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Sample records for population based analysis

  1. GIS-based poverty and population distribution analysis in China

    NASA Astrophysics Data System (ADS)

    Cui, Jing; Wang, Yingjie; Yan, Hong

    2009-07-01

    Geographically, poverty status is not only related with social-economic factors but also strongly affected by geographical environment. In the paper, GIS-based poverty and population distribution analysis method is introduced for revealing their regional differences. More than 100000 poor villages and 592 national key poor counties are chosen for the analysis. The results show that poverty distribution tends to concentrate in most of west China and mountainous rural areas of mid China. Furthermore, the fifth census data are overlaid to those poor areas in order to gain its internal diversity of social-economic characteristics. By overlaying poverty related social-economic parameters, such as sex ratio, illiteracy, education level, percentage of ethnic minorities, family composition, finding shows that poverty distribution is strongly correlated with high illiteracy rate, high percentage minorities, and larger family member.

  2. Distributions of personal VOC exposures: a population-based analysis.

    PubMed

    Jia, Chunrong; D'Souza, Jennifer; Batterman, Stuart

    2008-10-01

    Information regarding the distribution of volatile organic compound (VOC) concentrations and exposures is scarce, and there have been few, if any, studies using population-based samples from which representative estimates can be derived. This study characterizes distributions of personal exposures to ten different VOCs in the U.S. measured in the 1999--2000 National Health and Nutrition Examination Survey (NHANES). Personal VOC exposures were collected for 669 individuals over 2-3 days, and measurements were weighted to derive national-level statistics. Four common exposure sources were identified using factor analyses: gasoline vapor and vehicle exhaust, methyl tert-butyl ether (MBTE) as a gasoline additive, tap water disinfection products, and household cleaning products. Benzene, toluene, ethyl benzene, xylenes chloroform, and tetrachloroethene were fit to log-normal distributions with reasonably good agreement to observations. 1,4-Dichlorobenzene and trichloroethene were fit to Pareto distributions, and MTBE to Weibull distribution, but agreement was poor. However, distributions that attempt to match all of the VOC exposure data can lead to incorrect conclusions regarding the level and frequency of the higher exposures. Maximum Gumbel distributions gave generally good fits to extrema, however, they could not fully represent the highest exposures of the NHANES measurements. The analysis suggests that complete models for the distribution of VOC exposures require an approach that combines standard and extreme value distributions, and that carefully identifies outliers. This is the first study to provide national-level and representative statistics regarding the VOC exposures, and its results have important implications for risk assessment and probabilistic analyses.

  3. Public assistance, drug testing, and the law: the limits of population-based legal analysis.

    PubMed

    Player, Candice T

    2014-01-01

    In Populations, Public Health and the Law, legal scholar Wendy Parmet urges courts to embrace population-based legal analysis, a public health inspired approach to legal reasoning. Parmet contends that population-based legal analysis offers a way to analyze legal issues--not unlike law and economics--as well as a set of values from which to critique contemporary legal discourse. Population-based analysis has been warmly embraced by the health law community as a bold new way of analyzing legal issues. Still, population-based analysis is not without its problems. At times, Parmet claims too much territory for the population perspective. Moreover, Parmet urges courts to recognize population health as an important norm in legal reasoning. What should we do when the insights of public health and conventional legal reasoning conflict? Still in its infancy, population-based analysis offers little in the way of answers to these questions. This Article applies population-based legal analysis to the constitutional problems that arise when states condition public assistance benefits on passing a drug test, thereby highlighting the strengths of the population perspective and exposing its weaknesses.

  4. Medullary carcinoma of the large intestine: a population based analysis.

    PubMed

    Thirunavukarasu, Pragatheeshwar; Sathaiah, Magesh; Singla, Smit; Sukumar, Shyam; Karunamurthy, Arivarasan; Pragatheeshwar, Kothai Divya; Lee, Kenneth K W; Zeh, Herbert; Kane, Kevin M; Bartlett, David L

    2010-10-01

    Medullary carcinoma (MC) of the colorectum is a relatively new histological type of adenocarcinoma characterized by poor glandular differentiation and intraepithelial lymphocytic infiltrate. To date, there has been no epidemiological study of this rare tumor type, which has now been incorporated as a separate entity in the World Health Organization (WHO) classification of colorectal cancers. We used the population-based registries of the Surveillance, Epidemiology and End Results (SEER) database to identify all cases of colorectal MC between 1973 and 2006 and compared them to poorly and undifferentiated colonic adenocarcinomas (PDA and UDA, respectively). We observed that MCs were rare tumors, constituting approximately 5-8 cases for every 10,000 colon cancers diagnosed, with a mean annual incidence of 3.47 (+/-0.75) per 10 million population. Mean age at diagnosis was 69.3 (+/-12.5) years, with incidence increasing with age. MCs were twice as common in females, who presented at a later age, with a lower stage and a trend towards favorable prognosis. MCs were extremely rare among African-Americans. MCs were most common in the proximal colon (74%), where they present at a later age than the sigmoid colon. There were no cases reliably identified in the rectum or appendix. Serum carcinoembryonic antigen levels (CEA) were elevated prior to first course of treatment in 40% of the patients. MCs were more commonly poorly differentiated (72%), with 22% being undifferentiated. MCs commonly presented with Stage II disease, with 10% presenting with metastases. Only one patient presented with N2b disease (>7 positive nodes). Early outcome analyses showed that MCs have 1- and 2-year relative survival rates of 92.7 and 73.8% respectively. Although MCs showed a trend towards better early overall survival, undifferentiated MCs present more commonly with Stage III, with comparatively worse early outcomes.

  5. An individual-based model for population viability analysis of humpback chub in Grand Canyon

    USGS Publications Warehouse

    Pine, William Pine; Healy, Brian; Smith, Emily Omana; Trammell, Melissa; Speas, Dave; Valdez, Rich; Yard, Mike; Walters, Carl; Ahrens, Rob; Vanhaverbeke, Randy; Stone, Dennis; Wilson, Wade

    2013-01-01

    We developed an individual-based population viability analysis model (females only) for evaluating risk to populations from catastrophic events or conservation and research actions. This model tracks attributes (size, weight, viability, etc.) for individual fish through time and then compiles this information to assess the extinction risk of the population across large numbers of simulation trials. Using a case history for the Little Colorado River population of Humpback Chub Gila cypha in Grand Canyon, Arizona, we assessed extinction risk and resiliency to a catastrophic event for this population and then assessed a series of conservation actions related to removing specific numbers of Humpback Chub at different sizes for conservation purposes, such as translocating individuals to establish other spawning populations or hatchery refuge development. Our results suggested that the Little Colorado River population is generally resilient to a single catastrophic event and also to removals of larvae and juveniles for conservation purposes, including translocations to establish new populations. Our results also suggested that translocation success is dependent on similar survival rates in receiving and donor streams and low emigration rates from recipient streams. In addition, translocating either large numbers of larvae or small numbers of large juveniles has generally an equal likelihood of successful population establishment at similar extinction risk levels to the Little Colorado River donor population. Our model created a transparent platform to consider extinction risk to populations from catastrophe or conservation actions and should prove useful to managers assessing these risks for endangered species such as Humpback Chub.

  6. Challenges of cardiac image analysis in large-scale population-based studies.

    PubMed

    Medrano-Gracia, Pau; Cowan, Brett R; Suinesiaputra, Avan; Young, Alistair A

    2015-03-01

    Large-scale population-based imaging studies of preclinical and clinical heart disease are becoming possible due to the advent of standardized robust non-invasive imaging methods and infrastructure for big data analysis. This gives an exciting opportunity to gain new information about the development and progression of heart disease across population groups. However, the large amount of image data and prohibitive time required for image analysis present challenges for obtaining useful derived data from the images. Automated analysis tools for cardiac image analysis are only now becoming available. This paper reviews the challenges and possible solutions to the analysis of big imaging data in population studies. We also highlight the potential of recent large epidemiological studies using cardiac imaging to discover new knowledge on heart health and well-being.

  7. Genetic relationships among twelve Chinese indigenous goat populations based on microsatellite analysis

    PubMed Central

    Li, Meng-Hua; Zhao, Shu-Hong; Bian, Ci; Wang, Hai-Sheng; Wei, Hong; Liu, Bang; Yu, Mei; Fan, Bin; Chen, Shi-Lin; Zhu, Meng-Jin; Li, Shi-Jun; Xiong, Tong-An; Li, Kui

    2002-01-01

    Twelve Chinese indigenous goat populations were genotyped for twenty-six microsatellite markers recommended by the EU Sheep and Goat Biodiversity Project. A total of 452 goats were tested. Seventeen of the 26 microsatellite markers used in this analysis had four or more alleles. The mean expected heterozygosity and the mean observed heterozygosity for the population varied from 0.611 to 0.784 and 0.602 to 0.783 respectively. The mean FST (0.105) demonstrated that about 89.5% of the total genetic variation was due to the genetic differentiation within each population. A phylogenetic tree based on the Nei (1978) standard genetic distance displayed a remarkable degree of consistency with their different geographical origins and their presumed migration throughout China. The correspondence analysis did not only distinguish population groups, but also confirmed the above results, classifying the important populations contributing to diversity. Additionally, some specific alleles were shown to be important in the construction of the population structure. The study analyzed the recent origins of these populations and contributed to the knowledge and genetic characterization of Chinese indigenous goat populations. In addition, the seventeen microsatellites recommended by the EU Sheep and Goat Biodiversity Project proved to be useful for the biodiversity studies in goat breeds. PMID:12473236

  8. 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

  9. PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening Data.

    PubMed

    Matuszewski, Damian J; Wählby, Carolina; Puigvert, Jordi Carreras; Sintorn, Ida-Maria

    2016-01-01

    Image-based screening typically produces quantitative measurements of cell appearance. Large-scale screens involving tens of thousands of images, each containing hundreds of cells described by hundreds of measurements, result in overwhelming amounts of data. Reducing per-cell measurements to the averages across the image(s) for each treatment leads to loss of potentially valuable information on population variability. We present PopulationProfiler-a new software tool that reduces per-cell measurements to population statistics. The software imports measurements from a simple text file, visualizes population distributions in a compact and comprehensive way, and can create gates for subpopulation classes based on control samples. We validate the tool by showing how PopulationProfiler can be used to analyze the effect of drugs that disturb the cell cycle, and compare the results to those obtained with flow cytometry.

  10. Population history, biogeography, and taxonomy of orangutans (Genus: Pongo) based on a population genetic meta-analysis of multiple loci.

    PubMed

    Steiper, Michael E

    2006-05-01

    This paper examines orangutan population history and evolution through a meta-analysis of seven loci collected from both Sumatran and Bornean orangutans. Within orangutans, most loci show that the Sumatran population is about twice as diverse as the Bornean population. Orangutans are more diverse than African apes and humans. Sumatran and Bornean populations show significant genetic differentiation from one another and their history does not differ significantly from an 'island model' (population splitting without gene flow). Two different methods support a divergence of Bornean and Sumatran orangutans at 2.7-5 million years ago. This suggests that Pleistocene events, such as the cyclical exposure of the Sunda shelf and the Toba volcanic eruption, did not have a major impact on the divergence of Bornean and Sumatran orangutans. Pairwise mismatch analyses, however, suggest that Bornean orangutans have undergone a recent population expansion (beginning 39,000-64,000 years ago), while Sumatran orangutan populations were stable. Pleistocene events may have contributed to these aspects of orangutan population history. These conclusions are applied to the debate on orangutan taxonomy.

  11. MLPA-Based Analysis of Copy Number Variation in Plant Populations

    PubMed Central

    Samelak-Czajka, Anna; Marszalek-Zenczak, Malgorzata; Marcinkowska-Swojak, Malgorzata; Kozlowski, Piotr; Figlerowicz, Marek; Zmienko, Agnieszka

    2017-01-01

    Copy number variants (CNVs) are intraspecies duplications/deletions of large DNA segments (>1 kb). A growing number of reports highlight the functional and evolutionary impact of CNV in plants, increasing the need for appropriate tools that enable locus-specific CNV genotyping on a population scale. Multiplex ligation-dependent probe amplification (MLPA) is considered a gold standard in genotyping CNV in humans. Consequently, numerous commercial MLPA assays for CNV-related human diseases have been created. We routinely genotype complex multiallelic CNVs in human and plant genomes using the modified MLPA procedure based on fully synthesized oligonucleotide probes (90–200 nt), which greatly simplifies the design process and allows for the development of custom assays. Here, we present a step-by-step protocol for gene-specific MLPA probe design, multiplexed assay setup and data analysis in a copy number genotyping experiment in plants. As a case study, we present the results of a custom assay designed to genotype the copy number status of 12 protein coding genes in a population of 80 Arabidopsis accessions. The genes were pre-selected based on whole genome sequencing data and are localized in the genomic regions that display different levels of population-scale variation (non-variable, biallelic, or multiallelic, as well as CNVs overlapping whole genes or their fragments). The presented approach is suitable for population-scale validation of the CNV regions inferred from whole genome sequencing data analysis and for focused analysis of selected genes of interest. It can also be very easily adopted for any plant species, following optimization of the template amount and design of the appropriate control probes, according to the general guidelines presented in this paper. PMID:28270823

  12. DHLAS: A web-based information system for statistical genetic analysis of HLA population data.

    PubMed

    Thriskos, P; Zintzaras, E; Germenis, A

    2007-03-01

    DHLAS (database HLA system) is a user-friendly, web-based information system for the analysis of human leukocyte antigens (HLA) data from population studies. DHLAS has been developed using JAVA and the R system, it runs on a Java Virtual Machine and its user-interface is web-based powered by the servlet engine TOMCAT. It utilizes STRUTS, a Model-View-Controller framework and uses several GNU packages to perform several of its tasks. The database engine it relies upon for fast access is MySQL, but others can be used a well. The system estimates metrics, performs statistical testing and produces graphs required for HLA population studies: (i) Hardy-Weinberg equilibrium (calculated using both asymptotic and exact tests), (ii) genetics distances (Euclidian or Nei), (iii) phylogenetic trees using the unweighted pair group method with averages and neigbor-joining method, (iv) linkage disequilibrium (pairwise and overall, including variance estimations), (v) haplotype frequencies (estimate using the expectation-maximization algorithm) and (vi) discriminant analysis. The main merit of DHLAS is the incorporation of a database, thus, the data can be stored and manipulated along with integrated genetic data analysis procedures. In addition, it has an open architecture allowing the inclusion of other functions and procedures.

  13. Non-Linear Analysis Indicates Chaotic Dynamics and Reduced Resilience in Model-Based Daphnia Populations Exposed to Environmental Stress

    PubMed Central

    Ottermanns, Richard; Szonn, Kerstin; Preuß, Thomas G.; Roß-Nickoll, Martina

    2014-01-01

    In this study we present evidence that anthropogenic stressors can reduce the resilience of age-structured populations. Enhancement of disturbance in a model-based Daphnia population lead to a repression of chaotic population dynamics at the same time increasing the degree of synchrony between the population's age classes. Based on the theory of chaos-mediated survival an increased risk of extinction was revealed for this population exposed to high concentrations of a chemical stressor. The Lyapunov coefficient was supposed to be a useful indicator to detect disturbance thresholds leading to alterations in population dynamics. One possible explanation could be a discrete change in attractor orientation due to external disturbance. The statistical analysis of Lyapunov coefficient distribution is proposed as a methodology to test for significant non-linear effects of general disturbance on populations. Although many new questions arose, this study forms a theoretical basis for a dynamical definition of population recovery. PMID:24809537

  14. Comprehensive, Population-Based Sensitivity Analysis of a Two-Mass Vocal Fold Model

    PubMed Central

    Robertson, Daniel; Zañartu, Matías; Cook, Douglas

    2016-01-01

    Previous vocal fold modeling studies have generally focused on generating detailed data regarding a narrow subset of possible model configurations. These studies can be interpreted to be the investigation of a single subject under one or more vocal conditions. In this study, a broad population-based sensitivity analysis is employed to examine the behavior of a virtual population of subjects and to identify trends between virtual individuals as opposed to investigating a single subject or model instance. Four different sensitivity analysis techniques were used in accomplishing this task. Influential relationships between model input parameters and model outputs were identified, and an exploration of the model’s parameter space was conducted. Results indicate that the behavior of the selected two-mass model is largely dominated by complex interactions, and that few input-output pairs have a consistent effect on the model. Results from the analysis can be used to increase the efficiency of optimization routines of reduced-order models used to investigate voice abnormalities. Results also demonstrate the types of challenges and difficulties to be expected when applying sensitivity analyses to more complex vocal fold models. Such challenges are discussed and recommendations are made for future studies. PMID:26845452

  15. Population Analysis: Communicating in Context

    NASA Technical Reports Server (NTRS)

    Rajulu, Sudhakar; Thaxton, Sherry

    2008-01-01

    Providing accommodation to a widely varying user population presents a challenge to engineers and designers. It is often even difficult to quantify who is accommodated and who is not accommodated by designs, especially for equipment with multiple critical anthropometric dimensions. An approach to communicating levels of accommodation referred to as population analysis applies existing human factors techniques in novel ways. This paper discusses the definition of population analysis as well as major applications and case studies. The major applications of population analysis consist of providing accommodation information for multivariate problems and enhancing the value of feedback from human-in-the-loop testing. The results of these analyses range from the provision of specific accommodation percentages of the user population to recommendations of design specifications based on quantitative data. Such feedback is invaluable to designers and results in the design of products that accommodate the intended user population.

  16. Area-level poverty and preterm birth risk: A population-based multilevel analysis

    PubMed Central

    DeFranco, Emily A; Lian, Min; Muglia, Louis A; Schootman, Mario

    2008-01-01

    Background Preterm birth is a complex disease with etiologic influences from a variety of social, environmental, hormonal, genetic, and other factors. The purpose of this study was to utilize a large population-based birth registry to estimate the independent effect of county-level poverty on preterm birth risk. To accomplish this, we used a multilevel logistic regression approach to account for multiple co-existent individual-level variables and county-level poverty rate. Methods Population-based study utilizing Missouri's birth certificate database (1989–1997). We conducted a multilevel logistic regression analysis to estimate the effect of county-level poverty on PTB risk. Of 634,994 births nested within 115 counties in Missouri, two levels were considered. Individual-level variables included demographics factors, prenatal care, health-related behavioral risk factors, and medical risk factors. The area-level variable included the percentage of the population within each county living below the poverty line (US census data, 1990). Counties were divided into quartiles of poverty; the first quartile (lowest rate of poverty) was the reference group. Results PTB < 35 weeks occurred in 24,490 pregnancies (3.9%). The rate of PTB < 35 weeks was 2.8% in counties within the lowest quartile of poverty and increased through the 4th quartile (4.9%), p < 0.0001. High county-level poverty was significantly associated with PTB risk. PTB risk (< 35 weeks) was increased for women who resided in counties within the highest quartile of poverty, adjusted odds ratio (adjOR) 1.18 (95% CI 1.03, 1.35), with a similar effect at earlier gestational ages (< 32 weeks), adjOR 1.27 (95% CI 1.06, 1.52). Conclusion Women residing in socioeconomically deprived areas are at increased risk of preterm birth, above other underlying risk factors. Although the risk increase is modest, it affects a large number of pregnancies. PMID:18793437

  17. Historical sketch of Slovak Haban (Hutterite) population based on autosomal STR analysis.

    PubMed

    Soták, M; Petrejčíková, E; Siváková, D; Rębała, K; Bôžiková, A; Bernasovský, I; Carnogurská, J; Boronová, I; Mačeková, S; Homol'ová, L; Sovičová, A; Gabriková, D; Rusínová, L; Bernasovská, J

    2011-10-01

    According to the Hutterite chronicles, the Habans arrived from Austrian Tyrol, Switzerland, and northernmost Italy and stayed in four regions of Slovakia (Sobotište, Vel'ké Leváre, Moravský Svätý Ján, Trenčín). There are some communities in western Slovakia that retained their Haban cultural identity and still identify themselves as descendents of the Hutterite population with their own specific customs. Slovak Habans are typical founder population with significant social isolation for which high degree of inbreeding is typical. Present study investigated STR polymorphisms as a powerful genetic tool for population genetic studies. The aim was to perform a comparative, population genetic study based on 15 STR loci widely used in forensic genetics, of the Haban population, the Slovak majority population and the population of Tyrol. We analyzed allele frequencies and other statistical parameters in three selected populations in order to identify groups of specific ethnic origin and establish their genetic relationship. The data set included 110 unrelated Habans and 201 unrelated individuals from the Slovak majority population, as well as allelic frequencies for the population of Austrian Tyrol available in the literature. Population pairwise FST values used as a short term genetic distance between populations showed significant differentiation between the Habans and both reference populations (FST=0.0025 and 0.0042 for comparison with the Slovaks and Austrians, respectively; p<10(-3)). The Slovak Hutterites were demonstrated to be genetically distinct and more closely related to their geographic neighbors than to their historical ancestral population, which may be at least partially explained by gene flow between neighboring Haban and Slovak populations.

  18. Health: Policy or Law? A Population-Based Analysis of the Supreme Court's ACA Cases.

    PubMed

    Parmet, Wendy E

    2016-08-16

    This essay argues that it matters for the fate of health policies challenged in court whether courts consider health merely as a policy goal that must be subordinate to law, or as a legal norm warranting legal weight and consideration. Applying population-based legal analysis, this article demonstrates that courts have traditionally treated health as a legal norm. However, this norm appears to have weakened in recent years, a trend evident in the Supreme Court's first two decisions concerning the Affordable Care Act, NFIB v. Sebelius and Burwell v. Hobby Lobby However, in its more recent Affordable Care Act decision, King v. Burwell, the health legal norm is once again evident. Whether the Court will continue to treat health as a legal norm will prove critical to the deference and weight it grants health policies in the future.

  19. Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

    PubMed Central

    Li, Wenyuan; Kalhor, Reza; Dai, Chao; Hao, Shengli; Gong, Ke; Zhou, Yonggang; Li, Haochen; Zhou, Xianghong Jasmine; Le Gros, Mark A.; Larabell, Carolyn A.; Chen, Lin; Alber, Frank

    2016-01-01

    Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic approach for deconvoluting Hi-C data into a model population of distinct diploid 3D genome structures, which facilitates the detection of chromatin interactions likely to co-occur in individual cells. Our approach incorporates the stochastic nature of chromosome conformations and allows a detailed analysis of alternative chromatin structure states. For example, we predict and experimentally confirm the presence of large centromere clusters with distinct chromosome compositions varying between individual cells. The stability of these clusters varies greatly with their chromosome identities. We show that these chromosome-specific clusters can play a key role in the overall chromosome positioning in the nucleus and stabilizing specific chromatin interactions. By explicitly considering genome structural variability, our population-based method provides an important tool for revealing novel insights into the key factors shaping the spatial genome organization. PMID:26951677

  20. Data harmonization and federated analysis of population-based studies: the BioSHaRE project

    PubMed Central

    2013-01-01

    Abstracts Background Individual-level data pooling of large population-based studies across research centres in international research projects faces many hurdles. The BioSHaRE (Biobank Standardisation and Harmonisation for Research Excellence in the European Union) project aims to address these issues by building a collaborative group of investigators and developing tools for data harmonization, database integration and federated data analyses. Methods Eight population-based studies in six European countries were recruited to participate in the BioSHaRE project. Through workshops, teleconferences and electronic communications, participating investigators identified a set of 96 variables targeted for harmonization to answer research questions of interest. Using each study’s questionnaires, standard operating procedures, and data dictionaries, harmonization potential was assessed. Whenever harmonization was deemed possible, processing algorithms were developed and implemented in an open-source software infrastructure to transform study-specific data into the target (i.e. harmonized) format. Harmonized datasets located on server in each research centres across Europe were interconnected through a federated database system to perform statistical analysis. Results Retrospective harmonization led to the generation of common format variables for 73% of matches considered (96 targeted variables across 8 studies). Authenticated investigators can now perform complex statistical analyses of harmonized datasets stored on distributed servers without actually sharing individual-level data using the DataSHIELD method. Conclusion New Internet-based networking technologies and database management systems are providing the means to support collaborative, multi-center research in an efficient and secure manner. The results from this pilot project show that, given a strong collaborative relationship between participating studies, it is possible to seamlessly co

  1. A population based analysis of prognostic factors in advanced biliary tract cancer

    PubMed Central

    Renouf, Daniel; Lim, Howard

    2014-01-01

    Background Data regarding prognostic factors in advanced biliary tract cancer (BTC) remains scarce. The aim of this study was to review our institutional experience with cisplatin and gemcitabine in advanced BTC as well as to evaluate potential prognostic factors for overall survival (OS). Material and methods Consecutive patients with advanced BTC who initiated palliative chemotherapy with cisplatin and gemcitabine from 2009 to 2012 at the BC Cancer Agency were identified using the pharmacy database. Clinicopathologic variables and treatment outcome were retrospectively collected. Potential prognostic factors were assessed by univariate and multivariate analyses. Results A total of 106 patients were included in the analysis. Median OS was 8.5 months (95% CI: 6.5-10.5). On univariate analysis, poor ECOG performance status (ECOG PS) at diagnosis, primary tumor location (extra-hepatic cholangiocarcinoma, and unknown biliary cancer), and sites of advanced disease (extra-hepatic metastasis) were significantly associated with worse OS (P<0.001, 0.036 and 0.034, respectively). Age, gender, CA19-9, CEA, hemoglobin, neutrophil count, and prior stent were not significantly associated with OS. On multivariate analysis, ECOG PS 2/3 was the only predictor of poor OS (P<0.001), while primary location (P=0.089) and sites of advanced disease (P=0.079) had a non-significant trend towards prognostic significance. Conclusions In this population based analysis, a poorer performance status was significantly prognostic of worse OS. Although not significant in our analysis, primary tumor location and sites of advanced disease may also have prognostic relevance. PMID:25436121

  2. Detection of X chromosome aneuploidy using Southern blot analysis during routine population-based screening for fragile X syndrome.

    PubMed

    Adir, Vardit; Shahak, Elena; Dar, Hanna; Borochowitz, Zvi U

    2003-01-01

    We report herein two cases where detection of X chromosome aneuploidy (cytogenetically proved 45,X/46XX and 47,XXX) was made possible by molecular diagnosis during population-based carrier screening for Fragile X syndrome, using Southern blot analysis. This study emphasizes the value of molecular analysis for gene dosage to suggest chromosomal aneuploidy.

  3. Prevalence of exposure to suicide: A meta-analysis of population-based studies.

    PubMed

    Andriessen, Karl; Rahman, Bayzidur; Draper, Brian; Dudley, Michael; Mitchell, Philip B

    2017-05-01

    Those exposed to suicide are at increased risk of adverse outcomes including mental illness, impaired social functioning, and fatal and non-fatal suicidal behavior. However, it is unclear how many people are exposed to suicide in the general community. This first meta-analysis of population-based studies aimed to provide pooled estimates of past-year and lifetime prevalence of exposure to suicide among family, friends/peers, and all relationships. In addition, the study examined prevalence of exposure to suicide by age group: adolescents and adults. Systematic searches of the literature in Embase, Medline and PsycINFO identified eighteen studies that were included in the analysis. Pooled past-year prevalence was 4.31% (CI: 2.50 to 6.58) and life-time prevalence 21.83% (CI: 16.32 to 27.90). Both past-year and lifetime prevalences of exposure to suicide among friends and peers were significantly higher than the prevalence of exposure within families; there were no differences in the prevalence of exposure to suicide between adolescents and adults. Heterogeneity was highly significant. Future research should be conducted with large national representative samples and use standardised assessment instruments. Given the increased risks of adverse outcomes among those exposed to suicide, the high rate of exposure to suicide reported here has important ramifications for public health and mental health service delivery.

  4. Population-based analysis of Alzheimer’s disease risk alleles implicates genetic interactions

    PubMed Central

    Ebbert, Mark T. W.; Ridge, Perry G.; Wilson, Andrew R.; Sharp, Aaron R.; Bailey, Matthew; Norton, Maria C.; Tschanz, JoAnn T.; Munger, Ronald G.; Corcoran, Christopher D.; Kauwe, John S. K.

    2013-01-01

    Background Reported odds ratios and population attributable fractions (PAF) for late-onset Alzheimer’s disease (LOAD) risk loci (BIN1, ABCA7, CR1, MS4A4E, CD2AP, PICALM, MS4A6A, CD33, and CLU) come from clinically ascertained samples. Little is known about the combined PAF for these LOAD risk alleles and the utility of these combined markers for case-control prediction. Here we evaluate these loci in a large population-based sample to estimate PAF and explore the effects of additive and non-additive interactions on LOAD status prediction performance. Methods 2,419 samples from the Cache County Memory Study were genotyped for APOE and nine LOAD risk loci from AlzGene.org. We used logistic regression and ROC analysis to assess the LOAD status prediction performance of these loci using additive and non-additive models, and compared ORs and PAFs between AlzGene.org and Cache County. Results Odds ratios were comparable between Cache County and AlzGene.org when identical SNPs were genotyped. PAFs from AlzGene.org ranged from 2.25–37%; those from Cache County ranged from 0.05–20%. Including non-APOE alleles significantly improved LOAD status prediction performance (AUC = 0.80) over APOE alone (AUC = 0.78) when not constrained to an additive relationship (p < 0.03). We identified potential allelic interactions (p-values uncorrected): CD33-MS4A4E (Synergy Factor = 5.31; p < 0.003) and CLU-MS4A4E (SF = 3.81; p < 0.016). Conclusions While non-additive interactions between loci significantly improve diagnostic ability, the improvement does not reach the desired sensitivity or specificity for clinical use. Nevertheless, these results suggest that understanding gene-gene interactions may be important in resolving Alzheimer’s disease etiology. PMID:23954108

  5. Profiles of Cognitive Functioning in a Population-Based Sample of Centenarians Using Factor Mixture Analysis

    PubMed Central

    Davey, Adam; Dai, Ting; Woodard, John L.; Miller, L. Stephen; Gondo, Yasuyuki; Johnson, Mary Ann; Hausman, Dorothy B.; Martin, Peter; Green, Robert C.; Allen, Robert H.; Stabler, Sally P.; Poon, Leonard W.

    2013-01-01

    Background/Study Context The goal of the study was to identify and characterize latent profiles (clusters) of cognitive functioning in centenarians and the psychometric properties of cognitive measures within them. Methods Data were collected from cross-sectional, population-based sample of 244 centenarians (aged 98-108, 15.8% men, 20.5% African-American, 38.0% community-dwelling) from 44 counties in Northern Georgia participating in the Georgia Centenarian Study (2001-2009). Measures included the Mini-Mental State Examination (MMSE), Severe Impairment Battery (SIB), Wechsler Adult Intelligence Scale-III, Similarities sub-test (WAIS), Finger Tapping, Behavioral Dyscontrol Scale (BDS), Controlled Oral Word Association Test (COWAT), and Fuld Object Memory Evaluation (FOME). The Global Deterioration Rating Scale (GDRS) was used to independently evaluate criterion-related validity for distinguishing cognitively normal and impaired groups. Relevant covariates included directly assessed functional status for basic and instrumental activities of daily living (DAFS), race, gender, educational attainment, Geriatric Depression Scale Short Form (GDS), and vision and hearing problems. Results Results suggest two distinct classes of cognitive performance in this centenarian sample. Approximately one-third of the centenarians show a pattern of markedly lower cognitive performance on most measures. Group membership is independently well-predicted (AUC=.83) by GDRS scores (sensitivity 67.7%, specificity 82.4%). Membership in the lower cognitive performance group was more likely for individuals who were older, African Americans, had more depressive symptoms, lower plasma folate, carriers of the APOE ε4 allele, facility residents, and individuals who died in the two years following interview. Conclusions In a population expected to have high prevalence of dementia, latent subtypes can be distinguished via factor mixture analysis that provide normative values for cognitive

  6. Exploratory Factor Analysis of Self-Reported Symptoms in a Large, Population-Based Military Cohort

    DTIC Science & Technology

    2010-10-15

    analysis suggests that it could be a manifestation of it or another condition associated with anxiety such as fibromyalgia [33]. Factor 3...military population. However, general muscle pain can accompany many other illnesses, such as infectious diseases, autoimmune disorders, fibromyalgia ...Rosenberg R, Bach FW, Jensen TS. Depression, anxiety, health-related quality of life and pain in patients with chronic fibromyalgia and neuropathic pain

  7. [Spatial structure analysis and distribution simulation of Therioaphis trifolii population based on geostatistics and GIS].

    PubMed

    Zhang, Rong; Leng, Yun-fa; Zhu, Meng-meng; Wang, Fang

    2007-11-01

    Based on geographic information system and geostatistics, the spatial structure of Therioaphis trifolii population of different periods in Yuanzhou district of Guyuan City, the southern Ningxia Province, was analyzed. The spatial distribution of Therioaphis trifolii population was also simulated by ordinary Kriging interpretation. The results showed that Therioaphis trifolii population of different periods was correlated spatially in the study area. The semivariograms of Therioaphis trifolii could be described by exponential model, indicating an aggregated spatial arrangement. The spatial variance varied from 34.13%-48.77%, and the range varied from 8.751-12.049 km. The degree and direction of aggregation showed that the trend was increased gradually from southwest to northeast. The dynamic change of Therioaphis trifolii population in different periods could be analyzed intuitively on the simulated maps of the spatial distribution from the two aspects of time and space, The occurrence position and degree of Therioaphis trifolii to a state of certain time could be determined easily.

  8. Genetic Variability and Population Structure of Disanthus cercidifolius subsp. longipes (Hamamelidaceae) Based on AFLP Analysis

    PubMed Central

    Yu, Yi; Fan, Qiang; Shen, Rujiang; Guo, Wei; Jin, Jianhua; Cui, Dafang; Liao, Wenbo

    2014-01-01

    Disanthus cercidifolius subsp. longipes is an endangered species in China. Genetic diversity and structure analysis of this species was investigated using amplified fragments length polymorphism (AFLP) fingerprinting. Nei's gene diversity ranged from 0.1290 to 0.1394. The AMOVA indicated that 75.06% of variation was distributed within populations, while the between-group component 5.04% was smaller than the between populations-within-group component 19.90%. Significant genetic differentiation was detected between populations. Genetic and geographical distances were not correlated. PCA and genetic structure analysis showed that populations from East China were together with those of the Nanling Range. These patterns of genetic diversity and levels of genetic variation may be the result of D. c. subsp. longipes restricted to several isolated habitats and “excess flowers production, but little fruit set”. It is necessary to protect all existing populations of D. c. subsp. longipes in order to preserve as much genetic variation as possible. PMID:25250583

  9. Intensive care outcomes in bone marrow transplant recipients: a population-based cohort analysis

    PubMed Central

    Scales, Damon C; Thiruchelvam, Deva; Kiss, Alexander; Sibbald, William J; Redelmeier, Donald A

    2008-01-01

    Introduction Intensive care unit (ICU) admission for bone marrow transplant recipients immediately following transplantation is an ominous event, yet the survival of these patients with subsequent ICU admissions is unknown. Our objective was to determine the long-term outcome of bone marrow transplant recipients admitted to an ICU during subsequent hospitalizations. Methods We conducted a population-based cohort analysis of all adult bone marrow transplant recipients who received subsequent ICU care in Ontario, Canada from 1 January 1992 to 31 March 2002. The primary endpoint was mortality at 1 year. Results A total of 2,653 patients received bone marrow transplantation; 504 of which received ICU care during a subsequent hospitalization. Patients receiving any major procedure during their ICU stay had higher 1-year mortality than those patients who received no ICU procedure (87% versus 44%, P < 0.0001). Death rates at 1 year were highest for those receiving mechanical ventilation (87%), pulmonary artery catheterization (91%), or hemodialysis (94%). In combination, the strongest independent predictors of death at 1 year were mechanical ventilation (odds ratio, 7.4; 95% confidence interval, 4.8 to 11.4) and hemodialysis (odds ratio, 8.7; 95% confidence interval, 2.1 to 36.7), yet no combination of procedures uniformly predicted 100% mortality. Conclusion The prognosis of bone marrow transplant recipients receiving ICU care during subsequent hospitalizations is very poor but should not be considered futile. PMID:18547422

  10. Selective of informative metabolites using random forests based on model population analysis.

    PubMed

    Huang, Jian-Hua; Yan, Jun; Wu, Qing-Hua; Duarte Ferro, Miguel; Yi, Lun-Zhao; Lu, Hong-Mei; Xu, Qing-Song; Liang, Yi-Zeng

    2013-12-15

    One of the main goals of metabolomics studies is to discover informative metabolites or biomarkers, which may be used to diagnose diseases and to find out pathology. Sophisticated feature selection approaches are required to extract the information hidden in such complex 'omics' data. In this study, it is proposed a new and robust selective method by combining random forests (RF) with model population analysis (MPA), for selecting informative metabolites from three metabolomic datasets. According to the contribution to the classification accuracy, the metabolites were classified into three kinds: informative, no-informative, and interfering metabolites. Based on the proposed method, some informative metabolites were selected for three datasets; further analyses of these metabolites between healthy and diseased groups were then performed, showing by T-test that the P values for all these selected metabolites were lower than 0.05. Moreover, the informative metabolites identified by the current method were demonstrated to be correlated with the clinical outcome under investigation. The source codes of MPA-RF in Matlab can be freely downloaded from http://code.google.com/p/my-research-list/downloads/list.

  11. Estimating and modeling the cure fraction in population-based cancer survival analysis.

    PubMed

    Lambert, Paul C; Thompson, John R; Weston, Claire L; Dickman, Paul W

    2007-07-01

    In population-based cancer studies, cure is said to occur when the mortality (hazard) rate in the diseased group of individuals returns to the same level as that expected in the general population. The cure fraction (the proportion of patients cured of disease) is of interest to patients and is a useful measure to monitor trends in survival of curable disease. There are 2 main types of cure fraction model, the mixture cure fraction model and the non-mixture cure fraction model, with most previous work concentrating on the mixture cure fraction model. In this paper, we extend the parametric non-mixture cure fraction model to incorporate background mortality, thus providing estimates of the cure fraction in population-based cancer studies. We compare the estimates of relative survival and the cure fraction between the 2 types of model and also investigate the importance of modeling the ancillary parameters in the selected parametric distribution for both types of model.

  12. [Population bio-banks: a juridical analysis based on Icelandic and Estonian experience].

    PubMed

    Andorno, Roberto

    2006-01-01

    Large-scale collections of human biological samples and associated data are becoming increasingly common as a means of identifying, in a particular population, genetic predispositions to complex diseases that result from an interaction of environmental, lifestyle and genetic factors. This paper compares the recent experiences of Iceland and Estonia in the establishment of population biobanks as well as the specific law passed by both countries to deal with this matter. In the light of this comparative analysis, this paper summarizes the main ethical and policy dilemmas posed by large-scale biobanks and suggests some possible solutions to these new challenges.

  13. Long-term sedative use among community-dwelling adults: a population-based analysis

    PubMed Central

    Weymann, Deirdre; Gladstone, Emilie J.; Smolina, Kate; Morgan, Steven G.

    2017-01-01

    Background: Chronic use of benzodiazepines and benzodiazepine-like sedatives (z-drugs) presents substantial risks to people of all ages. We sought to assess trends in long-term sedative use among community-dwelling adults in British Columbia. Methods: Using population-based linked administrative databases, we examined longitudinal trends in age-standardized rates of sedative use among different age groups of community-dwelling adults (age ≥ 18 yr), from 2004 to 2013. For each calendar year, we classified adults as nonusers, short-term users, or long-term users of sedatives based on their patterns of sedative dispensation. For calendar year 2013, we applied cross-sectional analysis and estimated logistic regression models to identify health and socioeconomic risk factors associated with long-term sedative use. Results: More than half (53.4%) of long-term users of sedatives in British Columbia are between ages 18 and 64 years (young and middle-aged adults). From 2004 to 2013, long-term sedative use remained stable among adults more than 65 years of age (older adults) and increased slightly among young and middle-aged adults. Although the use of benzodiazepines decreased during the study period, the trend was offset by equal or greater increases in long-term use of z-drugs. Being an older adult, sick, poor and single were associated with increased odds of long-term sedative use. Interpretation: Despite efforts to stem such patterns of medication use, long-term use of sedatives increased in British Columbia between 2004 and 2013. This increase was driven largely by increased use among middle-aged adults. Future deprescribing efforts that target adults of all ages may help curb this trend.

  14. Trend analysis of cancer incidence in Japan using data from selected population-based cancer registries.

    PubMed

    Katanoda, Kota; Ajiki, Wakiko; Matsuda, Tomohiro; Nishino, Yoshikazu; Shibata, Akiko; Fujita, Manabu; Tsukuma, Hideaki; Ioka, Akiko; Soda, Midori; Sobue, Tomotaka

    2012-02-01

    Population-based cancer registries are operated by over 80% of prefectures in Japan. However, only a limited proportion of the registries can provide long-term incidence data. Here, we aimed to establish a method for monitoring cancer incidence trends in Japan using data from selected prefectures. Based on the availability of long-term (≥ 20 years) high-quality data, we collected incidence data from five prefectures (Miyagi, Yamagata, Fukui, Osaka, and Nagasaki), which included an annual average of 54,539 primary cancer cases diagnosed between 1985 and 2004. Cancer mortality data for 1995-2004 were obtained from the vital statistics. Representativeness and homogeneity of the trends were examined by funnel plot analysis of log-linear regression coefficients calculated for the most recent 10 years of data (1995-2004) of age-standardized rates (ASR). The ASR of incidence for five prefectures in total (5-pref total) showed a significant decrease, with an annual percent change (APC) of -1.0 (95% confidence interval [CI] -1.4: -0.6) for males and -0.4 (95% CI -0.8: -0.1) for females. Excluding data from Osaka (4-pref total) reversed the decreasing trend; the corresponding APC was +0.4 (95% CI -0.2: +1.0) for males and +0.7 (95% CI +0.5: +0.9) for females. The APCs for the ASR of mortality for the 4-pref total (males, -1.5; females, -1.3) were more representative of nationwide data (males, -1.4 [95% CI -1.7: -1.2]; females, -1.1 [95% CI -1.4: -0.9]) than those for the 5-pref total (males, -1.7; females, -1.4). We conclude that using data from Miyagi, Yamagata, Fukui, and Nagasaki prefectures, with continuous monitoring of the representativeness of the data, is a provisionally relevant way to evaluate cancer incidence trends in Japan.

  15. Physiologically based and population PK modeling in optimizing drug development: A predict-learn-confirm analysis.

    PubMed

    Suri, A; Chapel, S; Lu, C; Venkatakrishnan, K

    2015-09-01

    Physiologically based pharmacokinetic (PBPK) modeling and classical population pharmacokinetic (PK) model-based simulations are increasingly used to answer various drug development questions. In this study, we propose a methodology to optimize the development of drugs, primarily cleared by the kidney, using model-based approaches to determine the need for a dedicated renal impairment (RI) study. First, the impact of RI on drug exposure is simulated via PBPK modeling and then confirmed using classical population PK modeling of phase 2/3 data. This methodology was successfully evaluated and applied to an investigational agent, orteronel (nonsteroidal, reversible, selective 17,20-lyase inhibitor). A phase 1 RI study confirmed the accuracy of model-based predictions. Hence, for drugs eliminated primarily via renal clearance, this modeling approach can enable inclusion of patients with RI in phase 3 trials at appropriate doses, which may be an alternative to a dedicated RI study, or suggest that only a reduced-size study in severe RI may be sufficient.

  16. Stroke in systemic lupus erythematosus: a meta-analysis of population-based cohort studies

    PubMed Central

    Holmqvist, Marie; Simard, Julia F; Asplund, Kjell; Arkema, Elizabeth V

    2015-01-01

    Previous studies of stroke in systemic lupus erythematosus (SLE) have had limited statistical power, combined stroke subtypes into composite outcomes, and lacked a reference population estimate. Therefore, we conducted a systematic review and meta-analysis of cohort studies to summarise the stroke subtype-specific risk in patients with SLE compared to the general population. A systematic search of MEDLINE and EMBASE was performed for cohort studies examining the risk of stroke in SLE and including a general population comparator. Random effects models were used to pool the risk ratio (RR) for stroke. Subgroup analyses were carried out to investigate potential sources of heterogeneity. 10 studies were included which reported RRs for overall stroke (n=5), ischaemic stroke (n=6), intracerebral haemorrhage (n=3) and subarachnoid haemorrhage (n=3). The pooled RR for overall stroke was 2.53 (95% CI 1.96 to 3.26), ischaemic stroke 2.10 (95% CI 1.68 to 2.62), intracerebral haemorrhage 2.72 (95% CI 2.15 to 3.44) and subarachnoid haemorrhage 3.85 (95% CI 3.20 to 4.64). Significant heterogeneity among studies for ischaemic stroke was detected (p=0.002). Relative risk of stroke was highest among individuals younger than 50 years of age. Individuals with SLE have a twofold higher risk of ischaemic stroke, a threefold higher risk of intracerebral haemorrhage, and an almost fourfold higher risk of subarachnoid haemorrhage compared to the general population. Future studies should focus on whether comorbidity and disease flares are related to stroke, when individuals are at the highest risk, and how the targeting of specific groups of patients with SLE may reduce this risk. PMID:26719816

  17. Is Statin Use Associated With Tendon Rupture? A Population-Based Retrospective Cohort Analysis.

    PubMed

    Contractor, Tahmeed; Beri, Abhimanyu; Gardiner, Joseph C; Tang, Xiaoqin; Dwamena, Francesca C

    2015-01-01

    Previous case reports and small studies have suggested that 3-hydroxy-3-methylglutaryl-CoA reductase inhibitors (HMG-CoA-Is) may increase the risk of tendon rupture. We conducted a population-based retrospective cohort evaluation to better assess this relationship. From approximately 800,000 enrollees of a private insurance database, those who were aged ≤64 years with at least 1 year of continuous enrollment were selected. Exposure was defined as initiation of HMG-CoA-I after the beginning of the study period. Each exposed person was matched with 2 controls of similar age and gender. Baseline characteristics, including known risk factors for tendon rupture, were compared between exposed and control cohorts with fidelity to the study's matched design. After adjusting for differences in follow-up and baseline characteristics, incidence rate ratios for tendon rupture was assessed in HMG-CoA-I users and nonusers. A total of 34,749 exposed patients were matched with 69,498 controls. There was no difference in the occurrence of tendon ruptures in HMG-CoA-I users versus nonusers. The results remained unchanged after adjustment for age and gender. In conclusion, this population-based retrospective cohort evaluation suggests that use of HMG-CoA-Is as a group are not associated with tendon rupture.

  18. Prevalence of Intellectual Disability: A Meta-Analysis of Population-Based Studies

    ERIC Educational Resources Information Center

    Maulik, Pallab K.; Mascarenhas, Maya N.; Mathers, Colin D.; Dua, Tarun; Saxena, Shekhar

    2011-01-01

    Intellectual disability is an extremely stigmatizing condition and involves utilization of large public health resources, but most data about its burden is based on studies conducted in developed countries. The aim of this meta-analysis was to collate data from published literature and estimate the prevalence of intellectual disability across all…

  19. Antibiotic regimen based on population analysis of residing persister cells eradicates Staphylococcus epidermidis biofilms.

    PubMed

    Yang, Shoufeng; Hay, Iain D; Cameron, David R; Speir, Mary; Cui, Bintao; Su, Feifei; Peleg, Anton Y; Lithgow, Trevor; Deighton, Margaret A; Qu, Yue

    2015-12-21

    Biofilm formation is a major pathogenicity strategy of Staphylococcus epidermidis causing various medical-device infections. Persister cells have been implicated in treatment failure of such infections. We sought to profile bacterial subpopulations residing in S. epidermidis biofilms, and to establish persister-targeting treatment strategies to eradicate biofilms. Population analysis was performed by challenging single biofilm cells with antibiotics at increasing concentrations ranging from planktonic minimum bactericidal concentrations (MBCs) to biofilm MBCs (MBCbiofilm). Two populations of "persister cells" were observed: bacteria that survived antibiotics at MBCbiofilm for 24/48 hours were referred to as dormant cells; those selected with antibiotics at 8 X MICs for 3 hours (excluding dormant cells) were defined as tolerant-but-killable (TBK) cells. Antibiotic regimens targeting dormant cells were tested in vitro for their efficacies in eradicating persister cells and intact biofilms. This study confirmed that there are at least three subpopulations within a S. epidermidis biofilm: normal cells, dormant cells, and TBK cells. Biofilms comprise more TBK cells and dormant cells than their log-planktonic counterparts. Using antibiotic regimens targeting dormant cells, i.e. effective antibiotics at MBCbiofilm for an extended period, might eradicate S. epidermidis biofilms. Potential uses for this strategy are in antibiotic lock techniques and inhaled aerosolized antibiotics.

  20. Voxel-based population analysis for correlating local dose and rectal toxicity in prostate cancer radiotherapy

    PubMed Central

    Acosta, Oscar; Drean, Gael; Ospina, Juan David; Simon, Antoine; Haigron, Pascal; Lafond, Caroline; De Crevoisier, Renaud

    2013-01-01

    The majority of current models utilized for predicting toxicity in prostate cancer radiotherapy are based on dose-volume histograms. One of their main drawbacks is the lack of spatial accuracy, since they consider the organs as a whole volume and thus ignore the heterogeneous intra-organ radio-sensitivity. In this paper, we propose a dose-image-based framework to reveal the relationships between local dose and toxicity. In this approach, the three-dimensional (3D) planned dose distributions across a population are non-rigidly registered into a common coordinate system and compared at a voxel level, therefore enabling the identification of 3D anatomical patterns, which may be responsible for toxicity, at least to some extent. Additionally, different metrics were employed in order to assess the quality of the dose mapping. The value of this approach was demonstrated by prospectively analyzing rectal bleeding (≥Grade 1 at 2 years) according to the CTCAE v3.0 classification in a series of 105 patients receiving 80Gy to the prostate by IMRT. Within the patients presenting bleeding, a significant dose excess (6Gy on average, p<0.01) was found in a region of the anterior rectal wall. This region, close to the prostate (1cm), represented less than 10% of the rectum. This promising voxel-wise approach allowed subregions to be defined within the organ that may be involved in toxicity and, as such, must be considered during the inverse IMRT planning step. PMID:23528429

  1. Dynamic population flow based risk analysis of infectious disease propagation in a metropolis.

    PubMed

    Zhang, Nan; Huang, Hong; Duarte, Marlyn; Zhang, Junfeng Jim

    2016-09-01

    Knowledge on the characteristics of infectious disease propagation in metropolises plays a critical role in guiding public health intervention strategies to reduce death tolls, disease incidence, and possible economic losses. Based on the SIR model, we established a comprehensive spatiotemporal risk assessment model to compute infectious disease propagation within an urban setting using Beijing, China as a case study. The model was developed for a dynamic population distribution using actual data on location, density of residences and offices, and means of public transportation (e.g., subways, buses and taxis). We evaluated four influencing factors including biological, behavioral, environmental parameters and infectious sources. The model output resulted in a set of maps showing how the four influencing factors affected the trend and characteristics of airborne infectious disease propagation in Beijing. We compared the scenarios for the long-term dynamic propagation of infectious disease without governmental interventions versus scenarios with government intervention and hospital coordinated emergency responses. Lastly, the sensitivity of the average number of people at different location in spreading infections is analyzed. Based on our results, we provide valuable recommendations to governmental agencies and the public in order to minimize the disease propagation.

  2. Academic Outcomes in High-School Students after a Concussion: A Retrospective Population-Based Analysis

    PubMed Central

    Russell, Kelly; Hutchison, Michael G.; Selci, Erin; Leiter, Jeff; Chateau, Daniel; Ellis, Michael J.

