches representing 40 and 100 times the mean channel width (MCW; wetted channel) at base flow. Minimum sampling effort was assessed by comparing the relation between reach length sampled and change in IBI score. Thirty-two species of fish in the families Catostomidae, Centrarchidae, Cottidae, Cyprinidae, Ictaluridae, Percidae, and Salmonidae were collected. Of these, 12 alien species were collected at 80% (12 of 15) of the sample sites; alien species represented about 38% of all species (N = 32) collected during the study. A total of 60% (9 of 15) of the sample sites had poor IBI scores. A minimum reach length of about 36 times MCW was determined to be sufficient for collecting an adequate number of fish for estimating biotic condition based on an IBI score. For most sites, this equates to collecting 275 fish at a site. Results may be applicable to other semiarid, fifth-order through seventh-order rivers sampled during summer low-flow conditions.

Feasibility of biochemical verification in a web-based smoking cessation study.

PubMed

Cha, Sarah; Ganz, Ollie; Cohn, Amy M; Ehlke, Sarah J; Graham, Amanda L

2017-10-01

Cogent arguments have been made against the need for biochemical verification in population-based studies with low-demand characteristics. Despite this fact, studies involving digital interventions (low-demand) are often required in peer review to report biochemically verified abstinence. To address this discrepancy, we examined the feasibility and costs of biochemical verification in a web-based study conducted with a national sample. Participants were 600U.S. adult current smokers who registered on a web-based smoking cessation program and completed surveys at baseline and 3months. Saliva sampling kits were sent to participants who reported 7-day abstinence at 3months, and analyzed for cotinine. The response rate at 3-months was 41.2% (n=247): 93 participants reported 7-day abstinence (38%) and were mailed a saliva kit (71% returned). The discordance rate was 36.4%. Participants with discordant responses were more likely to report 3-month use of nicotine replacement therapy or e-cigarettes than those with concordant responses (79.2% vs. 45.2%, p=0.007). The total cost of saliva sampling was $8280 ($125/sample). Biochemical verification was both time- and cost-intensive, and yielded a relatively small number of samples due to low response rates and use of other nicotine products during the follow-up period. There was a high rate of discordance of self-reported abstinence and saliva testing. Costs for data collection may be prohibitive for studies with large sample sizes or limited budgets. Our findings echo previous statements that biochemical verification is not necessary in population-based studies, and add evidence specific to technology-based studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

The association between Internet addiction and personality disorders in a general population-based sample.

PubMed

Zadra, Sina; Bischof, Gallus; Besser, Bettina; Bischof, Anja; Meyer, Christian; John, Ulrich; Rumpf, Hans-Jürgen

2016-12-01

Background and aims Data on Internet addiction (IA) and its association with personality disorder are rare. Previous studies are largely restricted to clinical samples and insufficient measurement of IA. Methods Cross-sectional analysis data are based on a German sub-sample (n = 168; 86 males; 71 meeting criteria for IA) with increased levels of excessive Internet use derived from a general population sample (n = 15,023). IA was assessed with a comprehensive standardized interview using the structure of the Composite International Diagnostic Interview and the criteria of Internet Gaming Disorder as suggested in DSM-5. Impulsivity, attention deficit hyperactivity disorder, and self-esteem were assessed with the widely used questionnaires. Results Participants with IA showed higher frequencies of personality disorders (29.6%) compared to those without IA (9.3%; p < .001). In males with IA, Cluster C personality disorders were more prevalent than among non-addicted males. Compared to participants who had IA only, lower rates of remission of IA were found among participants with IA and additional cluster B personality disorder. Personality disorders were significantly associated with IA in multivariate analysis. Comorbidity of IA and personality disorders must be considered in prevention and treatment.

Efficiency of multi-breed genomic selection for dairy cattle breeds with different sizes of reference population.

PubMed

Hozé, C; Fritz, S; Phocas, F; Boichard, D; Ducrocq, V; Croiseau, P

2014-01-01

Single-breed genomic selection (GS) based on medium single nucleotide polymorphism (SNP) density (~50,000; 50K) is now routinely implemented in several large cattle breeds. However, building large enough reference populations remains a challenge for many medium or small breeds. The high-density BovineHD BeadChip (HD chip; Illumina Inc., San Diego, CA) containing 777,609 SNP developed in 2010 is characterized by short-distance linkage disequilibrium expected to be maintained across breeds. Therefore, combining reference populations can be envisioned. A population of 1,869 influential ancestors from 3 dairy breeds (Holstein, Montbéliarde, and Normande) was genotyped with the HD chip. Using this sample, 50K genotypes were imputed within breed to high-density genotypes, leading to a large HD reference population. This population was used to develop a multi-breed genomic evaluation. The goal of this paper was to investigate the gain of multi-breed genomic evaluation for a small breed. The advantage of using a large breed (Normande in the present study) to mimic a small breed is the large potential validation population to compare alternative genomic selection approaches more reliably. In the Normande breed, 3 training sets were defined with 1,597, 404, and 198 bulls, and a unique validation set included the 394 youngest bulls. For each training set, estimated breeding values (EBV) were computed using pedigree-based BLUP, single-breed BayesC, or multi-breed BayesC for which the reference population was formed by any of the Normande training data sets and 4,989 Holstein and 1,788 Montbéliarde bulls. Phenotypes were standardized by within-breed genetic standard deviation, the proportion of polygenic variance was set to 30%, and the estimated number of SNP with a nonzero effect was about 7,000. The 2 genomic selection (GS) approaches were performed using either the 50K or HD genotypes. The correlations between EBV and observed daughter yield deviations (DYD) were computed for 6 traits and using the different prediction approaches. Compared with pedigree-based BLUP, the average gain in accuracy with GS in small populations was 0.057 for the single-breed and 0.086 for multi-breed approach. This gain was up to 0.193 and 0.209, respectively, with the large reference population. Improvement of EBV prediction due to the multi-breed evaluation was higher for animals not closely related to the reference population. In the case of a breed with a small reference population size, the increase in correlation due to multi-breed GS was 0.141 for bulls without their sire in reference population compared with 0.016 for bulls with their sire in reference population. These results demonstrate that multi-breed GS can contribute to increase genomic evaluation accuracy in small breeds. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

A Simple Sampling Method for Estimating the Accuracy of Large Scale Record Linkage Projects.

PubMed

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.

A simulative comparison of respondent driven sampling with incentivized snowball sampling--the "strudel effect".

PubMed

Gyarmathy, V Anna; Johnston, Lisa G; Caplinskiene, Irma; Caplinskas, Saulius; Latkin, Carl A

2014-02-01

Respondent driven sampling (RDS) and incentivized snowball sampling (ISS) are two sampling methods that are commonly used to reach people who inject drugs (PWID). We generated a set of simulated RDS samples on an actual sociometric ISS sample of PWID in Vilnius, Lithuania ("original sample") to assess if the simulated RDS estimates were statistically significantly different from the original ISS sample prevalences for HIV (9.8%), Hepatitis A (43.6%), Hepatitis B (Anti-HBc 43.9% and HBsAg 3.4%), Hepatitis C (87.5%), syphilis (6.8%) and Chlamydia (8.8%) infections and for selected behavioral risk characteristics. The original sample consisted of a large component of 249 people (83% of the sample) and 13 smaller components with 1-12 individuals. Generally, as long as all seeds were recruited from the large component of the original sample, the simulation samples simply recreated the large component. There were no significant differences between the large component and the entire original sample for the characteristics of interest. Altogether 99.2% of 360 simulation sample point estimates were within the confidence interval of the original prevalence values for the characteristics of interest. When population characteristics are reflected in large network components that dominate the population, RDS and ISS may produce samples that have statistically non-different prevalence values, even though some isolated network components may be under-sampled and/or statistically significantly different from the main groups. This so-called "strudel effect" is discussed in the paper. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus) in New York City.

PubMed

Harris, Stephen E; Xue, Alexander T; Alvarado-Serrano, Diego; Boehm, Joel T; Joseph, Tyler; Hickerson, Michael J; Munshi-South, Jason

2016-04-01

How urbanization shapes population genomic diversity and evolution of urban wildlife is largely unexplored. We investigated the impact of urbanization on white-footed mice,Peromyscus leucopus,in the New York City (NYC) metropolitan area using coalescent-based simulations to infer demographic history from the site-frequency spectrum. We assigned individuals to evolutionary clusters and then inferred recent divergence times, population size changes and migration using genome-wide single nucleotide polymorphisms genotyped in 23 populations sampled along an urban-to-rural gradient. Both prehistoric climatic events and recent urbanization impacted these populations. Our modelling indicates that post-glacial sea-level rise led to isolation of mainland and Long Island populations. These models also indicate that several urban parks represent recently isolated P. leucopus populations, and the estimated divergence times for these populations are consistent with the history of urbanization in NYC. © 2016 The Author(s).

Multidisciplinary population monitoring when demographic data are sparse: a case study of remote trout populations

PubMed Central

Fraser, Dylan J; Calvert, Anna M; Bernatchez, Louis; Coon, Andrew

2013-01-01

The potential of genetic, genomic, and phenotypic metrics for monitoring population trends may be especially high in isolated regions, where traditional demographic monitoring is logistically difficult and only sporadic sampling is possible. This potential, however, is relatively underexplored empirically. Over eleven years, we assessed several such metrics along with traditional ecological knowledge and catch data in a socioeconomically important trout species occupying a large, remote lake. The data revealed largely stable characteristics in two populations over 2–3 generations, but possible contemporary changes in a third population. These potential shifts were suggested by reduced catch rates, reduced body size, and changes in selection implied at one gene-associated single nucleotide polymorphism. A demographic decline in this population, however, was ambiguously supported, based on the apparent lack of temporal change in effective population size, and corresponding traditional knowledge suggesting little change in catch. We illustrate how the pluralistic approach employed has practicality for setting future monitoring efforts of these populations, by guiding monitoring priorities according to the relative merits of different metrics and availability of resources. Our study also considers some advantages and disadvantages to adopting a pluralistic approach to population monitoring where demographic data are not easily obtained. PMID:24455128

Evaluation of type 2 diabetes genetic risk variants in Chinese adults: findings from 93,000 individuals from the China Kadoorie Biobank.

PubMed

Gan, Wei; Walters, Robin G; Holmes, Michael V; Bragg, Fiona; Millwood, Iona Y; Banasik, Karina; Chen, Yiping; Du, Huaidong; Iona, Andri; Mahajan, Anubha; Yang, Ling; Bian, Zheng; Guo, Yu; Clarke, Robert J; Li, Liming; McCarthy, Mark I; Chen, Zhengming

2016-07-01

Genome-wide association studies (GWAS) have discovered many risk variants for type 2 diabetes. However, estimates of the contributions of risk variants to type 2 diabetes predisposition are often based on highly selected case-control samples, and reliable estimates of population-level effect sizes are missing, especially in non-European populations. The individual and cumulative effects of 59 established type 2 diabetes risk loci were measured in a population-based China Kadoorie Biobank (CKB) study of 93,000 Chinese adults, including >7,100 diabetes cases. Association signals were directionally consistent between CKB and the original discovery GWAS: of 56 variants passing quality control, 48 showed the same direction of effect (binomial test, p = 2.3 × 10(-8)). We observed a consistent overall trend towards lower risk variant effect sizes in CKB than in case-control samples of GWAS meta-analyses (mean 19-22% decrease in log odds, p ≤ 0.0048), likely to reflect correction of both 'winner's curse' and spectrum bias effects. The association with risk of diabetes of a genetic risk score, based on lead variants at 25 loci considered to act through beta cell function, demonstrated significant interactions with several measures of adiposity (BMI, waist circumference [WC], WHR and percentage body fat [PBF]; all p interaction < 1 × 10(-4)), with a greater effect being observed in leaner adults. Our study provides further evidence of shared genetic architecture for type 2 diabetes between Europeans and East Asians. It also indicates that even very large GWAS meta-analyses may be vulnerable to substantial inflation of effect size estimates, compared with those observed in large-scale population-based cohort studies. Details of how to access China Kadoorie Biobank data and details of the data release schedule are available from www.ckbiobank.org/site/Data+Access .

Population specific biomarkers of human aging: a big data study using South Korean, Canadian and Eastern European patient populations.

PubMed

Mamoshina, Polina; Kochetov, Kirill; Putin, Evgeny; Cortese, Franco; Aliper, Alexander; Lee, Won-Suk; Ahn, Sung-Min; Uhn, Lee; Skjodt, Neil; Kovalchuk, Olga; Scheibye-Knudsen, Morten; Zhavoronkov, Alex

2018-01-11

Accurate and physiologically meaningful biomarkers for human aging are key to assessing anti-aging therapies. Given ethnic differences in health, diet, lifestyle, behaviour, environmental exposures and even average rate of biological aging, it stands to reason that aging clocks trained on datasets obtained from specific ethnic populations are more likely to account for these potential confounding factors, resulting in an enhanced capacity to predict chronological age and quantify biological age. Here we present a deep learning-based hematological aging clock modeled using the large combined dataset of Canadian, South Korean and Eastern European population blood samples that show increased predictive accuracy in individual populations compared to population-specific hematologic aging clocks. The performance of models was also evaluated on publicly-available samples of the American population from the National Health and Nutrition Examination Survey (NHANES). In addition, we explored the association between age predicted by both population-specific and combined hematological clocks and all-cause mortality. Overall, this study suggests a) the population-specificity of aging patterns and b) hematologic clocks predicts all-cause mortality. Proposed models added to the freely available Aging.AI system allowing improved ability to assess human aging. © The Author(s) 2018. Published by Oxford University Press on behalf of The Gerontological Society of America.

A simulative comparison of respondent driven sampling with incentivized snowball sampling – the “strudel effect”

PubMed Central

Gyarmathy, V. Anna; Johnston, Lisa G.; Caplinskiene, Irma; Caplinskas, Saulius; Latkin, Carl A.

2014-01-01

Background Respondent driven sampling (RDS) and Incentivized Snowball Sampling (ISS) are two sampling methods that are commonly used to reach people who inject drugs (PWID). Methods We generated a set of simulated RDS samples on an actual sociometric ISS sample of PWID in Vilnius, Lithuania (“original sample”) to assess if the simulated RDS estimates were statistically significantly different from the original ISS sample prevalences for HIV (9.8%), Hepatitis A (43.6%), Hepatitis B (Anti-HBc 43.9% and HBsAg 3.4%), Hepatitis C (87.5%), syphilis (6.8%) and Chlamydia (8.8%) infections and for selected behavioral risk characteristics. Results The original sample consisted of a large component of 249 people (83% of the sample) and 13 smaller components with 1 to 12 individuals. Generally, as long as all seeds were recruited from the large component of the original sample, the simulation samples simply recreated the large component. There were no significant differences between the large component and the entire original sample for the characteristics of interest. Altogether 99.2% of 360 simulation sample point estimates were within the confidence interval of the original prevalence values for the characteristics of interest. Conclusions When population characteristics are reflected in large network components that dominate the population, RDS and ISS may produce samples that have statistically non-different prevalence values, even though some isolated network components may be under-sampled and/or statistically significantly different from the main groups. This so-called “strudel effect” is discussed in the paper. PMID:24360650

Genetic determinants of freckle occurrence in the Spanish population: Towards ephelides prediction from human DNA samples.

PubMed

Hernando, Barbara; Ibañez, Maria Victoria; Deserio-Cuesta, Julio Alberto; Soria-Navarro, Raquel; Vilar-Sastre, Inca; Martinez-Cadenas, Conrado

2018-03-01

Prediction of human pigmentation traits, one of the most differentiable externally visible characteristics among individuals, from biological samples represents a useful tool in the field of forensic DNA phenotyping. In spite of freckling being a relatively common pigmentation characteristic in Europeans, little is known about the genetic basis of this largely genetically determined phenotype in southern European populations. In this work, we explored the predictive capacity of eight freckle and sunlight sensitivity-related genes in 458 individuals (266 non-freckled controls and 192 freckled cases) from Spain. Four loci were associated with freckling (MC1R, IRF4, ASIP and BNC2), and female sex was also found to be a predictive factor for having a freckling phenotype in our population. After identifying the most informative genetic variants responsible for human ephelides occurrence in our sample set, we developed a DNA-based freckle prediction model using a multivariate regression approach. Once developed, the capabilities of the prediction model were tested by a repeated 10-fold cross-validation approach. The proportion of correctly predicted individuals using the DNA-based freckle prediction model was 74.13%. The implementation of sex into the DNA-based freckle prediction model slightly improved the overall prediction accuracy by 2.19% (76.32%). Further evaluation of the newly-generated prediction model was performed by assessing the model's performance in a new cohort of 212 Spanish individuals, reaching a classification success rate of 74.61%. Validation of this prediction model may be carried out in larger populations, including samples from different European populations. Further research to validate and improve this newly-generated freckle prediction model will be needed before its forensic application. Together with DNA tests already validated for eye and hair colour prediction, this freckle prediction model may lead to a substantially more detailed physical description of unknown individuals from DNA found at the crime scene. Copyright © 2017 Elsevier B.V. All rights reserved.

Utilizing Big Data and Twitter to Discover Emergent Online Communities of Cannabis Users

PubMed Central

Baumgartner, Peter; Peiper, Nicholas

2017-01-01

Large shifts in medical, recreational, and illicit cannabis consumption in the United States have implications for personalizing treatment and prevention programs to a wide variety of populations. As such, considerable research has investigated clinical presentations of cannabis users in clinical and population-based samples. Studies leveraging big data, social media, and social network analysis have emerged as a promising mechanism to generate timely insights that can inform treatment and prevention research. This study extends a novel method called stochastic block modeling to derive communities of cannabis consumers as part of a complex social network on Twitter. A set of examples illustrate how this method can ascertain candidate samples of medical, recreational, and illicit cannabis users. Implications for research planning, intervention design, and public health surveillance are discussed. PMID:28615950

A new bathyal sipunculan from Southern California, with ecological notes

NASA Astrophysics Data System (ADS)

Thompson, Bruce E.

1980-11-01

Golfingia (Nephasoma) nicolasi n. sp. is described. It is a long, slender species with a filiform introvert that is 6 to 7 times the length of the trunk. The species was often the numerically dominant taxon in samples collected from the San Nicolas Basin, California, and was also callected from several other basins off southern California. Analyses of several collections from the San Nicolas Basin show that the population was spatially patchy; temporal variation was also indicated but only one year was sampled adequately. Average population densities were highest at the base of the slopes descending into the basin from the highly productive Santa Rosa-Cortes Ridge and Tanner Bank. G. nicolasi appears to feed on the large amounts of organic detritus that accumulate from this source.

Accuracy or precision: Implications of sample design and methodology on abundance estimation

USGS Publications Warehouse

Kowalewski, Lucas K.; Chizinski, Christopher J.; Powell, Larkin A.; Pope, Kevin L.; Pegg, Mark A.

2015-01-01

Sampling by spatially replicated counts (point-count) is an increasingly popular method of estimating population size of organisms. Challenges exist when sampling by point-count method, and it is often impractical to sample entire area of interest and impossible to detect every individual present. Ecologists encounter logistical limitations that force them to sample either few large-sample units or many small sample-units, introducing biases to sample counts. We generated a computer environment and simulated sampling scenarios to test the role of number of samples, sample unit area, number of organisms, and distribution of organisms in the estimation of population sizes using N-mixture models. Many sample units of small area provided estimates that were consistently closer to true abundance than sample scenarios with few sample units of large area. However, sample scenarios with few sample units of large area provided more precise abundance estimates than abundance estimates derived from sample scenarios with many sample units of small area. It is important to consider accuracy and precision of abundance estimates during the sample design process with study goals and objectives fully recognized, although and with consequence, consideration of accuracy and precision of abundance estimates is often an afterthought that occurs during the data analysis process.

Back pain in the German adult population: prevalence, severity, and sociodemographic correlates in a multiregional survey.

PubMed

Schmidt, Carsten Oliver; Raspe, Heiner; Pfingsten, Michael; Hasenbring, Monika; Basler, Heinz Dieter; Eich, Wolfgang; Kohlmann, Thomas

2007-08-15

A population-based cross-sectional multiregion postal survey. To provide a descriptive epidemiology of the prevalence and severity of back pain in German adults and to analyze sociodemographic correlates for disabling back pain within and across regions. Back pain is a leading health problem in Germany. However, comprehensive population-based evidence on the severity of back pain is still fragmentary for this country. Despite earlier findings concerning large prevalence differences across regions, systematic explanations remain to be ascertained. Questionnaire data were collected for 9263 subjects in 5 German cities and regions (population-based random samples, postal questionnaire). Point, 1-year, and lifetime prevalence were assessed using direct questions, and graded back pain was determined using the Graded Chronic Pain Scale. Poststratification was applied to adjust for cross-regional sociodemographic differences. Point-prevalence was 37.1%, 1-year prevalence 76.0%, and lifetime prevalence 85.5%. A substantial minority had severe (Grade II, 8.0%) or disabling back pain (Grade III-IV, 11.2%). Subjects with a low educational level reported substantially more disabling back pain. This variable was an important predictor for large cross-regional differences in the burden of back pain. Back pain is a highly prevalent condition in Germany. Disabling back pain in this country may be regarded as part of a social disadvantage syndrome. Educational level should receive greater attention in future cross-regional comparisons of back pain.

How Generalizable Is Your Experiment? An Index for Comparing Experimental Samples and Populations

ERIC Educational Resources Information Center

Tipton, Elizabeth

2014-01-01

Although a large-scale experiment can provide an estimate of the average causal impact for a program, the sample of sites included in the experiment is often not drawn randomly from the inference population of interest. In this article, we provide a generalizability index that can be used to assess the degree of similarity between the sample of…

Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach

PubMed Central

Boitard, Simon; Rodríguez, Willy; Jay, Flora; Mona, Stefano; Austerlitz, Frédéric

2016-01-01

Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles. PMID:26943927

Statistical properties of Faraday rotation measure in external galaxies - I. Intervening disc galaxies

NASA Astrophysics Data System (ADS)

Basu, Aritra; Mao, S. A.; Fletcher, Andrew; Kanekar, Nissim; Shukurov, Anvar; Schnitzeler, Dominic; Vacca, Valentina; Junklewitz, Henrik

2018-06-01

Deriving the Faraday rotation measure (RM) of quasar absorption line systems, which are tracers of high-redshift galaxies intervening background quasars, is a powerful tool for probing magnetic fields in distant galaxies. Statistically comparing the RM distributions of two quasar samples, with and without absorption line systems, allows one to infer magnetic field properties of the intervening galaxy population. Here, we have derived the analytical form of the probability distribution function (PDF) of RM produced by a single galaxy with an axisymmetric large-scale magnetic field. We then further determine the PDF of RM for one random sight line traversing each galaxy in a population with a large-scale magnetic field prescription. We find that the resulting PDF of RM is dominated by a Lorentzian with a width that is directly related to the mean axisymmetric large-scale field strength of the galaxy population if the dispersion of B0 within the population is smaller than . Provided that RMs produced by the intervening galaxies have been successfully isolated from other RM contributions along the line of sight, our simple model suggests that in galaxies probed by quasar absorption line systems can be measured within ≈50 per cent accuracy without additional constraints on the magneto-ionic medium properties of the galaxies. Finally, we discuss quasar sample selection criteria that are crucial to reliably interpret observations, and argue that within the limitations of the current data base of absorption line systems, high-metallicity damped Lyman-α absorbers are best suited to study galactic dynamo action in distant disc galaxies.

Lifestyle Factors and Premature Ejaculation: Are Physical Exercise, Alcohol Consumption, and Body Mass Index Associated With Premature Ejaculation and Comorbid Erectile Problems?

PubMed

Ventus, Daniel; Jern, Patrick

2016-10-01

Premature ejaculation (PE) is a common sexual problem in men, but its etiology remains uncertain. Lifestyle factors have long been hypothesized to be associated with sexual problems in general and have been proposed as risk factors for PE. To explore associations among physical exercise, alcohol use, body mass index, PE, and erectile dysfunction. A population-based sample of Finnish men and a sample of Finnish men diagnosed with PE were surveyed for statistical comparisons. Participants using selective serotonin reuptake inhibitors or other medications known to affect symptoms of PE were excluded from analyses. Self-report questionnaires: Multiple Indicators of Premature Ejaculation, International Index of Erectile Function-5, Alcohol Use Disorders Identification Test, and Godin Leisure-Time Exercise Questionnaire. The clinical sample reported lower levels of physical exercise (mean = 27.53, SD = 21.01, n = 69) than the population-based sample (mean = 34.68, SD = 22.82, n = 863, t930 = 2.52, P = .012), and the effect size was large (d = 0.85). There was a small negative correlation between levels of physical exercise and symptoms of PE (r = -0.09, P < .01, n = 863) in the population-based sample. The association between physical exercise and PE remained significant after controlling for effects of age, erectile dysfunction, alcohol use, and body mass index. If future studies show that the direction of causality of this association is such that physical activity alleviates PE symptoms, then including physical activity in PE treatment interventions could be a promising addition to treatment regimes. Copyright © 2016 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kendler, K.S.; Straub, R.E.; MacLean, C.J.

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/ormore » 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.« less

Methodology of a nationwide cross-sectional survey of prevalence and epidemiological patterns of hepatitis A, B and C infection in Brazil.

PubMed

Ximenes, Ricardo Arraes de Alencar; Pereira, Leila Maria Beltrão; Martelli, Celina Maria Turchi; Merchán-Hamann, Edgar; Stein, Airton Tetelbom; Figueiredo, Gerusa Maria; Braga, Maria Cynthia; Montarroyos, Ulisses Ramos; Brasil, Leila Melo; Turchi, Marília Dalva; Fonseca, José Carlos Ferraz da; Lima, Maria Luiza Carvalho de; Alencar, Luis Cláudio Arraes de; Costa, Marcelo; Coral, Gabriela; Moreira, Regina Celia; Cardoso, Maria Regina Alves

2010-09-01

A population-based survey to provide information on the prevalence of hepatitis viral infection and the pattern of risk factors was carried out in the urban population of all Brazilian state capitals and the Federal District, between 2005 and 2009. This paper describes the design and methodology of the study which involved a population aged 5 to 19 for hepatitis A and 10 to 69 for hepatitis B and C. Interviews and blood samples were obtained through household visits. The sample was selected using stratified multi-stage cluster sampling and was drawn with equal probability from each domain of study (region and age-group). Nationwide, 19,280 households and ~31,000 residents were selected. The study is large enough to detect prevalence of viral infection around 0.1% and risk factor assessments within each region. The methodology seems to be a viable way of differentiating between distinct epidemiological patterns of hepatitis A, B and C. These data will be of value for the evaluation of vaccination policies and for the design of control program strategies.

High-throughput telomere length quantification by FISH and its application to human population studies.

PubMed

Canela, Andrés; Vera, Elsa; Klatt, Peter; Blasco, María A

2007-03-27

A major limitation of studies of the relevance of telomere length to cancer and age-related diseases in human populations and to the development of telomere-based therapies has been the lack of suitable high-throughput (HT) assays to measure telomere length. We have developed an automated HT quantitative telomere FISH platform, HT quantitative FISH (Q-FISH), which allows the quantification of telomere length as well as percentage of short telomeres in large human sample sets. We show here that this technique provides the accuracy and sensitivity to uncover associations between telomere length and human disease.

A league of their own: demographics, motivations and patterns of use of 1,955 male adult non-medical anabolic steroid users in the United States

PubMed Central

Cohen, Jason; Collins, Rick; Darkes, Jack; Gwartney, Daniel

2007-01-01

Background Rule violations among elite-level sports competitors and tragedies among adolescents have largely defined the issue of non-medical anabolic-androgenic steroid (NMAAS) use for the public and policy makers. However, the predominant and oft-ignored segment of the NMAAS community exists in the general population that is neither participating in competitive sports nor adolescent. A clearer profile of NMAAS users within the general population is an initial step in developing a full understanding of NMAAS use and devising appropriate policy and interventions. This survey sought to provide a more comprehensive profile of NMAAS users by accessing a large sample of user respondents from around the United States. Methods U.S.-based male NMAAS users (n = 1955) were recruited from various Internet websites dedicated to resistance training activities and use of ergogenic substances, mass emails, and print media to participate in a 291-item web-based survey. The Internet was utilized to provide a large and geographically diverse sample with the greatest degree of anonymity to facilitate participation. Results The majority of respondents did not initiate AAS use during adolescence and their NMAAS use was not motivated by athletics. The typical user was a Caucasian, highly-educated, gainfully employed professional approximately 30 years of age, who was earning an above-average income, was not active in organized sports, and whose use was motivated by increases in skeletal muscle mass, strength, and physical attractiveness. These findings question commonly held views of the typical NMAAS user and the associated underlying motivations. Conclusion The focus on "cheating" athletes and at risk youth has led to ineffective policy as it relates to the predominant group of NMAAS users. Effective policy, prevention or intervention should address the target population(s) and their reasons for use while utilizing their desire for responsible use and education. PMID:17931410

Clinical characteristics of an Afrikaner founder population recruited for a schizophrenia genetic study.

PubMed

Roos, Johannes Lodewikus; Pretorius, Herman Walter; Karayiorgou, Maria

2009-01-01

The clinical characteristics of an Afrikaner founder population sample recruited for a schizophrenia genetic study are described. Comparisons on several clinical characteristics between this sample and a U.S. sample of schizophrenia patients show that generalization of findings in a founder population to the population at large is applicable. The assessment of the frequency of the 22q11 deletion in Afrikaner schizophrenia patients is approximately 2%, similar to findings in a U.S. sample. Results of analysis of early non-psychotic deviant behavior in subjects under the age of 10 years in the Afrikaner population broadly replicated findings in a U.S. sample. Approximately half of male schizophrenia patients and a quarter of female patients in the Afrikaner schizophrenia database used or abused cannabis. Male users of cannabis with severe early deviant behavior had the lowest mean age of criteria onset, namely 18.4 years. These findings confirm previous findings, indicating that early deviance is linked to later outcome of disease. The clinical characteristics and premorbid variables in 12 childhood-onset Afrikaner schizophrenia patients thus far recruited in this study compare favorably with what is known about childhood-onset schizophrenia in a U.S. sample. The prevalence of co-morbid OCD/OCS in this Afrikaner schizophrenia founder sample was 13.2% which is in keeping with that of co-morbid OCD in schizophrenia, estimated at 12.2% by the U.S. National Institute of Mental Health. These findings confirm that the clinical characteristics of a schizophrenia sample drawn from the Afrikaner founder population can be generalized to the schizophrenia population at large when compared to findings reported in the literature.

Paraphilic Sexual Interests and Sexually Coercive Behavior: A Population-Based Twin Study.

PubMed

Baur, Elena; Forsman, Mats; Santtila, Pekka; Johansson, Ada; Sandnabba, Kenneth; Långström, Niklas

2016-07-01

Prior research with selected clinical and forensic samples suggests associations between paraphilic sexual interests (e.g., exhibitionism and sexual sadism) and sexually coercive behavior. However, no study to date used a large, representative and genetically informative population sample to address the potential causal nature of this association. We used self-report data on paraphilic and sexually coercive behavior from 5990 18- to 32-year-old male and female twins from a contemporary Finnish population cohort. Logistic regression and co-twin control models were employed to examine if paraphilic behaviors were causally related to coercive behavior or if suggested links were confounded by familial (genetic or common family environment) risk factors. Results indicated that associations between four out of five tested paraphilic behaviors (exhibitionism, masochism, sadism, and voyeurism, respectively) and sexually coercive behavior were moderate to strong. Transvestic fetishism was not independently associated with sexual coercion. Comparisons of twins reporting paraphilic behavior with their paraphilic behavior-discordant twin further suggested that associations were largely independent of shared genetic and environmental confounds, consistent with a causal association. In conclusion, similar to previously reported predictive effects of paraphilias on sexual crime recidivism, paraphilic behavior among young adults in the general population increases sexual offending risk. Further, early identification of paraphilic interest and preventive interventions with at-risk individuals might also reduce perpetration of first-time sexual violence.

Cryptic Distant Relatives Are Common in Both Isolated and Cosmopolitan Genetic Samples

PubMed Central

Macpherson, J. Michael; Eriksson, Nick; Saxonov, Serge; Pe'er, Itsik; Mountain, Joanna L.

2012-01-01

Although a few hundred single nucleotide polymorphisms (SNPs) suffice to infer close familial relationships, high density genome-wide SNP data make possible the inference of more distant relationships such as 2nd to 9th cousinships. In order to characterize the relationship between genetic similarity and degree of kinship given a timeframe of 100–300 years, we analyzed the sharing of DNA inferred to be identical by descent (IBD) in a subset of individuals from the 23andMe customer database (n = 22,757) and from the Human Genome Diversity Panel (HGDP-CEPH, n = 952). With data from 121 populations, we show that the average amount of DNA shared IBD in most ethnolinguistically-defined populations, for example Native American groups, Finns and Ashkenazi Jews, differs from continentally-defined populations by several orders of magnitude. Via extensive pedigree-based simulations, we determined bounds for predicted degrees of relationship given the amount of genomic IBD sharing in both endogamous and ‘unrelated’ population samples. Using these bounds as a guide, we detected tens of thousands of 2nd to 9th degree cousin pairs within a heterogenous set of 5,000 Europeans. The ubiquity of distant relatives, detected via IBD segments, in both ethnolinguistic populations and in large ‘unrelated’ populations samples has important implications for genetic genealogy, forensics and genotype/phenotype mapping studies. PMID:22509285

Genetic and environmental contributions to the inverse association between specific autistic traits and experience seeking in adults.

PubMed

Romero-Martínez, Ángel; Moya-Albiol, Luís; Vinkhuyzen, Anna A E; Polderman, Tinca J C

2016-12-01

Autistic traits are characterized by social and communication problems, restricted, repetitive and stereotyped patterns of behavior, interests and activities. The relation between autistic traits and personality characteristics is largely unknown. This study focused on the relation between five specific autistic traits measured with the abridged version of the Autism Spectrum Quotient ("social problems," "preference for routine," "attentional switching difficulties," "imagination impairments," "fascination for numbers and patterns") and Experience Seeking (ES) in a general population sample of adults, and subsequently investigated the genetic and environmental etiology between these traits. Self-reported data on autistic traits and ES were collected in a population sample (n = 559) of unrelated individuals, and in a population based family sample of twins and siblings (n = 560). Phenotypic, genetic and environmental associations between traits were examined in a bivariate model, accounting for sex and age differences. Phenotypically, ES correlated significantly with "preference for routine" and "imagination impairments" in both samples but was unrelated to the other autistic traits. Genetic analyses in the family sample revealed that the association between ES and "preference for routine" and "imagination impairments" could largely be explained by a shared genetic factor (89% and 70%, respectively). Our analyses demonstrated at a phenotypic and genetic level an inverse relationship between ES and specific autistic traits in adults. ES is associated with risk taking behavior such as substance abuse, antisocial behavior and financial problems. Future research could investigate whether autistic traits, in particular strong routine preference and impaired imagination skills, serve as protective factors for such risky behaviors. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Calculating p-values and their significances with the Energy Test for large datasets

NASA Astrophysics Data System (ADS)

Barter, W.; Burr, C.; Parkes, C.

2018-04-01

The energy test method is a multi-dimensional test of whether two samples are consistent with arising from the same underlying population, through the calculation of a single test statistic (called the T-value). The method has recently been used in particle physics to search for samples that differ due to CP violation. The generalised extreme value function has previously been used to describe the distribution of T-values under the null hypothesis that the two samples are drawn from the same underlying population. We show that, in a simple test case, the distribution is not sufficiently well described by the generalised extreme value function. We present a new method, where the distribution of T-values under the null hypothesis when comparing two large samples can be found by scaling the distribution found when comparing small samples drawn from the same population. This method can then be used to quickly calculate the p-values associated with the results of the test.

A population-based study on health-related quality of life among urban community residents in Shenyang, Northeast of China.

PubMed

Song, Tian; Ding, Yan-wei; Sun, Yan; He, Yi-Ni; Qi, Dian-Jun; Wu, Ying; Wu, Bin; Lang, Lang; Yu, Kai; Zhao, Xin; Zhu, Liang-liang; Wang, Shuang; Yu, Xiao-Song

2015-09-19

Due to the rising standard of living environment and advances in public health and medical care in China, it has been a tendency in recent years that health-related quality of life (HRQoL) has been increasingly acknowledged in community health management. However, large-scale population-based study on evaluating HQRoL in northeast of China was not conducted. This article aims to investigate the HRQoL in community residents in Northeast China and explore the associated factors. Stratified multiple-stage sampling method was used in the cross-sectional survey to investigate HRQoL of community residents in northeast of China. Univariate analysis and multiple linear regressions were used to analyze the factors associated to HRQoL of the community residents. The results were confirmed that HRQoL in general population was well performed for the first time in northeast of China in a large scale population. Community residents had better mental health than physical health. The factors influencing HRQoL included gender, age, educational level, marital status, ethnic group, chronic disease status, having breakfast frequency weekly and sleep quality. However, drinking and smoking habits did not affect residents' HRQoL. In this study, the result of the large-scale survey was satisfactory in northeast of China, providing HRQoL status of community residents. Policies on specific health management in community public health would emphasize on lifestyle behaviors especially eating habits in order to improving HRQoL.

Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes.

PubMed

Bentzen, Amalie Kai; Marquard, Andrea Marion; Lyngaa, Rikke; Saini, Sunil Kumar; Ramskov, Sofie; Donia, Marco; Such, Lina; Furness, Andrew J S; McGranahan, Nicholas; Rosenthal, Rachel; Straten, Per Thor; Szallasi, Zoltan; Svane, Inge Marie; Swanton, Charles; Quezada, Sergio A; Jakobsen, Søren Nyboe; Eklund, Aron Charles; Hadrup, Sine Reker

2016-10-01

Identification of the peptides recognized by individual T cells is important for understanding and treating immune-related diseases. Current cytometry-based approaches are limited to the simultaneous screening of 10-100 distinct T-cell specificities in one sample. Here we use peptide-major histocompatibility complex (MHC) multimers labeled with individual DNA barcodes to screen >1,000 peptide specificities in a single sample, and detect low-frequency CD8 T cells specific for virus- or cancer-restricted antigens. When analyzing T-cell recognition of shared melanoma antigens before and after adoptive cell therapy in melanoma patients, we observe a greater number of melanoma-specific T-cell populations compared with cytometry-based approaches. Furthermore, we detect neoepitope-specific T cells in tumor-infiltrating lymphocytes and peripheral blood from patients with non-small cell lung cancer. Barcode-labeled pMHC multimers enable the combination of functional T-cell analysis with large-scale epitope recognition profiling for the characterization of T-cell recognition in various diseases, including in small clinical samples.

Decomposing Educational Inequalities in Child Mortality: A Temporal Trend Analysis of Access to Water and Sanitation in Peru

PubMed Central

Bohra, Tasneem; Benmarhnia, Tarik; McKinnon, Britt; Kaufman, Jay S.

2017-01-01

Previous studies of inequality in health and mortality have largely focused on income-based inequality. Maternal education plays an important role in determining access to water and sanitation, and inequalities in child mortality arising due to differential access, especially in low- and middle-income countries such as Peru. This article aims to explain education-related inequalities in child mortality in Peru using a regression-based decomposition of the concentration index of child mortality. The analysis combines a concentration index created along a cumulative distribution of the Demographic and Health Surveys sample ranked according to maternal education, and decomposition measures the contribution of water and sanitation to educational inequalities in child mortality. We observed a large education-related inequality in child mortality and access to water and sanitation. There is a need for programs and policies in child health to focus on ensuring equity and to consider the educational stratification of the population to target the most disadvantaged segments of the population. PMID:27821698

Approximate sample sizes required to estimate length distributions

USGS Publications Warehouse

Miranda, L.E.

2007-01-01

The sample sizes required to estimate fish length were determined by bootstrapping from reference length distributions. Depending on population characteristics and species-specific maximum lengths, 1-cm length-frequency histograms required 375-1,200 fish to estimate within 10% with 80% confidence, 2.5-cm histograms required 150-425 fish, proportional stock density required 75-140 fish, and mean length required 75-160 fish. In general, smaller species, smaller populations, populations with higher mortality, and simpler length statistics required fewer samples. Indices that require low sample sizes may be suitable for monitoring population status, and when large changes in length are evident, additional sampling effort may be allocated to more precisely define length status with more informative estimators. ?? Copyright by the American Fisheries Society 2007.

Evidence for population bottlenecks and subtle genetic structure in the yellow rail

USGS Publications Warehouse

Popper, Kenneth J.; Miller, Leonard F.; Green, Michael; Haig, Susan M.; Mullins, Thomas D.

2012-01-01

The Yellow Rail (Coturnicops noveboracencis) is among the most enigmatic and least studied North American birds. Nesting exclusively in marshes and wetlands, it breeds largely east of the Rocky Mountains in the northern United States and Canada, but there is an isolated population in southern Oregon once believed extirpated. The degree of connectivity of the Oregon population with the main population is unknown. We used mitochondrial DNA sequences (mtDNA) and six microsatellite loci to characterize the Yellow Rail's genetic structure and diversity patterns in six areas. Our mtDNA-based analyses of genetic structure identified significant population differentiation, but pairwise comparison of regions identified no clear geographic trends. In contrast, microsatellites suggested subtle genetic structure differentiating the Oregon population from those in the five regions sampled in the Yellow Rail's main breeding range. The genetic diversity of the Oregon population was also the lowest of the six regions sampled, and Oregon was one of three regions that demonstrated evidence of recent population bottlenecks. Factors that produced population reductions may include loss of wetlands to development and agricultural conversion, drought, and wildfire. At this time, we are unable to determine if the high percentage (50%) of populations having experienced bottlenecks is representative of the Yellow Rail's entire range. Further genetic data from additional breeding populations will be required for this issue to be addressed.

Brief Report: The Prevalence of Neurofibromatosis Type 1 among Children with Autism Spectrum Disorder Identified by the Autism and Developmental Disabilities Monitoring Network

ERIC Educational Resources Information Center

Bilder, Deborah A.; Bakian, Amanda V.; Stevenson, David A.; Carbone, Paul S.; Cunniff, Christopher; Goodman, Alyson B.; McMahon, William M.; Fisher, Nicole P.; Viskochil, David

2016-01-01

Neurofibromatosis type 1 (NF1) is an inherited neurocutaneous disorder associated with neurodevelopmental disorders including autism spectrum disorder (ASD). The frequency of ASD/NF1 co-occurrence has been subject to debate since the 1980s. This relationship was investigated in a large population-based sample of 8-year-old children identified with…

Autosomal STRs provide genetic evidence for the hypothesis that Tai people originate from southern China.

PubMed

Sun, Hao; Zhou, Chi; Huang, Xiaoqin; Lin, Keqin; Shi, Lei; Yu, Liang; Liu, Shuyuan; Chu, Jiayou; Yang, Zhaoqing

2013-01-01

Tai people are widely distributed in Thailand, Laos and southwestern China and are a large population of Southeast Asia. Although most anthropologists and historians agree that modern Tai people are from southwestern China and northern Thailand, the place from which they historically migrated remains controversial. Three popular hypotheses have been proposed: northern origin hypothesis, southern origin hypothesis or an indigenous origin. We compared the genetic relationships between the Tai in China and their "siblings" to test different hypotheses by analyzing 10 autosomal microsatellites. The genetic data of 916 samples from 19 populations were analyzed in this survey. The autosomal STR data from 15 of the 19 populations came from our previous study (Lin et al., 2010). 194 samples from four additional populations were genotyped in this study: Han (Yunnan), Dai (Dehong), Dai (Yuxi) and Mongolian. The results of genetic distance comparisons, genetic structure analyses and admixture analyses all indicate that populations from northern origin hypothesis have large genetic distances and are clearly differentiated from the Tai. The simulation-based ABC analysis also indicates this. The posterior probability of the northern origin hypothesis is just 0.04 [95%CI: (0.01-0.06)]. Conversely, genetic relationships were very close between the Tai and populations from southern origin or an indigenous origin hypothesis. Simulation-based ABC analyses were also used to distinguish the southern origin hypothesis from the indigenous origin hypothesis. The results indicate that the posterior probability of the southern origin hypothesis [0.640, 95%CI: (0.524-0.757)] is greater than that of the indigenous origin hypothesis [0.324, 95%CI: (0.211-0.438)]. Therefore, we propose that the genetic evidence does not support the hypothesis of northern origin. Our genetic data indicate that the southern origin hypothesis has higher probability than the other two hypotheses statistically, suggesting that the Tai people most likely originated from southern China.

Cross-cultural measurement invariance of the General Health Questionnaire-12 in a German and a Colombian population sample.

PubMed

Romppel, Matthias; Hinz, Andreas; Finck, Carolyn; Young, Jeremy; Brähler, Elmar; Glaesmer, Heide

2017-12-01

While the General Health Questionnaire, 12-item version (GHQ-12) has been widely used in cross-cultural comparisons, rigorous tests of the measurement equivalence of different language versions are still lacking. Thus, our study aims at investigating configural, metric and scalar invariance across the German and the Spanish version of the GHQ-12 in two population samples. The GHQ-12 was applied in two large-scale population-based samples in Germany (N = 1,977) and Colombia (N = 1,500). To investigate measurement equivalence, confirmatory factor analyses were conducted in both samples. In the German sample mean GHQ-12 total scores were higher than in the Colombian sample. A one-factor model including response bias on the negatively worded items showed superior fit in the German and the Colombian sample; thus both versions of the GHQ-12 showed configural invariance. Factor loadings and intercepts were not equal across both samples; thus GHQ-12 showed no metric and scalar invariance. As both versions of the GHQ-12 did not show measurement equivalence, it is not recommendable to compare both measures and to conclude that mental distress is higher in the German sample, although we do not know if the differences are attributable to measurement problems or represent a real difference in mental distress. The study underlines the importance of measurement equivalence in cross-cultural comparisons. Copyright © 2017 John Wiley & Sons, Ltd.

Understanding and estimating effective population size for practical application in marine species management.

PubMed

Hare, Matthew P; Nunney, Leonard; Schwartz, Michael K; Ruzzante, Daniel E; Burford, Martha; Waples, Robin S; Ruegg, Kristen; Palstra, Friso

2011-06-01

Effective population size (N(e)) determines the strength of genetic drift in a population and has long been recognized as an important parameter for evaluating conservation status and threats to genetic health of populations. Specifically, an estimate of N(e) is crucial to management because it integrates genetic effects with the life history of the species, allowing for predictions of a population's current and future viability. Nevertheless, compared with ecological and demographic parameters, N(e) has had limited influence on species management, beyond its application in very small populations. Recent developments have substantially improved N(e) estimation; however, some obstacles remain for the practical application of N(e) estimates. For example, the need to define the spatial and temporal scale of measurement makes the concept complex and sometimes difficult to interpret. We reviewed approaches to estimation of N(e) over both long-term and contemporary time frames, clarifying their interpretations with respect to local populations and the global metapopulation. We describe multiple experimental factors affecting robustness of contemporary N(e) estimates and suggest that different sampling designs can be combined to compare largely independent measures of N(e) for improved confidence in the result. Large populations with moderate gene flow pose the greatest challenges to robust estimation of contemporary N(e) and require careful consideration of sampling and analysis to minimize estimator bias. We emphasize the practical utility of estimating N(e) by highlighting its relevance to the adaptive potential of a population and describing applications in management of marine populations, where the focus is not always on critically endangered populations. Two cases discussed include the mechanisms generating N(e) estimates many orders of magnitude lower than census N in harvested marine fishes and the predicted reduction in N(e) from hatchery-based population supplementation. ©2011 Society for Conservation Biology.

Conspicuous carotenoid-based pelvic spine ornament in three-spined stickleback populations—occurrence and inheritance

PubMed Central

Amundsen, CR; Gjøen, HM; Larsen, B; Egeland, ES

2015-01-01

Reports on reddish carotenoid-based ornaments in female three-spined sticklebacks (Gasterosteus aculeatus) are few, despite the large interest in the species’ behaviour, ornamentation, morphology and evolution. We sampled sticklebacks from 17 sites in north-western Europe in this first extensive study on the occurrence of carotenoid-based female pelvic spines and throat ornaments. The field results showed that females, and males, with reddish spines were found in all 17 populations. Specimens of both sexes with conspicuous red spines were found in several of the sites. The pelvic spines of males were more intensely red compared to the females’ spines, and large specimens were more red than small ones. Fish infected with the tapeworm (Schistocephalus solidus) had drabber spines than uninfected fish. Both sexes had red spines both during and after the spawning period, but the intensity of the red colour was more exaggerated during the spawning period. As opposed to pelvic spines, no sign of red colour at the throat was observed in any female from any of the 17 populations. A rearing experiment was carried out to estimate a potential genetic component of the pelvic spine ornament by artificial crossing and rearing of 15 family groups during a 12 months period. The results indicated that the genetic component of the red colour at the spines was low or close to zero. Although reddish pelvic spines seem common in populations of stickleback, the potential adaptive function of the reddish pelvic spines remains largely unexplained. PMID:25861558

Sex Differences in DSM-IV Posttraumatic Stress Disorder Symptoms Expression Using Item Response Theory: a Population-based Study

PubMed Central

Rivollier, Fabrice; Peyre, Hugo; Hoertel, Nicolas; Blanco, Carlos; Limosin, Frédéric; Delorme, Richard

2015-01-01

Background Whether there are systematic sex differences in posttraumatic stress disorder (PTSD) symptom expression remains debated. Using methods based on item response theory (IRT), we aimed at examining differences in the likelihood of reporting DSM-IV symptoms of PTSD between women and men, while stratifying for major trauma type and equating for PTSD severity. Method We compared data from women and men in a large nationally representative adult sample, the National Epidemiologic Survey on Alcohol and Related Conditions. Analyses were conducted in the full population sample of individuals who met the DSM-IV criterion A (n = 23,860) and in subsamples according to trauma types. Results The clinical presentation of the 17 DSM-IV PTSD symptoms in the general population did not substantially differ in women and men in the full population and by trauma type after equating for levels of PTSD severity. The only exception was the symptom “foreshortened future”, which was more likely endorsed by men at equivalent levels of PTSD severity. Limitations The retrospective nature of the assessment of PTSD symptoms could have led to recall bias. Our sample size was too small to draw conclusions among individuals who experienced war-related traumas. Conclusions Our findings suggest that the clinical presentation of PTSD does not differ substantially between women and men. We also provide additional psychometric support to the exclusion of the symptom “foreshortened future” from the diagnostic criteria for PTSD in the DSM-5. PMID:26342916

Sex differences in DSM-IV posttraumatic stress disorder symptoms expression using item response theory: A population-based study.

PubMed

Rivollier, Fabrice; Peyre, Hugo; Hoertel, Nicolas; Blanco, Carlos; Limosin, Frédéric; Delorme, Richard

2015-11-15

Whether there are systematic sex differences in posttraumatic stress disorder (PTSD) symptom expression remains debated. Using methods based on item response theory (IRT), we aimed at examining differences in the likelihood of reporting DSM-IV symptoms of PTSD between women and men, while stratifying for major trauma type and equating for PTSD severity. We compared data from women and men in a large nationally representative adult sample, the National Epidemiologic Survey on Alcohol and Related Conditions. Analyses were conducted in the full population sample of individuals who met the DSM-IV criterion A (n=23,860) and in subsamples according to trauma types. The clinical presentation of the 17 DSM-IV PTSD symptoms in the general population did not substantially differ in women and men in the full population and by trauma type after equating for levels of PTSD severity. The only exception was the symptom "foreshortened future", which was more likely endorsed by men at equivalent levels of PTSD severity. The retrospective nature of the assessment of PTSD symptoms could have led to recall bias. Our sample size was too small to draw conclusions among individuals who experienced war-related traumas. Our findings suggest that the clinical presentation of PTSD does not differ substantially between women and men. We also provide additional psychometric support to the exclusion of the symptom "foreshortened future" from the diagnostic criteria for PTSD in the DSM-5. Copyright © 2015 Elsevier B.V. All rights reserved.

The Association between Childhood and Adolescent Sexual Abuse and Proxies for Sexual Risk Behavior: A Random Sample of the General Population of Sweden

ERIC Educational Resources Information Center

Steel, Jennifer L.; Herlitz, Claes A.

2005-01-01

Objective: Several studies with small and ''high risk'' samples have demonstrated that a history of childhood or adolescent sexual abuse (CASA) is associated with sexual risk behaviors (SRBs). However, few studies with large random samples from the general population have specifically examined the relationship between CASA and SRBs with a…

Localised estimates and spatial mapping of poverty incidence in the state of Bihar in India—An application of small area estimation techniques

PubMed Central

Aditya, Kaustav; Sud, U. C.

2018-01-01

Poverty affects many people, but the ramifications and impacts affect all aspects of society. Information about the incidence of poverty is therefore an important parameter of the population for policy analysis and decision making. In order to provide specific, targeted solutions when addressing poverty disadvantage small area statistics are needed. Surveys are typically designed and planned to produce reliable estimates of population characteristics of interest mainly at higher geographic area such as national and state level. Sample sizes are usually not large enough to provide reliable estimates for disaggregated analysis. In many instances estimates are required for areas of the population for which the survey providing the data was unplanned. Then, for areas with small sample sizes, direct survey estimation of population characteristics based only on the data available from the particular area tends to be unreliable. This paper describes an application of small area estimation (SAE) approach to improve the precision of estimates of poverty incidence at district level in the State of Bihar in India by linking data from the Household Consumer Expenditure Survey 2011–12 of NSSO and the Population Census 2011. The results show that the district level estimates generated by SAE method are more precise and representative. In contrast, the direct survey estimates based on survey data alone are less stable. PMID:29879202

Localised estimates and spatial mapping of poverty incidence in the state of Bihar in India-An application of small area estimation techniques.