    2016-01-01

    Background Many concussion symptoms, such as headaches, vision problems, or difficulty remembering or concentrating may deleteriously affect school functioning. Our objective was to determine if academic performance was lower in the academic calendar year that students sustain a concussion compared to the previous year when they did not sustain a concussion. Methods Using Manitoba Health and Manitoba Education data, we conducted a population-based, controlled before-after study from 2005–2006 to 2010–2011 academic years. Grade 9–12 students with an ICD9/10 code for concussion were matched to non-concussed controls. Overall changes in grade point average (GPA) were compared for the academic year prior to the concussion to the academic year the concussion occurred (or could have occurred among non-concussed matched students). Results Overall, 8240 students (1709 concussed, 6531 non-concussed students) were included. Both concussed and non-concussed students exhibited a lower overall GPA from one year to the next. Having sustained a concussion resulted in a -0.90% (95% CI: -1.88, 0.08) reduction in GPA. Over the same period, non-concussed matched students’ GPA reduced by -0.57% (95% CI: -1.32, 0.19). Students who sustained a concussion during high school were just as likely to graduate within four years as their non-concussed peers (ORadj: 0.84; 95% CI: 0.73, 1.02). Conclusions We found that, at a population level, a concussion had minimal long-term effects on academic performance during high school. While academic accommodations and Return-to-Learn programs are an important component of pediatric concussion management, research is needed to identify risk factors for poor academic performance after a concussion and who should receive these programs. PMID:27764223

  3. Sexting Leads to "Risky" Sex? An Analysis of Sexting Behaviors in a Nonuniversity-Based, Older Adult Population.

    PubMed

    Currin, Joseph M; Hubach, Randolph D; Sanders, Carissa; Hammer, Tonya R

    2016-10-12

    Since few researchers have analyzed sexting behaviors in nonuniversity-based adult samples, we sought to determine if sexting is associated with negative psychological correlates and risky sexual behaviors in this population. Analysis of individuals who indicated having vaginal or anal sex in the past 12 months and who identified as single (n = 377) showed that condomless sex is independent of sexting behaviors. Results for those in committed relationships (n = 374) and having had vaginal or anal sex in the past 12 months also demonstrated condomless sex and sexting behaviors were not related. Furthermore, alcohol consumption and relational health were predictive of sexting behaviors in adults in committed relationships. These findings demonstrate that while risky sexual behavior and negative psychological correlates are associated with sexting and younger populations, the same might not be true for a nonuniversity-based, older adult sample.

  4. Informed consent, participation in, and withdrawal from a population based cohort study involving genetic analysis

    PubMed Central

    Matsui, K; Kita, Y; Ueshima, H

    2005-01-01

    Design: Descriptive analyses. Setting and participants: The study evaluated two non-genetic subcohorts comprising 3166 people attending for a health checkup during 2002, and two genetic subcohorts comprising 2195 people who underwent a checkup during 2003. Main outcome measurements: Analysis endpoints were differences in participation rates between the non-genetic and genetic subcohorts, differences between providing non-extensive and extensive preliminary information, and changes in participation status between baseline and at 6 months. Results: Participation rates in the genetic subcohorts were 4·7–9·3% lower than those in the non-genetic subcohorts. The odds ratios (OR) of participation in genetic research were between 0·60 and 0·77, and the OR for withdrawal from the research was over 7·70; providing preliminary extensive information about genetic research reduced the withdrawal risks (OR 0·15 for all dependent variables) but worsened participation rates (OR 0·63–0·74). Conclusions: The general population responded sceptically towards genetic research. It is crucial that genetic researchers utilise an informative and educational consent process worthy of public trust. PMID:15994356

  5. Improving mesocosm data analysis through individual-based modelling of control population dynamics: a case study with mosquitofish (Gambusia holbrooki).

    PubMed

    Beaudouin, Rémy; Ginot, Vincent; Monod, Gilles

    2012-01-01

    Experimental ecosystems such as mesocosms have been developed to improve the ecological relevance of ecotoxicity test. However, in mesocosm studies, the number of replicates is limited by practical and financial constraints. In addition, high levels of biological organization are characterized by a high variability of descriptive variables. This variability and the poor number of replicates have been recognized as a major drawback for detecting significant effects of chemicals in mesocosm studies. In this context, a tool able to predict precisely control mesocosms outputs, to which endpoints in mesocosms exposed to chemicals could be compared should constitute a substantial improvement. We evaluated here a solution which consists in stochastic modelling of the control fish populations to assess the probabilistic distributions of population endpoints. An individual-based approach was selected, because it generates realistic fish length distributions and accounts for both individual and environmental sources of variability. This strategy was applied to mosquitofish (Gambusia holbrooki) populations monitored in lentic mesocosms. We chose the number of founders as a so-called "stressor" because subsequent consequences at the population level could be expected. Using this strategy, we were able to detect more significant and biologically relevant perturbations than using classical methods. We conclude that designing an individual-based model is very promising for improving mesocosm data analysis. This methodology is currently being applied to ecotoxicological issues.

  6. Analysis of amyotrophic lateral sclerosis as a multistep process: a population-based modelling study

    PubMed Central

    Al-Chalabi, Ammar; Calvo, Andrea; Chio, Adriano; Colville, Shuna; Ellis, Cathy M; Hardiman, Orla; Heverin, Mark; Howard, Robin S; Huisman, Mark H B; Keren, Noa; Leigh, P Nigel; Mazzini, Letizia; Mora, Gabriele; Orrell, Richard W; Rooney, James; Scott, Kirsten M; Scotton, William J; Seelen, Meinie; Shaw, Christopher E; Sidle, Katie S; Swingler, Robert; Tsuda, Miho; Veldink, Jan H; Visser, Anne E; van den Berg, Leonard H; Pearce, Neil

    2014-01-01

    Summary Background Amyotrophic lateral sclerosis shares characteristics with some cancers, such as onset being more common in later life, progression usually being rapid, the disease affecting a particular cell type, and showing complex inheritance. We used a model originally applied to cancer epidemiology to investigate the hypothesis that amyotrophic lateral sclerosis is a multistep process. Methods We generated incidence data by age and sex from amyotrophic lateral sclerosis population registers in Ireland (registration dates 1995–2012), the Netherlands (2006–12), Italy (1995–2004), Scotland (1989–98), and England (2002–09), and calculated age and sex-adjusted incidences for each register. We regressed the log of age-specific incidence against the log of age with least squares regression. We did the analyses within each register, and also did a combined analysis, adjusting for register. Findings We identified 6274 cases of amyotrophic lateral sclerosis from a catchment population of about 34 million people. We noted a linear relationship between log incidence and log age in all five registers: England r2=0·95, Ireland r2=0·99, Italy r2=0·95, the Netherlands r2=0·99, and Scotland r2=0·97; overall r2=0·99. All five registers gave similar estimates of the linear slope ranging from 4·5 to 5·1, with overlapping confidence intervals. The combination of all five registers gave an overall slope of 4·8 (95% CI 4·5–5·0), with similar estimates for men (4·6, 4·3–4·9) and women (5·0, 4·5–5·5). Interpretation A linear relationship between the log incidence and log age of onset of amyotrophic lateral sclerosis is consistent with a multistage model of disease. The slope estimate suggests that amyotrophic lateral sclerosis is a six-step process. Identification of these steps could lead to preventive and therapeutic avenues. Funding UK Medical Research Council; UK Economic and Social Research Council; Ireland Health Research Board; The

  7. Population-based survival-cure analysis of ER-negative breast cancer.

    PubMed

    Huang, Lan; Johnson, Karen A; Mariotto, Angela B; Dignam, James J; Feuer, Eric J

    2010-08-01

    This study investigated the trends over time in age and stage specific population-based survival of estrogen receptor negative (ER-) breast cancer patients by examining the fraction of cured patients and the median survival time for uncured patients. Cause-specific survival data from the Surveillance, Epidemiology, and End Results program for cases diagnosed during 1992-1998 were used in mixed survival cure models to evaluate the cure fraction and the extension in survival for uncured patients. Survival trends were compared with adjuvant chemotherapy data available from an overlapping patterns-of-care study. For stage II N+ disease, the largest increase in cure fraction was 44-60% (P = 0.0257) for women aged >or=70 in contrast to a 7-8% point increase for women aged <50 or 50-69 (P = 0.056 and 0.038, respectively). For women with stage III disease, the increases in the cure fraction were not statistically significant, although women aged 50-69 had a 10% point increase (P = 0.103). Increases in cure fraction correspond with increases in the use of adjuvant chemotherapy, particularly for the oldest age group. In this article, for the first time, we estimate the cure fraction for ER- patients. We notice that at age >o5r=70, the accelerated increase in cure fraction from 1992 to 1998 for women with stage II N+ compared with stage III suggests a selective benefit for chemotherapy in the lower stage group.

  8. Population-Based Analysis of Invasive Nontypeable Pneumococci Reveals That Most Have Defective Capsule Synthesis Genes

    PubMed Central

    Sherwood, Logan K.; Nahm, Moon H.; Beall, Bernard

    2014-01-01

    Since nasopharyngeal carriage of pneumococcus precedes invasive pneumococcal disease, characteristics of carriage isolates could be incorrectly assumed to reflect those of invasive isolates. While most pneumococci express a capsular polysaccharide, nontypeable pneumococci are sometimes isolated. Carriage nontypeables tend to encode novel surface proteins in place of a capsular polysaccharide synthetic locus, the cps locus. In contrast, capsular polysaccharide is believed to be indispensable for invasive pneumococcal disease, and nontypeables from population-based invasive pneumococcal disease surveillance have not been extensively characterized. We received 14,328 invasive pneumococcal isolates through the Active Bacterial Core surveillance program during 2006–2009. Isolates that were nontypeable by Quellung serotyping were characterized by PCR serotyping, sequence analyses of the cps locus, and multilocus sequence typing. Eighty-eight isolates were Quellung-nontypeable (0.61%). Of these, 79 (89.8%) contained cps loci. Twenty-two nontypeables exhibited serotype 8 cps loci with defects, primarily within wchA. Six of the remaining nine isolates contained previously-described aliB homologs in place of cps loci. Multilocus sequence typing revealed that most nontypeables that lacked capsular biosynthetic genes were related to established non-encapsulated lineages. Thus, invasive pneumococcal disease caused by nontypeable pneumococcus remains rare in the United States, and while carriage nontypeables lacking cps loci are frequently isolated, such nontypeable are extremely rare in invasive pneumococcal disease. Most invasive nontypeable pneumococci possess defective cps locus genes, with an over-representation of defective serotype 8 cps variants. PMID:24831650

  9. Voxel-based population analysis for correlating local dose and rectal toxicity in prostate cancer radiotherapy.

    PubMed

    Acosta, Oscar; Drean, Gael; Ospina, Juan D; Simon, Antoine; Haigron, Pascal; Lafond, Caroline; de Crevoisier, Renaud

    2013-04-21

    The majority of current models utilized for predicting toxicity in prostate cancer radiotherapy are based on dose-volume histograms. One of their main drawbacks is the lack of spatial accuracy, since they consider the organs as a whole volume and thus ignore the heterogeneous intra-organ radio-sensitivity. In this paper, we propose a dose-image-based framework to reveal the relationships between local dose and toxicity. In this approach, the three-dimensional (3D) planned dose distributions across a population are non-rigidly registered into a common coordinate system and compared at a voxel level, therefore enabling the identification of 3D anatomical patterns, which may be responsible for toxicity, at least to some extent. Additionally, different metrics were employed in order to assess the quality of the dose mapping. The value of this approach was demonstrated by prospectively analyzing rectal bleeding (≥Grade 1 at 2 years) according to the CTCAE v3.0 classification in a series of 105 patients receiving 80 Gy to the prostate by intensity modulated radiation therapy (IMRT). Within the patients presenting bleeding, a significant dose excess (6 Gy on average, p < 0.01) was found in a region of the anterior rectal wall. This region, close to the prostate (1 cm), represented less than 10% of the rectum. This promising voxel-wise approach allowed subregions to be defined within the organ that may be involved in toxicity and, as such, must be considered during the inverse IMRT planning step.

  10. Voxel-based population analysis for correlating local dose and rectal toxicity in prostate cancer radiotherapy

    NASA Astrophysics Data System (ADS)

    Acosta, Oscar; Drean, Gael; Ospina, Juan D.; Simon, Antoine; Haigron, Pascal; Lafond, Caroline; de Crevoisier, Renaud

    2013-04-01

    The majority of current models utilized for predicting toxicity in prostate cancer radiotherapy are based on dose-volume histograms. One of their main drawbacks is the lack of spatial accuracy, since they consider the organs as a whole volume and thus ignore the heterogeneous intra-organ radio-sensitivity. In this paper, we propose a dose-image-based framework to reveal the relationships between local dose and toxicity. In this approach, the three-dimensional (3D) planned dose distributions across a population are non-rigidly registered into a common coordinate system and compared at a voxel level, therefore enabling the identification of 3D anatomical patterns, which may be responsible for toxicity, at least to some extent. Additionally, different metrics were employed in order to assess the quality of the dose mapping. The value of this approach was demonstrated by prospectively analyzing rectal bleeding (⩾Grade 1 at 2 years) according to the CTCAE v3.0 classification in a series of 105 patients receiving 80 Gy to the prostate by intensity modulated radiation therapy (IMRT). Within the patients presenting bleeding, a significant dose excess (6 Gy on average, p < 0.01) was found in a region of the anterior rectal wall. This region, close to the prostate (1 cm), represented less than 10% of the rectum. This promising voxel-wise approach allowed subregions to be defined within the organ that may be involved in toxicity and, as such, must be considered during the inverse IMRT planning step.

  11. Population based MRI and DTI templates of the adult ferret brain and tools for voxelwise analysis.

    PubMed

    Hutchinson, E B; Schwerin, S C; Radomski, K L; Sadeghi, N; Jenkins, J; Komlosh, M E; Irfanoglu, M O; Juliano, S L; Pierpaoli, C

    2017-03-16

    Non-invasive imaging has the potential to play a crucial role in the characterization and translation of experimental animal models to investigate human brain development and disorders, especially when employed to study animal models that more accurately represent features of human neuroanatomy. The purpose of this study was to build and make available MRI and DTI templates and analysis tools for the ferret brain as the ferret is a well-suited species for pre-clinical MRI studies with folded cortical surface, relatively high white matter volume and body dimensions that allow imaging with pre-clinical MRI scanners. Four ferret brain templates were built in this study - in-vivo MRI and DTI and ex-vivo MRI and DTI - using brain images across many ferrets and region of interest (ROI) masks corresponding to established ferret neuroanatomy were generated by semi-automatic and manual segmentation. The templates and ROI masks were used to create a web-based ferret brain viewing software for browsing the MRI and DTI volumes with annotations based on the ROI masks. A second objective of this study was to provide a careful description of the imaging methods used for acquisition, processing, registration and template building and to demonstrate several voxelwise analysis methods including Jacobian analysis of morphometry differences between the female and male brain and bias-free identification of DTI abnormalities in an injured ferret brain. The templates, tools and methodological optimization presented in this study are intended to advance non-invasive imaging approaches for human-similar animal species that will enable the use of pre-clinical MRI studies for understanding and treating brain disorders.

  12. Population-based analysis of the frequency of HFE gene polymorphisms: Correlation with the susceptibility to develop hereditary hemochromatosis.

    PubMed

    Katsarou, Martha-Spyridoula; Latsi, Rosana; Papasavva, Maria; Demertzis, Nikolaos; Kalogridis, Thodoris; Tsatsakis, Aristides M; Spandidos, Demetrios A; Drakoulis, Nikolaos

    2016-07-01

    Hereditary hemochromatosis (HH) is an autosomal recessive genetic disease, characterized by increased dietary iron absorption. Due to the absence of an effective excretory mechanism, the excess iron in the body may accumulate resulting in toxic effects. The HFE gene also affects the activity of hepcidin, a hormone which acts as a negative regulator of iron metabolism. In this study, we performed a population-based analysis of the distribution of three hemochromatosis-related polymorphisms in the HFE gene (rs1800562, rs1799945 and rs1800730). DNA from 1,446 non‑related individuals of Greek ethnicity was collected and analyzed, either from whole blood or buccal swabs. The frequency distribution of these HFE gene polymorphisms was then determined. The results revealed that in our Greek population cohort (gr) the frequencies of each polymorphism were as follows: rs1800562: GG (wild‑type)=97.0%, GA=1.5%, AA=1.5%; rs1799945: CC (wild‑type)=74.4%, CG=23.4%, GG=2.2%; rs1800730: AA (wild‑type)=98.1%, AT=1.5% and TT=0.4%. No association between the HFE polymorphisms rs1800562, rs1799945 and rs1800730 and gender could be established. As regards the rs1800562 polymorphism, the A allele (mutant) was ~1.8‑fold more frequent in the European population (eur) than in the Greek population [(gr)=2,3%<(eur)=4%]. As for the rs1799945 polymorphism, the G allele (mutant) was 1.2‑fold more frequent in the European population than in the Greek population [(gr)=13,9%<(eur)=17%]. As regards the rs1800730 polymorphism, the T allele (mutant) was ~1.7‑fold more frequent in the European population than in the Greek population [(gr)=1.2%<(eur)=2%]. However, these pathogenic mutations were found more frequently in the Greek population compared to the global population (gl) [rs1800562: (gl)=1%<(gr)=2,3%; rs1799945: (gl)=7%<(gr)=13,9%; rs1800730: (gl)=<1%<(gr)=1.2%]. This suggests that the Greek population may differ genetically from the northern European population

  13. Survival analysis of children with primary malignant brain tumors in England and Wales: a population-based study.

    PubMed

    Tseng, Jen-Ho; Tseng, Ming-Yuan

    2006-01-01

    Primary malignant brain tumor is the second most common cancer in children. To investigate factors affecting children's survival at a population level, data of 3,169 patients (age<15 years) from the Cancer Registry in England and Wales were used. They were diagnosed during 1971-1990 and followed up until 1995. Variables including age, gender, morphology, WHO grade, tumor site, socioeconomic status, geographical region, and period of diagnosis were available for analysis using the Kaplan-Meier method and the Cox hazards ratio (HR) regression. Results showed that the median survival and the 1-, 5-, and 10-year crude survival rate for this population were 8.7 years, 72.4, 54.0, and 49.2% respectively. Survival was influenced by age (HR 0.88/5 years), morphology (ependymoma HR 2.43), WHO grades (HR 1.42/grade), tumor sites (brain stem HR 2.11), and periods of diagnosis (HR 0.88/5 years). Gender, socioeconomic status, and geographical region did not affect their survival. Results from this population-based data are very helpful for comparison with other hospital-based studies and for public health purposes.

  14. Population Education: A Knowledge Base.

    ERIC Educational Resources Information Center

    Jacobson, Willard J.

    To aid junior high and high school educators and curriculum planners as they develop population education programs, the book provides an overview of the population education knowledge base. In addition, it suggests learning activities, discussion questions, and background information which can be integrated into courses dealing with population,…

  15. Bone mineral density in statin users: a population-based analysis from a Spanish cohort.

    PubMed

    Hernández, José L; Olmos, José M; Romaña, Galo; Martinez, Josefina; Castillo, Jesús; Yezerska, Irina; Pinedo, Gabriel; González-Macías, Jesús

    2014-03-01

    We studied 2,315 subjects (1,422 women and 893 men) from the Camargo Cohort and analyzed the differences in BMD between statin or non-statin users. We also studied effects of the type of statin, dose, pharmacokinetic properties, and length of treatment on bone mineral density (BMD). Of the subjects, 478 (21 %) were taking statins (256 women and 222 men). Overall, they had higher BMD than non-users (p < 0.0001). In adjusted multivariate models, women taking statins had higher BMD at femoral neck (p = 0.002) and total hip (p = 0.04) than non- users. No differences were found in men. Women taking simvastatin had higher increases in BMD than non-statin users at femoral neck (p = 0.02) and total hip (p = 0.009), those taking fluvastatin had lower BMD values at lumbar spine (p = 0.028), and those receiving lovastatin had higher increases at femoral neck (p = 0.006). In men, only atorvastatin was associated with higher femoral neck BMD than non-statin use (p = 0.029). Comparing with non-statin users, only women receiving lipophilic statins had greater BMD at femoral neck (p = 0.003). According to drug potency, women on high- or lower-potency agents showed higher BMD values at femoral neck than non-users (p = 0.028 and 0.022, respectively). In men, only high-potency statins were associated with higher femoral neck BMD than non-use (p = 0.021). No differences between dose or length of statin therapy were noted regarding BMD in either sex. In summary, in a large population-based cohort, women on statins had higher BMD at the hip than non-users. Overall, this increase in BMD was more evident in subjects on lipophilic or high-potency statins.

  16. Feasibility of MR-Based Body Composition Analysis in Large Scale Population Studies

    PubMed Central

    West, Janne; Dahlqvist Leinhard, Olof; Romu, Thobias; Collins, Rory; Garratt, Steve; Bell, Jimmy D.; Borga, Magnus; Thomas, Louise

    2016-01-01

    Introduction Quantitative and accurate measurements of fat and muscle in the body are important for prevention and diagnosis of diseases related to obesity and muscle degeneration. Manually segmenting muscle and fat compartments in MR body-images is laborious and time-consuming, hindering implementation in large cohorts. In the present study, the feasibility and success-rate of a Dixon-based MR scan followed by an intensity-normalised, non-rigid, multi-atlas based segmentation was investigated in a cohort of 3,000 subjects. Materials and Methods 3,000 participants in the in-depth phenotyping arm of the UK Biobank imaging study underwent a comprehensive MR examination. All subjects were scanned using a 1.5 T MR-scanner with the dual-echo Dixon Vibe protocol, covering neck to knees. Subjects were scanned with six slabs in supine position, without localizer. Automated body composition analysis was performed using the AMRA Profiler™ system, to segment and quantify visceral adipose tissue (VAT), abdominal subcutaneous adipose tissue (ASAT) and thigh muscles. Technical quality assurance was performed and a standard set of acceptance/rejection criteria was established. Descriptive statistics were calculated for all volume measurements and quality assurance metrics. Results Of the 3,000 subjects, 2,995 (99.83%) were analysable for body fat, 2,828 (94.27%) were analysable when body fat and one thigh was included, and 2,775 (92.50%) were fully analysable for body fat and both thigh muscles. Reasons for not being able to analyse datasets were mainly due to missing slabs in the acquisition, or patient positioned so that large parts of the volume was outside of the field-of-view. Discussion and Conclusions In conclusion, this study showed that the rapid UK Biobank MR-protocol was well tolerated by most subjects and sufficiently robust to achieve very high success-rate for body composition analysis. This research has been conducted using the UK Biobank Resource. PMID:27662190

  17. Ten-Year Trend Analysis of Autism Severity: A Nationwide Population-Based Register Study

    ERIC Educational Resources Information Center

    Lin, Jin-Ding; Sung, Chang-Lin; Lin, Lan-Ping; Hsu, Shang-Wei; Chien, Wu-Chien; Su, Sui-Lung; Wu, Jia-Ling

    2011-01-01

    The severity of autism spectrum disorder was strongly related to the education and service outcome. Without a clear profile of autistic population and its change, efforts to understand its nature and improve the quality of service or education will be impossible. The present study aims to describe the over time reported rate of autism severity…

  18. [Analysis of genetic diversity of Russian regional populations based on common STR markers used in DNA identification].

    PubMed

    Pesik, V Yu; Fedunin, A A; Agdzhoyan, A T; Utevska, O M; Chukhraeva, M I; Evseeva, I V; Churnosov, M I; Lependina, I N; Bogunov, Yu V; Bogunova, A A; Ignashkin, M A; Yankovsky, N K; Balanovska, E V; Orekhov, V A; Balanovsky, O P

    2014-06-01

    We conducted the first genetic analysis of a wide a range of rural Russian populations in European Russia with a panel of common DNA markers commonly used in criminalistics genetic identification. We examined a total of 647 samples from indigenous ethnic Russian populations in Arkhangelsk, Belgorod, Voronezh, Kursk, Rostov, Ryazan, and Orel regions. We employed a multiplex genotyping kit, COrDIS Plus, to genotype Short Tandem Repeat (STR) loci, which included the genetic marker panel officially recommended for DNA identification in the Russian Federation, the United States, and the European Union. In the course of our study, we created a database of allelic frequencies, examined the distribution of alleles and genotypes in seven rural Russian populations, and defined the genetic relationships between these populations. We found that, although multidimensional analysis indicated a difference between the Northern gene pool and the rest of the Russian European populations, a pairwise comparison using 19 STR markers among all populations did not reveal significant differences. This is in concordance with previous studies, which examined up to 12 STR markers of urban Russian populations. Therefore, the database of allelic frequencies created in this study can be applied for forensic examinations and DNA identification among the ethnic Russian population over European Russia. We also noted a decrease in the levels of heterozygosity in the northern Russian population compared to ethnic populations in southern and central Russia, which is consistent with trends identified previously using classical gene markers and analysis of mitochondrial DNA.

  19. Understanding sexual orientation health disparities in smoking: a population-based analysis.

    PubMed

    Balsam, Kimberly F; Beadnell, Blair; Riggs, Karin R

    2012-10-01

    Lesbian, gay, and bisexual populations are at elevated risk for tobacco use compared to their heterosexual peers. However, there is little research examining reasons for this disparity. Drawing on prior literature regarding psychosocial variables associated with both sexual orientation and smoking, the authors tested a path model of risk and protective factors to help explain sexual orientation differences in smoking using data from the Washington State Behavioral Risk Factor Surveillance System from 2003 to 2007. The authors estimated separate models for men and women, comparing lesbians or gays and bisexuals to heterosexuals. Results indicated that the explanatory variables accounted for most of the variance in this relationship, with both risk-enhancing and risk-reducing pathways. Mental health, life dissatisfaction, alcohol use, exposure to tobacco marketing, and single relationship status were risk enhancers for most LGB participants. Health-care access and income level were risk enhancers for bisexual participants only. Neither emotional support nor attitudes and knowledge about tobacco use helped explain the relationship between sexual orientation and smoking. These findings have significant implications for tobacco prevention and control efforts in this high-risk population.

  20. [Analysis of genetic structure and differentiation of the bog and dry land populations of Pinus sibirica du tour based on nuclear microsatellite loci].

    PubMed

    Oreshkova, N V; Sedel'nikova, T S; Pimenov, A V; Efremov, S P

    2014-09-01

    We evaluated the population structure of the bog and dry land populations of the Siberian pine Pinus sibirica (P. sibrica) in Western Siberia using nuclear genome markers. Six pairs of nuclear microsatellite loci were used for this analysis. We detected 30 allelic variants in 120 individuals of four populations of P. Sibirica. We established that the studied populations differ by genetic structure. The most essential differences were identified between the Siberian pine population from oligotrophic bog and the group of populations from dry land within eutrophic bogs and near settlements P. sibirica forest (F(ST) = 0.019; D(N) = 0.053). We estimated that diversification of the West Siberian populations of P. sibirica exceeded 2.4% (F(ST) = 0.024), based on an analysis of SSR markers.

  1. Psychotic Experiences and Working Memory: A Population-Based Study Using Signal-Detection Analysis

    PubMed Central

    Rossi, Rodolfo; Zammit, Stanley; Button, Katherine S.; Munafò, Marcus R.; Lewis, Glyn; David, Anthony S.

    2016-01-01

    Psychotic Experiences (PEs) during adolescence index increased risk for psychotic disorders and schizophrenia in adult life. Working memory (WM) deficits are a core feature of these disorders. Our objective was to examine the relationship between PEs and WM in a general population sample of young people in a case control study. 4744 individuals of age 17–18 from Bristol and surrounding areas (UK) were analyzed in a cross-sectional study nested within the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort study. The dependent variable was PEs, assessed using the semi-structured Psychosis-Like Symptom Interview (PLIKSi). The independent variable was performance on a computerized numerical n-back working memory task. Signal-Detection Theory indices, including standardized hits rate, false alarms rate, discriminability index (d’) and response bias (c) from 2-Back and 3-Back tasks were calculated. 3576 and 3527 individuals had complete data for 2-Back and 3-Back respectively. Suspected/definite PEs prevalence was 7.9% (N = 374). Strongest evidence of association was seen between PEs and false alarms on the 2-Back, (odds ratio (OR) = 1.17 [95% confidence intervals (CI) 1.01, 1.35]) and 3-back (OR = 1.35 [1.18, 1.54]) and with c (OR = 1.59 [1.09, 2.34]), and lower d’ (OR = 0.76 [0.65, 0.89]), on the 3-Back. Adjustment for several potential confounders, including general IQ, drug exposure and different psycho-social factors, and subsequent multiple imputation of missing data did not materially alter the results. WM is impaired in young people with PEs in the general population. False alarms, rather than poor accuracy, are more closely related to PEs. Such impairment is consistent with different neuropsychological models of psychosis focusing on signal-to-noise discrimination, probabilistic reasoning and impaired reality monitoring as a basis of psychotic symptoms. PMID:27120349

  2. Image Based Biomarker of Breast Cancer Risk: Analysis of Risk Disparity Among Minority Populations

    DTIC Science & Technology

    2014-03-01

    Simulation of Microcalcification Clusters in Software Breast Phantoms , as well as a Computer Demo of the Software Pipeline for Breast Imaging Simulation...Breast Phantom Simulation and Analysis Software Pipeline for Breast Anatomy and Imaging Simulation The pipeline connects anatomy and imaging... Phantoms 3D clusters of microcalcifications, extracted from reconstructed clinical images, are inserted at randomly selected positions out of a set

  3. Structure analysis of an Aspergillus flavus kernels population in North Italy. First analysis of an Aspergillus flavus kernels population based on vegetative compatibility groups in Northern Italy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In order to gain insight into the causal agents of aflatoxin contamination of maize in Italy, populations of Aspergillus flavus on maize produced in the most affected area were characterized. Forty-six percent of A. flavus, isolated from maize kernels collected in 5 districts of northern Italy betwe...

  4. Model‐Based Population Pharmacokinetic Analysis of Nivolumab in Patients With Solid Tumors

    PubMed Central

    Bajaj, G; Wang, X; Agrawal, S; Gupta, M; Roy, A

    2016-01-01

    Nivolumab is a fully human monoclonal antibody that inhibits programmed death‐1 activation. The clinical pharmacology profile of nivolumab was analyzed by a population pharmacokinetics model that assessed covariate effects on nivolumab concentrations in 1,895 patients who received 0.3–10.0 mg/kg nivolumab in 11 clinical trials. Nivolumab pharmacokinetics is linear with a time‐varying clearance. A full covariate model was developed to assess covariate effects on pharmacokinetic parameters. Nivolumab clearance and volume of distribution increase with body weight. The final model included the effects of baseline performance status (PS), baseline body weight, and baseline estimated glomerular filtration rate (eGFR), sex, and race on clearance, and effects of baseline body weight and sex on volume of distribution in the central compartment. Sex, PS, baseline eGFR, age, race, baseline lactate dehydrogenase, mild hepatic impairment, tumor type, tumor burden, and programmed death ligand‐1 expression had a significant but not clinically relevant (<20%) effect on nivolumab clearance. PMID:28019091

  5. Model-Based Population Pharmacokinetic Analysis of Nivolumab in Patients With Solid Tumors.

    PubMed

    Bajaj, G; Wang, X; Agrawal, S; Gupta, M; Roy, A; Feng, Y

    2017-01-01

    Nivolumab is a fully human monoclonal antibody that inhibits programmed death-1 activation. The clinical pharmacology profile of nivolumab was analyzed by a population pharmacokinetics model that assessed covariate effects on nivolumab concentrations in 1,895 patients who received 0.3-10.0 mg/kg nivolumab in 11 clinical trials. Nivolumab pharmacokinetics is linear with a time-varying clearance. A full covariate model was developed to assess covariate effects on pharmacokinetic parameters. Nivolumab clearance and volume of distribution increase with body weight. The final model included the effects of baseline performance status (PS), baseline body weight, and baseline estimated glomerular filtration rate (eGFR), sex, and race on clearance, and effects of baseline body weight and sex on volume of distribution in the central compartment. Sex, PS, baseline eGFR, age, race, baseline lactate dehydrogenase, mild hepatic impairment, tumor type, tumor burden, and programmed death ligand-1 expression had a significant but not clinically relevant (<20%) effect on nivolumab clearance.

  6. Fatalism, optimism, spirituality, depressive symptoms and stroke outcome: A population-based analysis

    PubMed Central

    Morgenstern, Lewis B.; Sánchez, Brisa N.; Skolarus, Lesli E.; Garcia, Nelda; Risser, Jan M.H.; Wing, Jeffrey J.; Smith, Melinda A.; Zahuranec, Darin B.; Lisabeth, Lynda D.

    2011-01-01

    Background and Purpose We sought to describe the association of spirituality, optimism, fatalism and depressive symptoms with initial stroke severity, stroke recurrence and post-stroke mortality. Methods Stroke cases June 2004–December 2008 were ascertained in Nueces County, Texas. Patients without aphasia were queried on their recall of depressive symptoms, fatalism, optimism, and non-organizational spirituality before stroke using validated scales. The association between scales and stroke outcomes was studied using multiple linear regression with log-transformed NIHSS and Cox proportional hazards regression for recurrence and mortality. Results 669 patients participated, 48.7% were women. In fully adjusted models, an increase in fatalism from the first to third quartile was associated with all-cause mortality (HR=1.41, 95%CI: 1.06, 1.88), marginally associated with risk of recurrence (HR=1.35, 95%CI: 0.97, 1.88), but not stroke severity. Similarly, an increase in depressive symptoms was associated with increased mortality (HR=1.32, 95%CI: 1.02, 1.72), marginally associated with stroke recurrence (HR=1.22, CI: 0.93, 1.62), and with a 9.0% increase in stroke severity (95%CI: 0.01, 18.0). Depressive symptoms altered the fatalism-mortality association such that the association of fatalism and mortality was more pronounced for patients reporting no depressive symptoms. Neither spirituality nor optimism conferred a significant effect on stroke severity, recurrence or mortality. Conclusions Among patients who have already had a stroke, self-described pre-stroke depressive symptoms and fatalism, but not optimism or spirituality, are associated with increased risk of stroke recurrence and mortality. Unconventional risk factors may explain some of the variability in stroke outcomes observed in populations, and may be novel targets for intervention. PMID:21940963

  7. Age-structured mark-recapture analysis: A virtual-population-analysis-based model for analyzing age-structured capture-recapture data

    USGS Publications Warehouse

    Coggins, L.G.; Pine, William E.; Walters, C.J.; Martell, S.J.D.

    2006-01-01

    We present a new model to estimate capture probabilities, survival, abundance, and recruitment using traditional Jolly-Seber capture-recapture methods within a standard fisheries virtual population analysis framework. This approach compares the numbers of marked and unmarked fish at age captured in each year of sampling with predictions based on estimated vulnerabilities and abundance in a likelihood function. Recruitment to the earliest age at which fish can be tagged is estimated by using a virtual population analysis method to back-calculate the expected numbers of unmarked fish at risk of capture. By using information from both marked and unmarked animals in a standard fisheries age structure framework, this approach is well suited to the sparse data situations common in long-term capture-recapture programs with variable sampling effort. ?? Copyright by the American Fisheries Society 2006.

  8. Prevalence of familial hypercholesterolemia: a meta-analysis of six large, observational, population-based studies in Poland

    PubMed Central

    Szafraniec, Krystyna; Polak, Maciej; Drygas, Wojciech; Piotrowski, Walerian; Zdrojewski, Tomasz; Jankowski, Piotr

    2016-01-01

    Introduction Familial hypercholesterolemia (FH) is a severely underdiagnosed and undertreated genetic disorder. Little is known about regional variation in the prevalence of FH, and information for Central and Eastern Europe (CEE) is scarce. This paper assesses the prevalence of FH and related cardiovascular disease (CVD) risk factors in Poland. Material and methods We performed a meta-analysis of six population-based studies in Poland. The FH was assessed using the Dutch Lipids Clinics Network (DLCN) criteria. The categories “definite” (> 8 points) and “probable” (6–8 points) were combined into “potential FH”. Combined estimates of proportions across studies were pooled by meta-analysis with a random effects model. Results A total of 37,889 persons aged 20–79 years were included in the analysis. The distribution of DLCN scores was skewed, and there were only 7 cases of definite FH. Prevalence of potential FH was 404/100,000 people (95% CI = 277–531/100,000). Familial hypercholesterolemia was more prevalent in women than in men, and the prevalence was the highest in the age group 45–54 years in men and 55–64 years in women. After adjustment for age and sex, compared to participants with normal cholesterol, persons with potential FH had twice the prevalence of hypertension (p < 0.01); smoking was more prevalent by about 80% (p < 0.01) and hypertriglyceridemia was nine times more frequent (p < 0.001). There was no difference in the prevalence of low high-density lipoprotein (HDL)-cholesterol or diabetes. Conclusions We believe that our study might facilitate the planning of a strategy to manage the disease at a population level, i.e. to develop a national strategy for the detection, diagnosis, and treatment of FH. PMID:27478447

  9. Graph-based analysis of connectivity in spatially-explicit population models: HexSim and the Connectivity Analysis Toolkit

    EPA Science Inventory

    Background / Question / Methods Planning for the recovery of threatened species is increasingly informed by spatially-explicit population models. However, using simulation model results to guide land management decisions can be difficult due to the volume and complexity of model...

  10. A population-based analysis of germline BAP1 mutations in melanoma.

    PubMed

    O'Shea, Sally J; Robles-Espinoza, Carla Daniela; McLellan, Lauren; Harrigan, Jeanine; Jacq, Xavier; Hewinson, James; Iyer, Vivek; Merchant, Will; Elliott, Faye; Harland, Mark; Timothy Bishop, D; Newton-Bishop, Julia; Adams, David J

    2017-01-05

    Germline mutation of the BRCA1 associated protein-1 (BAP1) gene has been linked to uveal melanoma, mesothelioma, meningioma, renal cell carcinoma and basal cell carcinoma. Germline variants have also been found in familial cutaneous melanoma pedigrees, but their contribution to sporadic melanoma has not been fully assessed. We sequenced BAP1 in 1,977 melanoma cases and 754 controls and used deubiquitinase assays, a pedigree analysis, and a histopathological review to assess the consequences of the mutations found. Sequencing revealed 30 BAP1 variants in total, of which 27 were rare (ExAc allele frequency <0.002). Of the 27 rare variants, 22 were present in cases (18 missense, one splice acceptor, one frameshift and two near splice regions) and 5 in controls (all missense). A missense change (S98R) in a case that completely abolished BAP1 deubiquitinase activity was identified. Analysis of cancers in the pedigree of the proband carrying the S98R variant and in two other pedigrees carrying clear loss-of-function alleles showed the presence of BAP1-associated cancers such as renal cell carcinoma, mesothelioma and meningioma, but not uveal melanoma. Two of these three probands carrying BAP1 loss-of-function variants also had melanomas with histopathological features suggestive of a germline BAP1 mutation. The remaining cases with germline mutations, which were predominantly missense mutations, were associated with less typical pedigrees and tumours lacking a characteristic BAP1-associated histopathological appearances, but may still represent less penetrant variants. Germline BAP1 alleles defined as loss-of-function or predicted to be deleterious/damaging are rare in melanoma.

  11. Latent Class Analysis of Functional Somatic Symptoms in a Population-Based Sample of Twins

    PubMed Central

    Kato, Kenji; Sullivan, Patrick F.; Pedersen, Nancy L.

    2010-01-01

    Objective This study aimed to investigate empirically how and in what way individuals with symptoms of functional somatic syndromes should be classified. We also aimed to look into genetic and environmental influences on the classification. Method A total of 28531 twins aged 41–64 underwent screening interviews via a computer-assisted data collection system from 1998 to 2002. Nine functional somatic symptoms (abnormal tiredness, general muscular pain, recurrent abdominal discomfort, back pain, gastroesophageal reflux, recurrent headache, recurrent urinary problem, dizziness, breathlessness at rest) were assessed using structured questions in a blinded manner. Latent class analysis was applied to the data. Structural equation modeling was further performed in order to estimate the relative importance of genetic and environmental influences on class probability. Results Latent class analysis resulted in a 5-class solution. Individuals in the first class did not show any health problems. Those assigned to the second, third, and fourth classes tended to have abnormal tiredness, gastrointestinal problems, and pain-related symptoms, respectively. Individuals in the fifth class had multiple symptoms to a greater extent than the other classes. All the five classes showed modest genetic influences (7 – 29% of the total variation) with gender differences except Class 3; however, the majority of influences on the class membership derived from unique environmental effects. Conclusion The findings suggested the necessity of re-defining the existing classification criteria for functional somatic syndromes in terms of single (uncomplicated) or multiple (complicated) syndromes. Environmental influences are important for the aetiology of functional somatic syndromes. PMID:20403503

  12. Cervical cancer incidence trends in Canada: a 30-year population-based analysis.

    PubMed

    Mosavi-Jarrahi, Alireza; Kliewer, Erich V

    2013-07-01

    Objectifs : Utiliser les données les plus récentes pour offrir une mise à jour quant à la tendance pour ce qui est de l’incidence du cancer du col utérin au Canada au cours de la période de 30 ans s’étalant de 1978 à 2009. Méthodes : Les cas enregistrés de cancer du col utérin et les taux correspondants en personnes-années pour la population canadienne ont été récupérés auprès d’un dépôt de données en ligne du Centre International de Recherche sur le Cancer, ainsi qu’auprès de Statistique Canada, pour la période 1978 - 2009. Les taux annuels standardisés en fonction de l’âge ont été estimés pour l’ensemble des données et, de façon distincte, pour chacune des provinces. Les âges des cas ont été agrégés en trois groupes : 25 - 39 ans, 40 - 59 ans et 60 - 75 ans. Une analyse de régression Joinpoint a été utilisée pour décrire la tendance d’un groupe d’âge et d’une province à l’autre. Résultats : Entre 1978 et 2006, au Canada, le taux de cancer du col utérin corrigé en fonction de l’âge est passé de 20,05 à 12,66 par 100 000 femmes; après 2006, le taux a connu une hausse. Des baisses plus importantes ont été constatées au sein des groupes plus âgés. La modification annuelle moyenne en pourcentage (MAMP) était de −1,1 % (IC à 95 %, −1,1 % - 0,09 %), de −1,8 % (IC à 95 %, −2,5 % - −1,2 %) et de −2,6 % (IC à 95 %, −3,9 % - −1,4 %) pour les groupes d’âge de 25 à 39 ans, de 40 à 60 ans et de 60 à 75 ans, respectivement. La MAMP variait d’une province à l’autre, allant de −0,22 % (IC à 95 %, −1,4 % - 0,9 %) en Saskatchewan à −3,02 % (IC à 95 %, −4,5 % - −1,5 %) à Terre-Neuve-et-Labrador. En Ontario, l’incidence du cancer du col utérin a connu une hausse annuelle entre 2006 et 2009. En Colombie-Britannique, la tendance comptait une modification de pente significative en 1984. Conclusion : L’incidence du cancer du

  13. RECURRENCE OF HIGH-RISK BLADDER CANCER: A POPULATION-BASED ANALYSIS

    PubMed Central

    Chamie, Karim; Litwin, Mark S.; Bassett, Jeffrey C.; Daskivich, Timothy J.; Lai, Julie; Hanley, Jan M.; Konety, Badrinath R.; Saigal, Christopher S.

    2013-01-01

    Background Patients with bladder cancer are apt to develop multiple recurrences that require intervention. We examined the recurrence, progression and bladder cancer-related mortality rates in a cohort of individuals with high-grade non-muscle-invasive bladder cancer. Methods Using linked SEER-Medicare data, we identified subjects with a diagnosis of high-grade, non-muscle-invasive disease in 1992–2002 and were followed until 2007. We then used multivariate competing-risks regression analyses to examine recurrence, progression, and bladder cancer-related mortality rates. Results Of 7,410 subjects, 2,897 (39.1%) experienced a recurrence without progression, 2,449 (33.0%) experienced disease progression, of whom 981 succumbed to bladder cancer. Using competing-risks regression analysis, we found the 10-year recurrence, progression, and bladder cancer-related mortality rates to be 74.3%, 33.3%, and 12.3%, respectively. Stage T1 was the only variable associated with a higher rate of recurrence. Women, black race, undifferentiated grade, stage Tis and T1 were associated with a higher risk of progression and mortality. Advanced age (≥70) was associated with a higher risk of bladder cancer-related mortality. Conclusions Nearly three-fourths of patients diagnosed with high-risk bladder cancer will recur, progress, or die within ten years of their diagnosis. Even though most patients do not die of bladder cancer, the vast majority endures the morbidity of recurrence and progression of their cancer. Increasing efforts should be made to offer patients intravesical therapy with the goal of minimizing the incidence of recurrences. Furthermore, the high recurrence rate seen during the first two years of diagnosis warrants an intense surveillance schedule. PMID:23737352

  14. Institution-based cancer incidence in a local population in Pakistan: nine year data analysis.

    PubMed

    Hanif, Muhammad; Zaidi, Parveen; Kamal, Shahid; Hameed, Abid

    2009-01-01

    At present no national level of cancer registry program exists in Pakistan and the data available from different sources, necessary for incidence, prevalence, morbidity/mortality, and etiological assessment of cancer and cancer control programs, are from hospital or institutional databases. Karachi Institute of Radiotherapy and Nuclear Medicine (KIRAN) is a comprehensive healthcare facility for diagnosis, treatment and research of all cancers. This is a retrospective analysis of the cancer patients of both genders of all age groups to determine frequencies of different cancers presented to this Institute from 1st January 2000 to 31 December 2008. A total of 16,351 cancer patients were registered at KIRAN during the nine year period. Male cancers accounted for 48.1% and female cancers 51.8%. Some 558 (3.4%) were in children (0-15 years). The mean ages at presentation for males and females were 50-/+9.6 and 47-/+7.4 years respectively. In males the five most frequent malignancies were head and neck (32.6%), lung (15%), gastrointestinal tract (GIT) (6.9%), lymphoma (6.1%), and bone and soft tissue (4.9%). In females breast cancer was the most common cancer accounting for 38.2% followed by head and neck (15.1%), cervical (5.5%), ovarian (4.9%) and GIT cancer (4.9%) respectively. Cancer prevalence in different age groups with respect to gender and the epidemiologies of most common cancers with reference to our cultural and environmental factors and dietary habits are also discussed. Overall cancer incidence in nine years in this tertiary care cancer institution showed that head and neck cancers in males and breast cancers in females are most common, at rates almost highest in Asia. Mean age and male to female ratio in all other cancers are essentially comparable to other developing countries.

  15. Genetic diversity and population genetic structure analysis of Echinococcus granulosus sensu stricto complex based on mitochondrial DNA signature.

    PubMed

    Sharma, Monika; Fomda, Bashir Ahmad; Mazta, Saligram; Sehgal, Rakesh; Singh, Balbir Bagicha; Malla, Nancy

    2013-01-01

    The genetic diversity and population genetics of the Echinococcus granulosus sensu stricto complex were investigated based on sequencing of mitochondrial DNA (mtDNA). Total 81 isolates of hydatid cyst collected from ungulate animals from different geographical areas of North India were identified by sequencing of cytochrome c oxidase subunit1 (coxi) gene. Three genotypes belonging to E. granulosus sensu stricto complex were identified (G1, G2 and G3 genotypes). Further the nucleotide sequences (retrieved from GenBank) for the coxi gene from seven populations of E. granulosus sensu stricto complex covering 6 continents, were compared with sequences of isolates analysed in this study. Molecular diversity indices represent overall high mitochondrial DNA diversity for these populations, but low nucleotide diversity between haplotypes. The neutrality tests were used to analyze signatures of historical demographic events. The Tajima's D test and Fu's FS test showed negative value, indicating deviations from neutrality and both suggested recent population expansion for the populations. Pairwise fixation index was significant for pairwise comparison of different populations (except between South America and East Asia, Middle East and Europe, South America and Europe, Africa and Australia), indicating genetic differentiation among populations. Based on the findings of the present study and those from earlier studies, we hypothesize that demographic expansion occurred in E. granulosus after the introduction of founder haplotype particular by anthropogenic movements.

  16. 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.

  17. 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

  18. Education as a Predictor of Chronic Periodontitis: A Systematic Review with Meta-Analysis Population-Based Studies

    PubMed Central

    Boillot, Adrien; El Halabi, Bechara; Batty, George David; Rangé, Hélène; Czernichow, Sébastien; Bouchard, Philippe

    2011-01-01

    Background The impact of socioeconomic inequalities on health is well-documented. Despite the links of periodontal disease with cardiovascular diseases, adverse pregnancy outcomes and diabetes, no meta-analysis of socioeconomic variations in periodontal disease exists. This meta-analytic review was conducted to determine the extent to which education attainment influences risk of periodontitis in adults aged 35+ years in the general population. Methods The authors searched studies published until November 2010 using EMBASE and MEDLINE databases. References listed were then scrutinised, our own files were checked, and, finally, we contacted experts in the field. The authors included only general population-based studies conducted in adults aged 35 years and more. All articles were blind reviewed by two investigators. In the case of disagreement, a third investigator arbitrated. Using PRISMA statement, two reviewers independently extracted papers of interest. Results Relative to the higher education group, people with low education attainment experience a greater risk of periodontitis (OR: 1.86 [1.66–2.10]; p<0.00001). The association was partially attenuated after adjustment for covariates (OR: 1.55 [1.30–1.86]; p<0.00001). Sensitivity analyses showed that methods used to assess periodontitis, definition of cases, study country and categorization of education are largely responsible for the heterogeneity between studies. No significant bias of publication was shown using both the Egger (p = 0.16) and rank correlation tests (p = 0.35). Conclusions In the studies reviewed, low educational attainment was associated with an increased risk of periodontitis. Although this evidence should be cautiously interpreted due to methodological problems in selected studies, efforts to eliminate educational inequalities in periodontitis should focus on early life interventions. PMID:21814546

  19. Age-at-death estimation based on radiological and image analysis methods in clavicle in a current Spanish population.

    PubMed

    Benito, María; Sánchez, José Antonio; Codinha, Sónia

    2014-05-01

    Age-at-death estimation in adult individuals is one of the most challenging issues in forensic anthropology, namely, due to the large age intervals provided by the current methods, which demand the development of more reliable investigations. The clavicle has been studied as an age-at-death indicator in many researches for its accessibility, low biomechanical implication in locomotion and accuracy to predict age at death when other age indicators are not available. The present study was developed on a sample of 332 clavicles from adult individuals of known sex and age from the current Spanish population. They were x-rayed and digitalized, in a standardized way, using a Sedecal X-ray generator, model SHF 415. Three indices were calculated at the mid-diaphysis point (anterior index, posterior index, and total index) which relate the cortical thickness and the total clavicle thickness to age at death. The average grey level was also calculated in a 0.5-cm(2) area of the sternal and acromial ends (sternal grey average, acromial grey average), using Image J software. The data were subjected to a statistical analysis, using SPSS, version 15.0. The results show that average grey level has a weaker correlation with age than the variables which are based on the cortical thickness. On the other hand, the regression equations, which were calculated combining all the variables, provided smaller age-at-death intervals, demonstrating the usefulness of this method for adult age-at-death estimation in forensic anthropology.

  20. A new strategy to prevent over-fitting in partial least squares models based on model population analysis.

    PubMed

    Deng, Bai-Chuan; Yun, Yong-Huan; Liang, Yi-Zeng; Cao, Dong-Sheng; Xu, Qing-Song; Yi, Lun-Zhao; Huang, Xin

    2015-06-23

    Partial least squares (PLS) is one of the most widely used methods for chemical modeling. However, like many other parameter tunable methods, it has strong tendency of over-fitting. Thus, a crucial step in PLS model building is to select the optimal number of latent variables (nLVs). Cross-validation (CV) is the most popular method for PLS model selection because it selects a model from the perspective of prediction ability. However, a clear minimum of prediction errors may not be obtained in CV which makes the model selection difficult. To solve the problem, we proposed a new strategy for PLS model selection which combines the cross-validated coefficient of determination (Qcv(2)) and model stability (S). S is defined as the stability of PLS regression vectors which is obtained using model population analysis (MPA). The results show that, when a clear maximum of Qcv(2) is not obtained, S can provide additional information of over-fitting and it helps in finding the optimal nLVs. Compared with other regression vector based indictors such as the Euclidean 2-norm (B2), the Durbin Watson statistic (DW) and the jaggedness (J), S is more sensitive to over-fitting. The model selected by our method has both good prediction ability and stability.

  1. Resuscitative endovascular balloon occlusion of the aorta (REBOA): a population based gap analysis of trauma patients in England and Wales

    PubMed Central

    Barnard, Edward Benjamin Graham; Morrison, Jonathan James; Madureira, Ricardo Mondoni; Lendrum, Robbie; Fragoso-Iñiguez, Marisol; Edwards, Antoinette; Lecky, Fiona; Bouamra, Omar; Lawrence, Thomas; Jansen, Jan Olaf

    2015-01-01

    Introduction Non-compressible torso haemorrhage (NCTH) carries a high mortality in trauma as many patients exsanguinate prior to definitive haemorrhage control. Resuscitative endovascular balloon occlusion of the aorta (REBOA) is an adjunct that has the potential to bridge patients to definitive haemostasis. However, the proportion of trauma patients in whom REBOA may be utilised is unknown. Methods We conducted a population based analysis of 2012–2013 Trauma Audit and Research Network (TARN) data. We identified the number of patients in whom REBOA may have been utilised, defined by an Abbreviated Injury Scale score ≥3 to abdominal solid organs, abdominal or pelvic vasculature, pelvic fracture with ring disruption or proximal traumatic lower limb amputation, together with a systolic blood pressure <90 mm Hg. Patients with non-compressible haemorrhage in the mediastinum, axilla, face or neck were excluded. Results During 2012–2013, 72 677 adult trauma patients admitted to hospitals in England and Wales were identified. 397 patients had an indication(s) and no contraindications for REBOA with evidence of haemorrhagic shock: 69% men, median age 43 years and median Injury Severity Score 32. Overall mortality was 32%. Major trauma centres (MTCs) received the highest concentration of potential REBOA patients, and would be anticipated to receive a patient in whom REBOA may be utilised every 95 days, increasing to every 46 days in the 10 MTCs with the highest attendance of this injury type. Conclusions This TARN database analysis has identified a small group of severely injured, resource intensive patients with a highly lethal injury that is theoretically amenable to REBOA. The highest density of these patients is seen at MTCs, and as such a planned evaluation of REBOA should be further considered in these hospitals. PMID:26598631

  2. Analysis of population structure and genetic history of cattle breeds based on high-density SNP data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Advances in single nucleotide polymorphism (SNP) genotyping microarrays have facilitated a new understanding of population structure and evolutionary history for several species. Most existing studies in livestock were based on low density SNP arrays. The first wave of low density SNP studies on cat...

  3. Genetic diversity of cultured and wild populations of the freshwater prawn Macrobrachium rosenbergii based on microsatellite analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Freshwater prawn Macrobrachium rosenbergii culture in the Western Hemisphere is primarily, if not entirely, based on thirty-six individual prawn introduced to Hawaii from Malaysia in 1965 and 1966. Little information is available regarding the genetic background or current population status of cult...

  4. Genetic origin of Behçet's disease population in Denizli, Turkey; population genetics data analysis; historical demography and geographical perspectives based on β-globin gene cluster haplotype variation.

    PubMed

    Ozturk, O; Arikan, S; Bahadir, A; Atalay, A; Atalay, E O

    2017-01-01

    In our study, we aimed to investigate the possible genetic drift, relationships, expansion and historical origin based on haplotype frequencies of the β-globin gene cluster of normal and Behçet's disease (BD) population in Denizli, Turkey. We examined blood DNA samples obtained from our DNA bank. The association of population genetic parameters such as haplotypes, diversity, differentiation, Hardy-Weinberg equilibrium and demographic analysis for two populations was performed by Arlequin ver. 3.5. Our results show that both populations have high similarity in genetic parameters in terms of development and expansion based on haplotype diversity through the history. We found that historical levels of gene flow were significantly higher between the two populations. According to historical population, growth parameter of τ values for normal and BD populations dated approximately 42 000 to 38 000 ybp, respectively. In conclusion, historically, two populations show similar genetic parameters and unimodal growth distribution. Our results are consistent with the view that the BD may have occurred in area, independent from Silk Road.

  5. Analysis of population genetic structure from Bucaramanga (Colombia) based on gene polymorphisms associated with the regulation of blood pressure

    PubMed Central

    Rondón, Fernando; Vargas, Clara Inés; Oróstegui, Myriam; Bautista, Leonelo; Serrano, Norma Cecilia; Páez, María c; Castillo, Adriana

    2012-01-01

    Introduction: In spite of nearly 40% of variability in blood pressure being explained by genetic factors, the identification of genes associated with essential high blood pressure is difficult to determine in populations where individuals have different genetic backgrounds. In these circumstances it is necessary to determinate whether the population is sub-structured because this can bias studies associated with this disease. Objective: To determine the genetic structure of the population in Bucaramanga from genetic polymorphisms associated with the regulation of blood pressure: 448G>T, 679C>T y 1711C>T from the gene kinase 4 of the dopaminergic receptor linked to the protein G and Glu298Asp, -786T>C and the VNTR of the intron 4 of the gene of endothelial nitric oxide. Methods: A sample of 552 unrelated individuals was studied through analysis of restriction fragment length polymorphism. The allelic, haplotypic and genotypic frequencies were calculated, the Hardy-Weinberg equilibrium was determined and a molecular analysis of variance was performed to determine the genetic structure. Results: Thirty-eight (38) Haplotypes were identified with GCCTG4b being the most frequent (21.2%). The most diverse polymorphism was 448G>T with a frequency of 49.9% for heterozygous. The six polymorphisms were found in genetic equilibrium and a genetic structure of populations was not evidenced (FST= 0.0038). Conclusion: The population studied does not present a genetic sub-structure and the polymorphisms analyzed were found in genetic equilibrium. This indicates that the population mixes randomly and there are no sub-groups capable of affecting the results of the association studies. PMID:24893057

  6. Population structure of the predatory mite Neoseiulus womersleyi in a tea field based on an analysis of microsatellite DNA markers

    PubMed Central

    Todokoro, Yasuhiro; Higaki, Tomomi

    2010-01-01

    The predatory mite Neoseiulus womersleyi (Schicha) (Acari: Phytoseiidae) is an important natural enemy of the Kanzawa spider mite, Tetranychus kanzawaki Kishida (Acari: Tetranychidae), in tea fields. Attraction and preservation of natural enemies by habitat management to reduce the need for acaricide sprays is thought to enhance the activity of N. womersleyi. To better conserve N. womersleyi in the field, however, it is essential to elucidate the population genetic structure of this species. To this end, we developed ten microsatellite DNA markers for N. womersleyi. We then evaluated population structure of N. womersleyi collected from a tea field, where Mexican sunflower, Tithonia rotundifolia (Mill.), was planted to preserve N. womersleyi. Seventy-seven adult females were collected from four sites within 200 m. The fixation indexes FST among subpopulations were not significantly different. The kinship coefficients between individuals did not differ significantly within a site as a function of the sampling dates, but the coefficients gradually decreased with increasing distance. Bayesian clustering analysis revealed that the population consisted of three genetic clusters, and that subpopulations within 100 m, including those collected on T. rotundifolia, were genetically similar to each other. Given the previously observed population dynamics of N. womersleyi, it appears that the area inhabited by a given cluster of the mite did not exceed 100 m. The estimation of population structure using microsatellite markers will provide valuable information in conservation biological control. PMID:20625919

  7. Lipoprotein lipase gene variants and risk of coronary disease: a quantitative analysis of population-based studies.

    PubMed

    Hokanson, J E

    1997-01-01

    The purpose of this study is to quantify the magnitude of the association between common variants in the lipoprotein lipase gene and coronary disease, based on published population-based studies. Fourteen studies, representing 15,708 subjects, report allelic distribution for lipoprotein lipase gene variants among coronary disease patients and control subjects. Patient outcomes included clinical coronary disease events and documented coronary disease based on angiography. Allele frequencies are estimated for disease and non-disease groups within each study. A 2 x 2 contingency table is used to compute individual study odds ratios and 95% confidence intervals, relating the presence of the rare allele to disease status. Mantel-Haenszel-stratified analysis of each allelic variant results in a summary odds ratio and 95% confidence interval for the association between each rare allele in the lipoprotein lipase gene and coronary disease. The lipoprotein lipase D9N allele has a summary odds ratio of 1.59 (95% confidence interval 1.03-2.55), indicating a 59% increase in risk of coronary disease for carriers with this allelic variant. The lipoprotein lipase N291S allele showed no association with coronary disease (summary odds ratio 0.93, 95% confidence interval 0.73-1.19). The summary odds ratio for lipoprotein lipase S447Ter allele is 0.81 (95% confidence interval 0.65-1.0), indicating a marginal negative association between this variant and coronary disease. The common lipoprotein lipase Pvu II polymorphism shows no relation to coronary disease (summary odds ratio 0.90, 95% confidence interval 0.80-1.01). The rare allele of the lipoprotein lipase HindIII polymorphism is negatively associated with coronary disease (summary odds ratio 0.84, 95% confidence interval 0.73-0.96). The lipoprotein lipase D9N allele is associated with high levels of triglyceride and low levels of high-density lipoprotein. Similar atherogenic lipid levels are observed in subjects with structural

  8. Identifying associated factors with social capital using path analysis: A population-based survey in Tehran, Iran (Urban HEART-2).

    PubMed

    Asadi-Lari, Mohsen; Hassanzadeh, Jafar; Torabinia, Mansour; Vaez-Mahdavi, Mohammad Reza; Montazeri, Ali; Ghaem, Haleh; Menati, Rostam; Niazi, Mohsen; Kassani, Aziz

    2016-01-01

    Background: Social capital has been defined as norms, networks, and social links that facilitate collective actions. Social capital is related to a number of main social and public health variables. Therefore, the present study aimed to determine the factors associated with social capital among the residents of Tehran, Iran. Methods: In this large cross-sectional population-based study, 31531 residents aged 20 years and above were selected through multi-stage sampling method from 22 districts of Tehran in 2011. The social capital questionnaire, 28-item General Health Questionnaire (GHQ-28), and Short-Form Health Survey (SF-12) were used. Hypothetical causal models were designed to identify the pathways through which different variables influenced the components of social capital. Then, path analysis was conducted for identifying the determinants of social capital. Results: The most influential variables in 'individual trust' were job status (β=0.37, p=0.02), marital status (β=0.32, p=0.01), Physical Component Summary (PCS) (β=0.37, p=0.02), and age (β=0.34, p=0.03). On the other hand, education level (β=0.34, p=0.01), age (β=0.33, p=0.02), marital status (β=0.33, p=0.01), and job status (β=0.32, p=0.01) were effective in 'cohesion and social support'. Additionally, age (β=0.18, p=0.02), PCS (β=0.36, p=0.01), house ownership (β=0.23, p=0.03), and mental health (β=0.26, p=0.01) were influential in 'social trust/collective relations'. Conclusion: Social capital can be improved in communities by planning to improve education and occupation status, paying more attention to strengthening family bonds, and provision of local facilities and neighborhood bonds to reduce migration within the city.

  9. Identifying associated factors with social capital using path analysis: A population-based survey in Tehran, Iran (Urban HEART-2)

    PubMed Central

    Asadi-Lari, Mohsen; Hassanzadeh, Jafar; Torabinia, Mansour; Vaez-Mahdavi, Mohammad Reza; Montazeri, Ali; Ghaem, Haleh; Menati, Rostam; Niazi, Mohsen; Kassani, Aziz

    2016-01-01

    Background: Social capital has been defined as norms, networks, and social links that facilitate collective actions. Social capital is related to a number of main social and public health variables. Therefore, the present study aimed to determine the factors associated with social capital among the residents of Tehran, Iran. Methods: In this large cross-sectional population-based study, 31531 residents aged 20 years and above were selected through multi-stage sampling method from 22 districts of Tehran in 2011. The social capital questionnaire, 28-item General Health Questionnaire (GHQ-28), and Short-Form Health Survey (SF-12) were used. Hypothetical causal models were designed to identify the pathways through which different variables influenced the components of social capital. Then, path analysis was conducted for identifying the determinants of social capital. Results: The most influential variables in ‘individual trust’ were job status (β=0.37, p=0.02), marital status (β=0.32, p=0.01), Physical Component Summary (PCS) (β=0.37, p=0.02), and age (β=0.34, p=0.03). On the other hand, education level (β=0.34, p=0.01), age (β=0.33, p=0.02), marital status (β=0.33, p=0.01), and job status (β=0.32, p=0.01) were effective in ‘cohesion and social support’. Additionally, age (β=0.18, p=0.02), PCS (β=0.36, p=0.01), house ownership (β=0.23, p=0.03), and mental health (β=0.26, p=0.01) were influential in ‘social trust/collective relations’. Conclusion: Social capital can be improved in communities by planning to improve education and occupation status, paying more attention to strengthening family bonds, and provision of local facilities and neighborhood bonds to reduce migration within the city. PMID:28210579

  10. Evaluation of personal and built environment attributes to physical activity: a multilevel analysis on multiple population-based data sources.

    PubMed

    Yang, Wei; Spears, Karen; Zhang, Fan; Lee, Wai; Himler, Heidi L

    2012-01-01

    Background. Studies have documented that built environment factors potentially promote or impede leisure time physical activity (LTPA). This study explored the relationship between multiple built environment factors and individual characteristics on LTPA. Methods. Multiple data sources were utilized including individual level data for health behaviors and health status from the Nevada Behavioral Risk Factor Surveillance System (BRFSS) and community level data from different data sources including indicators for recreation facilities, safety, air quality, commute time, urbanization, population density, and land mix level. Mixed model logistic regression and geographic information system (GIS) spatial analysis were conducted. Results. Among 6,311 respondents, 24.4% reported no LTPA engagement during the past 30 days. No engagement in LTPA was significantly associated with (1) individual factors: older age, less education, lower income, being obesity, and low life satisfaction and (2) community factors: more commute time, higher crime rate, urban residence, higher population density, but not for density and distance to recreation facilities, air quality, and land mix. Conclusions. Multiple data systems including complex population survey and spatial analysis are valuable tools on health and built environment studies.

  11. Characterization and Scaling of Black Carbon Aerosol Concentration with City Population Based on In-Situ Measurements and Analysis

    NASA Astrophysics Data System (ADS)

    Paredes-Miranda, G.; Arnott, W. P.; Moosmuller, H.

    2010-12-01

    The global trend toward urbanization and the resulting increase in city population has directed attention toward air pollution in megacities. A closely related question of importance for urban planning and attainment of air quality standards is how pollutant concentrations scale with city population. In this study, we use measurements of light absorption and light scattering coefficients as proxies for primary (i.e., black carbon; BC) and total (i.e., particulate matter; PM) pollutant concentration, to start addressing the following questions: What patterns and generalizations are emerging from our expanding data sets on urban air pollution? How does the per-capita air pollution vary with economic, geographic, and meteorological conditions of an urban area? Does air pollution provide an upper limit on city size? Diurnal analysis of black carbon concentration measurements in suburban Mexico City, Mexico, Las Vegas, NV, USA, and Reno, NV, USA for similar seasons suggests that commonly emitted primary air pollutant concentrations scale approximately as the square root of the urban population N, consistent with a simple 2-d box model. The measured absorption coefficient Babs is approximately proportional to the BC concentration (primary pollution) and thus scales with the square root of population (N). Since secondary pollutants form through photochemical reactions involving primary pollutants, they scale also with square root of N. Therefore the scattering coefficient Bsca, a proxy for PM concentration is also expected to scale with square root of N. Here we present light absorption and scattering measurements and data on meteorological conditions and compare the population scaling of these pollutant measurements with predictions from the simple 2-d box model. We find that these basin cities are connected by the square root of N dependence. Data from other cities will be discussed as time permits.

  12. Combining family- and population-based imputation data for association analysis of rare and common variants in large pedigrees.

    PubMed

    Saad, Mohamad; Wijsman, Ellen M

    2014-11-01

    In the last two decades, complex traits have become the main focus of genetic studies. The hypothesis that both rare and common variants are associated with complex traits is increasingly being discussed. Family-based association studies using relatively large pedigrees are suitable for both rare and common variant identification. Because of the high cost of sequencing technologies, imputation methods are important for increasing the amount of information at low cost. A recent family-based imputation method, Genotype Imputation Given Inheritance (GIGI), is able to handle large pedigrees and accurately impute rare variants, but does less well for common variants where population-based methods perform better. Here, we propose a flexible approach to combine imputation data from both family- and population-based methods. We also extend the Sequence Kernel Association Test for Rare and Common variants (SKAT-RC), originally proposed for data from unrelated subjects, to family data in order to make use of such imputed data. We call this extension "famSKAT-RC." We compare the performance of famSKAT-RC and several other existing burden and kernel association tests. In simulated pedigree sequence data, our results show an increase of imputation accuracy from use of our combining approach. Also, they show an increase of power of the association tests with this approach over the use of either family- or population-based imputation methods alone, in the context of rare and common variants. Moreover, our results show better performance of famSKAT-RC compared to the other considered tests, in most scenarios investigated here.

  13. On the origin of Iberomaurusians: new data based on ancient mitochondrial DNA and phylogenetic analysis of Afalou and Taforalt populations.

    PubMed

    Kefi, Rym; Hechmi, Meriem; Naouali, Chokri; Jmel, Haifa; Hsouna, Sana; Bouzaid, Eric; Abdelhak, Sonia; Beraud-Colomb, Eliane; Stevanovitch, Alain

    2016-12-30

    The Western North African population was characterized by the presence of Iberomaurusian civilization at the Epiplaeolithic period (around 20,000 years before present (YBP) to 10,000 YBP). The origin of this population is still not clear: they may come from Europe, Near East, sub-Saharan Africa or they could have evolved in situ in North Africa. With the aim to contribute to a better knowledge of the settlement of North Africa we analysed the mitochondrial DNA extracted from Iberomaurusian skeletons exhumed from the archaeological site of Afalou (AFA) (15,000-11,000 YBP) in Algeria and from the archaeological site of Taforalt (TAF) (23,000-10,800 YBP) in Morocco. Then, we carried out a phylogenetic analysis relating these Iberomaurusians to 61 current Mediterranean populations. The genetic structure of TAF and AFA specimens contains only North African and Eurasian maternal lineages. These finding demonstrate the presence of these haplotypes in North Africa from at least 20,000 YBP. The very low contribution of a Sub-Saharan African haplotype in the Iberomaurusian samples is confirmed. We also highlighted the existence of genetic flows between Southern and Northern coast of the Mediterranean.

  14. Comparison of base composition analysis and Sanger sequencing of mitochondrial DNA for four U.S. population groups.

    PubMed

    Kiesler, Kevin M; Coble, Michael D; Hall, Thomas A; Vallone, Peter M

    2014-01-01

    A set of 711 samples from four U.S. population groups was analyzed using a novel mass spectrometry based method for mitochondrial DNA (mtDNA) base composition profiling. Comparison of the mass spectrometry results with Sanger sequencing derived data yielded a concordance rate of 99.97%. Length heteroplasmy was identified in 46% of samples and point heteroplasmy was observed in 6.6% of samples in the combined mass spectral and Sanger data set. Using discrimination capacity as a metric, Sanger sequencing of the full control region had the highest discriminatory power, followed by the mass spectrometry base composition method, which was more discriminating than Sanger sequencing of just the hypervariable regions. This trend is in agreement with the number of nucleotides covered by each of the three assays.

  15. Association between chronic osteomyelitis and deep-vein thrombosis. Analysis of a nationwide population-based registry.

    PubMed

    Lin, T-Y; Chen, Y-G; Huang, W-Y; Lin, C-L; Peng, C-L; Sung, F-C; Kao, C-H

    2014-09-02

    Studies on the association between chronic osteomyelitis and deep vein thrombosis (DVT) and pulmonary thromboembolism (PE) are scarce. The aim of this study was to analyse a nationwide population-based database for association between DVT or PE after a diagnosis of chronic osteomyelitis. This nationwide population-based cohort study was based on data obtained from the Taiwan National Health Insurance Database from 1998 to 2008, with a follow-up period extending to the end of 2010. We identified patients with chronic osteomyelitis using International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes. The patients with chronic osteomyelitis and comparison controls were selected by 1:1 matching on a propensity score. The propensity score was calculated by a logistic regression to estimate the probability of the treatment assignment given the baseline variables including age, sex, and Charlson comorbidity index score. We analysed the risks of DVT and PE by using Cox proportional hazards regression models, including sex, age, and comorbidities. In total, 24,335 chronic osteomyelitis patients and 24,335 controls were enrolled in the study. The risk of developing DVT was 2.49-fold in patients with chronic osteomyelitis compared with the comparison cohort, after adjusting for age, sex, and comorbidities. The multiplicative increased risks of DVT were also significant in patients with chronic osteomyelitis with any comorbidity. In conclusion, physicians should consider chronic osteomyelitis in their evaluation of risk factors for DVT.

  16. Cost-effectiveness analysis of population-based screening of hepatocellular carcinoma: Comparing ultrasonography with two-stage screening

    PubMed Central

    Kuo, Ming-Jeng; Chen, Hsiu-Hsi; Chen, Chi-Ling; Fann, Jean Ching-Yuan; Chen, Sam Li-Sheng; Chiu, Sherry Yueh-Hsia; Lin, Yu-Min; Liao, Chao-Sheng; Chang, Hung-Chuen; Lin, Yueh-Shih; Yen, Amy Ming-Fang

    2016-01-01

    AIM: To assess the cost-effectiveness of two population-based hepatocellular carcinoma (HCC) screening programs, two-stage biomarker-ultrasound method and mass screening using abdominal ultrasonography (AUS). METHODS: In this study, we applied a Markov decision model with a societal perspective and a lifetime horizon for the general population-based cohorts in an area with high HCC incidence, such as Taiwan. The accuracy of biomarkers and ultrasonography was estimated from published meta-analyses. The costs of surveillance, diagnosis, and treatment were based on a combination of published literature, Medicare payments, and medical expenditure at the National Taiwan University Hospital. The main outcome measure was cost per life-year gained with a 3% annual discount rate. RESULTS: The results show that the mass screening using AUS was associated with an incremental cost-effectiveness ratio of USD39825 per life-year gained, whereas two-stage screening was associated with an incremental cost-effectiveness ratio of USD49733 per life-year gained, as compared with no screening. Screening programs with an initial screening age of 50 years old and biennial screening interval were the most cost-effective. These findings were sensitive to the costs of screening tools and the specificity of biomarker screening. CONCLUSION: Mass screening using AUS is more cost effective than two-stage biomarker-ultrasound screening. The most optimal strategy is an initial screening age at 50 years old with a 2-year inter-screening interval. PMID:27022228

  17. Population structure of Cicada barbara Stål (Hemiptera, Cicadoidea) from the Iberian Peninsula and Morocco based on mitochondrial DNA analysis.

    PubMed

    Pinto-Juma, G A; Quartau, J A; Bruford, M W

    2008-02-01

    We assess the genetic history and population structure of Cicada barbara in Morocco and the Iberian Peninsula, based on analysis of the mitochondrial cytochrome b gene. The divergence between Morocco and the Iberian Peninsula populations was strongly corroborated by the molecular data, suggesting genetically isolated populations with a low level of gene flow. The Ceuta population from Spanish North Africa was more similar to the Iberian populations than the surrounding Moroccan populations, suggesting that the Strait of Gibraltar has not been acting as a strict barrier to dispersal while the Rif Mountains have. The Iberian Peninsula specimens showed a signature of demographic expansion before that which occurred in Morocco, but some of the assumptions related to the demographic parameters should be considered with caution due to the small genetic variation found. The high haplotype diversity found in Morocco implies higher demographic stability than in the Iberian Peninsula populations. These results do not, however, suggest a Moroccan origin for Iberian cicadas; but the most northwest region in Africa, such as Ceuta, might have acted as a southern refuge for Iberian cicadas during the most severe climatic conditions, from where they could expand north when climate improved. The separation of two subspecies within C. barbara (C. barbara lusitanica and C. barbara barbara) finds support with these results.

  18. Content-based image retrieval for brain MRI: an image-searching engine and population-based analysis to utilize past clinical data for future diagnosis.

    PubMed

    Faria, Andreia V; Oishi, Kenichi; Yoshida, Shoko; Hillis, Argye; Miller, Michael I; Mori, Susumu

    2015-01-01

    Radiological diagnosis is based on subjective judgment by radiologists. The reasoning behind this process is difficult to document and share, which is a major obstacle in adopting evidence-based medicine in radiology. We report our attempt to use a comprehensive brain parcellation tool to systematically capture image features and use them to record, search, and evaluate anatomical phenotypes. Anatomical images (T1-weighted MRI) were converted to a standardized index by using a high-dimensional image transformation method followed by atlas-based parcellation of the entire brain. We investigated how the indexed anatomical data captured the anatomical features of healthy controls and a population with Primary Progressive Aphasia (PPA). PPA was chosen because patients have apparent atrophy at different degrees and locations, thus the automated quantitative results can be compared with trained clinicians' qualitative evaluations. We explored and tested the power of individual classifications and of performing a search for images with similar anatomical features in a database using partial least squares-discriminant analysis (PLS-DA) and principal component analysis (PCA). The agreement between the automated z-score and the averaged visual scores for atrophy (r = 0.8) was virtually the same as the inter-evaluator agreement. The PCA plot distribution correlated with the anatomical phenotypes and the PLS-DA resulted in a model with an accuracy of 88% for distinguishing PPA variants. The quantitative indices captured the main anatomical features. The indexing of image data has a potential to be an effective, comprehensive, and easily translatable tool for clinical practice, providing new opportunities to mine clinical databases for medical decision support.

  19. Population pharmacokinetic analysis of bisoprolol.

    PubMed

    Grevel, J; Thomas, P; Whiting, B

    1989-07-01

    The technique of population pharmacokinetic analysis was employed to study the variability in the dose concentration relationship of bisoprolol during its clinical development. The influence of demographic factors on the variability of clearance was investigated in 3 different populations: group I, patients (including an elderly group) with essential hypertension receiving multiple oral doses of bisoprolol 10 or 20mg for 3 months; group II, patients with different degrees of renal impairment and healthy controls; and group III, patients with different types of hepatic impairment and healthy controls. Patients and controls in groups II and III received only a single oral dose of bisoprolol 10mg. The 3 data sets were analysed separately, using a non-linear mixed effects model (the NONMEM program). A 2-compartment pharmacokinetic model with first-order absorption described the data adequately. The typical values of volume of central compartment, volume of distribution at steady-state and the absorption rate constant for the 3 populations were: for group I, 68L, 235L, and 0.7h-1; for group II, 28L, 179L, and 0.3h-1; and for group III, 55L, 256L, and 0.4h-1, respectively. Plasma clearance was related to age in group I, to serum creatinine in group II and to aspartate transaminase activity in group III. The 68% confidence limits for clearance and elimination half-life were 8.2 to 21.5 L/h and 7.6 to 19.7h, respectively, for 50-year-old patients in group I. The analysis predicted that progressive increases in serum creatinine or aspartate transaminase activity will result in only a 50% reduction of clearance.

  20. A Microarray-Based Analysis of Gametogenesis in Two Portuguese Populations of the European Clam Ruditapes decussatus

    PubMed Central

    de Sousa, Joana Teixeira; Milan, Massimo; Bargelloni, Luca; Pauletto, Marianna; Matias, Domitília; Joaquim, Sandra; Matias, Ana Margarete; Quillien, Virgile; Leitão, Alexandra; Huvet, Arnaud

    2014-01-01

    The European clam, Ruditapes decussatus is a species with a high commercial importance in Portugal and other Southern European countries. Its production is almost exclusively based on natural recruitment, which is subject to high annual fluctuations. Increased knowledge of the natural reproductive cycle of R. decussatus and its molecular mechanisms would be particularly important in providing new highly valuable genomic information for better understanding the regulation of reproduction in this economically important aquaculture species. In this study, the transcriptomic bases of R. decussatus reproduction have been analysed using a custom oligonucleotide microarray representing 51,678 assembled contigs. Microarray analyses were performed in four gonadal maturation stages from two different Portuguese wild populations, characterized by different responses to spawning induction when used as progenitors in hatchery. A comparison between the two populations elucidated a specific pathway involved in the recognition signals and binding between the oocyte and components of the sperm plasma membrane. We suggest that this pathway can explain part of the differences in terms of spawning induction success between the two populations. In addition, sexes and reproductive stages were compared and a correlation between mRNA levels and gonadal area was investigated. The lists of differentially expressed genes revealed that sex explains most of the variance in gonadal gene expression. Additionally, genes like Foxl2, vitellogenin, condensing 2, mitotic apparatus protein p62, Cep57, sperm associated antigens 6, 16 and 17, motile sperm domain containing protein 2, sperm surface protein Sp17, sperm flagellar proteins 1 and 2 and dpy-30, were identified as being correlated with the gonad area and therefore supposedly with the number and/or the size of the gametes produced. PMID:24643002

  1. Choice of lumbar spine bone density reference database for fracture prediction in men and women: a population-based analysis.

    PubMed

    Leslie, William D; Langsetmo, Lisa; Zhou, Wei; Goltzman, David; Kovacs, Christopher S; Prior, Jerilynn; Josse, Robert; Olszynski, Wojciech P; Davison, K Shawn; Anastassiades, Tassos; Towheed, Tanveer; Hanley, David A; Kaiser, Stephanie M; Lentle, Brian; Kreiger, Nancy

    2014-01-01

    The diagnosis of osteoporosis in men is controversial, although most studies demonstrate similar fracture rates for men and women with the same level of hip bone mineral density (BMD). Whether this applies to the lumbar spine is currently uncertain and has important implications with respect to choice of reference population for T-score calculation and osteoporosis diagnosis. This question was specifically addressed in the population-based Canadian Multicentre Osteoporosis Study cohort of 4745 women and 1887 men ages 50+ yr at the time of baseline lumbar spine dual energy x-ray absorptiometry. In up to 10 yr of observation, incident clinical major osteoporotic fractures occurred in 110 men (5.8%) vs 543 women (11.4%) (p < 0.001). Mean lumbar spine BMD in men was greater than in women, both among those with and those without incident major osteoporotic fracture (p < 0.001). Men were at slightly lower risk for incident major osteoporotic fracture than women for an equivalent lumbar spine BMD (age- and BMD-adjusted rate ratio 0.75, 95% confidence interval 0.60-0.93, p = 0.008) with similar findings after adjustment for the World Health Organization fracture risk assessment clinical risk factors or competing mortality. No significant sex difference in the BMD relationship was seen for vertebral fractures (clinical or radiographic) or for all fractures. In summary, this large population-based longitudinal cohort study found similar or lower fracture risk for men vs women after adjustment for absolute lumbar spine BMD and additional covariates. The least complicated model for describing fracture risk is therefore to use the same reference lumbar spine data for generating T-scores in men and women.

  2. Choice of Lumbar Spine Bone Density Reference Database for Fracture Prediction in Men and Women: A Population-Based Analysis

    PubMed Central

    Leslie, William D.; Langsetmo, Lisa; Zhou, Wei; Goltzman, David; Kovacs, Christopher S.; Prior, Jerilynn; Josse, Robert; Olszynski, Wojciech P.; Davison, K. Shawn; Anastassiades, Tassos; Towheed, Tanveer; Hanley, David A.; Kaiser, Stephanie M.; Lentle, Brian; Kreiger, Nancy

    2016-01-01

    The diagnosis of osteoporosis in men is controversial, although most studies demonstrate similar fracture rates for men and women with the same level of hip bone mineral density (BMD). Whether this applies to the lumbar spine is currently uncertain and has important implications with respect to choice of reference population for T-score calculation and osteoporosis diagnosis. This question was specifically addressed in the population-based Canadian Multicentre Osteoporosis Study cohort of 4745 women and 1887 men ages 50+ yr at the time of baseline lumbar spine dual energy x-ray absorptiometry. In up to 10 yr of observation, incident clinical major osteoporotic fractures occurred in 110 men (5.8%) vs 543 women (11.4%) (p < 0.001). Mean lumbar spine BMD in men was greater than in women, both among those with and those without incident major osteoporotic fracture (p < 0.001). Men were at slightly lower risk for incident major osteoporotic fracture than women for an equivalent lumbar spine BMD (age- and BMD-adjusted rate ratio 0.75, 95% confidence interval 0.60–0.93, p = 0.008) with similar findings after adjustment for the World Health Organization fracture risk assessment clinical risk factors or competing mortality. No significant sex difference in the BMD relationship was seen for vertebral fractures (clinical or radiographic) or for all fractures. In summary, this large population-based longitudinal cohort study found similar or lower fracture risk for men vs women after adjustment for absolute lumbar spine BMD and additional covariates. The least complicated model for describing fracture risk is therefore to use the same reference lumbar spine data for generating T-scores in men and women. PMID:24613388

  3. Mean Field Analysis of Large-Scale Interacting Populations of Stochastic Conductance-Based Spiking Neurons Using the Klimontovich Method

    NASA Astrophysics Data System (ADS)

    Gandolfo, Daniel; Rodriguez, Roger; Tuckwell, Henry C.

    2017-01-01

    We investigate the dynamics of large-scale interacting neural populations, composed of conductance based, spiking model neurons with modifiable synaptic connection strengths, which are possibly also subjected to external noisy currents. The network dynamics is controlled by a set of neural population probability distributions (PPD) which are constructed along the same lines as in the Klimontovich approach to the kinetic theory of plasmas. An exact non-closed, nonlinear, system of integro-partial differential equations is derived for the PPDs. As is customary, a closing procedure leads to a mean field limit. The equations we have obtained are of the same type as those which have been recently derived using rigorous techniques of probability theory. The numerical solutions of these so called McKean-Vlasov-Fokker-Planck equations, which are only valid in the limit of infinite size networks, actually shows that the statistical measures as obtained from PPDs are in good agreement with those obtained through direct integration of the stochastic dynamical system for large but finite size networks. Although numerical solutions have been obtained for networks of Fitzhugh-Nagumo model neurons, which are often used to approximate Hodgkin-Huxley model neurons, the theory can be readily applied to networks of general conductance-based model neurons of arbitrary dimension.

  4. Mean Field Analysis of Large-Scale Interacting Populations of Stochastic Conductance-Based Spiking Neurons Using the Klimontovich Method

    NASA Astrophysics Data System (ADS)

    Gandolfo, Daniel; Rodriguez, Roger; Tuckwell, Henry C.

    2017-03-01

    We investigate the dynamics of large-scale interacting neural populations, composed of conductance based, spiking model neurons with modifiable synaptic connection strengths, which are possibly also subjected to external noisy currents. The network dynamics is controlled by a set of neural population probability distributions (PPD) which are constructed along the same lines as in the Klimontovich approach to the kinetic theory of plasmas. An exact non-closed, nonlinear, system of integro-partial differential equations is derived for the PPDs. As is customary, a closing procedure leads to a mean field limit. The equations we have obtained are of the same type as those which have been recently derived using rigorous techniques of probability theory. The numerical solutions of these so called McKean-Vlasov-Fokker-Planck equations, which are only valid in the limit of infinite size networks, actually shows that the statistical measures as obtained from PPDs are in good agreement with those obtained through direct integration of the stochastic dynamical system for large but finite size networks. Although numerical solutions have been obtained for networks of Fitzhugh-Nagumo model neurons, which are often used to approximate Hodgkin-Huxley model neurons, the theory can be readily applied to networks of general conductance-based model neurons of arbitrary dimension.

  5. CDKN2A and CDK4 variants in Latvian melanoma patients: analysis of a clinic-based population.

    PubMed

    Pjanova, Dace; Engele, Ludmila; Randerson-Moor, Juliette A; Harland, Mark; Bishop, D Timothy; Newton Bishop, Julia A; Taylor, Claire; Debniak, Tadeusz; Lubinski, Jan; Kleina, Regina; Heisele, Olita

    2007-06-01

    Germline mutations of the CDKN2A and CDK4 genes explain a significant proportion of familial melanoma. To date, there have been few published estimations of the prevalence of such mutations in sporadic melanoma patients. In this study, we investigated CDKN2A and CDK4 exon 2 for germline mutations in 125 consecutive cutaneous malignant melanoma patients recruited through the Latvian Oncological Center, using amplicon melting analysis and sequencing. No disease-related CDKN2A germline mutations were identified in any of the melanoma patients analysed but the previously described CDK4 mutation, Arg24His, was found in one patient with a family history of melanoma. CDKN2A polymorphisms were studied as putative low penetrance susceptibility genes. The proportion of cases with polymorphisms in this Latvian melanoma population was Ala148Thr (c.442G>A) (6%), 500 C/G (c.*29C>G) (18%), and 540 C/T (c.*69C>T) (20%); however, only the frequency of the Ala148Thr polymorphism was higher in melanoma patients than in 203 controls (6 versus 1%, P=0.03). Ala148Thr has also been reported in association with melanoma in a Polish series but not in an English series. We therefore examined the Ala148Thr carrier's haplotype in 10 Latvian and 39 Polish samples. No significant difference was seen between these populations and the predominant haplotype observed in English samples, giving no indication that the discrepancy could be explained by population differences in linkage disequilibrium. In summary, our results show that germline mutations at the CDKN2A locus are rare in sporadic melanoma in Latvia. The study does, however, provide some additional evidence for a role for the CDKN2A polymorphism Ala148Thr as a low penetrance susceptibility gene. The detected CDK4 exon 2 mutation was found in only the seventh family identified worldwide with a germline CDK4 mutation.

  6. [Population and environment. Requests for interdisciplinary analysis].

    PubMed

    Tudela, F

    1991-01-01

    Serious difficulties impede interdisciplinary research involving demographers, ecologists, and other students of the environment. The 1st problem concerns definitions of the different subject areas. Demographers have focused on the dynamics of some indicators that reflect complex and heterogeneous population processes. The relative autonomy of demography as a discipline was gained through an empirical orientation reflected in the statistical treatment of causality. But the traditional demographic paradigm is insufficient for untangling the causal mechanisms underlying population dynamics. Environmental disciplines on the other hand face methodologic difficulties in transcending a strictly biological focus to incorporate aspects of cultural and social influence on ecological processes. "Human ecology", a possible meeting ground for ecological and demographic studies, is more of an ambitious program of transdisciplinary research than an independent discipline. Relations between the environment and development processes, including population aspects, are of increasing international concern. A conceptual base has developed in Latin America which emphasizes the global and structural aspects of the environment and of development styles. It has been extremely difficult to apply the entire conceptualization to the concrete environmental problems that are of current interest to both civil society and governments. It may be time to replace the umbrella term "environment", defining it in more specific, systemic, and operational terms. It is time to delimit study topics in terms of concrete problems. A good example would be the situation of Lake Chapala, the largest lake in Mexico. Damage caused to it cannot be assessed by referring to the "population explosion" or an "overall development style". Environmental, economic, and sociodemographic aspects will however necessarily enter the analysis. Fragile and unstable situations are of special interest in the study of relations

  7. Rank-based genome-wide analysis reveals the association of Ryanodine receptor-2 gene variants with childhood asthma among human populations

    PubMed Central

    2013-01-01

    Background The standard approach to determine unique or shared genetic factors across populations is to identify risk alleles in one population and investigate replication in others. However, since populations differ in DNA sequence information, allele frequencies, effect sizes, and linkage disequilibrium patterns, SNP association using a uniform stringent threshold on p values may not be reproducible across populations. Here, we developed rank-based methods to investigate shared or population-specific loci and pathways for childhood asthma across individuals of diverse ancestry. We performed genome-wide association studies on 859,790 SNPs genotyped in 527 affected offspring trios of European, African, and Hispanic ancestry using publically available asthma database in the Genotypes and Phenotypes database. Results Rank-based analyses showed that there are shared genetic factors for asthma across populations, more at the gene and pathway levels than at the SNP level. Although the top 1,000 SNPs were not shared, 11 genes (RYR2, PDE4D, CSMD1, CDH13, ROBO2, RBFOX1, PTPRD, NPAS3, PDE1C, SEMA5A, and CTNNA2) mapped by these SNPs were shared across populations. Ryanodine receptor 2 (RYR2, a statin response-related gene) showed the strongest association in European (p value = 2.55 × 10−7) and was replicated in African (2.57 × 10−4) and Hispanic (1.18 × 10−3) Americans. Imputation analyses based on the 1000 Genomes Project uncovered additional RYR2 variants associated with asthma. Network and functional ontology analyses revealed that RYR2 is an integral part of dermatological or allergic disorder biological networks, specifically in the functional classes involving inflammatory, eosinophilic, and respiratory diseases. Conclusion Our rank-based genome-wide analysis revealed for the first time an association of RYR2 variants with asthma and replicated previously discovered PDE4D asthma gene across human populations. The replication of top

  8. Real world heart failure epidemiology and outcome: A population-based analysis of 88,195 patients

    PubMed Central

    Vela, Emili; Clèries, Montse; Bustins, Montse; Cainzos-Achirica, Miguel; Enjuanes, Cristina; Moliner, Pedro; Ruiz, Sonia; Verdú-Rotellar, José María; Comín-Colet, Josep

    2017-01-01

    Background Heart failure (HF) is frequent and its prevalence is increasing. We aimed to evaluate the epidemiologic features of HF patients, the 1-year follow-up outcomes and the independent predictors of those outcomes at a population level. Methods and results Population-based longitudinal study including all prevalent HF cases in Catalonia (Spain) on December 31st, 2012. Patients were divided in 3 groups: patients without a previous HF hospitalization, patients with a remote (>1 year) HF hospitalization and patients with a recent (<1 year) HF admission. We analyzed 1year all-cause and HF hospitalizations, and all-cause mortality. Logistic regression was used to identify the independent predictors of each of those outcomes. A total of 88,195 patients were included. Mean age was 77 years, 55% were women. Comorbidities were frequent. Fourteen percent of patients had never been hospitalized, 71% had a remote HF hospitalization and 15% a recent hospitalization. At 1-year follow-up, all-cause and HF hospitalization were 53% and 8.8%, respectively. One-year all-cause mortality rate was 14%, and was higher in patients with a recent HF hospitalization (24%). The presence of diabetes mellitus, atrial fibrillation or chronic kidney disease was independently associated with all-cause and HF hospitalization and all-cause mortality. Hospital admissions and emergency department visits the previous year were also found to be independently associated with the three study outcomes. Conclusions Outcomes are different depending on the HF population studied. Some comorbidity, an all-cause hospitalization or emergency department visit the previous year were associated with a worse outcome. PMID:28235067

  9. Generation-based life table analysis reveals manifold effects of inbreeding on the population fitness in Plutella xylostella

    PubMed Central

    Peng, Lu; Zou, Mingmin; Ren, Nana; Xie, Miao; Vasseur, Liette; Yang, Yifan; He, Weiyi; Yang, Guang; Gurr, Geoff M.; Hou, Youming; You, Shijun; You, Minsheng

    2015-01-01

    Understanding how inbreeding affects fitness is biologically important for conservation and pest management. Despite being a worldwide pest of many economically important cruciferous crops, the influence of inbreeding on diamondback moth, Plutella xylostella (L.), populations is currently unknown. Using age-stage-specific life tables, we quantified the inbreeding effects on fitness-related traits and demographic parameters of P. xylostella. Egg hatching rate, survival and fecundity of the inbred line significantly declined compared to those of the outbred line over time. The inbred P. xylostella line showed significantly lower intrinsic rate of increase (r), net reproduction rate (R0), and finite increase rate (λ), and increasing generation time (T). Inbreeding effects vary with developmental stages and the fitness-related traits can be profoundly affected by the duration of inbreeding. Our work provides a foundation for further studies on molecular and genetic bases of the inbreeding depression for P. xylostella. PMID:26227337

  10. AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set.

    PubMed

    Sorkheh, Karim; Masaeli, Mohammad; Chaleshtori, Maryam Hosseini; Adugna, Asfaw; Ercisli, Sezai

    2016-04-01

    Analysis of the genetic diversity and population structure of crops is very important for use in breeding programs and for genetic resources conservation. We analyzed the genetic diversity and population structure of 47 rice genotypes from diverse origins using amplified fragment length polymorphism (AFLP) markers and morphological characters. The 47 genotypes, which were composed of four populations: Iranian native varieties, Iranian improved varieties, International Rice Research Institute (IRRI) rice varieties, and world rice collections, were analyzed using ten primer combinations. A total of 221 scorable bands were produced with an average of 22.1 alleles per pair of primers, of which 120 (54.30%) were polymorphic. The polymorphism information content (PIC) values varied from 0.32 to 0.41 with an average of 0.35. The high percentage of polymorphic bands (%PB) was found to be 64.71 and the resolving power (R p) collections were 63.36. UPGMA clustering based on numerical data from AFLP patterns clustered all 47 genotypes into three large groups. The genetic similarity between individuals ranged from 0.54 to 0.94 with an average of 0.74. Population genetic tree showed that Iranian native cultivars formed far distant cluster from the other populations, which may indicate that these varieties had minimal genetic change over time. Analysis of molecular variance (AMOVA) revealed that the largest proportion of the variation (84%) to be within populations showing the inbreeding nature of rice. Therefore, Iranian native varieties (landraces) may have unique genes, which can be used for future breeding programs and there is a need to conserve this unique diversity. Furthermore, crossing of Iranian genotypes with the genetically distant genotypes in the other three populations may result in useful combinations, which can be used as varieties and/or lines for future rice breeding programs.

  11. Revisiting the impact of OXTR rs53576 on empathy: A population-based study and a meta-analysis.

    PubMed

    Gong, Pingyuan; Fan, Huiyong; Liu, Jinting; Yang, Xing; Zhang, Kejin; Zhou, Xiaolin

    2017-03-09

    Oxytocin in the brain is related to empathy, which refers to the ability to understand and share others' internal states or responses. Previous studies have investigated the impact of OXTR rs53576, the most intensively examined polymorphism in the oxytocin receptor (OXTR) gene, on individual differences in empathy. However, these studies produced inconsistent results. In the current study, we reexamined the association of OXTR rs53576 with empathy in a relatively large population (N=1830) and also evaluated the association by a comprehensive meta-analysis (N=6631, 13 independent samples). The replication study indicated that OXTR rs53576 was indeed associated with individual differences in empathy. Individuals with a greater number of G alleles showed better empathic ability, particularly in fantasizing other's feelings and actions. The meta-analysis not only confirmed this association, but also indicated that the impact of this polymorphism was significant in both Europeans and Asians. These findings provide convincing evidence for the impact of OXTR rs53576 on empathy, highlighting the importance of OXTR gene in individuals' social cognition.

  12. A Genome-Wide Association Meta-Analysis of Attention-Deficit/Hyperactivity Disorder Symptoms in Population-Based Paediatric Cohorts

    PubMed Central

    Groen-Blokhuis, Maria M.; Pourcain, Beate St.; Greven, Corina U.; Pappa, Irene; Tiesler, Carla M.T.; Ang, Wei; Nolte, Ilja M.; Vilor-Tejedor, Natalia; Bacelis, Jonas; Ebejer, Jane L.; Zhao, Huiying; Davies, Gareth E.; Ehli, Erik A.; Evans, David M.; Fedko, Iryna O.; Guxens, Mònica; Hottenga, Jouke-Jan; Hudziak, James J.; Jugessur, Astanand; Kemp, John P.; Krapohl, Eva; Martin, Nicholas G.; Murcia, Mario; Myhre, Ronny; Ormel, Johan; Ring, Susan M.; Standl, Marie; Stergiakouli, Evie; Stoltenberg, Camilla; Thiering, Elisabeth; Timpson, Nicholas J.; Trzaskowski, Maciej; van der Most, Peter J.; Wang, Carol; Nyholt, Dale R.; Medland, Sarah E.; Neale, Benjamin; Jacobsson, Bo; Sunyer, Jordi; Hartman, Catharina A.; Whitehouse, Andrew J.O.; Pennell, Craig E.; Heinrich, Joachim; Plomin, Robert; Smith, George Davey; Tiemeier, Henning; Posthuma, Danielle; Boomsma, Dorret I.

    2016-01-01

    Objective To elucidate the influence of common genetic variants on childhood attention-deficit/hyperactivity disorder (ADHD) symptoms, to identify genetic variants that explain its high heritability, and to investigate the genetic overlap of ADHD symptom scores with ADHD diagnosis. Method Within the EArly Genetics and Lifecourse Epidemiology (EAGLE) consortium, genome-wide single nucleotide polymorphisms (SNPs) and ADHD symptom scores were available for 17,666 children (< 13 years) from nine population-based cohorts. SNP-based heritability was estimated in data from the three largest cohorts. Meta-analysis based on genome-wide association (GWA) analyses with SNPs was followed by gene-based association tests, and the overlap in results with a meta-analysis in the Psychiatric Genomics Consortium (PGC) case-control ADHD study was investigated. Results SNP-based heritability ranged from 5% to 34%, indicating that variation in common genetic variants influences ADHD symptom scores. The meta-analysis did not detect genome-wide significant SNPs, but three genes, lying close to each other with SNPs in high linkage disequilibrium (LD), showed a gene-wide significant association (p values between 1.46×10-6 and 2.66×10-6). One gene, WASL, is involved in neuronal development. Both SNP- and gene-based analyses indicated overlap with the PGC meta-analysis results with the genetic correlation estimated at 0.96. Conclusion The SNP-based heritability for ADHD symptom scores indicates a polygenic architecture and genes involved in neurite outgrowth are possibly involved. Continuous and dichotomous measures of ADHD appear to assess a genetically common phenotype. A next step is to combine data from population-based and case-control cohorts in genetic association studies to increase sample size and improve statistical power for identifying genetic variants. PMID:27663945

  13. Physiogenomic analysis of the Puerto Rican population

    PubMed Central

    Ruaño, Gualberto; Duconge, Jorge; Windemuth, Andreas; Cadilla, Carmen L; Kocherla, Mohan; Villagra, David; Renta, Jessica; Holford, Theodore; Santiago-Borrero, Pedro J

    2009-01-01

    Aims Admixture in the population of the island of Puerto Rico is of general interest with regards to pharmacogenetics to develop comprehensive strategies for personalized healthcare in Latin Americans. This research was aimed at determining the frequencies of SNPs in key physiological, pharmacological and biochemical genes to infer population structure and ancestry in the Puerto Rican population. Materials & methods A noninterventional, cross-sectional, retrospective study design was implemented following a controlled, stratified-by-region, random sampling protocol. The sample was based on birthrates in each region of the island of Puerto Rico, according to the 2004 National Birth Registry. Genomic DNA samples from 100 newborns were obtained from the Puerto Rico Newborn Screening Program in dried-blood spot cards. Genotyping using a physiogenomic array was performed for 332 SNPs from 196 cardiometabolic and neuroendocrine genes. Population structure was examined using a Bayesian clustering approach as well as by allelic dissimilarity as a measure of allele sharing. Results The Puerto Rican sample was found to be broadly heterogeneous. We observed three main clusters in the population, which we hypothesize to reflect the historical admixture in the Puerto Rican population from Amerindian, African and European ancestors. We present evidence for this interpretation by comparing allele frequencies for the three clusters with those for the same SNPs available from the International HapMap project for Asian, African and European populations. Conclusion Our results demonstrate that population analysis can be performed with a physiogenomic array of cardiometabolic and neuroendocrine genes to facilitate the translation of genome diversity into personalized medicine. PMID:19374515

  14. Gene-Based Genome-Wide Association Analysis in European and Asian Populations Identified Novel Genes for Rheumatoid Arthritis

    PubMed Central

    Zhu, Hong; Xia, Wei; Mo, Xing-Bo; Lin, Xiang; Qiu, Ying-Hua; Yi, Neng-Jun; Zhang, Yong-Hong; Deng, Fei-Yan; Lei, Shu-Feng

    2016-01-01

    Objective Rheumatoid arthritis (RA) is a complex autoimmune disease. Using a gene-based association research strategy, the present study aims to detect unknown susceptibility to RA and to address the ethnic differences in genetic susceptibility to RA between European and Asian populations. Methods Gene-based association analyses were performed with KGG 2.5 by using publicly available large RA datasets (14,361 RA cases and 43,923 controls of European subjects, 4,873 RA cases and 17,642 controls of Asian Subjects). For the newly identified RA-associated genes, gene set enrichment analyses and protein-protein interactions analyses were carried out with DAVID and STRING version 10.0, respectively. Differential expression verification was conducted using 4 GEO datasets. The expression levels of three selected ‘highly verified’ genes were measured by ELISA among our in-house RA cases and controls. Results A total of 221 RA-associated genes were newly identified by gene-based association study, including 71‘overlapped’, 76 ‘European-specific’ and 74 ‘Asian-specific’ genes. Among them, 105 genes had significant differential expressions between RA patients and health controls at least in one dataset, especially for 20 genes including 11 ‘overlapped’ (ABCF1, FLOT1, HLA-F, IER3, TUBB, ZKSCAN4, BTN3A3, HSP90AB1, CUTA, BRD2, HLA-DMA), 5 ‘European-specific’ (PHTF1, RPS18, BAK1, TNFRSF14, SUOX) and 4 ‘Asian-specific’ (RNASET2, HFE, BTN2A2, MAPK13) genes whose differential expressions were significant at least in three datasets. The protein expressions of two selected genes FLOT1 (P value = 1.70E-02) and HLA-DMA (P value = 4.70E-02) in plasma were significantly different in our in-house samples. Conclusion Our study identified 221 novel RA-associated genes and especially highlighted the importance of 20 candidate genes on RA. The results addressed ethnic genetic background differences for RA susceptibility between European and Asian populations and

  15. Population-based analysis of health care contacts among suicide decedents: identifying opportunities for more targeted suicide prevention strategies.