PubMed

Chandra, Hukum; Aditya, Kaustav; Sud, U C

2018-01-01

Poverty affects many people, but the ramifications and impacts affect all aspects of society. Information about the incidence of poverty is therefore an important parameter of the population for policy analysis and decision making. In order to provide specific, targeted solutions when addressing poverty disadvantage small area statistics are needed. Surveys are typically designed and planned to produce reliable estimates of population characteristics of interest mainly at higher geographic area such as national and state level. Sample sizes are usually not large enough to provide reliable estimates for disaggregated analysis. In many instances estimates are required for areas of the population for which the survey providing the data was unplanned. Then, for areas with small sample sizes, direct survey estimation of population characteristics based only on the data available from the particular area tends to be unreliable. This paper describes an application of small area estimation (SAE) approach to improve the precision of estimates of poverty incidence at district level in the State of Bihar in India by linking data from the Household Consumer Expenditure Survey 2011-12 of NSSO and the Population Census 2011. The results show that the district level estimates generated by SAE method are more precise and representative. In contrast, the direct survey estimates based on survey data alone are less stable.

Performance Assessment PCR-Based Assays Targeting Bacteroidales Genetic Markers of Bovine Fecal Pollution▿

PubMed Central

Shanks, Orin C.; White, Karen; Kelty, Catherine A.; Hayes, Sam; Sivaganesan, Mano; Jenkins, Michael; Varma, Manju; Haugland, Richard A.

2010-01-01

There are numerous PCR-based assays available to characterize bovine fecal pollution in ambient waters. The determination of which approaches are most suitable for field applications can be difficult because each assay targets a different gene, in many cases from different microorganisms, leading to variation in assay performance. We describe a performance evaluation of seven end-point PCR and real-time quantitative PCR (qPCR) assays reported to be associated with either ruminant or bovine feces. Each assay was tested against a reference collection of DNA extracts from 247 individual bovine fecal samples representing 11 different populations and 175 fecal DNA extracts from 24 different animal species. Bovine-associated genetic markers were broadly distributed among individual bovine samples ranging from 39 to 93%. Specificity levels of the assays spanned 47.4% to 100%. End-point PCR sensitivity also varied between assays and among different bovine populations. For qPCR assays, the abundance of each host-associated genetic marker was measured within each bovine population and compared to results of a qPCR assay targeting 16S rRNA gene sequences from Bacteroidales. Experiments indicate large discrepancies in the performance of bovine-associated assays across different bovine populations. Variability in assay performance between host populations suggests that the use of bovine microbial source-tracking applications will require a priori characterization at each watershed of interest. PMID:20061457

Sampling through time and phylodynamic inference with coalescent and birth–death models

PubMed Central

Volz, Erik M.; Frost, Simon D. W.

2014-01-01

Many population genetic models have been developed for the purpose of inferring population size and growth rates from random samples of genetic data. We examine two popular approaches to this problem, the coalescent and the birth–death-sampling model (BDM), in the context of estimating population size and birth rates in a population growing exponentially according to the birth–death branching process. For sequences sampled at a single time, we found the coalescent and the BDM gave virtually indistinguishable results in terms of the growth rates and fraction of the population sampled, even when sampling from a small population. For sequences sampled at multiple time points, we find that the birth–death model estimators are subject to large bias if the sampling process is misspecified. Since BDMs incorporate a model of the sampling process, we show how much of the statistical power of BDMs arises from the sequence of sample times and not from the genealogical tree. This motivates the development of a new coalescent estimator, which is augmented with a model of the known sampling process and is potentially more precise than the coalescent that does not use sample time information. PMID:25401173

Analysis of five-year trends in self-reported language preference and issues of item non-response among Hispanic persons in a large cross-sectional health survey: implications for the measurement of an ethnic minority population

PubMed Central

2010-01-01

Background Significant differences in health outcomes have been documented among Hispanic persons, the fastest-growing demographic segment of the United States. The objective of this study was to examine trends in population growth and the collection of health data among Hispanic persons, including issues of language preference and survey completion using a national health survey to highlight issues of measurement of an increasingly important demographic segment of the United States. Design Data from the 2003-2007 United States Census and the Behavioral Risk Factor Surveillance System were used to compare trends in population growth and survey sample size as well as differences in survey response based on language preference among a Hispanic population. Percentages of item non-response on selected survey questions were compared for Hispanic respondents choosing to complete the survey in Spanish and those choosing to complete the survey in English. The mean number of attempts to complete the survey was also compared based on language preference among Hispanic respondents. Results The sample size of Hispanic persons in the Behavioral Risk Factor Surveillance System saw little growth compared to the actual growth of the Hispanic population in the United States. Significant differences in survey item non-response for nine of 15 survey questions were seen based on language preference. Hispanic respondents choosing to complete the survey in Spanish had a significantly fewer number of call attempts for survey completion compared to their Hispanic counterparts choosing to communicate in English. Conclusions Including additional measures of acculturation and increasing the sample size of Hispanic persons in a national health survey such as the Behavioral Risk Factor Surveillance System may result in more precise findings that could be used to better target prevention and health care needs for an ethnic minority population. PMID:20412575

Reference Intervals of Common Clinical Chemistry Analytes for Adults in Hong Kong.

PubMed

Lo, Y C; Armbruster, David A

2012-04-01

Defining reference intervals is a major challenge because of the difficulty in recruiting volunteers to participate and testing samples from a significant number of healthy reference individuals. Historical literature citation intervals are often suboptimal because they're be based on obsolete methods and/or only a small number of poorly defined reference samples. Blood donors in Hong Kong gave permission for additional blood to be collected for reference interval testing. The samples were tested for twenty-five routine analytes on the Abbott ARCHITECT clinical chemistry system. Results were analyzed using the Rhoads EP evaluator software program, which is based on the CLSI/IFCC C28-A guideline, and defines the reference interval as the 95% central range. Method specific reference intervals were established for twenty-five common clinical chemistry analytes for a Chinese ethnic population. The intervals were defined for each gender separately and for genders combined. Gender specific or combined gender intervals were adapted as appropriate for each analyte. A large number of healthy, apparently normal blood donors from a local ethnic population were tested to provide current reference intervals for a new clinical chemistry system. Intervals were determined following an accepted international guideline. Laboratories using the same or similar methodologies may adapt these intervals if deemed validated and deemed suitable for their patient population. Laboratories using different methodologies may be able to successfully adapt the intervals for their facilities using the reference interval transference technique based on a method comparison study.

Prevalence, Determinants, and Clinical Significance of Masked Hypertension in a Population-Based Sample of African Americans: The Jackson Heart Study.

PubMed

Diaz, Keith M; Veerabhadrappa, Praveen; Brown, Michael D; Whited, Matthew C; Dubbert, Patricia M; Hickson, DeMarc A

2015-07-01

The disproportionate rates of cardiovascular disease in African Americans may, in part, be due to suboptimal assessment of blood pressure (BP) with clinic BP measurements alone. To date, however, the prevalence of masked hypertension in African Americans has not been fully delineated. The purpose of this study was to evaluate masked hypertension prevalence in a large population-based sample of African Americans and examine its determinants and association with indices of target organ damage (TOD). Clinic and 24-hour ambulatory BP monitoring were conducted in 972 African Americans enrolled in the Jackson Heart Study. Common carotid artery intima-media thickness, left ventricular mass index, and the urinary albumin:creatinine excretion ratio were evaluated as indices of TOD. Masked hypertension prevalence was 25.9% in the overall sample and 34.4% in participants with normal clinic BP. All indices of TOD were significantly higher in masked hypertensives compared to sustained normotensives and were similar between masked hypertensives and sustained hypertensives. Male gender, smoking, diabetes, and antihypertensive medication use were independent determinants of masked hypertension in multivariate analyses. In this population-based cohort of African Americans, approximately one-third of participants with presumably normal clinic BP had masked hypertension when BP was assessed in their daily environment. Masked hypertension was accompanied by a greater degree of TOD in this cohort. © American Journal of Hypertension, Ltd 2014. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Chlamyweb Study I: rationale, design and acceptability of an internet-based chlamydia testing intervention.

PubMed

Lydié, Nathalie; de Barbeyrac, Bertille; Bluzat, Lucile; Le Roy, Chloé; Kersaudy-Rahib, Delphine

2017-05-01

In recent years, the internet has widely facilitated Chlamydia trachomatis home-sampling. In France (2012), the Chlamyweb Study evaluated an intervention (Chlamyweb) involving home-based self-sampling via the internet. One element of the study consisted of a randomised controlled trial (RCT), which is reported in detail elsewhere. The focus of this paper, however, is on describing the Chlamyweb Intervention and reporting on the non-RCT element of the evaluation of that intervention by the Chlamyweb Study. This involves (1) describing the design and roll-out of the Chlamyweb Intervention, (2) comparing the socio-behavioural profiles of the participants in the intervention with a nationally representative general population sample and (3) examining the factors that influence the acceptance and return of a self-sampling kit supplied to participants in the course of the intervention. Self-sampling kits were offered to sexually active people aged 18-24 years living on the mainland French. Participants' characteristics were compared with the general population to describe recruited and participant populations. Multivariate analyses by conditional logistic regression were performed to determine factors that were predictors of kit acceptation and use. 7215 people aged 18-24 years were included. Compared with the general population, Chlamyweb reached larger proportions of women, younger people and people with several partners in the previous year. 3372 (46.7%) agreed to receive a self-sampling kit and 2084 (61.8%) returned it, with more women doing so than men. The participation rate was associated with age, place of birth, occupational status, number of partners and condom use, differently for men and women. The offer of easy-to-use, self-sampling kits free of charge appeared to be a logistically feasible strategy for testing in France and reached a large and diverse population including individuals who have limited access to the traditional healthcare system. AFFSAPS n° IDRCB 0211-A01000-41; pre-results. 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/.

Large-scale parentage inference with SNPs: an efficient algorithm for statistical confidence of parent pair allocations.

PubMed

Anderson, Eric C

2012-11-08

Advances in genotyping that allow tens of thousands of individuals to be genotyped at a moderate number of single nucleotide polymorphisms (SNPs) permit parentage inference to be pursued on a very large scale. The intergenerational tagging this capacity allows is revolutionizing the management of cultured organisms (cows, salmon, etc.) and is poised to do the same for scientific studies of natural populations. Currently, however, there are no likelihood-based methods of parentage inference which are implemented in a manner that allows them to quickly handle a very large number of potential parents or parent pairs. Here we introduce an efficient likelihood-based method applicable to the specialized case of cultured organisms in which both parents can be reliably sampled. We develop a Markov chain representation for the cumulative number of Mendelian incompatibilities between an offspring and its putative parents and we exploit it to develop a fast algorithm for simulation-based estimates of statistical confidence in SNP-based assignments of offspring to pairs of parents. The method is implemented in the freely available software SNPPIT. We describe the method in detail, then assess its performance in a large simulation study using known allele frequencies at 96 SNPs from ten hatchery salmon populations. The simulations verify that the method is fast and accurate and that 96 well-chosen SNPs can provide sufficient power to identify the correct pair of parents from amongst millions of candidate pairs.

Reproductive health surveillance in the US-Mexico border region, 2003-2006: the Brownsville-Matamoros Sister City Project for Women's Health.

PubMed

McDonald, Jill A; Johnson, Christopher H; Smith, Ruben; Folger, Suzanne G; Chavez, Ana L; Mishra, Ninad; Hernández Jiménez, Antonio; MacDonald, Linda R; Hernández Rodríguez, Jorge Sebastián; Villalobos, Susie Ann

2008-10-01

High birth and immigration rates in the US-Mexico border region have led to large population increases in recent decades. Two national, 10 state, and more than 100 local government entities deliver reproductive health services to the region's 14 million residents. Limited standardized information about health risks in this population hampers capacity to address local needs and assess effectiveness of public health programs. We worked with binational partners to develop a system for reproductive health surveillance in the sister communities of Matamoros, Tamaulipas, Mexico, and Cameron County, Texas, as a model for a broader regional approach. We used a stratified, systematic cluster-sampling design to sample women giving birth in hospitals in each community during an 81-day period (August 21-November 9) in 2005. We conducted in-hospital computer-assisted personal interviews that addressed prenatal, behavioral, and lifestyle factors. We evaluated survey response rates, data quality, and other attributes of effective surveillance systems. We estimated population coverage using vital records data. Among the 999 women sampled, 947 (95%) completed interviews, and the item nonresponse rate was low. The study sample included 92.7% of live births in Matamoros and 98.3% in Cameron County. Differences between percentage distributions of birth certificate characteristics in the study and target populations did not exceed 2.0. Study population coverage among hospitals ranged from 92.9% to 100.0%, averaging 97.3% in Matamoros and 97.4% in Cameron County. Results indicate that hospital-based sampling and postpartum interviewing constitute an effective approach to reproductive health surveillance. Such a system can yield valuable information for public health programs serving the growing US-Mexico border population.

Software engineering the mixed model for genome-wide association studies on large samples

USDA-ARS?s Scientific Manuscript database

Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample siz...

Supernumerary heads to biceps brachii muscle and Asian population history.

PubMed

Techataweewan, N; Toomsan, Y; Maneenin, C; Tungsrithong, N; Tayles, N

2016-12-01

Supernumerary heads of biceps brachii are one of the most common anatomic variants in the muscular system and appear to develop under genetic control and vary in prevalence among populations. Variation in prevalence and morphology therefore has the potential to contribute to understanding of human population history. Until now, there has been no publication of the prevalence of the variant in Southeast Asian populations. The aim of this research is to document the prevalence and morphology of the variant in a sample of Thai cadavers and to consider the significance of the findings. The method used was dissection of arms of 162 donated cadavers at Khon Kaen University, Thailand. The sample showed high prevalence of third heads of biceps brachii in 35% of cadavers, compared with the prevalence of up to 25% reported in large samples worldwide. The sample also showed equal prevalence in males and females and one-third present bilaterally. This pattern is similar to that found in East Asia, and very different from the low prevalence found in South Asia. The morphology of the supernumerary heads does not appear to be different from elsewhere in the world based on the minimal comparable data available in the literature. The Southeast-East Asian pattern of prevalence is consistent with current theories of population history in the region and suggests anatomical variation of the postcranial soft tissues may ultimately contribute to understanding of past human migrations. Copyright © 2016 Elsevier GmbH. All rights reserved.

The episode of genetic drift defining the migration of humans out of Africa is derived from a large east African population size.

PubMed

Elhassan, Nuha; Gebremeskel, Eyoab Iyasu; Elnour, Mohamed Ali; Isabirye, Dan; Okello, John; Hussien, Ayman; Kwiatksowski, Dominic; Hirbo, Jibril; Tishkoff, Sara; Ibrahim, Muntaser E

2014-01-01

Human genetic variation particularly in Africa is still poorly understood. This is despite a consensus on the large African effective population size compared to populations from other continents. Based on sequencing of the mitochondrial Cytochrome C Oxidase subunit II (MT-CO2), and genome wide microsatellite data we observe evidence suggesting the effective size (Ne) of humans to be larger than the current estimates, with a foci of increased genetic diversity in east Africa, and a population size of east Africans being at least 2-6 fold larger than other populations. Both phylogenetic and network analysis indicate that east Africans possess more ancestral lineages in comparison to various continental populations placing them at the root of the human evolutionary tree. Our results also affirm east Africa as the likely spot from which migration towards Asia has taken place. The study reflects the spectacular level of sequence variation within east Africans in comparison to the global sample, and appeals for further studies that may contribute towards filling the existing gaps in the database. The implication of these data to current genomic research, as well as the need to carry out defined studies of human genetic variation that includes more African populations; particularly east Africans is paramount.

Genome-Wide Association Studies of a Broad Spectrum of Antisocial Behavior.

PubMed

Tielbeek, Jorim J; Johansson, Ada; Polderman, Tinca J C; Rautiainen, Marja-Riitta; Jansen, Philip; Taylor, Michelle; Tong, Xiaoran; Lu, Qing; Burt, Alexandra S; Tiemeier, Henning; Viding, Essi; Plomin, Robert; Martin, Nicholas G; Heath, Andrew C; Madden, Pamela A F; Montgomery, Grant; Beaver, Kevin M; Waldman, Irwin; Gelernter, Joel; Kranzler, Henry R; Farrer, Lindsay A; Perry, John R B; Munafò, Marcus; LoParo, Devon; Paunio, Tiina; Tiihonen, Jari; Mous, Sabine E; Pappa, Irene; de Leeuw, Christiaan; Watanabe, Kyoko; Hammerschlag, Anke R; Salvatore, Jessica E; Aliev, Fazil; Bigdeli, Tim B; Dick, Danielle; Faraone, Stephen V; Popma, Arne; Medland, Sarah E; Posthuma, Danielle

2017-12-01

Antisocial behavior (ASB) places a large burden on perpetrators, survivors, and society. Twin studies indicate that half of the variation in this trait is genetic. Specific causal genetic variants have, however, not been identified. To estimate the single-nucleotide polymorphism-based heritability of ASB; to identify novel genetic risk variants, genes, or biological pathways; to test for pleiotropic associations with other psychiatric traits; and to reevaluate the candidate gene era data through the Broad Antisocial Behavior Consortium. Genome-wide association data from 5 large population-based cohorts and 3 target samples with genome-wide genotype and ASB data were used for meta-analysis from March 1, 2014, to May 1, 2016. All data sets used quantitative phenotypes, except for the Finnish Crime Study, which applied a case-control design (370 patients and 5850 control individuals). This study adopted relatively broad inclusion criteria to achieve a quantitative measure of ASB derived from multiple measures, maximizing the sample size over different age ranges. The discovery samples comprised 16 400 individuals, whereas the target samples consisted of 9381 individuals (all individuals were of European descent), including child and adult samples (mean age range, 6.7-56.1 years). Three promising loci with sex-discordant associations were found (8535 female individuals, chromosome 1: rs2764450, chromosome 11: rs11215217; 7772 male individuals, chromosome X, rs41456347). Polygenic risk score analyses showed prognostication of antisocial phenotypes in an independent Finnish Crime Study (2536 male individuals and 3684 female individuals) and shared genetic origin with conduct problems in a population-based sample (394 male individuals and 431 female individuals) but not with conduct disorder in a substance-dependent sample (950 male individuals and 1386 female individuals) (R2 = 0.0017 in the most optimal model, P = 0.03). Significant inverse genetic correlation of ASB with educational attainment (r = -0.52, P = .005) was detected. The Broad Antisocial Behavior Consortium entails the largest collaboration to date on the genetic architecture of ASB, and the first results suggest that ASB may be highly polygenic and has potential heterogeneous genetic effects across sex.

A random spatial sampling method in a rural developing nation

Treesearch

Michelle C. Kondo; Kent D.W. Bream; Frances K. Barg; Charles C. Branas

2014-01-01

Nonrandom sampling of populations in developing nations has limitations and can inaccurately estimate health phenomena, especially among hard-to-reach populations such as rural residents. However, random sampling of rural populations in developing nations can be challenged by incomplete enumeration of the base population. We describe a stratified random sampling method...

The Next Generation Virgo Cluster Survey (NGVS). XXXII. A Search for Globular Cluster Substructures in the Virgo Galaxy Cluster Core

NASA Astrophysics Data System (ADS)

Powalka, Mathieu; Puzia, Thomas H.; Lançon, Ariane; Longobardi, Alessia; Peng, Eric W.; Duc, Pierre-Alain; Alamo-Martínez, Karla; Blakeslee, John P.; Côté, Patrick; Cuillandre, Jean-Charles; Durrell, Patrick; Eigenthaler, Paul; Ferrarese, Laura; Guhathakurta, Puragra; Gwyn, S. D. J.; Hudelot, Patrick; Liu, Chengze; Mei, Simona; Muñoz, Roberto P.; Roediger, Joel; Sánchez-Janssen, Rubén; Toloba, Elisa; Zhang, Hongxin

2018-03-01

Substructure in globular cluster (GC) populations around large galaxies is expected in galaxy formation scenarios that involve accretion or merger events, and it has been searched for using direct associations between GCs and structure in the diffuse galaxy light, or with GC kinematics. Here, we present a search for candidate substructures in the GC population around the Virgo cD galaxy M87 through the analysis of the spatial distribution of the GC colors. The study is based on a sample of ∼1800 bright GCs with high-quality u, g, r, i, z, K s photometry, selected to ensure a low contamination by foreground stars or background galaxies. The spectral energy distributions of the GCs are associated with formal estimates of age and metallicity, which are representative of its position in a 4D color space relative to standard single stellar population models. Dividing the sample into broad bins based on the relative formal ages, we observe inhomogeneities that reveal signatures of GC substructures. The most significant of these is a spatial overdensity of GCs with relatively young age labels, of diameter ∼0.°1 (∼30 kpc), located to the south of M87. The significance of this detection is larger than about 5σ after accounting for estimates of random and systematic errors. Surprisingly, no large Virgo galaxy is present in this area that could potentially host these GCs. But candidate substructures in the M87 halo with equally elusive hosts have been described based on kinematic studies in the past. The number of GC spectra available around M87 is currently insufficient to clarify the nature of the new candidate substructure.

Population structure of pigs determined by single nucleotide polymorphisms observed in assembled expressed sequence tags.

PubMed

Matsumoto, Toshimi; Okumura, Naohiko; Uenishi, Hirohide; Hayashi, Takeshi; Hamasima, Noriyuki; Awata, Takashi

2012-01-01

We have collected more than 190000 porcine expressed sequence tags (ESTs) from full-length complementary DNA (cDNA) libraries and identified more than 2800 single nucleotide polymorphisms (SNPs). In this study, we tentatively chose 222 SNPs observed in assembled ESTs to study pigs of different breeds; 104 were selected by comparing the cDNA sequences of a Meishan pig and samples of three-way cross pigs (Landrace, Large White, and Duroc: LWD), and 118 were selected from LWD samples. To evaluate the genetic variation between the chosen SNPs from pig breeds, we determined the genotypes for 192 pig samples (11 pig groups) from our DNA reference panel with matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Of the 222 reference SNPs, 186 were successfully genotyped. A neighbor-joining tree showed that the pig groups were classified into two large clusters, namely, Euro-American and East Asian pig populations. F-statistics and the analysis of molecular variance of Euro-American pig groups revealed that approximately 25% of the genetic variations occurred because of intergroup differences. As the F(IS) values were less than the F(ST) values(,) the clustering, based on the Bayesian inference, implied that there was strong genetic differentiation among pig groups and less divergence within the groups in our samples. © 2011 The Authors. Animal Science Journal © 2011 Japanese Society of Animal Science.

Concurrent Isolation of 3 Distinct Cardiac Stem Cell Populations From a Single Human Heart Biopsy.

PubMed

Monsanto, Megan M; White, Kevin S; Kim, Taeyong; Wang, Bingyan J; Fisher, Kristina; Ilves, Kelli; Khalafalla, Farid G; Casillas, Alexandria; Broughton, Kathleen; Mohsin, Sadia; Dembitsky, Walter P; Sussman, Mark A

2017-07-07

The relative actions and synergism between distinct myocardial-derived stem cell populations remain obscure. Ongoing debates on optimal cell population(s) for treatment of heart failure prompted implementation of a protocol for isolation of multiple stem cell populations from a single myocardial tissue sample to develop new insights for achieving myocardial regeneration. Establish a robust cardiac stem cell isolation and culture protocol to consistently generate 3 distinct stem cell populations from a single human heart biopsy. Isolation of 3 endogenous cardiac stem cell populations was performed from human heart samples routinely discarded during implantation of a left ventricular assist device. Tissue explants were mechanically minced into 1 mm 3 pieces to minimize time exposure to collagenase digestion and preserve cell viability. Centrifugation removes large cardiomyocytes and tissue debris producing a single cell suspension that is sorted using magnetic-activated cell sorting technology. Initial sorting is based on tyrosine-protein kinase Kit (c-Kit) expression that enriches for 2 c-Kit + cell populations yielding a mixture of cardiac progenitor cells and endothelial progenitor cells. Flowthrough c-Kit - mesenchymal stem cells are positively selected by surface expression of markers CD90 and CD105. After 1 week of culture, the c-Kit + population is further enriched by selection for a CD133 + endothelial progenitor cell population. Persistence of respective cell surface markers in vitro is confirmed both by flow cytometry and immunocytochemistry. Three distinct cardiac cell populations with individualized phenotypic properties consistent with cardiac progenitor cells, endothelial progenitor cells, and mesenchymal stem cells can be successfully concurrently isolated and expanded from a single tissue sample derived from human heart failure patients. © 2017 American Heart Association, Inc.

Single and simultaneous binary mergers in Wright-Fisher genealogies.

PubMed

Melfi, Andrew; Viswanath, Divakar

2018-05-01

The Kingman coalescent is a commonly used model in genetics, which is often justified with reference to the Wright-Fisher (WF) model. Current proofs of convergence of WF and other models to the Kingman coalescent assume a constant sample size. However, sample sizes have become quite large in human genetics. Therefore, we develop a convergence theory that allows the sample size to increase with population size. If the haploid population size is N and the sample size is N 1∕3-ϵ , ϵ>0, we prove that Wright-Fisher genealogies involve at most a single binary merger in each generation with probability converging to 1 in the limit of large N. Single binary merger or no merger in each generation of the genealogy implies that the Kingman partition distribution is obtained exactly. If the sample size is N 1∕2-ϵ , Wright-Fisher genealogies may involve simultaneous binary mergers in a single generation but do not involve triple mergers in the large N limit. The asymptotic theory is verified using numerical calculations. Variable population sizes are handled algorithmically. It is found that even distant bottlenecks can increase the probability of triple mergers as well as simultaneous binary mergers in WF genealogies. Copyright © 2018 Elsevier Inc. All rights reserved.

The population-based Barcelona-Asymptomatic Intracranial Atherosclerosis Study (ASIA): rationale and design

PubMed Central

2011-01-01

Background Large-artery intracranial atherosclerosis may be the most frequent cause of ischemic stroke worldwide. Traditional approaches have attempted to target the disease when it is already symptomatic. However, early detection of intracranial atherosclerosis may allow therapeutic intervention while the disease is still asymptomatic. The prevalence and natural history of asymptomatic intracranial atherosclerosis in Caucasians remain unclear. The aims of the Barcelona-ASymptomatic Intracranial Atherosclerosis (ASIA) study are (1) to determine the prevalence of ASIA in a moderate-high vascular risk population, (2) to study its prognostic impact on the risk of suffering future major ischemic events, and (3) to identify predictors of the development, progression and clinical expression of this condition. Methods/Design Cross-over and cohort, population-based study. A randomly selected representative sample of 1,503 subjects with a mild-moderate-high vascular risk (as defined by a REGICOR score ≥ 5%) and with neither a history of cerebrovascular nor ischemic heart disease will be studied. At baseline, all individuals will undergo extracranial and transcranial Color-Coded Duplex (TCCD) ultrasound examinations to detect presence and severity of extra and intracranial atherosclerosis. Intracranial stenoses will be assessed by magnetic resonance angiography (MRA). Clinical and demographic variables will be recorded and blood samples will be drawn to investigate clinical, biological and genetic factors associated with the presence of ASIA. A long-term clinical and sonographic follow-up will be conducted thereafter to identify predictors of disease progression and of incident vascular events. Discussion The Barcelona-ASIA is a population-based study aiming to evaluate the prevalence and clinical importance of asymptomatic intracranial large-artery atherosclerosis in Caucasians. The ASIA project may provide a unique scientific resource to better understand the dynamics of intracranial atherosclerosis from its early stages and to identify new potential therapeutic targets for this condition. PMID:21329527

Detecting selection effects in community implementations of family-based substance abuse prevention programs.

PubMed

Hill, Laura G; Goates, Scott G; Rosenman, Robert

2010-04-01

To calculate valid estimates of the costs and benefits of substance abuse prevention programs, selection effects must be identified and corrected. A supplemental comparison sample is typically used for this purpose, but in community-based program implementations, such a sample is often not available. We present an evaluation design and analytic approach that can be used in program evaluations of real-world implementations to identify selection effects, which in turn can help inform recruitment strategies, pinpoint possible selection influences on measured program outcomes, and refine estimates of program costs and benefits. We illustrate our approach with data from a multisite implementation of a popular substance abuse prevention program. Our results indicate that the program's participants differed significantly from the population at large.

Geographic differences in allele frequencies of susceptibility SNPs for cardiovascular disease

PubMed Central

2011-01-01

Background We hypothesized that the frequencies of risk alleles of SNPs mediating susceptibility to cardiovascular diseases differ among populations of varying geographic origin and that population-specific selection has operated on some of these variants. Methods From the database of genome-wide association studies (GWAS), we selected 36 cardiovascular phenotypes including coronary heart disease, hypertension, and stroke, as well as related quantitative traits (eg, body mass index and plasma lipid levels). We identified 292 SNPs in 270 genes associated with a disease or trait at P < 5 × 10-8. As part of the Human Genome-Diversity Project (HGDP), 158 (54.1%) of these SNPs have been genotyped in 938 individuals belonging to 52 populations from seven geographic areas. A measure of population differentiation, FST, was calculated to quantify differences in risk allele frequencies (RAFs) among populations and geographic areas. Results Large differences in RAFs were noted in populations of Africa, East Asia, America and Oceania, when compared with other geographic regions. The mean global FST (0.1042) for 158 SNPs among the populations was not significantly higher than the mean global FST of 158 autosomal SNPs randomly sampled from the HGDP database. Significantly higher global FST (P < 0.05) was noted in eight SNPs, based on an empirical distribution of global FST of 2036 putatively neutral SNPs. For four of these SNPs, additional evidence of selection was noted based on the integrated Haplotype Score. Conclusion Large differences in RAFs for a set of common SNPs that influence risk of cardiovascular disease were noted between the major world populations. Pairwise comparisons revealed RAF differences for at least eight SNPs that might be due to population-specific selection or demographic factors. These findings are relevant to a better understanding of geographic variation in the prevalence of cardiovascular disease. PMID:21507254

The short-form version of the Depression Anxiety Stress Scales (DASS-21): construct validity and normative data in a large non-clinical sample.

PubMed

Henry, Julie D; Crawford, John R

2005-06-01

To test the construct validity of the short-form version of the Depression anxiety and stress scale (DASS-21), and in particular, to assess whether stress as indexed by this measure is synonymous with negative affectivity (NA) or whether it represents a related, but distinct, construct. To provide normative data for the general adult population. Cross-sectional, correlational and confirmatory factor analysis (CFA). The DASS-21 was administered to a non-clinical sample, broadly representative of the general adult UK population (N = 1,794). Competing models of the latent structure of the DASS-21 were evaluated using CFA. The model with optimal fit (RCFI = 0.94) had a quadripartite structure, and consisted of a general factor of psychological distress plus orthogonal specific factors of depression, anxiety, and stress. This model was a significantly better fit than a competing model that tested the possibility that the Stress scale simply measures NA. The DASS-21 subscales can validly be used to measure the dimensions of depression, anxiety, and stress. However, each of these subscales also taps a more general dimension of psychological distress or NA. The utility of the measure is enhanced by the provision of normative data based on a large sample.

The association between Internet addiction and personality disorders in a general population-based sample

PubMed Central

Zadra, Sina; Bischof, Gallus; Besser, Bettina; Bischof, Anja; Meyer, Christian; John, Ulrich; Rumpf, Hans-Jürgen

2016-01-01

Background and aims Data on Internet addiction (IA) and its association with personality disorder are rare. Previous studies are largely restricted to clinical samples and insufficient measurement of IA. Methods Cross-sectional analysis data are based on a German sub-sample (n = 168; 86 males; 71 meeting criteria for IA) with increased levels of excessive Internet use derived from a general population sample (n = 15,023). IA was assessed with a comprehensive standardized interview using the structure of the Composite International Diagnostic Interview and the criteria of Internet Gaming Disorder as suggested in DSM-5. Impulsivity, attention deficit hyperactivity disorder, and self-esteem were assessed with the widely used questionnaires. Results Participants with IA showed higher frequencies of personality disorders (29.6%) compared to those without IA (9.3%; p < .001). In males with IA, Cluster C personality disorders were more prevalent than among non-addicted males. Compared to participants who had IA only, lower rates of remission of IA were found among participants with IA and additional cluster B personality disorder. Personality disorders were significantly associated with IA in multivariate analysis. Discussion and conclusion: Comorbidity of IA and personality disorders must be considered in prevention and treatment. PMID:28005417

Development and use of EST-SSR markers for assessing genetic diversity in the brown planthopper (Nilaparvata lugens Stål).

PubMed

Jing, S; Liu, B; Peng, L; Peng, X; Zhu, L; Fu, Q; He, G

2012-02-01

To assess genetic diversity in populations of the brown planthopper (Nilaparvata lugens Stål) (Homoptera: Delphacidae), we have developed and applied microsatellite, or simple sequence repeat (SSR), markers from expressed sequence tags (ESTs). We found that the brown planthopper clusters of ESTs were rich in SSRs with unique frequencies and distributions of SSR motifs. Three hundred and fifty-one EST-SSR markers were developed and yielded clear bands from samples of four brown planthopper populations. High cross-species transferability of these markers was detected in the closely related planthopper N. muiri. The newly developed EST-SSR markers provided sufficient resolution to distinguish within and among biotypes. Analyses based on SSR data revealed host resistance-based genetic differentiation among different brown planthopper populations; the genetic diversity of populations feeding on susceptible rice varieties was lower than that of populations feeding on resistant rice varieties. This is the first large-scale development of brown planthopper SSR markers, which will be useful for future molecular genetics and genomics studies of this serious agricultural pest.

Assessing tiger population dynamics using photographic capture-recapture sampling

USGS Publications Warehouse

Karanth, K.U.; Nichols, J.D.; Kumar, N.S.; Hines, J.E.

2006-01-01

Although wide-ranging, elusive, large carnivore species, such as the tiger, are of scientific and conservation interest, rigorous inferences about their population dynamics are scarce because of methodological problems of sampling populations at the required spatial and temporal scales. We report the application of a rigorous, noninvasive method for assessing tiger population dynamics to test model-based predictions about population viability. We obtained photographic capture histories for 74 individual tigers during a nine-year study involving 5725 trap-nights of effort. These data were modeled under a likelihood-based, ?robust design? capture?recapture analytic framework. We explicitly modeled and estimated ecological parameters such as time-specific abundance, density, survival, recruitment, temporary emigration, and transience, using models that incorporated effects of factors such as individual heterogeneity, trap-response, and time on probabilities of photo-capturing tigers. The model estimated a random temporary emigration parameter of =K' =Y' 0.10 ? 0.069 (values are estimated mean ? SE). When scaled to an annual basis, tiger survival rates were estimated at S = 0.77 ? 0.051, and the estimated probability that a newly caught animal was a transient was = 0.18 ? 0.11. During the period when the sampled area was of constant size, the estimated population size Nt varied from 17 ? 1.7 to 31 ? 2.1 tigers, with a geometric mean rate of annual population change estimated as = 1.03 ? 0.020, representing a 3% annual increase. The estimated recruitment of new animals, Bt, varied from 0 ? 3.0 to 14 ? 2.9 tigers. Population density estimates, D, ranged from 7.33 ? 0.8 tigers/100 km2 to 21.73 ? 1.7 tigers/100 km2 during the study. Thus, despite substantial annual losses and temporal variation in recruitment, the tiger density remained at relatively high levels in Nagarahole. Our results are consistent with the hypothesis that protected wild tiger populations can remain healthy despite heavy mortalities because of their inherently high reproductive potential. The ability to model the entire photographic capture history data set and incorporate reduced-parameter models led to estimates of mean annual population change that were sufficiently precise to be useful. This efficient, noninvasive sampling approach can be used to rigorously investigate the population dynamics of tigers and other elusive, rare, wide-ranging animal species in which individuals can be identified from photographs or other means.

Assessing tiger population dynamics using photographic capture-recapture sampling.

PubMed

Karanth, K Ullas; Nichols, James D; Kumar, N Samba; Hines, James E

2006-11-01

Although wide-ranging, elusive, large carnivore species, such as the tiger, are of scientific and conservation interest, rigorous inferences about their population dynamics are scarce because of methodological problems of sampling populations at the required spatial and temporal scales. We report the application of a rigorous, noninvasive method for assessing tiger population dynamics to test model-based predictions about population viability. We obtained photographic capture histories for 74 individual tigers during a nine-year study involving 5725 trap-nights of effort. These data were modeled under a likelihood-based, "robust design" capture-recapture analytic framework. We explicitly modeled and estimated ecological parameters such as time-specific abundance, density, survival, recruitment, temporary emigration, and transience, using models that incorporated effects of factors such as individual heterogeneity, trap-response, and time on probabilities of photo-capturing tigers. The model estimated a random temporary emigration parameter of gamma" = gamma' = 0.10 +/- 0.069 (values are estimated mean +/- SE). When scaled to an annual basis, tiger survival rates were estimated at S = 0.77 +/- 0.051, and the estimated probability that a newly caught animal was a transient was tau = 0.18 +/- 0.11. During the period when the sampled area was of constant size, the estimated population size N(t) varied from 17 +/- 1.7 to 31 +/- 2.1 tigers, with a geometric mean rate of annual population change estimated as lambda = 1.03 +/- 0.020, representing a 3% annual increase. The estimated recruitment of new animals, B(t), varied from 0 +/- 3.0 to 14 +/- 2.9 tigers. Population density estimates, D, ranged from 7.33 +/- 0.8 tigers/100 km2 to 21.73 +/- 1.7 tigers/100 km2 during the study. Thus, despite substantial annual losses and temporal variation in recruitment, the tiger density remained at relatively high levels in Nagarahole. Our results are consistent with the hypothesis that protected wild tiger populations can remain healthy despite heavy mortalities because of their inherently high reproductive potential. The ability to model the entire photographic capture history data set and incorporate reduced-parameter models led to estimates of mean annual population change that were sufficiently precise to be useful. This efficient, noninvasive sampling approach can be used to rigorously investigate the population dynamics of tigers and other elusive, rare, wide-ranging animal species in which individuals can be identified from photographs or other means.

[Genetic Differentiation of Sockeye Salmon Oncorhynchus nerka from Kamchatka River Basin and the Lake-River Systems of the West Coast of the Bering Sea as Inferred from Data on Single Nucleotide Polymorphism].

PubMed

Khrustaleva, A M; Klovach, N V; Vedischeva, E V; Seeb, J E

2015-10-01

The variability of 45 single nucleotide polymorphism loci (SNP) was studied in sockeye salmon from the Kamchatka River basin and four lake-river systems of the west coast of the Bering Sea. Based on the genetic differentiation estimates for the largest sockeye salmon populations of Eastern Kamchatka and Chukotka, the examined samples were combined into two regional groups represented by the population of the Kamchatka River drainage, which included numerous local subpopulations and seasonal races, and the northern population grouping from the rivers of Olutorsko-Navarinsky raion, wherein the sockeye salmon from Maynypilginskaya Lake-River system was relatively isolated. Considerable divergence was observed between the island (Sarannoe Lake, Bering Island) and continental populations. Genetic heterogeneity was revealed and groups of early- and late-maturing individuals were isolated in the sample of late-run sockeye salmon from Kamchatka River. In Apuka River, subdivision of the spawning run into two genetically distinct spatial and temporal groupings was also observed. The results suggest that the differentiation of sockeye salmon samples by single nucleotide substitution frequencies was largely due to differences in the direction and strength of local selection at some loci in the population complexes and intrapopulation groupings from the examined river basins of Eastern Kamchatka, Chukotka, and Commander Islands.

Genetic structuring and recent demographic history of red pandas (Ailurus fulgens) inferred from microsatellite and mitochondrial DNA.

PubMed

Hu, Yibo; Guo, Yu; Qi, Dunwu; Zhan, Xiangjiang; Wu, Hua; Bruford, Michael W; Wei, Fuwen

2011-07-01

Clarification of the genetic structure and population history of a species can shed light on the impacts of landscapes, historical climate change and contemporary human activities and thus enables evidence-based conservation decisions for endangered organisms. The red panda (Ailurus fulgens) is an endangered species distributing at the edge of the Qinghai-Tibetan Plateau and is currently subject to habitat loss, fragmentation and population decline, thus representing a good model to test the influences of the above-mentioned factors on a plateau edge species. We combined nine microsatellite loci and 551 bp of mitochondrial control region (mtDNA CR) to explore the genetic structure and demographic history of this species. A total of 123 individuals were sampled from 23 locations across five populations. High levels of genetic variation were identified for both mtDNA and microsatellites. Phylogeographic analyses indicated little geographic structure, suggesting historically wide gene flow. However, microsatellite-based Bayesian clustering clearly identified three groups (Qionglai-Liangshan, Xiaoxiangling and Gaoligong-Tibet). A significant isolation-by-distance pattern was detected only after removing Xiaoxiangling. For mtDNA data, there was no statistical support for a historical population expansion or contraction for the whole sample or any population except Xiaoxiangling where a signal of contraction was detected. However, Bayesian simulations of population history using microsatellite data did pinpoint population declines for Qionglai, Xiaoxiangling and Gaoligong, demonstrating significant influences of human activity on demography. The unique history of the Xiaoxiangling population plays a critical role in shaping the genetic structure of this species, and large-scale habitat loss and fragmentation is hampering gene flow among populations. The implications of our findings for the biogeography of the Qinghai-Tibetan Plateau, subspecies classification and conservation of red pandas are discussed. © 2011 Blackwell Publishing Ltd.

Classifier performance prediction for computer-aided diagnosis using a limited dataset.

PubMed

Sahiner, Berkman; Chan, Heang-Ping; Hadjiiski, Lubomir

2008-04-01

In a practical classifier design problem, the true population is generally unknown and the available sample is finite-sized. A common approach is to use a resampling technique to estimate the performance of the classifier that will be trained with the available sample. We conducted a Monte Carlo simulation study to compare the ability of the different resampling techniques in training the classifier and predicting its performance under the constraint of a finite-sized sample. The true population for the two classes was assumed to be multivariate normal distributions with known covariance matrices. Finite sets of sample vectors were drawn from the population. The true performance of the classifier is defined as the area under the receiver operating characteristic curve (AUC) when the classifier designed with the specific sample is applied to the true population. We investigated methods based on the Fukunaga-Hayes and the leave-one-out techniques, as well as three different types of bootstrap methods, namely, the ordinary, 0.632, and 0.632+ bootstrap. The Fisher's linear discriminant analysis was used as the classifier. The dimensionality of the feature space was varied from 3 to 15. The sample size n2 from the positive class was varied between 25 and 60, while the number of cases from the negative class was either equal to n2 or 3n2. Each experiment was performed with an independent dataset randomly drawn from the true population. Using a total of 1000 experiments for each simulation condition, we compared the bias, the variance, and the root-mean-squared error (RMSE) of the AUC estimated using the different resampling techniques relative to the true AUC (obtained from training on a finite dataset and testing on the population). Our results indicated that, under the study conditions, there can be a large difference in the RMSE obtained using different resampling methods, especially when the feature space dimensionality is relatively large and the sample size is small. Under this type of conditions, the 0.632 and 0.632+ bootstrap methods have the lowest RMSE, indicating that the difference between the estimated and the true performances obtained using the 0.632 and 0.632+ bootstrap will be statistically smaller than those obtained using the other three resampling methods. Of the three bootstrap methods, the 0.632+ bootstrap provides the lowest bias. Although this investigation is performed under some specific conditions, it reveals important trends for the problem of classifier performance prediction under the constraint of a limited dataset.

SAS procedures for designing and analyzing sample surveys

USGS Publications Warehouse

Stafford, Joshua D.; Reinecke, Kenneth J.; Kaminski, Richard M.

2003-01-01

Complex surveys often are necessary to estimate occurrence (or distribution), density, and abundance of plants and animals for purposes of re-search and conservation. Most scientists are familiar with simple random sampling, where sample units are selected from a population of interest (sampling frame) with equal probability. However, the goal of ecological surveys often is to make inferences about populations over large or complex spatial areas where organisms are not homogeneously distributed or sampling frames are in-convenient or impossible to construct. Candidate sampling strategies for such complex surveys include stratified,multistage, and adaptive sampling (Thompson 1992, Buckland 1994).

The effects of sample size on population genomic analyses--implications for the tests of neutrality.

PubMed

Subramanian, Sankar

2016-02-20

One of the fundamental measures of molecular genetic variation is the Watterson's estimator (θ), which is based on the number of segregating sites. The estimation of θ is unbiased only under neutrality and constant population growth. It is well known that the estimation of θ is biased when these assumptions are violated. However, the effects of sample size in modulating the bias was not well appreciated. We examined this issue in detail based on large-scale exome data and robust simulations. Our investigation revealed that sample size appreciably influences θ estimation and this effect was much higher for constrained genomic regions than that of neutral regions. For instance, θ estimated for synonymous sites using 512 human exomes was 1.9 times higher than that obtained using 16 exomes. However, this difference was 2.5 times for the nonsynonymous sites of the same data. We observed a positive correlation between the rate of increase in θ estimates (with respect to the sample size) and the magnitude of selection pressure. For example, θ estimated for the nonsynonymous sites of highly constrained genes (dN/dS < 0.1) using 512 exomes was 3.6 times higher than that estimated using 16 exomes. In contrast this difference was only 2 times for the less constrained genes (dN/dS > 0.9). The results of this study reveal the extent of underestimation owing to small sample sizes and thus emphasize the importance of sample size in estimating a number of population genomic parameters. Our results have serious implications for neutrality tests such as Tajima D, Fu-Li D and those based on the McDonald and Kreitman test: Neutrality Index and the fraction of adaptive substitutions. For instance, use of 16 exomes produced 2.4 times higher proportion of adaptive substitutions compared to that obtained using 512 exomes (24% vs 10 %).

Investigation of established genetic risk variants for glioma in prediagnostic samples from a population-based nested case-control study.

PubMed

Wibom, Carl; Späth, Florentin; Dahlin, Anna M; Langseth, Hilde; Hovig, Eivind; Rajaraman, Preetha; Johannesen, Tom Børge; Andersson, Ulrika; Melin, Beatrice

2015-05-01

Although glioma etiology is poorly understood in general, growing evidence indicates a genetic component. Four large genome-wide association studies (GWAS) have linked common genetic variants with an increased glioma risk. However, to date, these studies are based largely on a case-control design, where cases have been recruited at the time of or after diagnosis. They may therefore suffer from a degree of survival bias, introduced when rapidly fatal cases are not included. To confirm glioma risk variants in a prospective setting, we have analyzed 11 previously identified risk variants in a set of prediagnostic serum samples with 598 cases and 595 matched controls. Serum samples were acquired from The Janus Serum Bank, a Norwegian population-based biobank reserved for cancer research. We confirmed the association with glioma risk for variants within five genomic regions: 8q24.21 (CCDC26), 9p21.3 (CDKN2B-AS1), 11q23.3 (PHLDB1), 17p13.1 (TP53), and 20q13.33 (RTEL1). However, previously identified risk variants within the 7p11.2 (EGFR) region were not confirmed by this study. Our results indicate that the risk variants that were confirmed by this study are truly associated with glioma risk and may, consequently, affect gliomagenesis. Though the lack of positive confirmation of EGFR risk variants may be attributable to relatively limited statistical power, it nevertheless raises the question whether they truly are risk variants or markers for glioma prognosis. Our findings indicate the need for further studies to clarify the role of glioma risk loci with respect to prolonged survival versus etiology. ©2015 American Association for Cancer Research.

Migraine and Mental Health in a Population-Based Sample of Adolescents.

PubMed

Orr, Serena L; Potter, Beth K; Ma, Jinhui; Colman, Ian

2017-01-01

To explore the relationship between migraine and anxiety disorders, mood disorders and perceived mental health in a population-based sample of adolescents. The Canadian Community Health Survey (CCHS) is a cross-sectional health survey sampling a nationally representative group of Canadians. In this observational study, data on all 61,375 participants aged 12-19 years from six survey cycles were analyzed. The relationships between self-reported migraine, perceived mental health, and mood/anxiety disorders were modeled using univariate and multivariate logistic regression. The migraine-depression association was also explored in a subset of participants using the Composite International Diagnostic Interview-Short Form (CIDI-SF) depression scale. The odds of migraine were higher among those with mood disorders, with the strongest association in 2011-2 (adjusted odds ratio [aOR]=4.59; 95% confidence interval [CI 95%]=3.44-6.12), and the weakest in 2009-10 (aOR=3.06, CI 95%=2.06-4.55). The migraine-mood disorders association was also significant throughout all cycles, other than 2011-2, when the CIDI-SF depression scale was employed. The odds of migraine were higher among those with anxiety disorders, with the strongest association in 2011-2 (aOR=4.21, CI 95%=3.31-5.35) and the weakest in 2010 (aOR=1.87, CI 95%=1.10-3.37). The inverse association between high perceived mental health and the odds of migraine was observed in all CCHS cycles, with the strongest association in 2011-2 (aOR=0.58, CI 95%=0.48-0.69) and the weakest in 2003-4 (aOR=0.75, CI 95%=0.62-0.91). This study provides evidence, derived from a large population-based sample of adolescents, for a link between migraine and mood/anxiety disorders.

Genotype imputation in a coalescent model with infinitely-many-sites mutation

PubMed Central

Huang, Lucy; Buzbas, Erkan O.; Rosenberg, Noah A.

2012-01-01

Empirical studies have identified population-genetic factors as important determinants of the properties of genotype-imputation accuracy in imputation-based disease association studies. Here, we develop a simple coalescent model of three sequences that we use to explore the theoretical basis for the influence of these factors on genotype-imputation accuracy, under the assumption of infinitely-many-sites mutation. Employing a demographic model in which two populations diverged at a given time in the past, we derive the approximate expectation and variance of imputation accuracy in a study sequence sampled from one of the two populations, choosing between two reference sequences, one sampled from the same population as the study sequence and the other sampled from the other population. We show that under this model, imputation accuracy—as measured by the proportion of polymorphic sites that are imputed correctly in the study sequence—increases in expectation with the mutation rate, the proportion of the markers in a chromosomal region that are genotyped, and the time to divergence between the study and reference populations. Each of these effects derives largely from an increase in information available for determining the reference sequence that is genetically most similar to the sequence targeted for imputation. We analyze as a function of divergence time the expected gain in imputation accuracy in the target using a reference sequence from the same population as the target rather than from the other population. Together with a growing body of empirical investigations of genotype imputation in diverse human populations, our modeling framework lays a foundation for extending imputation techniques to novel populations that have not yet been extensively examined. PMID:23079542

Estimating population size with correlated sampling unit estimates

Treesearch

David C. Bowden; Gary C. White; Alan B. Franklin; Joseph L. Ganey

2003-01-01

Finite population sampling theory is useful in estimating total population size (abundance) from abundance estimates of each sampled unit (quadrat). We develop estimators that allow correlated quadrat abundance estimates, even for quadrats in different sampling strata. Correlated quadrat abundance estimates based on mark–recapture or distance sampling methods occur...

Imputation-Based Meta-Analysis of Severe Malaria in Three African Populations

PubMed Central

Band, Gavin; Le, Quang Si; Jostins, Luke; Pirinen, Matti; Kivinen, Katja; Jallow, Muminatou; Sisay-Joof, Fatoumatta; Bojang, Kalifa; Pinder, Margaret; Sirugo, Giorgio; Conway, David J.; Nyirongo, Vysaul; Kachala, David; Molyneux, Malcolm; Taylor, Terrie; Ndila, Carolyne; Peshu, Norbert; Marsh, Kevin; Williams, Thomas N.; Alcock, Daniel; Andrews, Robert; Edkins, Sarah; Gray, Emma; Hubbart, Christina; Jeffreys, Anna; Rowlands, Kate; Schuldt, Kathrin; Clark, Taane G.; Small, Kerrin S.; Teo, Yik Ying; Kwiatkowski, Dominic P.; Rockett, Kirk A.; Barrett, Jeffrey C.; Spencer, Chris C. A.