    PubMed

    Schaffer, Ayal; Sinyor, Mark; Kurdyak, Paul; Vigod, Simone; Sareen, Jitender; Reis, Catherine; Green, Diane; Bolton, James; Rhodes, Anne; Grigoriadis, Sophie; Cairney, John; Cheung, Amy

    2016-06-01

    The objective of this study was to detail the nature and correlates of mental health and non-mental health care contacts prior to suicide death. We conducted a systematic extraction of data from records at the Office of the Chief Coroner of Ontario of each person who died by suicide in the city of Toronto from 1998 to 2011. Data on 2,835 suicide deaths were linked with provincial health administrative data to identify health care contacts during the 12 months prior to suicide. Sub-populations of suicide decedents based on the presence and type of mental health care contact were described and compared across socio-demographic, clinical and suicide-specific variables. Time periods from last mental health contact to date of death were calculated and a Cox proportional hazards model examined covariates. Among suicide decedents, 91.7% had some type of past-year health care contact prior to death, 66.4% had a mental health care contact, and 25.3% had only non-mental health contacts. The most common type of mental health contact was an outpatient primary care visit (54.0%), followed by an outpatient psychiatric visit (39.8%), an emergency department visit (31.1%), and a psychiatric hospitalization (21.0%). The median time from last mental health contact to death was 18 days (interquartile range 5-63). Mental health contact was significantly associated with female gender, age 25-64, absence of a psychosocial stressor, diagnosis of schizophrenia or bipolar disorder, past suicide attempt, self-poisoning method and absence of a suicide note. Significant differences between sub-populations of suicide decedents based on the presence and nature of their health care contacts suggest the need for targeting of community and clinical-based suicide prevention strategies. The predominance of ambulatory mental health care contacts, often close to the time of death, reinforce the importance of concentrating efforts on embedding risk assessment and care pathways into all routine primary

  16. A systematic analysis of worldwide population-based data on the global burden of chronic kidney disease in 2010.

    PubMed

    Mills, Katherine T; Xu, Yu; Zhang, Weidong; Bundy, Joshua D; Chen, Chung-Shiuan; Kelly, Tanika N; Chen, Jing; He, Jiang

    2015-11-01

    Chronic kidney disease (CKD) is a major risk factor for end-stage renal disease, cardiovascular disease, and premature death. Here we estimated the global prevalence and absolute burden of CKD in 2010 by pooling data from population-based studies. We searched MEDLINE (January 1990 to December 2014), International Society of Nephrology Global Outreach Program-funded projects, and bibliographies of retrieved articles and selected 33 studies reporting gender- and age-specific prevalence of CKD in representative population samples. The age-standardized global prevalence of CKD stages 1-5 in adults aged 20 and older was 10.4% in men (95% confidence interval 9.3-11.9%) and 11.8% in women (11.2-12.6%). This consisted of 8.6% in men (7.3-9.8%) and 9.6% in women (7.7-11.1%) in high-income countries, and 10.6% in men (9.4-13.1%) and 12.5% in women (11.8-14.0%) in low- and middle-income countries. The total number of adults with CKD was 225.7 million (205.7-257.4 million) men and 271.8 million (258.0-293.7 million) women. This consisted of 48.3 million (42.3-53.3 million) men and 61.7 million (50.4-69.9 million) women in high-income countries, and 177.4 million (159.2-215.9 million) men and 210.1 million (200.8-231.7 million) women in low- and middle-income countries. Thus, CKD is an important global-health challenge, especially in low- and middle-income countries. National and international efforts for prevention, detection, and treatment of CKD are needed to reduce its morbidity and mortality worldwide.

  17. Knowledge and Attitudes towards Antibiotic Use and Resistance - A Latent Class Analysis of a Swedish Population-Based Sample

    PubMed Central

    Rosales-Klintz, Senia; Tegmark Wisell, Karin; Stålsby Lundborg, Cecilia

    2016-01-01

    Background In 2006, a study investigating knowledge and attitudes regarding antibiotic use and resistance in Sweden, indicated high level of knowledge but also areas in need of improvement. Objective (i) To provide an update on the knowledge and attitudes to antibiotic use and resistance of the Swedish population, and (ii) to identify which groups within the population are in particular need of improved knowledge or attitudes. Methods A questionnaire was sent by post in 2013 to 2,500 randomly-selected individuals aged 18–74, living in Sweden. Latent class analyses were conducted to group respondents based on their responses. The association between socio-demographic characteristics and the probability of belonging to each latent class was assessed. Results The response rate was 57%. Ninety-four per cent of the responders knew that bacteria could become resistant to antibiotics and the majority answered correctly to the questions regarding antibiotic resistance development. The respondents expressed confidence in doctors who decided not to prescribe antibiotics. Three latent classes related to ‘knowledge regarding antibiotic use and resistance’, two regarding ‘attitudes towards antibiotic accessibility and infection prevention’ and three regarding ‘attitudes towards antibiotic use and effects’ were revealed. Men, younger and more educated people were more knowledgeable but males had a less restrictive attitude. Respondents with high levels of knowledge on antibiotics were more likely to have appropriate restrictive attitudes to antibiotics. Conclusion Knowledge on antibiotic use and resistance is maintained high and has improved in Sweden compared to 2006. People with lower education and elderly are especially in need of improved knowledge about antibiotic use and resistance. PMID:27096751

  18. Budget Impact Analysis of Switching to Digital Mammography in a Population-Based Breast Cancer Screening Program: A Discrete Event Simulation Model

    PubMed Central

    Comas, Mercè; Arrospide, Arantzazu; Mar, Javier; Sala, Maria; Vilaprinyó, Ester; Hernández, Cristina; Cots, Francesc; Martínez, Juan; Castells, Xavier

    2014-01-01

    Objective To assess the budgetary impact of switching from screen-film mammography to full-field digital mammography in a population-based breast cancer screening program. Methods A discrete-event simulation model was built to reproduce the breast cancer screening process (biennial mammographic screening of women aged 50 to 69 years) combined with the natural history of breast cancer. The simulation started with 100,000 women and, during a 20-year simulation horizon, new women were dynamically entered according to the aging of the Spanish population. Data on screening were obtained from Spanish breast cancer screening programs. Data on the natural history of breast cancer were based on US data adapted to our population. A budget impact analysis comparing digital with screen-film screening mammography was performed in a sample of 2,000 simulation runs. A sensitivity analysis was performed for crucial screening-related parameters. Distinct scenarios for recall and detection rates were compared. Results Statistically significant savings were found for overall costs, treatment costs and the costs of additional tests in the long term. The overall cost saving was 1,115,857€ (95%CI from 932,147 to 1,299,567) in the 10th year and 2,866,124€ (95%CI from 2,492,610 to 3,239,638) in the 20th year, representing 4.5% and 8.1% of the overall cost associated with screen-film mammography. The sensitivity analysis showed net savings in the long term. Conclusions Switching to digital mammography in a population-based breast cancer screening program saves long-term budget expense, in addition to providing technical advantages. Our results were consistent across distinct scenarios representing the different results obtained in European breast cancer screening programs. PMID:24832200

  19. Risk of Second Cancers in Merkel Cell Carcinoma: A Meta-Analysis of Population Based Cohort Studies

    PubMed Central

    Saxena, Anshul; Ramamoorthy, Venkataraghavan; Khan, Hafiz

    2014-01-01

    The risk of second cancers in Merkel cell carcinoma (MCC) remains uncertain since risk estimates vary worldwide. The global MCC population is growing and there is a demand for better knowledge of prognosis of this disease. The Cochrane Database of Systematic Reviews, MEDLINE, and EMBASE search engines were searched for the relevant literature between January 1999 and September 2014 by use of explicit search criteria. The main outcome was second malignancies associated with MCC patients measured by standardized incidence ratios (SIRs) or other estimates of risks. Five papers fulfilled the inclusion criteria and reported SIRs of second cancer in MCC which varied from 1.07 to 2.80. Performing meta-analysis using random effects model revealed that there was an increased risk for second malignancies due to MCC (SIR, 1.52; 95% CI, 1.10–2.11). There was a significant increase in risk for malignant melanoma (SIR, 3.09; 95% CI, 2.02–4.73) as compared to all common second malignancies among the studies. Updated knowledge about risk of second malignancies in MCC will help in better assessment of the disease prognosis and will help in optimizing the medical and surgical treatment, radiotherapy, follow-up, and surveillance procedures. PMID:25574398

  20. Risk of second cancers in merkel cell carcinoma: a meta-analysis of population based cohort studies.

    PubMed

    Saxena, Anshul; Rubens, Muni; Ramamoorthy, Venkataraghavan; Khan, Hafiz

    2014-01-01

    The risk of second cancers in Merkel cell carcinoma (MCC) remains uncertain since risk estimates vary worldwide. The global MCC population is growing and there is a demand for better knowledge of prognosis of this disease. The Cochrane Database of Systematic Reviews, MEDLINE, and EMBASE search engines were searched for the relevant literature between January 1999 and September 2014 by use of explicit search criteria. The main outcome was second malignancies associated with MCC patients measured by standardized incidence ratios (SIRs) or other estimates of risks. Five papers fulfilled the inclusion criteria and reported SIRs of second cancer in MCC which varied from 1.07 to 2.80. Performing meta-analysis using random effects model revealed that there was an increased risk for second malignancies due to MCC (SIR, 1.52; 95% CI, 1.10-2.11). There was a significant increase in risk for malignant melanoma (SIR, 3.09; 95% CI, 2.02-4.73) as compared to all common second malignancies among the studies. Updated knowledge about risk of second malignancies in MCC will help in better assessment of the disease prognosis and will help in optimizing the medical and surgical treatment, radiotherapy, follow-up, and surveillance procedures.

  1. Spousal Violence in 5 Transitional Countries: A Population-Based Multilevel Analysis of Individual and Contextual Factors

    PubMed Central

    2015-01-01

    Objectives. I examined the individual- and community-level factors associated with spousal violence in post-Soviet countries. Methods. I used population-based data from the Demographic and Health Survey conducted between 2005 and 2012. My sample included currently married women of reproductive age (n = 3932 in Azerbaijan, n = 4053 in Moldova, n = 1932 in Ukraine, n = 4361 in Kyrgyzstan, and n = 4093 in Tajikistan). I selected respondents using stratified multistage cluster sampling. Because of the nested structure of the data, multilevel logistic regressions for survey data were fitted to examine factors associated with spousal violence in the last 12 months. Results. Partner’s problem drinking was the strongest risk factor associated with spousal violence in all 5 countries. In Moldova, Ukraine, and Kyrgyzstan, women with greater financial power than their spouses were more likely to experience violence. Effects of community economic deprivation and of empowerment status of women in the community on spousal violence differed across countries. Women living in communities with a high tolerance of violence faced a higher risk of spousal violence in Moldova and Ukraine. In more traditional countries (Azerbaijan, Kyrgyzstan, and Tajikistan), spousal violence was lower in conservative communities with patriarchal gender beliefs or higher financial dependency on husbands. Conclusions. My findings underscore the importance of examining individual risk factors in the context of community-level factors and developing individual- and community-level interventions. PMID:26378858

  2. Microbial Character Related Sulfur Cycle under Dynamic Environmental Factors Based on the Microbial Population Analysis in Sewerage System

    PubMed Central

    Dong, Qian; Shi, Hanchang; Liu, Yanchen

    2017-01-01

    The undesired sulfur cycle derived by microbial population can ultimately causes the serious problems of sewerage systems. However, the microbial community characters under dynamic environment factors in actual sewerage system is still not enough. This current study aimed to character the distributions and compositions of microbial communities that participate in the sulfur cycle under the dynamic environmental conditions in a local sewerage system. To accomplish this, microbial community compositions were assessed using 454 high-throughput sequencing (16S rDNA) combined with dsrB gene-based denaturing gradient gel electrophoresis. The results indicated that a higher diversity of microbial species was present at locations in sewers with high concentrations of H2S. Actinobacteria and Proteobacteria were dominant in the sewerage system, while Actinobacteria alone were dominant in regions with high concentrations of H2S. Specifically, the unique operational taxonomic units could aid to characterize the distinct microbial communities within a sewerage manhole. The proportion of sulfate-reducing bacteria, each sulfur-oxidizing bacteria (SOB) were strongly correlated with the liquid parameters (DO, ORP, COD, Sulfide, NH3-N), while the Mycobacterium and Acidophilic SOB (M&A) was strongly correlated with gaseous factors within the sewer, such as H2S, CH4, and CO. Identifying the distributions and proportions of critical microbial communities within sewerage systems could provide insights into how the microbial sulfur cycle is affected by the dynamic environmental conditions that exist in sewers and might be useful for explaining the potential sewerage problems. PMID:28261160

  3. Associations of All-Cause Mortality with Census-Based Neighbourhood Deprivation and Population Density in Japan: A Multilevel Survival Analysis

    PubMed Central

    Nakaya, Tomoki; Honjo, Kaori; Hanibuchi, Tomoya; Ikeda, Ai; Iso, Hiroyasu; Inoue, Manami; Sawada, Norie; Tsugane, Shoichiro

    2014-01-01

    Background Despite evidence that neighbourhood conditions affect residents' health, no prospective studies of the association between neighbourhood socio-demographic factors and all-cause mortality have been conducted in non-Western societies. Thus, we examined the effects of areal deprivation and population density on all-cause mortality in Japan. Methods We employed census and survival data from the Japan Public Health Center-based Prospective Study, Cohort I (n = 37,455), consisting of middle-aged residents (40 to 59 years at the baseline in 1990) living in four public health centre districts. Data spanned between 1990 and 2010. A multilevel parametric proportional-hazard regression model was applied to estimate the hazard ratios (HRs) of all-cause mortality by two census-based areal variables —areal deprivation index and population density—as well as individualistic variables such as socioeconomic status and various risk factors. Results We found that areal deprivation and population density had moderate associations with all-cause mortality at the neighbourhood level based on the survival data with 21 years of follow-ups. Even when controlling for individualistic socio-economic status and behavioural factors, the HRs of the two areal factors (using quartile categorical variables) significantly predicted mortality. Further, this analysis indicated an interaction effect of the two factors: areal deprivation prominently affects the health of residents in neighbourhoods with high population density. Conclusions We confirmed that neighbourhood socio-demographic factors are significant predictors of all-cause death in Japanese non-metropolitan settings. Although further study is needed to clarify the cause-effect relationship of this association, the present findings suggest that health promotion policies should consider health disparities between neighbourhoods and possibly direct interventions towards reducing mortality in densely populated and highly

  4. Extinction-effective population index: incorporating life-history variations in population viability analysis.

    PubMed

    Fujiwara, Masami

    2007-09-01

    Viability status of populations is a commonly used measure for decision-making in the management of populations. One of the challenges faced by managers is the need to consistently allocate management effort among populations. This allocation should in part be based on comparison of extinction risks among populations. Unfortunately, common criteria that use minimum viable population size or count-based population viability analysis (PVA) often do not provide results that are comparable among populations, primarily because they lack consistency in determining population size measures and threshold levels of population size (e.g., minimum viable population size and quasi-extinction threshold). Here I introduce a new index called the "extinction-effective population index," which accounts for differential effects of demographic stochasticity among organisms with different life-history strategies and among individuals in different life stages. This index is expected to become a new way of determining minimum viable population size criteria and also complement the count-based PVA. The index accounts for the difference in life-history strategies of organisms, which are modeled using matrix population models. The extinction-effective population index, sensitivity, and elasticity are demonstrated in three species of Pacific salmonids. The interpretation of the index is also provided by comparing them with existing demographic indices. Finally, a measure of life-history-specific effect of demographic stochasticity is derived.

  5. Reliable Quantification of the Potential for Equations Based on Spot Urine Samples to Estimate Population Salt Intake: Protocol for a Systematic Review and Meta-Analysis

    PubMed Central

    Huang, Liping; Crino, Michelle; Wu, Jason HY; Woodward, Mark; Land, Mary-Anne; McLean, Rachael; Webster, Jacqui; Enkhtungalag, Batsaikhan; Nowson, Caryl A; Elliott, Paul; Cogswell, Mary; Toft, Ulla; Mill, Jose G; Furlanetto, Tania W; Ilich, Jasminka Z; Hong, Yet Hoi; Cohall, Damian; Luzardo, Leonella; Noboa, Oscar; Holm, Ellen; Gerbes, Alexander L; Senousy, Bahaa; Pinar Kara, Sonat; Brewster, Lizzy M; Ueshima, Hirotsugu; Subramanian, Srinivas; Teo, Boon Wee; Allen, Norrina; Choudhury, Sohel Reza; Polonia, Jorge; Yasuda, Yoshinari; Campbell, Norm RC; Neal, Bruce

    2016-01-01

    Background Methods based on spot urine samples (a single sample at one time-point) have been identified as a possible alternative approach to 24-hour urine samples for determining mean population salt intake. Objective The aim of this study is to identify a reliable method for estimating mean population salt intake from spot urine samples. This will be done by comparing the performance of existing equations against one other and against estimates derived from 24-hour urine samples. The effects of factors such as ethnicity, sex, age, body mass index, antihypertensive drug use, health status, and timing of spot urine collection will be explored. The capacity of spot urine samples to measure change in salt intake over time will also be determined. Finally, we aim to develop a novel equation (or equations) that performs better than existing equations to estimate mean population salt intake. Methods A systematic review and meta-analysis of individual participant data will be conducted. A search has been conducted to identify human studies that report salt (or sodium) excretion based upon 24-hour urine samples and spot urine samples. There were no restrictions on language, study sample size, or characteristics of the study population. MEDLINE via OvidSP (1946-present), Premedline via OvidSP, EMBASE, Global Health via OvidSP (1910-present), and the Cochrane Library were searched, and two reviewers identified eligible studies. The authors of these studies will be invited to contribute data according to a standard format. Individual participant records will be compiled and a series of analyses will be completed to: (1) compare existing equations for estimating 24-hour salt intake from spot urine samples with 24-hour urine samples, and assess the degree of bias according to key demographic and clinical characteristics; (2) assess the reliability of using spot urine samples to measure population changes in salt intake overtime; and (3) develop a novel equation that performs

  6. A population-based analysis of incentive payments to primary care physicians for the care of patients with complex disease

    PubMed Central

    Lavergne, M. Ruth; Law, Michael R.; Peterson, Sandra; Garrison, Scott; Hurley, Jeremiah; Cheng, Lucy; McGrail, Kimberlyn

    2016-01-01

    Background: In 2007, the province of British Columbia implemented incentive payments to primary care physicians for the provision of comprehensive, continuous, guideline-informed care for patients with 2 or more chronic conditions. We examined the impact of this program on primary care access and continuity, rates of hospital admission and costs. Methods: We analyzed all BC patients who qualified for the incentive based on their diagnostic profile. We tracked primary care contacts and continuity, hospital admissions (total, via the emergency department and for targeted conditions), and cost of physician services, hospital care and pharmaceuticals, for 24 months before and 24 months after the intervention. Results: Of 155 754 eligible patients, 63.7% had at least 1 incentive payment billed. Incentive payments had no impact on primary care contacts (change in contacts per patient per month: 0.016, 95% confidence interval [CI] −0.047 to 0.078) or continuity of care (mean monthly change: 0.012, 95% CI −0.001 to 0.024) and were associated with increased total rates of hospital admission (change in hospital admissions per 1000 patients per month: 1.46, 95% CI 0.04 to 2.89), relative to preintervention trends. Annual costs per patient did not decline (mean change: $455.81, 95% CI −$2.44 to $914.08). Interpretation: British Columbia’s $240-million investment in this program improved compensation for physicians doing the important work of caring for complex patients, but did not appear to improve primary care access or continuity, or constrain resource use elsewhere in the health care system. Policymakers should consider other strategies to improve care for this patient population. PMID:27527484

  7. Association of Sjögrens Syndrome in Patients with Chronic Hepatitis Virus Infection: A Population-Based Analysis

    PubMed Central

    Yeh, Chih-Ching; Wang, Wen-Chang; Wu, Chien-Sheng; Sung, Fung-Chang; Su, Chien-Tien; Shieh, Ying-Hua; Chang, Shih-Ni; Su, Fu-Hsiung

    2016-01-01

    Objective The association between Sjögren’s syndrome (SS) and chronic hepatitis virus infection is inconclusive. Hepatitis B (HBV) and hepatitis C virus (HCV) infections are highly prevalent in Taiwan. We used a population-based case-control study to evaluate the associations between SS and HBV and HCV infections. Materials and Methods We identified 9,629 SS patients without other concomitant autoimmune diseases and 38,516 sex- and age-matched controls without SS from the Taiwan National Health Insurance claims data between 2000 and 2011. We utilized multivariate logistic regression to estimate the odds ratios (ORs) and 95% confidence intervals (CIs) of the associations between SS and HBV and HCV infections. Sex- and age-specific (<55 and ≥55 years) risks of SS were evaluated. Results The risk of SS was higher in patients with HCV than in those without chronic viral hepatitis (OR = 2.49, 95% CI = 2.16–2.86). Conversely, HBV infection was not associated with SS (OR = 1.10, 95% CI = 0.98–1.24). Younger HCV patients were at a higher risk for SS (<55 years: OR = 3.37, 95% CI = 2.62–4.35; ≥55 years: OR = 2.20, 95% CI = 1.84–2.62). Men with HCV were at a greater risk for SS (women: OR = 2.26, 95% CI = 1.94–2.63; men: OR = 4.22, 95% CI = 2.90–6.16). Only men with chronic HBV exhibited a higher risk of SS (OR = 1.61, 95% CI = 1.21–2.14). Conclusion HCV infection was associated with SS; however, HBV only associated with SS in men. PMID:27560377

  8. Population bases and the 2011 Census.

    PubMed

    Smallwood, Steve

    2011-01-01

    In an increasingly complex society there are a number of different population definitions that can be relevant for users, beyond the standard definition used in counting the population. This article describes the enumeration base for the 2011 Census and how alternative population outputs may be produced. It provides a background as to how the questions on the questionnaire were decided upon and how population bases can be constructed from the Census. Similarities and differences between the information collected across the three UK Censuses (England and Wales, Scotland and Northern Ireland) are discussed. Finally, issues around estimating the population on alternative bases are presented.

  9. Prevalence of human papillomavirus and cervical intraepithelial neoplasia in China: a pooled analysis of 17 population-based studies.

    PubMed

    Zhao, Fang-Hui; Lewkowitz, Adam K; Hu, Shang-Ying; Chen, Feng; Li, Long-Yu; Zhang, Qing-Ming; Wu, Rui-Fang; Li, Chang-Qing; Wei, Li-Hui; Xu, Ai-Di; Zhang, Wen-Hua; Pan, Qin-Jing; Zhang, Xun; Belinson, Jerome L; Sellors, John W; Smith, Jennifer S; Qiao, You-Lin; Franceschi, Silvia

    2012-12-15

    High-risk (HR) human papillomavirus (HPV) prevalence has been shown to correlate well with cervical cancer incidence rates. Our study aimed to estimate the prevalence of HR-HPV and cervical intraepithelial neoplasia (CIN) in China and indirectly informs on the cervical cancer burden in the country. A total of 30,207 women from 17 population-based studies throughout China were included. All women received HPV DNA testing (HC2, Qiagen, Gaithersburg, MD), visual inspection with acetic acid and liquid-based cytology. Women positive for any test received colposcopy-directed or four-quadrant biopsies. A total of 29,579 women had HR-HPV testing results, of whom 28,761 had biopsy confirmed (9,019, 31.4%) or assumed (19,742, 68.6%) final diagnosis. Overall crude HR-HPV prevalence was 17.7%. HR-HPV prevalence was similar in rural and urban areas but showed dips in different age groups: at age 25-29 (11.3%) in rural and at age 35-39 (11.3%) in urban women. In rural and urban women, age-standardized CIN2 prevalence was 1.5% [95% confidence interval (CI): 1.4-1.6%] and 0.7% (95% CI: 0.7-0.8%) and CIN3+ prevalence was 1.2% (95% CI: 1.2-1.3%) and 0.6% (95% CI: 0.5-0.7%), respectively. Prevalence of CIN3+ as a percentage of either all women or HR-HPV-positive women steadily increased with age, peaking in 45- to 49-year-old women. High prevalence of HR-HPV and CIN3+ was detected in both rural and urban China. The steady rise of CIN3+ up to the age group of 45-49 is attributable to lack of lesion removal through screening. Our findings document the inadequacy of current screening in China while indirectly raising the possibility that the cervical cancer burden in China is underreported.

  10. Optical Coherence Tomography in the UK Biobank Study – Rapid Automated Analysis of Retinal Thickness for Large Population-Based Studies

    PubMed Central

    Grossi, Carlota M.; Foster, Paul J.; Yang, Qi; Reisman, Charles A.; Chan, Kinpui; Peto, Tunde; Thomas, Dhanes; Patel, Praveen J.

    2016-01-01

    Purpose To describe an approach to the use of optical coherence tomography (OCT) imaging in large, population-based studies, including methods for OCT image acquisition, storage, and the remote, rapid, automated analysis of retinal thickness. Methods In UK Biobank, OCT images were acquired between 2009 and 2010 using a commercially available “spectral domain” OCT device (3D OCT-1000, Topcon). Images were obtained using a raster scan protocol, 6 mm x 6 mm in area, and consisting of 128 B-scans. OCT image sets were stored on UK Biobank servers in a central repository, adjacent to high performance computers. Rapid, automated analysis of retinal thickness was performed using custom image segmentation software developed by the Topcon Advanced Biomedical Imaging Laboratory (TABIL). This software employs dual-scale gradient information to allow for automated segmentation of nine intraretinal boundaries in a rapid fashion. Results 67,321 participants (134,642 eyes) in UK Biobank underwent OCT imaging of both eyes as part of the ocular module. 134,611 images were successfully processed with 31 images failing segmentation analysis due to corrupted OCT files or withdrawal of subject consent for UKBB study participation. Average time taken to call up an image from the database and complete segmentation analysis was approximately 120 seconds per data set per login, and analysis of the entire dataset was completed in approximately 28 days. Conclusions We report an approach to the rapid, automated measurement of retinal thickness from nearly 140,000 OCT image sets from the UK Biobank. In the near future, these measurements will be publically available for utilization by researchers around the world, and thus for correlation with the wealth of other data collected in UK Biobank. The automated analysis approaches we describe may be of utility for future large population-based epidemiological studies, clinical trials, and screening programs that employ OCT imaging. PMID:27716837

  11. Profile of Individuals Who Are Metabolically Healthy Obese Using Different Definition Criteria. A Population-Based Analysis in the Spanish Population

    PubMed Central

    Martínez-Larrad, María Teresa; Corbatón Anchuelo, Arturo; Del Prado, Náyade; Ibarra Rueda, José María; Gabriel, Rafael; Serrano-Ríos, Manuel

    2014-01-01

    Background Obesity is associated with numerous metabolic complications such as diabetes mellitus type 2, dyslipidemia, hypertension, cardiovascular diseases and several forms of cancer. Our goal was to compare different criteria to define the metabolically healthy obese (MHO) with metabolically unhealthy obese (MUHO) subjects. We applied Wildman (W), Wildman modified (WM) with insulin resistance (IR) with cut-off point ≥3.8 and levels of C- Reactive Protein (CRP) ≥3 mg/l; and Consensus Societies (CS) criteria. In these subjects cardiovascular-risk (CV-risk) was estimated by Framingham score and SCORE for MHO and MUHO. Methods A cross-sectional study was conducted in Spanish Caucasian adults. A total of 3,844 subjects completed the study, 45% males, aged 35–74 years. Anthropometric/biochemical variables were measured. Obesity was defined as BMI: ≥30 Kg/m2. Results The overall prevalence of obesity in our population was 27.5%, (23.7%/males and 30.2%/females). MHO prevalence according to W, WM, and CS definition criteria were: 9.65%, 16.29%, 39.94% respectively in obese participants. MHO has lower waist circumference (WC) measurements than MUHO. The estimated CV-risks by Framingham and SCORE Project charts were lower in MHO than MUHO subjects. WC showed high specificity and sensitivity in detecting high estimated CV risk by Framingham. However, WHR showed high specificity and sensitivity in detecting CV risk according to SCORE Project. MHO subjects as defined by any of the three criteria had higher adiponectin levels after adjustment by sex, age, WC, HOMA IR and Framingham or SCORE risks. This relationship was not found for CRP circulating levels neither leptin levels. Conclusions MHO prevalence is highly dependent on the definition criteria used to define those individuals. Results showed that MHO subjects had less WC, and a lower estimated CV-risk than MUHO subjects. Additionally, the high adiponectin circulating levels in MHO may suggest a protective role

  12. Population-Based Smoking Cessation Strategies

    PubMed Central

    2010-01-01

    , reviews examining individual-level smoking cessation strategies (i.e. self-help interventions, counselling, etc.), web-based smoking cessation interventions, and smoking cessation strategies for special population groups outside of those identified from reviews included in this analysis were excluded from the scope. Information on cessation programs or strategies in other provinces or an evaluation of current population-based programs in Ontario was also not included in the scope. Status in Ontario In 2005, the McGuinty government launched the Smoke-Free Ontario Strategy, focusing on initiatives aimed at young people to encourage them not to smoke, protection from exposure to second-hand smoke, and programs to help smokers quit. There are currently many smoking cessation programs funded across the province and in 2007/2008, Ontario invested $15 million in cessation programs, services and training. Ontario Health Insurance Plan (OHIP) fee codes for physician advice to quit also exist. Evidence-Based Analysis Research Question What are the efficacy and cost-effectiveness of the selected population-based strategies for smoking cessation? Literature Search A preliminary scan of Medline was conducted to identify major systematic reviews, meta-analyses, and health technology assessments (HTAs) in the area of smoking cessation. Based on the availability of a number of Cochrane Reviews on the topic of smoking cessation, a more systematic search of the literature was not conducted. For the economic analysis, a literature search was conducted of relevant databases for recently published article reviews, HTAs, and Cochrane Reviews of the nine identified population-based smoking cessation strategies. This analysis is limited as it is a summary of existing reviews and not a systematic review. Outcomes of Interest The primary outcome of interest for the clinical summary was abstinence from smoking at 6 months follow up; additional outcomes were examined where available. The primary

  13. Inbreeding and genetic diversity analysis in a hatchery release population and clones of Rhopilema esculentum based on microsatellite markers

    NASA Astrophysics Data System (ADS)

    Tian, Tao; Chen, Zaizhong; Wang, Mosang; Hu, Yulong; Wang, Weiji

    2016-07-01

    Ten microsatellite markers were used to analyze the levels of genetic diversity and inbreeding in a hatchery release population of Rhopilema esculentum Kishinouye (Scyphozoa: Rhizostomatidae). A total of 85 alleles were detected in 600 individuals. Within-population levels of observed (H o) and expected (H e) heterozygosity ranged from 0.152 to 0.839 (mean=0.464) and from 0.235 to 0.821 (mean=0.618), respectively. The polymorphism information content (PIC) of each marker ranged from 0.207 to 0.795 with an average of 0.580, indicating that the hatchery population maintained a high level of genetic diversity. Inbreeding levels were estimated in the hatchery population and the inbreeding coefficient was 0.203. This result revealed that a certain level of inbreeding occurred within the population. Meanwhile, we also determined genetic diversity at the clone level. Several polyps from the same scyphistomae were genotyped at the ten microsatellite loci and there was virtually no difference in their genotypes. Furthermore, we calculated the probabilities of exclusion. When both parents were known, the average exclusion probability of ten loci was 99.99%. Our data suggest that the ten microsatellite markers can not only be used to analyze the identity of individuals but they can also be applied to parentage identification. Our research provides a theoretical basis and technical support for genetic diversity detection and reasonable selection of R. esculentum hatchery populations. These findings support the use of releasing studies and conservation of R. esculentum germplasm resources.

  14. Effects of diabetes definition on global surveillance of diabetes prevalence and diagnosis: a pooled analysis of 96 population-based studies with 331 288 participants

    PubMed Central

    2015-01-01

    Summary Background Diabetes has been defined on the basis of different biomarkers, including fasting plasma glucose (FPG), 2-h plasma glucose in an oral glucose tolerance test (2hOGTT), and HbA1c. We assessed the effect of different diagnostic definitions on both the population prevalence of diabetes and the classification of previously undiagnosed individuals as having diabetes versus not having diabetes in a pooled analysis of data from population-based health examination surveys in different regions. Methods We used data from 96 population-based health examination surveys that had measured at least two of the biomarkers used for defining diabetes. Diabetes was defined using HbA1c (HbA1c ≥6·5% or history of diabetes diagnosis or using insulin or oral hypoglycaemic drugs) compared with either FPG only or FPG-or-2hOGTT definitions (FPG ≥7·0 mmol/L or 2hOGTT ≥11·1 mmol/L or history of diabetes or using insulin or oral hypoglycaemic drugs). We calculated diabetes prevalence, taking into account complex survey design and survey sample weights. We compared the prevalences of diabetes using different definitions graphically and by regression analyses. We calculated sensitivity and specificity of diabetes diagnosis based on HbA1c compared with diagnosis based on glucose among previously undiagnosed individuals (ie, excluding those with history of diabetes or using insulin or oral hypoglycaemic drugs). We calculated sensitivity and specificity in each survey, and then pooled results using a random-effects model. We assessed the sources of heterogeneity of sensitivity by meta-regressions for study characteristics selected a priori. Findings Population prevalence of diabetes based on FPG-or-2hOGTT was correlated with prevalence based on FPG alone (r=0·98), but was higher by 2–6 percentage points at different prevalence levels. Prevalence based on HbA1c was lower than prevalence based on FPG in 42·8% of age–sex–survey groups and higher in another 41·6%; in

  15. Microsatellite data analysis for population genetics.

    PubMed

    Kim, Kyung Seok; Sappington, Thomas W

    2013-01-01

    Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of variation at selectively neutral marker loci, and microsatellites continue to be a popular choice of marker. In recent decades, software programs to estimate population genetics parameters have been developed at an increasing pace as computational science and theoretical knowledge advance. Numerous population genetics software programs are presently available to analyze microsatellite genotype data, but only a handful are commonly employed for calculating parameters such as genetic variation, genetic structure, patterns of spatial and temporal gene flow, population demography, individual population assignment, and genetic relationships within and between populations. In this chapter, we introduce statistical analyses and relevant population genetic software programs that are commonly employed in the field of population genetics and molecular ecology.

  16. Genetic structure and distribution of pythium aphanidermatum populations in Pennsylvania greenhouses based on analysis of AFLP and SSR markers.

    PubMed

    Lee, Seonghee; Garzón, Carla D; Moorman, Gary W

    2010-01-01

    Pythium aphanidermatum is one of the most aggressive species in the genus and has a wide host range, but little is known about its population genetic structure. We tested 123 P. aphanidermatum isolates with six AFLP primer combinations and four SSR markers. The genetic diversity of P. aphanidermatum was 0.34 with AFLP and 0.55 with SSR markers. SSR genotypes totaled 3-8 for each locus, and a total of 14 SSR genotypes were found among all isolates. Three major genetic groups were identified with the combination of AFLP and SSR marker data. The genetic structure observed among P. aphanidermatum isolates was related to location and mefenoxam fungicide resistance instead of host. Four genotypes (PA1, PA2, PA5 and PA7) were found in the population from a commercial greenhouse, and the genetic diversity of a greenhouse population was similar to that found in the whole sample. The molecular tools for P. aphanidermatum isolates identified the possible gene flow within and among populations in Pennsylvania greenhouses.

  17. People living with HIV travel farther to access healthcare: a population-based geographic analysis from rural Uganda

    PubMed Central

    Akullian, Adam N; Mukose, Aggrey; Levine, Gillian A; Babigumira, Joseph B

    2016-01-01

    Introduction The availability of specialized HIV services is limited in rural areas of sub-Saharan Africa where the need is the greatest. Where HIV services are available, people living with HIV (PLHIV) must overcome large geographic, economic and social barriers to access healthcare. The objective of this study was to understand the unique barriers PLHIV face when accessing healthcare compared with those not living with HIV in a rural area of sub-Saharan Africa with limited availability of healthcare infrastructure. Methods We conducted a population-based cross-sectional study of 447 heads of household on Bugala Island, Uganda. Multiple linear regression models were used to compare travel time, cost and distance to access healthcare, and log binomial models were used to test for associations between HIV status and access to nearby health services. Results PLHIV travelled an additional 1.9 km (95% CI (0.6, 3.2 km), p=0.004) to access healthcare compared with those not living with HIV, and they were 56% less likely to access healthcare at the nearest health facility to their residence, so long as that facility lacked antiretroviral therapy (ART) services (aRR=0.44, 95% CI (0.24 to 0.83), p=0.011). We found no evidence that PLHIV travelled further for care if the nearest facility supplies ART services (aRR=0.95, 95% CI (0.86 to 1.05), p=0.328). Among those who reported uptake of care at one of two facilities on the island that provides ART (81% of PLHIV and 68% of HIV-negative individuals), PLHIV tended to seek care at a higher tiered facility that provides ART, even when this facility was not their closest facility (30% of PLHIV travelled further than the closest ART facility compared with 16% of HIV-negative individuals), and travelled an additional 2.2 km (p=0.001) to access that facility, relative to HIV-negative individuals (aRR=1.91, 95% CI (1.00 to 3.65), p=0.05). Among PLHIV, residential distance was associated with access to facilities providing ART (RR=0

  18. Missed diagnosis of stroke in the emergency department: a cross-sectional analysis of a large population-based sample

    PubMed Central

    Moy, Ernest; Valente, Ernest; Coffey, Rosanna; Hines, Anika L.

    2017-01-01

    Background Some cerebrovascular events are not diagnosed promptly, potentially resulting in death or disability from missed treatments. We sought to estimate the frequency of missed stroke and examine associations with patient, emergency department (ED), and hospital characteristics. Methods Cross-sectional analysis using linked inpatient discharge and ED visit records from the 2009 Healthcare Cost and Utilization Project State Inpatient Databases and 2008–2009 State ED Databases across nine US states. We identified adult patients admitted for stroke with a treat-and-release ED visit in the prior 30 days, considering those given a non-cerebrovascular diagnosis as probable (benign headache or dizziness diagnosis) or potential (any other diagnosis) missed strokes. Results There were 23,809 potential and 2243 probable missed strokes representing 12.7% and 1.2% of stroke admissions, respectively. Missed hemorrhages (n = 406) were linked to headache while missed ischemic strokes (n = 1435) and transient ischemic attacks (n = 402) were linked to headache or dizziness. Odds of a probable misdiagnosis were lower among men (OR 0.75), older individuals (18–44 years [base]; 45–64:OR 0.43; 65–74:OR 0.28; ≥ 75:OR 0.19), and Medicare (OR 0.66) or Medicaid (OR 0.70) recipients compared to privately insured patients. Odds were higher among Blacks (OR 1.18), Asian/Pacific Islanders (OR 1.29), and Hispanics (OR 1.30). Odds were higher in non-teaching hospitals (OR 1.45) and low-volume hospitals (OR 1.57). Conclusions We estimate 15,000–165,000 misdiagnosed cerebrovascular events annually in US EDs, disproportionately presenting with headache or dizziness. Physicians evaluating these symptoms should be particularly attuned to the possibility of stroke in younger, female, and non-White patients.

  19. A geographical information system-based analysis of cancer mortality and population exposure to coal mining activities in West Virginia, United States of America.

    PubMed

    Hendryx, Michael; Fedorko, Evan; Anesetti-Rothermel, Andrew

    2010-05-01

    Cancer incidence and mortality rates are high in West Virginia compared to the rest of the United States of America. Previous research has suggested that exposure to activities of the coal mining industry may contribute to elevated cancer mortality, although exposure measures have been limited. This study tests alternative specifications of exposure to mining activity to determine whether a measure based on location of mines, processing plants, coal slurry impoundments and underground slurry injection sites relative to population levels is superior to a previously-reported measure of exposure based on tons mined at the county level, in the prediction of age-adjusted cancer mortality rates. To this end, we utilize two geographical information system (GIS) techniques--exploratory spatial data analysis and inverse distance mapping--to construct new statistical analyses. Total, respiratory and "other" age-adjusted cancer mortality rates in West Virginia were found to be more highly associated with the GIS-exposure measure than the tonnage measure, before and after statistical control for smoking rates. The superior performance of the GIS measure, based on where people in the state live relative to mining activity, suggests that activities of the industry contribute to cancer mortality. Further confirmation of observed phenomena is necessary with person-level studies, but the results add to the body of evidence that coal mining poses environmental risks to population health in West Virginia.

  20. Comparative Outcome Analysis of Penicillin-Based Versus Fluoroquinolone-Based Antibiotic Therapy for Community-Acquired Pneumonia: A Nationwide Population-Based Cohort Study.

    PubMed

    Wang, Chi-Chuan; Lin, Chia-Hui; Lin, Kuan-Yin; Chuang, Yu-Chung; Sheng, Wang-Huei

    2016-02-01

    Community-acquired pneumonia (CAP) is a common but potentially life-threatening condition, but limited information exists on the effectiveness of fluoroquinolones compared to β-lactams in outpatient settings. We aimed to compare the effectiveness and outcomes of penicillins versus respiratory fluoroquinolones for CAP at outpatient clinics.This was a claim-based retrospective cohort study. Patients aged 20 years or older with at least 1 new pneumonia treatment episode were included, and the index penicillin or respiratory fluoroquinolone therapies for a pneumonia episode were at least 5 days in duration. The 2 groups were matched by propensity scores. Cox proportional hazard models were used to compare the rates of hospitalizations/emergence service visits and 30-day mortality. A logistic model was used to compare the likelihood of treatment failure between the 2 groups.After propensity score matching, 2622 matched pairs were included in the final model. The likelihood of treatment failure of fluoroquinolone-based therapy was lower than that of penicillin-based therapy (adjusted odds ratio [AOR], 0.88; 95% confidence interval [95%CI], 0.77-0.99), but no differences were found in hospitalization/emergence service (ES) visits (adjusted hazard ratio [HR], 1.27; 95% CI, 0.92-1.74) and 30-day mortality (adjusted HR, 0.69; 95% CI, 0.30-1.62) between the 2 groups.The likelihood of treatment failure of fluoroquinolone-based therapy was lower than that of penicillin-based therapy for CAP on an outpatient clinic basis. However, this effect may be marginal. Further investigation into the comparative effectiveness of these 2 treatment options is warranted.

  1. Population Viability Analysis of Riverine Fishes

    SciTech Connect

    Bates, P.; Chandler, J.; Jager, H.I.; Lepla, K.; Van Winkle, W.

    1999-04-12

    Many utilities face conflkts between two goals: cost-efficient hydropower generation and protecting riverine fishes. Research to develop ecological simulation tools that can evaluate alternative mitigation strategies in terms of their benefits to fish populations is vital to informed decision-making. In this paper, we describe our approach to population viability analysis of riverine fishes in general and Snake River white sturgeon in particular. We are finding that the individual-based modeling approach used in previous in-stream flow applications is well suited to addressing questions about the viability of species of concern for several reasons. Chief among these are: (1) the abiIity to represent the effects of individual variation in life history characteristics on predicted population viabili~, (2) the flexibili~ needed to quanti~ the ecological benefits of alternative flow management options by representing spatial and temporal variation in flow and temperaturty and (3) the flexibility needed to quantifi the ecological benefits of non-flow related manipulations (i.e., passage, screening and hatchery supplementation).

  2. Impact of Boost Radiation in the Treatment of Ductal Carcinoma In Situ: A Population-Based Analysis

    SciTech Connect

    Rakovitch, Eileen; Narod, Steven A.; Nofech-Moses, Sharon; Hanna, Wedad; Thiruchelvam, Deva; Saskin, Refik; Taylor, Carole; Tuck, Alan; Youngson, Bruce; Miller, Naomi; Done, Susan J.; Sengupta, Sandip; Elavathil, Leela; Jani, Prashant A.; Bonin, Michel; Metcalfe, Stephanie; Paszat, Lawrence

    2013-07-01

    Purpose: To report the outcomes of a population of women with ductal carcinoma in situ (DCIS) treated with breast-conserving surgery and radiation and to evaluate the independent effect of boost radiation on the development of local recurrence. Methods and Materials: All women diagnosed with DCIS and treated with breast-conserving surgery and radiation therapy in Ontario from 1994 to 2003 were identified. Treatments and outcomes were identified through administrative databases and validated by chart review. The impact of boost radiation on the development of local recurrence was determined using survival analyses. Results: We identified 1895 cases of DCIS that were treated by breast-conserving surgery and radiation therapy; 561 patients received boost radiation. The cumulative 10-year rate of local recurrence was 13% for women who received boost radiation and 12% for those who did not (P=.3). The 10-year local recurrence-free survival (LRFS) rate among women who did and who did not receive boost radiation was 88% and 87%, respectively (P=.27), 94% and 93% for invasive LRFS (P=.58), and was 95% and 93% for DCIS LRFS (P=.31). On multivariable analyses, boost radiation was not associated with a lower risk of local recurrence (hazard ratio = 0.82, 95% confidence interval 0.59-1.15) (P=.25). Conclusions: Among a population of women treated with breast-conserving surgery and radiation for DCIS, additional (boost) radiation was not associated with a lower risk of local or invasive recurrence.

  3. Responses of retinal ganglion cells to extracellular electrical stimulation, from single cell to population: model-based analysis.

    PubMed

    Tsai, David; Chen, Spencer; Protti, Dario A; Morley, John W; Suaning, Gregg J; Lovell, Nigel H

    2012-01-01

    Retinal ganglion cells (RGCs), which survive in large numbers following neurodegenerative diseases, could be stimulated with extracellular electric pulses to elicit artificial percepts. How do the RGCs respond to electrical stimulation at the sub-cellular level under different stimulus configurations, and how does this influence the whole-cell response? At the population level, why have experiments yielded conflicting evidence regarding the extent of passing axon activation? We addressed these questions through simulations of morphologically and biophysically detailed computational RGC models on high performance computing clusters. We conducted the analyses on both large-field RGCs and small-field midget RGCs. The latter neurons are unique to primates. We found that at the single cell level the electric potential gradient in conjunction with neuronal element excitability, rather than the electrode center location per se, determined the response threshold and latency. In addition, stimulus positioning strongly influenced the location of RGC response initiation and subsequent activity propagation through the cellular structure. These findings were robust with respect to inhomogeneous tissue resistivity perpendicular to the electrode plane. At the population level, RGC cellular structures gave rise to low threshold hotspots, which limited axonal and multi-cell activation with threshold stimuli. Finally, due to variations in neuronal element excitability over space, following supra-threshold stimulation some locations favored localized activation of multiple cells, while others favored axonal activation of cells over extended space.

  4. Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers.

    PubMed

    Zhou, L X; Xiao, Y; Xia, W; Yang, Y D

    2015-12-08

    Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species.

  5. Survival of multiple myeloma patients in the era of novel therapies confirms the improvement in patients younger than 75 years: a population-based analysis.

    PubMed

    Pozzi, Samantha; Marcheselli, Luigi; Bari, Alessia; Liardo, Eliana V; Marcheselli, Raffaella; Luminari, Stefano; Quaresima, Micol; Cirilli, Claudia; Ferri, Paola; Federico, Massimo; Sacchi, Stefano

    2013-10-01

    Novel treatments for multiple myeloma (MM) have shown promising results in clinical trials, but the advantage in unselected patients is still unclear. In order to evaluate whether novel therapies impact survival of MM patients, we performed a population-based analysis on data collected by the Modena Cancer Registry from 1989 to 2009. The analysis evaluated 1206 newly diagnosed MM patients collected in the years 1988-96 (conventional therapy), 1997-05 (high dose melphalan and autologous transplant), and 2006-09 (novel agents era). Both relative survival (RS) and overall survival (OS) improved over the years, but not equally in the three groups. For patients aged <65 years, RS improved in 1997-05 and 2006-09 compared with previous years and a trend to improvement was observed from 1997-05 to 2006-09. For patients aged 65-74 years, RS improved significantly in 2006-09 compared with 1988-96 and 1997-05. No amelioration was observed for patients 75+ years old. OS confirmed RS. In conclusion, the survival of MM patients aged <65 and, in particular, 65-74 years, has improved over time, especially after 2006. This observation provides circumstantial evidence that novel therapies might impact patient survival. Despite the limits of this study, these data refer to an unselected population, giving a picture of every day clinical practice.

  6. Cost-effectiveness of chemotherapy combined with thoracic radiotherapy versus chemotherapy alone for limited stage small cell lung cancer: A population-based propensity-score matched analysis

    PubMed Central

    Chien, Chun-Ru; Hsia, Te-Chun; Chen, Chih-Yi

    2014-01-01

    Background The addition of thoracic radiotherapy improves the outcome of limited stage small cell lung cancer (LS-SCLC), however, the cost-effectiveness of this process has never been reported. We aimed to estimate the short-term cost-effectiveness of chemotherapy combined with thoracic radiotherapy (C-TRT) versus chemotherapy alone (C/T) for LS-SCLC patients from the payer's perspective (Taiwan National Health Insurance). Methods We identified LS-SCLC patients diagnosed within 2007–2009 through a comprehensive population-based database containing cancer and death registries, and reimbursement data. The duration of interest was one year within diagnosis. We included potential confounding covariables through literature searching and our own experience, and used a propensity score to construct a 1:1 population for adjustment. We used a net benefit (NB) approach to evaluate the cost-effectiveness at various willingness-to-pay (WTP) levels. Sensitivity analysis regarding potential unmeasured confounder(s) was performed. Results Our study population constituted 74 patients. The mean cost (2013 USD) and survival (year) was higher for C-TRT (42 439 vs. 28 357; 0.94 vs. 0.88). At the common WTP level (50 000 USD/life-year), C-TRT was not cost effective (incremental NB − 11 082) and the probability for C-TRT to be cost effective (i.e. positive net benefit) was 0.005. The result was moderately sensitive to potential unmeasured confounder(s) in sensitivity analysis. Conclusions We provide evidence that when compared to C/T, C-TRT is effective in improving survival, but is not cost-effective in the short-term at a common WTP level from a payer's perspective. This information should be considered by clinicians when discussing thoracic radiotherapy with their LS-SCLC patients. PMID:26767048

  7. Performance and Cost-Effectiveness of Computed Tomography Lung Cancer Screening Scenarios in a Population-Based Setting: A Microsimulation Modeling Analysis in Ontario, Canada

    PubMed Central

    ten Haaf, Kevin; Tammemägi, Martin C.; Bondy, Susan J.; van der Aalst, Carlijn M.; Gu, Sumei; de Koning, Harry J.

    2017-01-01

    Background The National Lung Screening Trial (NLST) results indicate that computed tomography (CT) lung cancer screening for current and former smokers with three annual screens can be cost-effective in a trial setting. However, the cost-effectiveness in a population-based setting with >3 screening rounds is uncertain. Therefore, the objective of this study was to estimate the cost-effectiveness of lung cancer screening in a population-based setting in Ontario, Canada, and evaluate the effects of screening eligibility criteria. Methods and Findings This study used microsimulation modeling informed by various data sources, including the Ontario Health Insurance Plan (OHIP), Ontario Cancer Registry, smoking behavior surveys, and the NLST. Persons, born between 1940 and 1969, were examined from a third-party health care payer perspective across a lifetime horizon. Starting in 2015, 576 CT screening scenarios were examined, varying by age to start and end screening, smoking eligibility criteria, and screening interval. Among the examined outcome measures were lung cancer deaths averted, life-years gained, percentage ever screened, costs (in 2015 Canadian dollars), and overdiagnosis. The results of the base-case analysis indicated that annual screening was more cost-effective than biennial screening. Scenarios with eligibility criteria that required as few as 20 pack-years were dominated by scenarios that required higher numbers of accumulated pack-years. In general, scenarios that applied stringent smoking eligibility criteria (i.e., requiring higher levels of accumulated smoking exposure) were more cost-effective than scenarios with less stringent smoking eligibility criteria, with modest differences in life-years gained. Annual screening between ages 55–75 for persons who smoked ≥40 pack-years and who currently smoke or quit ≤10 y ago yielded an incremental cost-effectiveness ratio of $41,136 Canadian dollars ($33,825 in May 1, 2015, United States dollars) per

  8. Molecular variation and expansion of a rice black-streaked dwarf virus population based on analysis of segment 1 in Jining, China.

    PubMed

    Zhou, Yu; Meng, Qingchang; Chen, Yanping; Wu, Jirong; Hao, Zhuanfang; Wang, Zhenhua; Zhang, Degui; Li, Mingshun; Yong, Hongjun; Zhang, Shihuang; Li, Xinhai; Weng, Jianfeng

    2016-12-01

    To analyze the variation in rice black-streaked dwarf virus (RBSDV) in an area with high incidence of maize rough dwarf disease (MRDD), the RBSDV S1 segment in a collection of 100 maize isolates (sample population A100) from Jining, Shandong Province, was sequenced. An additional 21 maize and rice isolates (subpopulation B21) that were sampled from nine other geographic locations in China in 2012 and 2013 were used as a control. A total of 914 nucleotide mutations, including 239 singleton variable and 675 parsimony-informative sites were detected among the segment 1 (S1) sequences from A100. A total of 614 nucleotide mutation sites including 164 singleton variable and 450 parsimony-informative sites were detected among the S1 sequences from B21, while 97.55 % of the parsimony-informative sites from B21 were also detected in A100. The nucleotide sequence diversities of A100 (π = 0.0479) and B21 (π = 0.0396) were significantly different (P = 0.0002) but showed similar trends. Phylogenetic analysis showed that the 121 RBSDV isolates could be classified into two groups based on their S1 sequences, independent of subpopulation, with a combination of host species and locations. A100 and B21 were under the same level of negative and purifying selection, with Ka/Ks ratios of 0.0337 and 0.0369, respectively. The combined RBSDV population, including 121 isolates, was expanding, with negative values for Tajima's D, Fu and Li's D, and Fu and Li's F in both A100 and B21, except Tajima's D in A100. Based on S1, the RBSDV population in China has long-term phytogeographic stability, and there do not appear to be any newly-emerging strains.

  9. Microsatellite data analysis for population genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of ...

  10. A Powerful Procedure for Pathway-Based Meta-analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations

    PubMed Central

    Zhang, Han; Wheeler, William; Hyland, Paula L.; Yang, Yifan; Shi, Jianxin; Chatterjee, Nilanjan; Yu, Kai

    2016-01-01

    Meta-analysis of multiple genome-wide association studies (GWAS) has become an effective approach for detecting single nucleotide polymorphism (SNP) associations with complex traits. However, it is difficult to integrate the readily accessible SNP-level summary statistics from a meta-analysis into more powerful multi-marker testing procedures, which generally require individual-level genetic data. We developed a general procedure called Summary based Adaptive Rank Truncated Product (sARTP) for conducting gene and pathway meta-analysis that uses only SNP-level summary statistics in combination with genotype correlation estimated from a panel of individual-level genetic data. We demonstrated the validity and power advantage of sARTP through empirical and simulated data. We conducted a comprehensive pathway-based meta-analysis with sARTP on type 2 diabetes (T2D) by integrating SNP-level summary statistics from two large studies consisting of 19,809 T2D cases and 111,181 controls with European ancestry. Among 4,713 candidate pathways from which genes in neighborhoods of 170 GWAS established T2D loci were excluded, we detected 43 T2D globally significant pathways (with Bonferroni corrected p-values < 0.05), which included the insulin signaling pathway and T2D pathway defined by KEGG, as well as the pathways defined according to specific gene expression patterns on pancreatic adenocarcinoma, hepatocellular carcinoma, and bladder carcinoma. Using summary data from 8 eastern Asian T2D GWAS with 6,952 cases and 11,865 controls, we showed 7 out of the 43 pathways identified in European populations remained to be significant in eastern Asians at the false discovery rate of 0.1. We created an R package and a web-based tool for sARTP with the capability to analyze pathways with thousands of genes and tens of thousands of SNPs. PMID:27362418

  11. Two-compartmental population balance modeling of a pulsed spray fluidized bed granulation based on computational fluid dynamics (CFD) analysis.

    PubMed

    Liu, Huolong; Li, Mingzhong

    2014-11-20

    In this work a two-compartmental population balance model (TCPBM) was proposed to model a pulsed top-spray fluidized bed granulation. The proposed TCPBM considered the spatially heterogeneous granulation mechanisms of the granule growth by dividing the granulator into two perfectly mixed zones of the wetting compartment and drying compartment, in which the aggregation mechanism was assumed in the wetting compartment and the breakage mechanism was considered in the drying compartment. The sizes of the wetting and drying compartments were constant in the TCPBM, in which 30% of the bed was the wetting compartment and 70% of the bed was the drying compartment. The exchange rate of particles between the wetting and drying compartments was determined by the details of the flow properties and distribution of particles predicted by the computational fluid dynamics (CFD) simulation. The experimental validation has shown that the proposed TCPBM can predict evolution of the granule size and distribution within the granulator under different binder spray operating conditions accurately.

  12. Temporal trends in conduit urinary diversion with concomitant cystectomy for benign indications: a population-based analysis

    PubMed Central

    Brown, Elizabeth Timbrook; Osborn, David; Mock, Stephen; Ni, Shenghua; Graves, Amy J.; Milam, Laurel; Milam, Douglas; Kaufman, Melissa; Dmochowski, Roger; Reynolds, W. Stuart

    2016-01-01

    Objectives To describe national trends in cystectomy at the time of urinary diversion for benign indications. Multiple practice patterns exist regarding the necessity of concomitant cystectomy with urinary diversion for benign end-stage lower urinary tract dysfunction. Beyond single institution reports, limited data is available to describe how concurrent cystectomy is employed on a national level. Methods A representative sample of patients undergoing urinary diversion for benign indications with or without concurrent cystectomy was identified from the Healthcare Cost and Utilization Project Nationwide Inpatient Sample from 1998–2011. Using multivariate logistic regression models, we identified hospital and patient-level characteristics associated with concomitant cystectomy with urinary diversion. Results There was an increase in the proportion of concomitant cystectomy at the time of urinary diversion from 20% to 35% (p<0.001) between 1998 and 2011. The increase in simultaneous cystectomy over time occurred at teaching hospitals (vs. community hospitals), in older patients, in male patients, in the Medicare population (vs. private insurance and Medicaid), and in those with certain diagnoses. Conclusions There has been an overall increase in the use of cystectomy at the time of urinary diversion for benign indications on a national level, though the indications driving this clinical decision appear inconsistent. PMID:27374730

  13. Association between fluid intake and kidney function, and survival outcomes analysis: a nationwide population-based study

    PubMed Central

    Wu, Li-Wei; Chen, Wei-Liang; Liaw, Fang-Yih; Sun, Yu-Shan; Yang, Hui-Fang; Wang, Chung-Ching; Lin, Chien-Ming; Tsao, Yu-Tzu

    2016-01-01

    Objectives Fluid intake, one of the most common daily activities, has not been well studied in chronic kidney disease (CKD) populations, and clinical outcomes are rarely addressed. The aim of this nationwide study is to explore the influence of daily fluid intake on cardiovascular and all-cause mortality and its association with renal function. Design Observational cohort study. Participants In all, 2182 participants aged more than 20 years participated in the Third National Health and Nutrition Examination Survey (1988–1994). Main outcome measures Survival outcomes in patients with or without CKD, using multiple variable adjusted Cox proportional hazard models. Results In a longitudinal survey with a median follow-up length of 15.4 years, 1080 participants died and 473 cardiovascular deaths were recorded. For all-cause mortality in the CKD group, individuals in the highest quartile of fluid intake (≧3.576 L/day) had better survival outcomes than those in the lowest quartile of fluid intake (≤2.147 L/day) (p=0.029) after adjustment of several pertinent variables. Conclusions Although the interpretation of this observational study was limited by the failure to identify the compositions of ingested fluids, adequate hydration may offer some advantages in patients with CKD. However, the underlying pathophysiological mechanisms of the responses of normal and injured kidneys to chronic changes in fluid consumption warrant further investigation. PMID:27173809

  14. Trend analysis and survival of primary gallbladder cancer in the United States: a 1973-2009 population-based study.

    PubMed

    Rahman, Rubayat; Simoes, Eduardo J; Schmaltz, Chester; Jackson, Christian S; Ibdah, Jamal A

    2017-03-20

    Primary gallbladder cancer is an aggressive and uncommon cancer with poor outcomes. Our study examines epidemiology, trend, and survival of gallbladder cancer in the United States from 1973 to 2009. We utilized the Surveillance Epidemiology and End Results database (SEER). Frequency and rate analyses on demographics, stage, and survival were compared among non-Hispanic whites, Hispanics, African American, and Asian/Pacific Islanders. A total of 18,124 cases were reported in SEER from 1973 to 2009 comprising 1.4% of all reported gastrointestinal cancers. Gallbladder cancer was more common in females than males (71 vs. 29%, respectively). The age-adjusted incidence rate was 1.4 per 100,000, significantly higher in females than males (1.7 vs. 1.0). Trend analysis showed that the incidence rate has been decreasing over the last three decades for males. However, among females, the incidence rate had decreased from 1973 to mid-90s but has remained stable since then. Trend analysis for stage at diagnosis showed that the proportion of late-stage cases has been increasing significantly since 2001 after a decreasing pattern since 1973. Survival has improved considerably over time, and survival is better in females than males and in Asian/Pacific Islanders than other racial groups. The highest survival was in patients who received both surgery and radiation. Trend analysis revealed a recent increase of the incidence of late-stage gallbladder cancer. Highest survival was associated with receiving both surgery and radiation.

  15. Genetic variability and phylogenetic analysis of Han population from Guanzhong region of China based on 21 non-CODIS STR loci.

    PubMed

    Zhang, Yu-Dang; Tang, Xiao-Li; Meng, Hao-Tian; Wang, Hong-Dan; Jin, Rui; Yang, Chun-Hua; Yan, Jiang-Wei; Yang, Guang; Liu, Wen-Juan; Shen, Chun-Mei; Zhu, Bo-Feng

    2015-03-09

    In the present study, we presented the population genetic data and their forensic parameters of 21 non-CODIS autosomal STR loci in Chinese Guanzhong Han population. A total of 166 alleles were observed with corresponding allelic frequencies ranging from 0.0018 to 0.5564. No STR locus was observed to deviate from the Hardy-Weinberg equilibrium and linkage disequilibriums after applying Bonferroni correction. The cumulative power of discrimination and probability of exclusion of all the 21 STR loci were 0.99999999999999999993814 and 0.999998184, respectively. The results of genetic distances, phylogenetic trees and principal component analysis revealed that the Guanzhong Han population had a closer relationship with Ningxia Han, Tujia and Bai groups than other populations tested. In summary, these 21 STR loci showed a high level of genetic polymorphisms for the Guanzhong Han population and could be used for forensic applications and the studies of population genetics.

  16. Genetic Variability and Phylogenetic Analysis of Han Population from Guanzhong Region of China based on 21 non-CODIS STR Loci

    PubMed Central

    Zhang, Yu-Dang; Tang, Xiao-Li; Meng, Hao-Tian; Wang, Hong-Dan; Jin, Rui; Yang, Chun-Hua; Yan, Jiang-Wei; Yang, Guang; Liu, Wen-Juan; Shen, Chun-Mei; Zhu, Bo-Feng

    2015-01-01

    In the present study, we presented the population genetic data and their forensic parameters of 21 non-CODIS autosomal STR loci in Chinese Guanzhong Han population. A total of 166 alleles were observed with corresponding allelic frequencies ranging from 0.0018 to 0.5564. No STR locus was observed to deviate from the Hardy-Weinberg equilibrium and linkage disequilibriums after applying Bonferroni correction. The cumulative power of discrimination and probability of exclusion of all the 21 STR loci were 0.99999999999999999993814 and 0.999998184, respectively. The results of genetic distances, phylogenetic trees and principal component analysis revealed that the Guanzhong Han population had a closer relationship with Ningxia Han, Tujia and Bai groups than other populations tested. In summary, these 21 STR loci showed a high level of genetic polymorphisms for the Guanzhong Han population and could be used for forensic applications and the studies of population genetics. PMID:25747708

  17. A Population-Based Analysis of Ethnic Differences in Admission to the Intensive Care Unit after Stroke

    PubMed Central

    Fletcher, Jeffrey J.; Morgenstern, Lewis B.; Lisabeth, Lynda D.; Sánchez, Brisa N.; Skolarus, Lesli E.; Smith, Melinda A.; Garcia, Nelda M.; Zahuranec, Darin B.

    2012-01-01

    Background Mexican Americans (MAs) have shown lower post-stroke mortality compared to non-Hispanic whites (NHWs). Limited evidence suggests race/ethnic differences exist in intensive care unit (ICU)admissions following stroke. Our objective was to investigate the association of ethnicity with admission to the ICU following stroke. Methods Cases of intracerebral hemorrhage and acute ischemic stroke were prospectively ascertained as part of the Brain Attack Surveillance in Corpus Christi (BASIC) project for the period January, 2000 through December, 2009. Logistic regression models fitted within the generalized additive model framework were used to test associations between ethnicity and ICU admission and potential confounders. An interaction term between age and ethnicity was investigated in the final model. Results A total 1,464 cases were included in analysis. MAs were younger, more likely to have diabetes, and less likely to have atrial fibrillation, health insurance, or high school diploma than NHWs. On unadjusted analysis, there was a trend toward MAs being more likely to be admitted to ICU than NHWs (34.6% versus 30.3%; OR=1.22; 95% CI 0.98–1.52; p=0.08). However, on adjusted analysis, no overall association between MA ethnicity and ICU admission (OR=1.13; 95% CI 0.85–1.50) was found. When an interaction term for age and ethnicity was added to this model, there was only borderline evidence for effect modification by age of the ethnicity/ICU relationship (p=0.16). Conclusions No overall association between ethnicity and ICU admission was observed in this community. ICU utilization alone does not likely explain ethnic differences in survival following stroke between MAs and NHWs. PMID:22892883

  18. Population Analysis: Communicating About Anthropometry in Context

    NASA Technical Reports Server (NTRS)

    Thaxton, Sherry; Rajulu, Sudhakar

    2009-01-01

    This slide presentation reviews the importance of communications about anthropometry and population analysis in particular for the design of aerospace systems. The difficulty of providing anthropometric accomodation an entire range of the population is reviewed, and the importance of communication of the issues with human system integration is emphasized, and the analysis of population as it applies to existing human factors methodologies is a novel way to assist with the communication. The issues of space suit design and anthropometry is reviewed as an example.

  19. Facility-Based Delivery during the Ebola Virus Disease Epidemic in Rural Liberia: Analysis from a Cross-Sectional, Population-Based Household Survey

    PubMed Central

    Griffiths, Thomas; Kanjee, Zahir; Battistoli, Dale; Dorr, Lorenzo; Lorenzen, Breeanna; Thomson, Dana R.; Waters, Ami; Roberts, Ruth; Smith, Wilmot L.; Kraemer, John D.

    2016-01-01

    Background The Ebola virus disease (EVD) epidemic has threatened access to basic health services through facility closures, resource diversion, and decreased demand due to community fear and distrust. While modeling studies have attempted to estimate the impact of these disruptions, no studies have yet utilized population-based survey data. Methods and Findings We conducted a two-stage, cluster-sample household survey in Rivercess County, Liberia, in March–April 2015, which included a maternal and reproductive health module. We constructed a retrospective cohort of births beginning 4 y before the first day of survey administration (beginning March 24, 2011). We then fit logistic regression models to estimate associations between our primary outcome, facility-based delivery (FBD), and time period, defined as the pre-EVD period (March 24, 2011–June 14, 2014) or EVD period (June 15, 2014–April 13, 2015). We fit both univariable and multivariable models, adjusted for known predictors of facility delivery, accounting for clustering using linearized standard errors. To strengthen causal inference, we also conducted stratified analyses to assess changes in FBD by whether respondents believed that health facility attendance was an EVD risk factor. A total of 1,298 women from 941 households completed the survey. Median age at the time of survey was 29 y, and over 80% had a primary education or less. There were 686 births reported in the pre-EVD period and 212 in the EVD period. The unadjusted odds ratio of facility-based delivery in the EVD period was 0.66 (95% confidence interval [CI] 0.48–0.90, p-value = 0.010). Adjustment for potential confounders did not change the observed association, either in the principal model (adjusted odds ratio [AOR] = 0.70, 95%CI 0.50–0.98, p = 0.037) or a fully adjusted model (AOR = 0.69, 95%CI 0.50–0.97, p = 0.033). The association was robust in sensitivity analyses. The reduction in FBD during the EVD period was observed among

  20. Metastatic lymph node ratio can further stratify risk for mortality in medullary thyroid cancer patients: A population-based analysis

    PubMed Central

    Lu, Zhong-wu; Liao, Tian; Wen, Duo; Sun, Guo-hua; Li, Duan-shu; Ji, Qing-hai

    2016-01-01

    Medullary thyroid cancer (MTC) has a propensity to cervical lymph node metastases (LNM). Recent studies have shown that both the number of involved lymph nodes (LNs) and the metastatic lymph node ratio (MLNR) confer prognostic information. This study was to determine the predictive value of MLNR on cancer-specific survival (CSS) in SEER (Surveillance, Epidemiology and End Results)-registered MTC patients treated with thyroidectomy and lymphadenectomy between 1991 and 2012, investigate the cutoff points for MLNR in stratifying risk of mortality and provide evidence for selection of appropriate treatment strategies. X-tile program determined 0.5 as optimal cut-off value for MLNR in terms of CSS in 890 MTC patients. According to multivariate Cox regression analysis, MLNR (0.50–1.00) is a significant independent prognostic factor for CSS (hazard ratio 2.161, 95% confidence interval 1.327–3.519, p=0.002). MLNR (0.50–1.00) has a greater prognostic impact on CSS in female, non-Hispanic white, T3/4, N1b and M1 patients. The lymph node yield (LNY) influences the effect of MLNR on CSS; LNY ≥9 results in MLNR (0.50–1.00) having a higher HR for CSS than MLNR (0.00-0.49). In conclusion, higher MLNRs predict poorer survival in MTC patients. Eradication of involved nodes ensures accurate staging and maximizes the ability of MLNR to predict prognosis. PMID:27588396

  1. Empirical and targeted therapy of candidemia with fluconazole versus echinocandins: a propensity score-derived analysis of a population-based, multicentre prospective cohort.

    PubMed

    López-Cortés, L E; Almirante, B; Cuenca-Estrella, M; Garnacho-Montero, J; Padilla, B; Puig-Asensio, M; Ruiz-Camps, I; Rodríguez-Baño, J

    2016-08-01

    We compared the clinical efficacy of fluconazole and echinocandins in the treatment of candidemia in real practice. The CANDIPOP study is a prospective, population-based cohort study on candidemia carried out between May 2010 and April 2011 in 29 Spanish hospitals. Using strict inclusion criteria, we separately compared the impact of empirical and targeted therapy with fluconazole or echinocandins on 30-day mortality. Cox regression, including a propensity score (PS) for receiving echinocandins, stratified analysis on the PS quartiles and PS-based matched analyses, were performed. The empirical and targeted therapy cohorts comprised 316 and 421 cases, respectively; 30-day mortality was 18.7% with fluconazole and 33.9% with echinocandins (p 0.02) in the empirical therapy group and 19.8% with fluconazole and 27.7% with echinocandins (p 0.06) in the targeted therapy group. Multivariate Cox regression analysis including PS showed that empirical therapy with fluconazole was associated with better prognosis (adjusted hazard ratio 0.38; 95% confidence interval 0.17-0.81; p 0.01); no differences were found within each PS quartile or in cases matched according to PS. Targeted therapy with fluconazole did not show a significant association with mortality in the Cox regression analysis (adjusted hazard ratio 0.77; 95% confidence interval 0.41-1.46; p 0.63), in the PS quartiles or in PS-matched cases. The results were similar among patients with severe sepsis and septic shock. Empirical or targeted treatment with fluconazole was not associated with increased 30-day mortality compared to echinocandins among adults with candidemia.

  2. Cultivation-independent population analysis of bacterial endophytes in three potato varieties based on eubacterial and Actinomycetes-specific PCR of 16S rRNA genes.

    PubMed

    Sessitsch, Angela; Reiter, Birgit; Pfeifer, Ulrike; Wilhelm, Eva

    2002-01-01

    Abstract Endophytic bacteria are ubiquitous in most plants and colonise plants without exhibiting pathogenicity. Studies on the diversity of bacterial endophytes have been mainly approached by characterisation of isolates obtained from internal tissues. Despite the broad application of culture-independent techniques for the analysis of microbial communities in a wide range of natural habitats, little information is available on the species diversity of endophytes. In this study, microbial communities inhabiting stems, roots and tubers of three potato varieties were analysed by 16S rRNA-based techniques such as terminal restriction fragment length polymorphism analysis, denaturing gradient gel electrophoresis as well as 16S rDNA cloning and sequencing. Two individual plant experiments were conducted. In the first experiment plants suffered from light deficiency, whereas healthy and robust plants were obtained in the second experiment. Plants obtained from both experiments showed comparable endophytic populations, but healthy potato plants possessed a significantly higher diversity of endophytes than stressed plants. In addition, plant tissue and variety specific endophytes were detected. Sequence analysis of 16S rRNA genes indicated that a broad phylogenetic spectrum of bacteria is able to colonise plants internally including alpha-, beta-, and gamma-Proteobacteria, high-GC Gram-positives, microbes belonging to the Flexibacter/Cytophaga/Bacteroides group and Planctomycetales. Group-specific analysis of Actinomycetes indicated a higher abundance and diversity of Streptomyces scabiei-related species in the variety Mehlige Mühlviertler, which is known for its resistance against potato common scab caused by S. scabiei.

  3. Costs of detection bias in index-based population monitoring

    USGS Publications Warehouse

    Moore, C.T.; Kendall, W.L.

    2004-01-01

    Managers of wildlife populations commonly rely on indirect, count-based measures of the population in making decisions regarding conservation, harvest, or control. The main appeal in the use of such counts is their low material expense compared to methods that directly measure the population. However, their correct use rests on the rarely-tested but often-assumed premise that they proportionately reflect population size, i.e., that they constitute a population index. This study investigates forest management for the endangered Red-cockaded Woodpecker (Picoides borealis) and the Wood Thrush (Hylocichla mustelina) at the Piedmont National Wildlife Refuge in central Georgia, U.S.A. Optimal decision policies for a joint species objective were derived for two alternative models of Wood Thrush population dynamics. Policies were simulated under scenarios of unbiasedness, consistent negative bias, and habitat-dependent negative bias in observed Wood Thrush densities. Differences in simulation outcomes between biased and unbiased detection scenarios indicated the expected loss in resource objectives (here, forest habitat and birds) through decision-making based on biased population counts. Given the models and objective function used in our analysis, expected losses were as great as 11%, a degree of loss perhaps not trivial for applications such as endangered species management. Our analysis demonstrates that costs of uncertainty about the relationship between the population and its observation can be measured in units of the resource, costs which may offset apparent savings achieved by collecting uncorrected population counts.

  4. The Impact of Clinical, Demographic and Risk Factors on Rates of HIV Transmission: A Population-based Phylogenetic Analysis in British Columbia, Canada

    PubMed Central

    Poon, Art F. Y.; Joy, Jeffrey B.; Woods, Conan K.; Shurgold, Susan; Colley, Guillaume; Brumme, Chanson J.; Hogg, Robert S.; Montaner, Julio S. G.; Harrigan, P. Richard

    2015-01-01

    Background. The diversification of human immunodeficiency virus (HIV) is shaped by its transmission history. We therefore used a population based province wide HIV drug resistance database in British Columbia (BC), Canada, to evaluate the impact of clinical, demographic, and behavioral factors on rates of HIV transmission. Methods. We reconstructed molecular phylogenies from 27 296 anonymized bulk HIV pol sequences representing 7747 individuals in BC—about half the estimated HIV prevalence in BC. Infections were grouped into clusters based on phylogenetic distances, as a proxy for variation in transmission rates. Rates of cluster expansion were reconstructed from estimated dates of HIV seroconversion. Results. Our criteria grouped 4431 individuals into 744 clusters largely separated with respect to risk factors, including large established clusters predominated by injection drug users and more-recently emerging clusters comprising men who have sex with men. The mean log10 viral load of an individual's phylogenetic neighborhood (composed of 5 other individuals with shortest phylogenetic distances) increased their odds of appearing in a cluster by >2-fold per log10 viruses per milliliter. Conclusions. Hotspots of ongoing HIV transmission can be characterized in near real time by the secondary analysis of HIV resistance genotypes, providing an important potential resource for targeting public health initiatives for HIV prevention. PMID:25312037

  5. Short-term population-based non-linear concentration-response associations between fine particulate matter and respiratory diseases in Taipei (Taiwan): a spatiotemporal analysis.

    PubMed

    Yu, Hwa-Lung; Chien, Lung-Chang

    2016-01-01

    Fine particulate matter <2.5 μm (PM2.5) has been associated with human health issues; however, findings regarding the influence of PM2.5 on respiratory disease remain inconsistent. The short-term, population-based association between the respiratory clinic visits of children and PM2.5 exposure levels were investigated by considering both the spatiotemporal distributions of ambient pollution and clinic visit data. We applied a spatiotemporal structured additive regression model to examine the concentration-response (C-R) association between children's respiratory clinic visits and PM2.5 concentrations. This analysis was separately performed on three respiratory disease categories that were selected from the Taiwanese National Health Insurance database, which includes 41 districts in the Taipei area of Taiwan from 2005 to 2007. The findings reveal a non-linear C-R pattern of PM2.5, particularly in acute respiratory infections. However, a PM2.5 increase at relatively lower levels can elevate the same-day respiratory health risks of both preschool children (<6 years old) and schoolchildren (6-14 years old). In preschool children, same-day health risks rise when concentrations increase from 0.76 to 7.44 μg/m(3), and in schoolchildren, same-day health risks rise when concentrations increase from 0.76 to 7.52 μg/m(3). Changes in PM2.5 levels generally exhibited no significant association with same-day respiratory risks, except in instances where PM2.5 levels are extremely high, and these occurrences do exhibit a significant positive influence on respiratory health that is especially notable in schoolchildren. A significant high relative rate of respiratory clinic visits are concentrated in highly populated areas. We highlight the non-linearity of the respiratory health effects of PM2.5 on children to investigate this population-based association. The C-R relationship in this study can provide a highly valuable alternative for assessing the effects of ambient air

  6. Population-based study on infant mortality.

    PubMed

    Lima, Jaqueline Costa; Mingarelli, Alexandre Marchezoni; Segri, Neuber José; Zavala, Arturo Alejandro Zavala; Takano, Olga Akiko

    2017-03-01

    Although Brazil has reduced social, economic and health indicators disparities in the last decade, intra- and inter-regional differences in child mortality rates (CMR) persist in regions such as the state capital of Mato Grosso. This population-based study aimed to investigate factors associated with child mortality in five cohorts of live births (LB) of mothers living in Cuiabá (MT), Brazil, 2006-2010, through probabilistic linkage in 47,018 LB. We used hierarchical logistic regression analysis. Of the 617 child deaths, 48% occurred in the early neonatal period. CMR ranged from 14.6 to 12.0 deaths per thousand LB. The following remained independently associated with death: mothers without companion (OR = 1.32); low number of prenatal consultations (OR = 1.65); low birthweight (OR = 4.83); prematurity (OR = 3.05); Apgar ≤ 7 at the first minute (OR = 3.19); Apgar ≤ 7 at the fifth minute (OR = 4.95); congenital malformations (OR = 14.91) and male gender (OR = 1.26). CMR has declined in Cuiabá, however, there is need to guide public healthcare policies in the prenatal and perinatal period to reduce early neonatal mortality and further studies to identify the causes of preventable deaths.

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

    PubMed

    Fu, Yong-Bi

    2012-02-01

    Many plant disease resistance (R) genes have been cloned, but the potential of utilizing these plant R-gene genomic resources for genetic inferences of plant domestication history remains unexplored. A population-based resequencing analysis of the genomic region near the Rrs2 scald resistance gene was made in 51 accessions of wild and cultivated barley from 41 countries. Fifteen primer pairs were designed to sample the genomic region with a total length of 10 406 bp. More nucleotide diversity was found in wild (π = 0.01846) than cultivated (π = 0.01507) barley samples. Three distinct groups of 29 haplotypes were detected for all 51 samples, and they were well mixed with wild and cultivated barley samples from different countries and regions. The neutrality tests by Tajima's D were not significant, but a significant (P < 0.05) case by Fu and Li's D* and F* was found in the barley cultivar samples. The estimate of selection intensity by K(a)/K(s) was 0.691 in wild barley and 0.580 in cultivated barley. The estimate of the minimum recombination events was 16 in wild barley and 19 in cultivated barley. A coalescence simulation revealed a bottleneck intensity of 1.5 to 2 since barley domestication. Together, the domestication signal in the genomic region was weak both in human selection and domestication bottleneck.

  8. Next generation semiconductor based sequencing of bitter taste receptor genes in different pig populations and association analysis using a selective DNA pool-seq approach.

    PubMed

    Ribani, A; Bertolini, F; Schiavo, G; Scotti, E; Utzeri, V J; Dall'Olio, S; Trevisi, P; Bosi, P; Fontanesi, L

    2017-02-01

    Taste perception in animals affects feed intake and may influence production traits. In particular, bitter is sensed by receptors encoded by the family of TAS2R genes. In this research, using a DNA pool-seq approach coupled with next generation semiconductor based target resequencing, we analysed nine porcine TAS2R genes (TAS2R1, TAS2R3, TAS2R4, TAS2R7, TAS2R9, TAS2R10, TAS2R16, TAS2R38 and TAS2R39) to identify variability and, at the same time, estimate single nucleotide polymorphism (SNP) allele frequencies in several populations and testing differences in an association analysis. Equimolar DNA pools were prepared for five pig breeds (Italian Duroc, Italian Landrace, Pietrain, Meishan and Casertana) and wild boars (5-10 individuals each) and for two groups of Italian Large White pigs with extreme and divergent back fat thickness (50 + 50 pigs). About 1.8 million reads were obtained by sequencing amplicons generated from these pools. A total of 125 SNPs were identified, of which 37 were missense mutations. Three of them (p.Ile53Phe and p.Trp85Leu in TAS2R4; p.Leu37Ser in TAS2R39) could have important effects on the function of these bitter taste receptors, based on in silico predictions. Variability in wild boars seems lower than that in domestic breeds potentially as a result of selective pressure in the wild towards defensive bitter taste perception. Three SNPs in TAS2R38 and TAS2R39 were significantly associated with back fat thickness. These results may be important to understand the complexity of taste perception and their associated effects that could be useful to develop nutrigenetic approaches in pig breeding and nutrition.

  9. Development of a multiplex PCR assay for fine-scale population genetic analysis of the Komodo monitor Varanus komodoensis based on 18 polymorphic microsatellite loci.

    PubMed

    Ciofi, Claudio; Tzika, Athanasia C; Natali, Chiara; Watts, Phillip C; Sulandari, Sri; Zein, Moch S A; Milinkovitch, Michel C

    2011-05-01

    Multiplex PCR assays for the coamplification of microsatellite loci allow rapid and cost-effective genetic analyses and the production of efficient screening protocols for international breeding programs. We constructed a partial genomic library enriched for di-nucleotide repeats and characterized 14 new microsatellite loci for the Komodo monitor (or Komodo dragon, Varanus komodoensis). Using these novel microsatellites and four previously described loci, we developed multiplex PCR assays that may be loaded on a genetic analyser in three separate panels. We tested the novel set of microsatellites for polymorphism using 69 individuals from three island populations and evaluated the resolving power of the entire panel of 18 loci by conducting (i) a preliminary assignment test to determine population(s) of origin and (ii) a parentage analysis for 43 captive Komodo monitors. This panel of polymorphic loci proved useful for both purposes and thus can be exploited for fine-scale population genetic analyses and as part of international captive breeding programs directed at maintaining genetically viable ex situ populations and reintroductions.

  10. Long term survival with stereotactic ablative radiotherapy (SABR) versus thoracoscopic sublobar lung resection in elderly people: national population based study with propensity matched comparative analysis

    PubMed Central

    Paul, Subroto; Lee, Paul C; Mao, Jialin; Isaacs, Abby J

    2016-01-01

    Objectives To compare cancer specific survival after thoracoscopic sublobar lung resection and stereotactic ablative radiotherapy (SABR) for tumors ≤2 cm in size and thoracoscopic resection (sublobar resection or lobectomy) and SABR for tumors ≤5 cm in size. Design National population based retrospective cohort study with propensity matched comparative analysis. Setting Surveillance, Epidemiology, and End Results (SEER) registry linked with Medicare database in the United States. Participants Patients aged ≥66 with lung cancer undergoing SABR or thoracoscopic lobectomy or sublobar resection from 1 Oct 2007 to 31 June 2012 and followed up to 31 December 2013. Main outcome measures Cancer specific survival after SABR or thoracoscopic surgery for lung cancer. Results 690 (275 (39.9%) SABR and 415 (60.1%) thoracoscopic sublobar lung resection) and 2967 (714 (24.1%) SABR and 2253 (75.9%) thoracoscopic resection) patients were included in primary and secondary analyses. The average age of the entire cohort was 76. Follow-up of the entire cohort ranged from 0 to 6.25 years, with an average of three years. In the primary analysis of patients with tumors sized ≤2 cm, 37 (13.5%) undergoing SABR and 44 (10.6%) undergoing thoracoscopic sublobar resection died from lung cancer, respectively. The cancer specific survival diverged after one year, but in the matched analysis (201 matched patients in each group) there was no significant difference between the groups (SABR v sublobar lung resection mortality: hazard ratio 1.32, 95% confidence interval 0.77 to 2.26; P=0.32). Estimated cancer specific survival at three years after SABR and thoracoscopic sublobar lung resection was 82.6% and 86.4%, respectively. The secondary analysis (643 matched patients in each group) showed that thoracoscopic resection was associated with improved cancer specific survival over SABR in patients with tumors sized ≤5 cm (SABR v resection mortality: hazard ratio 2.10, 1.52 to 2.89; P<0

  11. The Impact of Brachytherapy on Prostate Cancer-Specific Mortality for Definitive Radiation Therapy of High-Grade Prostate Cancer: A Population-Based Analysis

    SciTech Connect

    Shen Xinglei; Keith, Scott W.; Mishra, Mark V.; Dicker, Adam P.; Showalter, Timothy N.

    2012-07-15

    Purpose: This population-based analysis compared prostate cancer-specific mortality (PCSM) in a cohort of patients with high-risk prostate cancer after nonsurgical treatment with external beam radiation therapy (EBRT), brachytherapy (BT), or combination (BT + EBRT). Methods and Materials: We identified from the Surveillance, Epidemiology and End Results database patients diagnosed from 1988 through 2002 with T1-T3N0M0 prostate adenocarcinoma of poorly differentiated grade and treated with BT, EBRT, or BT + EBRT. During this time frame, the database defined high grade as prostate cancers with Gleason score 8-10, or Gleason grade 4-5 if the score was not recorded. This corresponds to a cohort primarily with high-risk prostate cancer, although some cases where only Gleason grade was recorded may have included intermediate-risk cancer. We used multivariate models to examine patient and tumor characteristics associated with the likelihood of treatment with each radiation modality and the effect of radiation modality on PCSM. Results: There were 12,745 patients treated with EBRT (73.5%), BT (7.1%), or BT + EBRT (19.4%) included in the analysis. The median follow-up time for all patients was 6.4 years. The use of BT or BT + EBRT increased from 5.1% in 1988-1992 to 31.4% in 1998-2002. Significant predictors of use of BT or BT + EBRT were younger age, later year of diagnosis, urban residence, and earlier T-stage. On multivariate analysis, treatment with either BT (hazard ratio, 0.66; 95% confidence interval, 0.49-0.86) or BT + EBRT (hazard ratio, 0.77; 95% confidence ratio, 0.66-0.90) was associated with significant reduction in PCSM compared with EBRT alone. Conclusion: In patients with high-grade prostate cancer, treatment with brachytherapy is associated with reduced PCSM compared with EBRT alone. Our results suggest that brachytherapy should be investigated as a component of definitive treatment strategies for patients with high-risk prostate cancer.

  12. Analysis of the effect of inoculum characteristics on the first stages of a growing yeast population in beer fermentations by means of an individual-based model.

    PubMed

    Ginovart, M; Prats, C; Portell, X; Silbert, M

    2011-01-01

    The yeast Saccharomyces cerevisiae has a limited replicative lifespan. The cell mass at division is partitioned unequally between a larger, old parent cell and a smaller, new daughter cell. Industrial beer fermentations maintain and reuse yeast. At the end of fermentation a portion of the yeast is 'cropped' from the vessel for 'serial repitching'. Harvesting yeast may select a population with an imbalance of young and aged individuals, but the output of any bioprocess is dependent on the physiology of each single cell in the population. Unlike continuous models, individual-based modelling is an approach that considers each microbe as an individual, a unique and discrete entity, with characteristics that change throughout its life. The aim of this contribution is to explore, by means of individual-based simulations, the effects of inoculum size and cell genealogical age on the dynamics of virtual yeast fermentation, focussing on: (1) the first stages of population growth, (2) the mean biomass evolution of the population, (3) the rate of glucose uptake and ethanol production, and (4) the biomass and genealogical age distributions. The ultimate goal is to integrate these results in order to make progress in the understanding of the composition of yeast populations and their temporal evolution in beer fermentations. Simulation results show that there is a clear influence of these initial features of the inocula on the subsequent growth dynamics. By contrasting both the individual and global properties of yeast cells and populations, we gain insight into the interrelation between these two types of data, which helps us to deal with the macroscopic behaviour observed in experimental research.

  13. Yellow fever impact on brown howler monkeys (Alouatta guariba clamitans) in Argentina: a metamodelling approach based on population viability analysis and epidemiological dynamics.

    PubMed

    Moreno, Eduardo S; Agostini, Ilaria; Holzmann, Ingrid; Di Bitetti, Mario S; Oklander, Luciana I; Kowalewski, Martín M; Beldomenico, Pablo M; Goenaga, Silvina; Martínez, Mariela; Lestani, Eduardo; Desbiez, Arnaud L J; Miller, Philip

    2015-11-01

    In South America, yellow fever (YF) is an established infectious disease that has been identified outside of its traditional endemic areas, affecting human and nonhuman primate (NHP) populations. In the epidemics that occurred in Argentina between 2007-2009, several outbreaks affecting humans and howler monkeys (Alouatta spp) were reported, highlighting the importance of this disease in the context of conservation medicine and public health policies. Considering the lack of information about YF dynamics in New World NHP, our main goal was to apply modelling tools to better understand YF transmission dynamics among endangered brown howler monkey (Alouatta guariba clamitans) populations in northeastern Argentina. Two complementary modelling tools were used to evaluate brown howler population dynamics in the presence of the disease: Vortex, a stochastic demographic simulation model, and Outbreak, a stochastic disease epidemiology simulation. The baseline model of YF disease epidemiology predicted a very high probability of population decline over the next 100 years. We believe the modelling approach discussed here is a reasonable description of the disease and its effects on the howler monkey population and can be useful to support evidence-based decision-making to guide actions at a regional level.

  14. Yellow fever impact on brown howler monkeys (Alouatta guariba clamitans) in Argentina: a metamodelling approach based on population viability analysis and epidemiological dynamics

    PubMed Central

    Moreno, Eduardo S; Agostini, Ilaria; Holzmann, Ingrid; Di Bitetti, Mario S; Oklander, Luciana I; Kowalewski, Martín M; Beldomenico, Pablo M; Goenaga, Silvina; Martínez, Mariela; Lestani, Eduardo; Desbiez, Arnaud LJ; Miller, Philip

    2015-01-01

    In South America, yellow fever (YF) is an established infectious disease that has been identified outside of its traditional endemic areas, affecting human and nonhuman primate (NHP) populations. In the epidemics that occurred in Argentina between 2007-2009, several outbreaks affecting humans and howler monkeys (Alouatta spp) were reported, highlighting the importance of this disease in the context of conservation medicine and public health policies. Considering the lack of information about YF dynamics in New World NHP, our main goal was to apply modelling tools to better understand YF transmission dynamics among endangered brown howler monkey (Alouatta guariba clamitans) populations in northeastern Argentina. Two complementary modelling tools were used to evaluate brown howler population dynamics in the presence of the disease: Vortex, a stochastic demographic simulation model, and Outbreak, a stochastic disease epidemiology simulation. The baseline model of YF disease epidemiology predicted a very high probability of population decline over the next 100 years. We believe the modelling approach discussed here is a reasonable description of the disease and its effects on the howler monkey population and can be useful to support evidence-based decision-making to guide actions at a regional level. PMID:26517499

  15. The model adaptive space shrinkage (MASS) approach: a new method for simultaneous variable selection and outlier detection based on model population analysis.

    PubMed

    Wen, Ming; Deng, Bai-Chuan; Cao, Dong-Sheng; Yun, Yong-Huan; Yang, Rui-Han; Lu, Hong-Mei; Liang, Yi-Zeng

    2016-10-07

    Variable selection and outlier detection are important processes in chemical modeling. Usually, they affect each other. Their performing orders also strongly affect the modeling results. Currently, many studies perform these processes separately and in different orders. In this study, we examined the interaction between outliers and variables and compared the modeling procedures performed with different orders of variable selection and outlier detection. Because the order of outlier detection and variable selection can affect the interpretation of the model, it is difficult to decide which order is preferable when the predictabilities (prediction error) of the different orders are relatively close. To address this problem, a simultaneous variable selection and outlier detection approach called Model Adaptive Space Shrinkage (MASS) was developed. This proposed approach is based on model population analysis (MPA). Through weighted binary matrix sampling (WBMS) from model space, a large number of partial least square (PLS) regression models were built, and the elite parts of the models were selected to statistically reassign the weight of each variable and sample. Then, the whole process was repeated until the weights of the variables and samples converged. Finally, MASS adaptively found a high performance model which consisted of the optimized variable subset and sample subset. The combination of these two subsets could be considered as the cleaned dataset used for chemical modeling. In the proposed approach, the problem of the order of variable selection and outlier detection is avoided. One near infrared spectroscopy (NIR) dataset and one quantitative structure-activity relationship (QSAR) dataset were used to test this approach. The result demonstrated that MASS is a useful method for data cleaning before building a predictive model.

  16. Association of Change of Anthropometric Measurements With Incident Type 2 Diabetes Mellitus: A Pooled Analysis of the Prospective Population-Based CARLA and SHIP Cohort Studies.

    PubMed

    Hartwig, Saskia; Greiser, Karin Halina; Medenwald, Daniel; Tiller, Daniel; Herzog, Beatrice; Schipf, Sabine; Ittermann, Till; Völzke, Henry; Müller, Grit; Haerting, Johannes; Kluttig, Alexander

    2015-08-01

    Our objective was to investigate the association of change of anthropometric measurements and the incidence of type 2 diabetes mellitus (T2DM) within a pooled sample of 2 population-based cohorts.A final sample of 1324 women and 1278 men aged 31 to 83 years from 2 prospective cohorts in Germany, the CARLA (Cardiovascular Disease - Living and Ageing in Halle) and the SHIP study (Study of Health in Pomerania), were pooled. The association of change of body weight and waist circumference (WC) with incidence of T2DM was assessed by calculating sex-specific hazard ratios (HRs). We investigated the absolute change of markers of obesity as well as change relative to the baseline value and estimated crude and adjusted HRs. Furthermore, we conducted the analyses stratified by obesity status and age (<60 vs ≥60 years) at baseline.Associations were found for both change of body weight and WC and incidence of T2DM in the crude and adjusted analyses. In the stratified study sample, those participants with a body mass index of <30 kg/m at baseline showed considerably lower HRs compared with obese women and men for both weight and WC. In the age-stratified analysis, we still found associations between change of weight and WC and incident T2DM with only marginal differences between the age groups.Our study showed associations of change of weight and WC as markers of obesity with incidence of T2DM. Keeping a healthy and primarily stable weight should be the goal for preventing the development of T2DM.

  17. A multivariate analysis of factors determining tumor progression in childhood low-grade glioma: a population-based cohort study (CCLG CNS9702)

    PubMed Central

    Stokland, Tore; Liu, Jo-Fen; Ironside, James W.; Ellison, David W.; Taylor, Roger; Robinson, Kathryn J.; Picton, Susan V.; Walker, David A.

    2010-01-01

    The purpose of this study was to identify risk factors for the progression of low-grade glioma in children from a large population-based cohort. Patient and tumor details of a national cohort of children with low-grade glioma, recruited into an international multidisciplinary clinical strategy, were subjected to univariate and multivariate analyses of progression-free survival and overall survival. From the cohort of 798 patients, 639 patients were eligible, with a median age 6.71 years (0.26–16.75 years); 49% were males; 15.9% had neurofibromatosis type 1, 63.7% pilocytic astrocytoma, 5.9% fibrillary astrocytoma, 4.2% mixed neuronal-glial tumors, and 3.6% others; 21.1% were diagnosed clinically. Anatomically implicated were 31.6% cerebellum, 24.6% chiasma/hypothalamus, 16.0% cerebral hemispheres, 9.9% brain stem, 6.1% other supratentorial midline structures, 5.9% optic nerve only, 4.5% spinal cord, and 1.4% others. The 5-year overall survival and progression-free survival in the whole cohort were 94.6% and 69.4%, respectively. There was a significant association between age and site (P < .001) and extent of tumor resection and site (P < .001). Multivariate analysis identified young age, fibrillary astrocytoma, and extent of surgical resection as significant independent risk factors for progression. Hypothalamic/chiasmatic tumors demonstrated the most sustained tendency to progress. In conclusion, the influence of age and anatomical site upon the risk of tumor progression suggests that these factors strongly influence tumor behavior for the majority of pilocytic tumors. Age <1 year and 1–5 years, fibrillary histology, completeness of resection, and chiasmatic location are candidates for stratification in future studies. PMID:20861086

  18. Agriculture, population growth, and statistical analysis of the radiocarbon record.

    PubMed

    Zahid, H Jabran; Robinson, Erick; Kelly, Robert L

    2016-01-26

    The human population has grown significantly since the onset of the Holocene about 12,000 y ago. Despite decades of research, the factors determining prehistoric population growth remain uncertain. Here, we examine measurements of the rate of growth of the prehistoric human population based on statistical analysis of the radiocarbon record. We find that, during most of the Holocene, human populations worldwide grew at a long-term annual rate of 0.04%. Statistical analysis of the radiocarbon record shows that transitioning farming societies experienced the same rate of growth as contemporaneous foraging societies. The same rate of growth measured for populations dwelling in a range of environments and practicing a variety of subsistence strategies suggests that the global climate and/or endogenous biological factors, not adaptability to local environment or subsistence practices, regulated the long-term growth of the human population during most of the Holocene. Our results demonstrate that statistical analyses of large ensembles of radiocarbon dates are robust and valuable for quantitatively investigating the demography of prehistoric human populations worldwide.

  19. Agriculture, population growth, and statistical analysis of the radiocarbon record

    PubMed Central

    Zahid, H. Jabran; Robinson, Erick; Kelly, Robert L.

    2016-01-01

    The human population has grown significantly since the onset of the Holocene about 12,000 y ago. Despite decades of research, the factors determining prehistoric population growth remain uncertain. Here, we examine measurements of the rate of growth of the prehistoric human population based on statistical analysis of the radiocarbon record. We find that, during most of the Holocene, human populations worldwide grew at a long-term annual rate of 0.04%. Statistical analysis of the radiocarbon record shows that transitioning farming societies experienced the same rate of growth as contemporaneous foraging societies. The same rate of growth measured for populations dwelling in a range of environments and practicing a variety of subsistence strategies suggests that the global climate and/or endogenous biological factors, not adaptability to local environment or subsistence practices, regulated the long-term growth of the human population during most of the Holocene. Our results demonstrate that statistical analyses of large ensembles of radiocarbon dates are robust and valuable for quantitatively investigating the demography of prehistoric human populations worldwide. PMID:26699457

  20. Global surveillance of cancer survival 1995–2009: analysis of individual data for 25 676 887 patients from 279 population-based registries in 67 countries (CONCORD-2)

    PubMed Central

    Allemani, Claudia; Weir, Hannah K; Carreira, Helena; Harewood, Rhea; Spika, Devon; Wang, Xiao-Si; Bannon, Finian; Ahn, Jane V; Johnson, Christopher J; Bonaventure, Audrey; Marcos-Gragera, Rafael; Stiller, Charles; Silva, Gulnar Azevedo e; Chen, Wan-Qing; Ogunbiyi, Olufemi J; Rachet, Bernard; Soeberg, Matthew J; You, Hui; Matsuda, Tomohiro; Bielska-Lasota, Magdalena; Storm, Hans; Tucker, Thomas C; Coleman, Michel P

    2015-01-01

    Summary Background Worldwide data for cancer survival are scarce. We aimed to initiate worldwide surveillance of cancer survival by central analysis of population-based registry data, as a metric of the effectiveness of health systems, and to inform global policy on cancer control. Methods Individual tumour records were submitted by 279 population-based cancer registries in 67 countries for 25·7 million adults (age 15–99 years) and 75 000 children (age 0–14 years) diagnosed with cancer during 1995–2009 and followed up to Dec 31, 2009, or later. We looked at cancers of the stomach, colon, rectum, liver, lung, breast (women), cervix, ovary, and prostate in adults, and adult and childhood leukaemia. Standardised quality control procedures were applied; errors were corrected by the registry concerned. We estimated 5-year net survival, adjusted for background mortality in every country or region by age (single year), sex, and calendar year, and by race or ethnic origin in some countries. Estimates were age-standardised with the International Cancer Survival Standard weights. Findings 5-year survival from colon, rectal, and breast cancers has increased steadily in most developed countries. For patients diagnosed during 2005–09, survival for colon and rectal cancer reached 60% or more in 22 countries around the world; for breast cancer, 5-year survival rose to 85% or higher in 17 countries worldwide. Liver and lung cancer remain lethal in all nations: for both cancers, 5-year survival is below 20% everywhere in Europe, in the range 15–19% in North America, and as low as 7–9% in Mongolia and Thailand. Striking rises in 5-year survival from prostate cancer have occurred in many countries: survival rose by 10–20% between 1995–99 and 2005–09 in 22 countries in South America, Asia, and Europe, but survival still varies widely around the world, from less than 60% in Bulgaria and Thailand to 95% or more in Brazil, Puerto Rico, and the USA. For cervical cancer

  1. Bone fracture risk is not associated with the use of glucagon-like peptide-1 receptor agonists: a population-based cohort analysis.

    PubMed

    Driessen, Johanna H M; Henry, Ronald M A; van Onzenoort, Hein A W; Lalmohamed, Arief; Burden, Andrea M; Prieto-Alhambra, Daniel; Neef, Cees; Leufkens, Hubert G M; de Vries, Frank

    2015-08-01

    Glucagon-like Peptide-1 receptor agonists (GLP1-ra) are a relatively new class of anti-hyperglycemic drugs which may positively affect bone metabolism and thereby decrease (osteoporotic) bone fracture risk. Data on the effect of GLP1-ra on fracture risk are scarce and limited to clinical trial data only. The aim of this study was to investigate, in a population-based cohort, the association between the use of GLP1-ra and bone fracture risk. We conducted a population-based cohort study, with the use of data from the Clinical Practice Research Datalink (CPRD) database (2007-2012). The study population (N = 216,816) consisted of all individuals with type 2 diabetes patients with at least one prescription for a non-insulin anti-diabetic drug and were over 18 years of age. Cox proportional hazards models were used to estimate the hazard ratio of fracture in GLP1-ra users versus never-GLP1-ra users. Time-dependent adjustments were made for age, sex, lifestyle, comorbidity and the use of other drugs. There was no decreased risk of fracture with current use of GLP1-ra compared to never-GLP1-ra use (adjusted HR 0.99, 95 % CI 0.82-1.19). Osteoporotic fracture risk was also not decreased by current GLP1-ra use (adjusted HR 0.97; 95 % CI 0.72-1.32). In addition, stratification according to cumulative dose did not show a decreased bone fracture risk with increasing cumulative GLP1-ra dose. We showed in a population-based cohort study that GLP1-ra use is not associated with a decreased bone fracture risk compared to users of other anti-hyperglycemic drugs. Future research is needed to elucidate the potential working mechanisms of GLP1-ra on bone.