2013-01-01

Combining data from genome-wide association studies (GWAS) conducted at different locations, using genotype imputation and fixed-effects meta-analysis, has been a powerful approach for dissecting complex disease genetics in populations of European ancestry. Here we investigate the feasibility of applying the same approach in Africa, where genetic diversity, both within and between populations, is far more extensive. We analyse genome-wide data from approximately 5,000 individuals with severe malaria and 7,000 population controls from three different locations in Africa. Our results show that the standard approach is well powered to detect known malaria susceptibility loci when sample sizes are large, and that modern methods for association analysis can control the potential confounding effects of population structure. We show that pattern of association around the haemoglobin S allele differs substantially across populations due to differences in haplotype structure. Motivated by these observations we consider new approaches to association analysis that might prove valuable for multicentre GWAS in Africa: we relax the assumptions of SNP–based fixed effect analysis; we apply Bayesian approaches to allow for heterogeneity in the effect of an allele on risk across studies; and we introduce a region-based test to allow for heterogeneity in the location of causal alleles. PMID:23717212

Stellar Population Properties of Ultracompact Dwarfs in M87: A Mass–Metallicity Correlation Connecting Low-metallicity Globular Clusters and Compact Ellipticals

NASA Astrophysics Data System (ADS)

Zhang, Hong-Xin; Puzia, Thomas H.; Peng, Eric W.; Liu, Chengze; Côté, Patrick; Ferrarese, Laura; Duc, Pierre-Alain; Eigenthaler, Paul; Lim, Sungsoon; Lançon, Ariane; Muñoz, Roberto P.; Roediger, Joel; Sánchez-Janssen, Ruben; Taylor, Matthew A.; Yu, Jincheng

2018-05-01

We derive stellar population parameters for a representative sample of ultracompact dwarfs (UCDs) and a large sample of massive globular clusters (GCs) with stellar masses ≳ 106 M ⊙ in the central galaxy M87 of the Virgo galaxy cluster, based on model fitting to the Lick-index measurements from both the literature and new observations. After necessary spectral stacking of the relatively faint objects in our initial sample of 40 UCDs and 118 GCs, we obtain 30 sets of Lick-index measurements for UCDs and 80 for GCs. The M87 UCDs have ages ≳ 8 Gyr and [α/Fe] ≃ 0.4 dex, in agreement with previous studies based on smaller samples. The literature UCDs, located in lower-density environments than M87, extend to younger ages and smaller [α/Fe] (at given metallicities) than M87 UCDs, resembling the environmental dependence of the stellar nuclei of dwarf elliptical galaxies (dEs) in the Virgo cluster. The UCDs exhibit a positive mass–metallicity relation (MZR), which flattens and connects compact ellipticals at stellar masses ≳ 108 M ⊙. The Virgo dE nuclei largely follow the average MZR of UCDs, whereas most of the M87 GCs are offset toward higher metallicities for given stellar masses. The difference between the mass–metallicity distributions of UCDs and GCs may be qualitatively understood as a result of their different physical sizes at birth in a self-enrichment scenario or of galactic nuclear cluster star formation efficiency being relatively low in a tidal stripping scenario for UCD formation. The existing observations provide the necessary but not sufficient evidence for tidally stripped dE nuclei being the dominant contributors to the M87 UCDs.

Determinants of Viral Oncogene E6-E7 mRNA Overexpression in a Population-Based Large Sample of Women Infected by High-Risk Human Papillomavirus Types

PubMed Central

Bisanzi, Simonetta; Allia, Elena; Mongia, Alessandra; Carozzi, Francesca; Gillio-Tos, Anna; De Marco, Laura; Ronco, Guglielmo; Gustinucci, Daniela; Del Mistro, Annarosa; Frayle, Helena; Iossa, Anna; Fantacci, Giulia; Pompeo, Giampaolo; Cesarini, Elena; Bulletti, Simonetta; Passamonti, Basilio; Rizzi, Martina; Penon, Maria Gabriella; Barca, Alessandra; Benevolo, Maria

2017-01-01

ABSTRACT Cervical cancer screening by human papillomavirus (HPV) DNA testing with cytology triage is more effective than cytology testing. Compared to cytology, the HPV DNA test's higher sensitivity, which allows better protection with longer intervals, makes it necessary to triage the women with a positive result to compensate its lower specificity. We are conducting a large randomized clinical trial (New Technologies for Cervical Cancer 2 [NTCC2]) within organized population-based screening programs in Italy using HPV DNA as the primary screening test to evaluate, by the Aptima HPV assay (Hologic), the use of HPV E6-E7 mRNA in a triage test in comparison to cytology. By the end of June 2016, data were available for 35,877 of 38,535 enrolled women, 2,651 (7.4%) of whom were HPV DNA positive. Among the samples obtained, 2,453 samples were tested also by Aptima, and 1,649 (67.2%) gave a positive result. The proportion of mRNA positivity was slightly higher among samples tested for HPV DNA by the Cobas 4800 HPV assay (Roche) than by the Hybrid Capture 2 (HC2) assay (Qiagen). In our setting, the observed E6-E7 mRNA positivity rate, if used as a triage test, would bring a rate of immediate referral to colposcopy of about 4 to 5%. This value is higher than that observed with cytology triage for both immediate and delayed referrals to colposcopy. By showing only a very high sensitivity and thus allowing a longer interval for HPV DNA-positive/HPV mRNA-negative women, a triage by this test might be more efficient than by cytology. PMID:28100595

EvoSNP-DB: A database of genetic diversity in East Asian populations.

PubMed

Kim, Young Uk; Kim, Young Jin; Lee, Jong-Young; Park, Kiejung

2013-08-01

Genome-wide association studies (GWAS) have become popular as an approach for the identification of large numbers of phenotype-associated variants. However, differences in genetic architecture and environmental factors mean that the effect of variants can vary across populations. Understanding population genetic diversity is valuable for the investigation of possible population specific and independent effects of variants. EvoSNP-DB aims to provide information regarding genetic diversity among East Asian populations, including Chinese, Japanese, and Korean. Non-redundant SNPs (1.6 million) were genotyped in 54 Korean trios (162 samples) and were compared with 4 million SNPs from HapMap phase II populations. EvoSNP-DB provides two user interfaces for data query and visualization, and integrates scores of genetic diversity (Fst and VarLD) at the level of SNPs, genes, and chromosome regions. EvoSNP-DB is a web-based application that allows users to navigate and visualize measurements of population genetic differences in an interactive manner, and is available online at [http://biomi.cdc.go.kr/EvoSNP/].

Analysis of genetic population structure in Acacia caven (Leguminosae, Mimosoideae), comparing one exploratory and two Bayesian-model-based methods.

PubMed

Pometti, Carolina L; Bessega, Cecilia F; Saidman, Beatriz O; Vilardi, Juan C

2014-03-01

Bayesian clustering as implemented in STRUCTURE or GENELAND software is widely used to form genetic groups of populations or individuals. On the other hand, in order to satisfy the need for less computer-intensive approaches, multivariate analyses are specifically devoted to extracting information from large datasets. In this paper, we report the use of a dataset of AFLP markers belonging to 15 sampling sites of Acacia caven for studying the genetic structure and comparing the consistency of three methods: STRUCTURE, GENELAND and DAPC. Of these methods, DAPC was the fastest one and showed accuracy in inferring the K number of populations (K = 12 using the find.clusters option and K = 15 with a priori information of populations). GENELAND in turn, provides information on the area of membership probabilities for individuals or populations in the space, when coordinates are specified (K = 12). STRUCTURE also inferred the number of K populations and the membership probabilities of individuals based on ancestry, presenting the result K = 11 without prior information of populations and K = 15 using the LOCPRIOR option. Finally, in this work all three methods showed high consistency in estimating the population structure, inferring similar numbers of populations and the membership probabilities of individuals to each group, with a high correlation between each other.

Flexible sampling large-scale social networks by self-adjustable random walk

NASA Astrophysics Data System (ADS)

Xu, Xiao-Ke; Zhu, Jonathan J. H.

2016-12-01

Online social networks (OSNs) have become an increasingly attractive gold mine for academic and commercial researchers. However, research on OSNs faces a number of difficult challenges. One bottleneck lies in the massive quantity and often unavailability of OSN population data. Sampling perhaps becomes the only feasible solution to the problems. How to draw samples that can represent the underlying OSNs has remained a formidable task because of a number of conceptual and methodological reasons. Especially, most of the empirically-driven studies on network sampling are confined to simulated data or sub-graph data, which are fundamentally different from real and complete-graph OSNs. In the current study, we propose a flexible sampling method, called Self-Adjustable Random Walk (SARW), and test it against with the population data of a real large-scale OSN. We evaluate the strengths of the sampling method in comparison with four prevailing methods, including uniform, breadth-first search (BFS), random walk (RW), and revised RW (i.e., MHRW) sampling. We try to mix both induced-edge and external-edge information of sampled nodes together in the same sampling process. Our results show that the SARW sampling method has been able to generate unbiased samples of OSNs with maximal precision and minimal cost. The study is helpful for the practice of OSN research by providing a highly needed sampling tools, for the methodological development of large-scale network sampling by comparative evaluations of existing sampling methods, and for the theoretical understanding of human networks by highlighting discrepancies and contradictions between existing knowledge/assumptions of large-scale real OSN data.

Examination of participant flow in the CONSORT diagram can improve the understanding of the generalizability of study results.

PubMed

Andrade, Chittaranjan

2015-11-01

A fundamental principle in research is that the findings of a study can only be generalized to the population from which the sample of the study was drawn. What this population was can be discerned from an examination of the study selection criteria. Additional insights can sometimes be gleaned from the study flowchart or CONSORT diagram, which may show sample attenuation between subject screening and final recruitment. Such sample attenuation, if present, implies further limitation to the generalizability of the study outcomes. Two large, 2-year, randomized controlled maintenance therapy trials are described to illustrate sample attenuation that limits study generalizability, one in the context of mindfulness-based cognitive therapy versus antidepressant drugs for recurrent major depressive disorder and the other in the context of quetiapine versus placebo for bipolar disorder. Readers therefore need to examine both study selection criteria and the CONSORT diagram in order to better understand the extent to which study results apply to the patients whom they see. © Copyright 2015 Physicians Postgraduate Press, Inc.

Estimating snow leopard population abundance using photography and capture-recapture techniques

USGS Publications Warehouse

Jackson, R.M.; Roe, J.D.; Wangchuk, R.; Hunter, D.O.

2006-01-01

Conservation and management of snow leopards (Uncia uncia) has largely relied on anecdotal evidence and presence-absence data due to their cryptic nature and the difficult terrain they inhabit. These methods generally lack the scientific rigor necessary to accurately estimate population size and monitor trends. We evaluated the use of photography in capture-mark-recapture (CMR) techniques for estimating snow leopard population abundance and density within Hemis National Park, Ladakh, India. We placed infrared camera traps along actively used travel paths, scent-sprayed rocks, and scrape sites within 16- to 30-km2 sampling grids in successive winters during January and March 2003-2004. We used head-on, oblique, and side-view camera configurations to obtain snow leopard photographs at varying body orientations. We calculated snow leopard abundance estimates using the program CAPTURE. We obtained a total of 66 and 49 snow leopard captures resulting in 8.91 and 5.63 individuals per 100 trap-nights during 2003 and 2004, respectively. We identified snow leopards based on the distinct pelage patterns located primarily on the forelimbs, flanks, and dorsal surface of the tail. Capture probabilities ranged from 0.33 to 0.67. Density estimates ranged from 8.49 (SE = 0.22; individuals per 100 km2 in 2003 to 4.45 (SE = 0.16) in 2004. We believe the density disparity between years is attributable to different trap density and placement rather than to an actual decline in population size. Our results suggest that photographic capture-mark-recapture sampling may be a useful tool for monitoring demographic patterns. However, we believe a larger sample size would be necessary for generating a statistically robust estimate of population density and abundance based on CMR models.

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

PubMed Central

Johnston, Henry Richard; Hu, Yi-Juan; Gao, Jingjing; O’Connor, Timothy D.; Abecasis, Gonçalo R.; Wojcik, Genevieve L; Gignoux, Christopher R.; Gourraud, Pierre-Antoine; Lizee, Antoine; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Kenny, Eimear E.; Bustamante, Carlos; Beaty, Terri H.; Mathias, Rasika A.; Barnes, Kathleen C.; Qin, Zhaohui S.; Preethi Boorgula, Meher; Campbell, Monica; Chavan, Sameer; Ford, Jean G.; Foster, Cassandra; Gao, Li; Hansel, Nadia N.; Horowitz, Edward; Huang, Lili; Ortiz, Romina; Potee, Joseph; Rafaels, Nicholas; Ruczinski, Ingo; Scott, Alan F.; Taub, Margaret A.; Vergara, Candelaria; Levin, Albert M.; Padhukasahasram, Badri; Williams, L. Keoki; Dunston, Georgia M.; Faruque, Mezbah U.; Gietzen, Kimberly; Deshpande, Aniket; Grus, Wendy E.; Locke, Devin P.; Foreman, Marilyn G.; Avila, Pedro C.; Grammer, Leslie; Kim, Kwang-Youn A.; Kumar, Rajesh; Schleimer, Robert; De La Vega, Francisco M.; Shringarpure, Suyash S.; Musharoff, Shaila; Burchard, Esteban G.; Eng, Celeste; Hernandez, Ryan D.; Pino-Yanes, Maria; Torgerson, Dara G.; Szpiech, Zachary A.; Torres, Raul; Nicolae, Dan L.; Ober, Carole; Olopade, Christopher O; Olopade, Olufunmilayo; Oluwole, Oluwafemi; Arinola, Ganiyu; Song, Wei; Correa, Adolfo; Musani, Solomon; Wilson, James G.; Lange, Leslie A.; Akey, Joshua; Bamshad, Michael; Chong, Jessica; Fu, Wenqing; Nickerson, Deborah; Reiner, Alexander; Hartert, Tina; Ware, Lorraine B.; Bleecker, Eugene; Meyers, Deborah; Ortega, Victor E.; Maul, Pissamai; Maul, Trevor; Watson, Harold; Ilma Araujo, Maria; Riccio Oliveira, Ricardo; Caraballo, Luis; Marrugo, Javier; Martinez, Beatriz; Meza, Catherine; Ayestas, Gerardo; Francisco Herrera-Paz, Edwin; Landaverde-Torres, Pamela; Erazo, Said Omar Leiva; Martinez, Rosella; Mayorga, Alvaro; Mayorga, Luis F.; Mejia-Mejia, Delmy-Aracely; Ramos, Hector; Saenz, Allan; Varela, Gloria; Marina Vasquez, Olga; Ferguson, Trevor; Knight-Madden, Jennifer; Samms-Vaughan, Maureen; Wilks, Rainford J.; Adegnika, Akim; Ateba-Ngoa, Ulysse; Yazdanbakhsh, Maria

2017-01-01

A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an ‘African Diaspora Power Chip’ (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry. PMID:28429804

Composition and distribution of the health workforce in India: estimates based on data from the National Sample Survey.

PubMed

Rao, Krishna D; Shahrawat, Renu; Bhatnagar, Aarushi

2016-09-01

The availability of reliable and comprehensive information on the health workforce is crucial for workforce planning. In India, routine information sources on the health workforce are incomplete and unreliable. This paper addresses this issue and provides a comprehensive picture of India's health workforce. Data from the 68th round (July 2011 to June 2012) of the National Sample Survey on the Employment and unemployment situation in India were analysed to produce estimates of the health workforce in India. The estimates were based on self-reported occupations, categorized using a combination of both National Classification of Occupations (2004) and National Industrial Classification (2008) codes. Findings suggest that in 2011-2012, there were 2.5 million health workers (density of 20.9 workers per 10 000 population) in India. However, 56.4% of all health workers were unqualified, including 42.3% of allopathic doctors, 27.5% of dentists, 56.1% of Ayurveda, yoga and naturopathy, Unani, Siddha and homoeopathy (AYUSH) practitioners, 58.4% of nurses and midwives and 69.2% of health associates. By cadre, there were 3.3 qualified allopathic doctors and 3.1 nurses and midwives per 10 000 population; this is around one quarter of the World Health Organization benchmark of 22.8 doctors, nurses and midwives per 10 000 population. Out of all qualified workers, 77.4% were located in urban areas, even though the urban population is only 31% of the total population of the country. This urban-rural difference was higher for allopathic doctors (density 11.4 times higher in urban areas) compared to nurses and midwives (5.5 times higher in urban areas). The study highlights several areas of concern: overall low numbers of qualified health workers; a large presence of unqualified health workers, particularly in rural areas; and large urban-rural differences in the distribution of qualified health workers.

Extent of height variability explained by known height-associated genetic variants in an isolated population of the Adriatic coast of Croatia.

PubMed

Zhang, Ge; Karns, Rebekah; Sun, Guangyun; Indugula, Subba Rao; Cheng, Hong; Havas-Augustin, Dubravka; Novokmet, Natalija; Rudan, Dusko; Durakovic, Zijad; Missoni, Sasa; Chakraborty, Ranajit; Rudan, Pavao; Deka, Ranjan

2011-01-01

Human height is a classical example of a polygenic quantitative trait. Recent large-scale genome-wide association studies (GWAS) have identified more than 200 height-associated loci, though these variants explain only 2∼10% of overall variability of normal height. The objective of this study was to investigate the variance explained by these loci in a relatively isolated population of European descent with limited admixture and homogeneous genetic background from the Adriatic coast of Croatia. In a sample of 1304 individuals from the island population of Hvar, Croatia, we performed genome-wide SNP typing and assessed the variance explained by genetic scores constructed from different panels of height-associated SNPs extracted from five published studies. The combined information of the 180 SNPs reported by Lango Allen el al. explained 7.94% of phenotypic variation in our sample. Genetic scores based on 20~50 SNPs reported by the remaining individual GWA studies explained 3~5% of height variance. These percentages of variance explained were within ranges comparable to the original studies and heterogeneity tests did not detect significant differences in effect size estimates between our study and the original reports, if the estimates were obtained from populations of European descent. We have evaluated the portability of height-associated loci and the overall fitting of estimated effect sizes reported in large cohorts to an isolated population. We found proportions of explained height variability were comparable to multiple reference GWAS in cohorts of European descent. These results indicate similar genetic architecture and comparable effect sizes of height loci among populations of European descent. © 2011 Zhang et al.

Sampling pig farms at the abattoir in a cross-sectional study - Evaluation of a sampling method.

PubMed

Birkegård, Anna Camilla; Halasa, Tariq; Toft, Nils

2017-09-15

A cross-sectional study design is relatively inexpensive, fast and easy to conduct when compared to other study designs. Careful planning is essential to obtaining a representative sample of the population, and the recommended approach is to use simple random sampling from an exhaustive list of units in the target population. This approach is rarely feasible in practice, and other sampling procedures must often be adopted. For example, when slaughter pigs are the target population, sampling the pigs on the slaughter line may be an alternative to on-site sampling at a list of farms. However, it is difficult to sample a large number of farms from an exact predefined list, due to the logistics and workflow of an abattoir. Therefore, it is necessary to have a systematic sampling procedure and to evaluate the obtained sample with respect to the study objective. We propose a method for 1) planning, 2) conducting, and 3) evaluating the representativeness and reproducibility of a cross-sectional study when simple random sampling is not possible. We used an example of a cross-sectional study with the aim of quantifying the association of antimicrobial resistance and antimicrobial consumption in Danish slaughter pigs. It was not possible to visit farms within the designated timeframe. Therefore, it was decided to use convenience sampling at the abattoir. Our approach was carried out in three steps: 1) planning: using data from meat inspection to plan at which abattoirs and how many farms to sample; 2) conducting: sampling was carried out at five abattoirs; 3) evaluation: representativeness was evaluated by comparing sampled and non-sampled farms, and the reproducibility of the study was assessed through simulated sampling based on meat inspection data from the period where the actual data collection was carried out. In the cross-sectional study samples were taken from 681 Danish pig farms, during five weeks from February to March 2015. The evaluation showed that the sampling procedure was reproducible with results comparable to the collected sample. However, the sampling procedure favoured sampling of large farms. Furthermore, both under-sampled and over-sampled areas were found using scan statistics. In conclusion, sampling conducted at abattoirs can provide a spatially representative sample. Hence it is a possible cost-effective alternative to simple random sampling. However, it is important to assess the properties of the resulting sample so that any potential selection bias can be addressed when reporting the findings. Copyright © 2017 Elsevier B.V. All rights reserved.

Evolutionary history of Ichthyosaura alpestris (Caudata, Salamandridae) inferred from the combined analysis of nuclear and mitochondrial markers.

PubMed

Recuero, Ernesto; Buckley, David; García-París, Mario; Arntzen, Jan W; Cogălniceanu, Dan; Martínez-Solano, Iñigo

2014-12-01

Widespread species with morphologically and ecologically differentiated populations are key to understand speciation because they allow investigating the different stages of the continuous process of population divergence. The alpine newt, Ichthyosaura alpestris, with a range that covers a large part of Central Europe as well as isolated regions in all three European Mediterranean peninsulas, and with strong ecological and life-history differences among populations, is an excellent system for such studies. We sampled individuals across most of the range of the species, and analyzed mitochondrial (1442 bp) and nuclear (two nuclear genes -1554 bp- and 35 allozyme loci) markers to produce a time-calibrated phylogeny and reconstruct the historical biogeography of the species. Phylogenetic analyses of mtDNA data produced a fully resolved topology, with an endemic, Balkan clade (Vlasina) which is sister to a clade comprising an eastern and a western group. Within the former, one clade (subspecies I. a. veluchiensis) is sister to a clade containing subspecies I. a. montenegrina and I. a. serdara as well as samples from southern Romania, Bosnia-Herzegovina, Serbia and Bulgaria (subspecies I. a. reiseri and part of I. a. alpestris). Within the western group, populations from the Italian peninsula (subspecies I. a. apuana and I. a. inexpectata) are sister to a clade containing samples from the Iberian Peninsula (subspecies I. a. cyreni) and the remainder of the samples from subspecies I. a. alpestris (populations from Hungary, Austria, Poland, France, Germany and the larger part of Romania). Results of (∗)BEAST analyses on a combined mtDNA and nDNA dataset consistently recovered with high statistical support four lineages with unresolved inter-relationships: (1) subspecies I. a. veluchiensis; (2) subspecies I. a. apuana+I. a. inexpectata; (3) subspecies I. a. cyreni+part of subspecies I. a. alpestris (the westernmost populations, plus most Romanian populations); and (4) the remaining populations, including subspecies I. a. serdara, I. a. reiseri and I. a. montenegrina and part of subspecies I. a. alpestris, plus samples from Vlasina. Our time estimates are consistent with ages based on the fossil record and suggest a widespread distribution for the I. alpestris ancestor, with the split of the major eastern and western lineages during the Miocene, in the Tortonian. Our study provides a solid, comprehensive background on the evolutionary history of the species based on the most complete combined (mtDNA+nDNA+allozymes) dataset to date. The combination of the historical perspective provided by coalescent-based analyses of mitochondrial and nuclear DNA variation with individual-based multilocus assignment methods based on multiple nuclear markers (allozymes) also allowed identification of instances of discordance across markers that highlight the complexity and dynamism of past and ongoing evolutionary processes in the species. Copyright © 2014 Elsevier Inc. All rights reserved.

Population Stratification in the Context of Diverse Epidemiologic Surveys Sans Genome-Wide Data

PubMed Central

Oetjens, Matthew T.; Brown-Gentry, Kristin; Goodloe, Robert; Dilks, Holli H.; Crawford, Dana C.

2016-01-01

Population stratification or confounding by genetic ancestry is a potential cause of false associations in genetic association studies. Estimation of and adjustment for genetic ancestry has become common practice thanks in part to the availability of ancestry informative markers on genome-wide association study (GWAS) arrays. While array data is now widespread, these data are not ubiquitous as several large epidemiologic and clinic-based studies lack genome-wide data. One such large epidemiologic-based study lacking genome-wide data accessible to investigators is the National Health and Nutrition Examination Surveys (NHANES), population-based cross-sectional surveys of Americans linked to demographic, health, and lifestyle data conducted by the Centers for Disease Control and Prevention. DNA samples (n = 14,998) were extracted from biospecimens from consented NHANES participants between 1991–1994 (NHANES III, phase 2) and 1999–2002 and represent three major self-identified racial/ethnic groups: non-Hispanic whites (n = 6,634), non-Hispanic blacks (n = 3,458), and Mexican Americans (n = 3,950). We as the Epidemiologic Architecture for Genes Linked to Environment study genotyped candidate gene and GWAS-identified index variants in NHANES as part of the larger Population Architecture using Genomics and Epidemiology I study for collaborative genetic association studies. To enable basic quality control such as estimation of genetic ancestry to control for population stratification in NHANES san genome-wide data, we outline here strategies that use limited genetic data to identify the markers optimal for characterizing genetic ancestry. From among 411 and 295 autosomal SNPs available in NHANES III and NHANES 1999–2002, we demonstrate that markers with ancestry information can be identified to estimate global ancestry. Despite limited resolution, global genetic ancestry is highly correlated with self-identified race for the majority of participants, although less so for ethnicity. Overall, the strategies outlined here for a large epidemiologic study can be applied to other datasets accessible for genotype–phenotype studies but are sans genome-wide data. PMID:27200085

Reliability of confidence intervals calculated by bootstrap and classical methods using the FIA 1-ha plot design

Treesearch

H. T. Schreuder; M. S. Williams

2000-01-01

In simulation sampling from forest populations using sample sizes of 20, 40, and 60 plots respectively, confidence intervals based on the bootstrap (accelerated, percentile, and t-distribution based) were calculated and compared with those based on the classical t confidence intervals for mapped populations and subdomains within those populations. A 68.1 ha mapped...

Population Estimation Using a 3D City Model: A Multi-Scale Country-Wide Study in the Netherlands

PubMed Central

Arroyo Ohori, Ken; Ledoux, Hugo; Peters, Ravi; Stoter, Jantien

2016-01-01

The remote estimation of a region’s population has for decades been a key application of geographic information science in demography. Most studies have used 2D data (maps, satellite imagery) to estimate population avoiding field surveys and questionnaires. As the availability of semantic 3D city models is constantly increasing, we investigate to what extent they can be used for the same purpose. Based on the assumption that housing space is a proxy for the number of its residents, we use two methods to estimate the population with 3D city models in two directions: (1) disaggregation (areal interpolation) to estimate the population of small administrative entities (e.g. neighbourhoods) from that of larger ones (e.g. municipalities); and (2) a statistical modelling approach to estimate the population of large entities from a sample composed of their smaller ones (e.g. one acquired by a government register). Starting from a complete Dutch census dataset at the neighbourhood level and a 3D model of all 9.9 million buildings in the Netherlands, we compare the population estimates obtained by both methods with the actual population as reported in the census, and use it to evaluate the quality that can be achieved by estimations at different administrative levels. We also analyse how the volume-based estimation enabled by 3D city models fares in comparison to 2D methods using building footprints and floor areas, as well as how it is affected by different levels of semantic detail in a 3D city model. We conclude that 3D city models are useful for estimations of large areas (e.g. for a country), and that the 3D approach has clear advantages over the 2D approach. PMID:27254151

Genomic scan as a tool for assessing the genetic component of phenotypic variance in wild populations.

PubMed

Herrera, Carlos M

2012-01-01

Methods for estimating quantitative trait heritability in wild populations have been developed in recent years which take advantage of the increased availability of genetic markers to reconstruct pedigrees or estimate relatedness between individuals, but their application to real-world data is not exempt from difficulties. This chapter describes a recent marker-based technique which, by adopting a genomic scan approach and focusing on the relationship between phenotypes and genotypes at the individual level, avoids the problems inherent to marker-based estimators of relatedness. This method allows the quantification of the genetic component of phenotypic variance ("degree of genetic determination" or "heritability in the broad sense") in wild populations and is applicable whenever phenotypic trait values and multilocus data for a large number of genetic markers (e.g., amplified fragment length polymorphisms, AFLPs) are simultaneously available for a sample of individuals from the same population. The method proceeds by first identifying those markers whose variation across individuals is significantly correlated with individual phenotypic differences ("adaptive loci"). The proportion of phenotypic variance in the sample that is statistically accounted for by individual differences in adaptive loci is then estimated by fitting a linear model to the data, with trait value as the dependent variable and scores of adaptive loci as independent ones. The method can be easily extended to accommodate quantitative or qualitative information on biologically relevant features of the environment experienced by each sampled individual, in which case estimates of the environmental and genotype × environment components of phenotypic variance can also be obtained.

Childhood adversity and personality disorders: results from a nationally representative population-based study.

PubMed

Afifi, Tracie O; Mather, Amber; Boman, Jonathon; Fleisher, William; Enns, Murray W; Macmillan, Harriet; Sareen, Jitender

2011-06-01

Although, a large population-based literature exists on the relationship between childhood adversity and Axis I mental disorders, research on the link between childhood adversity and Axis II personality disorders (PDs) relies mainly on clinical samples. The purpose of the current study was to examine the relationship between a range of childhood adversities and PDs in a nationally representative sample while adjusting for Axis I mental disorders. Data were from the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC; n=34,653; data collection 2004-2005); a nationally representative sample of the United States population aged 20 years and older. The results indicated that many types of childhood adversity were highly prevalent among individuals with PDs in the general population and childhood adversity was most consistently associated with schizotypal, antisocial, borderline, and narcissistic PDs. The most robust childhood adversity findings were for child abuse and neglect with cluster A and cluster B PDs after adjusting for all other types of childhood adversity, mood disorders, anxiety disorders, substance use disorders, other PD clusters, and sociodemographic variables (Odd Ratios ranging from 1.22 to 1.63). In these models, mood disorders, anxiety disorders, and substance use disorders also remained significantly associated with PD clusters (Odds Ratios ranging from 1.26 to 2.38). Further research is necessary to understand whether such exposure has a causal role in the association with PDs. In addition to preventing child maltreatment, it is important to determine ways to prevent impairment among those exposed to adversity, as this may reduce the development of PDs. Copyright © 2010 Elsevier Ltd. All rights reserved.

Variation in the cranial base orientation and facial skeleton in dry skulls sampled from three major populations.

PubMed

Kuroe, Kazuto; Rosas, Antonio; Molleson, Theya

2004-04-01

The aim of this study was to analyse the effects of cranial base orientation on the morphology of the craniofacial system in human populations. Three geographically distant populations from Europe (72), Africa (48) and Asia (24) were chosen. Five angular and two linear variables from the cranial base component and six angular and six linear variables from the facial component based on two reference lines of the vertical posterior maxillary and Frankfort horizontal planes were measured. The European sample presented dolichofacial individuals with a larger face height and a smaller face depth derived from a raised cranial base and facial cranium orientation which tended to be similar to the Asian sample. The African sample presented brachyfacial individuals with a reduced face height and a larger face depth as a result of a lowered cranial base and facial cranium orientation. The Asian sample presented dolichofacial individuals with a larger face height and depth due to a raised cranial base and facial cranium orientation. The findings of this study suggest that cranial base orientation and posterior cranial base length appear to be valid discriminating factors between different human populations.

Developing a synthetic national population to investigate the impact of different cardiovascular disease risk management strategies: A derivation and validation study

PubMed Central

Jackson, Rod

2017-01-01

Background Many national cardiovascular disease (CVD) risk factor management guidelines now recommend that drug treatment decisions should be informed primarily by patients’ multi-variable predicted risk of CVD, rather than on the basis of single risk factor thresholds. To investigate the potential impact of treatment guidelines based on CVD risk thresholds at a national level requires individual level data representing the multi-variable CVD risk factor profiles for a country’s total adult population. As these data are seldom, if ever, available, we aimed to create a synthetic population, representing the joint CVD risk factor distributions of the adult New Zealand population. Methods and results A synthetic population of 2,451,278 individuals, representing the actual age, gender, ethnicity and social deprivation composition of people aged 30–84 years who completed the 2013 New Zealand census was generated using Monte Carlo sampling. Each ‘synthetic’ person was then probabilistically assigned values of the remaining cardiovascular disease (CVD) risk factors required for predicting their CVD risk, based on data from the national census national hospitalisation and drug dispensing databases and a large regional cohort study, using Monte Carlo sampling and multiple imputation. Where possible, the synthetic population CVD risk distributions for each non-demographic risk factor were validated against independent New Zealand data sources. Conclusions We were able to develop a synthetic national population with realistic multi-variable CVD risk characteristics. The construction of this population is the first step in the development of a micro-simulation model intended to investigate the likely impact of a range of national CVD risk management strategies that will inform CVD risk management guideline updates in New Zealand and elsewhere. PMID:28384217

Developing a synthetic national population to investigate the impact of different cardiovascular disease risk management strategies: A derivation and validation study.

PubMed

Knight, Josh; Wells, Susan; Marshall, Roger; Exeter, Daniel; Jackson, Rod

2017-01-01

Many national cardiovascular disease (CVD) risk factor management guidelines now recommend that drug treatment decisions should be informed primarily by patients' multi-variable predicted risk of CVD, rather than on the basis of single risk factor thresholds. To investigate the potential impact of treatment guidelines based on CVD risk thresholds at a national level requires individual level data representing the multi-variable CVD risk factor profiles for a country's total adult population. As these data are seldom, if ever, available, we aimed to create a synthetic population, representing the joint CVD risk factor distributions of the adult New Zealand population. A synthetic population of 2,451,278 individuals, representing the actual age, gender, ethnicity and social deprivation composition of people aged 30-84 years who completed the 2013 New Zealand census was generated using Monte Carlo sampling. Each 'synthetic' person was then probabilistically assigned values of the remaining cardiovascular disease (CVD) risk factors required for predicting their CVD risk, based on data from the national census national hospitalisation and drug dispensing databases and a large regional cohort study, using Monte Carlo sampling and multiple imputation. Where possible, the synthetic population CVD risk distributions for each non-demographic risk factor were validated against independent New Zealand data sources. We were able to develop a synthetic national population with realistic multi-variable CVD risk characteristics. The construction of this population is the first step in the development of a micro-simulation model intended to investigate the likely impact of a range of national CVD risk management strategies that will inform CVD risk management guideline updates in New Zealand and elsewhere.

Genome-wide analysis of the diversity and ancestry of Korean dogs.

PubMed

Choi, Bong Hwan; Wijayananda, Hasini I; Lee, Soo Hyun; Lee, Doo Ho; Kim, Jong Seok; Oh, Seok Il; Park, Eung Woo; Lee, Cheul Koo; Lee, Seung Hwan

2017-01-01

There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei's genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China.

Genome-wide analysis of the diversity and ancestry of Korean dogs

PubMed Central

Lee, Doo Ho; Kim, Jong Seok; Oh, Seok Il; Park, Eung Woo; Lee, Cheul Koo; Lee, Seung Hwan

2017-01-01

There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei’s genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China. PMID:29182674

CIHR Candrive Cohort Comparison with Canadian Household Population Holding Valid Driver's Licenses.

PubMed

Gagnon, Sylvain; Marshall, Shawn; Kadulina, Yara; Stinchcombe, Arne; Bédard, Michel; Gélinas, Isabelle; Man-Son-Hing, Malcolm; Mazer, Barbara; Naglie, Gary; Porter, Michelle M; Rapoport, Mark; Tuokko, Holly; Vrkljan, Brenda

2016-06-01

We investigated whether convenience sampling is a suitable method to generate a sample of older drivers representative of the older-Canadian driver population. Using equivalence testing, we compared a large convenience sample of older drivers (Candrive II prospective cohort study) to a similarly aged population of older Canadian drivers. The Candrive sample consists of 928 community-dwelling older drivers from seven metropolitan areas of Canada. The population data was obtained from the Canadian Community Health Survey - Healthy Aging (CCHS-HA), which is a representative sample of older Canadians. The data for drivers aged 70 and older were extracted from the CCHS-HA database, for a total of 3,899 older Canadian drivers. Two samples were demonstrated as equivalent on socio-demographic, health, and driving variables that we compared, but not on driving frequency. We conclude that convenience sampling used in the Candrive study created a fairly representative sample of Canadian older drivers, with a few exceptions.

Differential Item Functioning for Accommodated Students with Disabilities: Effect of Differences in Proficiency Distributions

ERIC Educational Resources Information Center

Quesen, Sarah

2016-01-01

When studying differential item functioning (DIF) with students with disabilities (SWD) focal groups typically suffer from small sample size, whereas the reference group population is usually large. This makes it possible for a researcher to select a sample from the reference population to be similar to the focal group on the ability scale. Doing…

How many infants are temperamentally difficult? Comparing norms from the Revised Infant Temperament Questionnaire to a population sample of UK infants.

PubMed

Chong, Shiau Yun; Chittleborough, Catherine R; Gregory, Tess; Lynch, John W; Smithers, Lisa G

2015-08-01

The original norms for the Revised Infant Temperament Questionnaire (RITQ) were published in 1978 and were based on a small sample from the US. The aim of this study is to compare temperament scores from the original RITQ against scores from a large population-based cohort of infants from the UK. This study consists of 10,937 infants from the Avon Longitudinal Study of Parents and Children (ALSPAC) born between April 1991 and December 1992 in the southwest of England. Infant temperament at 6 months of age was reported by parents using the adapted RITQ. Responses were scored according to the RITQ manual and then categorized into temperament groups (easy, intermediate low, intermediate high, and difficult) using either the RITQ norms or norms derived from the data. The scores for each temperament subscale and the proportion of children in each temperament group were compared across the two methods. Subscale scores for the ALSPAC sample were higher (more "difficult") than the RITQ norms for rhythmicity, approach, adaptability, intensity, and distractibility. When RITQ norms were applied, 24% infants were categorized as difficult and 25% as easy, compared with 15% difficult and 38% easy when ALSPAC norms were used. There are discrepancies between RITQ norms and the ALSPAC norms which resulted in differences in the distribution of temperament groups. There is a need to re-examine RITQ norms and categorization for use in primary care practice and contemporary population-based studies. Copyright © 2015 Elsevier Inc. All rights reserved.

First direct comparison of high and low ionization line kinematics in active galactic nuclei

NASA Technical Reports Server (NTRS)

Sulentic, J. W.; Marziani, P.; Dultzin-Hacyan, D.; Calvani, M.; Moles, M.

1995-01-01

We present first results of a comparison of emission line shift properties for the high (HILs) and low (LILs) ionization lines in 43 low-reshift quasars. We identify a core sample of C IV lambda 1549 and hydrogen beta profiles with a wide distribution of red- and blueshifts (less than or equal to +/- 1000 km/sec). We also identify two tails in this distribution: one with large hydrogen beta redshifts (greater than or equal to 2000 km/sec) and another with large C IV blueshifts (greater than or equal to 1500 km/sec). The tails are mutually exclusive. All objects with extreme hydrogen beta redshift are radio loud, and all objects with extreme C IV blueshift are radio quiet. The core samples of smaller shifts can be most simply divided into: (1) hydrogen beta - a redshifted radio-loud population (related to the tail) and a radio-quiet population with mean shift near zero, and (2) C IV - a blueshifted radio-quiet population (related to the tail) and a radio-loud population with mean shift near zero. The results suggest fundamentally different kinematics for the HILs and LILs. They also suggest very different kinematics for radio-loud and radio-quiet active galactic nuclei. They also favor a predominance of radial motion in a large fraction of the sample.

Observation of Spontaneous Expressive Language (OSEL): A New Measure for Spontaneous and Expressive Language of Children with Autism Spectrum Disorders and Other Communication Disorders

PubMed Central

Kim, So Hyun; Junker, Dörte; Lord, Catherine

2014-01-01

A new language measure, the Observation of Spontaneous Expressive Language (OSEL), is intended to document spontaneous use of syntax, pragmatics, and semantics in 2-12-year-old children with ASD and other communication disorders with expressive language levels comparable to typical 2-5 year olds. Because the purpose of the OSEL is to provide developmental norms for use of language, the first step involves assessment of the scale’s feasibility, validity, and reliability using a sample of 180 2-5 year-old typically developing children. Pilot data from the OSEL shows strong internal consistency, high reliabilities and validity. Once replicated with a large population-based sample and in special populations, the scale should be helpful in designing appropriate interventions for children with ASD and other communication disorders. PMID:25022249

Assessing power of large river fish monitoring programs to detect population changes: the Missouri River sturgeon example

USGS Publications Warehouse

Wildhaber, M.L.; Holan, S.H.; Bryan, J.L.; Gladish, D.W.; Ellersieck, M.

2011-01-01

In 2003, the US Army Corps of Engineers initiated the Pallid Sturgeon Population Assessment Program (PSPAP) to monitor pallid sturgeon and the fish community of the Missouri River. The power analysis of PSPAP presented here was conducted to guide sampling design and effort decisions. The PSPAP sampling design has a nested structure with multiple gear subsamples within a river bend. Power analyses were based on a normal linear mixed model, using a mixed cell means approach, with variance estimates from the original data. It was found that, at current effort levels, at least 20 years for pallid and 10 years for shovelnose sturgeon is needed to detect a 5% annual decline. Modified bootstrap simulations suggest power estimates from the original data are conservative due to excessive zero fish counts. In general, the approach presented is applicable to a wide array of animal monitoring programs.

Observation of Spontaneous Expressive Language (OSEL): a new measure for spontaneous and expressive language of children with autism spectrum disorders and other communication disorders.

PubMed

Kim, So Hyun; Junker, Dörte; Lord, Catherine

2014-12-01

A new language measure, the Observation of Spontaneous Expressive Language (OSEL), is intended to document spontaneous use of syntax, pragmatics, and semantics in 2-12-year-old children with Autism Spectrum Disorder (ASD) and other communication disorders with expressive language levels comparable to typical 2-5 year olds. Because the purpose of the OSEL is to provide developmental norms for use of language, the first step involves assessment of the scale's feasibility, validity, and reliability using a sample of 180 2-5 year-old typically developing children. Pilot data from the OSEL shows strong internal consistency, high reliabilities and validity. Once replicated with a large population-based sample and in special populations, the scale should be helpful in designing appropriate interventions for children with ASD and other communication disorders.

How are social capital and sense of coherence associated with hazardous alcohol use? Findings from a large population-based Swedish sample of adults.

PubMed

Larm, Peter; Åslund, Cecilia; Starrin, Bengt; Nilsson, K W

2016-07-01

This study examined whether social capital and a sense of coherence are associated with hazardous alcohol use in a large population-based Swedish sample. In particular, the objectives were (a) to examine which of five subdimensions of social capital is associated with hazardous alcohol use, (b) to investigate the moderating role of sense of coherence and (c) to examine possible sex differences. A postal survey was distributed to a sample of respondents (aged 18-84 years) from five Swedish counties that was stratified by sex, age and city; 40,674 (59.2%) participants responded, of which 45.5% were men and 54.5% were women with a mean±SD age of 53.8±17.9 years. Structural dimensions of social capital were associated with an increased probability of hazardous alcohol use among both men and women, whereas the increased probability associated with cognitive dimensions occurred mostly among women. Sense of coherence was robustly associated with a decreased probability of hazardous alcohol use among both men and women. There were few moderating effects of sense of coherence and sex differences emerged mainly for the cognitive dimension of social capital. CONCLUSIONS ASSOCIATIONS BETWEEN SOCIAL CAPITAL DIMENSIONS AND HAZARDOUS ALCOHOL USE WERE PARTLY SEX-SPECIFIC, WHEREAS THE BENEFITS OF A SENSE OF COHERENCE ACCRUED TO BOTH SEXES SOCIAL CAPITAL DIMENSIONS AND SENSE OF COHERENCE WERE GENERALLY UNRELATED TO EACH OTHER ONLY ASSOCIATIONS BETWEEN THE COGNITIVE DIMENSIONS OF SOCIAL CAPITAL AND HAZARDOUS ALCOHOL USE DIFFERED BY SEX. © 2016 the Nordic Societies of Public Health.

Pharmacological profiles of acute myeloid leukemia treatments in patient samples by automated flow cytometry: a bridge to individualized medicine.

PubMed

Bennett, Teresa A; Montesinos, Pau; Moscardo, Federico; Martinez-Cuadron, David; Martinez, Joaquin; Sierra, Jorge; García, Raimundo; de Oteyza, Jaime Perez; Fernandez, Pascual; Serrano, Josefina; Fernandez, Angeles; Herrera, Pilar; Gonzalez, Ataulfo; Bethancourt, Concepcion; Rodriguez-Macias, Gabriela; Alonso, Arancha; Vera, Juan A; Navas, Begoña; Lavilla, Esperanza; Lopez, Juan A; Jimenez, Santiago; Simiele, Adriana; Vidriales, Belen; Gonzalez, Bernardo J; Burgaleta, Carmen; Hernandez Rivas, Jose A; Mascuñano, Raul Cordoba; Bautista, Guiomar; Perez Simon, Jose A; Fuente, Adolfo de la; Rayón, Consolación; Troconiz, Iñaki F; Janda, Alvaro; Bosanquet, Andrew G; Hernandez-Campo, Pilar; Primo, Daniel; Lopez, Rocio; Liebana, Belen; Rojas, Jose L; Gorrochategui, Julian; Sanz, Miguel A; Ballesteros, Joan

2014-08-01

We have evaluated the ex vivo pharmacology of single drugs and drug combinations in malignant cells of bone marrow samples from 125 patients with acute myeloid leukemia using a novel automated flow cytometry-based platform (ExviTech). We have improved previous ex vivo drug testing with 4 innovations: identifying individual leukemic cells, using intact whole blood during the incubation, using an automated platform that escalates reliably data, and performing analyses pharmacodynamic population models. Samples were sent from 24 hospitals to a central laboratory and incubated for 48 hours in whole blood, after which drug activity was measured in terms of depletion of leukemic cells. The sensitivity of single drugs is assessed for standard efficacy (EMAX) and potency (EC50) variables, ranked as percentiles within the population. The sensitivity of drug-combination treatments is assessed for the synergism achieved in each patient sample. We found a large variability among patient samples in the dose-response curves to a single drug or combination treatment. We hypothesize that the use of the individual patient ex vivo pharmacological profiles may help to guide a personalized treatment selection. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Type I error probabilities based on design-stage strategies with applications to noninferiority trials.

PubMed

Rothmann, Mark

2005-01-01

When testing the equality of means from two different populations, a t-test or large sample normal test tend to be performed. For these tests, when the sample size or design for the second sample is dependent on the results of the first sample, the type I error probability is altered for each specific possibility in the null hypothesis. We will examine the impact on the type I error probabilities for two confidence interval procedures and procedures using test statistics when the design for the second sample or experiment is dependent on the results from the first sample or experiment (or series of experiments). Ways for controlling a desired maximum type I error probability or a desired type I error rate will be discussed. Results are applied to the setting of noninferiority comparisons in active controlled trials where the use of a placebo is unethical.

BayeSED: A General Approach to Fitting the Spectral Energy Distribution of Galaxies

NASA Astrophysics Data System (ADS)

Han, Yunkun; Han, Zhanwen

2014-11-01

We present a newly developed version of BayeSED, a general Bayesian approach to the spectral energy distribution (SED) fitting of galaxies. The new BayeSED code has been systematically tested on a mock sample of galaxies. The comparison between the estimated and input values of the parameters shows that BayeSED can recover the physical parameters of galaxies reasonably well. We then applied BayeSED to interpret the SEDs of a large Ks -selected sample of galaxies in the COSMOS/UltraVISTA field with stellar population synthesis models. Using the new BayeSED code, a Bayesian model comparison of stellar population synthesis models has been performed for the first time. We found that the 2003 model by Bruzual & Charlot, statistically speaking, has greater Bayesian evidence than the 2005 model by Maraston for the Ks -selected sample. In addition, while setting the stellar metallicity as a free parameter obviously increases the Bayesian evidence of both models, varying the initial mass function has a notable effect only on the Maraston model. Meanwhile, the physical parameters estimated with BayeSED are found to be generally consistent with those obtained using the popular grid-based FAST code, while the former parameters exhibit more natural distributions. Based on the estimated physical parameters of the galaxies in the sample, we qualitatively classified the galaxies in the sample into five populations that may represent galaxies at different evolution stages or in different environments. We conclude that BayeSED could be a reliable and powerful tool for investigating the formation and evolution of galaxies from the rich multi-wavelength observations currently available. A binary version of the BayeSED code parallelized with Message Passing Interface is publicly available at https://bitbucket.org/hanyk/bayesed.

Prevalence of depression: Comparisons of different depression definitions in population-based samples of older adults.

PubMed

Sjöberg, Linnea; Karlsson, Björn; Atti, Anna-Rita; Skoog, Ingmar; Fratiglioni, Laura; Wang, Hui-Xin

2017-10-15

Depression prevalence in older adults varies largely across studies, which probably reflects methodological rather than true differences. This study aims to explore whether and to what extent the prevalence of depression varies when using different diagnostic criteria and rating scales, and various samples of older adults. A population-based sample of 3353 individuals aged 60-104 years from the Swedish National Study on Aging and Care in Kungsholmen (SNAC-K) were examined in 2001-2004. Point prevalence of depression was estimated by: 1) diagnostic criteria, ICD-10 and DSM-IV-TR/DSM-5; 2) rating scales, MADRS and GDS-15; and 3) self-report. Depression prevalence in sub-samples by dementia status, living place, and socio-demographics were compared. The prevalence of any depression (including all severity grades) was 4.2% (moderate/severe: 1.6%) for ICD-10 and 9.3% (major: 2.1%) for DSM-IV-TR; 10.6% for MADRS and 9.2% for GDS-15; and 9.1% for self-report. Depression prevalence was lower in the dementia-free sample as compared to the total population. Furthermore, having poor physical function, or not having a partner were independently associated with higher depression prevalence, across most of the depression definitions. The response rate was 73.3% and this may have resulted in an underestimation of depression. Depression prevalence was similar across all depression definitions except for ICD-10, showing much lower figures. However, independent of the definition used, depression prevalence varies greatly by dementia status, physical functioning, and marital status. These findings may be useful for clinicians when assessing depression in older adults and for researchers when exploring and comparing depression prevalence across studies. Copyright © 2017 Elsevier B.V. All rights reserved.

BayeSED: A GENERAL APPROACH TO FITTING THE SPECTRAL ENERGY DISTRIBUTION OF GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Yunkun; Han, Zhanwen, E-mail: hanyk@ynao.ac.cn, E-mail: zhanwenhan@ynao.ac.cn

2014-11-01

We present a newly developed version of BayeSED, a general Bayesian approach to the spectral energy distribution (SED) fitting of galaxies. The new BayeSED code has been systematically tested on a mock sample of galaxies. The comparison between the estimated and input values of the parameters shows that BayeSED can recover the physical parameters of galaxies reasonably well. We then applied BayeSED to interpret the SEDs of a large K{sub s} -selected sample of galaxies in the COSMOS/UltraVISTA field with stellar population synthesis models. Using the new BayeSED code, a Bayesian model comparison of stellar population synthesis models has beenmore » performed for the first time. We found that the 2003 model by Bruzual and Charlot, statistically speaking, has greater Bayesian evidence than the 2005 model by Maraston for the K{sub s} -selected sample. In addition, while setting the stellar metallicity as a free parameter obviously increases the Bayesian evidence of both models, varying the initial mass function has a notable effect only on the Maraston model. Meanwhile, the physical parameters estimated with BayeSED are found to be generally consistent with those obtained using the popular grid-based FAST code, while the former parameters exhibit more natural distributions. Based on the estimated physical parameters of the galaxies in the sample, we qualitatively classified the galaxies in the sample into five populations that may represent galaxies at different evolution stages or in different environments. We conclude that BayeSED could be a reliable and powerful tool for investigating the formation and evolution of galaxies from the rich multi-wavelength observations currently available. A binary version of the BayeSED code parallelized with Message Passing Interface is publicly available at https://bitbucket.org/hanyk/bayesed.« less

A New Stratified Sampling Procedure which Decreases Error Estimation of Varroa Mite Number on Sticky Boards.

PubMed

Kretzschmar, A; Durand, E; Maisonnasse, A; Vallon, J; Le Conte, Y

2015-06-01

A new procedure of stratified sampling is proposed in order to establish an accurate estimation of Varroa destructor populations on sticky bottom boards of the hive. It is based on the spatial sampling theory that recommends using regular grid stratification in the case of spatially structured process. The distribution of varroa mites on sticky board being observed as spatially structured, we designed a sampling scheme based on a regular grid with circles centered on each grid element. This new procedure is then compared with a former method using partially random sampling. Relative error improvements are exposed on the basis of a large sample of simulated sticky boards (n=20,000) which provides a complete range of spatial structures, from a random structure to a highly frame driven structure. The improvement of varroa mite number estimation is then measured by the percentage of counts with an error greater than a given level. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Minimizing Artifacts and Biases in Chamber-Based Measurements of Soil Respiration

NASA Astrophysics Data System (ADS)

Davidson, E. A.; Savage, K.

2001-05-01

Soil respiration is one of the largest and most important fluxes of carbon in terrestrial ecosystems. The objectives of this paper are to review concerns about uncertainties of chamber-based measurements of CO2 emissions from soils, to evaluate the direction and magnitude of these potential errors, and to explain procedures that minimize these errors and biases. Disturbance of diffusion gradients cause underestimate of fluxes by less than 15% in most cases, and can be partially corrected for with curve fitting and/or can be minimized by using brief measurement periods. Under-pressurization or over-pressurization of the chamber caused by flow restrictions in air circulating designs can cause large errors, but can also be avoided with properly sized chamber vents and unrestricted flows. Somewhat larger pressure differentials are observed under windy conditions, and the accuracy of measurements made under such conditions needs more research. Spatial and temporal heterogeneity can be addressed with appropriate chamber sizes and numbers and frequency of sampling. For example, means of 8 randomly chosen flux measurements from a population of 36 measurements made with 300 cm2 chambers in tropical forests and pastures were within 25% of the full population mean 98% of the time and were within 10% of the full population mean 70% of the time. Comparisons of chamber-based measurements with tower-based measurements of total ecosystem respiration require analysis of the scale of variation within the purported tower footprint. In a forest at Howland, Maine, the differences in soil respiration rates among very poorly drained and well drained soils were large, but they mostly were fortuitously cancelled when evaluated for purported tower footprints of 600-2100 m length. While all of these potential sources of measurement error and sampling biases must be carefully considered, properly designed and deployed chambers provide a reliable means of accurately measuring soil respiration in terrestrial ecosystems.