  2. Principal-component-based population structure adjustment in the North American Rheumatoid Arthritis Consortium data: impact of single-nucleotide polymorphism set and analysis method

    PubMed Central

    2009-01-01

    Population structure occurs when a sample is composed of individuals with different ancestries and can result in excess type I error in genome-wide association studies. Genome-wide principal-component analysis (PCA) has become a popular method for identifying and adjusting for subtle population structure in association studies. Using the Genetic Analysis Workshop 16 (GAW16) NARAC data, we explore two unresolved issues concerning the use of genome-wide PCA to account for population structure in genetic associations studies: the choice of single-nucleotide polymorphism (SNP) subset and the choice of adjustment model. We computed PCs for subsets of genome-wide SNPs with varying levels of LD. The first two PCs were similar for all subsets and the first three PCs were associated with case status for all subsets. When the PCs associated with case status were included as covariates in an association model, the reduction in genomic inflation factor was similar for all SNP sets. Several models have been proposed to account for structure using PCs, but it is not yet clear whether the different methods will result in substantively different results for association studies with individuals of European descent. We compared genome-wide association p-values and results for two positive-control SNPs previously associated with rheumatoid arthritis using four PC adjustment methods as well as no adjustment and genomic control. We found that in this sample, adjusting for the continuous PCs or adjusting for discrete clusters identified using the PCs adequately accounts for the case-control population structure, but that a recently proposed randomization test performs poorly. PMID:20017972

  3. GIS-Based Population Model Applied to Nevada Transportation Routes

    SciTech Connect

    Mills, G.S.; Neuhauser, K.S.

    1999-03-04

    Recently, a model based on geographic information system (GIS) processing of US Census Block data has made high-resolution population analysis for transportation risk analysis technically and economically feasible. Population density bordering each kilometer of a route may be tabulated with specific route sections falling into each of three categories (Rural, Suburban or Urban) identified for separate risk analysis. In addition to the improvement in resolution of Urban areas along a route, the model provides a statistically-based correction to population densities in Rural and Suburban areas where Census Block dimensions may greatly exceed the 800-meter scale of interest. A semi-automated application of the GIS model to a subset of routes in Nevada (related to the Yucca Mountain project) are presented, and the results compared to previous models including a model based on published Census and other data. These comparisons demonstrate that meaningful improvement in accuracy and specificity of transportation risk analyses is dependent on correspondingly accurate and geographically-specific population density data.

  4. Population-based case-control association studies.

    PubMed

    Hancock, Dana B; Scott, William K

    2012-07-01

    This unit provides an overview of the design and analysis of population-based case-control studies of genetic risk factors for complex disease. Considerations specific to genetic studies are emphasized. The unit reviews basic study designs differentiating case-control studies from others, presents different genetic association strategies (candidate gene, genome-wide association, and high-throughput sequencing), introduces basic methods of statistical analysis for case-control data and approaches to combining case-control studies, and discusses measures of association and impact. Admixed populations, controlling for confounding (including population stratification), consideration of multiple loci and environmental risk factors, and complementary analyses of haplotypes, genes, and pathways are briefly discussed. Readers are referred to basic texts on epidemiology for more details on general conduct of case-control studies.

  5. Analysis of Intervention Strategies for Inhalation Exposure to Polycyclic Aromatic Hydrocarbons and Associated Lung Cancer Risk Based on a Monte Carlo Population Exposure Assessment Model

    PubMed Central

    Zhou, Bin; Zhao, Bin

    2014-01-01

    It is difficult to evaluate and compare interventions for reducing exposure to air pollutants, including polycyclic aromatic hydrocarbons (PAHs), a widely found air pollutant in both indoor and outdoor air. This study presents the first application of the Monte Carlo population exposure assessment model to quantify the effects of different intervention strategies on inhalation exposure to PAHs and the associated lung cancer risk. The method was applied to the population in Beijing, China, in the year 2006. Several intervention strategies were designed and studied, including atmospheric cleaning, smoking prohibition indoors, use of clean fuel for cooking, enhancing ventilation while cooking and use of indoor cleaners. Their performances were quantified by population attributable fraction (PAF) and potential impact fraction (PIF) of lung cancer risk, and the changes in indoor PAH concentrations and annual inhalation doses were also calculated and compared. The results showed that atmospheric cleaning and use of indoor cleaners were the two most effective interventions. The sensitivity analysis showed that several input parameters had major influence on the modeled PAH inhalation exposure and the rankings of different interventions. The ranking was reasonably robust for the remaining majority of parameters. The method itself can be extended to other pollutants and in different places. It enables the quantitative comparison of different intervention strategies and would benefit intervention design and relevant policy making. PMID:24416436

  6. Genetic analysis of oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) populations based on mitochondrial cox1 and nad1 gene sequences from India and other Asian countries.

    PubMed

    Choudhary, Jaipal S; Naaz, Naiyar; Prabhakar, Chandra S; Lemtur, Moanaro

    2016-10-01

    The study examined the genetic diversity and demographic history of Bactrocera dorsalis, a destructive and polyphagous insect pest of fruit crops in diverse geographic regions of India. 19 widely dispersed populations of the fly from India and other Asian countries were analysed using partial sequences of mitochondrial cytochrome oxidase I (cox1) and NADH dehydrogenase 1 (nad1) genes to investigate genetic diversity, genetic structure, and demographic history in the region. Genetic diversity indices [number of haplotypes (H), haloptype diversity (Hd), nucleotide diversity (π) and average number of nucleotide difference (k)] of populations revealed that B. dorsalis maintains fairly high level of genetic diversity without isolation by distance among the geographic regions. Demographic analysis showed significant (negative) Tajimas' D and Fu's F S with non significant sum of squared deviations (SSD) values, which indicate the possibility of recent sudden expansion of species and is further supported through distinctively star-like distribution structure of haplotypes among populations. Thus, the results indicate that both ongoing and historical factors have played important role in determining the genetic structure and diversity of the species in India. Consequently, sterile insect technique (SIT) could be a possible management strategy of species in the regions.

  7. Predictors of Surgery Types after Neoadjuvant Therapy for Advanced Stage Breast Cancer: Analysis from Florida Population-Based Cancer Registry (1996–2009)

    PubMed Central

    Al-Azhri, Jamila; Koru-Sengul, Tulay; Miao, Feng; Saclarides, Constantine; Byrne, Margaret M.; Avisar, Eli

    2015-01-01

    PURPOSE Despite the established guidelines for breast cancer treatment, there is still variability in surgical treatment after neoadjuvant therapy (NT) for women with large breast tumors. Our objective was to identify predictors of the type of surgical treatment: mastectomy versus breast-conserving surgery (BCS) in women with T3/T4 breast cancer who received NT. METHODS Population-based Florida Cancer Data System Registry, Florida’s Agency for Health Care Administration, and US census from 1996 to 2009 were linked for women diagnosed with T3/T4 breast cancer and received NT followed by either BCS or mastectomy. Analysis of multiple variables, such as sociodemographic characteristics (race, ethnicity, socioeconomic status, age, marital status, and urban/rural residency), tumor’s characteristics (estrogen/progesterone receptor status, histology, grade, SEER stage, and regional nodes positivity), treatment facilities (hospital volume and teaching status), patients’ comorbidities, and type of NT, was performed. RESULTS Of 1,056 patients treated with NT for T3/T4 breast cancer, 107 (10%) had BCS and 949 (90%) had mastectomy. After adjusting with extensive covariables, Hispanic patients (adjusted odds ratio (aOR) = [3.50], 95% confidence interval (CI): 1.38–8.84, P = 0.008) were more likely to have mastectomy than BCS. Compared to localized SEER stage, regional stage with direct extension (aOR = [3.24], 95% CI: 1.60–6.54, P = 0.001), regional stage with direct extension and nodes (aOR = [4.35], 95% CI: 1.72–11.03, P = 0.002), and distant stage (aOR = [4.44], 95% CI: 1.81–10.88, P = 0.001) were significantly more likely to have mastectomy than BCS. Compared to patients who received both chemotherapy and hormonal therapy, patients who received hormonal NT only (aOR = [0.29], 95% CI: 0.12–0.68, P = 0.004) were less likely to receive mastectomy. CONCLUSION Our study suggests that Hispanic ethnicity, advanced SEER stage, and type of NT are significant

  8. MLST-Based Population Genetic Analysis in a Global Context Reveals Clonality amongst Cryptococcus neoformans var. grubii VNI Isolates from HIV Patients in Southeastern Brazil

    PubMed Central

    Ferreira-Paim, Kennio; Andrade-Silva, Leonardo; Fonseca, Fernanda M.; Ferreira, Thatiana B.; Mora, Delio J.; Andrade-Silva, Juliana; Khan, Aziza; Dao, Aiken; Reis, Eduardo C.; Almeida, Margarete T. G.; Maltos, Andre; Junior, Virmondes R.; Trilles, Luciana; Rickerts, Volker; Chindamporn, Ariya; Sykes, Jane E.; Cogliati, Massimo; Nielsen, Kirsten; Boekhout, Teun; Fisher, Matthew; Kwon-Chung, June; Engelthaler, David M.; Lazéra, Marcia; Meyer, Wieland; Silva-Vergara, Mario L.

    2017-01-01

    Cryptococcosis is an important fungal infection in immunocompromised individuals, especially those infected with HIV. In Brazil, despite the free availability of antiretroviral therapy (ART) in the public health system, the mortality rate due to Cryptococcus neoformans meningitis is still high. To obtain a more detailed picture of the population genetic structure of this species in southeast Brazil, we studied 108 clinical isolates from 101 patients and 35 environmental isolates. Among the patients, 59% had a fatal outcome mainly in HIV-positive male patients. All the isolates were found to be C. neoformans var. grubii major molecular type VNI and mating type locus alpha. Twelve were identified as diploid by flow cytometry, being homozygous (AαAα) for the mating type and by PCR screening of the STE20, GPA1, and PAK1 genes. Using the ISHAM consensus multilocus sequence typing (MLST) scheme, 13 sequence types (ST) were identified, with one being newly described. ST93 was identified from 81 (75%) of the clinical isolates, while ST77 and ST93 were identified from 19 (54%) and 10 (29%) environmental isolates, respectively. The southeastern Brazilian isolates had an overwhelming clonal population structure. When compared with populations from different continents based on data extracted from the ISHAM-MLST database (mlst.mycologylab.org) they showed less genetic variability. Two main clusters within C. neoformans var. grubii VNI were identified that diverged from VNB around 0.58 to 4.8 million years ago. PMID:28099434

  9. MLST-Based Population Genetic Analysis in a Global Context Reveals Clonality amongst Cryptococcus neoformans var. grubii VNI Isolates from HIV Patients in Southeastern Brazil.

    PubMed

    Ferreira-Paim, Kennio; Andrade-Silva, Leonardo; Fonseca, Fernanda M; Ferreira, Thatiana B; Mora, Delio J; Andrade-Silva, Juliana; Khan, Aziza; Dao, Aiken; Reis, Eduardo C; Almeida, Margarete T G; Maltos, Andre; Junior, Virmondes R; Trilles, Luciana; Rickerts, Volker; Chindamporn, Ariya; Sykes, Jane E; Cogliati, Massimo; Nielsen, Kirsten; Boekhout, Teun; Fisher, Matthew; Kwon-Chung, June; Engelthaler, David M; Lazéra, Marcia; Meyer, Wieland; Silva-Vergara, Mario L

    2017-01-01

    Cryptococcosis is an important fungal infection in immunocompromised individuals, especially those infected with HIV. In Brazil, despite the free availability of antiretroviral therapy (ART) in the public health system, the mortality rate due to Cryptococcus neoformans meningitis is still high. To obtain a more detailed picture of the population genetic structure of this species in southeast Brazil, we studied 108 clinical isolates from 101 patients and 35 environmental isolates. Among the patients, 59% had a fatal outcome mainly in HIV-positive male patients. All the isolates were found to be C. neoformans var. grubii major molecular type VNI and mating type locus alpha. Twelve were identified as diploid by flow cytometry, being homozygous (AαAα) for the mating type and by PCR screening of the STE20, GPA1, and PAK1 genes. Using the ISHAM consensus multilocus sequence typing (MLST) scheme, 13 sequence types (ST) were identified, with one being newly described. ST93 was identified from 81 (75%) of the clinical isolates, while ST77 and ST93 were identified from 19 (54%) and 10 (29%) environmental isolates, respectively. The southeastern Brazilian isolates had an overwhelming clonal population structure. When compared with populations from different continents based on data extracted from the ISHAM-MLST database (mlst.mycologylab.org) they showed less genetic variability. Two main clusters within C. neoformans var. grubii VNI were identified that diverged from VNB around 0.58 to 4.8 million years ago.

  10. Health-Specific Information and Communication Technology Use and Its Relationship to Obesity in High-Poverty, Urban Communities: Analysis of a Population-Based Biosocial Survey

    PubMed Central

    Makelarski, Jennifer A; Garibay, Lori B; Escamilla, Veronica; Merchant, Raina M; Wolfe Sr, Marcus B; Holbrook, Rebecca; Lindau, Stacy Tessler

    2016-01-01

    Background More than 35% of American adults are obese. For African American and Hispanic adults, as well as individuals residing in poorer or more racially segregated urban neighborhoods, the likelihood of obesity is even higher. Information and communication technologies (ICTs) may substitute for or complement community-based resources for weight management. However, little is currently known about health-specific ICT use among urban-dwelling people with obesity. Objective We describe health-specific ICT use and its relationship to measured obesity among adults in high-poverty urban communities. Methods Using data collected between November 2012 and July 2013 from a population-based probability sample of urban-dwelling African American and Hispanic adults residing on the South Side of Chicago, we described patterns of ICT use in relation to measured obesity defined by a body mass index (BMI) of ≥30 kg/m2. Among those with BMI≥30 kg/m2, we also assessed the association between health-specific ICT use and diagnosed versus undiagnosed obesity as well as differences in health-specific ICT use by self-reported comorbidities, including diabetes and hypertension. Results The survey response rate was 44.6% (267 completed surveys/598.4 eligible or likely eligible individuals); 53.2% were African American and 34.6% were Hispanic. More than 35% of the population reported an annual income of less than US $25,000. The population prevalence of measured obesity was 50.2%. People with measured obesity (BMI≥30 kg/m2) were more likely to report both general (81.5% vs 67.0%, P=.04) and health-specific (61.1% vs 41.2%, P=.01) ICT use. In contrast, among those with measured obesity, being told of this diagnosis by a physician was not associated with increased health-specific ICT use. People with measured obesity alone had higher rates of health-specific use than those with comorbid hypertension and/or diabetes diagnoses (77.1% vs 60.7% vs 47.4%, P=.04). Conclusions In conclusion

  11. Population Analysis: A Methodology for Understanding Populations in COIN Environments

    DTIC Science & Technology

    2008-12-01

    predict cause and effect of human 30 behavior. In the late 19th century, Wilhelm Wundt founded the first psychology department at the University of...on the application of power with respect to managing people, organizations, markets, and populations. Philosophers and authors such as Friedrich ... Nietzsche , Jeffery Pfeffer, Bertram Raven, and John French have each laid out models by which power, and its implementation can be better understood

  12. Association between population prevalence of smoking and incidence of meningococcal disease in Norway, Sweden, Denmark and the Netherlands between 1975 and 2009: a population-based time series analysis

    PubMed Central

    Norheim, Gunnstein; Sadarangani, Manish; Omar, Omar; Yu, Ly-Mee; Mølbak, Kåre; Howitz, Michael; Olcén, Per; Haglund, Margaretha; van der Ende, Arie; Pollard, Andrew J

    2014-01-01

    Objective To investigate the relationship between the prevalence of smoking in the population and incidence of invasive meningococcal disease (IMD) among children under 5 years of age. Design Retrospective, longitudinal, observational study. Poisson regression controlled for confounding factors. Setting Norway, Sweden, Denmark and the Netherlands between 1975 and 2009. Population Total population of approximately 35 million people in these four countries. Data sources Data were collected from the Ministries of Health, National Statistics Bureaus and other relevant national institutes. Results In Norway, there was a significant positive relationship between the annual prevalence of daily smokers among individuals aged 25–49 years and the incidence of IMD in children under 5 years of age, unadjusted (RR=1.04–1.06, 95% CI 1.02 to 1.07, p<0.001) and after adjustment for time of year (quarter), incidence of influenza-like illness and household crowding (RR=1.05–1.07, 95% CI 1.03 to 1.09, p<0.001). Depending on age group, the risk of IMD increased by 5.2–6.9% per 1% increase in smoking prevalence among individuals aged 25–49 years in adjusted analyses. Using limited datasets from the three other countries, unadjusted analysis showed positive associations between IMD in children related to older smokers in Sweden and the Netherlands and negative associations related to younger smokers in Sweden. However, there were no demonstrable associations between incidence of IMD and prevalence of smoking, after adjustment for the same confounding variables. Conclusions The reduced incidence of IMD in Norway between 1975 and 2009 may partly be explained by the reduced prevalence of smoking during this period. High-quality surveillance data are required to confirm this in other countries. Strong efforts to reduce smoking in the whole population including targeted campaigns to reduce smoking among adults may have a role to play in the prevention of IMD in children

  13. A biopsychosocial profile of adult Canadians with and without chronic back disorders: a population-based analysis of the 2009-2010 Canadian Community Health Surveys.

    PubMed

    Bath, Brenna; Trask, Catherine; McCrosky, Jesse; Lawson, Josh

    2014-01-01

    Chronic back disorders (CBD) are a significant public health concern. Profiling Canadians with CBD and the associated biopsychosocial factors at a national population level is important to understand the burden of this condition and how clinicians, health systems, and related policies might address this potentially growing problem. We performed a secondary analysis of the 2009 and 2010 Canadian Community Health Surveys to calculate prevalence and to better understand the differences between people with and without CBD. An estimated 20.2% of the adult Canadian population reports having back problems lasting for 6 months or more. Among people with CBD, there was significantly greater likelihood of living in a more rural or remote location, being Aboriginal, being a former or current smoker, being overweight, having other chronic health conditions, having greater activity limitations, having higher levels of stress, and having lower perceived mental health. People who were single/never married or had an ethnicity other than Caucasian or Aboriginal were less likely to report having CBD. These results contribute to a growing body of research in the area that may assist with strategic prioritization and tailoring of health promotion efforts and health services for people with CBD, particularly among vulnerable groups.

  14. Characterization of the metabolic profile associated with serum 25-hydroxyvitamin D: a cross-sectional analysis in population-based data

    PubMed Central

    Vogt, Susanne; Wahl, Simone; Kettunen, Johannes; Breitner, Susanne; Kastenmüller, Gabi; Gieger, Christian; Suhre, Karsten; Waldenberger, Melanie; Kratzsch, Jürgen; Perola, Markus; Salomaa, Veikko; Blankenberg, Stefan; Zeller, Tanja; Soininen, Pasi; Kangas, Antti J; Peters, Annette; Grallert, Harald; Ala-Korpela, Mika; Thorand, Barbara

    2016-01-01

    Background: Numerous observational studies have observed associations between vitamin D deficiency and cardiometabolic diseases, but these findings might be confounded by obesity. A characterization of the metabolic profile associated with serum 25-hydroxyvitamin D [25(OH)D] levels, in general and stratified by abdominal obesity, may help to untangle the relationship between vitamin D, obesity and cardiometabolic health. Methods: Serum metabolomics measurements were obtained from a nuclear magnetic resonance spectroscopy (NMR)- and a mass spectrometry (MS)-based platform. The discovery was conducted in 1726 participants of the population-based KORA-F4 study, in which the associations of the concentrations of 415 metabolites with 25(OH)D levels were assessed in linear models. The results were replicated in 6759 participants (NMR) and 609 (MS) participants, respectively, of the population-based FINRISK 1997 study. Results: Mean [standard deviation (SD)] 25(OH)D levels were 15.2 (7.5) ng/ml in KORA F4 and 13.8 (5.9) ng/ml in FINRISK 1997; 37 metabolites were associated with 25(OH)D in KORA F4 at P < 0.05/415. Of these, 30 associations were replicated in FINRISK 1997 at P < 0.05/37. Among these were constituents of (very) large very-low-density lipoprotein and small low-density lipoprotein subclasses and related measures like serum triglycerides as well as fatty acids and measures reflecting the degree of fatty acid saturation. The observed associations were independent of waist circumference and generally similar in abdominally obese and non-obese participants. Conclusions: Independently of abdominal obesity, higher 25(OH)D levels were associated with a metabolite profile characterized by lower concentrations of atherogenic lipids and a higher degree of fatty acid polyunsaturation. These results indicate that the relationship between vitamin D deficiency and cardiometabolic diseases is unlikely to merely reflect obesity-related pathomechanisms. PMID:27605587

  15. Venous thromboembolism in adults screened for sickle cell trait: a population-based cohort study with nested case–control analysis

    PubMed Central

    Little, Iain; Vinogradova, Yana; Orton, Elizabeth; Kai, Joe; Qureshi, Nadeem

    2017-01-01

    Objective To determine whether sickle cell carriers (‘sickle cell trait’) have an increased risk of venous thromboembolism (VTE). Design Cohort study with nested case–control analysis. Setting General population with data from 609 UK general practices in the Clinical Practice Research Datalink (CPRD). Participants All individuals registered with a CPRD general practice between 1998 and 2013, with a medical record of screening for sickle cell between 18 and 75 years of age. Main outcomes measures Incidence of VTE per 10 000 person-years (PY) among sickle cell carriers and non-carriers; and adjusted OR for VTE among sickle cell carriers compared with non-carriers. Results We included 30 424 individuals screened for sickle cell, with a follow-up time of 179 503 PY, identifying 55 VTEs in 6758 sickle cell carriers and 125 VTEs in 23 666 non-carriers. VTE incidence among sickle cell carriers (14.9/10 000 PY; 95% CI 11.4 to 19.4) was significantly higher than non-carriers (8.8/10 000 PY; 95% CI 7.4 to 10.4). Restricting analysis to confirmed non-carriers was non-significant, but performed on a small sample. In the case–control analysis (180 cases matched to 1775 controls by age and gender), sickle cell carriers remained at increased risk of VTE after adjusting for body mass index, pregnancy, smoking status and ethnicity (OR 1.78, 95% CI 1.18 to 2.69, p=0.006), with the greatest risk for pulmonary embolism (PE) (OR 2.27, 95% CI 1.17 to 4.39, p=0.011). Conclusions Although absolute numbers are small, in a general population screened for sickle cell, carriers have a higher incidence and risk of VTE, particularly PE, than non-carriers. Clinicians should be aware of this elevated risk in the clinical care of sickle cell carriers, or when discussing carrier screening, and explicitly attend to modifiable risk factors for VTE in these individuals. More complete primary care coding of carrier status could improve analysis. PMID:28360235

  16. Microsatellite and Wolbachia analysis in Rhagoletis cerasi natural populations: population structuring and multiple infections

    PubMed Central

    Augustinos, Antonios A; Asimakopoulou, Anastasia K; Moraiti, Cleopatra A; Mavragani-Tsipidou, Penelope; Papadopoulos, Nikolaos T; Bourtzis, Kostas

    2014-01-01

    Rhagoletis cerasi (Diptera: Tephritidae) is a major pest of sweet and sour cherries in Europe and parts of Asia. Despite its economic significance, there is a lack of studies on the genetic structure of R. cerasi populations. Elucidating the genetic structure of insects of economic importance is crucial for developing phenological-predictive models and environmental friendly control methods. All natural populations of R. cerasi have been found to harbor the endosymbiont Wolbachia pipientis, which widely affects multiple biological traits contributing to the evolution of its hosts, and has been suggested as a tool for the biological control of insect pests and disease vectors. In the current study, the analysis of 18 R. cerasi populations collected in Greece, Germany, and Russia using 13 microsatellite markers revealed structuring of R. cerasi natural populations, even at close geographic range. We also analyzed the Wolbachia infection status of these populations using 16S rRNA-, MLST- and wsp-based approaches. All 244 individuals screened were positive for Wolbachia. Our results suggest the fixation of the wCer1 strain in Greece while wCer2, wCer4, wCer5, and probably other uncharacterized strains were also detected in multiply infected individuals. The role of Wolbachia and its potential extended phenotypes needs a thorough investigation in R. cerasi. Our data suggest an involvement of this symbiont in the observed restriction in the gene flow in addition to a number of different ecological factors. PMID:24963388

  17. Multilocus family-based association analysis of seven candidate polymorphisms with essential hypertension in an african-derived semi-isolated brazilian population.

    PubMed

    Kimura, L; Angeli, C B; Auricchio, M T B M; Fernandes, G R; Pereira, A C; Vicente, J P; Pereira, T V; Mingroni-Netto, R C

    2012-01-01

    Background. It has been widely suggested that analyses considering multilocus effects would be crucial to characterize the relationship between gene variability and essential hypertension (EH). Objective. To test for the presence of multilocus effects between/among seven polymorphisms (six genes) on blood pressure-related traits in African-derived semi-isolated Brazilian populations (quilombos). Methods. Analyses were carried out using a family-based design in a sample of 652 participants (97 families). Seven variants were investigated: ACE (rs1799752), AGT (rs669), ADD2 (rs3755351), NOS3 (rs1799983), GNB3 (rs5441 and rs5443), and GRK4 (rs1801058). Sensitivity analyses were further performed under a case-control design with unrelated participants only. Results. None of the investigated variants were associated individually with both systolic and diastolic BP levels (SBP and DBP, respectively) or EH (as a binary outcome). Multifactor dimensionality reduction-based techniques revealed a marginal association of the combined effect of both GNB3 variants on DBP levels in a family-based design (P = 0.040), whereas a putative NOS3-GRK4 interaction also in relation to DBP levels was observed in the case-control design only (P = 0.004). Conclusion. Our results provide limited support for the hypothesis of multilocus effects between/among the studied variants on blood pressure in quilombos. Further larger studies are needed to validate our findings.

  18. Multilocus Family-Based Association Analysis of Seven Candidate Polymorphisms with Essential Hypertension in an African-Derived Semi-Isolated Brazilian Population

    PubMed Central

    Kimura, L.; Angeli, C. B.; Auricchio, M. T. B. M.; Fernandes, G. R.; Pereira, A. C.; Vicente, J. P.; Pereira, T. V.; Mingroni-Netto, R. C.

    2012-01-01

    Background. It has been widely suggested that analyses considering multilocus effects would be crucial to characterize the relationship between gene variability and essential hypertension (EH). Objective. To test for the presence of multilocus effects between/among seven polymorphisms (six genes) on blood pressure-related traits in African-derived semi-isolated Brazilian populations (quilombos). Methods. Analyses were carried out using a family-based design in a sample of 652 participants (97 families). Seven variants were investigated: ACE (rs1799752), AGT (rs669), ADD2 (rs3755351), NOS3 (rs1799983), GNB3 (rs5441 and rs5443), and GRK4 (rs1801058). Sensitivity analyses were further performed under a case-control design with unrelated participants only. Results. None of the investigated variants were associated individually with both systolic and diastolic BP levels (SBP and DBP, respectively) or EH (as a binary outcome). Multifactor dimensionality reduction-based techniques revealed a marginal association of the combined effect of both GNB3 variants on DBP levels in a family-based design (P = 0.040), whereas a putative NOS3-GRK4 interaction also in relation to DBP levels was observed in the case-control design only (P = 0.004). Conclusion. Our results provide limited support for the hypothesis of multilocus effects between/among the studied variants on blood pressure in quilombos. Further larger studies are needed to validate our findings. PMID:23056922

  19. Worldwide trends in diabetes since 1980: a pooled analysis of 751 population-based studies with 4·4 million participants

    PubMed Central

    2016-01-01

    Summary Background One of the global targets for non-communicable diseases is to halt, by 2025, the rise in the age-standardised adult prevalence of diabetes at its 2010 levels. We aimed to estimate worldwide trends in diabetes, how likely it is for countries to achieve the global target, and how changes in prevalence, together with population growth and ageing, are affecting the number of adults with diabetes. Methods We pooled data from population-based studies that had collected data on diabetes through measurement of its biomarkers. We used a Bayesian hierarchical model to estimate trends in diabetes prevalence—defined as fasting plasma glucose of 7·0 mmol/L or higher, or history of diagnosis with diabetes, or use of insulin or oral hypoglycaemic drugs—in 200 countries and territories in 21 regions, by sex and from 1980 to 2014. We also calculated the posterior probability of meeting the global diabetes target if post-2000 trends continue. Findings We used data from 751 studies including 4 372 000 adults from 146 of the 200 countries we make estimates for. Global age-standardised diabetes prevalence increased from 4·3% (95% credible interval 2·4–7·0) in 1980 to 9·0% (7·2–11·1) in 2014 in men, and from 5·0% (2·9–7·9) to 7·9% (6·4–9·7) in women. The number of adults with diabetes in the world increased from 108 million in 1980 to 422 million in 2014 (28·5% due to the rise in prevalence, 39·7% due to population growth and ageing, and 31·8% due to interaction of these two factors). Age-standardised adult diabetes prevalence in 2014 was lowest in northwestern Europe, and highest in Polynesia and Micronesia, at nearly 25%, followed by Melanesia and the Middle East and north Africa. Between 1980 and 2014 there was little change in age-standardised diabetes prevalence in adult women in continental western Europe, although crude prevalence rose because of ageing of the population. By contrast, age-standardised adult prevalence rose by 15

  20. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.

    PubMed

    Khanshour, Anas; Conant, Eleanore; Juras, Rytis; Cothran, Ernest Gus

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations.

  1. A population-based Habitable Zone perspective

    NASA Astrophysics Data System (ADS)

    Zsom, Andras

    2015-08-01

    What can we tell about exoplanet habitability if currently only the stellar properties, planet radius, and the incoming stellar flux are known? The Habitable Zone (HZ) is the region around stars where planets can harbor liquid water on their surfaces. The HZ is traditionally conceived as a sharp region around the star because it is calculated for one planet with specific properties e.g., Earth-like or desert planets , or rocky planets with H2 atmospheres. Such planet-specific approach is limiting because the planets’ atmospheric and geophysical properties, which influence the surface climate and the presence of liquid water, are currently unknown but expected to be diverse.A statistical HZ description is outlined which does not select one specific planet type. Instead the atmospheric and surface properties of exoplanets are treated as random variables and a continuous range of planet scenarios are considered. Various probability density functions are assigned to each observationally unconstrained random variable, and a combination of Monte Carlo sampling and climate modeling is used to generate synthetic exoplanet populations with known surface climates. Then, the properties of the liquid water bearing subpopulation is analyzed.Given our current observational knowledge of small exoplanets, the HZ takes the form of a weakly-constrained but smooth probability function. The model shows that the HZ has an inner edge: it is unlikely that planets receiving two-three times more stellar radiation than Earth can harbor liquid water. But a clear outer edge is not seen: a planet that receives a fraction of Earth's stellar radiation (1-10%) can be habitable, if the greenhouse effect of the atmosphere is strong enough. The main benefit of the population-based approach is that it will be refined over time as new data on exoplanets and their atmospheres become available.

  2. Association of volunteering with mental well-being: a lifecourse analysis of a national population-based longitudinal study in the UK

    PubMed Central

    Tabassum, Faiza; Mohan, John; Smith, Peter

    2016-01-01

    Objectives The association of volunteering with well-being has been found in previous research, but mostly among older people. The aim of this study was to examine the association of volunteering with mental well-being among the British population across the life course. Design British Household Panel Survey, a population-based longitudinal study. Setting UK. Participants 66 343 observations (person-years). Main outcome measures Mental well-being was measured by using the General Health Questionnaire (GHQ-12 or GHQ); high values denote high mental disorder. Four groups of volunteering participation were created: frequent (once a week), infrequent (once a month/several times a year), rare (once or less a year) and never. Multilevel linear models were used to analyse variations in mental well-being over the life course by levels of volunteering. Results When not considering age, those who engaged in volunteering regularly appeared to experience higher levels of mental well-being than those who never volunteered. To explore the association of volunteering with the GHQ across the life course, interaction terms were fitted between age and volunteering. The interactions were significant, demonstrating that these associations vary by age. The association between volunteering and well-being did not emerge during early adulthood to mid-adulthood, instead becoming apparent above the age of 40 years and continuing up to old age. Moreover, in early adulthood, the absence of engagement in voluntary activity was not related to mental well-being, but GHQ scores for this group increased sharply with age, levelling off after the age of 40 and then increasing again above the age of 70 years. The study also indicates variation in GHQ scores (65%) within individuals across time, suggesting evidence of lifecourse effects. Conclusions We conclude that volunteering may be more meaningful for mental well-being at some points of time in the life course. PMID:27503861

  3. Non-invasive Assessment of Lower Limb Geometry and Strength Using Hip Structural Analysis and Peripheral Quantitative Computed Tomography: A Population-Based Comparison.

    PubMed

    Litwic, A E; Clynes, M; Denison, H J; Jameson, K A; Edwards, M H; Sayer, A A; Taylor, P; Cooper, C; Dennison, E M

    2016-02-01

    Hip fracture is the most significant complication of osteoporosis in terms of mortality, long-term disability and decreased quality of life. In the recent years, different techniques have been developed to assess lower limb strength and ultimately fracture risk. Here we examine relationships between two measures of lower limb bone geometry and strength; proximal femoral geometry and tibial peripheral quantitative computed tomography. We studied a sample of 431 women and 488 men aged in the range 59-71 years. The hip structural analysis (HSA) programme was employed to measure the structural geometry of the left hip for each DXA scan obtained using a Hologic QDR 4500 instrument while pQCT measurements of the tibia were obtained using a Stratec 2000 instrument in the same population. We observed strong sex differences in proximal femoral geometry at the narrow neck, intertrochanteric and femoral shaft regions. There were significant (p < 0.001) associations between pQCT-derived measures of bone geometry (tibial width; endocortical diameter and cortical thickness) and bone strength (strength strain index) with each corresponding HSA variable (all p < 0.001) in both men and women. These results demonstrate strong correlations between two different methods of assessment of lower limb bone strength: HSA and pQCT. Validation in prospective cohorts to study associations of each with incident fracture is now indicated.

  4. Analysis of genetic diversity and population structure in a tomato (Solanum lycopersicum L.) germplasm collection based on single nucleotide polymorphism markers.

    PubMed

    Wang, T; Zou, Q D; Qi, S Y; Wang, X F; Wu, Y Y; Liu, N; Zhang, Y M; Zhang, Z J; Li, H T

    2016-07-29

    Knowledge of genetic diversity is important to assist breeders in the selection of parental materials and in the design of breeding programs. In this study, we genotyped 348 inbred tomato lines, representing vintage and contemporary fresh-market varieties, by using 52 single nucleotide polymorphisms (SNPs); 45 of these were found to be polymorphic. The average minor allele frequency and unbiased expected heterozygosity were 0.315 and 0.356, respectively. Population structure analysis revealed that contemporary germplasm could be distinctly divided into six subpopulations representing three market classes and breeding programs (pink, green, and red). Vintage germplasm could be separated into at least two subpopulations, and more admixtures were found in vintage lines than in contemporary lines. These findings indicate that contemporary inbred lines are more diversified than vintage inbred lines. AMOVA of vintage and contemporary lines was performed. A significant difference was found (P < 0.01), which explained 17.4% of the total genetic variance. Subsequently, we constructed a core collection using 45 polymorphic SNP markers. The data showed that all alleles were captured by only 2% of lines, indicating that more alleles, as well as rare alleles, could enable more variation to be captured in the core collection. These data allow us to discard redundant inbred tomato lines and to select elite inbred lines, which will accelerate the breeding process.

  5. Analysis of Patients with Helicobacter pylori Infection and the Subsequent Risk of Developing Osteoporosis after Eradication Therapy: A Nationwide Population-Based Cohort Study

    PubMed Central

    Shih, Hong-Mo; Hsu, Tai-Yi; Chen, Chih-Yu; Lin, Cheng-Li; Kao, Chia-Hung; Chen, Chao-Hsien

    2016-01-01

    Purpose Previous studies have reported conflicting results on the association between Helicobacter pylori infection and osteoporosis. A few studies have discussed the influence of H. pylori eradication therapy on bone mineral density. Methods We assessed the prevalence of osteoporosis among the H. pylori-infected population in Taiwan and the influence of early and late H. pylori eradication therapy on bone mineral density. Results Using data from Taiwan's National Health Insurance Research Database, we identified 5,447 patients who received H. pylori eradication therapy from 2000 to 2010 and 21,788 controls, frequency-matched according to age, sex, and year of receiving H. pylori eradication therapy. Those who received H. pylori eradication therapy were divided into two groups based on the time interval between the diagnosis of a peptic ulcer and commencement of eradication therapy. The risk of developing osteoporosis was higher in the early H. pylori treatment cohort (hazard ratio [HR] = 1.52, 95% confidence interval [CI] = 1.23–1.89) and late H. pylori treatment cohort (HR = 1.69, 95% CI = 1.39–2.05), compared with the risk in the control cohort. When followed for less than 5 years, both the early and late cohorts had a higher risk of developing osteoporosis (HR = 1.69, 95% CI = 1.32–2.16 and HR = 1.72, 95% CI = 1.38–2.14). However, when the follow-up period was over 5 years, only the late eradication group exhibited a higher incidence of osteoporosis (HR = 1.62, 95% CI = 1.06–2.47). Conclusion The development of osteoporosis is complex and multi-factorial. Via this population-based cohort study and adjustment of possible confounding variables, we found H. pylori infection may be associated with an increased risk of developing osteoporosis in Taiwan. Early eradication could reduce the influence of H. pylori infection on osteoporosis when the follow-up period is greater than 5 years. Further prospective studies are necessary to discover the connection of

  6. Does the Intent to Irradiate the Internal Mammary Nodes Impact Survival in Women With Breast Cancer? A Population-Based Analysis in British Columbia

    SciTech Connect

    Olson, Robert A.; Woods, Ryan; Speers, Caroline; Lau, Jeffrey; Lo, Andrea; Truong, Pauline T.; Tyldesley, Scott; Olivotto, Ivo A.; Weir, Lorna

    2012-05-01

    Purpose: To determine the value of the intent to include internal mammary nodes (IMNs) in the radiation therapy (RT) volume for patients receiving adjuvant locoregional (breast or chest wall plus axillary and supraclavicular fossa) RT for breast cancer. Methods and Materials: 2413 women with node-positive or T3/4N0 invasive breast cancer, treated with locoregional RT from 2001 to 2006, were identified in a prospectively maintained, population-based database. Intent to include IMNs in RT volume was determined through review of patient charts and RT plans. Distant relapse free survival (D-RFS), breast cancer-specific survival (BCSS), and overall survival (OS) were compared between the two groups. Prespecified pN1 subgroup analyses were performed. Results: The median follow-up time was 6.2 years. Forty-one percent of study participants received IMN RT. The 5-year D-RFS for IMN inclusion and exclusion groups were 82% vs. 82% (p = 0.82), BCSS was 87% vs. 87% (p = 0.81), and OS was 85% vs. 83% (p = 0.06). In the pN1 subgroup, D-RFS was 90% vs. 88% (p = 0.31), BCSS was 94% vs. 92% (p = 0.18), and OS was 91% vs. 88% (p = 0.01). After potential confounding variables were controlled for, women who received IMN RT did not have significantly different D-RFS (hazard ratio [HR] = 1.02 (95% confidence interval [CI], 0.84-1.24; p = 0.85), BCSS (HR = 0.98 (95% CI, 0.79-1.22; p = 0.88), or OS (HR = 0.95; 95% CI, 0.78-1.15; p = 0.57). In the pN1 subgroup, IMN RT was associated with trends for improved survival that were not statistically significant: D-RFS (HR = 0.87; 95% CI, 0.63-1.22; p = 0.42), BCSS (HR = 0.85; 95% CI, 0.57-1.25; p = 0.39), and OS (HR = 0.78; 95% CI, 0.56-1.09; p = 0.14). Conclusions: After a median follow-up time of 6.2 years, although intentional IMN RT was not associated with a significant improvement in survival, this population-based study suggests that IMN RT may contribute to improved outcomes in selected patients with N1 disease.

  7. Assessing population exposure for landslide risk analysis using dasymetric cartography

    NASA Astrophysics Data System (ADS)

    Garcia, Ricardo A. C.; Oliveira, Sérgio C.; Zêzere, José L.

    2016-12-01

    Assessing the number and locations of exposed people is a crucial step in landslide risk management and emergency planning. The available population statistical data frequently have insufficient detail for an accurate assessment of potentially exposed people to hazardous events, mainly when they occur at the local scale, such as with landslides. The present study aims to apply dasymetric cartography to improving population spatial resolution and to assess the potentially exposed population. An additional objective is to compare the results with those obtained with a more common approach that uses, as spatial units, basic census units, which are the best spatial data disaggregation and detailed information available for regional studies in Portugal. Considering the Portuguese census data and a layer of residential building footprint, which was used as ancillary information, the number of exposed inhabitants differs significantly according to the approach used. When the census unit approach is used, considering the three highest landslide susceptible classes, the number of exposed inhabitants is in general overestimated. Despite the associated uncertainties of a general cost-benefit analysis, the presented methodology seems to be a reliable approach for gaining a first approximation of a more detailed estimation of exposed people. The approach based on dasymetric cartography allows the spatial resolution of population over large areas to be increased and enables the use of detailed landslide susceptibility maps, which are valuable for improving the exposed population assessment.

  8. Automated analysis of a diverse synapse population.

    PubMed

    Busse, Brad; Smith, Stephen

    2013-01-01

    Synapses of the mammalian central nervous system are highly diverse in function and molecular composition. Synapse diversity per se may be critical to brain function, since memory and homeostatic mechanisms are thought to be rooted primarily in activity-dependent plastic changes in specific subsets of individual synapses. Unfortunately, the measurement of synapse diversity has been restricted by the limitations of methods capable of measuring synapse properties at the level of individual synapses. Array tomography is a new high-resolution, high-throughput proteomic imaging method that has the potential to advance the measurement of unit-level synapse diversity across large and diverse synapse populations. Here we present an automated feature extraction and classification algorithm designed to quantify synapses from high-dimensional array tomographic data too voluminous for manual analysis. We demonstrate the use of this method to quantify laminar distributions of synapses in mouse somatosensory cortex and validate the classification process by detecting the presence of known but uncommon proteomic profiles. Such classification and quantification will be highly useful in identifying specific subpopulations of synapses exhibiting plasticity in response to perturbations from the environment or the sensory periphery.

  9. Molecular and epidemiological population-based integrative analysis of human and animal Mycobacterium bovis infections in a low-prevalence setting.

    PubMed

    Palacios, Juan José; Navarro, Yurena; Romero, Beatriz; Penedo, Ana; Menéndez González, Ángela; Pérez Hernández, M Dolores; Fernández-Verdugo, Ana; Copano, Francisca; Torreblanca, Aurora; Bouza, Emilio; Domínguez, Lucas; de Juan, Lucía; García-de-Viedma, Darío

    2016-11-15

    Human Mycobacterium bovis infections are considered to be due to reactivations, when involve elderly people, or to recent transmissions, when exposure is occupational. We determined the cause of M. bovis infections by genotyping M. bovis isolates in a population-based study integrating human and animal databases. Among the 1,586 tuberculosis (TB) cases in Asturias, Northern Spain (1,080,000 inhabitants), 1,567 corresponded to M. tuberculosis and 19 to M. bovis. The number of human isolates sharing genotype with cattle isolates was higher than expected (47%) for a setting with low prevalence of bovine TB and efficient control programs in cattle. The risk of exposure to infected animals was probable/possible in most of these matched cases (77.7%). Recent transmission was the likely explanation of most M. bovis infections in elderly people. A potential human-to-human transmission was found. Our study illustrates a model of collaboration between human and animal health professionals to provide a precise snapshot of the transmission of M. bovis in the human-animal interface.

  10. Analysis of the effects of applying external fields and device dimensions alterations on GaAs/AlGaAs multiple quantum well slow light devices based on excitonic population oscillation.

    PubMed

    Kohandani, Reza; Zandi, Ashkan; Kaatuzian, Hassan

    2014-02-20

    This paper demonstrates the effects of applying magnetic and electric fields and physical dimensions alterations on AlGaAs/GaAs multiple quantum well (QW) slow light devices. Physical parameters include quantum well sizes and number of quantum wells. To the best of our knowledge, this is the first analysis of the effects of both applying magnetic/electric fields and physical parameters alterations and the first suggestion for matching the prefabrication and post fabrication tuning of the slow light devices based on excitonic population oscillations. The aim of our theoretical analysis is controlling the optical properties such as central frequency, bandwidth, and slow down factor (SDF) in slow light devices based on excitonic population oscillation to achieve better tuning. To reach these purposes, first we investigate the quantum well size and number of quantum wells alteration effects. Next, we analyze the effects of applying magnetic and electric fields to the multiple quantum well structure, separately. Finally, physical parameters and applied external fields are changed for measuring frequency shift and SDF for coherent population oscillation slow light devices. The results show the available central frequency shifts in about 1.6 THz at best. Also the SDF value improvement is about one order of magnitude. These results will be applicable for optical nonlinearity enhancements, all-optical signal processing, optical communications, all-optical switches, optical modulators, and variable true delays.

  11. Population-based genetic epidemiologic analysis of Chlamydia trachomatis serotypes and lack of association between ompA polymorphisms and clinical phenotypes.

    PubMed

    Millman, Kim; Black, Carolyn M; Stamm, Walter E; Jones, Robert B; Hook, Edward W; Martin, David H; Bolan, Gail; Tavaré, Simon; Dean, Deborah

    2006-03-01

    Chlamydia trachomatis is the leading cause of bacterial sexually transmitted diseases worldwide. Urogenital strains are classified into serotypes and genotypes based on the major outer membrane protein and its gene, ompA, respectively. Studies of the association of serotypes with clinical signs and symptoms have produced conflicting results while no studies have evaluated associations with ompA polymorphisms. We designed a population-based cross-sectional study of 344 men and women with urogenital chlamydial infections (excluding co-pathogen infections) presenting to clinics serving five U.S. cities from 1995 to 1997. Signs, symptoms and sequelae of chlamydial infection (mucopurulent cervicitis, vaginal or urethral discharge; dysuria; lower abdominal pain; abnormal vaginal bleeding; and pelvic inflammatory disease) were analyzed for associations with serotype and ompA polymorphisms. One hundred and fifty-three (44.5%) of 344 patients had symptoms consistent with urogenital chlamydial infection. Gender, reason for visit and city were significant independent predictors of symptom status. Men were 2.2 times more likely than women to report any symptoms (P=0.03) and 2.8 times more likely to report a urethral discharge than women were to report a vaginal discharge in adjusted analyses (P=0.007). Differences in serotype or ompA were not predictive except for an association between serotype F and pelvic inflammatory disease (P=0.046); however, the number of these cases was small. While there was no clinically prognostic value associated with serotype or ompA polymorphism for urogenital chlamydial infections except for serotype F, future studies might utilize multilocus genomic typing to identify chlamydial strains associated with clinical phenotypes.

  12. Validation of ‘Variable Number of Tandem Repeat’-Based Approach for Examination of ‘Candidatus Liberibacter asiaticus’ Diversity and Its Applications for the Analysis of the Pathogen Populations in the Areas of Recent Introduction

    PubMed Central

    Matos, Luis A.; Hilf, Mark E.; Chen, Jianchi; Folimonova, Svetlana Y.

    2013-01-01

    Citrus greening (Huanglongbing, HLB) is one of the most destructive diseases of citrus worldwide. In South Asia HLB has been known for more than a century, while in Americas the disease was found relatively recently. HLB is associated with three species of ‘Candidatus Liberibacter’ among which ‘Ca. Liberibacter asiaticus’ (CLas) has most wide distribution. Recently, a number of studies identified different regions in the CLas genome with variable number of tandem repeats (VNTRs) that could be used for examination of CLas diversity. One of the objectives of the work presented here was to further validate the VNTR analysis-based approach by assessing the stability of these repeats upon multiplication of the pathogen in a host over an extended period of time and upon its passaging from a host to a host using CLas populations from Florida. Our results showed that the numbers of tandem repeats in the four loci tested display very distinguishable “signature profiles” for the two Florida-type CLas haplotype groups. Remarkably, the profiles do not change upon passage of the pathogen in citrus and psyllid hosts as well as after its presence within a host over a period of five years, suggesting that VNTR analysis-based approach represents a valid methodology for examination of the pathogen populations in various geographical regions. Interestingly, an extended analysis of CLas populations in different locations throughout Florida and in several countries in the Caribbean and Central America regions and in Mexico where the pathogen has been introduced recently demonstrated the dispersion of the same haplotypes of CLas. On the other hand, these CLas populations appeared to differ significantly from those obtained from locations where the disease has been present for a much longer time. PMID:24223873

  13. Morphological and morphometrical analysis of Heterodera spp. populations in Jordan

    PubMed Central

    Lafi, Hamzeh A.; Al-Banna, Luma; Sadder, Monther T.; Migdadi, Hussein M.

    2015-01-01

    Phenotypic diversity of five Jordanian populations of cyst nematodes, Heterodera spp. collected from five regions from Jordan (Ar-Ramtha, Madaba, Dana, Al-Karak, and Jerash) was investigated. Soil samples were collected from one representative field in each region. Morphological and morphometrical characteristics revealed that Heterodera latipons is dominated in cereal fields at Ar-Ramtha, Madaba, Dana and Al-Karak regions and Heterodera schachtii in Jerash. Cysts populations from all cereal fields had bifenestrate vulval cone and a strong underbridge. Wherever, cysts of the cabbage population had ambifenestrate vulval cone with long vulval slit. The bullae were absent in Ar-Ramtha, Madaba and Dana populations, but present in Al-Karak and Jerash. Based on 12 morphometrical characters, the first three functions in canonical discriminant analysis accounted 99.3% of the total variation. Distance from dorsal gland duct opening to stylet base, underbridge length, a = L/W (body length/midbody width) and length of hyaline tail tip had strong and significant contributions in the first function. While the second function was strongly influenced by length of hyaline tail, fenestral length, fenestral width and tail length. However, the third canonical discriminate function was found to be influenced by stylet length, fenestral length, a = L/W (body length/midbody width) and underbridge width. The graphical representation of the distribution of the samples showed that the first canonical discriminant function clearly separated H. schachtii from Jerash from other populations. Whereas, H. latipons collected from Madaba and Dana were clearly separated in the second function. The results indicated that differences at morphological and morphometrical levels revealed diverse populations of Heterodera spp. in Jordan. PMID:26858546

  14. Characteristics and Outcomes of Patients With Nodular Lymphocyte-Predominant Hodgkin Lymphoma Versus Those With Classical Hodgkin Lymphoma: A Population-Based Analysis

    SciTech Connect

    Gerber, Naamit K.; Atoria, Coral L.; Elkin, Elena B.; Yahalom, Joachim

    2015-05-01

    Purpose: Nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) is rare, comprising approximately 5% of all Hodgkin lymphoma (HL) cases. Patients with NLPHL tend to have better prognoses than those with classical HL (CHL). Our goal was to assess differences in survival between NLPHL and CHL patients, controlling for differences in patient and disease characteristics. Methods and Materials: Using data from the population-based Surveillance, Epidemiology and End Results (SEER) cancer registry program, we identified patients diagnosed with pathologically confirmed HL between 1988 and 2010. Results: We identified 1,162 patients with NLPHL and 29,083 patients with CHL. With a median follow-up of 7 years, 5- and 10-year overall survival (OS) rates were 91% and 83% for NLPHL, respectively, and 81% and 74% for CHL, respectively. After adjusting for all available characteristics, NLPHL (vs CHL) was associated with higher OS (hazard ratio [HR]: 0.62, P<.01) and disease-specific survival (DSS; HR: 0.48, P<.01). The male predominance of NLPHL, compared to CHL, as well as the more favorable prognostic features in NLPHL patients are most pronounced in NLPHL patients <20 years old. Among all NLPHL patients, younger patients were less likely to receive radiation, and radiation use has declined by 40% for all patients from 1988 to 2010. Receipt of radiation was associated with better OS (HR: 0.64, P=.03) and DSS (HR: 0.45, P=.01) in NLPHL patients after controlling for available baseline characteristics. Other factors associated with OS and DSS in NLPHL patients are younger age and early stage. Conclusions: Our results in a large population dataset demonstrated that NLPHL patients have improved prognosis compared to CHL patients, even after accounting for stage and baseline characteristics. Use of radiation is declining among NLPHL patients despite an association in this series between radiation and better DSS and OS. Unique treatment strategies for NLPHL are warranted in both

  15. Psychotropic Medication Burden and Factors Associated with Antipsychotic Use: An Analysis of a Population-Based Sample of Community-Dwelling Older Persons with Dementia

    PubMed Central

    Rhee, YongJoo; Csernansky, John G.; Emanuel, Linda L.; Chang, Chang-Gok; Shega, Joseph W.