A fast least-squares algorithm for population inference

PubMed Central

2013-01-01

Background Population inference is an important problem in genetics used to remove population stratification in genome-wide association studies and to detect migration patterns or shared ancestry. An individual’s genotype can be modeled as a probabilistic function of ancestral population memberships, Q, and the allele frequencies in those populations, P. The parameters, P and Q, of this binomial likelihood model can be inferred using slow sampling methods such as Markov Chain Monte Carlo methods or faster gradient based approaches such as sequential quadratic programming. This paper proposes a least-squares simplification of the binomial likelihood model motivated by a Euclidean interpretation of the genotype feature space. This results in a faster algorithm that easily incorporates the degree of admixture within the sample of individuals and improves estimates without requiring trial-and-error tuning. Results We show that the expected value of the least-squares solution across all possible genotype datasets is equal to the true solution when part of the problem has been solved, and that the variance of the solution approaches zero as its size increases. The Least-squares algorithm performs nearly as well as Admixture for these theoretical scenarios. We compare least-squares, Admixture, and FRAPPE for a variety of problem sizes and difficulties. For particularly hard problems with a large number of populations, small number of samples, or greater degree of admixture, least-squares performs better than the other methods. On simulated mixtures of real population allele frequencies from the HapMap project, Admixture estimates sparsely mixed individuals better than Least-squares. The least-squares approach, however, performs within 1.5% of the Admixture error. On individual genotypes from the HapMap project, Admixture and least-squares perform qualitatively similarly and within 1.2% of each other. Significantly, the least-squares approach nearly always converges 1.5- to 6-times faster. Conclusions The computational advantage of the least-squares approach along with its good estimation performance warrants further research, especially for very large datasets. As problem sizes increase, the difference in estimation performance between all algorithms decreases. In addition, when prior information is known, the least-squares approach easily incorporates the expected degree of admixture to improve the estimate. PMID:23343408

A fast least-squares algorithm for population inference.

PubMed

Parry, R Mitchell; Wang, May D

2013-01-23

Population inference is an important problem in genetics used to remove population stratification in genome-wide association studies and to detect migration patterns or shared ancestry. An individual's genotype can be modeled as a probabilistic function of ancestral population memberships, Q, and the allele frequencies in those populations, P. The parameters, P and Q, of this binomial likelihood model can be inferred using slow sampling methods such as Markov Chain Monte Carlo methods or faster gradient based approaches such as sequential quadratic programming. This paper proposes a least-squares simplification of the binomial likelihood model motivated by a Euclidean interpretation of the genotype feature space. This results in a faster algorithm that easily incorporates the degree of admixture within the sample of individuals and improves estimates without requiring trial-and-error tuning. We show that the expected value of the least-squares solution across all possible genotype datasets is equal to the true solution when part of the problem has been solved, and that the variance of the solution approaches zero as its size increases. The Least-squares algorithm performs nearly as well as Admixture for these theoretical scenarios. We compare least-squares, Admixture, and FRAPPE for a variety of problem sizes and difficulties. For particularly hard problems with a large number of populations, small number of samples, or greater degree of admixture, least-squares performs better than the other methods. On simulated mixtures of real population allele frequencies from the HapMap project, Admixture estimates sparsely mixed individuals better than Least-squares. The least-squares approach, however, performs within 1.5% of the Admixture error. On individual genotypes from the HapMap project, Admixture and least-squares perform qualitatively similarly and within 1.2% of each other. Significantly, the least-squares approach nearly always converges 1.5- to 6-times faster. The computational advantage of the least-squares approach along with its good estimation performance warrants further research, especially for very large datasets. As problem sizes increase, the difference in estimation performance between all algorithms decreases. In addition, when prior information is known, the least-squares approach easily incorporates the expected degree of admixture to improve the estimate.

Sampling Migrants from their Social Networks: The Demography and Social Organization of Chinese Migrants in Dar es Salaam, Tanzania.

PubMed

Merli, M Giovanna; Verdery, Ashton; Mouw, Ted; Li, Jing

2016-07-01

The streams of Chinese migration to Africa are growing in tandem with rising Chinese investments and trade flows in and to the African continent. In spite of the high profile of this phenomenon in the media, there are few rich and broad descriptions of Chinese communities in Africa. Reasons for this include the rarity of official statistics on foreign-born populations in African censuses, the absence of predefined sampling frames required to draw representative samples with conventional survey methods and difficulties to reach certain segments of this population. Here, we use a novel network-based approach, Network Sampling with Memory, which overcomes the challenges of sampling 'hidden' populations in the absence of a sampling frame, to recruit a sample of recent Chinese immigrants in Dar es Salaam, Tanzania and collect information on the demographic characteristics, migration histories and social ties of members of this sample. These data reveal a heterogeneous Chinese community composed of "state-led" migrants who come to Africa to work on projects undertaken by large Chinese state-owned enterprises and "independent" migrants who come on their own accord to engage in various types of business ventures. They offer a rich description of the demographic profile and social organization of this community, highlight key differences between the two categories of migrants and map the structure of the social ties linking them. We highlight needs for future research on inter-group differences in individual motivations for migration, economic activities, migration outcomes, expectations about future residence in Africa, social integration and relations with local communities.

Sampling Migrants from their Social Networks: The Demography and Social Organization of Chinese Migrants in Dar es Salaam, Tanzania

PubMed Central

Merli, M. Giovanna; Verdery, Ashton; Mouw, Ted; Li, Jing

2016-01-01

The streams of Chinese migration to Africa are growing in tandem with rising Chinese investments and trade flows in and to the African continent. In spite of the high profile of this phenomenon in the media, there are few rich and broad descriptions of Chinese communities in Africa. Reasons for this include the rarity of official statistics on foreign-born populations in African censuses, the absence of predefined sampling frames required to draw representative samples with conventional survey methods and difficulties to reach certain segments of this population. Here, we use a novel network-based approach, Network Sampling with Memory, which overcomes the challenges of sampling ‘hidden’ populations in the absence of a sampling frame, to recruit a sample of recent Chinese immigrants in Dar es Salaam, Tanzania and collect information on the demographic characteristics, migration histories and social ties of members of this sample. These data reveal a heterogeneous Chinese community composed of “state-led” migrants who come to Africa to work on projects undertaken by large Chinese state-owned enterprises and “independent” migrants who come on their own accord to engage in various types of business ventures. They offer a rich description of the demographic profile and social organization of this community, highlight key differences between the two categories of migrants and map the structure of the social ties linking them. We highlight needs for future research on inter-group differences in individual motivations for migration, economic activities, migration outcomes, expectations about future residence in Africa, social integration and relations with local communities. PMID:27746912

Predictors of Disordered Eating in Adolescence and Young Adulthood: A Population-Based, Longitudinal Study of Females and Males in Norway

ERIC Educational Resources Information Center

Abebe, Dawit Shawel; Torgersen, Leila; Lien, Lars; Hafstad, Gertrud S.; von Soest, Tilmann

2014-01-01

We investigated longitudinal predictors for disordered eating from early adolescence to young adulthood (12-34 years) across gender and different developmental phases among Norwegian young people. Survey data from a population-based sample were collected at four time points (T) over a 13-year time span. A population-based sample of 5,679 females…

Estimating the Size of a Large Network and its Communities from a Random Sample

PubMed Central

Chen, Lin; Karbasi, Amin; Crawford, Forrest W.

2017-01-01

Most real-world networks are too large to be measured or studied directly and there is substantial interest in estimating global network properties from smaller sub-samples. One of the most important global properties is the number of vertices/nodes in the network. Estimating the number of vertices in a large network is a major challenge in computer science, epidemiology, demography, and intelligence analysis. In this paper we consider a population random graph G = (V, E) from the stochastic block model (SBM) with K communities/blocks. A sample is obtained by randomly choosing a subset W ⊆ V and letting G(W) be the induced subgraph in G of the vertices in W. In addition to G(W), we observe the total degree of each sampled vertex and its block membership. Given this partial information, we propose an efficient PopULation Size Estimation algorithm, called PULSE, that accurately estimates the size of the whole population as well as the size of each community. To support our theoretical analysis, we perform an exhaustive set of experiments to study the effects of sample size, K, and SBM model parameters on the accuracy of the estimates. The experimental results also demonstrate that PULSE significantly outperforms a widely-used method called the network scale-up estimator in a wide variety of scenarios. PMID:28867924

Estimating the Size of a Large Network and its Communities from a Random Sample.

PubMed

Chen, Lin; Karbasi, Amin; Crawford, Forrest W

2016-01-01

Most real-world networks are too large to be measured or studied directly and there is substantial interest in estimating global network properties from smaller sub-samples. One of the most important global properties is the number of vertices/nodes in the network. Estimating the number of vertices in a large network is a major challenge in computer science, epidemiology, demography, and intelligence analysis. In this paper we consider a population random graph G = ( V, E ) from the stochastic block model (SBM) with K communities/blocks. A sample is obtained by randomly choosing a subset W ⊆ V and letting G ( W ) be the induced subgraph in G of the vertices in W . In addition to G ( W ), we observe the total degree of each sampled vertex and its block membership. Given this partial information, we propose an efficient PopULation Size Estimation algorithm, called PULSE, that accurately estimates the size of the whole population as well as the size of each community. To support our theoretical analysis, we perform an exhaustive set of experiments to study the effects of sample size, K , and SBM model parameters on the accuracy of the estimates. The experimental results also demonstrate that PULSE significantly outperforms a widely-used method called the network scale-up estimator in a wide variety of scenarios.

Viewing child pornography: prevalence and correlates in a representative community sample of young Swedish men.

PubMed

Seto, Michael C; Hermann, Chantal A; Kjellgren, Cecilia; Priebe, Gisela; Svedin, Carl Göran; Långström, Niklas

2015-01-01

Most research on child pornography use has been based on selected clinical or criminal justice samples; risk factors for child pornography use in the general population remain largely unexplored. In this study, we examined prevalence, risk factors, and correlates of viewing depictions of adult-child sex in a population-representative sample of 1,978 young Swedish men (17-20 years, Mdn = 18 years, overall response rate, 77 %). In an anonymous, school-based survey, participants self-reported sexual coercion experiences, attitudes and beliefs about sex, perceived peer attitudes, and sexual interests and behaviors; including pornography use, sexual interest in children, and sexually coercive behavior. A total of 84 (4.2 %) young men reported they had ever viewed child pornography. Most theory-based variables were moderately and significantly associated with child pornography viewing and were consistent with models of sexual offending implicating both antisociality and sexual deviance. In multivariate logistic regression analysis, 7 of 15 tested factors independently predicted child pornography viewing and explained 42 % of the variance: ever had sex with a male, likely to have sex with a child aged 12-14, likely to have sex with a child 12 or less, perception of children as seductive, having friends who have watched child pornography, frequent pornography use, and ever viewed violent pornography. From these, a 6-item Child Pornography Correlates Scale was constructed and then cross-validated in a similar but independent Norwegian sample.

Internet Exposure Associated With Canadian Parents' Perception of Risk on Childhood Immunization: Cross-Sectional Study.

PubMed

Tustin, Jordan Lee; Crowcroft, Natasha Sarah; Gesink, Dionne; Johnson, Ian; Keelan, Jennifer

2018-01-19

There is a large presence of provaccination and antivaccination content on the Internet. The Internet has been identified as an important source for parents to seek and share vaccine information. There are concerns that parental fears or hesitancy on childhood immunizations are increasing due to the popularity of social media and exposure to online antivaccination sentiment. No other studies have investigated the association between seeking vaccine information online and Canadian parents' perception of risk on childhood immunization. We aimed to investigate the potential association between seeking vaccine information on the Internet and Canadian parents' perception of risk on childhood immunization in order to quantify the perceived association and increase our understanding on the impact of the Internet to help guide public health interventions. We analyzed this association in two population samples: a self-selecting Web-based sample of Canadian parents recruited through Facebook (n=966) and a population-based sample of parents recruited by random digit dialing (RDD; n=951). The outcome was parental perception of vaccine safety on a seven-point ordinal scale from "not safe" to "extremely safe." An ordinal regression model was used to investigate if Internet information seeking on childhood vaccination predicted parental perception of vaccine safety. After adjusting for income level, Internet reliability, age of parent, and region, the odds of perceiving vaccines as less safe rather than more safe were 1.6 times higher (95% CI 1.3-2.1) for parents who used the Internet to search for vaccination information compared to parents who did not search the Internet in the Web-based sample, and 2.0 times higher (95% CI 1.6-2.5) in the population-based RDD sample. The results suggest the Internet is significantly associated with Canadian parents' negative perception of vaccine risk. Governmental and scientific sectors should consider the development and implementation of Web-based vaccine interventions to promote confidence in immunization. ©Jordan Lee Tustin, Natasha Sarah Crowcroft, Dionne Gesink, Ian Johnson, Jennifer Keelan. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 19.01.2018.

Tracing the geographic origin of traded leopard body parts in the indian subcontinent with DNA-based assignment tests.

PubMed

Mondol, Samrat; Sridhar, Vanjulavalli; Yadav, Prasanjeet; Gubbi, Sanjay; Ramakrishnan, Uma

2015-04-01

Illicit trade in wildlife products is rapidly decimating many species across the globe. Such trade is often underestimated for wide-ranging species until it is too late for the survival of their remaining populations. Policing this trade could be vastly improved if one could reliably determine geographic origins of illegal wildlife products and identify areas where greater enforcement is needed. Using DNA-based assignment tests (i.e., samples are assigned to geographic locations), we addressed these factors for leopards (Panthera pardus) on the Indian subcontinent. We created geography-specific allele frequencies from a genetic reference database of 173 leopards across India to infer geographic origins of DNA samples from 40 seized leopard skins. Sensitivity analyses of samples of known geographic origins and assignments of seized skins demonstrated robust assignments for Indian leopards. We found that confiscated pelts seized in small numbers were not necessarily from local leopards. The geographic footprint of large seizures appeared to be bigger than the cumulative footprint of several smaller seizures, indicating widespread leopard poaching across the subcontinent. Our seized samples had male-biased sex ratios, especially the large seizures. From multiple seized sample assignments, we identified central India as a poaching hotspot for leopards. The techniques we applied can be used to identify origins of seized illegal wildlife products and trade routes at the subcontinent scale and beyond. © 2014 Society for Conservation Biology.

Nonprobability and probability-based sampling strategies in sexual science.

PubMed

Catania, Joseph A; Dolcini, M Margaret; Orellana, Roberto; Narayanan, Vasudah

2015-01-01

With few exceptions, much of sexual science builds upon data from opportunistic nonprobability samples of limited generalizability. Although probability-based studies are considered the gold standard in terms of generalizability, they are costly to apply to many of the hard-to-reach populations of interest to sexologists. The present article discusses recent conclusions by sampling experts that have relevance to sexual science that advocates for nonprobability methods. In this regard, we provide an overview of Internet sampling as a useful, cost-efficient, nonprobability sampling method of value to sex researchers conducting modeling work or clinical trials. We also argue that probability-based sampling methods may be more readily applied in sex research with hard-to-reach populations than is typically thought. In this context, we provide three case studies that utilize qualitative and quantitative techniques directed at reducing limitations in applying probability-based sampling to hard-to-reach populations: indigenous Peruvians, African American youth, and urban men who have sex with men (MSM). Recommendations are made with regard to presampling studies, adaptive and disproportionate sampling methods, and strategies that may be utilized in evaluating nonprobability and probability-based sampling methods.

Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma).

PubMed

Blair, Christopher; Bryson, Robert W

2017-11-01

Biodiversity reduction and loss continues to progress at an alarming rate, and thus, there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods has been tested repeatedly with simulations, additional studies are needed to assess congruence with empirical data. We compiled a large data set of mitochondrial ND4 sequences from horned lizards (Phrynosoma) to elucidate congruence using four tree-based (single-threshold GMYC, multiple-threshold GMYC, bPTP, mPTP) and one distance-based (ABGD) species delimitation models. We were particularly interested in cases with highly uneven sampling and/or large differences in intraspecific diversity. Results showed a high degree of discordance among methods, with multiple-threshold GMYC and bPTP suggesting an unrealistically high number of species (29 and 26 species within the P. douglasii complex alone). The single-threshold GMYC model was the most conservative, likely a result of difficulty in locating the inflection point in the genealogies. mPTP and ABGD appeared to be the most stable across sampling regimes and suggested the presence of additional cryptic species that warrant further investigation. These results suggest that the mPTP model may be preferable in empirical data sets with highly uneven sampling or large differences in effective population sizes of species. © 2017 John Wiley & Sons Ltd.

Qualitative Meta-Analysis on the Hospital Task: Implications for Research

ERIC Educational Resources Information Center

Noll, Jennifer; Sharma, Sashi

2014-01-01

The "law of large numbers" indicates that as sample size increases, sample statistics become less variable and more closely estimate their corresponding population parameters. Different research studies investigating how people consider sample size when evaluating the reliability of a sample statistic have found a wide range of…

Concerted evolution at the population level: pupfish HindIII satellite DNA sequences.

PubMed Central

Elder, J F; Turner, B J

1994-01-01

The canonical monomers (approximately 170 bp) of an abundant (1.9 x 10(6) copies per diploid genome) satellite DNA sequence family in the genome of Cyprinodon variegatus, a "pupfish" that ranges along the Atlantic coast from Cape Cod to central Mexico, are divergent in base sequence in 10 of 12 samples collected from natural populations. The divergence involves substitutions, deletions, and insertions, is marked in scope (mean pairwise sequence similarity = 61.6%; range = 35-95.9%), is largely confined to the 3' half of the monomer, and is not correlated with the distance among collecting sites. Repetitive cloning and direct genomic sequencing experiments failed to detect intrapopulation and intraindividual variation, suggesting high levels of sequence homogeneity within populations. The satellite sequence has therefore undergone "concerted evolution," at the level of the local population. Concerted evolution has previously almost always been discussed in terms of the divergence of species or higher taxa; its intraspecific occurrence apparently has not been reported previously. The generality of the observation is difficult to evaluate, for although satellite DNAs from a large number of organisms have been studied in detail, there appear to be little or no other data on their sequence variation in natural populations. The relationship (if any) between concerted, population level, satellite DNA divergence and the extent of gene flow/genetic isolation among conspecific natural populations remains to be established. Images PMID:8302879

The Nature and Origin of UCDs in the Coma Cluster

NASA Astrophysics Data System (ADS)

Chiboucas, Kristin; Tully, R. Brent; Madrid, Juan; Phillipps, Steven; Carter, David; Peng, Eric

2018-01-01

UCDs are super massive star clusters found largely in dense regions but have also been found around individual galaxies and in smaller groups. Their origin is still under debate but currently favored scenarios include formation as giant star clusters, either as the brightest globular clusters or through mergers of super star clusters, themselves formed during major galaxy mergers, or as remnant nuclei from tidal stripping of nucleated dwarf ellipticals. Establishing the nature of these enigmatic objects has important implications for our understanding of star formation, star cluster formation, the missing satellite problem, and galaxy evolution. We are attempting to disentangle these competing formation scenarios with a large survey of UCDs in the Coma cluster. Using ACS two-passband imaging from the HST/ACS Coma Cluster Treasury Survey, we are using colors and sizes to identify the UCD cluster members. With a large size limited sample of the UCD population within the core region of the Coma cluster, we are investigating the population size, properties, and spatial distribution, and comparing that with the Coma globular cluster and nuclear star cluster populations to discriminate between the threshing and globular cluster scenarios. In previous work, we had found a possible correlation of UCD colors with host galaxy and a possible excess of UCDs around a non-central giant galaxy with an unusually large globular cluster population, both suggestive of a globular cluster origin. With a larger sample size and additional imaging fields that encompass the regions around these giant galaxies, we have found that the color correlation with host persists and the giant galaxy with unusually large globular cluster population does appear to host a large UCD population as well. We present the current status of the survey.

Reference-based phasing using the Haplotype Reference Consortium panel.

PubMed

Loh, Po-Ru; Danecek, Petr; Palamara, Pier Francesco; Fuchsberger, Christian; A Reshef, Yakir; K Finucane, Hilary; Schoenherr, Sebastian; Forer, Lukas; McCarthy, Shane; Abecasis, Goncalo R; Durbin, Richard; L Price, Alkes

2016-11-01

Haplotype phasing is a fundamental problem in medical and population genetics. Phasing is generally performed via statistical phasing in a genotyped cohort, an approach that can yield high accuracy in very large cohorts but attains lower accuracy in smaller cohorts. Here we instead explore the paradigm of reference-based phasing. We introduce a new phasing algorithm, Eagle2, that attains high accuracy across a broad range of cohort sizes by efficiently leveraging information from large external reference panels (such as the Haplotype Reference Consortium; HRC) using a new data structure based on the positional Burrows-Wheeler transform. We demonstrate that Eagle2 attains a ∼20× speedup and ∼10% increase in accuracy compared to reference-based phasing using SHAPEIT2. On European-ancestry samples, Eagle2 with the HRC panel achieves >2× the accuracy of 1000 Genomes-based phasing. Eagle2 is open source and freely available for HRC-based phasing via the Sanger Imputation Service and the Michigan Imputation Server.

The Utility of an Online Convenience Panel for Reaching Rare and Dispersed Populations.

PubMed

Sell, Randall; Goldberg, Shoshana; Conron, Kerith

2015-01-01

Gaps in data collection systems, as well as challenges associated with gathering data from rare and dispersed populations, render current health surveillance systems inadequate to identify and monitor efforts to reduce health disparities. Using sexual and gender minorities we investigated the utility of using a large nonprobability online panel to conduct rapid population assessments of such populations using brief surveys. Surveys of the Google Android Panel (four assessing sexual orientation and one assessing gender identity and sex assigned at birth) were conducted resulting in invitation of 53,739 application users (37,505 of whom viewed the invitation) to generate a total of 34,759 who completed screening questions indicating their sexual orientation, or gender identity and sex at birth. Where possible we make comparisons to similar data from two population-based surveys (NHIS and NESARC). We found that 99.4% to 100.0% of respondents across our Google Android panel samples completed the screening questions and 97.8% to 99.2% of those that consented to participate in our surveys indicated they were "OK" with the content of surveys that assessed sexual orientation and sex/gender. In our Google Android panel samples there was a higher percentage of sexual minority respondents than in either NHIS or NESARC with 7.4% of men and 12.4% of women reporting gay, lesbian or bisexual identities. The proportion sexual minority was 2.8 to 5.6 times higher in the Google Android panel samples than was found in the 2012 NHIS sample, for men and women, respectively. The percentage of "transgender" identified individuals in the Google sample was 0.7%, which is similar to 0.5% transgender identified through the Massachusetts BRFSS, and using a transgender status item we found that 2.0% of the overall sample fit could be classified as transgender. The Google samples sometimes more closely approximated national averages for ethnicity and race than NHIS.

The Utility of an Online Convenience Panel for Reaching Rare and Dispersed Populations

PubMed Central

Sell, Randall; Goldberg, Shoshana; Conron, Kerith

2015-01-01

Gaps in data collection systems, as well as challenges associated with gathering data from rare and dispersed populations, render current health surveillance systems inadequate to identify and monitor efforts to reduce health disparities. Using sexual and gender minorities we investigated the utility of using a large nonprobability online panel to conduct rapid population assessments of such populations using brief surveys. Surveys of the Google Android Panel (four assessing sexual orientation and one assessing gender identity and sex assigned at birth) were conducted resulting in invitation of 53,739 application users (37,505 of whom viewed the invitation) to generate a total of 34,759 who completed screening questions indicating their sexual orientation, or gender identity and sex at birth. Where possible we make comparisons to similar data from two population-based surveys (NHIS and NESARC). We found that 99.4% to 100.0% of respondents across our Google Android panel samples completed the screening questions and 97.8% to 99.2% of those that consented to participate in our surveys indicated they were “OK” with the content of surveys that assessed sexual orientation and sex/gender. In our Google Android panel samples there was a higher percentage of sexual minority respondents than in either NHIS or NESARC with 7.4% of men and 12.4% of women reporting gay, lesbian or bisexual identities. The proportion sexual minority was 2.8 to 5.6 times higher in the Google Android panel samples than was found in the 2012 NHIS sample, for men and women, respectively. The percentage of “transgender” identified individuals in the Google sample was 0.7%, which is similar to 0.5% transgender identified through the Massachusetts BRFSS, and using a transgender status item we found that 2.0% of the overall sample fit could be classified as transgender. The Google samples sometimes more closely approximated national averages for ethnicity and race than NHIS. PMID:26641840

Decomposing Educational Inequalities in Child Mortality: A Temporal Trend Analysis of Access to Water and Sanitation in Peru.

PubMed

Bohra, Tasneem; Benmarhnia, Tarik; McKinnon, Britt; Kaufman, Jay S

2017-01-11

Previous studies of inequality in health and mortality have largely focused on income-based inequality. Maternal education plays an important role in determining access to water and sanitation, and inequalities in child mortality arising due to differential access, especially in low- and middle-income countries such as Peru. This article aims to explain education-related inequalities in child mortality in Peru using a regression-based decomposition of the concentration index of child mortality. The analysis combines a concentration index created along a cumulative distribution of the Demographic and Health Surveys sample ranked according to maternal education, and decomposition measures the contribution of water and sanitation to educational inequalities in child mortality. We observed a large education-related inequality in child mortality and access to water and sanitation. There is a need for programs and policies in child health to focus on ensuring equity and to consider the educational stratification of the population to target the most disadvantaged segments of the population. © The American Society of Tropical Medicine and Hygiene.

Sample features associated with success rates in population-based EGFR mutation testing.

PubMed

Shiau, Carolyn J; Babwah, Jesse P; da Cunha Santos, Gilda; Sykes, Jenna R; Boerner, Scott L; Geddie, William R; Leighl, Natasha B; Wei, Cuihong; Kamel-Reid, Suzanne; Hwang, David M; Tsao, Ming-Sound

2014-07-01

Epidermal growth factor receptor (EGFR) mutation testing has become critical in the treatment of patients with advanced non-small-cell lung cancer. This study involves a large cohort and epidemiologically unselected series of EGFR mutation testing for patients with nonsquamous non-small-cell lung cancer in a North American population to determine sample-related factors that influence success in clinical EGFR testing. Data from consecutive cases of Canadian province-wide testing at a centralized diagnostic laboratory for a 24-month period were reviewed. Samples were tested for exon-19 deletion and exon-21 L858R mutations using a validated polymerase chain reaction method with 1% to 5% detection sensitivity. From 2651 samples submitted, 2404 samples were tested with 2293 samples eligible for analysis (1780 histology and 513 cytology specimens). The overall test-failure rate was 5.4% with overall mutation rate of 20.6%. No significant differences in the failure rate, mutation rate, or mutation type were found between histology and cytology samples. Although tumor cellularity was significantly associated with test-success or mutation rates in histology and cytology specimens, respectively, mutations could be detected in all specimen types. Significant rates of EGFR mutation were detected in cases with thyroid transcription factor (TTF)-1-negative immunohistochemistry (6.7%) and mucinous component (9.0%). EGFR mutation testing should be attempted in any specimen, whether histologic or cytologic. Samples should not be excluded from testing based on TTF-1 status or histologic features. Pathologists should report the amount of available tumor for testing. However, suboptimal samples with a negative EGFR mutation result should be considered for repeat testing with an alternate sample.

The sexual attitudes and lifestyles of London's Eastern Europeans (SALLEE Project): design and methods.

PubMed

Evans, Alison R; Parutis, Violetta; Hart, Graham; Mercer, Catherine H; Gerry, Christopher; Mole, Richard; French, Rebecca S; Imrie, John; Burns, Fiona

2009-10-30

Since May 2004, ten Central and Eastern European (CEE) countries have joined the European Union, leading to a large influx of CEE migrants to the United Kingdom (UK). The SALLEE project (sexual attitudes and lifestyles of London's Eastern Europeans) set out to establish an understanding of the sexual lifestyles and reproductive health risks of CEE migrants. CEE nationals make up a small minority of the population resident in the UK with no sampling frame from which to select a probability sample. There is also difficulty estimating the socio-demographic and geographical distribution of the population. In addition, measuring self-reported sexual behaviour which is generally found to be problematic, may be compounded among people from a range of different cultural and linguistic backgrounds. This paper will describe the methods adopted by the SALLEE project to address these challenges. The research was undertaken using quantitative and qualitative methods: a cross-sectional survey of CEE migrants based on three convenience samples (recruited from community venues, sexual health clinics and from the Internet) and semi-structured in-depth interviews with a purposively selected sample of CEE migrants. A detailed social mapping exercise of the CEE community was conducted prior to commencement of the survey to identify places where CEE migrants could be recruited. A total of 3,005 respondents took part in the cross-sectional survey, including 2,276 respondents in the community sample, 357 in the clinic sample and 372 in the Internet sample. 40 in-depth qualitative interviews were undertaken with a range of individuals, as determined by the interview quota matrix. The SALLEE project has benefited from using quantitative research to provide generalisable data on a range of variables and qualitative research to add in-depth understanding and interpretation. The social mapping exercise successfully located a large number of CEE migrants for the community sample and is recommended for other migrant populations, especially when little or no official data are available for this purpose. The project has collected timely data that will help us to understand the sexual lifestyles, reproductive health risks and health service needs of CEE communities in the UK.

Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm.

PubMed

Lee, Hea-Young; Ro, Na-Young; Jeong, Hee-Jin; Kwon, Jin-Kyung; Jo, Jinkwan; Ha, Yeaseong; Jung, Ayoung; Han, Ji-Woong; Venkatesh, Jelli; Kang, Byoung-Cheorl

2016-11-14

Conservation of genetic diversity is an essential prerequisite for developing new cultivars with desirable agronomic traits. Although a large number of germplasm collections have been established worldwide, many of them face major difficulties due to large size and a lack of adequate information about population structure and genetic diversity. Core collection with a minimum number of accessions and maximum genetic diversity of pepper species and its wild relatives will facilitate easy access to genetic material as well as the use of hidden genetic diversity in Capsicum. To explore genetic diversity and population structure, we investigated patterns of molecular diversity using a transcriptome-based 48 single nucleotide polymorphisms (SNPs) in a large germplasm collection comprising 3,821 accessions. Among the 11 species examined, Capsicum annuum showed the highest genetic diversity (H E  = 0.44, I = 0.69), whereas the wild species C. galapagoense showed the lowest genetic diversity (H E  = 0.06, I = 0.07). The Capsicum germplasm collection was divided into 10 clusters (cluster 1 to 10) based on population structure analysis, and five groups (group A to E) based on phylogenetic analysis. Capsicum accessions from the five distinct groups in an unrooted phylogenetic tree showed taxonomic distinctness and reflected their geographic origins. Most of the accessions from European countries are distributed in the A and B groups, whereas the accessions from Asian countries are mainly distributed in C and D groups. Five different sampling strategies with diverse genetic clustering methods were used to select the optimal method for constructing the core collection. Using a number of allelic variations based on 48 SNP markers and 32 different phenotypic/morphological traits, a core collection 'CC240' with a total of 240 accessions (5.2 %) was selected from within the entire Capsicum germplasm. Compared to the other core collections, CC240 displayed higher genetic diversity (I = 0.95) and genetic evenness (J' = 0.80), and represented a wider range of phenotypic variation (MD = 9.45 %, CR = 98.40 %). A total of 240 accessions were selected from 3,821 Capsicum accessions based on transcriptome-based 48 SNP markers with genome-wide distribution and 32 traits using a systematic approach. This core collection will be a primary resource for pepper breeders and researchers for further genetic association and functional analyses.

LookSeq: a browser-based viewer for deep sequencing data.

PubMed

Manske, Heinrich Magnus; Kwiatkowski, Dominic P

2009-11-01

Sequencing a genome to great depth can be highly informative about heterogeneity within an individual or a population. Here we address the problem of how to visualize the multiple layers of information contained in deep sequencing data. We propose an interactive AJAX-based web viewer for browsing large data sets of aligned sequence reads. By enabling seamless browsing and fast zooming, the LookSeq program assists the user to assimilate information at different levels of resolution, from an overview of a genomic region to fine details such as heterogeneity within the sample. A specific problem, particularly if the sample is heterogeneous, is how to depict information about structural variation. LookSeq provides a simple graphical representation of paired sequence reads that is more revealing about potential insertions and deletions than are conventional methods.

Web based health surveys: Using a Two Step Heckman model to examine their potential for population health analysis.

PubMed

Morrissey, Karyn; Kinderman, Peter; Pontin, Eleanor; Tai, Sara; Schwannauer, Mathias

2016-08-01

In June 2011 the BBC Lab UK carried out a web-based survey on the causes of mental distress. The 'Stress Test' was launched on 'All in the Mind' a BBC Radio 4 programme and the test's URL was publicised on radio and TV broadcasts, and made available via BBC web pages and social media. Given the large amount of data created, over 32,800 participants, with corresponding diagnosis, demographic and socioeconomic characteristics; the dataset are potentially an important source of data for population based research on depression and anxiety. However, as respondents self-selected to participate in the online survey, the survey may comprise a non-random sample. It may be only individuals that listen to BBC Radio 4 and/or use their website that participated in the survey. In this instance using the Stress Test data for wider population based research may create sample selection bias. Focusing on the depression component of the Stress Test, this paper presents an easy-to-use method, the Two Step Probit Selection Model, to detect and statistically correct selection bias in the Stress Test. Using a Two Step Probit Selection Model; this paper did not find a statistically significant selection on unobserved factors for participants of the Stress Test. That is, survey participants who accessed and completed an online survey are not systematically different from non-participants on the variables of substantive interest. Copyright © 2016 Elsevier Ltd. All rights reserved.

Child mental health differences amongst ethnic groups in Britain: a systematic review

PubMed Central

Goodman, Anna; Patel, Vikram; Leon, David A

2008-01-01

Background Inter-ethnic differences have been reported for many mental health outcomes in the UK, but no systematic review on child mental health has been published. The aim of this review is to compare the population-based prevalence of child mental disorders between ethnic groups in Britain, and relate these findings to ethnic differences in mental health service use. Methods A systematic search of bibliographic databases for population-based and clinic-based studies of children aged 0–19, including all ethnic groups and the main child mental disorders. We synthesised findings by comparing each minority group to the White British study sample. Results 31 population-based and 18 clinic-based studies met the inclusion criteria. Children in the main minority groups have similar or better mental health than White British children for common disorders, but may have higher rates for some less common conditions. The causes of these differences are unclear. There may be unmet need for services among Pakistani and Bangladeshi children. Conclusion Inter-ethnic differences exist but are largely unexplained. Future studies should address the challenges of cross-cultural psychiatry and investigate reasons for inter-ethnic differences. PMID:18655701

Recruiting hard-to-reach United States population sub-groups via adaptations of snowball sampling strategy

PubMed Central

Sadler, Georgia Robins; Lee, Hau-Chen; Seung-Hwan Lim, Rod; Fullerton, Judith

2011-01-01

Nurse researchers and educators often engage in outreach to narrowly defined populations. This article offers examples of how variations on the snowball sampling recruitment strategy can be applied in the creation of culturally appropriate, community-based information dissemination efforts related to recruitment to health education programs and research studies. Examples from the primary author’s program of research are provided to demonstrate how adaptations of snowball sampling can be effectively used in the recruitment of members of traditionally underserved or vulnerable populations. The adaptation of snowball sampling techniques, as described in this article, helped the authors to gain access to each of the more vulnerable population groups of interest. The use of culturally sensitive recruitment strategies is both appropriate and effective in enlisting the involvement of members of vulnerable populations. Adaptations of snowball sampling strategies should be considered when recruiting participants for education programs or subjects for research studies when recruitment of a population based sample is not essential. PMID:20727089

Recruitment of hard-to-reach population subgroups via adaptations of the snowball sampling strategy.

PubMed

Sadler, Georgia Robins; Lee, Hau-Chen; Lim, Rod Seung-Hwan; Fullerton, Judith

2010-09-01

Nurse researchers and educators often engage in outreach to narrowly defined populations. This article offers examples of how variations on the snowball sampling recruitment strategy can be applied in the creation of culturally appropriate, community-based information dissemination efforts related to recruitment to health education programs and research studies. Examples from the primary author's program of research are provided to demonstrate how adaptations of snowball sampling can be used effectively in the recruitment of members of traditionally underserved or vulnerable populations. The adaptation of snowball sampling techniques, as described in this article, helped the authors to gain access to each of the more-vulnerable population groups of interest. The use of culturally sensitive recruitment strategies is both appropriate and effective in enlisting the involvement of members of vulnerable populations. Adaptations of snowball sampling strategies should be considered when recruiting participants for education programs or for research studies when the recruitment of a population-based sample is not essential.

Performing monkeys of Bangladesh: characterizing their source and genetic variation.

PubMed

Hasan, M Kamrul; Feeroz, M Mostafa; Jones-Engel, Lisa; Engel, Gregory A; Akhtar, Sharmin; Kanthaswamy, Sree; Smith, David Glenn

2016-04-01

The acquisition and training of monkeys to perform is a centuries-old tradition in South Asia, resulting in a large number of rhesus macaques kept in captivity for this purpose. The performing monkeys are reportedly collected from free-ranging populations, and may escape from their owners or may be released into other populations. In order to determine whether this tradition involving the acquisition and movement of animals has influenced the population structure of free-ranging rhesus macaques in Bangladesh, we first characterized the source of these monkeys. Biological samples from 65 performing macaques collected between January 2010 and August 2013 were analyzed for genetic variation using 716 base pairs of mitochondrial DNA. Performing monkey sequences were compared with those of free-ranging rhesus macaque populations in Bangladesh, India and Myanmar. Forty-five haplotypes with 116 (16 %) polymorphic nucleotide sites were detected among the performing monkeys. As for the free-ranging rhesus population, most of the substitutions (89 %) were transitions, and no indels (insertion/deletion) were observed. The estimate of the mean number of pair-wise differences for the performing monkey population was 10.1264 ± 4.686, compared to 14.076 ± 6.363 for the free-ranging population. Fifteen free-ranging rhesus macaque populations were identified as the source of performing monkeys in Bangladesh; several of these populations were from areas where active provisioning has resulted in a large number of macaques. The collection of performing monkeys from India was also evident.

Performing monkeys of Bangladesh: characterizing their source and genetic variation

PubMed Central

Hasan, M Kamrul; Feeroz, M Mostafa; Jones-Engel, Lisa; Engel, Gregory A; Akhtar, Sharmin; Kanthaswamy, Sree; Smith, David Glenn

2016-01-01

The acquisition and training of monkeys to perform is a century's old tradition in South Asia, resulting in a large number of rhesus macaques kept in captivity for this purpose. The performing monkeys are reportedly collected from free-ranging populations and may escape from their owners or be released into other populations. In order to determine whether this tradition, that involves the acquisition and movement of animals, has influenced the population structure of free-ranging rhesus macaques in Bangladesh we first characterized the source of these monkeys. Biological samples from 65 performing macaques, collected between January 2010 and August 2013 were analyzed for genetic variation using 716 base pairs of mitochondrial DNA. Performing monkey sequences were compared with those of free-ranging rhesus macaque populations in Bangladesh, India and Myanmar. Forty-five haplotypes with 116 (16%) polymorphic nucleotide sites were detected among the performing monkeys. As for the free-ranging rhesus population, most of the substitutions (89%) were transitions and no indels (insertion/deletion) were observed. The estimate of the mean number of pair-wise difference for the performing monkey population was 10.1264 ± 4.686, compared to 14.076 ± 6.363 for the free-ranging population. Fifteen free-ranging rhesus macaque populations were identified as the source of performing monkeys in Bangladesh; several of these populations were from areas where active provisioning has resulted in a large number of macaques. Collection of performing monkeys from India was also evident. PMID:26758818

Investigations of potential bias in the estimation of lambda using Pradel's (1996) model for capture-recapture data

USGS Publications Warehouse

Hines, James E.; Nichols, James D.

2002-01-01

Pradel's (1996) temporal symmetry model permitting direct estimation and modelling of population growth rate, u i , provides a potentially useful tool for the study of population dynamics using marked animals. Because of its recent publication date, the approach has not seen much use, and there have been virtually no investigations directed at robustness of the resulting estimators. Here we consider several potential sources of bias, all motivated by specific uses of this estimation approach. We consider sampling situations in which the study area expands with time and present an analytic expression for the bias in u i We next consider trap response in capture probabilities and heterogeneous capture probabilities and compute large-sample and simulation-based approximations of resulting bias in u i . These approximations indicate that trap response is an especially important assumption violation that can produce substantial bias. Finally, we consider losses on capture and emphasize the importance of selecting the estimator for u i that is appropriate to the question being addressed. For studies based on only sighting and resighting data, Pradel's (1996) u i ' is the appropriate estimator.

[Factor structure of the German version of the BIS/BAS Scales in a population-based sample].

PubMed

Müller, A; Smits, D; Claes, L; de Zwaan, M

2013-02-01

The Behavioural Inhibition System/Behavioural Activation System Scale (BIS/BAS-Scales) developed by Carver and White 1 is a self-rating instrument to assess the dispositional sensitivity to punishment and reward. The present work aims to examine the factor structure of the German version of the BIS/BAS-Scales. In a large German population-based sample (n = 1881) the model fit of several factor models was tested by using confirmatory factor analyses. The best model fit was found for the 5-factor model with two BIS (anxiety, fear) and three BAS (drive, reward responsiveness, fun seeking) scales, whereas the BIS-fear, the BAS-reward responsiveness, and the BAS-fun seeking subscales showed low internal consistency. The BIS/BAS scales were negatively correlated with age, and women reported higher BIS subscale scores than men. Confirmatory factor analyses suggest a 5-factor model. However, due to the low internal reliability of some of the subscales the use of this model is questionable. © Georg Thieme Verlag KG Stuttgart · New York.

SNP-based heritability estimates of the personality dimensions and polygenic prediction of both neuroticism and major depression: findings from CONVERGE.

PubMed

Docherty, A R; Moscati, A; Peterson, R; Edwards, A C; Adkins, D E; Bacanu, S A; Bigdeli, T B; Webb, B T; Flint, J; Kendler, K S

2016-10-25

Biometrical genetic studies suggest that the personality dimensions, including neuroticism, are moderately heritable (~0.4 to 0.6). Quantitative analyses that aggregate the effects of many common variants have recently further informed genetic research on European samples. However, there has been limited research to date on non-European populations. This study examined the personality dimensions in a large sample of Han Chinese descent (N=10 064) from the China, Oxford, and VCU Experimental Research on Genetic Epidemiology study, aimed at identifying genetic risk factors for recurrent major depression among a rigorously ascertained cohort. Heritability of neuroticism as measured by the Eysenck Personality Questionnaire (EPQ) was estimated to be low but statistically significant at 10% (s.e.=0.03, P=0.0001). In addition to EPQ, neuroticism based on a three-factor model, data for the Big Five (BF) personality dimensions (neuroticism, openness, conscientiousness, extraversion and agreeableness) measured by the Big Five Inventory were available for controls (n=5596). Heritability estimates of the BF were not statistically significant despite high power (>0.85) to detect heritabilities of 0.10. Polygenic risk scores constructed by best linear unbiased prediction weights applied to split-half samples failed to significantly predict any of the personality traits, but polygenic risk for neuroticism, calculated with LDpred and based on predictive variants previously identified from European populations (N=171 911), significantly predicted major depressive disorder case-control status (P=0.0004) after false discovery rate correction. The scores also significantly predicted EPQ neuroticism (P=6.3 × 10 -6 ). Factor analytic results of the measures indicated that any differences in heritabilities across samples may be due to genetic variation or variation in haplotype structure between samples, rather than measurement non-invariance. Findings demonstrate that neuroticism can be significantly predicted across ancestry, and highlight the importance of studying polygenic contributions to personality in non-European populations.

Joint modeling and registration of cell populations in cohorts of high-dimensional flow cytometric data.

PubMed

Pyne, Saumyadipta; Lee, Sharon X; Wang, Kui; Irish, Jonathan; Tamayo, Pablo; Nazaire, Marc-Danie; Duong, Tarn; Ng, Shu-Kay; Hafler, David; Levy, Ronald; Nolan, Garry P; Mesirov, Jill; McLachlan, Geoffrey J

2014-01-01

In biomedical applications, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multivariate responses of a panel of markers such as from a signaling network. In multiparametric cytometry, which is often used for analyzing patient samples, such issues are critical. While computational methods can identify cell populations in individual samples, without the ability to automatically match them across samples, it is difficult to compare and characterize the populations in typical experiments, such as those responding to various stimulations or distinctive of particular patients or time-points, especially when there are many samples. Joint Clustering and Matching (JCM) is a multi-level framework for simultaneous modeling and registration of populations across a cohort. JCM models every population with a robust multivariate probability distribution. Simultaneously, JCM fits a random-effects model to construct an overall batch template--used for registering populations across samples, and classifying new samples. By tackling systems-level variation, JCM supports practical biomedical applications involving large cohorts. Software for fitting the JCM models have been implemented in an R package EMMIX-JCM, available from http://www.maths.uq.edu.au/~gjm/mix_soft/EMMIX-JCM/.

Otoacoustic emissions in the general adult population of Nord-Trøndelag, Norway: III. Relationships with pure-tone hearing thresholds.

PubMed

Engdahl, Bo; Tambs, Kristian; Borchgrevink, Hans M; Hoffman, Howard J

2005-01-01

This study aims to describe the association between otoacoustic emissions (OAEs) and pure-tone hearing thresholds (PTTs) in an unscreened adult population (N =6415), to determine the efficiency by which TEOAEs and DPOAEs can identify ears with elevated PTTs, and to investigate whether a combination of DPOAE and TEOAE responses improves this performance. Associations were examined by linear regression analysis and ANOVA. Test performance was assessed by receiver operator characteristic (ROC) curves. The relation between OAEs and PTTs appeared curvilinear with a moderate degree of non-linearity. Combining DPOAEs and TEOAEs improved performance. Test performance depended on the cut-off thresholds defining elevated PTTs with optimal values between 25 and 45 dB HL, depending on frequency and type of OAE measure. The unique constitution of the present large sample, which reflects the general adult population, makes these results applicable to population-based studies and screening programs.

A nonparametric method to generate synthetic populations to adjust for complex sampling design features.

PubMed

Dong, Qi; Elliott, Michael R; Raghunathan, Trivellore E

2014-06-01

Outside of the survey sampling literature, samples are often assumed to be generated by a simple random sampling process that produces independent and identically distributed (IID) samples. Many statistical methods are developed largely in this IID world. Application of these methods to data from complex sample surveys without making allowance for the survey design features can lead to erroneous inferences. Hence, much time and effort have been devoted to develop the statistical methods to analyze complex survey data and account for the sample design. This issue is particularly important when generating synthetic populations using finite population Bayesian inference, as is often done in missing data or disclosure risk settings, or when combining data from multiple surveys. By extending previous work in finite population Bayesian bootstrap literature, we propose a method to generate synthetic populations from a posterior predictive distribution in a fashion inverts the complex sampling design features and generates simple random samples from a superpopulation point of view, making adjustment on the complex data so that they can be analyzed as simple random samples. We consider a simulation study with a stratified, clustered unequal-probability of selection sample design, and use the proposed nonparametric method to generate synthetic populations for the 2006 National Health Interview Survey (NHIS), and the Medical Expenditure Panel Survey (MEPS), which are stratified, clustered unequal-probability of selection sample designs.

A nonparametric method to generate synthetic populations to adjust for complex sampling design features

PubMed Central

Dong, Qi; Elliott, Michael R.; Raghunathan, Trivellore E.

2017-01-01

Outside of the survey sampling literature, samples are often assumed to be generated by a simple random sampling process that produces independent and identically distributed (IID) samples. Many statistical methods are developed largely in this IID world. Application of these methods to data from complex sample surveys without making allowance for the survey design features can lead to erroneous inferences. Hence, much time and effort have been devoted to develop the statistical methods to analyze complex survey data and account for the sample design. This issue is particularly important when generating synthetic populations using finite population Bayesian inference, as is often done in missing data or disclosure risk settings, or when combining data from multiple surveys. By extending previous work in finite population Bayesian bootstrap literature, we propose a method to generate synthetic populations from a posterior predictive distribution in a fashion inverts the complex sampling design features and generates simple random samples from a superpopulation point of view, making adjustment on the complex data so that they can be analyzed as simple random samples. We consider a simulation study with a stratified, clustered unequal-probability of selection sample design, and use the proposed nonparametric method to generate synthetic populations for the 2006 National Health Interview Survey (NHIS), and the Medical Expenditure Panel Survey (MEPS), which are stratified, clustered unequal-probability of selection sample designs. PMID:29200608

Intensity of Territorial Marking Predicts Wolf Reproduction: Implications for Wolf Monitoring

PubMed Central

García, Emilio J.

2014-01-01

Background The implementation of intensive and complex approaches to monitor large carnivores is resource demanding, restricted to endangered species, small populations, or small distribution ranges. Wolf monitoring over large spatial scales is difficult, but the management of such contentious species requires regular estimations of abundance to guide decision-makers. The integration of wolf marking behaviour with simple sign counts may offer a cost-effective alternative to monitor the status of wolf populations over large spatial scales. Methodology/Principal Findings We used a multi-sampling approach, based on the collection of visual and scent wolf marks (faeces and ground scratching) and the assessment of wolf reproduction using howling and observation points, to test whether the intensity of marking behaviour around the pup-rearing period (summer-autumn) could reflect wolf reproduction. Between 1994 and 2007 we collected 1,964 wolf marks in a total of 1,877 km surveyed and we searched for the pups' presence (1,497 howling and 307 observations points) in 42 sampling sites with a regular presence of wolves (120 sampling sites/year). The number of wolf marks was ca. 3 times higher in sites with a confirmed presence of pups (20.3 vs. 7.2 marks). We found a significant relationship between the number of wolf marks (mean and maximum relative abundance index) and the probability of wolf reproduction. Conclusions/Significance This research establishes a real-time relationship between the intensity of wolf marking behaviour and wolf reproduction. We suggest a conservative cutting point of 0.60 for the probability of wolf reproduction to monitor wolves on a regional scale combined with the use of the mean relative abundance index of wolf marks in a given area. We show how the integration of wolf behaviour with simple sampling procedures permit rapid, real-time, and cost-effective assessments of the breeding status of wolf packs with substantial implications to monitor wolves at large spatial scales. PMID:24663068

Genealogical relationships between early medieval and modern inhabitants of Piedmont.

PubMed

Vai, Stefania; Ghirotto, Silvia; Pilli, Elena; Tassi, Francesca; Lari, Martina; Rizzi, Ermanno; Matas-Lalueza, Laura; Ramirez, Oscar; Lalueza-Fox, Carles; Achilli, Alessandro; Olivieri, Anna; Torroni, Antonio; Lancioni, Hovirag; Giostra, Caterina; Bedini, Elena; Pejrani Baricco, Luisella; Matullo, Giuseppe; Di Gaetano, Cornelia; Piazza, Alberto; Veeramah, Krishna; Geary, Patrick; Caramelli, David; Barbujani, Guido

2015-01-01

In the period between 400 to 800 AD, also known as the period of the Barbarian invasions, intense migration is documented in the historical record of Europe. However, little is known about the demographic impact of these historical movements, potentially ranging from negligible to substantial. As a pilot study in a broader project on Medieval Europe, we sampled 102 specimens from 5 burial sites in Northwestern Italy, archaeologically classified as belonging to Lombards or Longobards, a Germanic people ruling over a vast section of the Italian peninsula from 568 to 774. We successfully amplified and typed the mitochondrial hypervariable region I (HVR-I) of 28 individuals. Comparisons of genetic diversity with other ancient populations and haplotype networks did not suggest that these samples are heterogeneous, and hence allowed us to jointly compare them with three isolated contemporary populations, and with a modern sample of a large city, representing a control for the effects of recent immigration. We then generated by serial coalescent simulations 16 millions of genealogies, contrasting a model of genealogical continuity with one in which the contemporary samples are genealogically independent from the medieval sample. Analyses by Approximate Bayesian Computation showed that the latter model fits the data in most cases, with one exception, Trino Vercellese, in which the evidence was compatible with persistence up to the present time of genetic features observed among this early medieval population. We conclude that it is possible, in general, to detect evidence of genealogical ties between medieval and specific modern populations. However, only seldom did mitochondrial DNA data allow us to reject with confidence either model tested, which indicates that broader analyses, based on larger assemblages of samples and genetic markers, are needed to understand in detail the effects of medieval migration.

Genealogical Relationships between Early Medieval and Modern Inhabitants of Piedmont

PubMed Central

Vai, Stefania; Ghirotto, Silvia; Pilli, Elena; Tassi, Francesca; Lari, Martina; Rizzi, Ermanno; Matas-Lalueza, Laura; Ramirez, Oscar; Lalueza-Fox, Carles; Achilli, Alessandro; Olivieri, Anna; Torroni, Antonio; Lancioni, Hovirag; Giostra, Caterina; Bedini, Elena; Baricco, Luisella Pejrani; Matullo, Giuseppe; Di Gaetano, Cornelia; Piazza, Alberto; Veeramah, Krishna; Geary, Patrick; Caramelli, David; Barbujani, Guido

2015-01-01

In the period between 400 to 800 AD, also known as the period of the Barbarian invasions, intense migration is documented in the historical record of Europe. However, little is known about the demographic impact of these historical movements, potentially ranging from negligible to substantial. As a pilot study in a broader project on Medieval Europe, we sampled 102 specimens from 5 burial sites in Northwestern Italy, archaeologically classified as belonging to Lombards or Longobards, a Germanic people ruling over a vast section of the Italian peninsula from 568 to 774. We successfully amplified and typed the mitochondrial hypervariable region I (HVR-I) of 28 individuals. Comparisons of genetic diversity with other ancient populations and haplotype networks did not suggest that these samples are heterogeneous, and hence allowed us to jointly compare them with three isolated contemporary populations, and with a modern sample of a large city, representing a control for the effects of recent immigration. We then generated by serial coalescent simulations 16 millions of genealogies, contrasting a model of genealogical continuity with one in which the contemporary samples are genealogically independent from the medieval sample. Analyses by Approximate Bayesian Computation showed that the latter model fits the data in most cases, with one exception, Trino Vercellese, in which the evidence was compatible with persistence up to the present time of genetic features observed among this early medieval population. We conclude that it is possible, in general, to detect evidence of genealogical ties between medieval and specific modern populations. However, only seldom did mitochondrial DNA data allow us to reject with confidence either model tested, which indicates that broader analyses, based on larger assemblages of samples and genetic markers, are needed to understand in detail the effects of medieval migration. PMID:25635682

Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India.

PubMed

Pemberton, T J; Jakobsson, M; Conrad, D F; Coop, G; Wall, J D; Pritchard, J K; Patel, P I; Rosenberg, N A

2008-07-01

When performing association studies in populations that have not been the focus of large-scale investigations of haplotype variation, it is often helpful to rely on genomic databases in other populations for study design and analysis - such as in the selection of tag SNPs and in the imputation of missing genotypes. One way of improving the use of these databases is to rely on a mixture of database samples that is similar to the population of interest, rather than using the single most similar database sample. We demonstrate the effectiveness of the mixture approach in the application of African, European, and East Asian HapMap samples for tag SNP selection in populations from India, a genetically intermediate region underrepresented in genomic studies of haplotype variation.

Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress.

PubMed

Fernández, Jesús; Toro, Miguel Á; Sonesson, Anna K; Villanueva, Beatriz

2014-01-01

The success of an aquaculture breeding program critically depends on the way in which the base population of breeders is constructed since all the genetic variability for the traits included originally in the breeding goal as well as those to be included in the future is contained in the initial founders. Traditionally, base populations were created from a number of wild strains by sampling equal numbers from each strain. However, for some aquaculture species improved strains are already available and, therefore, mean phenotypic values for economically important traits can be used as a criterion to optimize the sampling when creating base populations. Also, the increasing availability of genome-wide genotype information in aquaculture species could help to refine the estimation of relationships within and between candidate strains and, thus, to optimize the percentage of individuals to be sampled from each strain. This study explores the advantages of using phenotypic and genome-wide information when constructing base populations for aquaculture breeding programs in terms of initial and subsequent trait performance and genetic diversity level. Results show that a compromise solution between diversity and performance can be found when creating base populations. Up to 6% higher levels of phenotypic performance can be achieved at the same level of global diversity in the base population by optimizing the selection of breeders instead of sampling equal numbers from each strain. The higher performance observed in the base population persisted during 10 generations of phenotypic selection applied in the subsequent breeding program.

Phenotypic Association Analyses With Copy Number Variation in Recurrent Depressive Disorder.

PubMed

Rucker, James J H; Tansey, Katherine E; Rivera, Margarita; Pinto, Dalila; Cohen-Woods, Sarah; Uher, Rudolf; Aitchison, Katherine J; Craddock, Nick; Owen, Michael J; Jones, Lisa; Jones, Ian; Korszun, Ania; Barnes, Michael R; Preisig, Martin; Mors, Ole; Maier, Wolfgang; Rice, John; Rietschel, Marcella; Holsboer, Florian; Farmer, Anne E; Craig, Ian W; Scherer, Stephen W; McGuffin, Peter; Breen, Gerome

2016-02-15

Defining the molecular genomic basis of the likelihood of developing depressive disorder is a considerable challenge. We previously associated rare, exonic deletion copy number variants (CNV) with recurrent depressive disorder (RDD). Sex chromosome abnormalities also have been observed to co-occur with RDD. In this reanalysis of our RDD dataset (N = 3106 cases; 459 screened control samples and 2699 population control samples), we further investigated the role of larger CNVs and chromosomal abnormalities in RDD and performed association analyses with clinical data derived from this dataset. We found an enrichment of Turner's syndrome among cases of depression compared with the frequency observed in a large population sample (N = 34,910) of live-born infants collected in Denmark (two-sided p = .023, odds ratio = 7.76 [95% confidence interval = 1.79-33.6]), a case of diploid/triploid mosaicism, and several cases of uniparental isodisomy. In contrast to our previous analysis, large deletion CNVs were no more frequent in cases than control samples, although deletion CNVs in cases contained more genes than control samples (two-sided p = .0002). After statistical correction for multiple comparisons, our data do not support a substantial role for CNVs in RDD, although (as has been observed in similar samples) occasional cases may harbor large variants with etiological significance. Genetic pleiotropy and sample heterogeneity suggest that very large sample sizes are required to study conclusively the role of genetic variation in mood disorders. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

A European Concern? Genetic Structure and Expansion of Golden Jackals (Canis aureus) in Europe and the Caucasus

PubMed Central

Rutkowski, Robert; Krofel, Miha; Giannatos, Giorgos; Ćirović, Duško; Männil, Peep; Volokh, Anatoliy M.; Lanszki, József; Heltai, Miklós; Szabó, László; Banea, Ovidiu C.; Yavruyan, Eduard; Hayrapetyan, Vahram; Kopaliani, Natia; Miliou, Anastasia; Tryfonopoulos, George A.; Lymberakis, Petros; Penezić, Aleksandra; Pakeltytė, Giedrė; Suchecka, Ewa; Bogdanowicz, Wiesław

2015-01-01

In the first continent-wide study of the golden jackal (Canis aureus), we characterised its population genetic structure and attempted to identify the origin of European populations. This provided a unique insight into genetic characteristics of a native carnivore population with rapid large-scale expansion. We analysed 15 microsatellite markers and a 406 base-pair fragment of the mitochondrial control region. Bayesian-based and principal components methods were applied to evaluate whether the geographical grouping of samples corresponded with genetic groups. Our analysis revealed low levels of genetic diversity, reflecting the unique history of the golden jackal among Europe’s native carnivores. The results suggest ongoing gene flow between south-eastern Europe and the Caucasus, with both contributing to the Baltic population, which appeared only recently. The population from the Peloponnese Peninsula in southern Greece forms a common genetic cluster with samples from south-eastern Europe (ΔK approach in STRUCTURE, Principal Components Analysis [PCA]), although the results based on BAPS and the estimated likelihood in STRUCTURE indicate that Peloponnesian jackals may represent a distinct population. Moreover, analyses of population structure also suggest either genetic distinctiveness of the island population from Samos near the coast of Asia Minor (BAPS, most STRUCTURE, PCA), or possibly its connection with the Caucasus population (one analysis in STRUCTURE). We speculate from our results that ancient Mediterranean jackal populations have persisted to the present day, and have merged with jackals colonising from Asia. These data also suggest that new populations of the golden jackal may be founded by long-distance dispersal, and thus should not be treated as an invasive alien species, i.e. an organism that is “non-native to an ecosystem, and which may cause economic or environmental harm or adversely affect human health”. These insights into the genetic structure and ancestry of Baltic jackals have important implications for management and conservation of jackals in Europe. The golden jackal is listed as an Annex V species in the EU Habitats Directive and as such, considering also the results presented here, should be legally protected in all EU member states. PMID:26540195

USING A COMMERCIAL TELEPHONE DIRECTORY TO IDENTIFY A POPULATION-BASED SAMPLE OF WOMEN OF REPRODUCTIVE AGE

EPA Science Inventory

Using a commercial telephone directory to identify a population-based sample of women of reproductive age
*DT Lobdell, GM Buck, JM Weiner, P Mendola (United States Environmental Protection Agency, Research Triangle Park, NC 27711)

In the United States, sampling women o...

Using Approximate Bayesian Computation to Probe Multiple Transiting Planet Systems

NASA Astrophysics Data System (ADS)

Morehead, Robert C.

2015-08-01

The large number of multiple transiting planet systems (MTPS) uncovered with Kepler suggest a population of well-aligned planetary systems. Previously, the distribution of transit duration ratios in MTPSs has been used to place constraints on the distributions of mutual orbital inclinations and orbital eccentricities in these systems. However, degeneracies with the underlying number of planets in these systems pose added challenges and make explicit likelihood functions intractable. Approximate Bayesian computation (ABC) offers an intriguing path forward. In its simplest form, ABC proposes from a prior on the population parameters to produce synthetic datasets via a physically-motivated model. Samples are accepted or rejected based on how close they come to reproducing the actual observed dataset to some tolerance. The accepted samples then form a robust and useful approximation of the true posterior distribution of the underlying population parameters. We will demonstrate the utility of ABC in exoplanet populations by presenting new constraints on the mutual inclination and eccentricity distributions in the Kepler MTPSs. We will also introduce Simple-ABC, a new open-source Python package designed for ease of use and rapid specification of general models, suitable for use in a wide variety of applications in both exoplanet science and astrophysics as a whole.

Modeling trends from North American Breeding Bird Survey data: a spatially explicit approach

USGS Publications Warehouse

Bled, Florent; Sauer, John R.; Pardieck, Keith L.; Doherty, Paul; Royle, J. Andy

2013-01-01

Population trends, defined as interval-specific proportional changes in population size, are often used to help identify species of conservation interest. Efficient modeling of such trends depends on the consideration of the correlation of population changes with key spatial and environmental covariates. This can provide insights into causal mechanisms and allow spatially explicit summaries at scales that are of interest to management agencies. We expand the hierarchical modeling framework used in the North American Breeding Bird Survey (BBS) by developing a spatially explicit model of temporal trend using a conditional autoregressive (CAR) model. By adopting a formal spatial model for abundance, we produce spatially explicit abundance and trend estimates. Analyses based on large-scale geographic strata such as Bird Conservation Regions (BCR) can suffer from basic imbalances in spatial sampling. Our approach addresses this issue by providing an explicit weighting based on the fundamental sample allocation unit of the BBS. We applied the spatial model to three species from the BBS. Species have been chosen based upon their well-known population change patterns, which allows us to evaluate the quality of our model and the biological meaning of our estimates. We also compare our results with the ones obtained for BCRs using a nonspatial hierarchical model (Sauer and Link 2011). Globally, estimates for mean trends are consistent between the two approaches but spatial estimates provide much more precise trend estimates in regions on the edges of species ranges that were poorly estimated in non-spatial analyses. Incorporating a spatial component in the analysis not only allows us to obtain relevant and biologically meaningful estimates for population trends, but also enables us to provide a flexible framework in order to obtain trend estimates for any area.

A fosmid cloning strategy for detecting the widest possible spectrum of microbes from the international space station drinking water system.

PubMed

Choi, Sangdun; Chang, Mi Sook; Stuecker, Tara; Chung, Christine; Newcombe, David A; Venkateswaran, Kasthuri

2012-12-01

In this study, fosmid cloning strategies were used to assess the microbial populations in water from the International Space Station (ISS) drinking water system (henceforth referred to as Prebiocide and Tank A water samples). The goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16S rRNA-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. Initially, microbes could not be cultivated, and conventional PCR failed to amplify 16S rDNA fragments from these low biomass samples. Therefore, randomly primed rolling-circle amplification was used to amplify any DNA that might be present in the samples, followed by size selection by using pulsed-field gel electrophoresis. The amplified high-molecular-weight DNA from both samples was cloned into fosmid vectors. Several hundred clones were randomly selected for sequencing, followed by Blastn/Blastx searches. Sequences encoding specific genes from Burkholderia, a species abundant in the soil and groundwater, were found in both samples. Bradyrhizobium and Mesorhizobium, which belong to rhizobia, a large community of nitrogen fixers often found in association with plant roots, were present in the Prebiocide samples. Ralstonia, which is prevalent in soils with a high heavy metal content, was detected in the Tank A samples. The detection of many unidentified sequences suggests the presence of potentially novel microbial fingerprints. The bacterial diversity detected in this pilot study using a fosmid vector approach was higher than that detected by conventional 16S rRNA gene sequencing.

Methods and feasibility of collecting occupational data for a large population-based cohort study in the United States: the reasons for geographic and racial differences in stroke study

PubMed Central

2014-01-01

Background Coronary heart disease and stroke are major contributors to preventable mortality. Evidence links work conditions to these diseases; however, occupational data are perceived to be difficult to collect for large population-based cohorts. We report methodological details and the feasibility of conducting an occupational ancillary study for a large U.S. prospective cohort being followed longitudinally for cardiovascular disease and stroke. Methods Current and historical occupational information were collected from active participants of the REasons for Geographic And Racial Differences in Stroke (REGARDS) Study. A survey was designed to gather quality occupational data among this national cohort of black and white men and women aged 45 years and older (enrolled 2003–2007). Trained staff conducted Computer-Assisted Telephone Interviews (CATI). After a brief pilot period, interviewers received additional training in the collection of narrative industry and occupation data before administering the survey to remaining cohort members. Trained coders used a computer-assisted coding system to assign U.S. Census codes for industry and occupation. All data were double coded; discrepant codes were independently resolved. Results Over a 2-year period, 17,648 participants provided consent and completed the occupational survey (87% response rate). A total of 20,427 jobs were assigned Census codes. Inter-rater reliability was 80% for industry and 74% for occupation. Less than 0.5% of the industry and occupation data were uncodable, compared with 12% during the pilot period. Concordance between the current and longest-held jobs was moderately high. The median time to collect employment status plus narrative and descriptive job information by CATI was 1.6 to 2.3 minutes per job. Median time to assign Census codes was 1.3 minutes per rater. Conclusions The feasibility of conducting high-quality occupational data collection and coding for a large heterogeneous population-based sample was demonstrated. We found that training for interview staff was important in ensuring that narrative responses for industry and occupation were adequately specified for coding. Estimates of survey administration time and coding from digital records provide an objective basis for planning future studies. The social and environmental conditions of work are important understudied risk factors that can be feasibly integrated into large population-based health studies. PMID:24512119

Methods and feasibility of collecting occupational data for a large population-based cohort study in the United States: the reasons for geographic and racial differences in stroke study.

PubMed

MacDonald, Leslie A; Pulley, LeaVonne; Hein, Misty J; Howard, Virginia J

2014-02-10

Coronary heart disease and stroke are major contributors to preventable mortality. Evidence links work conditions to these diseases; however, occupational data are perceived to be difficult to collect for large population-based cohorts. We report methodological details and the feasibility of conducting an occupational ancillary study for a large U.S. prospective cohort being followed longitudinally for cardiovascular disease and stroke. Current and historical occupational information were collected from active participants of the REasons for Geographic And Racial Differences in Stroke (REGARDS) Study. A survey was designed to gather quality occupational data among this national cohort of black and white men and women aged 45 years and older (enrolled 2003-2007). Trained staff conducted Computer-Assisted Telephone Interviews (CATI). After a brief pilot period, interviewers received additional training in the collection of narrative industry and occupation data before administering the survey to remaining cohort members. Trained coders used a computer-assisted coding system to assign U.S. Census codes for industry and occupation. All data were double coded; discrepant codes were independently resolved. Over a 2-year period, 17,648 participants provided consent and completed the occupational survey (87% response rate). A total of 20,427 jobs were assigned Census codes. Inter-rater reliability was 80% for industry and 74% for occupation. Less than 0.5% of the industry and occupation data were uncodable, compared with 12% during the pilot period. Concordance between the current and longest-held jobs was moderately high. The median time to collect employment status plus narrative and descriptive job information by CATI was 1.6 to 2.3 minutes per job. Median time to assign Census codes was 1.3 minutes per rater. The feasibility of conducting high-quality occupational data collection and coding for a large heterogeneous population-based sample was demonstrated. We found that training for interview staff was important in ensuring that narrative responses for industry and occupation were adequately specified for coding. Estimates of survey administration time and coding from digital records provide an objective basis for planning future studies. The social and environmental conditions of work are important understudied risk factors that can be feasibly integrated into large population-based health studies.

Hibernating black holes revealed by photometric mass functions

NASA Astrophysics Data System (ADS)

Casares, Jorge

2018-02-01

We present a novel strategy to uncover the Galactic population of quiescent black holes (BHs). This is based on a new concept, the photometric mass function (PMF), which opens up the possibility of an efficient identification of dynamical BHs in large fields-of-view. This exploits the width of the disc H α emission line, combined with orbital period information. We here show that H α widths can be recovered using a combination of customized H α filters. By setting a width cut-off at 2200 km s-1 we are able to cleanly remove other Galactic populations of H α emitters, including ∼99.9 per cent of cataclysmic variables (CVs). Only short-period (Porb <2.1 h) eclipsing CVs and AGNs will contaminate the sample but these can be easily flagged through photometric variability and, in the latter case, also mid-IR colours. We also describe the strategy of a deep (r = 22) Galactic plane survey based on the concept of PMFs: HAWKs, the HAlpha-Width Kilo-deg Survey. We estimate that ∼800 deg2 are required to unveil ∼50 new dynamical BHs, a three-fold improvement over the known population. For comparison, a century would be needed to produce an enlarged sample of 50 dynamical BHs from X-ray transients at the current discovery rate.

Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions.

PubMed

Ballenghien, Marion; Faivre, Nicolas; Galtier, Nicolas

2017-03-29

Contamination is a well-known but often neglected problem in molecular biology. Here, we investigated the prevalence of cross-contamination among 446 samples from 116 distinct species of animals, which were processed in the same laboratory and subjected to subcontracted transcriptome sequencing. Using cytochrome oxidase 1 as a barcode, we identified a minimum of 782 events of between-species contamination, with approximately 80% of our samples being affected. An analysis of laboratory metadata revealed a strong effect of the sequencing center: nearly all the detected events of between-species contamination involved species that were sent the same day to the same company. We introduce new methods to address the amount of within-species, between-individual contamination, and to correct for this problem when calling genotypes from base read counts. We report evidence for pervasive within-species contamination in this data set, and show that classical population genomic statistics, such as synonymous diversity, the ratio of non-synonymous to synonymous diversity, inbreeding coefficient F IT , and Tajima's D, are sensitive to this problem to various extents. Control analyses suggest that our published results are probably robust to the problem of contamination. Recommendations on how to prevent or avoid contamination in large-scale population genomics/molecular ecology are provided based on this analysis.

Optical stretching as a tool to investigate the mechanical properties of lipid bilayers.

PubMed

Solmaz, Mehmet E; Sankhagowit, Shalene; Biswas, Roshni; Mejia, Camilo A; Povinelli, Michelle L; Malmstadt, Noah

2013-10-07

Measurements of lipid bilayer bending modulus by various techniques produce widely divergent results. We attempt to resolve some of this ambiguity by measuring bending modulus in a system that can rapidly process large numbers of samples, yielding population statistics. This system is based on optical stretching of giant unilamellar vesicles (GUVs) in a microfluidic dual-beam optical trap (DBOT). The microfluidic DBOT system is used here to measure three populations of GUVs with distinct lipid compositions. We find that gel-phase membranes are significantly stiffer than liquid-phase membranes, consistent with previous reports. We also find that the addition of cholesterol does not alter the bending modulus of membranes composed of a monounsaturated phospholipid.

Characterizing the WISE-selected heavily obscured quasar population with optical spectroscopy from the Southern African Large Telescope

NASA Astrophysics Data System (ADS)

Hviding, Raphael E.; Hickox, Ryan C.; Hainline, Kevin N.; Carroll, Christopher M.; DiPompeo, Michael A.; Yan, Wei; Jones, Mackenzie L.

2018-02-01

We present the results of an optical spectroscopic survey of 46 heavily obscured quasar candidates. Objects are selected using their mid-infrared (mid-IR) colours and magnitudes from the Wide-Field Infrared Survey Explorer (WISE) anzd their optical magnitudes from the Sloan Digital Sky Survey. Candidate Active Galactic Nuclei (AGNs) are selected to have mid-IR colours indicative of quasar activity and lie in a region of mid-IR colour space outside previously published X-ray based selection regions. We obtain optical spectra for our sample using the Robert Stobie Spectrograph on the Southern African Large Telescope. 30 objects (65 per cent) have identifiable emission lines, allowing for the determination of spectroscopic redshifts. Other than one object at z ˜ 2.6, candidates have moderate redshifts ranging from z = 0.1 to 0.8 with a median of 0.3. 21 (70 per cent) of our objects with identified redshift (46 per cent of the whole sample) are identified as AGNs through common optical diagnostics. We model the spectral energy distributions of our sample and found that all require a strong AGN component, with an average intrinsic AGN fraction at 8 μm of 0.91. Additionally, the fits require large extinction coefficients with an average E(B - V)AGN = 17.8 (average A(V)AGN = 53.4). By focusing on the area outside traditional mid-IR photometric cuts, we are able to capture and characterize a population of deeply buried quasars that were previously unattainable through X-ray surveys alone.

Oral Microbiota of Children in a School-based Dental Clinic

PubMed Central

Soncini, Jennifer A; Kanasi, Eleni; Lu, Shulin C.; Nunn, Martha E.; Henshaw, Michelle M; Tanner, Anne CR

2010-01-01

Objectives Dental caries disproportionately affects disadvantaged subjects. This study hypothesized that there were greater caries extent and higher levels of caries-associated and anaerobic subgingival bacterial species in oral samples of Hispanic and immigrant children compared with non-Hispanic and US born children. Methods Children from a school-based dental clinic serving a community with a large Hispanic component were examined, and the extent of caries was recorded. Microbial samples were taken from teeth and the tongues of children. Samples were analyzed using DNA probes to 18 oral bacterial species. Results Seventy five children were examined. Extent of caries increased with child age in immigrant, but not in US born or Hispanic children. There were no differences in the microbiota based on ethnicity or whether the child was born in US or not. There was a higher species detection frequency from teeth than tongue samples. Levels of Streptococcus mutans and other Streptococcus species increased with caries extent. Prevotella intermedia, Tannerella forsythia and Selenomonas species were detected at low levels in these children. Conclusions We conclude that, while there was a high rate of dental caries in disadvantaged school children, there were no differences in the caries-associated microbiota, including S. mutans, based on ethnicity or immigration status. Furthermore, while anaerobic subgingival, periodontal pathogens were also detected in children, there was no difference in species detection based on ethnicity or immigration status. Increased levels of streptococci, including S. mutans, however, were detected with high caries levels. This suggested that while it is beneficial to target preventive and treatment programs to disadvantaged populations, there is likely no additional benefit to focus on subgroups within a population already at high risk for dental disease. PMID:19879369

Oral microbiota of children in a school-based dental clinic.

PubMed

Soncini, Jennifer A; Kanasi, Eleni; Lu, Shulin C; Nunn, Martha E; Henshaw, Michelle M; Tanner, Anne C R

2010-06-01

Dental caries disproportionately affects disadvantaged subjects. This study hypothesized that there were greater caries extent and higher levels of caries-associated and anaerobic subgingival bacterial species in oral samples of Hispanic and immigrant children compared with non-Hispanic and US born children. Children from a school-based dental clinic serving a community with a large Hispanic component were examined, and the extent of caries was recorded. Microbial samples were taken from teeth and the tongues of children. Samples were analyzed using DNA probes to 18 oral bacterial species. Seventy five children were examined. Extent of caries increased with child age in immigrant, but not in US born or Hispanic children. There were no differences in the microbiota based on ethnicity or whether the child was born in US or not. There was a higher species detection frequency from teeth than tongue samples. Levels of Streptococcus mutans and other Streptococcus spp increased with caries extent. Prevotella intermedia, Tannerella forsythia and Selenomonas spp were detected at low levels in these children. We conclude that, while there was a high rate of dental caries in disadvantaged school children, there were no differences in the caries-associated microbiota, including S. mutans, based on ethnicity or immigration status. Furthermore, while anaerobic subgingival, periodontal pathogens were also detected in children, there was no difference in species detection based on ethnicity or immigration status. Increased levels of streptococci, including S. mutans, however, were detected with high caries levels. This suggested that while it is beneficial to target preventive and treatment programs to disadvantaged populations, there is likely no additional benefit to focus on subgroups within a population already at high risk for dental disease. 2009 Elsevier Ltd. All rights reserved.

Do You See What I See? Exploring the Consequences of Luminosity Limits in Black Hole-Galaxy Evolution Studies

NASA Astrophysics Data System (ADS)

Jones, Mackenzie L.; Hickox, Ryan C.; Mutch, Simon J.; Croton, Darren J.; Ptak, Andrew F.; DiPompeo, Michael A.

2017-07-01

In studies of the connection between active galactic nuclei (AGNs) and their host galaxies, there is widespread disagreement on some key aspects of the connection. These disagreements largely stem from a lack of understanding of the nature of the full underlying AGN population. Recent attempts to probe this connection utilize both observations and simulations to correct for a missed population, but presently are limited by intrinsic biases and complicated models. We take a simple simulation for galaxy evolution and add a new prescription for AGN activity to connect galaxy growth to dark matter halo properties and AGN activity to star formation. We explicitly model selection effects to produce an “observed” AGN population for comparison with observations and empirically motivated models of the local universe. This allows us to bypass the difficulties inherent in models that attempt to infer the AGN population by inverting selection effects. We investigate the impact of selecting AGNs based on thresholds in luminosity or Eddington ratio on the “observed” AGN population. By limiting our model AGN sample in luminosity, we are able to recreate the observed local AGN luminosity function and specific star formation-stellar mass distribution, and show that using an Eddington ratio threshold introduces less bias into the sample by selecting the full range of growing black holes, despite the challenge of selecting low-mass black holes. We find that selecting AGNs using these various thresholds yield samples with different AGN host galaxy properties.

Population genetic structure of traditional populations in the Peruvian Central Andes and implications for South American population history.

PubMed

Cabana, Graciela S; Lewis, Cecil M; Tito, Raúl Y; Covey, R Alan; Cáceres, Angela M; Cruz, Augusto F De La; Durand, Diana; Housman, Genevieve; Hulsey, Brannon I; Iannacone, Gian Carlo; López, Paul W; Martínez, Rolando; Medina, Ángel; Dávila, Olimpio Ortega; Pinto, Karla Paloma Osorio; Santillán, Susan I Polo; Domínguez, Percy Rojas; Rubel, Meagan; Smith, Heather F; Smith, Silvia E; Massa, Verónica Rubín de Celis; Lizárraga, Beatriz; Stone, Anne C

2014-01-01

Molecular-based characterizations of Andean peoples are traditionally conducted in the service of elucidating continent-level evolutionary processes in South America. Consequently, genetic variation among "western" Andean populations is often represented in relation to variation among "eastern" Amazon and Orinoco River Basin populations. This west-east contrast in patterns of population genetic variation is typically attributed to large-scale phenomena, such as dual founder colonization events or differing long-term microevolutionary histories. However, alternative explanations that consider the nature and causes of population genetic diversity within the Andean region remain underexplored. Here we examine population genetic diversity in the Peruvian Central Andes using data from the mtDNA first hypervariable region and Y-chromosome short tandem repeats among 17 newly sampled populations and 15 published samples. Using this geographically comprehensive data set, we first reassessed the currently accepted pattern of western versus eastern population genetic structure, which our results ultimately reject: mtDNA population diversities were lower, rather than higher, within Andean versus eastern populations, and only highland Y-chromosomes exhibited significantly higher within-population diversities compared with eastern groups. Multiple populations, including several highland samples, exhibited low genetic diversities for both genetic systems. Second, we explored whether the implementation of Inca state and Spanish colonial policies starting at about ad 1400 could have substantially restructured population genetic variation and consequently constitute a primary explanation for the extant pattern of population diversity in the Peruvian Central Andes. Our results suggest that Peruvian Central Andean population structure cannot be parsimoniously explained as the sole outcome of combined Inca and Spanish policies on the region's population demography: highland populations differed from coastal and lowland populations in mtDNA genetic structure only; highland groups also showed strong evidence of female-biased gene flow and/or effective sizes relative to other Peruvian ecozones. Taken together, these findings indicate that population genetic structure in the Peruvian Central Andes is considerably more complex than previously reported and that characterizations of and explanations for genetic variation may be best pursued within more localized regions and defined time periods.

The Peru Cervical Cancer Prevention Study (PERCAPS): the technology to make screening accessible.

PubMed

Levinson, Kimberly L; Abuelo, Carolina; Salmeron, Jorge; Chyung, Eunice; Zou, Jing; Belinson, Suzanne E; Wang, Guixiang; Ortiz, Carlos Santos; Vallejos, Carlos Santiago; Belinson, Jerome L

2013-05-01

This study utilized a combination of HPV self-sampling, iFTA elute specimen cards, and long distance transport for centralized processing of specimens to determine the feasibility of large-scale screening in remote and transient populations. This study was performed in two locations in Peru (Manchay and Iquitos). The "Just For Me" cervico-vaginal brush and iFTA elute cards were used for the collection and transport of specimens. Samples were shipped via FedEx to China and tested for 14 types of high-risk HPV using PCR based MALDI-TOF. HPV positive women were treated with cryotherapy after VIA triage, and followed-up with colposcopy, biopsy, ECC, and repeat HPV testing at 6 months. Six hundred and forty three women registered, and 632 returned a sample over a 10 day period. Within 2 weeks, specimens were shipped, samples tested, and results received by study staff. Sixty-eight women (10.8%) tested positive, and these results were delivered over 4 days. Fifty-nine HPV positive women (87%) returned for evaluation and treatment, and 2 had large lesions not suitable for cryotherapy. At 6 months, 42 women (74%) returned for follow-up, and 3 had CIN 2 (all positive samples from the endocervical canal). Ninety eight percent of participants reported that they would participate in this type of program again. Utilizing HPV self-sampling, solid media specimen cards for long distance transport, and centralized high throughput processing, we achieved rapid delivery of results, high satisfaction levels, and low loss to follow-up for cervical cancer screening in remote and transient populations. Copyright © 2013 Elsevier Inc. All rights reserved.

Haemangiomas and Associated Congenital Malformations in a Large Population-Based Sample of Infants

DTIC Science & Technology

2008-01-01

Clusters found to be associated with haemangioma were characterised by anomalies of the cervix, vagina, and external female genitalia, anophthalmia or...genitalia 2 228 55 (2.5) 2.23 ɘ.0001 Anophthalmia /microphthalmia 141 5 (3.5) 3.24 ɘ.01 Hydrocephalus without spina bifida 591 18 (3.0) 2.77 ɘ.0001...were characterised by: anomalies of the cervix, vagina and external female genitalia (OR = 2.23, P < 0.0001); anophthalmia or microphthalmia (OR = 3.24

Genetic assessment of connectivity in the common reef sponge, Callyspongia vaginalis (Demospongiae: Haplosclerida) reveals high population structure along the Florida reef tract

NASA Astrophysics Data System (ADS)

Debiasse, M. B.; Richards, V. P.; Shivji, M. S.

2010-03-01

The genetic population structure of the common branching vase sponge, Callyspongia vaginalis, was determined along the entire length (465 km) of the Florida reef system from Palm Beach to the Dry Tortugas based on sequences of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene. Populations of C. vaginalis were highly structured (overall ΦST = 0.33), in some cases over distances as small as tens of kilometers. However, nonsignificant pairwise ΦST values were also found between a few relatively distant sampling sites suggesting that some long distance larval dispersal may occur via ocean currents or transport in sponge fragments along continuous, shallow coastlines. Indeed, sufficient gene flow appears to occur along the Florida reef tract to obscure a signal of isolation by distance, but not to homogenize COI haplotype frequencies. The strong genetic differentiation among most of the sampling locations suggests that recruitment in this species is largely local source-driven, pointing to the importance of further elucidating general connectivity patterns along the Florida reef tract to guide the spatial scale of management efforts.

Rasch model based analysis of the Force Concept Inventory

NASA Astrophysics Data System (ADS)

Planinic, Maja; Ivanjek, Lana; Susac, Ana

2010-06-01

The Force Concept Inventory (FCI) is an important diagnostic instrument which is widely used in the field of physics education research. It is therefore very important to evaluate and monitor its functioning using different tools for statistical analysis. One of such tools is the stochastic Rasch model, which enables construction of linear measures for persons and items from raw test scores and which can provide important insight in the structure and functioning of the test (how item difficulties are distributed within the test, how well the items fit the model, and how well the items work together to define the underlying construct). The data for the Rasch analysis come from the large-scale research conducted in 2006-07, which investigated Croatian high school students’ conceptual understanding of mechanics on a representative sample of 1676 students (age 17-18 years). The instrument used in research was the FCI. The average FCI score for the whole sample was found to be (27.7±0.4)% , indicating that most of the students were still non-Newtonians at the end of high school, despite the fact that physics is a compulsory subject in Croatian schools. The large set of obtained data was analyzed with the Rasch measurement computer software WINSTEPS 3.66. Since the FCI is routinely used as pretest and post-test on two very different types of population (non-Newtonian and predominantly Newtonian), an additional predominantly Newtonian sample ( N=141 , average FCI score of 64.5%) of first year students enrolled in introductory physics course at University of Zagreb was also analyzed. The Rasch model based analysis suggests that the FCI has succeeded in defining a sufficiently unidimensional construct for each population. The analysis of fit of data to the model found no grossly misfitting items which would degrade measurement. Some items with larger misfit and items with significantly different difficulties in the two samples of students do require further examination. The analysis revealed some problems with item distribution in the FCI and suggested that the FCI may function differently in non-Newtonian and predominantly Newtonian population. Some possible improvements of the test are suggested.

Increasing the health promotion practices of workplaces in Australia with a proactive telephone-based intervention.

PubMed

Daly, Justine; Licata, Milly; Gillham, Karen; Wiggers, John

2005-01-01

The aim of this study was to explore the potential effectiveness of a proactive telephone-based intervention in increasing workplace adoption of health promotion initiatives. A telephone-based direct marketing strategy was used to contact a sample of Australian workplaces to encourage the adoption of health promotion initiatives. Workplaces were offered free services and resources designed to facilitate adoption of health promotion initiatives. A total of 227 (71%) workplaces provided informed consent to participate in both baseline and 4-year follow-up surveys. Significant increases were evident for seven of the eight health promotion initiatives. The findings of this study suggest that a proactive telephone-based intervention has the potential to be effective in increasing the prevalence of health promotion initiatives across a range of health topics in a large population of workplaces. Given the capacity to reach an entire population of workplaces, this approach represents a promising means of achieving the established potential of workplace health promotion.

The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography.

PubMed

Lapierre, Marguerite; Blin, Camille; Lambert, Amaury; Achaz, Guillaume; Rocha, Eduardo P C

2016-07-01

Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Sample and population exponents of generalized Taylor's law.

PubMed

Giometto, Andrea; Formentin, Marco; Rinaldo, Andrea; Cohen, Joel E; Maritan, Amos

2015-06-23

Taylor's law (TL) states that the variance V of a nonnegative random variable is a power function of its mean M; i.e., V = aM(b). TL has been verified extensively in ecology, where it applies to population abundance, physics, and other natural sciences. Its ubiquitous empirical verification suggests a context-independent mechanism. Sample exponents b measured empirically via the scaling of sample mean and variance typically cluster around the value b = 2. Some theoretical models of population growth, however, predict a broad range of values for the population exponent b pertaining to the mean and variance of population density, depending on details of the growth process. Is the widely reported sample exponent b ≃ 2 the result of ecological processes or could it be a statistical artifact? Here, we apply large deviations theory and finite-sample arguments to show exactly that in a broad class of growth models the sample exponent is b ≃ 2 regardless of the underlying population exponent. We derive a generalized TL in terms of sample and population exponents b(jk) for the scaling of the kth vs. the jth cumulants. The sample exponent b(jk) depends predictably on the number of samples and for finite samples we obtain b(jk) ≃ k = j asymptotically in time, a prediction that we verify in two empirical examples. Thus, the sample exponent b ≃ 2 may indeed be a statistical artifact and not dependent on population dynamics under conditions that we specify exactly. Given the broad class of models investigated, our results apply to many fields where TL is used although inadequately understood.

Geospatial techniques for developing a sampling frame of watersheds across a region

USGS Publications Warehouse

Gresswell, Robert E.; Bateman, Douglas S.; Lienkaemper, George; Guy, T.J.

2004-01-01

Current land-management decisions that affect the persistence of native salmonids are often influenced by studies of individual sites that are selected based on judgment and convenience. Although this approach is useful for some purposes, extrapolating results to areas that were not sampled is statistically inappropriate because the sampling design is usually biased. Therefore, in recent investigations of coastal cutthroat trout (Oncorhynchus clarki clarki) located above natural barriers to anadromous salmonids, we used a methodology for extending the statistical scope of inference. The purpose of this paper is to apply geospatial tools to identify a population of watersheds and develop a probability-based sampling design for coastal cutthroat trout in western Oregon, USA. The population of mid-size watersheds (500-5800 ha) west of the Cascade Range divide was derived from watershed delineations based on digital elevation models. Because a database with locations of isolated populations of coastal cutthroat trout did not exist, a sampling frame of isolated watersheds containing cutthroat trout had to be developed. After the sampling frame of watersheds was established, isolated watersheds with coastal cutthroat trout were stratified by ecoregion and erosion potential based on dominant bedrock lithology (i.e., sedimentary and igneous). A stratified random sample of 60 watersheds was selected with proportional allocation in each stratum. By comparing watershed drainage areas of streams in the general population to those in the sampling frame and the resulting sample (n = 60), we were able to evaluate the how representative the subset of watersheds was in relation to the population of watersheds. Geospatial tools provided a relatively inexpensive means to generate the information necessary to develop a statistically robust, probability-based sampling design.

Identifying Multiple Populations in M71 using CN

NASA Astrophysics Data System (ADS)

Gerber, Jeffrey M.; Friel, Eileen D.; Vesperini, Enrico

2018-01-01

It is now well established that globular clusters (GCs) host multiple stellar populations characterized by differences in several light elements. While these populations have been found in nearly all GCs, we still lack an entirely successful model to explain their formation. A key constraint to these models is the detailed pattern of light element abundances seen among the populations; different techniques for identifying these populations probe different elements and do not always yield the same results. We study a large sample of stars in the GC M71 for light elements C and N, using the CN and CH band strength to identify multiple populations. Our measurements come from low-resolution spectroscopy obtained with the WIYN-3.5m telescope for ~150 stars from the tip of the red-giant branch down to the main-sequence turn-off. The large number of stars and broad spatial coverage of our sample (out to ~3.5 half-light radii) allows us to carry out a comprehensive characterization of the multiple populations in M71. We use a combination of the various spectroscopic and photometric indicators to draw a more complete picture of the properties of the populations and to investigate the consistency of classifications using different techniques.

Analysis of genetic population structure in Acacia caven (Leguminosae, Mimosoideae), comparing one exploratory and two Bayesian-model-based methods

PubMed Central

Pometti, Carolina L.; Bessega, Cecilia F.; Saidman, Beatriz O.; Vilardi, Juan C.

2014-01-01

Bayesian clustering as implemented in STRUCTURE or GENELAND software is widely used to form genetic groups of populations or individuals. On the other hand, in order to satisfy the need for less computer-intensive approaches, multivariate analyses are specifically devoted to extracting information from large datasets. In this paper, we report the use of a dataset of AFLP markers belonging to 15 sampling sites of Acacia caven for studying the genetic structure and comparing the consistency of three methods: STRUCTURE, GENELAND and DAPC. Of these methods, DAPC was the fastest one and showed accuracy in inferring the K number of populations (K = 12 using the find.clusters option and K = 15 with a priori information of populations). GENELAND in turn, provides information on the area of membership probabilities for individuals or populations in the space, when coordinates are specified (K = 12). STRUCTURE also inferred the number of K populations and the membership probabilities of individuals based on ancestry, presenting the result K = 11 without prior information of populations and K = 15 using the LOCPRIOR option. Finally, in this work all three methods showed high consistency in estimating the population structure, inferring similar numbers of populations and the membership probabilities of individuals to each group, with a high correlation between each other. PMID:24688293

Arterial waveform parameters in a large, population-based sample of adults: relationships with ethnicity and lifestyle factors.

PubMed

Sluyter, J D; Hughes, A D; Thom, S A McG; Lowe, A; Camargo, C A; Hametner, B; Wassertheurer, S; Parker, K H; Scragg, R K R

2017-05-01

Little is known about how aortic waveform parameters vary with ethnicity and lifestyle factors. We investigated these issues in a large, population-based sample. We carried out a cross-sectional analysis of 4798 men and women, aged 50-84 years from Auckland, New Zealand. Participants were 3961 European, 321 Pacific, 266 Maori and 250 South Asian people. We assessed modifiable lifestyle factors via questionnaires, and measured body mass index (BMI) and brachial blood pressure (BP). Suprasystolic oscillometry was used to derive aortic pressure, from which several haemodynamic parameters were calculated. Heavy alcohol consumption and BMI were positively related to most waveform parameters. Current smokers had higher levels of aortic augmentation index than non-smokers (difference=3.7%, P<0.0001). Aortic waveform parameters, controlling for demographics, antihypertensives, diabetes and cardiovascular disease (CVD), were higher in non-Europeans than in Europeans. Further adjustment for brachial BP or lifestyle factors (particularly BMI) reduced many differences but several remained. Despite even further adjustment for mean arterial pressure, pulse rate, height and total:high-density lipoprotein cholesterol, compared with Europeans, South Asians had higher levels of all measured aortic waveform parameters (for example, for backward pressure amplitude: β=1.5 mm Hg; P<0.0001), whereas Pacific people had 9% higher log e (excess pressure integral) (P<0.0001). In conclusion, aortic waveform parameters varied with ethnicity in line with the greater prevalence of CVD among non-white populations. Generally, this was true even after accounting for brachial BP, suggesting that waveform parameters may have increased usefulness in capturing ethnic variations in cardiovascular risk. Heavy alcohol consumption, smoking and especially BMI may partially contribute to elevated levels of these parameters.

Arterial waveform parameters in a large, population-based sample of adults: relationships with ethnicity and lifestyle factors

PubMed Central

Sluyter, J D; Hughes, A D; Thom, S A McG; Lowe, A; Camargo Jr, C A; Hametner, B; Wassertheurer, S; Parker, K H; Scragg, R K R

2017-01-01

Little is known about how aortic waveform parameters vary with ethnicity and lifestyle factors. We investigated these issues in a large, population-based sample. We carried out a cross-sectional analysis of 4798 men and women, aged 50–84 years from Auckland, New Zealand. Participants were 3961 European, 321 Pacific, 266 Maori and 250 South Asian people. We assessed modifiable lifestyle factors via questionnaires, and measured body mass index (BMI) and brachial blood pressure (BP). Suprasystolic oscillometry was used to derive aortic pressure, from which several haemodynamic parameters were calculated. Heavy alcohol consumption and BMI were positively related to most waveform parameters. Current smokers had higher levels of aortic augmentation index than non-smokers (difference=3.7%, P<0.0001). Aortic waveform parameters, controlling for demographics, antihypertensives, diabetes and cardiovascular disease (CVD), were higher in non-Europeans than in Europeans. Further adjustment for brachial BP or lifestyle factors (particularly BMI) reduced many differences but several remained. Despite even further adjustment for mean arterial pressure, pulse rate, height and total:high-density lipoprotein cholesterol, compared with Europeans, South Asians had higher levels of all measured aortic waveform parameters (for example, for backward pressure amplitude: β=1.5 mm Hg; P<0.0001), whereas Pacific people had 9% higher loge (excess pressure integral) (P<0.0001). In conclusion, aortic waveform parameters varied with ethnicity in line with the greater prevalence of CVD among non-white populations. Generally, this was true even after accounting for brachial BP, suggesting that waveform parameters may have increased usefulness in capturing ethnic variations in cardiovascular risk. Heavy alcohol consumption, smoking and especially BMI may partially contribute to elevated levels of these parameters. PMID:28004730

Metapopulation models for historical inference.

PubMed

Wakeley, John

2004-04-01

The genealogical process for a sample from a metapopulation, in which local populations are connected by migration and can undergo extinction and subsequent recolonization, is shown to have a relatively simple structure in the limit as the number of populations in the metapopulation approaches infinity. The result, which is an approximation to the ancestral behaviour of samples from a metapopulation with a large number of populations, is the same as that previously described for other metapopulation models, namely that the genealogical process is closely related to Kingman's unstructured coalescent. The present work considers a more general class of models that includes two kinds of extinction and recolonization, and the possibility that gamete production precedes extinction. In addition, following other recent work, this result for a metapopulation divided into many populations is shown to hold both for finite population sizes and in the usual diffusion limit, which assumes that population sizes are large. Examples illustrate when the usual diffusion limit is appropriate and when it is not. Some shortcomings and extensions of the model are considered, and the relevance of such models to understanding human history is discussed.

Large genetic differentiation and low variation in vector competence for dengue and yellow fever viruses of Aedes albopictus from Brazil, the United States, and the Cayman Islands.

PubMed

Lourenço de Oliveira, Ricardo; Vazeille, Marie; de Filippis, Ana Maria Bispo; Failloux, Anna-Bella

2003-07-01

We conducted a population genetic analysis of Aedes albopictus collected from 20 sites in Brazil, the United States (Florida, Georgia, and Illinois), and the Cayman Islands. Using isoenzyme analysis, we examined genetic diversity and patterns of gene flow. High genetic differentiation was found among Brazilian samples, and between them and North American samples. Regression analysis of genetic differentiation according to geographic distances indicated that Ae. albopictus samples from Florida were genetically isolated by distance. Infection rates with dengue and yellow fever viruses showed greater differences between two Brazilian samples than between the two North American samples or between a Brazilian sample and a North American sample. Introductions and establishments of new Ae. albopictus populations in the Americas are still in progress, shaping population genetic composition and potentially modifying both dengue and yellow fever transmission patterns.

The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.

PubMed

Lack, Justin B; Cardeno, Charis M; Crepeau, Marc W; Taylor, William; Corbett-Detig, Russell B; Stevens, Kristian A; Langley, Charles H; Pool, John E

2015-04-01

Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets. Copyright © 2015 by the Genetics Society of America.

A Genome-Wide Linkage Scan for Age at Menarche in Three Populations of European Descent

PubMed Central

Anderson, Carl A.; Zhu, Gu; Falchi, Mario; van den Berg, Stéphanie M.; Treloar, Susan A.; Spector, Timothy D.; Martin, Nicholas G.; Boomsma, Dorret I.; Visscher, Peter M.; Montgomery, Grant W.

2008-01-01

Context: Age at menarche (AAM) is an important trait both biologically and socially, a clearly defined event in female pubertal development, and has been associated with many clinically significant phenotypes. Objective: The objective of the study was to identify genetic loci influencing variation in AAM in large population-based samples from three countries. Design/Participants: Recalled AAM data were collected from 13,697 individuals and 4,899 pseudoindependent sister-pairs from three different populations (Australia, The Netherlands, and the United Kingdom) by mailed questionnaire or interview. Genome-wide variance components linkage analysis was implemented on each sample individually and in combination. Results: The mean, sd, and heritability of AAM across the three samples was 13.1 yr, 1.5 yr, and 0.69, respectively. No loci were detected that reached genome-wide significance in the combined analysis, but a suggestive locus was detected on chromosome 12 (logarithm of the odds = 2.0). Three loci of suggestive significance were seen in the U.K. sample on chromosomes 1, 4, and 18 (logarithm of the odds = 2.4, 2.2 and 3.2, respectively). Conclusions: There was no evidence for common highly penetrant variants influencing AAM. Linkage and association suggest that one trait locus for AAM is located on chromosome 12, but further studies are required to replicate these results. PMID:18647812

Life-history and habitat features influence the within-river genetic structure of Atlantic salmon.

PubMed

Vähä, Juha-Pekka; Erkinaro, Jaakko; Niemelä, Eero; Primmer, Craig R

2007-07-01

Defining populations and identifying ecological and life-history characteristics affecting genetic structure is important for understanding species biology and hence, for managing threatened or endangered species or populations. In this study, populations of the world's largest indigenous Atlantic salmon (Salmo salar) stock were first inferred using model-based clustering methods, following which life-history and habitat variables best predicting the genetic diversity of populations were identified. This study revealed that natal homing of Atlantic salmon within the Teno River system is accurate at least to the tributary level. Generally, defining populations by main tributaries was observed to be a reasonable approach in this large river system, whereas in the mainstem of the river, the number of inferred populations was fewer than the number of distinct sampling sites. Mainstem and headwater populations were genetically more diverse and less diverged, while each tributary fostered a distinct population with high genetic differentiation and lower genetic diversity. Population structure and variation in genetic diversity among populations were poorly explained by geographical distance. In contrast, age-structure, as estimated by the proportion of multisea-winter spawners, was the most predictive variable in explaining the variation in the genetic diversity of the populations. This observation, being in agreement with theoretical predictions, emphasizes the essence of large multisea-winter females in maintaining the genetic diversity of populations. In addition, the unique genetic diversity of populations, as estimated by private allele richness, was affected by the ease of accessibility of a site, with more difficult to access sites having lower unique genetic diversity. Our results show that despite this species' high capacity for migration, tributaries foster relatively closed populations with little gene flow which will be important to consider when developing management strategies for the system.

Evaluating and improving count-based population inference: A case study from 31 years of monitoring Sandhill Cranes

USGS Publications Warehouse

Gerber, Brian D.; Kendall, William L.

2017-01-01

Monitoring animal populations can be difficult. Limited resources often force monitoring programs to rely on unadjusted or smoothed counts as an index of abundance. Smoothing counts is commonly done using a moving-average estimator to dampen sampling variation. These indices are commonly used to inform management decisions, although their reliability is often unknown. We outline a process to evaluate the biological plausibility of annual changes in population counts and indices from a typical monitoring scenario and compare results with a hierarchical Bayesian time series (HBTS) model. We evaluated spring and fall counts, fall indices, and model-based predictions for the Rocky Mountain population (RMP) of Sandhill Cranes (Antigone canadensis) by integrating juvenile recruitment, harvest, and survival into a stochastic stage-based population model. We used simulation to evaluate population indices from the HBTS model and the commonly used 3-yr moving average estimator. We found counts of the RMP to exhibit biologically unrealistic annual change, while the fall population index was largely biologically realistic. HBTS model predictions suggested that the RMP changed little over 31 yr of monitoring, but the pattern depended on assumptions about the observational process. The HBTS model fall population predictions were biologically plausible if observed crane harvest mortality was compensatory up to natural mortality, as empirical evidence suggests. Simulations indicated that the predicted mean of the HBTS model was generally a more reliable estimate of the true population than population indices derived using a moving 3-yr average estimator. Practitioners could gain considerable advantages from modeling population counts using a hierarchical Bayesian autoregressive approach. Advantages would include: (1) obtaining measures of uncertainty; (2) incorporating direct knowledge of the observational and population processes; (3) accommodating missing years of data; and (4) forecasting population size.

Validation of a Cost-Efficient Multi-Purpose SNP Panel for Disease Based Research

PubMed Central

Hou, Liping; Phillips, Christopher; Azaro, Marco; Brzustowicz, Linda M.; Bartlett, Christopher W.

2011-01-01

Background Here we present convergent methodologies using theoretical calculations, empirical assessment on in-house and publicly available datasets as well as in silico simulations, that validate a panel of SNPs for a variety of necessary tasks in human genetics disease research before resources are committed to larger-scale genotyping studies on those samples. While large-scale well-funded human genetic studies routinely have up to a million SNP genotypes, samples in a human genetics laboratory that are not yet part of such studies may be productively utilized in pilot projects or as part of targeted follow-up work though such smaller scale applications require at least some genome-wide genotype data for quality control purposes such as DNA “barcoding” to detect swaps or contamination issues, determining familial relationships between samples and correcting biases due to population effects such as population stratification in pilot studies. Principal Findings Empirical performance in classification of relative types for any two given DNA samples (e.g., full siblings, parental, etc) indicated that for outbred populations the panel performs sufficiently to classify relationship in extended families and therefore also for smaller structures such as trios and for twin zygosity testing. Additionally, familial relationships do not significantly diminish the (mean match) probability of sharing SNP genotypes in pedigrees, further indicating the uniqueness of the “barcode.” Simulation using these SNPs for an African American case-control disease association study demonstrated that population stratification, even in complex admixed samples, can be adequately corrected under a range of disease models using the SNP panel. Conclusion The panel has been validated for use in a variety of human disease genetics research tasks including sample barcoding, relationship verification, population substructure detection and statistical correction. Given the ease of genotyping our specific assay contained herein, this panel represents a useful and economical panel for human geneticists. PMID:21611176

Software engineering the mixed model for genome-wide association studies on large samples.

PubMed

Zhang, Zhiwu; Buckler, Edward S; Casstevens, Terry M; Bradbury, Peter J

2009-11-01

Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample size and number of markers used for GWAS is increasing dramatically, resulting in greater statistical power to detect those associations. The use of mixed models with increasingly large data sets depends on the availability of software for analyzing those models. While multiple software packages implement the mixed model method, no single package provides the best combination of fast computation, ability to handle large samples, flexible modeling and ease of use. Key elements of association analysis with mixed models are reviewed, including modeling phenotype-genotype associations using mixed models, population stratification, kinship and its estimation, variance component estimation, use of best linear unbiased predictors or residuals in place of raw phenotype, improving efficiency and software-user interaction. The available software packages are evaluated, and suggestions made for future software development.