    2011-01-01

    Objectives To estimate the proportion of community dwelling older adults with dementia being prescribed a psychotropic and identify patient and caregiver factors associated with antipsychotics use. Methods Retrospective cohort study of The Aging, Demographics, and Memory Study (ADAMS) from 2002 to 2004 designed to assess dementia severity and service use among community-dwelling older adults. The frequency of psychotropic medication (antipsychotics, antidepressants, anticonvulsants and benzodiazepines) use was tabulated and weighted to the US population by dementia diagnosis. Logistic regression analysis identified factors associated with antipsychotic use. Results The 307 participants of ADAMS had the following dementia diagnosis: Alzheimer’s disease (69.29%), vascular dementia (17.74%) and other dementia (12.39%). The proportion of participants prescribed a psychotropic medication broken down by therapeutic class was as 19.07% antipsychotics, 29.08% antidepressants, 9.84% benzodiazepines, and 8.85% anticonvulsants. Older adults with dementia were significantly more likely to receive an antipsychotic if they had moderate dementia (OR =7.4, p<0.05), or severe dementia (OR=5.80, p<0.05), compared to mild dementia or were diagnosed with Alzheimer (OR =6.7, p<0.05) dementia compared to vascular dementia. Older adults with dementia who lived with their caregivers in were significantly less likely to be medicated with antipsychotics (OR= 0.19, p<0.05) compared to those who lived alone. Also, persons with dementia were significantly less likely to be prescribed an antipsychotic if the caregivers were clinically depressed (OR=0.03, p<0.05) compared to those who were not depressed. Conclusion We found psychotropic medication use is common among community-dwelling older adults with dementia. Caregivers appear to have a substantial impact on whether or not an antipsychotic is prescribed, which adds additional complexity to conversations discussing the risk-benefit ratio of

  16. Coherent Population Oscillation-Based Light Storage.

    PubMed

    Neveu, P; Maynard, M-A; Bouchez, R; Lugani, J; Ghosh, R; Bretenaker, F; Goldfarb, F; Brion, E

    2017-02-17

    We theoretically study the propagation and storage of a classical field in a Λ-type atomic medium using coherent population oscillations (CPOs). We show that the propagation eigenmodes strongly relate to the different CPO modes of the system. Light storage in such modes is discussed by introducing a "populariton" quantity, a mixture of populations and field, by analogy to the dark state polariton used in the context of electromagnetically induced transparency light storage protocol. As experimentally shown, this memory relies on populations and is then-by contrast with usual Raman coherence optical storage protocols-robust to dephasing effects.

  17. Coherent Population Oscillation-Based Light Storage

    NASA Astrophysics Data System (ADS)

    Neveu, P.; Maynard, M.-A.; Bouchez, R.; Lugani, J.; Ghosh, R.; Bretenaker, F.; Goldfarb, F.; Brion, E.

    2017-02-01

    We theoretically study the propagation and storage of a classical field in a Λ -type atomic medium using coherent population oscillations (CPOs). We show that the propagation eigenmodes strongly relate to the different CPO modes of the system. Light storage in such modes is discussed by introducing a "populariton" quantity, a mixture of populations and field, by analogy to the dark state polariton used in the context of electromagnetically induced transparency light storage protocol. As experimentally shown, this memory relies on populations and is then—by contrast with usual Raman coherence optical storage protocols—robust to dephasing effects.

  18. Analysis of the bereavement effect after the death of a spouse in the Amish: a population-based retrospective cohort study

    PubMed Central

    Seifter, Ari; Singh, Sarabdeep; McArdle, Patrick F; Ryan, Kathleen A; Shuldiner, Alan R; Mitchell, Braxton D; Schäffer, Alejandro A

    2014-01-01

    Objective This study investigates the association between bereavement and the mortality of a surviving spouse among Amish couples. We hypothesised that the bereavement effect would be relatively small in the Amish due to the unusually cohesive social structure of the Amish that might attenuate the loss of spousal support. Design Population-based cohort study. Setting The USA. Participants 10 892 Amish couples born during 1725–1900 located in Pennsylvania, Ohio and Indiana. All the participants are deceased. Outcome measures The survival time is ‘age’; event is ‘death’. Hazard ratios (HRs) of widowed individuals with respect to gender, age at widowhood, remarriage, the number of surviving children and time since bereavement. Results We observed HRs for widowhood ranging from 1.06 to 1.26 over the study period (nearly all differences significant at p<0.05). Mortality risks tended to be higher in men than in women and in younger compared with older bereaved spouses. There were significantly increased mortality risks in widows and widowers who did not remarry. We observed a higher number of surviving children to be associated with increased mortality in men and women. Mortality risk following bereavement was higher in the first 6 months among men and women. Conclusions We conclude that bereavement effects remain apparent even in this socially cohesive Amish community. Remarriage is associated with a significant decrease in the mortality risk among Amish individuals. Contrary to results from previous studies, an increase in the number of surviving children was associated with decreased survival rate. PMID:24435888

  19. Use of Single- versus Multiple-Fraction Palliative Radiation Therapy for Bone Metastases: Population-Based Analysis of 16,898 Courses in a Canadian Province

    SciTech Connect

    Olson, Robert A.; Tiwana, Manpreet S.; Barnes, Mark; Kiraly, Andrew; Beecham, Kwamena; Miller, Stacy; Hoegler, David; Olivotto, Ivo

    2014-08-01

    Purpose: There is abundant evidence that a single fraction (SF) of palliative radiation therapy (RT) for bone metastases is equivalent to more protracted and costly multiple fraction courses. Despite this, there is low utilization of SFRT internationally. We sought to determine the utilization of SFRT in a population-based, publicly funded health care system. Methods and Materials: All consecutive patients with bone metastases treated with RT during 2007 to 2011 in British Columbia (BC) were identified. Associations between utilization of SFRT and patient and provider characteristics were investigated. Results: A total of 16,898 courses of RT were delivered to 8601 patients. SFRT was prescribed 49% of the time. There were positive relationships among SFRT utilization and primary tumor group (P<.001; most commonly in prostate cancer), worse prognosis (P<.001), increasing physician experience (P<.001), site of metastases (P<.001; least for spine metastases), and area of training (P<.001; most commonly for oncologists trained in the United Kingdom). There was wide variation in the prescription of SFRT across 5 regional cancer centers, ranging from 25.5% to 73.4%, which persisted after controlling for other, potentially confounding factors (P<.001). Conclusions: The large variability in SFRT utilization across BC Cancer Agency (BCCA) cancer centers suggests there is a strong cultural effect, where physicians' use of SFRT is influenced by their colleagues' practice. SFRT use in BC was similar to that in other Canadian and western European reports but strikingly higher than in the United States. Further work is needed to standardize SFRT prescribing practices internationally for this common indication for RT, with the potential for huge health system cost savings and substantial improvements in patients' quality of life.

  20. Influence of early life factors on body mass index trajectory during childhood: a population-based longitudinal analysis in the Western Brazilian Amazon.

    PubMed

    Lourenço, Barbara H; Villamor, Eduardo; Augusto, Rosângela A; Cardoso, Marly A

    2015-04-01

    Low- to middle-income countries may experience the occurrence of a dual burden of under and overnutrition. To better understand the overall progression of body mass index (BMI) during childhood, we estimated average BMI-for-age z-score (BAZ) growth curves in a population-based longitudinal study of 255 children living in the Brazilian Amazon. Children were aged 0.1-5.5 years at recruitment (2003). We collected data on socio-economic and maternal characteristics, children's birthweight and infant feeding practices. Child anthropometric measurements were taken in 2003, 2007 and 2009. BAZ differences among categories of exposure variables were calculated at 6 and 12 months, and 2, 7 and 10 years. At baseline, the mean (standard deviation) age was 2.6 (1.4) years; 12.9% were overweight and 3.9% thin. After adjustment, mean BAZ estimates were mostly negative. Boys were close to the median value for BAZ until 12 months, whereas girls were below the median (P=0.05). Children from households above the wealth median were 0.36 z- and 0.49 z-less underweight than poorer children at 7 and 10 years, respectively (P<0.01). Maternal BMI was positively associated with children's BAZ since 12 months old; BAZ in children from overweight mothers was higher by 0.69 compared with their counterparts at 10 years (P<0.01). Birthweight was positively related to BAZ up until 2 years (P=0.01). Socio-economic background and maternal nutritional status are important predictors of BAZ throughout childhood. Although excessive weight gain is a public health concern, it is critical to restrict inequities, while promoting healthier growth in developing countries.

  1. Do women spend longer on wait lists for coronary bypass surgery? Analysis of a population-based registry in British Columbia, Canada

    PubMed Central

    Levy, Adrian R; Sobolev, Boris G; Kuramoto, Lisa; Hayden, Robert; MacLeod, Stuart M

    2007-01-01

    Background Studies have shown patients who are delayed for surgical cardiac revascularization are faced with increased risks of symptom deterioration and death. This could explain the observation that operative mortality among persons undergoing coronary artery bypass surgery (CABG) is higher among women than men. However, in jurisdictions that employ priority wait lists to manage access to elective cardiac surgery, there is little information on whether women wait longer than men for CABG. It is therefore difficult to ascertain whether higher operative mortality among women is due to biological differences or to delayed access to elective CABG. Methods Using records from a population-based registry, we compared the wait-list time between women and men in British Columbia (BC) between 1990 and 2000. We compared the number of weeks from registration to surgery for equal proportions of women and men, after adjusting for priority, comorbidity and age. Results In BC in the 1990s, 9,167 patients aged 40 years and over were registered on wait lists for CABG and spent a total of 136,071 person-weeks waiting. At the time of registration for CABG, women were more likely to have a comorbid condition than men. We found little evidence to suggest that women waited longer than men for CABG after registration, after adjusting for comorbidity and age, either overall or within three priority groups. Conclusion Our findings support the hypothesis that higher operative mortality during elective CABG operations observed among women is not due to longer delays for the procedure. PMID:17683535

  2. Asthma–COPD overlap syndrome in the US: a prospective population-based analysis of patient-reported outcomes and health care utilization

    PubMed Central

    Vaz Fragoso, Carlos A; Murphy, Terrence E; Agogo, George O; Allore, Heather G; McAvay, Gail J

    2017-01-01

    Background Prior work suggests that asthma–COPD overlap syndrome (ACOS) has a greater health burden than asthma alone or COPD alone. In the current study, we have further evaluated the health burden of ACOS in a nationally representative sample of the US population, focusing on patient-reported outcomes and health care utilization and on comparisons with asthma alone and COPD alone. Patient-reported outcomes are especially meaningful, as these include functional activities that are highly valued by patients and are the basis for patient-centered care. Methods Using data from the Medical Expenditure Panel Survey (MEPS), we evaluated patient-reported outcomes and health care utilization among participants who were aged 40–85 years and had self-reported, physician-diagnosed asthma or COPD. MEPS administered five rounds of interviews, at baseline and approximately every 6 months over 2.5 years. Patient-reported outcomes included activities of daily living (ADLs), mobility, social/recreational activities, disability days in bed, and health status (Short Form 12, Version 2). Health care utilization included outpatient and emergency department (ED) visits, and hospitalization. Results Of 3,486 participants with asthma or COPD, 1,585 (45.4%) had asthma alone, 1,294 (37.1%) had COPD alone, and 607 (17.4%) had ACOS. Relative to asthma alone, ACOS was significantly associated with higher odds of prevalent disability in ADLs and limitations in mobility and social/recreational activities (adjusted odds ratios [adjORs]: 1.91–3.98), as well as with higher odds of incident limitations in mobility and social/recreational activities, disability days in bed, and respiratory-based outpatient and ED visits, and hospitalization (adjORs: 1.86–2.35). In addition, ACOS had significantly worse physical and mental health scores than asthma alone (P-values <0.0001). Relative to COPD alone, ACOS was significantly associated with higher odds of prevalent limitations in mobility and

  3. Genetic Diversity and Phylogenetic Analysis of South-East Asian Duck Populations Based on the mtDNA D-loop Sequences

    PubMed Central

    Sultana, H.; Seo, D. W.; Bhuiyan, M. S. A.; Choi, N. R.; Hoque, M. R.; Heo, K. N.; Lee, J. H.

    2016-01-01

    The maternally inherited mitochondrial DNA (mtDNA) D–loop region is widely used for exploring genetic relationships and for investigating the origin of various animal species. Currently, domestic ducks play an important role in animal protein supply. In this study, partial mtDNA D–loop sequences were obtained from 145 samples belonging to six South-East Asian duck populations and commercial duck population. All these populations were closely related to the mallard duck (Anas platyrhynchos), as indicated by their mean overall genetic distance. Sixteen nucleotide substitutions were identified in sequence analyses allowing the distinction of 28 haplotypes. Around 42.76% of the duck sequences were classified as Hap_02, which completely matched with Anas platyrhynchos duck species. The neighbor-joining phylogenetic tree also revealed that South-East Asian duck populations were closely related to Anas platyrhynchos. Network profiles were also traced using the 28 haplotypes. Overall, results showed that those duck populations D-loop haplotypes were shared between several duck breeds from Korea and Bangladesh sub continental regions. Therefore, these results confirmed that South-East Asian domestic duck populations have been domesticated from Anas platyrhynchos duck as the maternal origins. PMID:27004808

  4. Wealth Inequality and Mental Disability Among the Chinese Population: A Population Based Study.

    PubMed

    Wang, Zhenjie; Du, Wei; Pang, Lihua; Zhang, Lei; Chen, Gong; Zheng, Xiaoying

    2015-10-19

    In the study described herein, we investigated and explored the association between wealth inequality and the risk of mental disability in the Chinese population. We used nationally represented, population-based data from the second China National Sample Survey on Disability, conducted in 2006. A total of 1,724,398 study subjects between the ages of 15 and 64, including 10,095 subjects with mental disability only, were used for the analysis. Wealth status was estimated by a wealth index that was derived from a principal component analysis of 10 household assets and four other variables related to wealth. Logistic regression analysis was used to estimate the odds ratio (OR) and 95% confidence interval (CI) for mental disability for each category, with the lowest quintile category as the referent. Confounding variables under consideration were age, gender, residence area, marital status, ethnicity, education, current employment status, household size, house type, homeownership and living arrangement. The distribution of various types and severities of mental disability differed significantly by wealth index category in the present population. Wealth index category had a positive association with mild mental disability (p for trend <0.01), but had a negative association with extremely severe mental disability (p for trend <0.01). Moreover, wealth index category had a significant, inverse association with mental disability when all severities of mental disability were taken into consideration. This study's results suggest that wealth is a significant factor in the distribution of mental disability and it might have different influences on various types and severities of mental disability.

  5. The long-term relationship between population growth and vegetation cover: an empirical analysis based on the panel data of 21 cities in Guangdong Province, China.

    PubMed

    Li, Chao; Kuang, Yaoqiu; Huang, Ningsheng; Zhang, Chao

    2013-02-07

    It is generally believed that there is an inverse relationship between population growth and vegetation cover. However, reports about vegetation protection and reforestation around the World have been continuously increasing in recent decades, which seems to indicate that this relationship may not be true. In this paper, we have taken 21 cities in Guangdong Province, China as the study area to test the long-term relationship between population growth and vegetation cover, using an AVHRR NDVI data set and the panel cointegrated regression method. The results show that there is a long-term inverted N-shaped curve relationship between population growth and vegetation cover in the region where there are frequent human activities and the influence of climate change on vegetation cover changes is relatively small. The two turning points of the inverted N-shaped curve for the case of Guangdong Province correspond to 2,200 persons · km(-2) and 3,820 persons · km(-2), and they can provide a reference range for similar regions of the World. It also states that the population urbanization may have a negative impact on the vegetation cover at the early stage, but have a positive impact at the later stage. In addition, the Panel Error Correction Model (PECM) is used to investigate the causality direction between population growth and vegetation cover. The results show that not only will the consuming destruction effect and planting construction effect induced by the population growth have a great impact on vegetation cover changes, but vegetation cover changes in turn will also affect the population growth in the long term.

  6. The Long-Term Relationship between Population Growth and Vegetation Cover: An Empirical Analysis Based on the Panel Data of 21 Cities in Guangdong Province, China

    PubMed Central

    Li, Chao; Kuang, Yaoqiu; Huang, Ningsheng; Zhang, Chao

    2013-01-01

    It is generally believed that there is an inverse relationship between population growth and vegetation cover. However, reports about vegetation protection and reforestation around the World have been continuously increasing in recent decades, which seems to indicate that this relationship may not be true. In this paper, we have taken 21 cities in Guangdong Province, China as the study area to test the long-term relationship between population growth and vegetation cover, using an AVHRR NDVI data set and the panel cointegrated regression method. The results show that there is a long-term inverted N-shaped curve relationship between population growth and vegetation cover in the region where there are frequent human activities and the influence of climate change on vegetation cover changes is relatively small. The two turning points of the inverted N-shaped curve for the case of Guangdong Province correspond to 2,200 persons·km−2 and 3,820 persons·km−2, and they can provide a reference range for similar regions of the World. It also states that the population urbanization may have a negative impact on the vegetation cover at the early stage, but have a positive impact at the later stage. In addition, the Panel Error Correction Model (PECM) is used to investigate the causality direction between population growth and vegetation cover. The results show that not only will the consuming destruction effect and planting construction effect induced by the population growth have a great impact on vegetation cover changes, but vegetation cover changes in turn will also affect the population growth in the long term. PMID:23435589

  7. Smoking and poverty in Brazil: an analysis of the profile of the smoking population based on the 2008-09 Brazilian government Family Budget Survey.

    PubMed

    Bazotti, Angelita; Finokiet, Manuela; Conti, Irio Luiz; França, Marco Tulio Aniceto; Waquil, Paulo Dabdab

    2016-01-01

    This paper aims to characterize the Brazilian population who spent money with tobacco products. POF dataset was used from IBGE of the years 2008 and 2009. The same definition that IBGE usually use for tobacco consumer was applied, which is someone has spent money with any kind of tobacco products and its derivatives. It was used individual aspects taking into account such as gender, schooling, age (over 14 years old), income lines, regions and ethnics to characterize these populations. Descriptive statistics were employed to estimate the results and the complex sample design of the survey was considered. According to our results, on average, 10% of the Brazilian population have spent money with tobacco products. Besides, these people are older, earn low salaries and have less schooling than someone who does not consume tobacco. Moreover, for this population 1.5% of the family budget is spent on tobacco products. Last but not least, the most of tobacco consumers are men. In general, money which is spent on tobacco products can cause impressive effects on domestic budget because this value could supply other important necessities to the family. Although there are many monitoring and prevention strategies to avoid tobacco consume, deep knowledge about this population that actually consume these products can increase the efficacy of more specific policies.

  8. Cancer survival in Australia, Canada, Denmark, Norway, Sweden, and the UK, 1995–2007 (the International Cancer Benchmarking Partnership): an analysis of population-based cancer registry data

    PubMed Central

    Coleman, MP; Forman, D; Bryant, H; Butler, J; Rachet, B; Maringe, C; Nur, U; Tracey, E; Coory, M; Hatcher, J; McGahan, CE; Turner, D; Marrett, L; Gjerstorff, ML; Johannesen, TB; Adolfsson, J; Lambe, M; Lawrence, G; Meechan, D; Morris, EJ; Middleton, R; Steward, J; Richards, MA

    2011-01-01

    Summary Background Cancer survival is a key measure of the effectiveness of health-care systems. Persistent regional and international differences in survival represent many avoidable deaths. Differences in survival have prompted or guided cancer control strategies. This is the first study in a programme to investigate international survival disparities, with the aim of informing health policy to raise standards and reduce inequalities in survival. Methods Data from population-based cancer registries in 12 jurisdictions in six countries were provided for 2·4 million adults diagnosed with primary colorectal, lung, breast (women), or ovarian cancer during 1995–2007, with follow-up to Dec 31, 2007. Data quality control and analyses were done centrally with a common protocol, overseen by external experts. We estimated 1-year and 5-year relative survival, constructing 252 complete life tables to control for background mortality by age, sex, and calendar year. We report age-specific and age-standardised relative survival at 1 and 5 years, and 5-year survival conditional on survival to the first anniversary of diagnosis. We also examined incidence and mortality trends during 1985–2005. Findings Relative survival improved during 1995–2007 for all four cancers in all jurisdictions. Survival was persistently higher in Australia, Canada, and Sweden, intermediate in Norway, and lower in Denmark, England, Northern Ireland, and Wales, particularly in the first year after diagnosis and for patients aged 65 years and older. International differences narrowed at all ages for breast cancer, from about 9% to 5% at 1 year and from about 14% to 8% at 5 years, but less or not at all for the other cancers. For colorectal cancer, the international range narrowed only for patients aged 65 years and older, by 2–6% at 1 year and by 2–3% at 5 years. Interpretation Up-to-date survival trends show increases but persistent differences between countries. Trends in cancer incidence and

  9. MLST and Whole-Genome-Based Population Analysis of Cryptococcus gattii VGIII Links Clinical, Veterinary and Environmental Strains, and Reveals Divergent Serotype Specific Sub-populations and Distant Ancestors

    PubMed Central

    Firacative, Carolina; Roe, Chandler C.; Malik, Richard; Ferreira-Paim, Kennio; Escandón, Patricia; Sykes, Jane E.; Castañón-Olivares, Laura Rocío; Contreras-Peres, Cudberto; Samayoa, Blanca; Sorrell, Tania C.; Castañeda, Elizabeth; Lockhart, Shawn R.; Engelthaler, David M.; Meyer, Wieland

    2016-01-01

    The emerging pathogen Cryptococcus gattii causes life-threatening disease in immunocompetent and immunocompromised hosts. Of the four major molecular types (VGI-VGIV), the molecular type VGIII has recently emerged as cause of disease in otherwise healthy individuals, prompting a need to investigate its population genetic structure to understand if there are potential genotype-dependent characteristics in its epidemiology, environmental niche(s), host range and clinical features of disease. Multilocus sequence typing (MLST) of 122 clinical, environmental and veterinary C. gattii VGIII isolates from Australia, Colombia, Guatemala, Mexico, New Zealand, Paraguay, USA and Venezuela, and whole genome sequencing (WGS) of 60 isolates representing all established MLST types identified four divergent sub-populations. The majority of the isolates belong to two main clades, corresponding either to serotype B or C, indicating an ongoing species evolution. Both major clades included clinical, environmental and veterinary isolates. The C. gattii VGIII population was genetically highly diverse, with minor differences between countries, isolation source, serotype and mating type. Little to no recombination was found between the two major groups, serotype B and C, at the whole and mitochondrial genome level. C. gattii VGIII is widespread in the Americas, with sporadic cases occurring elsewhere, WGS revealed Mexico and USA as a likely origin of the serotype B VGIII population and Colombia as a possible origin of the serotype C VGIII population. Serotype B isolates are more virulent than serotype C isolates in a murine model of infection, causing predominantly pulmonary cryptococcosis. No specific link between genotype and virulence was observed. Antifungal susceptibility testing against six antifungal drugs revealed that serotype B isolates are more susceptible to azoles than serotype C isolates, highlighting the importance of strain typing to guide effective treatment to improve the

  10. MLST and Whole-Genome-Based Population Analysis of Cryptococcus gattii VGIII Links Clinical, Veterinary and Environmental Strains, and Reveals Divergent Serotype Specific Sub-populations and Distant Ancestors.

    PubMed

    Firacative, Carolina; Roe, Chandler C; Malik, Richard; Ferreira-Paim, Kennio; Escandón, Patricia; Sykes, Jane E; Castañón-Olivares, Laura Rocío; Contreras-Peres, Cudberto; Samayoa, Blanca; Sorrell, Tania C; Castañeda, Elizabeth; Lockhart, Shawn R; Engelthaler, David M; Meyer, Wieland

    2016-08-01

    The emerging pathogen Cryptococcus gattii causes life-threatening disease in immunocompetent and immunocompromised hosts. Of the four major molecular types (VGI-VGIV), the molecular type VGIII has recently emerged as cause of disease in otherwise healthy individuals, prompting a need to investigate its population genetic structure to understand if there are potential genotype-dependent characteristics in its epidemiology, environmental niche(s), host range and clinical features of disease. Multilocus sequence typing (MLST) of 122 clinical, environmental and veterinary C. gattii VGIII isolates from Australia, Colombia, Guatemala, Mexico, New Zealand, Paraguay, USA and Venezuela, and whole genome sequencing (WGS) of 60 isolates representing all established MLST types identified four divergent sub-populations. The majority of the isolates belong to two main clades, corresponding either to serotype B or C, indicating an ongoing species evolution. Both major clades included clinical, environmental and veterinary isolates. The C. gattii VGIII population was genetically highly diverse, with minor differences between countries, isolation source, serotype and mating type. Little to no recombination was found between the two major groups, serotype B and C, at the whole and mitochondrial genome level. C. gattii VGIII is widespread in the Americas, with sporadic cases occurring elsewhere, WGS revealed Mexico and USA as a likely origin of the serotype B VGIII population and Colombia as a possible origin of the serotype C VGIII population. Serotype B isolates are more virulent than serotype C isolates in a murine model of infection, causing predominantly pulmonary cryptococcosis. No specific link between genotype and virulence was observed. Antifungal susceptibility testing against six antifungal drugs revealed that serotype B isolates are more susceptible to azoles than serotype C isolates, highlighting the importance of strain typing to guide effective treatment to improve the

  11. Who Should Be Targeted for the Prevention of Birth Defects? A Latent Class Analysis Based on a Large, Population-Based, Cross-Sectional Study in Shaanxi Province, Western China

    PubMed Central

    Yang, Wenfang; Li, Danyang; Yang, Xue; Liu, Danli; Zhang, Min; Yan, Hong; Zeng, Lingxia

    2016-01-01

    Background The wide range and complex combinations of factors that cause birth defects impede the development of primary prevention strategies targeted at high-risk subpopulations. Methods Latent class analysis (LCA) was conducted to identify mutually exclusive profiles of factors associated with birth defects among women between 15 and 49 years of age using data from a large, population-based, cross-sectional study conducted in Shaanxi Province, western China, between August and October, 2013. The odds ratios (ORs) and 95% confidence intervals (CIs) of associated factors and the latent profiles of indicators of birth defects and congenital heart defects were computed using a logistic regression model. Results Five discrete subpopulations of participants were identified as follows: No folic acid supplementation in the periconceptional period (reference class, 21.37%); low maternal education level + unhealthy lifestyle (class 2, 39.75%); low maternal education level + unhealthy lifestyle + disease (class 3, 23.71%); unhealthy maternal lifestyle + advanced age (class 4, 4.71%); and multi-risk factor exposure (class 5, 10.45%). Compared with the reference subgroup, the other subgroups consistently had a significantly increased risk of birth defects (ORs and 95% CIs: class 2, 1.75 and 1.21–2.54; class 3, 3.13 and 2.17–4.52; class 4, 5.02 and 3.20–7.88; and class 5, 12.25 and 8.61–17.42, respectively). For congenital heart defects, the ORs and 95% CIs were all higher, and the magnitude of OR differences ranged from 1.59 to 16.15. Conclusions A comprehensive intervention strategy targeting maternal exposure to multiple risk factors is expected to show the strongest results in preventing birth defects. PMID:27183231

  12. Revisiting the Physico-Chemical Hypothesis of Code Origin: An Analysis Based on Code-Sequence Coevolution in a Finite Population

    NASA Astrophysics Data System (ADS)

    Bandhu, Ashutosh Vishwa; Aggarwal, Neha; Sengupta, Supratim

    2013-12-01

    The origin of the genetic code marked a major transition from a plausible RNA world to the world of DNA and proteins and is an important milestone in our understanding of the origin of life. We examine the efficacy of the physico-chemical hypothesis of code origin by carrying out simulations of code-sequence coevolution in finite populations in stages, leading first to the emergence of ten amino acid code(s) and subsequently to 14 amino acid code(s). We explore two different scenarios of primordial code evolution. In one scenario, competition occurs between populations of equilibrated code-sequence sets while in another scenario; new codes compete with existing codes as they are gradually introduced into the population with a finite probability. In either case, we find that natural selection between competing codes distinguished by differences in the degree of physico-chemical optimization is unable to explain the structure of the standard genetic code. The code whose structure is most consistent with the standard genetic code is often not among the codes that have a high fixation probability. However, we find that the composition of the code population affects the code fixation probability. A physico-chemically optimized code gets fixed with a significantly higher probability if it competes against a set of randomly generated codes. Our results suggest that physico-chemical optimization may not be the sole driving force in ensuring the emergence of the standard genetic code.

  13. Inference of population structure and demographic history in Taxodium distichum, a coniferous tree in North America, based on amplicon sequence analysis

    USGS Publications Warehouse

    Ikezaki, Yuka; Suyama, Yoshihisa; Middleton, Beth A.; Tsumura, Yoshihiko; Teshima, Kousuke; Tachida, Hidenori; Kusumi, Junko

    2016-01-01

    PREMISE OF THE STUDY: Studies of natural genetic variation can elucidate the genetic basis of phenotypic variation and the past population structure of species. Our study species, Taxodium distichum, is a unique conifer that inhabits the flood plains and swamps of North America. Morphological and ecological differences in two varieties, T. distichum var. distichum (bald cypress) and T. distichum var. imbricarium (pond cypress), are well known, but little is known about the level of genetic differentiation between the varieties and the demographic history of local populations.METHODS: We analyzed nucleotide polymorphisms at 47 nuclear loci from 96 individuals collected from the Mississippi River Alluvial Valley (MRAV), and Gulf Coastal populations in Texas, Louisiana, and Florida using high-throughput DNA sequencing. Standard population genetic statistics were calculated, and demographic parameters were estimated using a composite-likelihood approach.KEY RESULTS: Taxodium distichum in North America can be divided into at least three genetic groups, bald cypress in the MRAV and Texas, bald cypress in Florida, and pond cypress in Florida. The levels of genetic differentiation among the groups were low but significant. Several loci showed the signatures of positive selection, which might be responsible for local adaptation or varietal differentiation.CONCLUSIONS: Bald cypress was genetically differentiated into two geographical groups, and the boundary was located between the MRAV and Florida. This differentiation could be explained by population expansion from east to west. Despite the overlap of the two varieties’ ranges, they were genetically differentiated in Florida. The estimated demographic parameters suggested that pond cypress split from bald cypress during the late Miocene.

  14. Subdural haemorrhages in infants: population based study

    PubMed Central

    Jayawant, S; Rawlinson, A; Gibbon, F; Price, J; Schulte, J; Sharples, P; Sibert, J R; Kemp, A M

    1998-01-01

    Objectives To identify the incidence, clinical outcome, and associated factors of subdural haemorrhage in children under 2 years of age, and to determine how such cases were investigated and how many were due to child abuse. Design Population based case series. Setting South Wales and south west England. Subjects Children under 2 years of age who had a subdural haemorrhage. We excluded neonates who developed subdural haemorrhage during their stay on a neonatal unit and infants who developed a subdural haemorrhage after infection or neurosurgical intervention. Main outcome measures Incidence and clinical outcome of subdural haemorrhage in infants, the number of cases caused by child abuse, the investigations such children received, and associated risk factors. Results Thirty three children (23 boys and 10 girls) were identified with subdural haemorrhage. The incidence was 12.8/100 000 children/year (95% confidence interval 5.4 to 20.2). Twenty eight cases (85%) were under 1 year of age. The incidence of subdural haemorrhage in children under 1 year of age was 21.0/100 000 children/year and was therefore higher than in the older children. The clinical outcome was poor: nine infants died and 15 had profound disability. Only 22 infants had the basic investigations of a full blood count, coagulation screen, computed tomography or magnetic resonance imaging, skeletal survey or bone scan, and ophthalmological examination. In retrospect, 27 cases (82%) were highly suggestive of abuse. Conclusion Subdural haemorrhage is common in infancy and carries a poor prognosis; three quarters of such infants die or have profound disability. Most cases are due to child abuse, but in a few the cause is unknown. Some children with subdural haemorrhage do not undergo appropriate investigations. We believe the clinical investigation of such children should include a full multidisciplinary social assessment, an ophthalmic examination, a skeletal survey supplemented with a bone scan or a

  15. Model-Based Exposure–Response Analysis of Apixaban to Quantify Bleeding Risk in Special Populations of Subjects Undergoing Orthopedic Surgery

    PubMed Central

    Leil, T A; Frost, C; Wang, X; Pfister, M; LaCreta, F

    2014-01-01

    Population pharmacokinetic (PK) and exposure–response analyses of apixaban were performed using data from phase I–III studies to predict bleeding risks for patients receiving apixaban 2.5 mg b.i.d. after total knee or hip replacement (TKR, THR) surgery (N = 5,510). Renal function, age, gender, and body weight impacted apixaban exposure. Bleeding risk increased as a function of exposure. Predicted bleeding frequencies for TKR and THR populations at risk for high apixaban exposure (female, age > 75 years, calculated creatinine clearance (cCrCL) < 30 ml/min, body weight < 50 kg) (6.85 and 10.3%, respectively) were comparable to the reference population (male/female, age 65−75 years, cCrCL ≥ 80 ml/min, body weight 65−85 kg) (6.18 and 9.32%, respectively). A 100% increase in apixaban exposure is expected to raise bleeding frequencies to 7.25% (TKR) and 10.9% (THR), whereas a 200% increase would raise them to 8.49 and 12.7%. Coexistence of combined patient risk factors or doubling of exposure is not likely to result in a substantial, clinically relevant increase in bleeding risk with 2.5 mg b.i.d. apixaban. PMID:25229619

  16. Global Population Genetic Analysis of Aspergillus fumigatus

    PubMed Central

    Ashu, Eta Ebasi; Hagen, Ferry; Chowdhary, Anuradha

    2017-01-01

    ABSTRACT Aspergillus fumigatus is a ubiquitous opportunistic fungal pathogen capable of causing invasive aspergillosis, a globally distributed disease with a mortality rate of up to 90% in high-risk populations. Effective control and prevention of this disease require a thorough understanding of its epidemiology. However, despite significant efforts, the global molecular epidemiology of A. fumigatus remains poorly understood. In this study, we analyzed 2,026 A. fumigatus isolates from 13 countries in four continents using nine highly polymorphic microsatellite markers. Genetic cluster analyses suggest that our global sample of A. fumigatus isolates belonged to eight genetic clusters, with seven of the eight clusters showing broad geographic distributions. We found common signatures of sexual recombination within individual genetic clusters and clear evidence of hybridization between several clusters. Limited but statistically significant genetic differentiations were found among geographic and ecological populations. However, there was abundant evidence for gene flow at the local, regional, and global scales. Interestingly, the triazole-susceptible and triazole-resistant populations showed different population structures, consistent with antifungal drug pressure playing a significant role in local adaptation. Our results suggest that global populations of A. fumigatus are shaped by historical differentiation, contemporary gene flow, sexual reproduction, and the localized antifungal drug selection that is driving clonal expansion of genotypes resistant to multiple triazole drugs. IMPORTANCE The genetic diversity and geographic structure of the human fungal pathogen A. fumigatus have been the subject of many studies. However, most previous studies had relatively limited sample ranges and sizes and/or used genetic markers with low-level polymorphisms. In this paper, we characterize a global collection of strains of A. fumigatus using a panel of 9 highly

  17. Textural analysis of crystal populations: Looking towards the third dimention

    NASA Astrophysics Data System (ADS)

    Jerram, D. A.; Mock, A.

    2003-04-01

    Crystal populations that erupt at the Earths surface or are frozen in shallow level intrusions contain a record of the evolution, crystallisation history and dynamics of the magma system from which they originate. This information is often recorded from both a geochemical and a textural perspective. Here the information recorded from a textural perspective is investigated with case studies. It is possible to characterise the crystal population in terms of the size variation (Crystal Size Distribution CSD) and their spatial packing arrangement (Spatial Distribution Pattern - SDP). In both cases the rock textures are digitised into Image Analysis packages providing statistical data on crystal sizes and positions. CSD studies provide insight into the growth history of the crystal population and can identify mixed populations of crystals from different parts of the magma system. SDP analysis can define if crystals are forming touching frameworks in 3D and the nature of packing arrangements. Examination of known touching crystal frameworks in olivine (Komatiite cumulates and experimental data) and plagioclase dominant crystal populations (e.g. Holyoke flood basalt, USA) reveals that many touching frameworks involve complex, high porosity, clustered crystal frameworks. Olivine frameworks in Komatiite flows form in days to 10s of days. Plagioclase frameworks are calculated to have formed in less than 17 years for a crystal growth rate of 1x10-10 mm/s and can be less than 3 years for a growth rate of 5x10-10 mm/s based on Crystal Size Distributions. Using serial sections and 3D reconstruction of crystal populations it is possible to test the CSD and SDP techniques that are commonly applied to 2D sections. For example the preliminary results of a 3D reconstruction of Felsic phenocrysts in the Petersberg laccolith, Halle, Germany show that they do not form a touching framework, a confirmation of their 2D SDP data, and that they are irregularly shaped and deviate

  18. Demographic analysis from summaries of an age-structured population.

    PubMed

    Link, William A; Royle, J Andrew; Hatfield, Jeff S

    2003-12-01

    Demographic analyses of age-structured populations typically rely on life history data for individuals, or when individual animals are not identified, on information about the numbers of individuals in each age class through time. While it is usually difficult to determine the age class of a randomly encountered individual, it is often the case that the individual can be readily and reliably assigned to one of a set of age classes. For example, it is often possible to distinguish first-year from older birds. In such cases, the population age structure can be regarded as a latent variable governed by a process prior, and the data as summaries of this latent structure. In this article, we consider the problem of uncovering the latent structure and estimating process parameters from summaries of age class information. We present a demographic analysis for the critically endangered migratory population of whooping cranes (Grus americana), based only on counts of first-year birds and of older birds. We estimate age and year-specific survival rates. We address the controversial issue of whether management action on the breeding grounds has influenced recruitment, relating recruitment rates to the number of seventh-year and older birds, and examining the pattern of variation through time in this rate.

  19. Demographic analysis from summaries of an age-structured population

    USGS Publications Warehouse

    Link, William A.; Royle, J. Andrew; Hatfield, Jeff S.

    2003-01-01

    Demographic analyses of age-structured populations typically rely on life history data for individuals, or when individual animals are not identified, on information about the numbers of individuals in each age class through time. While it is usually difficult to determine the age class of a randomly encountered individual, it is often the case that the individual can be readily and reliably assigned to one of a set of age classes. For example, it is often possible to distinguish first-year from older birds. In such cases, the population age structure can be regarded as a latent variable governed by a process prior, and the data as summaries of this latent structure. In this article, we consider the problem of uncovering the latent structure and estimating process parameters from summaries of age class information. We present a demographic analysis for the critically endangered migratory population of whooping cranes (Grus americana), based only on counts of first-year birds and of older birds. We estimate age and year-specific survival rates. We address the controversial issue of whether management action on the breeding grounds has influenced recruitment, relating recruitment rates to the number of seventh-year and older birds, and examining the pattern of variation through time in this rate.

  20. Projecting the success of plant restoration with population viability analysis

    USGS Publications Warehouse

    Bell, T.J.; Bowles, M.L.; McEachern, A.K.; Brigham, C.A.; Schwartz, M.W.

    2003-01-01

    Conserving viable populations of plant species requires that they have high probabilities of long-term persistence within natural habitats, such as a chance of extinction in 100 years of less than 5% (Menges 1991, 1998; Brown 1994; Pavlik 1994; Chap. 1, this Vol.). For endangered and threatened species that have been severely reduces in range and whose habitats have been fragmented, important species conservation strategies may include augmenting existing populations or restoring new viable populations (Bowles and Whelan 1994; Chap. 2, this Vol.). Restoration objectives may include increasing population numbers to reduce extinction probability, deterministic manipulations to develop a staged cohort structure, or more complex restoration of a desired genetic structure to allow outcrossing or increase effective population size (DeMauro 1993, 1994; Bowles et al. 1993, 1998; Pavlik 1994; Knapp and Dyer 1998; Chap. 2, this Vol.). These efforts may require translocation of propagules from existing (in situ) populations, or from ex situ botanic gardens or seed storage facilities (Falk et al. 1996; Guerrant and Pavlik 1998; Chap. 2, this Vol.). Population viability analysis (PVA) can provide a critical foundation for plant restoration, as it models demographic projections used to evaluate the probability of population persistence and links plant life history with restoration strategies. It is unknown how well artificially created populations will meet demographic modeling requirements (e.g., due to artificial cohort transitions) and few, if any, PVAs have been applied to restorations. To guide application of PVA to restored populations and to illustrate potential difficulties, we examine effects of planting different life stages, model initial population sizes needed to achieve population viability, and compare demographic characteristics between natural and restored populations. We develop and compare plant population restoration viability analysis (PRVA) case studies of

  1. Community-Based Education for Indigenous Populations.

    ERIC Educational Resources Information Center

    Corson, David

    1998-01-01

    Provides an overview of key issues that community-based education initiatives presuppose and highlight. Argues that community-based education is fundamentally different from the more widely-known notion of community education because its implication extends beyond the local community through a critical questioning and contesting of wider…

  2. Evaluation of mixed-population flood-frequency analysis

    USGS Publications Warehouse

    Murphy, P.J.

    2001-01-01

    A mixed population of flood flows was shown to cause quality-of-fit problems if a single-population flood-frequency distribution was used to describe the flood data. The three populations in this mix were "ordinary," tropical cyclone, and ice-jam-release floods. Parametric descriptions of the single and separated flood populations were evaluated using probability-plot correlation-coefficient tests. These tests quantified how well the flood-probability distributions agreed with plotting-position descriptions of the data and quantified the differences due to the mixed-population analysis. High outliers caused the high skewness found in the single- population analyses. The tropical cyclone component was underestimated by single-population analyses at gauging stations in Massachusetts that had little data.

  3. Coverage and predictors of vaccination against 2012/13 seasonal influenza in Madrid, Spain: analysis of population-based computerized immunization registries and clinical records.

    PubMed

    Jiménez-García, Rodrigo; Esteban-Vasallo, María D; Rodríguez-Rieiro, Cristina; Hernandez-Barrera, Valentín; Domínguez-Berjón, M A Felicitas; Carrasco Garrido, Pilar; Lopez de Andres, Ana; Cameno Heras, Moises; Iniesta Fornies, Domingo; Astray-Mochales, Jenaro

    2014-01-01

    We aim to determine 2012-13 seasonal influenza vaccination coverage. Data were analyzed by age group and by coexistence of concomitant chronic conditions. Factors associated with vaccine uptake were identified. We also analyze a possible trend in vaccine uptake in post pandemic seasons. We used computerized immunization registries and clinical records of the entire population of the Autonomous Community of Madrid, Spain (6,284,128 persons) as data source. A total of 871,631 individuals were vaccinated (13.87%). Coverage for people aged ≥ 65 years was 56.57%. Global coverage in people with a chronic condition was 15.7% in children and 18.69% in adults aged 15-59 years. The variables significantly associated with a higher likelihood of being vaccinated in the 2012-13 campaign for the age groups studied were higher age, being Spanish-born, higher number of doses of seasonal vaccine received in previous campaigns, uptake of pandemic vaccination, and having a chronic condition. We conclude that vaccination coverage in persons aged<60 years with chronic conditions is less than acceptable. The very low coverage among children with chronic conditions calls for urgent interventions. Among those aged ≥60 years, uptake is higher but still far from optimal and seems to be descending in post-pandemic campaigns. For those aged ≥65 years the mean percentage of decrease from the 2009/10 to the actual campaign has been 12%. Computerized clinical and immunization registers are useful tools for providing rapid and detailed information about influenza vaccination coverage in the population.

  4. A genetic linkage map of the Durum x Triticum dicoccoides backcross population based on SSRs and AFLP markers, and QTL analysis for milling traits.

    PubMed

    Elouafi, I; Nachit, M M

    2004-02-01

    Durum wheat ( Triticum turgidum L. var durum) is mainly produced and consumed in the Mediterranean region; it is used to produce several specific end-products; such as local pasta, couscous and burghul. To study the genetics of grain-milling quality traits, chromosomal locations, and interaction with the environment, a genetic linkage map of durum was constructed and the quantitative trait loci QTLs for the milling-related traits, test weight (TW) and thousand-kernel weight (TKW), were identified. The population constituted 114 recombinant inbred lines derived from the cross: Omrabi 5 /Triticum dicoccoides 600545// Omrabi 5. TW and TKW were analyzed over 18 environments (sites x years). Single-sequence-repeat markers (SSRs), Amplified-fragment-length-polymorphism markers (AFLPs), and seed storage proteins (SSPs) showed a high level of polymorphism (>60%). The map was constructed with 124 SSRs, 149 AFLPs and 6 SSPs; its length covered 2,288.8 cM (8.2 cM/marker). The map showed high synteny with previous wheat maps, and both SSRs and AFLPs mapped evenly across the genome, with more markers in the B genome. However, some rearrangements were observed. For TW, a high genotypic effect was detected and two QTLs with epistasic effect were identified on 7AS and 6BS, explaining 30% of the total variation. The TKW showed a significant transgressive inheritance and five QTLs were identified, explaining 32% of the total variation, out of which 25% was of a genetic nature, and showing QTLxE interaction. The major TKW-QTLs were around the centromere region of 6B. For both traits, Omrabi 5 alleles had a significant positive effect. This population will be used to determine other QTLs of interest, as its parents are likely to harbor different genes for diseases and drought tolerance.

  5. Bayesian Analysis of Multiple Populations in Galactic Globular Clusters

    NASA Astrophysics Data System (ADS)

    Wagner-Kaiser, Rachel A.; Sarajedini, Ata; von Hippel, Ted; Stenning, David; Piotto, Giampaolo; Milone, Antonino; van Dyk, David A.; Robinson, Elliot; Stein, Nathan

    2016-01-01

    We use GO 13297 Cycle 21 Hubble Space Telescope (HST) observations and archival GO 10775 Cycle 14 HST ACS Treasury observations of Galactic Globular Clusters to find and characterize multiple stellar populations. Determining how globular clusters are able to create and retain enriched material to produce several generations of stars is key to understanding how these objects formed and how they have affected the structural, kinematic, and chemical evolution of the Milky Way. We employ a sophisticated Bayesian technique with an adaptive MCMC algorithm to simultaneously fit the age, distance, absorption, and metallicity for each cluster. At the same time, we also fit unique helium values to two distinct populations of the cluster and determine the relative proportions of those populations. Our unique numerical approach allows objective and precise analysis of these complicated clusters, providing posterior distribution functions for each parameter of interest. We use these results to gain a better understanding of multiple populations in these clusters and their role in the history of the Milky Way.Support for this work was provided by NASA through grant numbers HST-GO-10775 and HST-GO-13297 from the Space Telescope Science Institute, which is operated by AURA, Inc., under NASA contract NAS5-26555. This material is based upon work supported by the National Aeronautics and Space Administration under Grant NNX11AF34G issued through the Office of Space Science. This project was supported by the National Aeronautics & Space Administration through the University of Central Florida's NASA Florida Space Grant Consortium.

  6. Young adults' trajectories of Ecstasy use: a population based study.

    PubMed

    Smirnov, Andrew; Najman, Jake M; Hayatbakhsh, Reza; Plotnikova, Maria; Wells, Helene; Legosz, Margot; Kemp, Robert

    2013-11-01

    Young adults' Ecstasy use trajectories have important implications for individual and population-level consequences of Ecstasy use, but little relevant research has been conducted. This study prospectively examines Ecstasy trajectories in a population-based sample. Data are from the Natural History Study of Drug Use, a retrospective/prospective cohort study conducted in Australia. Population screening identified a probability sample of Ecstasy users aged 19-23 years. Complete data for 30 months of follow-up, comprising 4 time intervals, were available for 297 participants (88.4% of sample). Trajectories were derived using cluster analysis based on recent Ecstasy use at each interval. Trajectory predictors were examined using a generalized ordered logit model and included Ecstasy dependence (World Mental Health Composite International Diagnostic Instrument), psychological distress (Hospital Anxiety Depression Scale), aggression (Young Adult Self Report) and contextual factors (e.g. attendance at electronic/dance music events). Three Ecstasy trajectories were identified (low, intermediate and high use). At its peak, the high-use trajectory involved 1-2 days Ecstasy use per week. Decreasing frequency of use was observed for intermediate and high-use trajectories from 12 months, independently of market factors. Intermediate and high-use trajectory membership was predicted by past Ecstasy consumption (>70 pills) and attendance at electronic/dance music events. High-use trajectory members were unlikely to have used Ecstasy for more than 3 years and tended to report consistently positive subjective effects at baseline. Given the social context and temporal course of Ecstasy use, Ecstasy trajectories might be better understood in terms of instrumental rather than addictive drug use patterns.

  7. Population and genomic lessons from genetic analysis of two Indian populations.

    PubMed

    Juyal, Garima; Mondal, Mayukh; Luisi, Pierre; Laayouni, Hafid; Sood, Ajit; Midha, Vandana; Heutink, Peter; Bertranpetit, Jaume; Thelma, B K; Casals, Ferran

    2014-10-01

    Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.

  8. 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.

  9. A Population-based Habitable Zone Perspective

    NASA Astrophysics Data System (ADS)

    Zsom, Andras

    2015-11-01

    What can we tell about exoplanet habitability if currently only the stellar properties, planet radius, and the incoming stellar flux are known? A planet is in the habitable zone (HZ) if it harbors liquid water on its surface. The HZ is traditionally conceived as a sharp region around stars because it is calculated for one planet with specific properties. Such an approach is limiting because the planet’s atmospheric and geophysical properties, which influence the presence of liquid water on the surface, are currently unknown but expected to be diverse. A statistical HZ description is outlined that does not favor one planet type. Instead, the stellar and planet properties are treated as random variables, and a continuous range of planet scenarios is considered. Various probability density functions are assigned to each random variable, and a combination of Monte Carlo sampling and climate modeling is used to generate synthetic exoplanet populations with known surface climates. Then, the properties of the subpopulation bearing liquid water is analyzed. Given our current observational knowledge, the HZ takes the form of a weakly constrained but smooth probability function. The HZ has an inner edge, but a clear outer edge is not seen. Currently only optimistic upper limits can be derived for the potentially observable HZ occurrence rate. Finally, we illustrate through an example how future data on exoplanet atmospheres will help to narrow down the probability that an exoplanet harbors liquid water, and we identify the greatest observational challenge in the way of finding a habitable exoplanet.

  10. The ethical dilemma of population-based medical decision making.

    PubMed

    Kirsner, R S; Federman, D G

    1998-11-01

    Over the past several years, there has been a growing interest in population-based medicine. Some elements in healthcare have used population-based medicine as a technique to decrease healthcare expenditures. However, in their daily practice of medicine, physicians must grapple with the question of whether they incorporate population-based medicine when making decisions for an individual patient. They therefore may encounter an ethical dilemma. Physicians must remember that the physician-patient relationship is of paramount importance and that even well-conducted research may not be applicable to an individual patient.

  11. Ultrasonographic fetal growth charts: an informatic approach by quantitative analysis of the impact of ethnicity on diagnoses based on a preliminary report on Salentinian population.