Spatio-temporal population structuring and genetic diversity retention in depleted Atlantic Bluefin tuna of the Mediterranean Sea

PubMed Central

Riccioni, Giulia; Landi, Monica; Ferrara, Giorgia; Milano, Ilaria; Cariani, Alessia; Zane, Lorenzo; Sella, Massimo; Barbujani, Guido; Tinti, Fausto

2010-01-01

Fishery genetics have greatly changed our understanding of population dynamics and structuring in marine fish. In this study, we show that the Atlantic Bluefin tuna (ABFT, Thunnus thynnus), an oceanic predatory species exhibiting highly migratory behavior, large population size, and high potential for dispersal during early life stages, displays significant genetic differences over space and time, both at the fine and large scales of variation. We compared microsatellite variation of contemporary (n = 256) and historical (n = 99) biological samples of ABFTs of the central-western Mediterranean Sea, the latter dating back to the early 20th century. Measures of genetic differentiation and a general heterozygote deficit suggest that differences exist among population samples, both now and 96–80 years ago. Thus, ABFTs do not represent a single panmictic population in the Mediterranean Sea. Statistics designed to infer changes in population size, both from current and past genetic variation, suggest that some Mediterranean ABFT populations, although still not severely reduced in their genetic potential, might have suffered from demographic declines. The short-term estimates of effective population size are straddled on the minimum threshold (effective population size = 500) indicated to maintain genetic diversity and evolutionary potential across several generations in natural populations. PMID:20080643

Evaluation of three gears for sampling spawning populations of rainbow trout in a large Alaskan river

USGS Publications Warehouse

Schwanke, C.J.; Hubert, W.A.

2004-01-01

Alternatives to electrofishing are needed for sampling sexually mature rainbow trout Oncorhynchus mykiss during the spawning season in large Alaskan rivers. We compared hook and line, beach seining, and actively fished gill nets as sampling tools. Beach seining and active gill netting yielded similar catch rates, length frequencies, and sex ratios of sexually mature fish. Hook-and-line sampling was less effective, with a lower catch rate and selectivity for immature fish and sexually mature females. We conclude that both beach seining and active gill netting can serve as alternatives to electrofishing for sampling sexually mature rainbow trout stocks during the spawning season in large rivers with stable spring flows and spawning areas with few snags.

Sub-sampling genetic data to estimate black bear population size: A case study

USGS Publications Warehouse

Tredick, C.A.; Vaughan, M.R.; Stauffer, D.F.; Simek, S.L.; Eason, T.

2007-01-01

Costs for genetic analysis of hair samples collected for individual identification of bears average approximately US$50 [2004] per sample. This can easily exceed budgetary allowances for large-scale studies or studies of high-density bear populations. We used 2 genetic datasets from 2 areas in the southeastern United States to explore how reducing costs of analysis by sub-sampling affected precision and accuracy of resulting population estimates. We used several sub-sampling scenarios to create subsets of the full datasets and compared summary statistics, population estimates, and precision of estimates generated from these subsets to estimates generated from the complete datasets. Our results suggested that bias and precision of estimates improved as the proportion of total samples used increased, and heterogeneity models (e.g., Mh[CHAO]) were more robust to reduced sample sizes than other models (e.g., behavior models). We recommend that only high-quality samples (>5 hair follicles) be used when budgets are constrained, and efforts should be made to maximize capture and recapture rates in the field.

Occurence of internet addiction in a general population sample: a latent class analysis.

PubMed

Rumpf, Hans-Jürgen; Vermulst, Ad A; Bischof, Anja; Kastirke, Nadin; Gürtler, Diana; Bischof, Gallus; Meerkerk, Gert-Jan; John, Ulrich; Meyer, Christian

2014-01-01

Prevalence studies of Internet addiction in the general population are rare. In addition, a lack of approved criteria hampers estimation of its occurrence. This study conducted a latent class analysis (LCA) in a large general population sample to estimate prevalence. A telephone survey was conducted based on a random digit dialling procedure including landline telephone (n=14,022) and cell phone numbers (n=1,001) in participants aged 14-64. The Compulsive Internet Use Scale (CIUS) served as the basis for a LCA used to look for subgroups representing participants with Internet addiction or at-risk use. CIUS was given to participants reporting to use the Internet for private purposes at least 1 h on a typical weekday or at least 1 h on a day at the weekend (n=8,130). A 6-class model showed best model fit and included two groups likely to represent Internet addiction and at-risk Internet use. Both groups showed less social participation and the Internet addiction group less general trust in other people. Proportions of probable Internet addiction were 1.0% (CI 0.9-1.2) among the entire sample, 2.4% (CI 1.9-3.1) in the age group 14-24, and 4.0% (CI 2.7-5.7) in the age group 14-16. No difference in estimated proportions between males and females was found. Unemployment (OR 3.13; CI 1.74-5.65) and migration background (OR 3.04; CI 2.12-4.36) were related to Internet addiction. This LCA-based study differentiated groups likely to have Internet addiction and at-risk use in the general population and provides characteristics to further define this rather new disorder. © 2013 S. Karger AG, Basel.

Scalable population estimates using spatial-stream-network (SSN) models, fish density surveys, and national geospatial database frameworks for streams

Treesearch

Daniel J. Isaak; Jay M. Ver Hoef; Erin E. Peterson; Dona L. Horan; David E. Nagel

2017-01-01

Population size estimates for stream fishes are important for conservation and management, but sampling costs limit the extent of most estimates to small portions of river networks that encompass 100s–10 000s of linear kilometres. However, the advent of large fish density data sets, spatial-stream-network (SSN) models that benefit from nonindependence among samples,...

Hierarchial mark-recapture models: a framework for inference about demographic processes

USGS Publications Warehouse

Link, W.A.; Barker, R.J.

2004-01-01

The development of sophisticated mark-recapture models over the last four decades has provided fundamental tools for the study of wildlife populations, allowing reliable inference about population sizes and demographic rates based on clearly formulated models for the sampling processes. Mark-recapture models are now routinely described by large numbers of parameters. These large models provide the next challenge to wildlife modelers: the extraction of signal from noise in large collections of parameters. Pattern among parameters can be described by strong, deterministic relations (as in ultrastructural models) but is more flexibly and credibly modeled using weaker, stochastic relations. Trend in survival rates is not likely to be manifest by a sequence of values falling precisely on a given parametric curve; rather, if we could somehow know the true values, we might anticipate a regression relation between parameters and explanatory variables, in which true value equals signal plus noise. Hierarchical models provide a useful framework for inference about collections of related parameters. Instead of regarding parameters as fixed but unknown quantities, we regard them as realizations of stochastic processes governed by hyperparameters. Inference about demographic processes is based on investigation of these hyperparameters. We advocate the Bayesian paradigm as a natural, mathematically and scientifically sound basis for inference about hierarchical models. We describe analysis of capture-recapture data from an open population based on hierarchical extensions of the Cormack-Jolly-Seber model. In addition to recaptures of marked animals, we model first captures of animals and losses on capture, and are thus able to estimate survival probabilities w (i.e., the complement of death or permanent emigration) and per capita growth rates f (i.e., the sum of recruitment and immigration rates). Covariation in these rates, a feature of demographic interest, is explicitly described in the model.

Computer re-sampling for demographically representative user populations in anthropometry: a case of doorway and clear floor space widths.

PubMed

Paquet, Victor; Joseph, Caroline; D'Souza, Clive

2012-01-01

Anthropometric studies typically require a large number of individuals that are selected in a manner so that demographic characteristics that impact body size and function are proportionally representative of a user population. This sampling approach does not allow for an efficient characterization of the distribution of body sizes and functions of sub-groups within a population and the demographic characteristics of user populations can often change with time, limiting the application of the anthropometric data in design. The objective of this study is to demonstrate how demographically representative user populations can be developed from samples that are not proportionally representative in order to improve the application of anthropometric data in design. An engineering anthropometry problem of door width and clear floor space width is used to illustrate the value of the approach.

Stigma, Mental Health, and Resilience in an Online Sample of the US Transgender Population

PubMed Central

Miner, Michael H.; Swinburne Romine, Rebecca E.; Hamilton, Autumn; Coleman, Eli

2013-01-01

Objectives. We assessed the association between minority stress, mental health, and potential ameliorating factors in a large, community-based, geographically diverse sample of the US transgender population. Methods. In 2003, we recruited through the Internet a sample of 1093 male-to-female and female-to-male transgender persons, stratified by gender. Participants completed an online survey that included standardized measures of mental health. Guided by the minority stress model, we evaluated associations between stigma and mental health and tested whether indicators of resilience (family support, peer support, identity pride) moderated these associations. Results. Respondents had a high prevalence of clinical depression (44.1%), anxiety (33.2%), and somatization (27.5%). Social stigma was positively associated with psychological distress. Peer support (from other transgender people) moderated this relationship. We found few differences by gender identity. Conclusions. Our findings support the minority stress model. Prevention needs to confront social structures, norms, and attitudes that produce minority stress for gender-variant people; enhance peer support; and improve access to mental health and social services that affirm transgender identity and promote resilience. PMID:23488522

On the Simultaneous Identification and Quantification of Microalgae Populations Based on Fluorometric Techniques.

PubMed

Gsponer, Natalia S; Rodríguez, María Claudia; Palacios, Rodrigo E; Chesta, Carlos A

2018-05-16

In this study, the phytoplankton structure of a freshwater reservoir located in central Argentina (Embalse Río Tercero) was analyzed using Beutler's method (Photosynthesis Research 72: 39-53, 2002), aiming to provide water quality control agencies with a reliable tool for early detection of algae blooms, particularly cyanobacteria. The method estimated the concentration of chlorophyll a (Chl a) contributed by individual algal groups in a real sample by fitting its fluorescence excitation spectrum to a linear combination of norm spectra of relevant algae groups. To this purpose, norm spectra for five algae genera usually found in Embalse Río Tercero, Microcystis, Chlorella, Cyclotella, Ceratium and Porphyridium, were constructed and posteriorly used to analyze samples collected in the reservoir in years 2014-2016. Results showed that the method worked well for the quick identification of the algae present in the samples, but it tended to overestimate its Chl a contents. This error was attributed to the large heterogeneity of the algal populations due to the aging of cells grown in environmental conditions. © 2018 The American Society of Photobiology.

Classifying sensory profiles of children in the general population.

PubMed

Little, L M; Dean, E; Tomchek, S D; Dunn, W

2017-01-01

The aim of this study was to subtype groups of children in a community sample with and without developmental conditions, based on sensory processing patterns. We used latent profile analysis to determine the number of sensory subtypes in a sample of n = 1132 children aged 3-14 years with typical development and developmental conditions, including autism spectrum disorder (ASD), attention-deficit hyperactivity disorder and learning disabilities. A five-subtype solution was found to best characterize the sample, which differed on overall degree and differential presentation of sensory processing patterns. Children with and without developmental conditions presented across subtypes, and one subtype was significantly younger in age than others (P < 0.05). Our results show that sensory subtypes include both children with typical development and those with developmental conditions. Sensory subtypes have previously been investigated in ASD only, and our results suggest that similar sensory subtypes are present in a sample reflective of the general population of children including those largely with typical development. Elevated scores on sensory processing patterns are not unique to ASD but rather are reflections of children's abilities to respond to environmental demands. © 2016 John Wiley & Sons Ltd.

A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa

PubMed Central

Petegrosso, Raphael; Tolar, Jakub

2018-01-01

Single-cell RNA sequencing (scRNA-seq) has been widely applied to discover new cell types by detecting sub-populations in a heterogeneous group of cells. Since scRNA-seq experiments have lower read coverage/tag counts and introduce more technical biases compared to bulk RNA-seq experiments, the limited number of sampled cells combined with the experimental biases and other dataset specific variations presents a challenge to cross-dataset analysis and discovery of relevant biological variations across multiple cell populations. In this paper, we introduce a method of variance-driven multitask clustering of single-cell RNA-seq data (scVDMC) that utilizes multiple single-cell populations from biological replicates or different samples. scVDMC clusters single cells in multiple scRNA-seq experiments of similar cell types and markers but varying expression patterns such that the scRNA-seq data are better integrated than typical pooled analyses which only increase the sample size. By controlling the variance among the cell clusters within each dataset and across all the datasets, scVDMC detects cell sub-populations in each individual experiment with shared cell-type markers but varying cluster centers among all the experiments. Applied to two real scRNA-seq datasets with several replicates and one large-scale droplet-based dataset on three patient samples, scVDMC more accurately detected cell populations and known cell markers than pooled clustering and other recently proposed scRNA-seq clustering methods. In the case study applied to in-house Recessive Dystrophic Epidermolysis Bullosa (RDEB) scRNA-seq data, scVDMC revealed several new cell types and unknown markers validated by flow cytometry. MATLAB/Octave code available at https://github.com/kuanglab/scVDMC. PMID:29630593

An automated, high-throughput plant phenotyping system using machine learning-based plant segmentation and image analysis.

PubMed

Lee, Unseok; Chang, Sungyul; Putra, Gian Anantrio; Kim, Hyoungseok; Kim, Dong Hwan

2018-01-01

A high-throughput plant phenotyping system automatically observes and grows many plant samples. Many plant sample images are acquired by the system to determine the characteristics of the plants (populations). Stable image acquisition and processing is very important to accurately determine the characteristics. However, hardware for acquiring plant images rapidly and stably, while minimizing plant stress, is lacking. Moreover, most software cannot adequately handle large-scale plant imaging. To address these problems, we developed a new, automated, high-throughput plant phenotyping system using simple and robust hardware, and an automated plant-imaging-analysis pipeline consisting of machine-learning-based plant segmentation. Our hardware acquires images reliably and quickly and minimizes plant stress. Furthermore, the images are processed automatically. In particular, large-scale plant-image datasets can be segmented precisely using a classifier developed using a superpixel-based machine-learning algorithm (Random Forest), and variations in plant parameters (such as area) over time can be assessed using the segmented images. We performed comparative evaluations to identify an appropriate learning algorithm for our proposed system, and tested three robust learning algorithms. We developed not only an automatic analysis pipeline but also a convenient means of plant-growth analysis that provides a learning data interface and visualization of plant growth trends. Thus, our system allows end-users such as plant biologists to analyze plant growth via large-scale plant image data easily.

Influence of population versus convenience sampling on sample characteristics in studies of cognitive aging.

PubMed

Brodaty, Henry; Mothakunnel, Annu; de Vel-Palumbo, Melissa; Ames, David; Ellis, Kathryn A; Reppermund, Simone; Kochan, Nicole A; Savage, Greg; Trollor, Julian N; Crawford, John; Sachdev, Perminder S

2014-01-01

We examined whether differences in findings of studies examining mild cognitive impairment (MCI) were associated with recruitment methods by comparing sample characteristics in two contemporaneous Australian studies, using population-based and convenience sampling. The Sydney Memory and Aging Study invited participants randomly from the electoral roll in defined geographic areas in Sydney. The Australian Imaging, Biomarkers and Lifestyle Study of Ageing recruited cognitively normal (CN) individuals via media appeals and MCI participants via referrals from clinicians in Melbourne and Perth. Demographic and cognitive variables were harmonized, and similar diagnostic criteria were applied to both samples retrospectively. CN participants recruited via convenience sampling were younger, better educated, more likely to be married and have a family history of dementia, and performed better cognitively than those recruited via population-based sampling. MCI participants recruited via population-based sampling had better memory performance and were less likely to carry the apolipoprotein E ε4 allele than clinically referred participants but did not differ on other demographic variables. A convenience sample of normal controls is likely to be younger and better functioning and that of an MCI group likely to perform worse than a purportedly random sample. Sampling bias should be considered when interpreting findings. Copyright © 2014 Elsevier Inc. All rights reserved.

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

PubMed

Ramos, Enrique; Levinson, Benjamin T; Chasnoff, Sara; Hughes, Andrew; Young, Andrew L; Thornton, Katherine; Li, Allie; Vallania, Francesco L M; Province, Michael; Druley, Todd E

2012-12-06

Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regions and comparing against unaffected cohorts. However, despite persistent declines in sequencing costs, population-based rare variant detection across large genomic target regions remains cost prohibitive for most investigators. In addition, DNA samples are often precious and hybridization methods typically require large amounts of input DNA. Pooled sample DNA sequencing is a cost and time-efficient strategy for surveying populations of individuals for rare variants. We set out to 1) create a scalable, multiplexing method for custom capture with or without individual DNA indexing that was amenable to low amounts of input DNA and 2) expand the functionality of the SPLINTER algorithm for calling substitutions, insertions and deletions across either candidate genes or the entire exome by integrating the variant calling algorithm with the dynamic programming aligner, Novoalign. We report methodology for pooled hybridization capture with pre-enrichment, indexed multiplexing of up to 48 individuals or non-indexed pooled sequencing of up to 92 individuals with as little as 70 ng of DNA per person. Modified solid phase reversible immobilization bead purification strategies enable no sample transfers from sonication in 96-well plates through adapter ligation, resulting in 50% less library preparation reagent consumption. Custom Y-shaped adapters containing novel 7 base pair index sequences with a Hamming distance of ≥2 were directly ligated onto fragmented source DNA eliminating the need for PCR to incorporate indexes, and was followed by a custom blocking strategy using a single oligonucleotide regardless of index sequence. These results were obtained aligning raw reads against the entire genome using Novoalign followed by variant calling of non-indexed pools using SPLINTER or SAMtools for indexed samples. With these pipelines, we find sensitivity and specificity of 99.4% and 99.7% for pooled exome sequencing. Sensitivity, and to a lesser degree specificity, proved to be a function of coverage. For rare variants (≤2% minor allele frequency), we achieved sensitivity and specificity of ≥94.9% and ≥99.99% for custom capture of 2.5 Mb in multiplexed libraries of 22-48 individuals with only ≥5-fold coverage/chromosome, but these parameters improved to ≥98.7 and 100% with 20-fold coverage/chromosome. This highly scalable methodology enables accurate rare variant detection, with or without individual DNA sample indexing, while reducing the amount of required source DNA and total costs through less hybridization reagent consumption, multi-sample sonication in a standard PCR plate, multiplexed pre-enrichment pooling with a single hybridization and lesser sequencing coverage required to obtain high sensitivity.

Safe Schools? Transgender Youth's School Experiences and Perceptions of School Climate.

PubMed

Day, Jack K; Perez-Brumer, Amaya; Russell, Stephen T

2018-06-01

The magnitude of gender identity-related disparities in school-based outcomes is unknown because of a lack of representative studies that include measures of gender identity. By utilizing a representative sample generalizable to a broader population, this study elucidates the size of gender identity-related disparities, independent of sexual orientation, in school experiences associated with school connectedness and perceptions of school climate. Additionally, the inclusion of and comparison to results of a large non-representative sample allows for more direct comparisons to previous studies of the school experiences of transgender youth. The analyses in this study primarily draw on a sample of 31,896 youth representative of the middle and high school population in California who participated in the 2013-2015 California Student Survey (a subsample of the California Healthy Kids Survey, which includes the largest known sample of transgender youth). Over half the sample identified their sex as female (51.3%), and 398 identified as transgender (1.0%). The sample was racially and ethnically diverse: 30.7% identified as multiracial, 33.0% as White, 11.1% as Asian, 7.4% as Black, and 52.9% as Hispanic. Findings from multilevel analyses show that relative to non-transgender youth, transgender youth were more likely to be truant from school, to experience victimization and bias-based bullying, and to report more negative perceptions of school climate, though did not differ in self-reported grades. The findings have implications for improving school policies and practices to create safer and more supportive school climates for all youth.

Self-fertilization, long-distance flash invasion and biogeography shape the population structure of Pseudosuccinea columella at the worldwide scale.

PubMed

Lounnas, M; Correa, A C; Vázquez, A A; Dia, A; Escobar, J S; Nicot, A; Arenas, J; Ayaqui, R; Dubois, M P; Gimenez, T; Gutiérrez, A; González-Ramírez, C; Noya, O; Prepelitchi, L; Uribe, N; Wisnivesky-Colli, C; Yong, M; David, P; Loker, E S; Jarne, P; Pointier, J P; Hurtrez-Boussès, S

2017-02-01

Population genetic studies are efficient for inferring the invasion history based on a comparison of native and invasive populations, especially when conducted at species scale. An expected outcome in invasive populations is variability loss, and this is especially true in self-fertilizing species. We here focus on the self-fertilizing Pseudosuccinea columella, an invasive hermaphroditic freshwater snail that has greatly expanded its geographic distribution and that acts as intermediate host of Fasciola hepatica, the causative agent of human and veterinary fasciolosis. We evaluated the distribution of genetic diversity at the largest geographic scale analysed to date in this species by surveying 80 populations collected during 16 years from 14 countries, using eight nuclear microsatellites and two mitochondrial genes. As expected, populations from North America, the putative origin area, were strongly structured by selfing and history and harboured much more genetic variability than invasive populations. We found high selfing rates (when it was possible to infer it), none-to-low genetic variability and strong population structure in most invasive populations. Strikingly, we found a unique genotype/haplotype in populations from eight invaded regions sampled all over the world. Moreover, snail populations resistant to infection by the parasite are genetically distinct from susceptible populations. Our results are compatible with repeated introductions in South America and flash worldwide invasion by this unique genotype/haplotype. Our study illustrates the population genetic consequences of biological invasion in a highly selfing species at very large geographic scale. We discuss how such a large-scale flash invasion may affect the spread of fasciolosis. © 2016 John Wiley & Sons Ltd.

Landbird trends in national parks of the North Coast and Cascades Network, 2005-12

USGS Publications Warehouse

Saracco, James F.; Holmgren, Amanda L.; Wilkerson, Robert L.; Siegel, Rodney B.; Kuntz, Robert C.; Jenkins, Kurt J.; Happe, Patricia J.; Boetsch, John R.; Huff, Mark H.

2014-01-01

National parks in the North Coast and Cascades Network (NCCN) can fulfill vital roles as refuges for bird species dependent on late-successional forest conditions and as reference sites for assessing the effects of land-use and land-cover changes on bird populations throughout the larger Pacific Northwest region. Additionally, long-term monitoring of landbirds throughout the NCCN provides information that can inform decisions about important management issues in the parks, including visitor impacts, fire management, and the effects of introduced species. In 2005, the NCCN began implementing a network-wide Landbird Monitoring Project as part of the NPS Inventory and Monitoring Program. In this report, we discuss 8-year trends (2005–12) of bird populations in the NCCN, based on a sampling framework of point counts established in three large wilderness parks (Mount Rainier, North Cascades, and Olympic National Parks), 7-year trends at Lewis and Clark National Historical Park (sampled in 2006, 2008, 2010, and 2012), and 5-year trends at San Juan Islands National Historical Park (sampled in 2007, 2009, and 2011). Our analysis encompasses a fairly short time span for this long-term monitoring program. The first 2 years of the time series (2005 and 2006) were implemented as part of a limited pilot study that included only a small subset of the transects. The subsequent 6 years (2007–12) represent just a single cycle through 5 years of alternating panels of transects in the large parks, with the first of five alternating panels revisited for the first time in 2012. Of 204 transects that comprise the six sampling panels in the large parks, only 68 (one-third) have thus been eligible for revisit surveys (34 during every year after 2005, and an additional 34 only in 2012) and can contribute to our current trend estimates. We therefore initiated the current analysis with a primary goal of testing our analytical procedures rather than detecting trends that might be strong enough to drive conservation or management decisions in the parks or elsewhere. We expect that aggregated trend detection results may change substantially over the next several years, as the number of transects with revisit histories triples and the spatial dispersion of transects contributing to trend estimates also improves greatly. In the meantime, caution should be exercised in interpreting the importance of trends, as individual years can have very large influences on the direction and magnitude of trends in a time series of such limited duration (and limited numbers of repeat visits at the small parks). Nevertheless, we estimated trends for 43 species at Mount Rainier National Park, 53 species at North Cascades National Park Complex, and 41 species at Olympic National Park. Of 137 park-species combinations (including combined-park analyses), we found 16 significant decreases (12 percent) and five significant increases (4 percent). We identify several limitations of the current analytical framework for trend assessment but suggest that the overall sampling design is strong and amenable to analysis by more recently developed model-based methods. These could provide a more flexible framework for examining trends and other population parameters of interest, as well as testing hypotheses that relate the distribution and abundance of species to environmental covariates. A model-based approach would allow for modeling various components of the detection process and analyzing observations (detection process), population state (occupancy, population size, density), and change (trend, local extinction and colonization rates turnover) simultaneously. Finally, we also evaluate operational aspects of NCCN Landbird Monitoring Project, and conclude that our robust, multi-party partnership is successfully implementing the project as it was envisioned.

Structure and evolution of cereal genomes.

PubMed

Paterson, Andrew H; Bowers, John E; Peterson, Daniel G; Estill, James C; Chapman, Brad A

2003-12-01

The cereal species, of central importance to our diet, began to diverge 50-70 million years ago. For the past few thousand years, these species have undergone largely parallel selection regimes associated with domestication and improvement. The rice genome sequence provides a platform for organizing information about diverse cereals, and together with genetic maps and sequence samples from other cereals is yielding new insights into both the shared and the independent dimensions of cereal evolution. New data and population-based approaches are identifying genes that have been involved in cereal improvement. Reduced-representation sequencing promises to accelerate gene discovery in many large-genome cereals, and to better link the under-explored genomes of 'orphan' cereals with state-of-the-art knowledge.

Population dynamics of the Concho water snake in rivers and reservoirs

USGS Publications Warehouse

Whiting, M.J.; Dixon, J.R.; Greene, B.D.; Mueller, J.M.; Thornton, O.W.; Hatfield, J.S.; Nichols, J.D.; Hines, J.E.

2008-01-01

The Concho Water Snake (Nerodia harteri paucimaculata) is confined to the Concho–Colorado River valley of central Texas, thereby occupying one of the smallest geographic ranges of any North American snake. In 1986, N. h. paucimaculata was designated as a federally threatened species, in large part because of reservoir projects that were perceived to adversely affect the amount of habitat available to the snake. During a ten-year period (1987–1996), we conducted capture–recapture field studies to assess dynamics of five subpopulations of snakes in both natural (river) and man-made (reservoir) habitats. Because of differential sampling of subpopulations, we present separate results for all five subpopulations combined (including large reservoirs) and three of the five subpopulations (excluding large reservoirs). We used multistate capture–recapture models to deal with stochastic transitions between pre-reproductive and reproductive size classes and to allow for the possibility of different survival and capture probabilities for the two classes. We also estimated both the finite rate of increase (λ) for a deterministic, stage-based, female-only matrix model using the average litter size, and the average rate of adult population change, λ ˆ, which describes changes in numbers of adult snakes, using a direct capture–recapture approach to estimation. Average annual adult survival was about 0.23 and similar for males and females. Average annual survival for subadults was about 0.14. The parameter estimates from the stage-based projection matrix analysis all yielded asymptotic values of λ < 1, suggesting populations that are not viable. However, the direct estimates of average adult λ for the three subpopulations excluding major reservoirs were λ ˆ  =  1.26, SE ˆ(λ ˆ)  =  0.18 and λ ˆ  =  0.99, SE ˆ(λ ˆ)  =  0.79, based on two different models. Thus, the direct estimation approach did not provide strong evidence of population declines of the riverine subpopulations, but the estimates are characterized by substantial uncertainty.

Population-based multicase-control study in common tumors in Spain (MCC-Spain): rationale and study design.

PubMed

Castaño-Vinyals, Gemma; Aragonés, Nuria; Pérez-Gómez, Beatriz; Martín, Vicente; Llorca, Javier; Moreno, Victor; Altzibar, Jone M; Ardanaz, Eva; de Sanjosé, Sílvia; Jiménez-Moleón, José Juan; Tardón, Adonina; Alguacil, Juan; Peiró, Rosana; Marcos-Gragera, Rafael; Navarro, Carmen; Pollán, Marina; Kogevinas, Manolis

2015-01-01

We present the protocol of a large population-based case-control study of 5 common tumors in Spain (MCC-Spain) that evaluates environmental exposures and genetic factors. Between 2008-2013, 10,183 persons aged 20-85 years were enrolled in 23 hospitals and primary care centres in 12 Spanish provinces including 1,115 cases of a new diagnosis of prostate cancer, 1,750 of breast cancer, 2,171 of colorectal cancer, 492 of gastro-oesophageal cancer, 554 cases of chronic lymphocytic leukaemia (CLL) and 4,101 population-based controls matched by frequency to cases by age, sex and region of residence. Participation rates ranged from 57% (stomach cancer) to 87% (CLL cases) and from 30% to 77% in controls. Participants completed a face-to-face computerized interview on sociodemographic factors, environmental exposures, occupation, medication, lifestyle, and personal and family medical history. In addition, participants completed a self-administered food-frequency questionnaire and telephone interviews. Blood samples were collected from 76% of participants while saliva samples were collected in CLL cases and participants refusing blood extractions. Clinical information was recorded for cases and paraffin blocks and/or fresh tumor samples are available in most collaborating hospitals. Genotyping was done through an exome array enriched with genetic markers in specific pathways. Multiple analyses are planned to assess the association of environmental, personal and genetic risk factors for each tumor and to identify pleiotropic effects. This study, conducted within the Spanish Consortium for Biomedical Research in Epidemiology & Public Health (CIBERESP), is a unique initiative to evaluate etiological factors for common cancers and will promote cancer research and prevention in Spain. Copyright © 2014 SESPAS. Published by Elsevier Espana. All rights reserved.

Genome-wide SNP analysis reveals a genetic basis for sea-age variation in a wild population of Atlantic salmon (Salmo salar).

PubMed

Johnston, Susan E; Orell, Panu; Pritchard, Victoria L; Kent, Matthew P; Lien, Sigbjørn; Niemelä, Eero; Erkinaro, Jaakko; Primmer, Craig R

2014-07-01

Delaying sexual maturation can lead to larger body size and higher reproductive success, but carries an increased risk of death before reproducing. Classical life history theory predicts that trade-offs between reproductive success and survival should lead to the evolution of an optimal strategy in a given population. However, variation in mating strategies generally persists, and in general, there remains a poor understanding of genetic and physiological mechanisms underlying this variation. One extreme case of this is in the Atlantic salmon (Salmo salar), which can show variation in the age at which they return from their marine migration to spawn (i.e. their 'sea age'). This results in large size differences between strategies, with direct implications for individual fitness. Here, we used an Illumina Infinium SNP array to identify regions of the genome associated with variation in sea age in a large population of Atlantic salmon in Northern Europe, implementing individual-based genome-wide association studies (GWAS) and population-based FST outlier analyses. We identified several regions of the genome which vary in association with phenotype and/or selection between sea ages, with nearby genes having functions related to muscle development, metabolism, immune response and mate choice. In addition, we found that individuals of different sea ages belong to different, yet sympatric populations in this system, indicating that reproductive isolation may be driven by divergence between stable strategies. Overall, this study demonstrates how genome-wide methodologies can be integrated with samples collected from wild, structured populations to understand their ecology and evolution in a natural context. © 2014 John Wiley & Sons Ltd.

[The research protocol III. Study population].

PubMed

Arias-Gómez, Jesús; Villasís-Keever, Miguel Ángel; Miranda-Novales, María Guadalupe

2016-01-01

The study population is defined as a set of cases, determined, limited, and accessible, that will constitute the subjects for the selection of the sample, and must fulfill several characteristics and distinct criteria. The objectives of this manuscript are focused on specifying each one of the elements required to make the selection of the participants of a research project, during the elaboration of the protocol, including the concepts of study population, sample, selection criteria and sampling methods. After delineating the study population, the researcher must specify the criteria that each participant has to comply. The criteria that include the specific characteristics are denominated selection or eligibility criteria. These criteria are inclusion, exclusion and elimination, and will delineate the eligible population. The sampling methods are divided in two large groups: 1) probabilistic or random sampling and 2) non-probabilistic sampling. The difference lies in the employment of statistical methods to select the subjects. In every research, it is necessary to establish at the beginning the specific number of participants to be included to achieve the objectives of the study. This number is the sample size, and can be calculated or estimated with mathematical formulas and statistic software.

Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring

PubMed Central

Miller, Carolyn A.; Moore, Michael J.; Durban, John W.; Fearnbach, Holly; Barrett-Lennard, Lance G.

2017-01-01

ABSTRACT The pulmonary system is a common site for bacterial infections in cetaceans, but very little is known about their respiratory microbiome. We used a small, unmanned hexacopter to collect exhaled breath condensate (blow) from two geographically distinct populations of apparently healthy humpback whales (Megaptera novaeangliae), sampled in the Massachusetts coastal waters off Cape Cod (n = 17) and coastal waters around Vancouver Island (n = 9). Bacterial and archaeal small-subunit rRNA genes were amplified and sequenced from blow samples, including many of sparse volume, as well as seawater and other controls, to characterize the associated microbial community. The blow microbiomes were distinct from the seawater microbiomes and included 25 phylogenetically diverse bacteria common to all sampled whales. This core assemblage comprised on average 36% of the microbiome, making it one of the more consistent animal microbiomes studied to date. The closest phylogenetic relatives of 20 of these core microbes were previously detected in marine mammals, suggesting that this core microbiome assemblage is specialized for marine mammals and may indicate a healthy, noninfected pulmonary system. Pathogen screening was conducted on the microbiomes at the genus level, which showed that all blow and few seawater microbiomes contained relatives of bacterial pathogens; no known cetacean respiratory pathogens were detected in the blow. Overall, the discovery of a shared large core microbiome in humpback whales is an important advancement for health and disease monitoring of this species and of other large whales. IMPORTANCE The conservation and management of large whales rely in part upon health monitoring of individuals and populations, and methods generally necessitate invasive sampling. Here, we used a small, unmanned hexacopter drone to noninvasively fly above humpback whales from two populations, capture their exhaled breath (blow), and examine the associated microbiome. In the first extensive examination of the large-whale blow microbiome, we present surprising results about the discovery of a large core microbiome that was shared across individual whales from geographically separated populations in two ocean basins. We suggest that this core microbiome, in addition to other microbiome characteristics, could be a useful feature for health monitoring of large whales worldwide. PMID:29034331

Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring.

PubMed

Apprill, Amy; Miller, Carolyn A; Moore, Michael J; Durban, John W; Fearnbach, Holly; Barrett-Lennard, Lance G

2017-01-01

The pulmonary system is a common site for bacterial infections in cetaceans, but very little is known about their respiratory microbiome. We used a small, unmanned hexacopter to collect exhaled breath condensate (blow) from two geographically distinct populations of apparently healthy humpback whales ( Megaptera novaeangliae ), sampled in the Massachusetts coastal waters off Cape Cod ( n = 17) and coastal waters around Vancouver Island ( n = 9). Bacterial and archaeal small-subunit rRNA genes were amplified and sequenced from blow samples, including many of sparse volume, as well as seawater and other controls, to characterize the associated microbial community. The blow microbiomes were distinct from the seawater microbiomes and included 25 phylogenetically diverse bacteria common to all sampled whales. This core assemblage comprised on average 36% of the microbiome, making it one of the more consistent animal microbiomes studied to date. The closest phylogenetic relatives of 20 of these core microbes were previously detected in marine mammals, suggesting that this core microbiome assemblage is specialized for marine mammals and may indicate a healthy, noninfected pulmonary system. Pathogen screening was conducted on the microbiomes at the genus level, which showed that all blow and few seawater microbiomes contained relatives of bacterial pathogens; no known cetacean respiratory pathogens were detected in the blow. Overall, the discovery of a shared large core microbiome in humpback whales is an important advancement for health and disease monitoring of this species and of other large whales. IMPORTANCE The conservation and management of large whales rely in part upon health monitoring of individuals and populations, and methods generally necessitate invasive sampling. Here, we used a small, unmanned hexacopter drone to noninvasively fly above humpback whales from two populations, capture their exhaled breath (blow), and examine the associated microbiome. In the first extensive examination of the large-whale blow microbiome, we present surprising results about the discovery of a large core microbiome that was shared across individual whales from geographically separated populations in two ocean basins. We suggest that this core microbiome, in addition to other microbiome characteristics, could be a useful feature for health monitoring of large whales worldwide.

Salivary Cortisol Protocol Adherence and Reliability by Sociodemographic Features: the Multi-Ethnic Study of Atherosclerosis

PubMed Central

Golden, Sherita Hill; Sánchez, Brisa N.; DeSantis, Amy S.; Wu, Meihua; Castro, Cecilia; Seeman, Teresa E.; Tadros, Sameh; Shrager, Sandi; Diez Roux, Ana V.

2014-01-01

Collection of salivary cortisol has become increasingly popular in large population-based studies. However, the impact of protocol compliance on day-to-day reliabilities of measures, and the extent to which reliabilities differ systematically according to socio-demographic characteristics, has not been well characterized in large-scale population-based studies to date. Using data on 935 men and women from the Multi-ethnic Study of Atherosclerosis, we investigated whether sampling protocol compliance differs systematically according to socio-demographic factors and whether compliance was associated with cortisol estimates, as well as whether associations of cortisol with both compliance and socio-demographic characteristics were robust to adjustments for one another. We further assessed the day-to-day reliability for cortisol features and the extent to which reliabilities vary according to socio-demographic factors and sampling protocol compliance. Overall, we found higher compliance among persons with higher levels of income and education. Lower compliance was significantly associated with a less pronounced cortisol awakening response (CAR) but was not associated with any other cortisol features, and adjustment for compliance did not affect associations of socio-demographic characteristics with cortisol. Reliability was higher for area under the curve (AUC) and wake up values than for other features, but generally did not vary according to socio-demographic characteristics, with few exceptions. Our findings regarding intra-class correlation coefficients (ICCs) support prior research indicating that multiple day collection is preferable to single day collection, particularly for CAR and slopes, more so than wakeup and AUC. There were few differences in reliability by socio-demographic characteristics. Thus, it is unlikely that group-specific sampling protocols are warranted. PMID:24703168

Reducing Individual Variation for fMRI Studies in Children by Minimizing Template Related Errors

PubMed Central

Weng, Jian; Dong, Shanshan; He, Hongjian; Chen, Feiyan; Peng, Xiaogang

2015-01-01

Spatial normalization is an essential process for group comparisons in functional MRI studies. In practice, there is a risk of normalization errors particularly in studies involving children, seniors or diseased populations and in regions with high individual variation. One way to minimize normalization errors is to create a study-specific template based on a large sample size. However, studies with a large sample size are not always feasible, particularly for children studies. The performance of templates with a small sample size has not been evaluated in fMRI studies in children. In the current study, this issue was encountered in a working memory task with 29 children in two groups. We compared the performance of different templates: a study-specific template created by the experimental population, a Chinese children template and the widely used adult MNI template. We observed distinct differences in the right orbitofrontal region among the three templates in between-group comparisons. The study-specific template and the Chinese children template were more sensitive for the detection of between-group differences in the orbitofrontal cortex than the MNI template. Proper templates could effectively reduce individual variation. Further analysis revealed a correlation between the BOLD contrast size and the norm index of the affine transformation matrix, i.e., the SFN, which characterizes the difference between a template and a native image and differs significantly across subjects. Thereby, we proposed and tested another method to reduce individual variation that included the SFN as a covariate in group-wise statistics. This correction exhibits outstanding performance in enhancing detection power in group-level tests. A training effect of abacus-based mental calculation was also demonstrated, with significantly elevated activation in the right orbitofrontal region that correlated with behavioral response time across subjects in the trained group. PMID:26207985

The Point-of-Care Laboratory in Clinical Microbiology

PubMed Central

Michel-Lepage, Audrey; Boyer, Sylvie; Raoult, Didier

2016-01-01

SUMMARY Point-of-care (POC) laboratories that deliver rapid diagnoses of infectious diseases were invented to balance the centralization of core laboratories. POC laboratories operate 24 h a day and 7 days a week to provide diagnoses within 2 h, largely based on immunochromatography and real-time PCR tests. In our experience, these tests are conveniently combined into syndrome-based kits that facilitate sampling, including self-sampling and test operations, as POC laboratories can be operated by trained operators who are not necessarily biologists. POC laboratories are a way of easily providing clinical microbiology testing for populations distant from laboratories in developing and developed countries and on ships. Modern Internet connections enable support from core laboratories. The cost-effectiveness of POC laboratories has been established for the rapid diagnosis of tuberculosis and sexually transmitted infections in both developed and developing countries. PMID:27029593

Characterization of Metabolically Active Bacterial Populations in Subseafloor Nankai Trough Sediments above, within, and below the Sulfate–Methane Transition Zone

PubMed Central

Mills, Heath J.; Reese, Brandi Kiel; Shepard, Alicia K.; Riedinger, Natascha; Dowd, Scot E.; Morono, Yuki; Inagaki, Fumio

2012-01-01

A remarkable number of microbial cells have been enumerated within subseafloor sediments, suggesting a biological impact on geochemical processes in the subseafloor habitat. However, the metabolically active fraction of these populations is largely uncharacterized. In this study, an RNA-based molecular approach was used to determine the diversity and community structure of metabolically active bacterial populations in the upper sedimentary formation of the Nankai Trough seismogenic zone. Samples used in this study were collected from the slope apron sediment overlying the accretionary prism at Site C0004 during the Integrated Ocean Drilling Program Expedition 316. The sediments represented microbial habitats above, within, and below the sulfate–methane transition zone (SMTZ), which was observed approximately 20 m below the seafloor (mbsf). Small subunit ribosomal RNA were extracted, quantified, amplified, and sequenced using high-throughput 454 pyrosequencing, indicating the occurrence of metabolically active bacterial populations to a depth of 57 mbsf. Transcript abundance and bacterial diversity decreased with increasing depth. The two communities below the SMTZ were similar at the phylum level, however only a 24% overlap was observed at the genus level. Active bacterial community composition was not confined to geochemically predicted redox stratification despite the deepest sample being more than 50 m below the oxic/anoxic interface. Genus-level classification suggested that the metabolically active subseafloor bacterial populations had similarities to previously cultured organisms. This allowed predictions of physiological potential, expanding understanding of the subseafloor microbial ecosystem. Unique community structures suggest very diverse active populations compared to previous DNA-based diversity estimates, providing more support for enhancing community characterizations using more advanced sequencing techniques. PMID:22485111

How to infer relative fitness from a sample of genomic sequences.

PubMed

Dayarian, Adel; Shraiman, Boris I

2014-07-01

Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from those expected under neutral evolution and described statistically by Kingman's coalescent. While differences in the statistical structure of genealogies have long been used as a test for the presence of selection, the full extent of the information that they contain has not been exploited. Here we demonstrate that the shape of the reconstructed genealogical tree for a moderately large number of random genomic samples taken from a fitness diverse, but otherwise unstructured, asexual population can be used to predict the relative fitness of individuals within the sample. To achieve this we define a heuristic algorithm, which we test in silico, using simulations of a Wright-Fisher model for a realistic range of mutation rates and selection strength. Our inferred fitness ranking is based on a linear discriminator that identifies rapidly coalescing lineages in the reconstructed tree. Inferred fitness ranking correlates strongly with actual fitness, with a genome in the top 10% ranked being in the top 20% fittest with false discovery rate of 0.1-0.3, depending on the mutation/selection parameters. The ranking also enables us to predict the genotypes that future populations inherit from the present one. While the inference accuracy increases monotonically with sample size, samples of 200 nearly saturate the performance. We propose that our approach can be used for inferring relative fitness of genomes obtained in single-cell sequencing of tumors and in monitoring viral outbreaks. Copyright © 2014 by the Genetics Society of America.

Job strain and blood pressure in employed men and women: a pooled analysis of four northern italian population samples.

PubMed

Cesana, Giancarlo; Sega, Roberto; Ferrario, Marco; Chiodini, Paolo; Corrao, Giovanni; Mancia, Giuseppe

2003-01-01

The extent to which psychosocial stress concurs to raise blood pressure is still uncertain. Here the association between job strain and office blood pressure in a pooled analysis of four population samples from northern Italy is assessed. Four surveys assessing prevalence of major coronary risk factors were performed in 1986, 1990, 1991, and 1993 in area "Brianza" (Milan), a World Health Organization-MONItoring cardiovascular disease (WHO-MONICA) Project collaborating center. Ten year age- and gender-stratified independent samples were randomly recruited from the 25- to 64-year-old residents. The methods used to assess coronary risk factors strictly adhered to the MONICA manual, were kept constant, and underwent internal and external quality controls. Job strain was investigated through the administration to employed participants of a questionnaire derived from the Karasek model, assessing job demand/control latitude. Analysis was restricted to 25- to 54-year-old participants, untreated for hypertension (1799 men and 1010 women). Among men, there was a 3 mm Hg increase of systolic blood pressure (p<.001) moving from low to high strain job categories. This difference was independent from age, education, body mass index, alcohol intake, smoking habits, leisure time physical activity, and survey. No relevant differences among job strain categories were found in women and for diastolic blood pressure in both gender groups. These results carried out on a large population-based sample confirm previous findings obtained adopting ambulatory blood pressure measurements in more restricted samples of population or patients. Further research is needed to clarify the relationship between perceived work stress and blood pressure in women.

Associations of childhood adversity and adulthood trauma with C-reactive protein: A cross-sectional population-based study.

PubMed

Lin, Joy E; Neylan, Thomas C; Epel, Elissa; O'Donovan, Aoife

2016-03-01

Mounting evidence highlights specific forms of psychological stress as risk factors for ill health. Particularly strong evidence indicates that childhood adversity and adulthood trauma exposure increase risk for physical and psychiatric disorders, and there is emerging evidence that inflammation may play a key role in these relationships. In a population-based sample from the Health and Retirement Study (n=11,198, mean age 69 ± 10), we examine whether childhood adversity, adulthood trauma, and the interaction between them are associated with elevated levels of the systemic inflammatory marker high sensitivity C-reactive protein (hsCRP). All models were adjusted for age, gender, race, education, and year of data collection, as well as other possible confounds in follow-up sensitivity analyses. In our sample, 67% of individuals had experienced at least one traumatic event during adulthood, and those with childhood adversity were almost three times as likely to have experienced trauma as an adult. Childhood adversities and adulthood traumas were independently associated with elevated levels of hsCRP (β=0.03, p=0.01 and β=0.05, p<0.001, respectively). Those who had experienced both types of stress had higher levels of hsCRP than those with adulthood trauma alone, Estimate=-0.06, 95% CI [-0.003, -0.12], p=0.04, but not compared to those with childhood adversity alone, Estimate=-0.06, 95% CI [0.03, -0.16], p=0.19. There was no interaction between childhood and adulthood trauma exposure. To our knowledge, this is the first study to examine adulthood trauma exposure and inflammation in a large population-based sample, and the first to explore the interaction of childhood adversity and adulthood trauma with inflammation. Our study demonstrates the prevalence of trauma-related inflammation in the general population and suggests that childhood adversity and adulthood trauma are independently associated with elevated inflammation. Copyright © 2015 Elsevier Inc. All rights reserved.

Associations of childhood adversity and adulthood trauma with C-reactive protein: a cross-sectional population-based study

PubMed Central

Lin, Joy E.; Neylan, Thomas C.; Epel, Elissa; O’Donovan, Aoife

2016-01-01

Mounting evidence highlights specific forms of psychological stress as risk factors for ill health. Particularly strong evidence indicates that childhood adversity and adulthood trauma exposure increase risk for physical and psychiatric disorders, and there is emerging evidence that inflammation may play a key role in these relationships. In a population-based sample from the Health and Retirement Study (n = 11,198, mean age 69 ± 10), we examine whether childhood adversity, adulthood trauma, and the interaction between them are associated with elevated levels of the systemic inflammatory marker high sensitivity C-reactive protein (hsCRP). All models were adjusted for age, gender, race, education, and year of data collection, as well as other possible confounds in follow-up sensitivity analyses. In our sample, 67% of individuals had experienced at least one traumatic event during adulthood, and those with childhood adversity were almost three times as likely to have experienced trauma as an adult. Childhood adversities and adulthood traumas were independently associated with elevated levels of hsCRP (β = 0.03, p = 0.01 and β = 0.05, p < 0.001, respectively). Those who had experienced both types of stress had higher levels of hsCRP than those with adulthood trauma alone, Estimate = −0.06, 95% CI [−0.003, −0.12], p = 0.04, but not compared to those with childhood adversity alone, Estimate = −0.06, 95% CI [0.03, −0.16], p = 0.19. There was no interaction between childhood and adulthood trauma exposure. To our knowledge, this is the first study to examine adulthood trauma exposure and inflammation in a large population-based sample, and the first to explore the interaction of childhood adversity and adulthood trauma with inflammation. Our study demonstrates the prevalence of trauma-related inflammation in the general population and suggests that childhood adversity and adulthood trauma are independently associated with elevated inflammation. PMID:26616398

Do Humans Really Prefer Semi-open Natural Landscapes? A Cross-Cultural Reappraisal

PubMed Central

Hägerhäll, Caroline M.; Ode Sang, Åsa; Englund, Jan-Eric; Ahlner, Felix; Rybka, Konrad; Huber, Juliette; Burenhult, Niclas

2018-01-01

There is an assumption in current landscape preference theory of universal consensus in human preferences for moderate to high openness in a natural landscape. This premise is largely based on empirical studies of urban Western populations. Here we examine for the first time landscape preference across a number of geographically, ecologically and culturally diverse indigenous populations. Included in the study were two urban Western samples of university students (from southern Sweden) and five non-Western, indigenous and primarily rural communities: Jahai (Malay Peninsula), Lokono (Suriname), Makalero (Timor), Makasae (Timor), and Wayuu (Colombia). Preference judgements were obtained using pairwise forced choice assessments of digital visualizations of a natural landscape varied systematically on three different levels of topography and vegetation density. The results show differences between the Western and non-Western samples, with interaction effects between topography and vegetation being present for the two Swedish student samples but not for the other five samples. The theoretical claim of human preferences for half-open landscapes was only significantly confirmed for the student sample comprising landscape architects. The five non Western indigenous groups all preferred the highest level of vegetation density. Results show there are internal similarities between the two Western samples on the one hand, and between the five non-Western samples on the other. To some extent this supports the idea of consensus in preference, not universally but within those categories respectively. PMID:29896141

Socioeconomic status and prevalence of self-reported diabetes among adults in Tehran: results from a large population-based cross-sectional study (Urban HEART-2).

PubMed

Asadi-Lari, M; Khosravi, A; Nedjat, S; Mansournia, M A; Majdzadeh, R; Mohammad, K; Vaez-Mahdavi, M R; Faghihzadeh, S; Haeri Mehrizi, A A; Cheraghian, B

2016-05-01

Diabetes mellitus is an important public health challenge worldwide. The prevalence of type 2 diabetes varies across countries. The aim of this study is to estimate the prevalence of type 2 diabetes and to determine related factors including socioeconomic factors in a large random sample of Tehran population in 2011. In this cross-sectional study, 91,814 individuals aged over 20 years were selected randomly based on a multistage, cluster sampling. All participants were interviewed by trained personnel using standard questionnaires. Prevalence and Townsend deprivation indexes were calculated. Principal component analysis (PCA) was used to construct wealth index. Logistic regression model was used in multivariate analysis. The estimated prevalence of self-reported diabetes was 4.98 % overall, 4.76 %in men and 5.19 % in women (P < 0.003). In multivariate analysis, age, marital status (married and divorced/widow) and BMI were positively associated with the prevalence of self-reported diabetes. Of the socioeconomic variables, educational level and wealth status were negatively and Townsend Index was positively associated with diabetes. Our study findings highlight low reported prevalence of diabetes among adults in Tehran. Subjects with low socioeconomic status (SES) had a higher prevalence of type 2 diabetes. Weight gain and obesity were the most important risk factors associated with type 2 diabetes. Wealth index and educational level were better socioeconomic indicators for presenting the inequality in diabetes prevalence in relation to Townsend deprivation index.

Mutation supply and the repeatability of selection for antibiotic resistance

NASA Astrophysics Data System (ADS)

van Dijk, Thomas; Hwang, Sungmin; Krug, Joachim; de Visser, J. Arjan G. M.; Zwart, Mark P.

2017-10-01

Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution, which is a necessary condition for predictability. We explored experimentally the effect of mutation supply and the strength of selective pressure on the repeatability of selection from standing genetic variation. Different sizes of mutant libraries of antibiotic resistance gene TEM-1 β-lactamase in Escherichia coli, generated by error-prone PCR, were subjected to different antibiotic concentrations. We determined whether populations went extinct or survived, and sequenced the TEM gene of the surviving populations. The distribution of mutations per allele in our mutant libraries followed a Poisson distribution. Extinction patterns could be explained by a simple stochastic model that assumed the sampling of beneficial mutations was key for survival. In most surviving populations, alleles containing at least one known large-effect beneficial mutation were present. These genotype data also support a model which only invokes sampling effects to describe the occurrence of alleles containing large-effect driver mutations. Hence, evolution is largely predictable given cursory knowledge of mutational fitness effects, the mutation rate and population size. There were no clear trends in the repeatability of selected mutants when we considered all mutations present. However, when only known large-effect mutations were considered, the outcome of selection is less repeatable for large libraries, in contrast to expectations. We show experimentally that alleles carrying multiple mutations selected from large libraries confer higher resistance levels relative to alleles with only a known large-effect mutation, suggesting that the scarcity of high-resistance alleles carrying multiple mutations may contribute to the decrease in repeatability at large library sizes.

The Large-scale Structure of the Halo of the Andromeda Galaxy. I. Global Stellar Density, Morphology and Metallicity Properties

NASA Astrophysics Data System (ADS)

Ibata, Rodrigo A.; Lewis, Geraint F.; McConnachie, Alan W.; Martin, Nicolas F.; Irwin, Michael J.; Ferguson, Annette M. N.; Babul, Arif; Bernard, Edouard J.; Chapman, Scott C.; Collins, Michelle; Fardal, Mark; Mackey, A. D.; Navarro, Julio; Peñarrubia, Jorge; Rich, R. Michael; Tanvir, Nial; Widrow, Lawrence

2014-01-01

We present an analysis of the large-scale structure of the halo of the Andromeda galaxy, based on the Pan-Andromeda Archeological Survey (PAndAS), currently the most complete map of resolved stellar populations in any galactic halo. Despite the presence of copious substructures, the global halo populations follow closely power-law profiles that become steeper with increasing metallicity. We divide the sample into stream-like populations and a smooth halo component (defined as the population that cannot be resolved into spatially distinct substructures with PAndAS). Fitting a three-dimensional halo model reveals that the most metal-poor populations ([{{Fe/H}] \\lt -1.7}) are distributed approximately spherically (slightly prolate with ellipticity c/a = 1.09 ± 0.03), with only a relatively small fraction residing in discernible stream-like structures (f stream = 42%). The sphericity of the ancient smooth component strongly hints that the dark matter halo is also approximately spherical. More metal-rich populations contain higher fractions of stars in streams, with f stream becoming as high as 86% for [{Fe/H] \\gt -0.6}. The space density of the smooth metal-poor component has a global power-law slope of γ = -3.08 ± 0.07, and a non-parametric fit shows that the slope remains nearly constant from 30 kpc to ~300 kpc. The total stellar mass in the halo at distances beyond 2° is ~1.1 × 1010 M ⊙, while that of the smooth component is ~3 × 109 M ⊙. Extrapolating into the inner galaxy, the total stellar mass of the smooth halo is plausibly ~8 × 109 M ⊙. We detect a substantial metallicity gradient, which declines from lang[Fe/H]rang = -0.7 at R = 30 kpc to lang[Fe/H]rang = -1.5 at R = 150 kpc for the full sample, with the smooth halo being ~0.2 dex more metal poor than the full sample at each radius. While qualitatively in line with expectations from cosmological simulations, these observations are of great importance as they provide a prototype template that such simulations must now be able to reproduce in quantitative detail. Based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and CEA/DAPNIA, at the Canada-France-Hawaii Telescope (CFHT), which is operated by the National Research Council (NRC) of Canada, the Institute National des Sciences de l'Univers of the Centre National de la Recherche Scientifique of France, and the University of Hawaii.

Genetic variation between populations of the stable fly, Stomoxys calcitrans (L.)(Diptera: Muscidae) from Nebraska, Denmark and Australia

USDA-ARS?s Scientific Manuscript database

The stable fly, Stomoxys calcitrans L., is a cosmopolitan, major pest of livestock. Previous studies on this insect, from samples within the United States, suggested a large amount of gene flow; more genetic variation was detected within populations than between populations. To compare the genetic v...

Patterns of cannabis use in patients with Inflammatory Bowel Disease: A population based analysis.

PubMed

Weiss, Alexandra; Friedenberg, Frank

2015-11-01

Tobacco use patterns and effects in patients with Inflammatory Bowel Disease have been extensively studied, however the role and patterns of cannabis use remains poorly defined. Our aim was to evaluate patterns of marijuana use in a large population based survey. Cases were identified from the NHANES database from the National Center for Health Statistics for the time period from January, 2009 through December, 2010 as having ulcerative colitis or Crohn's disease, and exact matched with controls using the Propensity Score Module of SPSS, based on age, gender, and sample weighted using the nearest neighbor method. After weighting, 2084,895 subjects with IBD and 2013,901 control subjects were identified with no significant differences in demographic characteristics. Subjects with IBD had a higher incidence of ever having used marijuana/hashish (M/H) (67.3% vs. 60.0%) and an earlier age of onset of M/H use (15.7 years vs. 19.6 years). Patients with IBD were less likely to have used M/H every month for a year, but more likely to use a heavier amount per day (64.9% subjects with IBD used three or more joints per day vs. 80.5% of subjects without IBD used two or fewer joints per day). In multivariable logistic regression, presence of IBD, male gender, and age over 40 years predicted M/H use. Our study is the first to evaluate marijuana patterns in a large-scale population based survey. Older, male IBD patients have the highest odds of marijuana use. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Differential Item Functioning in the SF-36 Physical Functioning and Mental Health Sub-Scales: A Population-Based Investigation in the Canadian Multicentre Osteoporosis Study.

PubMed

Lix, Lisa M; Wu, Xiuyun; Hopman, Wilma; Mayo, Nancy; Sajobi, Tolulope T; Liu, Juxin; Prior, Jerilynn C; Papaioannou, Alexandra; Josse, Robert G; Towheed, Tanveer E; Davison, K Shawn; Sawatzky, Richard

2016-01-01

Self-reported health status measures, like the Short Form 36-item Health Survey (SF-36), can provide rich information about the overall health of a population and its components, such as physical, mental, and social health. However, differential item functioning (DIF), which arises when population sub-groups with the same underlying (i.e., latent) level of health have different measured item response probabilities, may compromise the comparability of these measures. The purpose of this study was to test for DIF on the SF-36 physical functioning (PF) and mental health (MH) sub-scale items in a Canadian population-based sample. Study data were from the prospective Canadian Multicentre Osteoporosis Study (CaMos), which collected baseline data in 1996-1997. DIF was tested using a multiple indicators multiple causes (MIMIC) method. Confirmatory factor analysis defined the latent variable measurement model for the item responses and latent variable regression with demographic and health status covariates (i.e., sex, age group, body weight, self-perceived general health) produced estimates of the magnitude of DIF effects. The CaMos cohort consisted of 9423 respondents; 69.4% were female and 51.7% were less than 65 years. Eight of 10 items on the PF sub-scale and four of five items on the MH sub-scale exhibited DIF. Large DIF effects were observed on PF sub-scale items about vigorous and moderate activities, lifting and carrying groceries, walking one block, and bathing or dressing. On the MH sub-scale items, all DIF effects were small or moderate in size. SF-36 PF and MH sub-scale scores were not comparable across population sub-groups defined by demographic and health status variables due to the effects of DIF, although the magnitude of this bias was not large for most items. We recommend testing and adjusting for DIF to ensure comparability of the SF-36 in population-based investigations.

Assessing respondent-driven sampling.

PubMed

Goel, Sharad; Salganik, Matthew J

2010-04-13

Respondent-driven sampling (RDS) is a network-based technique for estimating traits in hard-to-reach populations, for example, the prevalence of HIV among drug injectors. In recent years RDS has been used in more than 120 studies in more than 20 countries and by leading public health organizations, including the Centers for Disease Control and Prevention in the United States. Despite the widespread use and growing popularity of RDS, there has been little empirical validation of the methodology. Here we investigate the performance of RDS by simulating sampling from 85 known, network populations. Across a variety of traits we find that RDS is substantially less accurate than generally acknowledged and that reported RDS confidence intervals are misleadingly narrow. Moreover, because we model a best-case scenario in which the theoretical RDS sampling assumptions hold exactly, it is unlikely that RDS performs any better in practice than in our simulations. Notably, the poor performance of RDS is driven not by the bias but by the high variance of estimates, a possibility that had been largely overlooked in the RDS literature. Given the consistency of our results across networks and our generous sampling conditions, we conclude that RDS as currently practiced may not be suitable for key aspects of public health surveillance where it is now extensively applied.

Assessing respondent-driven sampling

PubMed Central

Goel, Sharad; Salganik, Matthew J.

2010-01-01

Respondent-driven sampling (RDS) is a network-based technique for estimating traits in hard-to-reach populations, for example, the prevalence of HIV among drug injectors. In recent years RDS has been used in more than 120 studies in more than 20 countries and by leading public health organizations, including the Centers for Disease Control and Prevention in the United States. Despite the widespread use and growing popularity of RDS, there has been little empirical validation of the methodology. Here we investigate the performance of RDS by simulating sampling from 85 known, network populations. Across a variety of traits we find that RDS is substantially less accurate than generally acknowledged and that reported RDS confidence intervals are misleadingly narrow. Moreover, because we model a best-case scenario in which the theoretical RDS sampling assumptions hold exactly, it is unlikely that RDS performs any better in practice than in our simulations. Notably, the poor performance of RDS is driven not by the bias but by the high variance of estimates, a possibility that had been largely overlooked in the RDS literature. Given the consistency of our results across networks and our generous sampling conditions, we conclude that RDS as currently practiced may not be suitable for key aspects of public health surveillance where it is now extensively applied. PMID:20351258

Into the depth of population genetics: pattern of structuring in mesophotic red coral populations

NASA Astrophysics Data System (ADS)

Costantini, Federica; Abbiati, Marco

2016-03-01

Deep-sea reef-building corals are among the most conspicuous invertebrates inhabiting the hard-bottom habitats worldwide and are particularly susceptible to human threats. The precious red coral ( Corallium rubrum, L. 1758) has a wide bathymetric distribution, from shallow up to 800 m depth, and represents a key species in the Mediterranean mesophotic reefs. Several studies have investigated genetic variability in shallow-water red coral populations, while geographic patterns in mesophotic habitats are largely unknown. This study investigated genetic variability of C. rubrum populations dwelling between 55 and 120 m depth, from the Ligurian to the Ionian Sea along about 1500 km of coastline. A total of 18 deep rocky banks were sampled. Colonies were analyzed by means of a set of microsatellite loci and the putative control region of the mitochondrial DNA. Collected data were compared with previous studies. Both types of molecular markers showed high genetic similarity between populations within the northern (Ligurian Sea and Tuscan Archipelago) and the southern (Tyrrhenian and Ionian seas) study areas. Variability in habitat features between the sampling sites did not affect the genetic variability of the populations. Conversely, the patchy distribution of suitable habitats affected populations' connectivity within and among deep coral banks. Based on these results and due to the emphasis on red coral protection in the Mediterranean Sea by international institutions, red coral could be promoted as a `focal species' to develop management plans for the conservation of deep coralligenous reefs, a reservoir of marine biodiversity.

Applications of species accumulation curves in large-scale biological data analysis.

PubMed

Deng, Chao; Daley, Timothy; Smith, Andrew D

2015-09-01

The species accumulation curve, or collector's curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional sampling. Traditional applications have focused on ecological populations but emerging large-scale applications, for example in DNA sequencing, are orders of magnitude larger and present new challenges. We developed a method to estimate accumulation curves for predicting the complexity of DNA sequencing libraries. This method uses rational function approximations to a classical non-parametric empirical Bayes estimator due to Good and Toulmin [Biometrika, 1956, 43, 45-63]. Here we demonstrate how the same approach can be highly effective in other large-scale applications involving biological data sets. These include estimating microbial species richness, immune repertoire size, and k -mer diversity for genome assembly applications. We show how the method can be modified to address populations containing an effectively infinite number of species where saturation cannot practically be attained. We also introduce a flexible suite of tools implemented as an R package that make these methods broadly accessible.

Applications of species accumulation curves in large-scale biological data analysis

PubMed Central

Deng, Chao; Daley, Timothy; Smith, Andrew D

2016-01-01

The species accumulation curve, or collector’s curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional sampling. Traditional applications have focused on ecological populations but emerging large-scale applications, for example in DNA sequencing, are orders of magnitude larger and present new challenges. We developed a method to estimate accumulation curves for predicting the complexity of DNA sequencing libraries. This method uses rational function approximations to a classical non-parametric empirical Bayes estimator due to Good and Toulmin [Biometrika, 1956, 43, 45–63]. Here we demonstrate how the same approach can be highly effective in other large-scale applications involving biological data sets. These include estimating microbial species richness, immune repertoire size, and k-mer diversity for genome assembly applications. We show how the method can be modified to address populations containing an effectively infinite number of species where saturation cannot practically be attained. We also introduce a flexible suite of tools implemented as an R package that make these methods broadly accessible. PMID:27252899

Species collapse via hybridization in Darwin's tree finches.

PubMed

Kleindorfer, Sonia; O'Connor, Jody A; Dudaniec, Rachael Y; Myers, Steven A; Robertson, Jeremy; Sulloway, Frank J

2014-03-01

Species hybridization can lead to fitness costs, species collapse, and novel evolutionary trajectories in changing environments. Hybridization is predicted to be more common when environmental conditions change rapidly. Here, we test patterns of hybridization in three sympatric tree finch species (small tree finch Camarhynchus parvulus, medium tree finch Camarhynchus pauper, and large tree finch: Camarhynchus psittacula) that are currently recognized on Floreana Island, Galápagos Archipelago. Genetic analysis of microsatellite data from contemporary samples showed two genetic populations and one hybrid cluster in both 2005 and 2010; hybrid individuals were derived from genetic population 1 (small morph) and genetic population 2 (large morph). Females of the large and rare species were more likely to pair with males of the small common species. Finch populations differed in morphology in 1852-1906 compared with 2005/2010. An unsupervised clustering method showed (a) support for three morphological clusters in the historical tree finch sample (1852-1906), which is consistent with current species recognition; (b) support for two or three morphological clusters in 2005 with some (19%) hybridization; and (c) support for just two morphological clusters in 2010 with frequent (41%) hybridization. We discuss these findings in relation to species demarcations of Camarhynchus tree finches on Floreana Island.

Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure

PubMed Central

Basu, Analabha; Sarkar-Roy, Neeta; Majumder, Partha P.

2016-01-01

India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform. PMID:26811443

Head and facial anthropometry of mixed-race US Army male soldiers for military design and sizing: a pilot study.

PubMed

Yokota, Miyo

2005-05-01

In the United States, the biologically admixed population is increasing. Such demographic changes may affect the distribution of anthropometric characteristics, which are incorporated into the design of equipment and clothing for the US Army and other large organizations. The purpose of this study was to examine multivariate craniofacial anthropometric distributions between biologically admixed male populations and single racial groups of Black and White males. Multivariate statistical results suggested that nose breadth and lip length were different between Blacks and Whites. Such differences may be considered for adjustments to respirators and chemical-biological protective masks. However, based on this pilot study, multivariate anthropometric distributions of admixed individuals were within the distributions of single racial groups. Based on the sample reported, sizing and designing for the admixed groups are not necessary if anthropometric distributions of single racial groups comprising admixed groups are known.

The Moderated Influence of Perceived Behavioral Control on Intentions among the General U.S. Population: Implications for Public Communication Campaigns

PubMed Central

Martinez, Lourdes S.; Lewis, Nehama

2016-01-01

This study reports results from a large population-based survey of U.S. adults showing perceived behavioral control (PBC) moderations of associations between (1) attitude and intention, and (2) perceived norms and intention to engage in six health behaviors. Results are based on data collected from a nationally representative sample of U.S. adults ages 40-70 (N=2,489) and extend understanding of how behavioral theory can be used to guide the design and evaluation of health communication campaigns. OLS regression analyses show evidence for a significant positive PBC moderation of (1) attitude and intention, and (2) perceived norms and intention such that attitude or perceived norms toward the behavior is more strongly associated with behavioral intention among participants reporting higher levels of PBC. Implications for message design and the evaluation of communication campaigns are discussed. PMID:27565188

Factors associated with lower gait speed among the elderly living in a developing country: a cross-sectional population-based study.

PubMed

Busch, Telma de Almeida; Duarte, Yeda Aparecida; Pires Nunes, Daniella; Lebrão, Maria Lucia; Satya Naslavsky, Michel; dos Santos Rodrigues, Anelise; Amaro, Edson

2015-04-01

Among community-dwelling older adults, mean values for gait speed vary substantially depending not only on the population studied, but also on the methodology used. Despite the large number of studies published in developed countries, there are few population-based studies in developing countries with socioeconomic inequality and different health conditions, and this is the first study with a representative sample of population. To explore this, the association of lower gait speed with sociodemographic, anthropometric factors, mental status and physical health was incorporated participants' weight (main weight) in the analysis of population of community-dwelling older adults living in a developing country. This was a cross-sectional population based on a sample of 1112 older adults aged 60 years and over from Health, Wellbeing and Aging Study cohort 2010. Usual gait speed (s) to walk 3 meters was stratified by sex and height into quartiles. Multiple regression analysis was performed to investigate the independent effect of each factor associated with a slower usual gait speed. The average walking speed of the elderly was 0.81 m/s-0.78 m/s among women and 0.86 m/s among men. In the final model, the factors associated with lower gait speed were age (OR = 3.56), literacy (OR = 3.20), difficulty in one or more IADL (OR = 2.74), presence of cardiovascular disease (OR = 2.15) and sedentarism. When we consider the 50% slower, we can add the variables handgrip strength, and the presence of COPD. Gait speed is a clinical marker and an important measure of functional capacity among the elderly. Our findings suggest that lower walking speed is associated with age, education, but especially with modifiable factors such as impairment of IADL, physical inactivity and cardiovascular disease. These results reinforce how important it is for the elderly to remain active and healthy.

Mental health of a police force: estimating prevalence of work-related depression in Australia without a direct national measure.

PubMed

Lawson, Katrina J; Rodwell, John J; Noblet, Andrew J

2012-06-01

The risk of work-related depression in Australia was estimated based on a survey of 631 police officers. Psychological wellbeing and psychological distress items were mapped onto a measure of depression to identify optimal cutoff points. Based on a sample of police officers, Australian workers, in general, are at risk of depression when general psychological wellbeing is considerably compromised. Large-scale estimation of work-related depression in the broader population of employed persons in Australia is reasonable. The relatively high prevalence of depression among police officers emphasizes the need to examine prevalence rates of depression among Australian employees.

Application of Response Surface Methods To Determine Conditions for Optimal Genomic Prediction

PubMed Central

Howard, Réka; Carriquiry, Alicia L.; Beavis, William D.

2017-01-01

An epistatic genetic architecture can have a significant impact on prediction accuracies of genomic prediction (GP) methods. Machine learning methods predict traits comprised of epistatic genetic architectures more accurately than statistical methods based on additive mixed linear models. The differences between these types of GP methods suggest a diagnostic for revealing genetic architectures underlying traits of interest. In addition to genetic architecture, the performance of GP methods may be influenced by the sample size of the training population, the number of QTL, and the proportion of phenotypic variability due to genotypic variability (heritability). Possible values for these factors and the number of combinations of the factor levels that influence the performance of GP methods can be large. Thus, efficient methods for identifying combinations of factor levels that produce most accurate GPs is needed. Herein, we employ response surface methods (RSMs) to find the experimental conditions that produce the most accurate GPs. We illustrate RSM with an example of simulated doubled haploid populations and identify the combination of factors that maximize the difference between prediction accuracies of best linear unbiased prediction (BLUP) and support vector machine (SVM) GP methods. The greatest impact on the response is due to the genetic architecture of the population, heritability of the trait, and the sample size. When epistasis is responsible for all of the genotypic variance and heritability is equal to one and the sample size of the training population is large, the advantage of using the SVM method vs. the BLUP method is greatest. However, except for values close to the maximum, most of the response surface shows little difference between the methods. We also determined that the conditions resulting in the greatest prediction accuracy for BLUP occurred when genetic architecture consists solely of additive effects, and heritability is equal to one. PMID:28720710

A Fosmid Cloning Strategy for Detecting the Widest Possible Spectrum of Microbes from the International Space Station Drinking Water System

PubMed Central

Choi, Sangdun; Chang, Mi Sook; Stuecker, Tara; Chung, Christine; Newcombe, David A.; Venkateswaran, Kasthuri

2012-01-01

In this study, fosmid cloning strategies were used to assess the microbial populations in water from the International Space Station (ISS) drinking water system (henceforth referred to as Prebiocide and Tank A water samples). The goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16S rRNA-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. Initially, microbes could not be cultivated, and conventional PCR failed to amplify 16S rDNA fragments from these low biomass samples. Therefore, randomly primed rolling-circle amplification was used to amplify any DNA that might be present in the samples, followed by size selection by using pulsed-field gel electrophoresis. The amplified high-molecular-weight DNA from both samples was cloned into fosmid vectors. Several hundred clones were randomly selected for sequencing, followed by Blastn/Blastx searches. Sequences encoding specific genes from Burkholderia, a species abundant in the soil and groundwater, were found in both samples. Bradyrhizobium and Mesorhizobium, which belong to rhizobia, a large community of nitrogen fixers often found in association with plant roots, were present in the Prebiocide samples. Ralstonia, which is prevalent in soils with a high heavy metal content, was detected in the Tank A samples. The detection of many unidentified sequences suggests the presence of potentially novel microbial fingerprints. The bacterial diversity detected in this pilot study using a fosmid vector approach was higher than that detected by conventional 16S rRNA gene sequencing. PMID:23346038

Exploring Collaborative Culture and Leadership in Large High Schools

ERIC Educational Resources Information Center

Jeffers, Michael P.

2013-01-01

The purpose of this exploratory study was to analyze how high school principals approached developing a collaborative culture and providing collaborative leadership in a large high school setting. The population sample for this study was 82 principals of large comprehensive high schools of grades 9 through 12 or some combination thereof with…

The VLT-FLAMES Tarantula Survey. XII. Rotational velocities of the single O-type stars

NASA Astrophysics Data System (ADS)

Ramírez-Agudelo, O. H.; Simón-Díaz, S.; Sana, H.; de Koter, A.; Sabín-Sanjulían, C.; de Mink, S. E.; Dufton, P. L.; Gräfener, G.; Evans, C. J.; Herrero, A.; Langer, N.; Lennon, D. J.; Maíz Apellániz, J.; Markova, N.; Najarro, F.; Puls, J.; Taylor, W. D.; Vink, J. S.

2013-12-01

Context. The 30 Doradus (30 Dor) region of the Large Magellanic Cloud, also known as the Tarantula nebula, is the nearest starburst region. It contains the richest population of massive stars in the Local Group, and it is thus the best possible laboratory to investigate open questions on the formation and evolution of massive stars. Aims: Using ground-based multi-object optical spectroscopy obtained in the framework of the VLT-FLAMES Tarantula Survey (VFTS), we aim to establish the (projected) rotational velocity distribution for a sample of 216 presumably single O-type stars in 30 Dor. The sample is large enough to obtain statistically significant information and to search for variations among subpopulations - in terms of spectral type, luminosity class, and spatial location - in the field of view. Methods: We measured projected rotational velocities, νesini, by means of a Fourier transform method and a profile fitting method applied to a set of isolated spectral lines. We also used an iterative deconvolution procedure to infer the probability density, P(νe), of the equatorial rotational velocity, νe. Results: The distribution of νesini shows a two-component structure: a peak around 80 kms-1 and a high-velocity tail extending up to ~600 kms-1. This structure is also present in the inferred distribution P(νe) with around 80% of the sample having 0 < νe ≤ 300 kms-1 and the other 20% distributed in the high-velocity region. The presence of the low-velocity peak is consistent with what has been found in other studies for late O- and early B-type stars. Conclusions: Most of the stars in our sample rotate with a rate less than 20% of their break-up velocity. For the bulk of the sample, mass loss in a stellar wind and/or envelope expansion is not efficient enough to significantly spin down these stars within the first few Myr of evolution. If massive-star formation results in stars rotating at birth with a large portion of their break-up velocities, an alternative braking mechanism, possibly magnetic fields, is thus required to explain the present-day rotational properties of the O-type stars in 30 Dor. The presence of a sizeable population of fast rotators is compatible with recent population synthesis computations that investigate the influence of binary evolution on the rotation rate of massive stars. Even though we have excluded stars that show significant radial velocity variations, our sample may have remained contaminated by post-interaction binary products. That the high-velocity tail may be populated primarily (and perhaps exclusively) by post-binary interaction products has important implications for the evolutionary origin of systems that produce gamma-ray bursts. Based on observations collected at the European Southern Observatory under program ID 182.D-0222.Full Tables 3 and 4 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/560/A29

Use of inequality constrained least squares estimation in small area estimation

NASA Astrophysics Data System (ADS)

Abeygunawardana, R. A. B.; Wickremasinghe, W. N.

2017-05-01

Traditional surveys provide estimates that are based only on the sample observations collected for the population characteristic of interest. However, these estimates may have unacceptably large variance for certain domains. Small Area Estimation (SAE) deals with determining precise and accurate estimates for population characteristics of interest for such domains. SAE usually uses least squares or maximum likelihood procedures incorporating prior information and current survey data. Many available methods in SAE use constraints in equality form. However there are practical situations where certain inequality restrictions on model parameters are more realistic. It will lead to Inequality Constrained Least Squares (ICLS) estimates if the method used is least squares. In this study ICLS estimation procedure is applied to many proposed small area estimates.

Optical stretching as a tool to investigate the mechanical properties of lipid bilayers†

PubMed Central

Solmaz, Mehmet E.; Sankhagowit, Shalene; Biswas, Roshni; Mejia, Camilo A.; Povinelli, Michelle L.; Malmstadt, Noah

2013-01-01

Measurements of lipid bilayer bending modulus by various techniques produce widely divergent results. We attempt to resolve some of this ambiguity by measuring bending modulus in a system that can rapidly process large numbers of samples, yielding population statistics. This system is based on optical stretching of giant unilamellar vesicles (GUVs) in a microfluidic dual-beam optical trap (DBOT). The microfluidic DBOT system is used here to measure three populations of GUVs with distinct lipid compositions. We find that gel-phase membranes are significantly stiffer than liquid-phase membranes, consistent with previous reports. We also find that the addition of cholesterol does not alter the bending modulus of membranes composed of a monounsaturated phospholipid. PMID:24244843

Population structure and connectivity of tiger sharks (Galeocerdo cuvier) across the Indo-Pacific Ocean basin

PubMed Central

Williams, Samuel M.; Otway, Nicholas M.; Nielsen, Einar E.; Maher, Safia L.; Bennett, Mike B.; Ovenden, Jennifer R.

2017-01-01

Population genetic structure using nine polymorphic nuclear microsatellite loci was assessed for the tiger shark (Galeocerdo cuvier) at seven locations across the Indo-Pacific, and one location in the southern Atlantic. Genetic analyses revealed considerable genetic structuring (FST > 0.14, p < 0.001) between all Indo-Pacific locations and Brazil. By contrast, no significant genetic differences were observed between locations from within the Pacific or Indian Oceans, identifying an apparent large, single Indo-Pacific population. A lack of differentiation between tiger sharks sampled in Hawaii and other Indo-Pacific locations identified herein is in contrast to an earlier global tiger shark nDNA study. The results of our power analysis provide evidence to suggest that the larger sample sizes used here negated any weak population subdivision observed previously. These results further highlight the need for cross-jurisdictional efforts to manage the sustainable exploitation of large migratory sharks like G. cuvier. PMID:28791159

Population structure and connectivity of tiger sharks (Galeocerdo cuvier) across the Indo-Pacific Ocean basin.

PubMed

Holmes, Bonnie J; Williams, Samuel M; Otway, Nicholas M; Nielsen, Einar E; Maher, Safia L; Bennett, Mike B; Ovenden, Jennifer R

2017-07-01

Population genetic structure using nine polymorphic nuclear microsatellite loci was assessed for the tiger shark ( Galeocerdo cuvier ) at seven locations across the Indo-Pacific, and one location in the southern Atlantic. Genetic analyses revealed considerable genetic structuring ( F ST  > 0.14, p  < 0.001) between all Indo-Pacific locations and Brazil. By contrast, no significant genetic differences were observed between locations from within the Pacific or Indian Oceans, identifying an apparent large, single Indo-Pacific population. A lack of differentiation between tiger sharks sampled in Hawaii and other Indo-Pacific locations identified herein is in contrast to an earlier global tiger shark nDNA study. The results of our power analysis provide evidence to suggest that the larger sample sizes used here negated any weak population subdivision observed previously. These results further highlight the need for cross-jurisdictional efforts to manage the sustainable exploitation of large migratory sharks like G. cuvier .

Maximum likelihood estimation for Cox's regression model under nested case-control sampling.

PubMed

Scheike, Thomas H; Juul, Anders

2004-04-01

Nested case-control sampling is designed to reduce the costs of large cohort studies. It is important to estimate the parameters of interest as efficiently as possible. We present a new maximum likelihood estimator (MLE) for nested case-control sampling in the context of Cox's proportional hazards model. The MLE is computed by the EM-algorithm, which is easy to implement in the proportional hazards setting. Standard errors are estimated by a numerical profile likelihood approach based on EM aided differentiation. The work was motivated by a nested case-control study that hypothesized that insulin-like growth factor I was associated with ischemic heart disease. The study was based on a population of 3784 Danes and 231 cases of ischemic heart disease where controls were matched on age and gender. We illustrate the use of the MLE for these data and show how the maximum likelihood framework can be used to obtain information additional to the relative risk estimates of covariates.

Socio-demographic predictors of sleep complaints in indigenous Siberians with a mixed economy.

PubMed

Wilson, Hannah J; Klimova, Tatiana M; Knuston, Kristen L; Fedorova, Valentina I; Fedorov, Afanasy; Yegorovna, Baltakhinova M; Leonard, William R

2015-08-01

Socio-demographic indicators closely relate to sleep in industrialized populations. However we know very little about how such factors impact sleep in populations undergoing industrialization. Within populations transitioning to the global economy, the preliminary evidence has found an inconsistent relationship between socio-demographics and sleep complaints across countries and social strata. Surveys were conducted on a sample of rural Sakha (Yakut) adults (n = 168) during the autumn of 2103 to assess variation in socio-demographics and sleep complaints, including trouble sleeping and daytime sleepiness. Socio-demographic variables included age, gender, socioeconomic measures, and markers of traditional/market-based lifestyle. We tested whether the socio-demographic variables predicted sleep complaints using bivariate analyses and multiple logistic regressions. Trouble sleeping was reported by 18.5% of the participants and excessive daytime sleepiness (EDS) by 17.3%. Trouble sleeping was significantly predicted by older age, female gender, and mixing traditional and market-based lifestyles. EDS was not significantly predicted by any socio-demographic variable. These findings support the few large-scale studies that found inconsistent relationships between measures of socioeconomic status and sleep complaints in transitioning populations. Employing a mix of traditional and market-based lifestyles may leave Sakha in a space of vulnerability, leading to trouble sleeping. © 2015 Wiley Periodicals, Inc.

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

PubMed Central

Nowicka, Malgorzata; Krieg, Carsten; Weber, Lukas M.; Hartmann, Felix J.; Guglietta, Silvia; Becher, Burkhard; Levesque, Mitchell P.; Robinson, Mark D.

2017-01-01

High dimensional mass and flow cytometry (HDCyto) experiments have become a method of choice for high throughput interrogation and characterization of cell populations.Here, we present an R-based pipeline for differential analyses of HDCyto data, largely based on Bioconductor packages. We computationally define cell populations using FlowSOM clustering, and facilitate an optional but reproducible strategy for manual merging of algorithm-generated clusters. Our workflow offers different analysis paths, including association of cell type abundance with a phenotype or changes in signaling markers within specific subpopulations, or differential analyses of aggregated signals. Importantly, the differential analyses we show are based on regression frameworks where the HDCyto data is the response; thus, we are able to model arbitrary experimental designs, such as those with batch effects, paired designs and so on. In particular, we apply generalized linear mixed models to analyses of cell population abundance or cell-population-specific analyses of signaling markers, allowing overdispersion in cell count or aggregated signals across samples to be appropriately modeled. To support the formal statistical analyses, we encourage exploratory data analysis at every step, including quality control (e.g. multi-dimensional scaling plots), reporting of clustering results (dimensionality reduction, heatmaps with dendrograms) and differential analyses (e.g. plots of aggregated signals). PMID:28663787

Sun Exposure Prevalence and Associated Skin Health Habits: Results from the Austrian Population-Based UVSkinRisk Survey

PubMed Central

Haluza, Daniela; Simic, Stana; Moshammer, Hanns

2016-01-01

Recreational sun exposure accounts for a large number of acute and chronic dermatological diseases, including skin cancer. This study aimed at estimating the one-year prevalence of sun exposure and skin health-associated knowledge and attitudes among Austrian citizens. The population-based UVSkinRisk survey investigated a representative sample of Austrian adults using a structured questionnaire. In total, 1500 study subjects (median age 33.0 years, 50.5% females) participated in this questionnaire survey. Among study participants, prevalence of sun exposure was 47%, with slightly higher rates in males (48%) compared to females (46%). Younger age, lower professional category, darker skin type, motives to tan, sunbed use, sunburn, and outdoor sport activity increased the odds for prevalent sun exposure. This is the first population-based study evaluating the prevailing sun exposure and recreational habits influencing skin health among Austrian citizens. Despite public media campaigns educating on the harmful effects of sunlight exposure, we found a high prevalence of self-reported sunlight exposure. The results suggest that multifaceted socio-cultural characteristics stimulate recreational sun exposure and tanning habits. Communicating individualized Public (Skin) Health messages might be the key to prevent photo-induced skin health hazards in light-skinned populations. The practical and theoretical implications of these findings are discussed. PMID:26797627

Detecting Small Amounts of Gene Flow from Phylogenies of Alleles

PubMed Central

Slatkin, M.

1989-01-01

The method of coalescents is used to find the probability that none of the ancestors of alleles sampled from a population are immigrants. If that is the case for samples from two or more populations, then there would be concordance between the phylogenies of those alleles and the geographic locations from which they are drawn. This type of concordance has been found in several studies of mitochondrial DNA from natural populations. It is shown that if the number of sequences sampled from each population is reasonably large (10 or more), then this type of concordance suggests that the average number of individuals migrating between populations is likely to be relatively small (Nm < 1) but the possibility of occasional migrants cannot be excluded. The method is applied to the data of E. Bermingham and J. C. Avise on mtDNA from the bowfin, Amia calva. PMID:2714639

Lipid Vesicle Shape Analysis from Populations Using Light Video Microscopy and Computer Vision

PubMed Central

Zupanc, Jernej; Drašler, Barbara; Boljte, Sabina; Kralj-Iglič, Veronika; Iglič, Aleš; Erdogmus, Deniz; Drobne, Damjana

2014-01-01

We present a method for giant lipid vesicle shape analysis that combines manually guided large-scale video microscopy and computer vision algorithms to enable analyzing vesicle populations. The method retains the benefits of light microscopy and enables non-destructive analysis of vesicles from suspensions containing up to several thousands of lipid vesicles (1–50 µm in diameter). For each sample, image analysis was employed to extract data on vesicle quantity and size distributions of their projected diameters and isoperimetric quotients (measure of contour roundness). This process enables a comparison of samples from the same population over time, or the comparison of a treated population to a control. Although vesicles in suspensions are heterogeneous in sizes and shapes and have distinctively non-homogeneous distribution throughout the suspension, this method allows for the capture and analysis of repeatable vesicle samples that are representative of the population inspected. PMID:25426933

A Systematic Review of Rural, Theory-based Physical Activity Interventions.

PubMed

Walsh, Shana M; Meyer, M Renée Umstattd; Gamble, Abigail; Patterson, Megan S; Moore, Justin B

2017-05-01

This systematic review synthesized the scientific literature on theory-based physical activity (PA) interventions in rural populations. PubMed, PsycINFO, and Web of Science databases were searched to identify studies with a rural study sample, PA as a primary outcome, use of a behavioral theory or model, randomized or quasi-experimental research design, and application at the primary and/or secondary level of prevention. Thirty-one studies met our inclusion criteria. The Social Cognitive Theory (N = 14) and Transtheoretical Model (N = 10) were the most frequently identified theories; however, most intervention studies were informed by theory but lacked higher-level theoretical application and testing. Interventions largely took place in schools (N = 10) and with female-only samples (N = 8). Findings demonstrated that theory-based PA interventions are mostly successful at increasing PA in rural populations but require improvement. Future studies should incorporate higher levels of theoretical application, and should explore adapting or developing rural-specific theories. Study designs should employ more rigorous research methods to decrease bias and increase validity of findings. Follow-up assessments to determine behavioral maintenance and/or intervention sustainability are warranted. Finally, funding agencies and journals are encouraged to adopt rural-urban commuting area codes as the standard for defining rural.

Modeling 3D Facial Shape from DNA

PubMed Central

Claes, Peter; Liberton, Denise K.; Daniels, Katleen; Rosana, Kerri Matthes; Quillen, Ellen E.; Pearson, Laurel N.; McEvoy, Brian; Bauchet, Marc; Zaidi, Arslan A.; Yao, Wei; Tang, Hua; Barsh, Gregory S.; Absher, Devin M.; Puts, David A.; Rocha, Jorge; Beleza, Sandra; Pereira, Rinaldo W.; Baynam, Gareth; Suetens, Paul; Vandermeulen, Dirk; Wagner, Jennifer K.; Boster, James S.; Shriver, Mark D.

2014-01-01

Human facial diversity is substantial, complex, and largely scientifically unexplained. We used spatially dense quasi-landmarks to measure face shape in population samples with mixed West African and European ancestry from three locations (United States, Brazil, and Cape Verde). Using bootstrapped response-based imputation modeling (BRIM), we uncover the relationships between facial variation and the effects of sex, genomic ancestry, and a subset of craniofacial candidate genes. The facial effects of these variables are summarized as response-based imputed predictor (RIP) variables, which are validated using self-reported sex, genomic ancestry, and observer-based facial ratings (femininity and proportional ancestry) and judgments (sex and population group). By jointly modeling sex, genomic ancestry, and genotype, the independent effects of particular alleles on facial features can be uncovered. Results on a set of 20 genes showing significant effects on facial features provide support for this approach as a novel means to identify genes affecting normal-range facial features and for approximating the appearance of a face from genetic markers. PMID:24651127

Serum testosterone levels in males are not associated with entrepreneurial behavior in two independent observational studies.

PubMed

van der Loos, Matthijs J H M; Haring, Robin; Rietveld, Cornelius A; Baumeister, Sebastian E; Groenen, Patrick J F; Hofman, Albert; de Jong, Frank H; Koellinger, Philipp D; Kohlmann, Thomas; Nauck, Matthias A; Rivadeneira, Fernando; Uitterlinden, André G; van Rooij, Frank J A; Wallaschofski, Henri; Thurik, A Roy

2013-07-02

Previous research has suggested a positive association between testosterone (T) and entrepreneurial behavior in males. However, this evidence was found in a study with a small sample size and has not been replicated. In the present study, we aimed to verify this association using two large, independent, population-based samples of males. We tested the association of T with entrepreneurial behavior, operationalized as self-employment, using data from the Rotterdam Study (N=587) and the Study of Health in Pomerania (N=1697). Total testosterone (TT) and sex hormone-binding globulin (SHBG) were measured in the serum. Free testosterone (FT), non-SHBG-bound T (non-SHBG-T), and the TT/SHBG ratio were calculated and used as measures of bioactive serum T, in addition to TT adjusted for SHBG. Using logistic regression models, we found no significant associations between any of the serum T measures and self-employment in either of the samples. To our knowledge, this is the first large-scale study on the relationship between serum T and entrepreneurial behavior. Copyright © 2013 Elsevier Inc. All rights reserved.

Do You See What I See? Exploring the Consequences of Luminosity Limits in Black Hole–Galaxy Evolution Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Mackenzie L.; Hickox, Ryan C.; DiPompeo, Michael A.

In studies of the connection between active galactic nuclei (AGNs) and their host galaxies, there is widespread disagreement on some key aspects of the connection. These disagreements largely stem from a lack of understanding of the nature of the full underlying AGN population. Recent attempts to probe this connection utilize both observations and simulations to correct for a missed population, but presently are limited by intrinsic biases and complicated models. We take a simple simulation for galaxy evolution and add a new prescription for AGN activity to connect galaxy growth to dark matter halo properties and AGN activity to starmore » formation. We explicitly model selection effects to produce an “observed” AGN population for comparison with observations and empirically motivated models of the local universe. This allows us to bypass the difficulties inherent in models that attempt to infer the AGN population by inverting selection effects. We investigate the impact of selecting AGNs based on thresholds in luminosity or Eddington ratio on the “observed” AGN population. By limiting our model AGN sample in luminosity, we are able to recreate the observed local AGN luminosity function and specific star formation-stellar mass distribution, and show that using an Eddington ratio threshold introduces less bias into the sample by selecting the full range of growing black holes, despite the challenge of selecting low-mass black holes. We find that selecting AGNs using these various thresholds yield samples with different AGN host galaxy properties.« less

Single nucleotide polymorphisms in native South American Atlantic coast populations of smooth shelled mussels: hybridization with invasive European Mytilus galloprovincialis.

PubMed

Zbawicka, Małgorzata; Trucco, María I; Wenne, Roman

2018-02-22

Throughout the world, harvesting of mussels Mytilus spp. is based on the exploitation of natural populations and aquaculture. Aquaculture activities include transfers of spat and live adult mussels between various geographic locations, which may result in large-scale changes in the world distribution of Mytilus taxa. Mytilus taxa are morphologically similar and difficult to distinguish. In spite of much research on taxonomy, evolution and geographic distribution, the native Mytilus taxa of the Southern Hemisphere are poorly understood. Recently, single nucleotide polymorphisms (SNPs) have been used to clarify the taxonomic status of populations of smooth shelled mussels from the Pacific coast of South America. In this paper, we used a set of SNPs to characterize, for the first time, populations of smooth shelled mussels Mytilus from the Atlantic coast of South America. Mytilus spp. samples were collected from eastern South America. Six reference samples from the Northern Hemisphere were used: Mytilus edulis from USA and Northern Ireland, Mytilus trossulus from Canada, and Mytilus galloprovincialis from Spain and Italy. Two other reference samples from the Southern Hemisphere were included: M. galloprovincialis from New Zealand and Mytilus chilensis from Chile. Fifty-five SNPs were successfully genotyped, of which 51 were polymorphic. Population genetic analyses using the STRUCTURE program revealed the clustering of eight populations from Argentina (Mytilus platensis) and the clustering of the sample from Ushuaia with M. chilensis from Chile. All individuals in the Puerto Madryn (Argentina) sample were identified as M. platensis × M. galloprovincialis F2 (88.89%) hybrids, except one that was classified as Mediterranean M. galloprovincialis. No F1 hybrids were observed. We demonstrate that M. platensis (or Mytilus edulis platensis) and M. chilensis are distinct native taxa in South America, which indicates that the evolutionary histories of Mytilus taxa along the Atlantic and Pacific coasts differ. M. platensis is endangered by hybridization with M. galloprovincialis that was introduced from Europe into the Puerto Madryn area in Argentina, presumably by accidental introduction via ship traffic. We confirm the occurrence of a native M. chilensis population in southern Argentina on the coast of Patagonia.

The Nutrinet-Santé Study: a web-based prospective study on the relationship between nutrition and health and determinants of dietary patterns and nutritional status.

PubMed

Hercberg, Serge; Castetbon, Katia; Czernichow, Sébastien; Malon, Aurélie; Mejean, Caroline; Kesse, Emmanuelle; Touvier, Mathilde; Galan, Pilar

2010-05-11

Nutrition-related chronic diseases such as cardiovascular diseases and cancer are of multiple origin, and may be due to genetic, biologic, behavioural and environmental factors. In order to detangle the specific role of nutritional factors, very large population sample cohort studies comprising precisely measured dietary intake and all necessary information for accurately assessing potential confounding factors are needed. Widespread use of internet is an opportunity to gradually collect huge amounts of data from a large sample of volunteers that can be automatically verified and processed. The objectives of the NutriNet-Santé study are: 1) to investigate the relationship between nutrition (nutrients, foods, dietary patterns, physical activity), mortality and health outcomes; and 2) to examine the determinants of dietary patterns and nutritional status (sociological, economic, cultural, biological, cognitive, perceptions, preferences, etc.), using a web-based approach. Our web-based prospective cohort study is being conducted for a scheduled follow-up of 10 years. Using a dedicated web site, recruitment will be carried out for 5 years so as to register 500 000 volunteers aged >/= 18 years among whom 60% are expected to be included (having complete baseline data) and followed-up for at least 5 years for 240 000 participants. Questionnaires administered via internet at baseline and each year thereafter will assess socio-demographic and lifestyle characteristics, anthropometry, health status, physical activity and diet. Surveillance of health events will be implemented via questionnaires on hospitalisation and use of medication, and linkage with a national database on vital statistics. Biochemical samples and clinical examination will be collected in a subsample of volunteers. Self-administered data collection using internet as a complement to collection of biological data will enable identifying nutrition-related risks and protective factors, thereby more clearly elucidating determinants of nutritional status and their interactions. These are necessary steps for further refining nutritional recommendations aimed at improving the health status of populations.

Sea-level rise and archaeological site destruction: An example from the southeastern United States using DINAA (Digital Index of North American Archaeology).

PubMed

Anderson, David G; Bissett, Thaddeus G; Yerka, Stephen J; Wells, Joshua J; Kansa, Eric C; Kansa, Sarah W; Myers, Kelsey Noack; DeMuth, R Carl; White, Devin A

2017-01-01

The impact of changing climate on terrestrial and underwater archaeological sites, historic buildings, and cultural landscapes can be examined through quantitatively-based analyses encompassing large data samples and broad geographic and temporal scales. The Digital Index of North American Archaeology (DINAA) is a multi-institutional collaboration that allows researchers online access to linked heritage data from multiple sources and data sets. The effects of sea-level rise and concomitant human population relocation is examined using a sample from nine states encompassing much of the Gulf and Atlantic coasts of the southeastern United States. A 1 m rise in sea-level will result in the loss of over >13,000 recorded historic and prehistoric archaeological sites, as well as over 1000 locations currently eligible for inclusion on the National Register of Historic Places (NRHP), encompassing archaeological sites, standing structures, and other cultural properties. These numbers increase substantially with each additional 1 m rise in sea level, with >32,000 archaeological sites and >2400 NRHP properties lost should a 5 m rise occur. Many more unrecorded archaeological and historic sites will also be lost as large areas of the landscape are flooded. The displacement of millions of people due to rising seas will cause additional impacts where these populations resettle. Sea level rise will thus result in the loss of much of the record of human habitation of the coastal margin in the Southeast within the next one to two centuries, and the numbers indicate the magnitude of the impact on the archaeological record globally. Construction of large linked data sets is essential to developing procedures for sampling, triage, and mitigation of these impacts.

Sea-level rise and archaeological site destruction: An example from the southeastern United States using DINAA (Digital Index of North American Archaeology)

PubMed Central

Wells, Joshua J.; Kansa, Eric C.; Kansa, Sarah W.; Myers, Kelsey Noack; DeMuth, R. Carl; White, Devin A.

2017-01-01

The impact of changing climate on terrestrial and underwater archaeological sites, historic buildings, and cultural landscapes can be examined through quantitatively-based analyses encompassing large data samples and broad geographic and temporal scales. The Digital Index of North American Archaeology (DINAA) is a multi-institutional collaboration that allows researchers online access to linked heritage data from multiple sources and data sets. The effects of sea-level rise and concomitant human population relocation is examined using a sample from nine states encompassing much of the Gulf and Atlantic coasts of the southeastern United States. A 1 m rise in sea-level will result in the loss of over >13,000 recorded historic and prehistoric archaeological sites, as well as over 1000 locations currently eligible for inclusion on the National Register of Historic Places (NRHP), encompassing archaeological sites, standing structures, and other cultural properties. These numbers increase substantially with each additional 1 m rise in sea level, with >32,000 archaeological sites and >2400 NRHP properties lost should a 5 m rise occur. Many more unrecorded archaeological and historic sites will also be lost as large areas of the landscape are flooded. The displacement of millions of people due to rising seas will cause additional impacts where these populations resettle. Sea level rise will thus result in the loss of much of the record of human habitation of the coastal margin in the Southeast within the next one to two centuries, and the numbers indicate the magnitude of the impact on the archaeological record globally. Construction of large linked data sets is essential to developing procedures for sampling, triage, and mitigation of these impacts. PMID:29186200

The power to detect trends in Missouri River fish populations within the Pallid Sturgeon Population Assessment Program

USGS Publications Warehouse

Bryan, Janice L.; Wildhaber, Mark L.; Gladish, Dan; Holan, Scott; Ellerseick, Mark

2010-01-01

As with all large rivers in the United States, the Missouri River has been altered, with approximately 32.5 percent of the main stem length impounded and 32.5 percent channelized. These physical alterations to the environment have had effects on the fisheries, but studies examining the effects of alterations have been localized and for short periods of time. In response to the U.S. Fish and Wildlife Service biological opinion, the U.S. Army Corps of Engineers initiated monitoring of the fish community of the Missouri River in 2003. The goal of the Pallid Sturgeon Population Assessment Program is to provide information to detect changes in populations and habitat preferences with time for pallid sturgeon (Scaphirhynchus albus) and native target species in the Missouri River Basin. To determine statistical power of the Pallid Sturgeon Population Assessment Program, a power analysis was conducted using a normal linear mixed model with variance component estimates based on the first 3 years of data (2003 to 2005). In cases where 3 years of data were unavailable, estimates were obtained using those data. It was determined that at least 20 years of data, sampling 12 bends with 8 subsamples per bend, would be required to detect a 5 percent annual decline in most of the target fish populations. Power varied between Zones. Zone 1 (upstream from Lake Sakakawea) did not have any species/gear type combinations with adequate power, whereas Zone 3 (downstream from Gavins Point Dam) had 19 species/gear type combinations with adequate power. With a slight increase in the sampling effort to 12 subsamples per bend, the Pallid Sturgeon Population Assessment Program has adequate power to detect declines in shovelnose sturgeon (S. platorynchus) throughout the entire Missouri River because of large catch rates. The lowest level of non-occurrence (in other words, zero catches) at the bend level for pallid sturgeon was 0.58 using otter trawls in Zone 1. Consequently, the power of the pallid sturgeon models was not as high as other species at the current level of sampling, but an increase in the sampling effort to 16 subsamples for each of 24 bends for 20 years would generate adequate power for the pallid sturgeon in all Zones. Since gear types are selective in their species efficiency, the strength of the Pallid Sturgeon Population Assessment Program approach is using multiple gears that have statistical power to detect population trends at the same time in different fish species within the Missouri River. As often is the case with monitoring studies involving endangered species, the data used to conduct the analyses exhibit some departures from the parametric model assumptions; however, preliminary simulations indicate that the results of this study are appropriate.

Excavating past population structures by surname-based sampling: the genetic legacy of the Vikings in northwest England

PubMed Central

Bowden, Georgina R.; Balaresque, Patricia; King, Turi E.; Hansen, Ziff; Lee, Andrew C.; Pergl-Wilson, Giles; Hurley, Emma; Roberts, Stephen J.; Waite, Patrick; Jesch, Judith; Jones, Abigail L.; Thomas, Mark G.; Harding, Stephen E.; Jobling, Mark A.

2009-01-01

The genetic structures of past human populations are obscured by recent migrations and expansions, and can been observed only indirectly by inference from modern samples. However, the unique link between a heritable cultural marker, the patrilineal surname, and a genetic marker, the Y chromosome, provides a means to target sets of modern individuals that might resemble populations at the time of surname establishment. As a test case, we studied samples from the Wirral peninsula and West Lancashire, in northwest England. Place names and archaeology show clear evidence of a past Viking presence, but heavy immigration and population growth since the Industrial Revolution are likely to have weakened the genetic signal of a thousand-year-old Scandinavian contribution. Samples ascertained on the basis of two generations of residence were compared with independent samples based on known ancestry in the region, plus the possession of a surname known from historical records to have been present there in medieval times. The Y-chromosomal haplotypes of these two sets of samples are significantly different, and in admixture analyses the surname-ascertained samples show markedly greater Scandinavian ancestry proportions, supporting the idea that northwest England was once heavily populated by Scandinavian settlers. The method of historical surname-based ascertainment promises to allow investigation of the influence of migration and drift over the last few centuries in changing the population structure of Britain, and will have general utility in other regions where surnames are patrilineal and suitable historical records survive. PMID:18032405

USE OF COMMERCIAL TELEPHONE DIRECTORY FOR OBTAINING A POPULATION-BASED SAMPLE OF WOMEN OF REPRODUCTIVE AGE

EPA Science Inventory

Using Commercial Telephone Directories to Obtain a Population-Based Sample for Mail Survey of Women of Reproductive Age

Danelle T. Lobdella, Germaine M. Buckb, John M. Weinerc, Pauline Mendolaa

aUnited States Environmental Protection Agency, Office of Research and ...

The impact of demographic and perceptual variables on a young adult's decision to be covered by private health insurance.

PubMed

Cantiello, John; Fottler, Myron D; Oetjen, Dawn; Zhang, Ning Jackie

2015-05-12

The large number of uninsured individuals in the United States creates negative consequences for those who are uninsured and for those who are covered by health insurance plans. Young adults between the ages of 18 and 24 are the largest uninsured population subgroup. This subgroup warrants analysis. The major aim of this study is to determine why young adults between the ages of 18 and 24 are the largest uninsured population subgroup. The present study seeks to determine why young adults between the ages of 18 and 24 are the largest population subgroup that is not covered by private health insurance. Data on perceived health status, perceived need, perceived value, socioeconomic status, gender, and race was obtained from a national sample of 1,340 young adults from the 2005 Medical Expenditure Panel Survey and examined for possible explanatory variables, as well as data on the same variables from a national sample of 1,463 from the 2008 Medical Expenditure Panel Survey. Results of the structural equation model analysis indicate that insurance coverage in the 2005 sample was largely a function of higher socioeconomic status and being a non-minority. Perceived health status, perceived need, perceived value, and gender were not significant predictors of private health insurance coverage in the 2005 sample. However, in the 2008 sample, these indicators changed. Socioeconomic status, minority status, perceived health, perceived need, and perceived value were significant predictors of private health insurance coverage. The results of this study show that coverage by a private health insurance plan in the 2005 sample was largely a matter of having a higher socioeconomic status and having a non-minority status. In 2008 each of the attitudinal variables (perceived health, perceived value, and perceived need) predicted whether subjects carried private insurance. Our findings suggest that among those sampled, the young adult subgroup between the ages of 18 and 24 does not necessarily represent a unique segment of the population, with behaviors differing from the rest of the sample.

Antimicrobial susceptibility and distribution of inhibition zone diameters of bovine mastitis pathogens in Flanders, Belgium.

PubMed

Supré, K; Lommelen, K; De Meulemeester, L

2014-07-16

In dairy farms, antimicrobial drugs are frequently used for treatment of (sub)clinical mastitis. Determining the antimicrobial susceptibility of mastitis pathogens is needed to come to a correct use of antimicrobials. Strains of Staphylococcus aureus (n=768), Streptococcus uberis (n=939), Streptococcus dysgalactiae (n=444), Escherichia coli (n=563), and Klebsiella species (n=59) originating from routine milk samples from (sub)clinical mastitis were subjected to the disk diffusion method. Disks contained representatives of frequently used antibiotics in dairy. A limited number of clinical breakpoints were available through CLSI, and showed that susceptibility of Staph. aureus, E. coli, and Klebsiella was moderate to high. For streptococcal species however, a large variation between the tested species and the different antimicrobials was observed. In a next step, wild type populations were described based on epidemiological cut off values (EUCAST). Because of the limited number of official cut off values, the data were observed as a mastitis subpopulation and self-generated cut off values were created and a putative wild type population was suggested. The need for accurate clinical breakpoints for veterinary pathogens is high. Despite the lack of these breakpoints, however, a population study can be performed based on the distribution of inhibition zone diameters on the condition that a large number of strains is tested. Copyright © 2014 Elsevier B.V. All rights reserved.

Birth outcomes of male and female patients with infantile hypertrophic pyloric stenosis--a population-based case-control study.

PubMed

Vermes, Gabor; Mátrai, Ákos; Czeizel, Andrew E; Ács, Nándor

2016-01-01

Most of the patients are affected by isolated infantile hypertrophic pyloric stenosis (IHPS) beyond the polygenic predisposition, the other factors in the multifactorial etiology are largely unknown. The main characteristic of IHPS is the robust male predominance, thus the aim of this study was to analyze birth outcomes in males and females whether they are different or not. The study samples included 241 cases with IHPS, 357 matched, and 38,151 population controls without any defect in the population-based large dataset of the Hungarian Case-Control Surveillance of Congenital Abnormalities, 1980-1996. The findings of this case-control study confirmed the well-known strong male excess (85.5%). The mean gestational age was somewhat longer and it is associated with a lower rate of preterm births. Mean birth weight did not show significant differences among the study groups, but the rate of low birthweight was higher in cases with IHPS. However, these differences were found only in males. Thus, intrauterine fetal growth restriction is characteristic only for male cases with IHPS. Our study confirmed the well-known obvious male excess of cases with IHPS, but our findings suggest some differences in birth outcomes of male and female cases. Male cases with IHPS had intrauterine fetal growth restriction while females did not. These data may indicate some differences in the pathogenesis of IHPS in males and females.

Demography and genetic structure of a recovering grizzly bear population

USGS Publications Warehouse

Kendall, K.C.; Stetz, J.B.; Boulanger, J.; Macleod, A.C.; Paetkau, David; White, Gary C.

2009-01-01

Grizzly bears (brown bears; Ursus arctos) are imperiled in the southern extent of their range worldwide. The threatened population in northwestern Montana, USA, has been managed for recovery since 1975; yet, no rigorous data were available to monitor program success. We used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population. We combined data from our 3 sampling methods (hair trap, bear rub, and physical capture) to construct individual bear encounter histories for use in Huggins-Pledger closed mark-recapture models. Our population estimate, N?? = 765 (95% CI = 715-831) was more than double the existing estimate derived from sightings of females with young. Based on our results, the estimated known, human-caused mortality rate in 2004 was 4.6% (95% CI = 4.2-4.9%), slightly above the 4% considered sustainable; however, the high proportion of female mortalities raises concern. We used location data from telemetry, confirmed sightings, and genetic sampling to estimate occupied habitat. We found that grizzly bears occupied 33,480 km2 in the Northern Continental Divide Ecosystem (NCDE) during 1994-2007, including 10,340 km beyond the Recovery Zone. We used factorial correspondence analysis to identify potential barriers to gene flow within this population. Our results suggested that genetic interchange recently increased in areas with low gene flow in the past; however, we also detected evidence of incipient fragmentation across the major transportation corridor in this ecosystem. Our results suggest that the NCDE population is faring better than previously thought, and they highlight the need for a more rigorous monitoring program.

Population impact of a high cardiovascular risk management program delivered by village doctors in rural China: design and rationale of a large, cluster-randomized controlled trial.

PubMed

Yan, Lijing L; Fang, Weigang; Delong, Elizabeth; Neal, Bruce; Peterson, Eric D; Huang, Yining; Sun, Ningling; Yao, Chen; Li, Xian; MacMahon, Stephen; Wu, Yangfeng

2014-04-11

The high-risk strategy has been proven effective in preventing cardiovascular disease; however, the population benefits from these interventions remain unknown. This study aims to assess, at the population level, the effects of an evidence-based high cardiovascular risk management program delivered by village doctors in rural China. The study will employ a cluster-randomized controlled trial in which a total of 120 villages in five northern provinces of China, will be assigned to either intervention (60 villages) or control (60 villages). Village doctors in intervention villages will be trained to implement a simple evidence-based management program designed to identify, treat and follow-up as many as possible individuals at high-risk of cardiovascular disease in the village. The intervention will also include performance feedback as well as a performance-based incentive payment scheme and will last for 2 years. We will draw two different (independent) random samples, before and after the intervention, 20 men aged≥50 years and 20 women aged≥60 years from each village in each sample and a total of 9,600 participants from 2 samples to measure the study outcomes at the population level. The primary outcome will be the pre-post difference in mean systolic blood pressure, analyzed with a generalized estimating equations extension of linear regression model to account for cluster effect. Secondary outcomes will include monthly clinic visits, provision of lifestyle advice, use of antihypertensive medications and use of aspirin. Process and economic evaluations will also be conducted. This trial will be the first implementation trial in the world to evaluate the population impact of the high-risk strategy in prevention and control of cardiovascular disease. The results are expected to provide important information (effectiveness, cost-effectiveness, feasibility and acceptability) to guide policy making for rural China as well as other resource-limited countries. The trial is registered at ClinicalTrials.gov (NCT01259700). Date of initial registration is December 13, 2010.

Genetic Variation in the Acorn Barnacle from Allozymes to Population Genomics

PubMed Central

Flight, Patrick A.; Rand, David M.

2012-01-01

Understanding the patterns of genetic variation within and among populations is a central problem in population and evolutionary genetics. We examine this question in the acorn barnacle, Semibalanus balanoides, in which the allozyme loci Mpi and Gpi have been implicated in balancing selection due to varying selective pressures at different spatial scales. We review the patterns of genetic variation at the Mpi locus, compare this to levels of population differentiation at mtDNA and microsatellites, and place these data in the context of genome-wide variation from high-throughput sequencing of population samples spanning the North Atlantic. Despite considerable geographic variation in the patterns of selection at the Mpi allozyme, this locus shows rather low levels of population differentiation at ecological and trans-oceanic scales (FST ∼ 5%). Pooled population sequencing was performed on samples from Rhode Island (RI), Maine (ME), and Southwold, England (UK). Analysis of more than 650 million reads identified approximately 335,000 high-quality SNPs in 19 million base pairs of the S. balanoides genome. Much variation is shared across the Atlantic, but there are significant examples of strong population differentiation among samples from RI, ME, and UK. An FST outlier screen of more than 22,000 contigs provided a genome-wide context for interpretation of earlier studies on allozymes, mtDNA, and microsatellites. FST values for allozymes, mtDNA and microsatellites are close to the genome-wide average for random SNPs, with the exception of the trans-Atlantic FST for mtDNA. The majority of FST outliers were unique between individual pairs of populations, but some genes show shared patterns of excess differentiation. These data indicate that gene flow is high, that selection is strong on a subset of genes, and that a variety of genes are experiencing diversifying selection at large spatial scales. This survey of polymorphism in S. balanoides provides a number of genomic tools that promise to make this a powerful model for ecological genomics of the rocky intertidal. PMID:22767487

Steps Toward Unveiling the True Population of AGN: Photometric Selection of Broad-Line AGN

NASA Astrophysics Data System (ADS)

Schneider, Evan; Impey, C.

2012-01-01

We present an AGN selection technique that enables identification of broad-line AGN using only photometric data. An extension of infrared selection techniques, our method involves fitting a given spectral energy distribution with a model consisting of three physically motivated components: infrared power law emission, optical accretion disk emission, and host galaxy emission. Each component can be varied in intensity, and a reduced chi-square minimization routine is used to determine the optimum parameters for each object. Using this model, both broad- and narrow-line AGN are seen to fall within discrete ranges of parameter space that have plausible bounds, allowing physical trends with luminosity and redshift to be determined. Based on a fiducial sample of AGN from the catalog of Trump et al. (2009), we find the region occupied by broad-line AGN to be distinct from that of quiescent or star-bursting galaxies. Because this technique relies only on photometry, it will allow us to find AGN at fainter magnitudes than are accessible in spectroscopic surveys, and thus probe a population of less luminous and/or higher redshift objects. With the vast availability of photometric data in large surveys, this technique should have broad applicability and result in large samples that will complement X-ray AGN catalogs.

Moving on From Representativeness: Testing the Utility of the Global Drug Survey.

PubMed

Barratt, Monica J; Ferris, Jason A; Zahnow, Renee; Palamar, Joseph J; Maier, Larissa J; Winstock, Adam R

2017-01-01

A decline in response rates in traditional household surveys, combined with increased internet coverage and decreased research budgets, has resulted in increased attractiveness of web survey research designs based on purposive and voluntary opt-in sampling strategies. In the study of hidden or stigmatised behaviours, such as cannabis use, web survey methods are increasingly common. However, opt-in web surveys are often heavily criticised due to their lack of sampling frame and unknown representativeness. In this article, we outline the current state of the debate about the relevance of pursuing representativeness, the state of probability sampling methods, and the utility of non-probability, web survey methods especially for accessing hidden or minority populations. Our article has two aims: (1) to present a comprehensive description of the methodology we use at Global Drug Survey (GDS), an annual cross-sectional web survey and (2) to compare the age and sex distributions of cannabis users who voluntarily completed (a) a household survey or (b) a large web-based purposive survey (GDS), across three countries: Australia, the United States, and Switzerland. We find that within each set of country comparisons, the demographic distributions among recent cannabis users are broadly similar, demonstrating that the age and sex distributions of those who volunteer to be surveyed are not vastly different between these non-probability and probability methods. We conclude that opt-in web surveys of hard-to-reach populations are an efficient way of gaining in-depth understanding of stigmatised behaviours and are appropriate, as long as they are not used to estimate drug use prevalence of the general population.

Moving on From Representativeness: Testing the Utility of the Global Drug Survey

PubMed Central

Barratt, Monica J; Ferris, Jason A; Zahnow, Renee; Palamar, Joseph J; Maier, Larissa J; Winstock, Adam R

2017-01-01

A decline in response rates in traditional household surveys, combined with increased internet coverage and decreased research budgets, has resulted in increased attractiveness of web survey research designs based on purposive and voluntary opt-in sampling strategies. In the study of hidden or stigmatised behaviours, such as cannabis use, web survey methods are increasingly common. However, opt-in web surveys are often heavily criticised due to their lack of sampling frame and unknown representativeness. In this article, we outline the current state of the debate about the relevance of pursuing representativeness, the state of probability sampling methods, and the utility of non-probability, web survey methods especially for accessing hidden or minority populations. Our article has two aims: (1) to present a comprehensive description of the methodology we use at Global Drug Survey (GDS), an annual cross-sectional web survey and (2) to compare the age and sex distributions of cannabis users who voluntarily completed (a) a household survey or (b) a large web-based purposive survey (GDS), across three countries: Australia, the United States, and Switzerland. We find that within each set of country comparisons, the demographic distributions among recent cannabis users are broadly similar, demonstrating that the age and sex distributions of those who volunteer to be surveyed are not vastly different between these non-probability and probability methods. We conclude that opt-in web surveys of hard-to-reach populations are an efficient way of gaining in-depth understanding of stigmatised behaviours and are appropriate, as long as they are not used to estimate drug use prevalence of the general population. PMID:28924351

Characterizing abnormal behavior in a large population of zoo-housed chimpanzees: prevalence and potential influencing factors

PubMed Central

Jacobson, Sarah L.; Bloomsmith, Mollie A.

2016-01-01

Abnormal behaviors in captive animals are generally defined as behaviors that are atypical for the species and are often considered to be indicators of poor welfare. Although some abnormal behaviors have been empirically linked to conditions related to elevated stress and compromised welfare in primates, others have little or no evidence on which to base such a relationship. The objective of this study was to investigate a recent claim that abnormal behavior is endemic in the captive population by surveying a broad sample of chimpanzees (Pan troglodytes), while also considering factors associated with the origins of these behaviors. We surveyed animal care staff from 26 accredited zoos to assess the prevalence of abnormal behavior in a large sample of chimpanzees in the United States for which we had information on origin and rearing history. Our results demonstrated that 64% of this sample was reported to engage in some form of abnormal behavior in the past two years and 48% of chimpanzees engaged in abnormal behavior other than coprophagy. Logistic regression models were used to analyze the historical variables that best predicted the occurrence of all abnormal behavior, any abnormal behavior that was not coprophagy, and coprophagy. Rearing had opposing effects on the occurrence of coprophagy and the other abnormal behaviors such that mother-reared individuals were more likely to perform coprophagy, whereas non-mother-reared individuals were more likely to perform other abnormal behaviors. These results support the assertion that coprophagy may be classified separately when assessing abnormal behavior and the welfare of captive chimpanzees. This robust evaluation of the prevalence of abnormal behavior in our sample from the U.S. zoo population also demonstrates the importance of considering the contribution of historical variables to present behavior, in order to better understand the causes of these behaviors and any potential relationship to psychological wellbeing. PMID:27478710

Genetic differentiation among North Atlantic killer whale populations.

PubMed

Foote, Andrew D; Vilstrup, Julia T; De Stephanis, Renaud; Verborgh, Philippe; Abel Nielsen, Sandra C; Deaville, Robert; Kleivane, Lars; Martín, Vidal; Miller, Patrick J O; Oien, Nils; Pérez-Gil, Monica; Rasmussen, Morten; Reid, Robert J; Robertson, Kelly M; Rogan, Emer; Similä, Tiu; Tejedor, Maria L; Vester, Heike; Víkingsson, Gísli A; Willerslev, Eske; Gilbert, M Thomas P; Piertney, Stuart B

2011-02-01

Population genetic structure of North Atlantic killer whale samples was resolved from differences in allele frequencies of 17 microsatellite loci, mtDNA control region haplotype frequencies and for a subset of samples, using complete mitogenome sequences. Three significantly differentiated populations were identified. Differentiation based on microsatellite allele frequencies was greater between the two allopatric populations than between the two pairs of partially sympatric populations. Spatial clustering of individuals within each of these populations overlaps with the distribution of particular prey resources: herring, mackerel and tuna, which each population has been seen predating. Phylogenetic analyses using complete mitogenomes suggested two populations could have resulted from single founding events and subsequent matrilineal expansion. The third population, which was sampled at lower latitudes and lower density, consisted of maternal lineages from three highly divergent clades. Pairwise population differentiation was greater for estimates based on mtDNA control region haplotype frequencies than for estimates based on microsatellite allele frequencies, and there were no mitogenome haplotypes shared among populations. This suggests low or no female migration and that gene flow was primarily male mediated when populations spatially and temporally overlap. These results demonstrate that genetic differentiation can arise through resource specialization in the absence of physical barriers to gene flow. © 2010 Blackwell Publishing Ltd.

Variance Estimation, Design Effects, and Sample Size Calculations for Respondent-Driven Sampling

PubMed Central

2006-01-01

Hidden populations, such as injection drug users and sex workers, are central to a number of public health problems. However, because of the nature of these groups, it is difficult to collect accurate information about them, and this difficulty complicates disease prevention efforts. A recently developed statistical approach called respondent-driven sampling improves our ability to study hidden populations by allowing researchers to make unbiased estimates of the prevalence of certain traits in these populations. Yet, not enough is known about the sample-to-sample variability of these prevalence estimates. In this paper, we present a bootstrap method for constructing confidence intervals around respondent-driven sampling estimates and demonstrate in simulations that it outperforms the naive method currently in use. We also use simulations and real data to estimate the design effects for respondent-driven sampling in a number of situations. We conclude with practical advice about the power calculations that are needed to determine the appropriate sample size for a study using respondent-driven sampling. In general, we recommend a sample size twice as large as would be needed under simple random sampling. PMID:16937083

Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps.

PubMed

Garud, Nandita R; Messer, Philipp W; Buzbas, Erkan O; Petrov, Dmitri A

2015-02-01

Adaptation from standing genetic variation or recurrent de novo mutation in large populations should commonly generate soft rather than hard selective sweeps. In contrast to a hard selective sweep, in which a single adaptive haplotype rises to high population frequency, in a soft selective sweep multiple adaptive haplotypes sweep through the population simultaneously, producing distinct patterns of genetic variation in the vicinity of the adaptive site. Current statistical methods were expressly designed to detect hard sweeps and most lack power to detect soft sweeps. This is particularly unfortunate for the study of adaptation in species such as Drosophila melanogaster, where all three confirmed cases of recent adaptation resulted in soft selective sweeps and where there is evidence that the effective population size relevant for recent and strong adaptation is large enough to generate soft sweeps even when adaptation requires mutation at a specific single site at a locus. Here, we develop a statistical test based on a measure of haplotype homozygosity (H12) that is capable of detecting both hard and soft sweeps with similar power. We use H12 to identify multiple genomic regions that have undergone recent and strong adaptation in a large population sample of fully sequenced Drosophila melanogaster strains from the Drosophila Genetic Reference Panel (DGRP). Visual inspection of the top 50 candidates reveals that in all cases multiple haplotypes are present at high frequencies, consistent with signatures of soft sweeps. We further develop a second haplotype homozygosity statistic (H2/H1) that, in combination with H12, is capable of differentiating hard from soft sweeps. Surprisingly, we find that the H12 and H2/H1 values for all top 50 peaks are much more easily generated by soft rather than hard sweeps. We discuss the implications of these results for the study of adaptation in Drosophila and in species with large census population sizes.

Are Antarctic minke whales unusually abundant because of 20th century whaling?

PubMed

Ruegg, Kristen C; Anderson, Eric C; Scott Baker, C; Vant, Murdoch; Jackson, Jennifer A; Palumbi, Stephen R

2010-01-01

Severe declines in megafauna worldwide illuminate the role of top predators in ecosystem structure. In the Antarctic, the Krill Surplus Hypothesis posits that the killing of more than 2 million large whales led to competitive release for smaller krill-eating species like the Antarctic minke whale. If true, the current size of the Antarctic minke whale population may be unusually high as an indirect result of whaling. Here, we estimate the long-term population size of the Antarctic minke whale prior to whaling by sequencing 11 nuclear genetic markers from 52 modern samples purchased in Japanese meat markets. We use coalescent simulations to explore the potential influence of population substructure and find that even though our samples are drawn from a limited geographic area, our estimate reflects ocean-wide genetic diversity. Using Bayesian estimates of the mutation rate and coalescent-based analyses of genetic diversity across loci, we calculate the long-term population size of the Antarctic minke whale to be 670,000 individuals (95% confidence interval: 374,000-1,150,000). Our estimate of long-term abundance is similar to, or greater than, contemporary abundance estimates, suggesting that managing Antarctic ecosystems under the assumption that Antarctic minke whales are unusually abundant is not warranted.

Developmental Stuttering in Children Who Are Hard of Hearing

PubMed Central

Walker, Elizabeth A.; Oleson, Jacob J.

2017-01-01

Purpose A number of studies with large sample sizes have reported lower prevalence of stuttering in children with significant hearing loss compared to children without hearing loss. This study used a parent questionnaire to investigate the characteristics of stuttering (e.g., incidence, prevalence, and age of onset) in children who are hard of hearing (CHH). Method Three hundred three parents of CHH who participated in the Outcomes of Children With Hearing Loss study (Moeller & Tomblin, 2015) were sent questionnaires asking about their child's history of stuttering. Results One hundred ninety-four parents of CHH responded to the survey. Thirty-three CHH were reported to have stuttered at one point in time (an incidence of 17.01%), and 10 children were still stuttering at the time of survey submission (a prevalence of 5.15%). Compared to estimates in the general population, this sample displayed a significantly higher incidence and prevalence. The age of onset, recovery rate, and other characteristics were similar to hearing children. Conclusions Based on this sample, mild to moderately severe hearing loss does not appear to be a protective factor for stuttering in the preschool years. In fact, the incidence and prevalence of stuttering may be higher in this population compared to the general population. Despite the significant speech and language needs that children with mild to moderately severe hearing loss may have, speech-language pathologists should appropriately prioritize stuttering treatment as they would in the hearing population. Supplemental Material https://doi.org/10.23641/asha.5397154 PMID:28915514

Developmental Stuttering in Children Who Are Hard of Hearing.

PubMed

Arenas, Richard M; Walker, Elizabeth A; Oleson, Jacob J

2017-10-05

A number of studies with large sample sizes have reported lower prevalence of stuttering in children with significant hearing loss compared to children without hearing loss. This study used a parent questionnaire to investigate the characteristics of stuttering (e.g., incidence, prevalence, and age of onset) in children who are hard of hearing (CHH). Three hundred three parents of CHH who participated in the Outcomes of Children With Hearing Loss study (Moeller & Tomblin, 2015) were sent questionnaires asking about their child's history of stuttering. One hundred ninety-four parents of CHH responded to the survey. Thirty-three CHH were reported to have stuttered at one point in time (an incidence of 17.01%), and 10 children were still stuttering at the time of survey submission (a prevalence of 5.15%). Compared to estimates in the general population, this sample displayed a significantly higher incidence and prevalence. The age of onset, recovery rate, and other characteristics were similar to hearing children. Based on this sample, mild to moderately severe hearing loss does not appear to be a protective factor for stuttering in the preschool years. In fact, the incidence and prevalence of stuttering may be higher in this population compared to the general population. Despite the significant speech and language needs that children with mild to moderately severe hearing loss may have, speech-language pathologists should appropriately prioritize stuttering treatment as they would in the hearing population. https://doi.org/10.23641/asha.5397154.

Does Exposure to Agricultural Chemicals Increase the Risk of Prostate Cancer among Farmers?

PubMed Central

Parent, Marie-Élise; Désy, Marie; Siemiatycki, Jack

2009-01-01

Several studies suggest that farmers may be at increased risk of prostate cancer. The present analysis, based on a large population-based case-control study conducted among men in the Montreal area in the early 1980’s, aim at identifying occupational chemicals which may be responsible for such increases. The original study enrolled 449 prostate cancer cases, nearly 4,000 patients with other cancers, as well as 533 population controls. Subjects were interviewed about their occupation histories, and a team of industrial hygienists assigned their past exposures using a checklist of some 300 chemicals. The present analysis was restricted to a study base of men who had worked as farmers earlier in their lives. There were a total of 49 men with prostate cancers, 127 with other cancers and 56 population controls. We created a pool of 183 controls combining the patients with cancers at sites other than the prostate and the population controls. We then estimated the odds ratio for prostate cancer associated with exposure to each of 10 agricultural chemicals, i.e., pesticides, arsenic compounds, acetic acid, gasoline engine emissions, diesel engine emissions, polycyclic aromatic hydrocarbons from petroleum, lubricating oils and greases, alkanes with ≥18 carbons, solvents, and mononuclear aromatic hydrocarbons. Based on a model adjusting for age, ethnicity, education, and respondent status, there was evidence of a two-fold excess risk of prostate cancer among farmers with substantial exposure to pesticides [odds ratio (OR)=2.3, 95% confidence interval (CI) 1.1–5.1], as compared to unexposed farmers. There was some suggestion, based on few subjects, of increased risks among farmers ever exposed to diesel engine emissions (OR=5.7, 95% CI 1.2–26.5). The results for pesticides are particularly noteworthy in the light of findings from previous studies. Suggestions of trends for elevated risks were noted with other agricultural chemicals, but these are largely novel and need further confirmation in larger samples. PMID:19753293

Zoonotic Babesia microti in the northeastern U.S.: Evidence for the expansion of a specific parasite lineage

PubMed Central

Molloy, Philip; Weeks, Karen

2018-01-01

The recent range expansion of human babesiosis in the northeastern United States, once found only in restricted coastal sites, is not well understood. This study sought to utilize a large number of samples to examine the population structure of the parasites on a fine scale to provide insights into the mode of emergence across the region. 228 B. microti samples collected in endemic northeastern U.S. sites were genotyped using published Variable number tandem repeat (VNTR) markers. The genetic diversity and population structure were analysed on a geographic scale using Phyloviz and TESS, programs that utilize two different methods to identify population membership without predefined population data. Three distinct populations were detected in northeastern US, each dominated by a single ancestral type. In contrast to the limited range of the Nantucket and Cape Cod populations, the mainland population dominated from New Jersey eastward to Boston. Ancestral populations of B. microti were sufficiently isolated to differentiate into distinct populations. Despite this, a single population was detected across a large geographic area of the northeast that historically had at least 3 distinct foci of transmission, central New Jersey, Long Island and southeastern Connecticut. We conclude that a single B. microti genotype has expanded across the northeastern U.S. The biological attributes associated with this parasite genotype that have contributed to such a selective sweep remain to be identified. PMID:29565993

Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure.

PubMed

Bohmann, Kristine; Gopalakrishnan, Shyam; Nielsen, Martin; Nielsen, Luisa Dos Santos Bay; Jones, Gareth; Streicker, Daniel G; Gilbert, M Thomas P

2018-04-19

Metabarcoding diet analysis has become a valuable tool in animal ecology; however, co-amplified predator sequences are not generally used for anything other than to validate predator identity. Exemplified by the common vampire bat, we demonstrate the use of metabarcoding to infer predator population structure alongside diet assessments. Growing populations of common vampire bats impact human, livestock and wildlife health in Latin America through transmission of pathogens, such as lethal rabies viruses. Techniques to determine large-scale variation in vampire bat diet and bat population structure would empower locality- and species-specific projections of disease transmission risks. However, previously used methods are not cost-effective and efficient for large-scale applications. Using bloodmeal and faecal samples from common vampire bats from coastal, Andean and Amazonian regions of Peru, we showcase metabarcoding as a scalable tool to assess vampire bat population structure and feeding preferences. Dietary metabarcoding was highly effective, detecting vertebrate prey in 93.2% of the samples. Bats predominantly preyed on domestic animals, but fed on tapirs at one Amazonian site. In addition, we identified arthropods in 9.3% of samples, likely reflecting consumption of ectoparasites. Using the same data, we document mitochondrial geographic population structure in the common vampire bat in Peru. Such simultaneous inference of vampire bat diet and population structure can enable new insights into the interplay between vampire bat ecology and disease transmission risks. Importantly, the methodology can be incorporated into metabarcoding diet studies of other animals to couple information on diet and population structure. © 2018 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Investigations of potential bias in the estimation of lambda using Pradel's (1996) model for capture-recapture data

USGS Publications Warehouse

Hines, J.E.; Nichols, J.D.

2002-01-01

Pradel's (1996) temporal symmetry model permitting direct estimation and modelling of population growth rate, lambda sub i provides a potentially useful tool for the study of population dynamics using marked animals. Because of its recent publication date, the approach has not seen much use, and there have been virtually no investigations directed at robustness of the resulting estimators. Here we consider several potential sources of bias, all motivated by specific uses of this estimation approach. We consider sampling situations in which the study area expands with time and present an analytic expression for the bias in lambda hat sub i. We next consider trap response in capture probabilities and heterogeneous capture probabilities and compute large-sample and simulation-based approximations of resulting bias in lambda hat sub i. These approximations indicate that trap response is an especially important assumption violation that can produce substantial bias. Finally, we consider losses on capture and emphasize the importance of selecting the estimator for lambda sub i that is appropriate to the question being addressed. For studies based on only sighting and resighting data, Pradel's (1996) lambda hat prime sub i is the appropriate estimator.

Sexual orientation and substance abuse treatment utilization in the United States: results from a national survey.

PubMed

McCabe, Sean Esteban; West, Brady T; Hughes, Tonda L; Boyd, Carol J

2013-01-01

This study examined substance abuse treatment utilization across three dimensions of sexual orientation (identity, attraction, and behavior) in a large national sample of adults in the United States. Prevalence estimates were based on data collected from the 2004-2005 National Epidemiologic Survey on Alcohol and Related Conditions. The sample consisted of 34,653 adults 20 years and older, and represented a population that was 52% women, 71% White, 12% Hispanic, 11% African American, 4% Asian, and 2% other race/ethnicities. An estimated 2% of the target population self-identified as lesbian, gay or bisexual; 4% reported same-sex sexual behavior, and 6% reported same-sex sexual attraction. Sexual minorities, especially women, had a greater likelihood of lifetime substance use disorders and earlier age of drinking onset. The majority of respondents with substance use disorders were untreated and lifetime substance abuse treatment utilization differed based on sexual orientation. Sexual minorities were found to have more extensive family histories of substance abuse problems. The findings indicate the underutilization of substance abuse treatment among all adults, and highlight some important factors to consider when working with sexual minorities. Copyright © 2013 Elsevier Inc. All rights reserved.

Mapping cell populations in flow cytometry data for cross‐sample comparison using the Friedman–Rafsky test statistic as a distance measure

PubMed Central

Hsiao, Chiaowen; Liu, Mengya; Stanton, Rick; McGee, Monnie; Qian, Yu

2015-01-01

Abstract Flow cytometry (FCM) is a fluorescence‐based single‐cell experimental technology that is routinely applied in biomedical research for identifying cellular biomarkers of normal physiological responses and abnormal disease states. While many computational methods have been developed that focus on identifying cell populations in individual FCM samples, very few have addressed how the identified cell populations can be matched across samples for comparative analysis. This article presents FlowMap‐FR, a novel method for cell population mapping across FCM samples. FlowMap‐FR is based on the Friedman–Rafsky nonparametric test statistic (FR statistic), which quantifies the equivalence of multivariate distributions. As applied to FCM data by FlowMap‐FR, the FR statistic objectively quantifies the similarity between cell populations based on the shapes, sizes, and positions of fluorescence data distributions in the multidimensional feature space. To test and evaluate the performance of FlowMap‐FR, we simulated the kinds of biological and technical sample variations that are commonly observed in FCM data. The results show that FlowMap‐FR is able to effectively identify equivalent cell populations between samples under scenarios of proportion differences and modest position shifts. As a statistical test, FlowMap‐FR can be used to determine whether the expression of a cellular marker is statistically different between two cell populations, suggesting candidates for new cellular phenotypes by providing an objective statistical measure. In addition, FlowMap‐FR can indicate situations in which inappropriate splitting or merging of cell populations has occurred during gating procedures. We compared the FR statistic with the symmetric version of Kullback–Leibler divergence measure used in a previous population matching method with both simulated and real data. The FR statistic outperforms the symmetric version of KL‐distance in distinguishing equivalent from nonequivalent cell populations. FlowMap‐FR was also employed as a distance metric to match cell populations delineated by manual gating across 30 FCM samples from a benchmark FlowCAP data set. An F‐measure of 0.88 was obtained, indicating high precision and recall of the FR‐based population matching results. FlowMap‐FR has been implemented as a standalone R/Bioconductor package so that it can be easily incorporated into current FCM data analytical workflows. © 2015 International Society for Advancement of Cytometry PMID:26274018

Mapping cell populations in flow cytometry data for cross-sample comparison using the Friedman-Rafsky test statistic as a distance measure.

PubMed

Hsiao, Chiaowen; Liu, Mengya; Stanton, Rick; McGee, Monnie; Qian, Yu; Scheuermann, Richard H

2016-01-01

Flow cytometry (FCM) is a fluorescence-based single-cell experimental technology that is routinely applied in biomedical research for identifying cellular biomarkers of normal physiological responses and abnormal disease states. While many computational methods have been developed that focus on identifying cell populations in individual FCM samples, very few have addressed how the identified cell populations can be matched across samples for comparative analysis. This article presents FlowMap-FR, a novel method for cell population mapping across FCM samples. FlowMap-FR is based on the Friedman-Rafsky nonparametric test statistic (FR statistic), which quantifies the equivalence of multivariate distributions. As applied to FCM data by FlowMap-FR, the FR statistic objectively quantifies the similarity between cell populations based on the shapes, sizes, and positions of fluorescence data distributions in the multidimensional feature space. To test and evaluate the performance of FlowMap-FR, we simulated the kinds of biological and technical sample variations that are commonly observed in FCM data. The results show that FlowMap-FR is able to effectively identify equivalent cell populations between samples under scenarios of proportion differences and modest position shifts. As a statistical test, FlowMap-FR can be used to determine whether the expression of a cellular marker is statistically different between two cell populations, suggesting candidates for new cellular phenotypes by providing an objective statistical measure. In addition, FlowMap-FR can indicate situations in which inappropriate splitting or merging of cell populations has occurred during gating procedures. We compared the FR statistic with the symmetric version of Kullback-Leibler divergence measure used in a previous population matching method with both simulated and real data. The FR statistic outperforms the symmetric version of KL-distance in distinguishing equivalent from nonequivalent cell populations. FlowMap-FR was also employed as a distance metric to match cell populations delineated by manual gating across 30 FCM samples from a benchmark FlowCAP data set. An F-measure of 0.88 was obtained, indicating high precision and recall of the FR-based population matching results. FlowMap-FR has been implemented as a standalone R/Bioconductor package so that it can be easily incorporated into current FCM data analytical workflows. © The Authors. Published by Wiley Periodicals, Inc. on behalf of ISAC.

Production and characterization of single-chain antibody (scFv) against 3ABC non-structural protein in Escherichia coli for sero-diagnosis of Foot and Mouth Disease virus.

PubMed

Sharma, Gaurav K; Mahajan, Sonalika; Matura, Rakesh; Subramaniam, Saravanan; Mohapatra, Jajati K; Pattnaik, Bramhadev

2014-11-01

Differentiation of Foot-and-Mouth Disease infected from vaccinated animals is essential for effective implementation of vaccination based control programme. Detection of antibodies against 3ABC non-structural protein of FMD virus by immunodiagnostic assays provides reliable indication of FMD infection. Sero-monitoring of FMD in the large country like India is a big task where thousands of serum samples are annually screened. Currently, monoclonal or polyclonal antibodies are widely used in these immunodiagnostic assays. Considering the large population of livestock in the country, an economical and replenishable alternative of these antibodies was required. In this study, specific short chain variable fragment (scFv) antibody against 3B region of 3ABC poly-protein was developed. High level of scFv expression in Escherichia coli system was obtained by careful optimization in four different strains. Two formats of enzyme immunoassays (sandwich and competitive ELISAs) were optimized using scFv with objective to differentiate FMD infected among the vaccinated population. The assays were statistically validated by testing 2150 serum samples. Diagnostic sensitivity/specificity of sandwich and competitive ELISAs were determined by ROC method as 92.2%/95.5% and 89.5%/93.5%, respectively. This study demonstrated that scFv is a suitable alternate for immunodiagnosis of FMD on large scale. Copyright © 2014 The International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

HLA imputation in an admixed population: An assessment of the 1000 Genomes data as a training set.

PubMed

Nunes, Kelly; Zheng, Xiuwen; Torres, Margareth; Moraes, Maria Elisa; Piovezan, Bruno Z; Pontes, Gerlandia N; Kimura, Lilian; Carnavalli, Juliana E P; Mingroni Netto, Regina C; Meyer, Diogo

2016-03-01

Methods to impute HLA alleles based on dense single nucleotide polymorphism (SNP) data provide a valuable resource to association studies and evolutionary investigation of the MHC region. The availability of appropriate training sets is critical to the accuracy of HLA imputation, and the inclusion of samples with various ancestries is an important pre-requisite in studies of admixed populations. We assess the accuracy of HLA imputation using 1000 Genomes Project data as a training set, applying it to a highly admixed Brazilian population, the Quilombos from the state of São Paulo. To assess accuracy, we compared imputed and experimentally determined genotypes for 146 samples at 4 HLA classical loci. We found imputation accuracies of 82.9%, 81.8%, 94.8% and 86.6% for HLA-A, -B, -C and -DRB1 respectively (two-field resolution). Accuracies were improved when we included a subset of Quilombo individuals in the training set. We conclude that the 1000 Genomes data is a valuable resource for construction of training sets due to the diversity of ancestries and the potential for a large overlap of SNPs with the target population. We also show that tailoring training sets to features of the target population substantially enhances imputation accuracy. Copyright © 2016 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping.

PubMed

Frickenhaus, Stephan; Kannan, Srinivasaraghavan; Zacharias, Martin

2009-02-01

A direct conformational clustering and mapping approach for peptide conformations based on backbone dihedral angles has been developed and applied to compare conformational sampling of Met-enkephalin using two molecular dynamics (MD) methods. Efficient clustering in dihedrals has been achieved by evaluating all combinations resulting from independent clustering of each dihedral angle distribution, thus resolving all conformational substates. In contrast, Cartesian clustering was unable to accurately distinguish between all substates. Projection of clusters on dihedral principal component (PCA) subspaces did not result in efficient separation of highly populated clusters. However, representation in a nonlinear metric by Sammon mapping was able to separate well the 48 highest populated clusters in just two dimensions. In addition, this approach also allowed us to visualize the transition frequencies between clusters efficiently. Significantly, higher transition frequencies between more distinct conformational substates were found for a recently developed biasing-potential replica exchange MD simulation method allowing faster sampling of possible substates compared to conventional MD simulations. Although the number of theoretically possible clusters grows exponentially with peptide length, in practice, the number of clusters is only limited by the sampling size (typically much smaller), and therefore the method is well suited also for large systems. The approach could be useful to rapidly and accurately evaluate conformational sampling during MD simulations, to compare different sampling strategies and eventually to detect kinetic bottlenecks in folding pathways.

Intuitive statistics by 8-month-old infants

PubMed Central

Xu, Fei; Garcia, Vashti

2008-01-01

Human learners make inductive inferences based on small amounts of data: we generalize from samples to populations and vice versa. The academic discipline of statistics formalizes these intuitive statistical inferences. What is the origin of this ability? We report six experiments investigating whether 8-month-old infants are “intuitive statisticians.” Our results showed that, given a sample, the infants were able to make inferences about the population from which the sample had been drawn. Conversely, given information about the entire population of relatively small size, the infants were able to make predictions about the sample. Our findings provide evidence that infants possess a powerful mechanism for inductive learning, either using heuristics or basic principles of probability. This ability to make inferences based on samples or information about the population develops early and in the absence of schooling or explicit teaching. Human infants may be rational learners from very early in development. PMID:18378901

Reference intervals for plasma-free amino acid in a Japanese population.

PubMed

Yamamoto, Hiroyuki; Kondo, Kazuhiro; Tanaka, Takayuki; Muramatsu, Takahiko; Yoshida, Hiroo; Imaizumi, Akira; Nagao, Kenji; Noguchi, Yasushi; Miyano, Hiroshi

2016-05-01

Plasma amino acid concentrations vary with various diseases. Although reference intervals are useful in daily clinical practice, no reference intervals have been reported for plasma amino acids in a large Japanese population. Reference individuals were selected from 7685 subjects examined with the Japanese Ningen Dock in 2008. A total of 1890 individuals were selected based on exclusion criteria, and the reference samples were selected after the outlier samples for each amino acid concentration were excluded. The lower limit of the reference intervals for the plasma amino acid concentrations was set at the 2.5th percentile and the upper limit at the 97.5th percentile. By use of the nested analysis of variance, we analysed a large dataset of plasma samples and the effects of background factors (sex, age and body mass index [BMI]) on the plasma amino acid concentrations. Most amino acid concentrations were related to sex, especially those of branched-chained amino acid. The citrulline, glutamine, ornithine and lysine concentrations were related to age. The glutamate concentration was related to body mass index. The concentrations of most amino acids are more strongly related to sex than to age or body mass index. Our results indicate that the reference intervals for plasma amino acid concentrations should be stratified by sex when the background factors of age and body mass index are considered. © The Author(s) 2015 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

A Spatial Framework for Understanding Population Structure and Admixture.

PubMed

Bradburd, Gideon S; Ralph, Peter L; Coop, Graham M

2016-01-01

Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build "geogenetic maps," which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix.

A Spatial Framework for Understanding Population Structure and Admixture

PubMed Central

Bradburd, Gideon S.; Ralph, Peter L.; Coop, Graham M.

2016-01-01

Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build “geogenetic maps,” which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix. PMID:26771578

Differential Risk of Injury to Child Occupants by SUV Size

PubMed Central

Kallan, Michael J.; Durbin, Dennis R.; Elliott, Michael R.; Arbogast, Kristy B.; Winston, Flaura K.

2004-01-01

In the United States, the sport utility vehicle (SUV) is the fastest growing segment of the passenger vehicle fleet, yet SUVs vary widely in size and crashworthiness. Using data collected from a population-based sample of crashes in insured vehicles, we quantified the risk of injury to child occupants in SUVs by vehicle weight. There is an increased risk in both Small and Midsize SUVs when compared to Large SUVs. Parents who are purchasing a SUV should strongly consider the size of the vehicle and its crashworthiness. PMID:15319119

Psychometric properties and confirmatory factor analysis of the CASP-19, a measure of quality of life in early old age: the HAPIEE study

PubMed Central

Kim, Gyu Ri; Netuveli, Gopalakrishnan; Blane, David; Peasey, Anne; Malyutina, Sofia; Simonova, Galina; Kubinova, Ruzena; Pajak, Andrzej; Croezen, Simone; Bobak, Martin; Pikhart, Hynek

2015-01-01

Objectives: The aim was to assess the reliability and validity of the quality of life (QoL) instrument CASP-19, and three shorter versions of CASP-12 in large population sample of older adults from the HAPIEE (Health, Alcohol, and Psychosocial factors In Eastern Europe) study. Methods: From the Czech Republic, Russia, and Poland, 13,210 HAPIEE participants aged 50 or older completed the retirement questionnaire including CASP-19 at baseline. Three shorter 12-item versions were also derived from original 19-item instrument. Psychometric validation used confirmatory factor analysis, Cronbach's alpha, Pearson's correlation, and construct validity. Results: The second-order four-factor model of CASP-19 did not provide a good fit to the data. Two-factor CASP-12v.3 including residual covariances for negative items to account for the method effect of negative items had the best fit to the data in all countries (CFI = 0.98, TLI = 0.97, RMSEA = 0.05, and WRMR = 1.65 in the Czech Republic; 0.96, 0.94, 0.07, and 2.70 in Poland; and 0.93, 0.90, 0.08, and 3.04 in Russia). Goodness-of-fit indices for the two-factor structure were substantially better than second-order models. Conclusions: This large population-based study is the first validation study of CASP scale in Central and Eastern Europe (CEE), which includes a general population sample in Russia, Poland, and the Czech Republic. The results of this study have demonstrated that the CASP-12v.3 is a valid and reliable tool for assessing QoL among adults aged 50 years or older. This version of CASP is recommended for use in future studies investigating QoL in the CEE populations. PMID:25059754

Exploring differences in pain beliefs within and between a large nonclinical (workplace) population and a clinical (chronic low back pain) population using the pain beliefs questionnaire.

PubMed

Baird, Andrew J; Haslam, Roger A

2013-12-01

Beliefs, cognitions, and behaviors relating to pain can be associated with a range of negative outcomes. In patients, certain beliefs are associated with increased levels of pain and related disability. There are few data, however, showing the extent to which beliefs of patients differ from those of the general population. This study explored pain beliefs in a large nonclinical population and a chronic low back pain (CLBP) sample using the Pain Beliefs Questionnaire (PBQ) to identify differences in scores and factor structures between and within the samples. This was a cross-sectional study. The samples comprised patients attending a rehabilitation program and respondents to a workplace survey. Pain beliefs were assessed using the PBQ, which incorporates 2 scales: organic and psychological. Exploratory factor analysis was used to explore variations in factor structure within and between samples. The relationship between the 2 scales also was examined. Patients reported higher organic scores and lower psychological scores than the nonclinical sample. Within the nonclinical sample, those who reported frequent pain scored higher on the organic scale than those who did not. Factor analysis showed variations in relation to the presence of pain. The relationship between scales was stronger in those not reporting frequent pain. This was a cross-sectional study; therefore, no causal inferences can be made. Patients experiencing CLBP adopt a more biomedical perspective on pain than nonpatients. The presence of pain is also associated with increased biomedical thinking in a nonclinical sample. However, the impact is not only on the strength of beliefs, but also on the relationship between elements of belief and the underlying belief structure.

Aerial survey methodology for bison population estimation in Yellowstone National Park

USGS Publications Warehouse

Hess, Steven C.

2002-01-01

I developed aerial survey methods for statistically rigorous bison population estimation in Yellowstone National Park to support sound resource management decisions and to understand bison ecology. Survey protocols, data recording procedures, a geographic framework, and seasonal stratifications were based on field observations from February 1998-September 2000. The reliability of this framework and strata were tested with long-term data from 1970-1997. I simulated different sample survey designs and compared them to high-effort censuses of well-defined large areas to evaluate effort, precision, and bias. Sample survey designs require much effort and extensive information on the current spatial distribution of bison and therefore do not offer any substantial reduction in time and effort over censuses. I conducted concurrent ground surveys, or 'double sampling' to estimate detection probability during aerial surveys. Group size distribution and habitat strongly affected detection probability. In winter, 75% of the groups and 92% of individual bison were detected on average from aircraft, while in summer, 79% of groups and 97% of individual bison were detected. I also used photography to quantify the bias due to counting large groups of bison accurately and found that undercounting increased with group size and could reach 15%. I compared survey conditions between seasons and identified optimal time windows for conducting surveys in both winter and summer. These windows account for the habitats and total area bison occupy, and group size distribution. Bison became increasingly scattered over the Yellowstone region in smaller groups and more occupied unfavorable habitats as winter progressed. Therefore, the best conditions for winter surveys occur early in the season (Dec-Jan). In summer, bison were most spatially aggregated and occurred in the largest groups by early August. Low variability between surveys and high detection probability provide population estimates with an overall coefficient of variation of approximately 8% and have high power for detecting trends in population change. I demonstrated how population estimates from winter and summer can be integrated into a comprehensive monitoring program to estimate annual growth rates, overall winter mortality, and an index of calf production, requiring about 30 hours of flight per year.

Transgender Population Size in the United States: a Meta-Regression of Population-Based Probability Samples

PubMed Central

Sevelius, Jae M.

2017-01-01

Background. Transgender individuals have a gender identity that differs from the sex they were assigned at birth. The population size of transgender individuals in the United States is not well-known, in part because official records, including the US Census, do not include data on gender identity. Population surveys today more often collect transgender-inclusive gender-identity data, and secular trends in culture and the media have created a somewhat more favorable environment for transgender people. Objectives. To estimate the current population size of transgender individuals in the United States and evaluate any trend over time. Search methods. In June and July 2016, we searched PubMed, Cumulative Index to Nursing and Allied Health Literature, and Web of Science for national surveys, as well as “gray” literature, through an Internet search. We limited the search to 2006 through 2016. Selection criteria. We selected population-based surveys that used probability sampling and included self-reported transgender-identity data. Data collection and analysis. We used random-effects meta-analysis to pool eligible surveys and used meta-regression to address our hypothesis that the transgender population size estimate would increase over time. We used subsample and leave-one-out analysis to assess for bias. Main results. Our meta-regression model, based on 12 surveys covering 2007 to 2015, explained 62.5% of model heterogeneity, with a significant effect for each unit increase in survey year (F = 17.122; df = 1,10; b = 0.026%; P = .002). Extrapolating these results to 2016 suggested a current US population size of 390 adults per 100 000, or almost 1 million adults nationally. This estimate may be more indicative for younger adults, who represented more than 50% of the respondents in our analysis. Authors’ conclusions. Future national surveys are likely to observe higher numbers of transgender people. The large variety in questions used to ask about transgender identity may account for residual heterogeneity in our models. Public health implications. Under- or nonrepresentation of transgender individuals in population surveys is a barrier to understanding social determinants and health disparities faced by this population. We recommend using standardized questions to identify respondents with transgender and nonbinary gender identities, which will allow a more accurate population size estimate. PMID:28075632

On spatial coalescents with multiple mergers in two dimensions.

PubMed

Heuer, Benjamin; Sturm, Anja

2013-08-01

We consider the genealogy of a sample of individuals taken from a spatially structured population when the variance of the offspring distribution is relatively large. The space is structured into discrete sites of a graph G. If the population size at each site is large, spatial coalescents with multiple mergers, so called spatial Λ-coalescents, for which ancestral lines migrate in space and coalesce according to some Λ-coalescent mechanism, are shown to be appropriate approximations to the genealogy of a sample of individuals. We then consider as the graph G the two dimensional torus with side length 2L+1 and show that as L tends to infinity, and time is rescaled appropriately, the partition structure of spatial Λ-coalescents of individuals sampled far enough apart converges to the partition structure of a non-spatial Kingman coalescent. From a biological point of view this means that in certain circumstances both the spatial structure as well as larger variances of the underlying offspring distribution are harder to detect from the sample. However, supplemental simulations show that for moderately large L the different structure is still evident. Copyright © 2012 Elsevier Inc. All rights reserved.

"Diminished" association between the serotonin transporter linked polymorphism (5HTTLPR) and body mass index in a large psychiatric sample.

PubMed

Shinozaki, Gen; Kumar, Yingying; Rosen, Brooke H; Rundell, James R; Mrazek, David A; Kung, Simon

2013-10-01

The role of the promoter polymorphism (5HTTLPR) of the serotonin transporter gene (SLC6A4) in psychiatric illnesses has been studied extensively. Serotonergic function also regulates many central nervous system, including appetite and feeding behaviors. The 5HTTLPR short allele was found to be associated with increased body mass index and obesity risk among the general population. No data is available to support generalizability of such association among psychiatric population. We examined the relationship between BMI and the 5HTTLPR genotype in a large sample of 1831 psychiatric patients at Mayo Clinic, Rochester, Minnesota, using a retrospective chart review. Average BMI among groups with the short/short (28.29 ± 7.27 kg/m(2)), the short/long (28.07 ± 6.45 kg/m(2)) and the long/long (28.15 ± 7.51 kg/m(2)) genotypes of 5HTTLPR were not statistically different. This negative association persisted even with the sub-analysis of the Caucasians. However, we observed an increased rate of obesity among our psychiatric patient sample compared to the general population of Minnesota (36.6% versus 27.6%, p=0.0001 for males, 30.3% versus 24.4%, p=0.0001 for females). Also, sub-analysis showed female inpatients to have a significantly higher average BMI than outpatients (28.64 ± 8.08 kg/m(2) versus 27.13 ± 6.92 kg/m(2), p=0.026). This confirmed a significant association between mental health disorder and BMI. Retrospective study design with limited control for potential confounders. In this large sample of psychiatric patients we found no significant association between 5HTTLPR genotype and BMI, which is different from the case with general population reported in the literature. Published by Elsevier B.V.

Bayesian Inference on the Effect of Density Dependence and Weather on a Guanaco Population from Chile

PubMed Central

Zubillaga, María; Skewes, Oscar; Soto, Nicolás; Rabinovich, Jorge E.; Colchero, Fernando

2014-01-01

Understanding the mechanisms that drive population dynamics is fundamental for management of wild populations. The guanaco (Lama guanicoe) is one of two wild camelid species in South America. We evaluated the effects of density dependence and weather variables on population regulation based on a time series of 36 years of population sampling of guanacos in Tierra del Fuego, Chile. The population density varied between 2.7 and 30.7 guanaco/km2, with an apparent monotonic growth during the first 25 years; however, in the last 10 years the population has shown large fluctuations, suggesting that it might have reached its carrying capacity. We used a Bayesian state-space framework and model selection to determine the effect of density and environmental variables on guanaco population dynamics. Our results show that the population is under density dependent regulation and that it is currently fluctuating around an average carrying capacity of 45,000 guanacos. We also found a significant positive effect of previous winter temperature while sheep density has a strong negative effect on the guanaco population growth. We conclude that there are significant density dependent processes and that climate as well as competition with domestic species have important effects determining the population size of guanacos, with important implications for management and conservation. PMID:25514510

Bayesian inference on the effect of density dependence and weather on a guanaco population from Chile.

PubMed

Zubillaga, María; Skewes, Oscar; Soto, Nicolás; Rabinovich, Jorge E; Colchero, Fernando

2014-01-01

Understanding the mechanisms that drive population dynamics is fundamental for management of wild populations. The guanaco (Lama guanicoe) is one of two wild camelid species in South America. We evaluated the effects of density dependence and weather variables on population regulation based on a time series of 36 years of population sampling of guanacos in Tierra del Fuego, Chile. The population density varied between 2.7 and 30.7 guanaco/km2, with an apparent monotonic growth during the first 25 years; however, in the last 10 years the population has shown large fluctuations, suggesting that it might have reached its carrying capacity. We used a Bayesian state-space framework and model selection to determine the effect of density and environmental variables on guanaco population dynamics. Our results show that the population is under density dependent regulation and that it is currently fluctuating around an average carrying capacity of 45,000 guanacos. We also found a significant positive effect of previous winter temperature while sheep density has a strong negative effect on the guanaco population growth. We conclude that there are significant density dependent processes and that climate as well as competition with domestic species have important effects determining the population size of guanacos, with important implications for management and conservation.