    PubMed

    Tinelli, Andrea; Bochicchio, Mario Alessandro; Vaira, Lucia; Malvasi, Antonio

    2014-01-01

    Clear guidance on fetal growth assessment is important because of the strong links between growth restriction or macrosomia and adverse perinatal outcome in order to reduce associated morbidity and mortality. Fetal growth curves are extensively adopted to track fetal sizes from the early phases of pregnancy up to delivery. In the literature, a large variety of reference charts are reported but they are mostly up to five decades old. Furthermore, they do not address several variables and factors (e.g., ethnicity, foods, lifestyle, smoke, and physiological and pathological variables), which are very important for a correct evaluation of the fetal well-being. Therefore, currently adopted fetal growth charts are inadequate to support the melting pot of ethnic groups and lifestyles of our society. Customized fetal growth charts are needed to provide an accurate fetal assessment and to avoid unnecessary obstetric interventions at the time of delivery. Starting from the development of a growth chart purposely built for a specific population, in the paper, authors quantify and analyse the impact of the adoption of wrong growth charts on fetal diagnoses. These results come from a preliminary evaluation of a new open service developed to produce personalized growth charts for specific ethnicity, lifestyle, and other parameters.

  12. Genetic diversity and population structure analysis of the tropical pasture grass Brachiaria humidicola based on microsatellites, cytogenetics, morphological traits, and geographical origin.

    PubMed

    Jungmann, L; Vigna, B B Z; Boldrini, K R; Sousa, A C B; do Valle, C B; Resende, R M S; Pagliarini, M S; Zucchi, M I; de Souza, A P

    2010-09-01

    Brachiaria humidicola (Rendle) Schweick. is a warm-season grass commonly used as forage in the tropics. Accessions of this species were collected in eastern Africa and massively introduced into South America in the 1980s. Several of these accessions form a germplasm collection at the Brazilian Agricultural Research Corporation. However, apomixis, ploidy, and limited knowledge of the genetic basis of this germplasm collection have constrained breeding activities. The objectives of this work were to identify genetic variability in the Brazilian B. humidicola germplasm collection using microsatellite markers and to compare the results with information on the following: (1) collection sites of the accessions; (2) reproductive mode and ploidy levels; and (3) genetic diversity revealed by morphological traits. The evaluated germplasm population is highly structured into four major groups. The sole sexual accession did not group with any of the clusters. Genetic dissimilarities did not correlate with either geographic distances or genetic distances inferred from morphological descriptors. Additionally, the genetic structure identified in this collection did not correspond to differences in ploidy level. Alleles exclusive to either sexual or apomictic accessions were identified, suggesting that further evaluation of the association of these loci with apospory should be carried out.

  13. AN INDIVIDUAL-BASED MODEL OF COTTUS POPULATION DYNAMICS

    EPA Science Inventory

    We explored population dynamics of a southern Appalachian population of Cottus bairdi using a spatially-explicit, individual-based model. The model follows daily growth, mortality, and spawning of individuals as a function of flow and temperature. We modeled movement of juveniles...

  14. National trends in incidence and survival of chronic lymphocytic leukemia in Norway for 1953-2012: a systematic analysis of population-based data.

    PubMed

    Lenartova, Andrea; Johannesen, Tom Børge; Tjønnfjord, Geir Erland

    2016-12-01

    Chronic lymphocytic leukemia is a disease of the elderly, and despite major advances in treatment, remains incurable. The Cancer Registry of Norway has registered data on patients with chronic lymphocytic leukemia since 1953. We aimed to analyze trends in incidence and survival of chronic lymphocytic leukemia in Norway. We identified 7664 patients reported with chronic lymphocytic leukemia to the registry between 1953 and 2012. We gathered information on sex, age at diagnosis, date of death and basis for diagnosis. The age-standardized incidence increased from 0.6/100.000 person-years in 1953 to 3.1/100,000 person-years in 2012. We found a significant decrease in median age between 1993-2002 and 2003-2012 (75 vs. 72 years, 95%CI: 2.52-3.98, P < 0.001). Men were diagnosed at a significantly younger age than women. Immunophenotyping has become the most important diagnostic method after 2002. Median observed survival increased from 3 years in 1952-1963 to 8.5 years in 2003-2012. Five- and 10-year age-standardized net survival increased throughout the whole period across age groups and reached 79% and 57%, respectively. Median observed survival was significantly shorter in men than in women in 1993-2002 (4.9 vs. 6.1 years, P < 0.001). The gap between survival rates for men and women was diminishing in 2003-2012 in patients younger than 60 years while it remained considerable in older patients. Despite an aging Norwegian population, chronic lymphocytic leukemia (CLL) patients become younger at diagnosis. A fourfold increase in incidence, a prolonged survival, and major changes in diagnostic methods in Norway were observed.

  15. Socio-Economic Differences in the Association between Self-Reported and Clinically Present Diabetes and Hypertension: Secondary Analysis of a Population-Based Cross-Sectional Study

    PubMed Central

    Tompkins, Gerald; Forrest, Lynne F.; Adams, Jean

    2015-01-01

    Background Diabetes and hypertension are key risk factors for coronary heart disease. Prevalence of both conditions is socio-economically patterned. Awareness of presence of the conditions may influence risk behaviour and use of preventative services. Our aim was to examine whether there were socio-economic differences in awareness of hypertension and diabetes in a UK population. Method Data from the Scottish Health Survey was used to compare self-reported awareness of hypertension and diabetes amongst those found on examination to have these conditions, by socioeconomic position (SEP) (measured by occupation, education and income). Odds ratios of self-reported awareness against presence, and the sensitivity, specificity and predictive value of self-reporting as a measure of the presence of the condition, were calculated. Results Presence and self-reported awareness of both conditions increased as SEP decreased, on most measures. There was only one significant difference in awareness by SEP once other factors had been taken into account. Sensitivity showed that those in the most disadvantaged groups were most likely to self-report awareness of their hypertension, and specificity showed that those in the least disadvantaged groups were most likely to self-report awareness of its absence. There were few differences of note for diabetes. Conclusion We found no consistent pattern in the associations between SEP and the presence and self-reported awareness of hypertension and diabetes amongst those with these conditions. Without evidence of differences, it is important that universal approaches continue to be applied to the identification and management of those at risk of these and other conditions that underpin cardiovascular disease. PMID:26466384

  16. Survival after Abdominoperineal and Sphincter-Preserving Resection in Nonmetastatic Rectal Cancer: A Population-Based Time-Trend and Propensity Score-Matched SEER Analysis

    PubMed Central

    Warschkow, Rene; Ebinger, Sabrina M.; Brunner, Walter; Schmied, Bruno M.

    2017-01-01

    Background. Abdominoperineal resection (APR) has been associated with impaired survival in nonmetastatic rectal cancer patients. It is unclear whether this adverse outcome is due to the surgical procedure itself or is a consequence of tumor-related characteristics. Study Design. Patients were identified from the Surveillance, Epidemiology, and End Results database. The impact of APR compared to coloanal anastomosis (CAA) on survival was assessed by Cox regression and propensity-score matching. Results. In 36,488 patients with rectal cancer resection, the APR rate declined from 31.8% in 1998 to 19.2% in 2011, with a significant trend change in 2004 at 21.6% (P < 0.001). To minimize a potential time-trend bias, survival analysis was limited to patients diagnosed after 2004. APR was associated with an increased risk of cancer-specific mortality after unadjusted analysis (HR = 1.61, 95% CI: 1.28–2.03, P < 0.01) and multivariable adjustment (HR = 1.39, 95% CI: 1.10–1.76, P < 0.01). After optimal adjustment of highly biased patient characteristics by propensity-score matching, APR was not identified as a risk factor for cancer-specific mortality (HR = 0.85, 95% CI: 0.56–1.29, P = 0.456). Conclusions. The current propensity score-adjusted analysis provides evidence that worse oncological outcomes in patients undergoing APR compared to CAA are caused by different patient characteristics and not by the surgical procedure itself. PMID:28197206

  17. Multimorbidity and healthcare utilization among home care clients with dementia in Ontario, Canada: A retrospective analysis of a population-based cohort

    PubMed Central

    Mondor, Luke; Maxwell, Colleen J.; Hogan, David B.; Gruneir, Andrea

    2017-01-01

    main limitations of this study include use of fixed (versus time-varying) covariates and focus on all-cause rather than cause-specific hospitalizations and ED visits, which could potentially inform interventions. Conclusions Older adults with dementia and multimorbidity pose a particular challenge for health systems. Findings from this study highlight the need to reshape models of care for this complex population, and to further investigate health system and other factors that may modify patients’ risk of health outcomes. PMID:28267802

  18. Associations of Steroid Sex Hormones and Sex Hormone-Binding Globulin With the Risk of Type 2 Diabetes in Women: A Population-Based Cohort Study and Meta-analysis.

    PubMed

    Muka, Taulant; Nano, Jana; Jaspers, Loes; Meun, Cindy; Bramer, Wichor M; Hofman, Albert; Dehghan, Abbas; Kavousi, Maryam; Laven, Joop S E; Franco, Oscar H

    2017-03-01

    It remains unclear whether endogenous sex hormones (ESH) are associated with risk of type 2 diabetes (T2D) in women. Data of 3,117 postmenopausal women participants of the Rotterdam Study were analyzed to examine whether ESH and sex hormone-binding globulin (SHBG) were associated with the risk of incident T2D. Additionally, we performed a systematic review and meta-analysis of studies assessing the prospective association of ESH and SHBG with T2D in women. During a median follow-up of 11.1 years, we identified 384 incident cases of T2D in the Rotterdam Study. No association was observed between total testosterone (TT) or bioavailable testosterone (BT) with T2D. SHBG was inversely associated with the risk of T2D, whereas total estradiol (TE) was associated with increased risk of T2D. Similarly, in the meta-analysis of 13 population-based prospective studies involving more than 1,912 incident T2D cases, low levels of SHBG and high levels of TE were associated with increased risk of T2D, whereas no associations were found for other hormones. The association of SHBG with T2D did not change by menopause status, whereas the associations of ESH and T2D were based only in postmenopausal women. SHBG and TE are independent risk factors for the development of T2D in women.

  19. Demographics of reintroduced populations: estimation, modeling, and decision analysis

    USGS Publications Warehouse

    Converse, Sarah J.; Moore, Clinton T.; Armstrong, Doug P.

    2013-01-01

    Reintroduction can be necessary for recovering populations of threatened species. However, the success of reintroduction efforts has been poorer than many biologists and managers would hope. To increase the benefits gained from reintroduction, management decision making should be couched within formal decision-analytic frameworks. Decision analysis is a structured process for informing decision making that recognizes that all decisions have a set of components—objectives, alternative management actions, predictive models, and optimization methods—that can be decomposed, analyzed, and recomposed to facilitate optimal, transparent decisions. Because the outcome of interest in reintroduction efforts is typically population viability or related metrics, models used in decision analysis efforts for reintroductions will need to include population models. In this special section of the Journal of Wildlife Management, we highlight examples of the construction and use of models for informing management decisions in reintroduced populations. In this introductory contribution, we review concepts in decision analysis, population modeling for analysis of decisions in reintroduction settings, and future directions. Increased use of formal decision analysis, including adaptive management, has great potential to inform reintroduction efforts. Adopting these practices will require close collaboration among managers, decision analysts, population modelers, and field biologists.

  20. Stochastic population forecasts based on conditional expert opinions

    PubMed Central

    Billari, F C; Graziani, R; Melilli, E

    2012-01-01

    The paper develops and applies an expert-based stochastic population forecasting method, which can also be used to obtain a probabilistic version of scenario-based official forecasts. The full probability distribution of population forecasts is specified by starting from expert opinions on the future development of demographic components. Expert opinions are elicited as conditional on the realization of scenarios, in a two-step (or multiple-step) fashion. The method is applied to develop a stochastic forecast for the Italian population, starting from official scenarios from the Italian National Statistical Office. PMID:22879704

  1. 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

  2. A longitudinal population-based analysis of relationship status and mortality in KwaZulu-Natal, South Africa 2001–2011

    PubMed Central

    Channon, Melanie; Hosegood, Victoria; McGrath, Nuala

    2016-01-01

    Background Mortality risk is lower in married than in unmarried men and women. However, little is known about the association between mortality and relationship status in South Africa where marriage rates are low, migration is common, many couples are not co-resident and HIV prevalence is high. Method Using demographic surveillance data collected from 2001 to 2011, relationship status was categorised as conjugal (partners belong to the same household), non-conjugal (partners do not belong to the same household) or not partnered. Rates of relationship formation and dissolution were calculated by age and sex. Controlling for antiretroviral treatment (ART) introduction in 2005 as well as education, sex-specific and age-specific Cox proportional hazards models were used to investigate the association between relationship status and (1) all-cause mortality and (2) non-AIDS mortality. Results Before 2005, individuals in conjugal relationships had a lower hazard of all-cause mortality in all age groups than not partnered men and women. Non-conjugal relationships lowered the risk of dying compared with not partnered men and women in fewer age groups. After ART introduction, the protective association of conjugal relationships was weaker but remained generally significant for men and women but not in non-conjugal relationships. In the later period, the association is reversed in young men (20–29 years) with mortality higher in conjugal and non-conjugal relationships compared with men not partnered. The analysis of non-AIDS deaths provided similar results. Conclusions The higher degree of social connections within a shared household environment that characterises conjugal relationships affords men and women greater protection against mortality. PMID:26254290

  3. Surgical Outcomes of Balanced Deep Lateral and Medial Orbital Wall Decompression in Korean Population: Clinical and Computed Tomography-based Analysis

    PubMed Central

    Choi, Sang Uk; Kim, Kyoung Woo

    2016-01-01

    Purpose To evaluate the clinical outcomes of balanced deep lateral and medial orbital wall decompression and to estimate surgical effects using computed tomography (CT) images in Korean patients with thyroid-associated ophthalmopathy (TAO). Methods Retrospective chart review was conducted in TAO patients with exophthalmos who underwent balanced deep lateral and medial orbital wall decompression. Exophthalmos was measured preoperatively and postoperatively at 1 and 3 months. Postoperative complications were evaluated in all study periods. In addition, decompressed bone volume was estimated using CT images. Thereafter, decompression volume in each decompressed orbital wall was analyzed to evaluate the surgical effect and predictability. Results Twenty-four patients (48 orbits) with an average age of 34.08 ± 7.03 years were evaluated. The mean preoperative and postoperative exophthalmos at 1 and 3 months was 18.91 ± 1.43, 15.10 ± 1.53, and 14.91 ± 1.49 mm, respectively. Bony decompression volume was 0.80 ± 0.29 cm3 at the medial wall and 0.68 ± 0.23 cm3 at the deep lateral wall. Postoperative complications included strabismus (one patient, 2.08%), upper eyelid fold change (four patients, 8.33%), and dysesthesia (four patients, 8.33%). Postsurgical exophthalmos reduction was more highly correlated with the deep lateral wall than the medial wall. Conclusions In TAO patients with exophthalmos, balanced deep lateral and medial orbital wall decompression is a good surgical method with a low-risk of complications. In addition, deep lateral wall decompression has higher surgical predictability than medial wall decompression, as seen with CT analysis. PMID:27051255

  4. FISH-Based Analysis of Clonally Derived CHO Cell Populations Reveals High Probability for Transgene Integration in a Terminal Region of Chromosome 1 (1q13)

    PubMed Central

    Li, Shengwei; Gao, Xiaoping; Peng, Rui; Zhang, Sheng; Fu, Wei

    2016-01-01

    A basic goal in the development of recombinant proteins is the generation of cell lines that express the desired protein stably over many generations. Here, we constructed engineered Chinese hamster ovary cell lines (CHO-S) with a pCHO-hVR1 vector that carried an extracellular domain of a VEGF receptor (VR) fusion gene. Forty-five clones with high hVR1 expression were selected for karyotype analysis. Using fluorescence in situ hybridization (FISH) and G-banding, we found that pCHO-hVR1 was integrated into three chromosomes, including chromosomes 1, Z3 and Z4. Four clones were selected to evaluate their productivity under non-fed, non-optimized shake flask conditions. The results showed that clones 1 and 2 with integration sites on chromosome 1 revealed high levels of hVR1 products (shake flask of approximately 800 mg/L), whereas clones 3 and 4 with integration sites on chromosomes Z3 or Z4 had lower levels of hVR1 products. Furthermore, clones 1 and 2 maintained their productivity stabilities over a continuous period of 80 generations, and clones 3 and 4 showed significant declines in their productivities in the presence of selection pressure. Finally, pCHO-hVR1 localized to the same region at chromosome 1q13, the telomere region of normal chromosome 1. In this study, these results demonstrate that the integration of exogenous hVR1 gene on chromosome 1, band q13, may create a high protein-producing CHO-S cell line, suggesting that chromosome 1q13 may contain a useful target site for the high expression of exogenous protein. This study shows that the integration into the target site of chromosome 1q13 may avoid the problems of random integration that cause gene silencing or also overcome position effects, facilitating exogenous gene expression in CHO-S cells. PMID:27684722

  5. A population-based analysis of predictors of influenza vaccination uptake in pregnant women: The effect of gestational and calendar time.

    PubMed

    Vilca, Luz Maria; Verma, Aman; Buckeridge, David; Campins, Magda

    2017-02-16

    Pregnant women are vaccinated against influenza less frequently than other high-risk groups. To design effective vaccination strategies, we must understand how decisions regarding vaccination may vary by trimester and over vaccination campaigns. We used a Cox model indexed by calendar time to estimate the effect of gestational trimester and other factors on vaccination uptake in a large cohort of pregnant women in Catalonia (Spain) during 2008-09 to 2012-13 influenza vaccination campaigns. We analyzed 247,316 pregnancies. Vaccination coverage was 3.7%, 5.2%, 4.8%, 5.6% and 4.6% from 2008-09 to 2012-13 seasonal vaccination campaigns and 8.3% for the 2009 pandemic vaccination campaign. Pregnant women previously vaccinated had higher uptake than women not previously vaccinated and the hazard ratios (HRs) comparing these 2 groups decreased from 10, the first day of seasonal campaigns, to 1.3 the last day. During the pandemic campaign, HRs decreased over the course of the campaign from 8.6 to 1.9. Women in second and third trimester had higher uptake than women in first trimester, with HR=2.8 and 2.3, respectively, at the start of seasonal campaigns. Influenza vaccination coverage among this cohort of pregnant women was alarmingly low. Our analysis reveals that gestational and calendar time have distinct and interacting effects on vaccination uptake; women in their second trimester and third trimester and previously vaccinated were more prone to be vaccinated, but this effect wanes as the influenza season progresses.

  6. Associations of Serum Manganese Levels with Prediabetes and Diabetes among ≥60-Year-Old Chinese Adults: A Population-Based Cross-Sectional Analysis.

    PubMed

    Wang, Xuan; Zhang, Mingyue; Lui, Guang; Chang, Hong; Zhang, Meilin; Liu, Wei; Li, Ziwei; Liu, Yixin; Huang, Guowei

    2016-08-13

    Older adults can experience glucose metabolism dysfunction, and although manganese may help regulate glucose metabolism, there is little information regarding this association among older people. This cross-sectional study included 2402 Chinese adults who were ≥60 years old in 2013 (Tianjin, China), and evaluated the associations of serum manganese with prediabetes and diabetes. Serum manganese levels were measured using inductively coupled plasma mass spectrometry. Multivariable logistic regression models were used to evaluate the sex-specific associations of manganese levels with diabetes and prediabetes after adjusting for confounding factors (age, sex, life style factors, and health status). Based on the WHO criteria, prediabetes was observed in 15.1% of men and 13.4% of women, while diabetes was observed in 30.0% of men and 34.4% of women. In the final model, the odds ratios (95% confidence interval) for prediabetes according to manganese quartile were 1.000, 0.463 (0.269-0.798), 0.639 (0.383-1.065), and 0.614 (0.365-1.031) among men and 1.000, 0.773 (0.498-1.200), 0.602 (0.382-0.947), and 0.603 (0.381-0.953) among women (p for trend = 0.134 and 0.015, respectively). The lowest prevalence of diabetes among men occurred at a moderate range of serum manganese (p < 0.05). Therefore, appropriate serum manganese levels may help prevent and control prediabetes and diabetes.

  7. Comorbidity profile of poliomyelitis survivors in a Chinese population: a population-based study.

    PubMed

    Kang, Jiunn-Horng; Lin, Herng-Ching

    2011-06-01

    Previous reports of comorbid conditions in poliomyelitis survivors mainly focused on some disease categories, such as respiratory diseases, gastrointestinal diseases, psychiatric diseases, neurological diseases and cancer. Data regarding a wide spectrum of medical comorbidities in patients with poliomyelitis is still sparse. This study aimed to investigate and profile the wide range of comorbidities among the survivors of paralytic poliomyelitis in a Chinese population. In total, 2,032 paralytic poliomyelitis patients were selected as the study group and the comparison group consisted of 10,160 randomly selected enrollees. The comorbidities for analysis were based on a modified version of the Elixhauser Comorbidity Index. Conditional logistic regression analyses were computed to investigate the risk of comorbidities for these two groups. As compared to controls, patients with paralytic poliomyelitis had significantly higher prevalence of hypertension, ischemic heart disease, hyperlipidemia, congestive heart failure, cardiac arrhythmias, peripheral vascular disorder, stroke, paralysis, migraines, Parkinson's disease, rheumatoid arthritis, ankylosing spondylitis, pulmonary circulation disorders, chronic pulmonary disease, liver disease, peptic ulcers, hepatitis B or C, deficiency anemias, depression, and lymphoma. Most of the differences are of clinical interest, ORs often being between 2 and 3. No significant difference between poliomyelitis patients and controls was observed in the prevalence of SLE, tuberculosis, alcohol abuse and drug abuse. Our findings demonstrate that survivors of paralytic poliomyelitis in Taiwan are at higher risk of having multiple medical comorbidities although some potential confounding factors including educational level, marital status, obesity and physical activity are not available in our database. The pattern is generally consistent with previous observations from Western populations. Nevertheless, we found several novel associations

  8. The incidence of cervical spondylosis decreases with aging in the elderly, and increases with aging in the young and adult population: a hospital-based clinical analysis

    PubMed Central

    Wang, Chuanling; Tian, Fuming; Zhou, Yingjun; He, Wenbo; Cai, Zhiyou

    2016-01-01

    Background and purpose Cervical spondylosis is well accepted as a common degenerative change in the cervical spine. Compelling evidence has shown that the incidence of cervical spondylosis increases with age. However, the relationship between age and the incidence of cervical spondylosis remains obscure. It is essential to note the relationship between age and the incidence of cervical spondylosis through more and more clinical data. Methods In the case-controlled study reported here, retrospective clinical analysis of 1,276 cases of cervical spondylosis has been conducted. We analyzed the general clinical data, the relationship between age and the incidence of cervical spondylosis, and the relationship between age-related risk factors and the incidence of cervical spondylosis. A chi-square test was used to analyze the associations between different variables. Statistical significance was defined as a P-value of less than 0.05. Results The imaging examination demonstrated the most prominent characteristic features of cervical spondylosis: bulge or herniation at C3-C4, C4-C5, and C5-C6. The incidence of cervical spondylosis increased with aging before age 50 years and decreased with aging after age 50 years, especially in the elderly after 60 years old. The occurrence rate of bulge or herniation at C3-C4, C4-C5, C5-C6, and C6-C7 increased with aging before age 50 years and decreased with aging after age 50 years, especially after 60 years. Moreover, the incidence of hyperosteogeny and spinal stenosis increased with aging before age 60 years and decreased with aging after age 60 years, although there was no obvious change in calcification. The age-related risk factors, such as hypertension, hyperlipidemia, diabetes, cerebral infarct, cardiovascular diseases, smoking, and drinking, have no relationship with the incidence of cervical spondylosis. Conclusion A decreasing proportion of cervical spondylosis with aging occurs in the elderly, while the proportion of

  9. Associations of Serum Manganese Levels with Prediabetes and Diabetes among ≥60-Year-Old Chinese Adults: A Population-Based Cross-Sectional Analysis

    PubMed Central

    Wang, Xuan; Zhang, Mingyue; Lui, Guang; Chang, Hong; Zhang, Meilin; Liu, Wei; Li, Ziwei; Liu, Yixin; Huang, Guowei

    2016-01-01

    Older adults can experience glucose metabolism dysfunction, and although manganese may help regulate glucose metabolism, there is little information regarding this association among older people. This cross-sectional study included 2402 Chinese adults who were ≥60 years old in 2013 (Tianjin, China), and evaluated the associations of serum manganese with prediabetes and diabetes. Serum manganese levels were measured using inductively coupled plasma mass spectrometry. Multivariable logistic regression models were used to evaluate the sex-specific associations of manganese levels with diabetes and prediabetes after adjusting for confounding factors (age, sex, life style factors, and health status). Based on the WHO criteria, prediabetes was observed in 15.1% of men and 13.4% of women, while diabetes was observed in 30.0% of men and 34.4% of women. In the final model, the odds ratios (95% confidence interval) for prediabetes according to manganese quartile were 1.000, 0.463 (0.269–0.798), 0.639 (0.383–1.065), and 0.614 (0.365–1.031) among men and 1.000, 0.773 (0.498–1.200), 0.602 (0.382–0.947), and 0.603 (0.381–0.953) among women (p for trend = 0.134 and 0.015, respectively). The lowest prevalence of diabetes among men occurred at a moderate range of serum manganese (p < 0.05). Therefore, appropriate serum manganese levels may help prevent and control prediabetes and diabetes. PMID:27529280

  10. Stratification of ALS patients' survival: a population-based study.

    PubMed

    Marin, Benoît; Couratier, Philippe; Arcuti, Simona; Copetti, Massimiliano; Fontana, Andrea; Nicol, Marie; Raymondeau, Marie; Logroscino, Giancarlo; Preux, Pierre Marie

    2016-01-01

    The natural history of amyotrophic lateral sclerosis (ALS) and patient risk stratification are areas of considerable research interest. We aimed (1) to describe the survival of a representative cohort of French ALS patients, and (2) to identify covariates associated with various patterns of survival using a risk classification analysis. ALS patients recruited in the FRALim register (2000-2013) were included. Time-to-death analyses were performed using Kaplan-Meier method and Cox model. A recursive partitioning and amalgamation (RECPAM) algorithm analysis identified subgroups of patients with different patterns of survival. Among 322 patients, median survival times were 26.2 and 15.6 months from time of onset and of diagnosis, respectively. Four groups of patients were identified, depending on their baseline characteristics and survival (1) ALSFRS-R slope >0.46/month and definite or probable ALS (median survival time (MST) 10.6 months); (2) ALSFRS-R slope >0.46/month and possible or probable laboratory-supported ALS (MST: 18.1 months); (3) ALSFRS-R slope ≤0.46/month and definite or probable ALS (MST: 22.5 months), and (4) ALSFRS-R slope ≤0.46/month and possible or probable laboratory-supported ALS (MST: 37.6 months). Median survival time is among the shortest ever reported by a worldwide population-based study. This is probably related to the age structure of the patients (the oldest identified to date), driven by the underlying population (30 % of subjects older than 60 years). Further research in the field of risk stratification could help physicians better anticipate prognosis of ALS patients, and help improve the design of randomized controlled trials.

  11. Analysis of mercury in hair of EPA region V population.

    PubMed

    Pellizzari, E D; Fernando, R; Cramer, G M; Meaburn, G M; Bangerter, K

    1999-01-01

    A scoping study, the National Human Exposure Assessment Survey (NHEXAS) was conducted in EPA Region V from July 1995 to May 1997. This probability-based population study provided an opportunity to examine the mercury levels in 182 participants who provided hair samples. A sensitive analytical procedure based on atomic fluorescence spectrometry was developed and evaluated for the analysis of Hg in approximately 5 mg of human hair. The correlation coefficient (r), the precision, and bias were 0.9983, < or = 1.6%, and < or = 8%, respectively, for standard curves in the hair matrix. The method detection limit (MDL), recovery of Hg in a certified sample (NIES-13), precision (% RSD) for duplicate extract analysis, and precision for duplicate sample analysis averaged 12 ppb (range 4 to 22 ppb), 100 +/- 3% (N=27), 4.6 +/- 2.8 (N=18), and 12.5 +/- 7.4 (N=17), respectively, over the 7 to 8 months of sample analysis. The low MDL yielded 95% of the samples with measurable values, permitting the entire distribution of Hg levels to be characterized. Comparison of annualized Hg distribution in hair with and without background correction revealed a negligible bias on the distribution (1.47% at the 90th percentile). Also, a comparison of the unweighted and nonannualized weighted Hg levels throughout the percentile distribution indicated a small deviation in the upper tail (95th percentile) and is attributable to the small sample size (N=182). The mean, median, and maximum of the annualized Hg levels in hair were 287, 204, and 3505 ppb, respectively. The 75th percentiles were 335 and 368 ppb for the weighted annualized and unweighted distributions, respectively. The percent of individuals in three age categories (0-24, 25-49, and 50 years and older) who exceeded the 75th percentile showed a linear increase with age. Males (N=81) had 10% and 20% lower mean levels than females (N=101) for unweighted and annualized weighted Hg data, respectively. The application of this methodology for

  12. A Latent Class Analysis of Multimorbidity and the Relationship to Socio-Demographic Factors and Health-Related Quality of Life. A National Population-Based Study of 162,283 Danish Adults

    PubMed Central

    Larsen, Finn Breinholt; Pedersen, Marie Hauge; Friis, Karina; Glümer, Charlotte; Lasgaard, Mathias

    2017-01-01

    Objectives To identify patterns of multimorbidity in the general population and examine how these patterns are related to socio-demographic factors and health-related quality of life. Study design and setting We used latent class analysis to identify subgroups with statistically distinct and clinically meaningful disease patterns in a nationally representative sample of Danish adults (N = 162,283) aged 16+ years. The analysis was based on 15 chronic diseases. Results Seven classes with different disease patterns were identified: a class with no or only a single chronic condition (59% of the population) labeled “1) Relatively Healthy” and six classes with a very high prevalence of multimorbidity labeled; “2) Hypertension” (14%); “3) Musculoskeletal Disorders” (10%); “4) Headache-Mental Disorders” (7%); “5) Asthma-Allergy” (6%); “6) Complex Cardiometabolic Disorders” (3%); and “7) Complex Respiratory Disorders” (2%). Female gender was associated with an increased likelihood of belonging to any of the six multimorbidity classes except for class 2 (Hypertension). Low educational attainment predicted membership of all of the multimorbidity classes except for class 5 (Asthma-Allergy). Marked differences in health-related quality of life between the seven latent classes were found. Poor health-related quality of life was highly associated with membership of class 6 (Complex Cardiometabolic Disorders) and class 7 (Complex Respiratory Disorders). Despite different disease patterns, these two classes had nearly identical profiles in relation to health-related quality of life. Conclusion The results clearly support that diseases tend to compound and interact, which suggests that a differentiated public health and treatment approach towards multimorbidity is needed. PMID:28056050

  13. Population-based prevention of influenza in Dutch general practice.

    PubMed Central

    Hak, E; Hermens, R P; van Essen, G A; Kuyvenhoven, M M; de Melker, R A

    1997-01-01

    BACKGROUND: Although the effectiveness of influenza vaccination in high-risk groups has been proven, vaccine coverage continues to be less than 50% in The Netherlands. To improve vaccination rates, data on the organizational factors, which should be targeted in population-based prevention of influenza, is essential. AIM: To assess the organizational factors in Dutch general practice, which were associated with the influenza vaccination rate in 1994. METHOD: A retrospective questionnaire study was undertaken in 1586 of the 4758 Dutch general practices, which were randomly selected. A total of 1251 (79%) practices returned a questionnaire. The items verified were practice profile, urbanization, delegation index, use of computer-based patient records, influenza vaccination characteristics and influenza vaccination rate. RESULTS: No differences were found with regard to the percentage of single-handed practices (65%), practices situated in urban area (38%), practices with a pharmacy (12%), patients insured by the National Health Service (59%) and use of computer-based patient records (57%) when compared with national statistics. The mean overall influenza vaccination rate was 9.0% (SD 4.0%). Using a logistic regression analysis, a high vaccination rate (> or = 9%) was associated with the use of personal reminders (odds ratio (OR) 1.7, 1.3-2.2), monitoring patient compliance (OR 1.8, 1.3-2.4), marking risk patients in computer-based patient records (OR 1.3, 1.0-1.6), a small number of patients per full-time practice assistant (OR 1.5, 1.1-1.9), urban areas (OR 1.6, 1.3-2.1) and single-handed practices (OR 1.5, 1.1-1.9). CONCLUSION: Improvement of vaccination rates in high-risk patients may be achievable by promoting the use of personal reminders and computer-based patient records, as well as monitoring patient compliance. In addition, the role of practice assistants with regard to preventive activities should be developed further. Practices situated in rural areas and

  14. IBSEM: An Individual-Based Atlantic Salmon Population Model.

    PubMed

    Castellani, Marco; Heino, Mikko; Gilbey, John; Araki, Hitoshi; Svåsand, Terje; Glover, Kevin A

    2015-01-01

    Ecology and genetics can influence the fate of individuals and populations in multiple ways. However, to date, few studies consider them when modelling the evolutionary trajectory of populations faced with admixture with non-local populations. For the Atlantic salmon, a model incorporating these elements is urgently needed because many populations are challenged with gene-flow from non-local and domesticated conspecifics. We developed an Individual-Based Salmon Eco-genetic Model (IBSEM) to simulate the demographic and population genetic change of an Atlantic salmon population through its entire life-cycle. Processes such as growth, mortality, and maturation are simulated through stochastic procedures, which take into account environmental variables as well as the genotype of the individuals. IBSEM is based upon detailed empirical data from salmon biology, and parameterized to reproduce the environmental conditions and the characteristics of a wild population inhabiting a Norwegian river. Simulations demonstrated that the model consistently and reliably reproduces the characteristics of the population. Moreover, in absence of farmed escapees, the modelled populations reach an evolutionary equilibrium that is similar to our definition of a 'wild' genotype. We assessed the sensitivity of the model in the face of assumptions made on the fitness differences between farm and wild salmon, and evaluated the role of straying as a buffering mechanism against the intrusion of farm genes into wild populations. These results demonstrate that IBSEM is able to capture the evolutionary forces shaping the life history of wild salmon and is therefore able to model the response of populations under environmental and genetic stressors.

  15. IBSEM: An Individual-Based Atlantic Salmon Population Model

    PubMed Central

    Castellani, Marco; Heino, Mikko; Gilbey, John; Araki, Hitoshi; Svåsand, Terje; Glover, Kevin A.

    2015-01-01

    Ecology and genetics can influence the fate of individuals and populations in multiple ways. However, to date, few studies consider them when modelling the evolutionary trajectory of populations faced with admixture with non-local populations. For the Atlantic salmon, a model incorporating these elements is urgently needed because many populations are challenged with gene-flow from non-local and domesticated conspecifics. We developed an Individual-Based Salmon Eco-genetic Model (IBSEM) to simulate the demographic and population genetic change of an Atlantic salmon population through its entire life-cycle. Processes such as growth, mortality, and maturation are simulated through stochastic procedures, which take into account environmental variables as well as the genotype of the individuals. IBSEM is based upon detailed empirical data from salmon biology, and parameterized to reproduce the environmental conditions and the characteristics of a wild population inhabiting a Norwegian river. Simulations demonstrated that the model consistently and reliably reproduces the characteristics of the population. Moreover, in absence of farmed escapees, the modelled populations reach an evolutionary equilibrium that is similar to our definition of a ‘wild’ genotype. We assessed the sensitivity of the model in the face of assumptions made on the fitness differences between farm and wild salmon, and evaluated the role of straying as a buffering mechanism against the intrusion of farm genes into wild populations. These results demonstrate that IBSEM is able to capture the evolutionary forces shaping the life history of wild salmon and is therefore able to model the response of populations under environmental and genetic stressors. PMID:26383256

  16. The association between ALS and population density: A population based study.

    PubMed

    Scott, Kirsten M; Abhinav, Kumar; Wijesekera, Lokesh; Ganesalingam, Jeban; Goldstein, Laura H; Janssen, Anna; Dougherty, Andrew; Willey, Emma; Stanton, Biba R; Turner, Martin R; Ampong, Mary-Ann; Sakel, Mohammed; Orrell, Richard; Howard, Robin; Shaw, Christopher E; Nigel Leigh, P; Al-Chalabi, Ammar

    2010-10-01

    We aimed to assess whether rural residence is associated with amyotrophic lateral sclerosis in the south-east of England using a population based register. Previous studies in different populations have produced contradictory findings. Residence defined by London borough or non-metropolitan district at time of diagnosis was recorded for each incident case in the South-East England ALS Register between 1995 and 2005. Each of the 26 boroughs or districts of the catchment area of the register was classified according to population density. Age- and sex-adjusted incidence of ALS was calculated for each region and the relationship with population density tested by linear regression, thereby controlling for the underlying population structure. We found that population density in region of residence at diagnosis explained 25% of the variance in ALS rates (r = 0.5, p < 0.01). Thus, in this cohort in the south-east of England, people with ALS were more likely to be resident in areas of high population density at diagnosis.

  17. The use of metabolomics in population-based research.

    PubMed

    Su, L Joseph; Fiehn, Oliver; Maruvada, Padma; Moore, Steven C; O'Keefe, Stephen J; Wishart, David S; Zanetti, Krista A

    2014-11-01

    The NIH has made a significant commitment through the NIH Common Fund's Metabolomics Program to build infrastructure and capacity for metabolomics research, which should accelerate the field. Given this investment, it is the ideal time to start planning strategies to capitalize on the infrastructure being established. An obvious gap in the literature relates to the effective use of metabolomics in large-population studies. Although published reports from population-based studies are beginning to emerge, the number to date remains relatively small. Yet, there is great potential for using metabolomics in population-based studies to evaluate the effects of nutritional, pharmaceutical, and environmental exposures (the "exposome"); conduct risk assessments; predict disease development; and diagnose diseases. Currently, the majority of the metabolomics studies in human populations are in nutrition or nutrition-related fields. This symposium provided a timely venue to highlight the current state-of-science on the use of metabolomics in population-based research. This session provided a forum at which investigators with extensive experience in performing research within large initiatives, multi-investigator grants, and epidemiology consortia could stimulate discussion and ideas for population-based metabolomics research and, in turn, improve knowledge to help devise effective methods of health research.

  18. Analysis of Population Substructure in Two Sympatric Populations of Gran Chaco, Argentina

    PubMed Central

    Sevini, Federica; Yao, Daniele Yang; Lomartire, Laura; Barbieri, Annalaura; Vianello, Dario; Ferri, Gianmarco; Moretti, Edgardo; Dasso, Maria Cristina; Garagnani, Paolo; Pettener, Davide; Franceschi, Claudio; Luiselli, Donata; Franceschi, Zelda Alice

    2013-01-01

    Sub-population structure and intricate kinship dynamics might introduce biases in molecular anthropology studies and could invalidate the efforts to understand diseases in highly admixed populations. In order to clarify the previously observed distribution pattern and morbidity of Chagas disease in Gran Chaco, Argentina, we studied two populations (Wichí and Criollos) recruited following an innovative bio-cultural model considering their complex cultural interactions. By reconstructing the genetic background and the structure of these two culturally different populations, the pattern of admixture, the correspondence between genealogical and genetic relationships, this integrated perspective had the power to validate data and to link the gap usually relying on a singular discipline. Although Wichí and Criollos share the same area, these sympatric populations are differentiated from the genetic point of view as revealed by Non Recombinant Y Chromosome genotyping resulting in significantly high Fst values and in a lower genetic variability in the Wichí population. Surprisingly, the Amerindian and the European components emerged with comparable amounts (20%) among Criollos and Wichí respectively. The detailed analysis of mitochondrial DNA showed that the two populations have as much as 87% of private haplotypes. Moreover, from the maternal perspective, despite a common Amerindian origin, an Andean and an Amazonian component emerged in Criollos and in Wichí respectively. Our approach allowed us to highlight that quite frequently there is a discrepancy between self-reported and genetic kinship. Indeed, if self-reported identity and kinship are usually utilized in population genetics as a reliable proxy for genetic identity and parental relationship, in our model populations appear to be the result not only and not simply of the genetic background but also of complex cultural determinants. This integrated approach paves the way to a rigorous reconstruction of

  19. Population viability analysis of the Endangered shortnose sturgeon

    SciTech Connect

    Jager, Yetta; Bevelhimer, Mark S; Peterson, Douglas L.

    2011-07-01

    This study used population viability analysis (PVA) to partition the influences of potential threats to the endangered shortnose sturgeon (Acipenser brevirostrum). A workshop brought together experts to help identify potential threats including groundwater withdrawal, poor water quality, saltwater intrusion, mercury effects, harvest as by-catch, and sedimentation of spawning habitat. During the course of the project, we eliminated some threats and added new ones. Groundwater withdrawal was dismissed after a study failed to identify connection with groundwater and the majority of pumping is from a confined aquifer. We also eliminated activities on Fort Stewart as influences on spawning habitat because any successful spawning must occur upstream of Fort Stewart. We added climate change to the list of threats based on our assessment of temperature effects and expectations of sea-level rise. Our study highlighted the role of populations in nearby rivers in providing metapopulation support, raising the concern that the population in the Ogeechee River acts as a demographic sink. As part of this study, we carried out a field sampling study to analyze effects of training activities on headwater streams. We developed a new methodology for sampling design as part of this effort and used a mixed-modeling approach to identify relationships between land cover-land use, including those associated with military training activity and water quality. We found that tank training was associated with higher suspended sediment and equipment training was associated with higher organic carbon) and water quality. We detected effects of training on suspended sediment and organic carbon. We also carried out a field sampling effort in the Canoochee and Ogeechee Rivers. In the Ogeechee River, we found that dissolved oxygen in 40% of measurements during summer were below 4 mg L-1. To evaluate mercury as a potential threat, we developed a mercury uptake model and analyzed mercury levels in

  20. Genetic analysis in the Collaborative Cross breeding population

    PubMed Central

    Philip, Vivek M.; Sokoloff, Greta; Ackert-Bicknell, Cheryl L.; Striz, Martin; Branstetter, Lisa; Beckmann, Melissa A.; Spence, Jason S.; Jackson, Barbara L.; Galloway, Leslie D.; Barker, Paul; Wymore, Ann M.; Hunsicker, Patricia R.; Durtschi, David C.; Shaw, Ginger S.; Shinpock, Sarah; Manly, Kenneth F.; Miller, Darla R.; Donohue, Kevin D.; Culiat, Cymbeline T.; Churchill, Gary A.; Lariviere, William R.; Palmer, Abraham A.; O'Hara, Bruce F.; Voy, Brynn H.; Chesler, Elissa J.

    2011-01-01

    Genetic reference populations in model organisms are critical resources for systems genetic analysis of disease related phenotypes. The breeding history of these inbred panels may influence detectable allelic and phenotypic diversity. The existing panel of common inbred strains reflects historical selection biases, and existing recombinant inbred panels have low allelic diversity. All such populations may be subject to consequences of inbreeding depression. The Collaborative Cross (CC) is a mouse reference population with high allelic diversity that is being constructed using a randomized breeding design that systematically outcrosses eight founder strains, followed by inbreeding to obtain new recombinant inbred strains. Five of the eight founders are common laboratory strains, and three are wild-derived. Since its inception, the partially inbred CC has been characterized for physiological, morphological, and behavioral traits. The construction of this population provided a unique opportunity to observe phenotypic variation as new allelic combinations arose through intercrossing and inbreeding to create new stable genetic combinations. Processes including inbreeding depression and its impact on allelic and phenotypic diversity were assessed. Phenotypic variation in the CC breeding population exceeds that of existing mouse genetic reference populations due to both high founder genetic diversity and novel epistatic combinations. However, some focal evidence of allele purging was detected including a suggestive QTL for litter size in a location of changing allele frequency. Despite these inescapable pressures, high diversity and precision for genetic mapping remain. These results demonstrate the potential of the CC population once completed and highlight implications for development of related populations. PMID:21734011

  1. Stellar populations in ω Centauri: a multivariate analysis

    NASA Astrophysics Data System (ADS)

    Fraix-Burnet, D.; Davoust, E.

    2015-07-01

    We have performed multivariate statistical analyses of photometric and chemical abundance parameters of three large samples of stars in the globular cluster ω Centauri. The statistical analysis of a sample of 735 stars based on seven chemical abundances with the method of Maximum Parsimony (cladistics) yields the most promising results: seven groups are found, distributed along three branches with distinct chemical, spatial and kinematical properties. A progressive chemical evolution can be traced from one group to the next, but also within groups, suggestive of an inhomogeneous chemical enrichment of the initial interstellar matter. The adjustment of stellar evolution models shows that the groups with metallicities [Fe/H] > -1.5 are Helium enriched, thus presumably of second generation. The spatial concentration of the groups increases with chemical evolution, except for two groups, which stand out in their other properties as well. The amplitude of rotation decreases with chemical evolution, except for two of the three metal-rich groups, which rotate fastest, as predicted by recent hydrodynamical simulations. The properties of the groups are interpreted in terms of star formation in gas clouds of different origins. In conclusion, our multivariate analysis has shown that metallicity alone cannot segregate the different populations of ω Centauri.

  2. Population genetics of Parascaris equorum based on DNA fingerprinting.

    PubMed

    Tydén, E; Morrison, D A; Engström, A; Nielsen, M K; Eydal, M; Höglund, J

    2013-01-01

    The large roundworm of horses, Parascaris equorum is considered ubiquitous in breeding operations, and is regarded as a most important helminth pathogen of foals. Over the past decade, this parasite has been reported increasingly resistant to anthelmintic drugs worldwide. This paper reports analysis of the population genetic structure of P. equorum. Adult parasites (n=194) collected from Sweden, Norway, Iceland, Germany, Brazil and the USA were investigated by amplified restriction fragment length polymorphism (AFLP) analysis. The genetic variation was low (Hj=0.12-0.4), for the global population of worms. This was accompanied by a weak degree of population structure (Fst=0.2), low gene flow (Nm=1.0) and low mutation rate (4 Nμ=0.07). Thus, the low genetic diversity is probably a result of a low mutation rate in DNA, although the gene flow (due to global movement of horses) is large enough to allow the spread of novel mutations. Surprisingly, isolates from Icelandic horses were not found to be different from other isolates, in spite of the fact that these have been isolated for thousands of years. The study indicates that the global P. equorum population is essentially homogenous, and continents do not appear to be strong barriers for the population structure of this species. Consequently, the potential spread of rare anthelmintic resistance genes may be rapid in a homogenous population.

  3. Important population viability analysis parameters for giant pandas (Aliuropoda melanoleuca).

    PubMed

    Gong, Minghao; Song, Yanling; Yang, Zhisong; Lin, Chen

    2012-06-01

    Population viability analysis (PVA) is a tool to evaluate the risk of extinction for endangered species and aid conservation decision-making. The quality of PVA output is dependent on parameters related to population dynamics and life-history; however, it has been difficult to collect this information for the giant panda (Aliuropoda melanoleuca), a rare and endangered mammal native to China, confined to some 30 fragmented habitat patches. Since giant pandas are long-lived, mature late, have lower reproductive rates, and show little sexual dimorphism, obtaining data to perform adequate PVA has been difficult. Here, we develop a parameter sensitivity index by modeling the dynamics of six giant panda populations in the Minshan Mountains, in order to determine the parameters most influential to giant panda populations. Our data shows that the giant panda populations are most sensitive to changes in four female parameters: initial breeding age, reproductive rate, mortality rate between age 0 and 1, and mortality rate of adults. The parameter sensitivity index strongly correlated with initial population size, as smaller populations were more sensitive to changes in these four variables. This model suggests that demographic parameters of females have more influence on the results of PVA, indicating that females may play a more important role in giant panda population dynamics than males. Consequently, reintroduction of female individuals to a small giant panda population should be a high priority for conservation efforts. Our findings form a technical basis for the coming program of giant panda reintroduction, and inform which parameters are crucial to successfully and feasibly monitoring wild giant panda populations.

  4. Population viability analysis of plant and animal populations with stochastic integral projection models.

    PubMed

    Jaffré, Malo; Le Galliard, Jean-François

    2016-12-01

    Integral projection models (IPM) make it possible to study populations structured by continuous traits. Recently, Vindenes et al. (Ecology 92:1146-1156, 2011) proposed an extended IPM to analyse the dynamics of small populations in stochastic environments, but this model has not yet been used to conduct population viability analyses. Here, we used the extended IPM to analyse the stochastic dynamics of IPM of small size-structured populations in one plant and one animal species (evening primrose and common lizard) including demographic stochasticity in both cases and environmental stochasticity in the lizard model. We also tested the accuracy of a diffusion approximation of the IPM for the two empirical systems. In both species, the elasticity for λ was higher with respect to parameters linked to body growth and size-dependent reproduction rather than survival. An analytical approach made it possible to quantify demographic and environmental variance to calculate the average stochastic growth rate. Demographic variance was further decomposed to gain insights into the most important size classes and demographic components. A diffusion approximation provided a remarkable fit to the stochastic dynamics and cumulative extinction risk, except for very small populations where stochastic growth rate was biased upward or downward depending on the model. These results confirm that the extended IPM provides a powerful tool to assess the conservation status and compare the stochastic demography of size-structured species, but should be complemented with individual based models to obtain unbiased estimates for very small populations of conservation concern.

  5. Unbiased methods for population-based association studies.

    PubMed

    Devlin, B; Roeder, K; Bacanu, S A

    2001-12-01

    Large, population-based samples and large-scale genotyping are being used to evaluate disease/gene associations. A substantial drawback to such samples is the fact that population substructure can induce spurious associations between genes and disease. We review two methods, called genomic control (GC) and structured association (SA), that obviate many of the concerns about population substructure by using the features of the genomes present in the sample to correct for stratification. The GC approach exploits the fact that population substructure generates "over dispersion" of statistics used to assess association. By testing multiple polymorphisms throughout the genome, only some of which are pertinent to the disease of interest, the degree of overdispersion generated by population substructure can be estimated and taken into account. The SA approach assumes that the sampled population, although heterogeneous, is composed of subpopulations that are themselves homogeneous. By using multiple polymorphisms throughout the genome, this "latent class method" estimates the probability sampled individuals derive from each of these latent subpopulations. GC has the advantage of robustness, simplicity, and wide applicability, even to experimental designs such as DNA pooling. SA is a bit more complicated but has the advantage of greater power in some realistic settings, such as admixed populations or when association varies widely across subpopulations. It, too, is widely applicable. Both also have weaknesses, as elaborated in our review.

  6. [Life table and spectral analysis of endangered plant Taxus chinensis var. mairei population].

    PubMed

    Hong, Wei; Wang, Xingong; Wu, Chengzhen; He, Dongjin; Liao, Chengzhang; Cheng, Yu; Feng, Lei

    2004-06-01

    Based on the investigation in Longxi Mountain National Nature Reserve and the theory of survival analysis, a static life table of Taxus chinensis var. mairei population was worked out, the curves of its survival rate, mortality rate and killing power were drawn, and the population dynamics was analyzed by spectral analysis. The results showed that the survival curve of the population appeared to be a type of Deevey-III, and the high mortality of seeding was one of the important reasons which caused Taxus chinensis var. mairei to be endangered. The spectral analysis of the population showed that there was a marked periodic regularity in the process of natural regeneration of Taxus chinensis var. mairei.

  7. [Analysis of population stratification using random SNPs in genome-wide association studies].

    PubMed

    Cao, Zong-Fu; Ma, Chuan-Xiang; Wang, Lei; Cai, Bin

    2010-09-01

    Since population genetic STRUCTURE can increase false-positive rate in genome-wide association studies (GWAS) for complex diseases, the effect of population stratification should be taken into account in GWAS. However, the effect of randomly selected SNPs in population stratification analysis is underdetermined. In this study, based on the genotype data generated on Genome-Wide Human SNP Array 6.0 from unrelated individuals of HapMap Phase2, we randomly selected SNPs that were evenly distributed across the whole-genome, and acquired Ancestry Informative Markers (AIMs) by the method of f value and allelic Fisher exact test. F-statistics and STRUCTURE analysis based on the select different sets of SNPs were used to evaluate the effect of distinguishing the populations from HapMap Phase3. We found that randomly selected SNPs that were evenly distributed across the whole-genome were able to be used to identify the population structure. This study further indicated that more than 3 000 randomly selected SNPs that were evenly distributed across the whole-genome were substituted for AIMs in population stratification analysis, when there were no available AIMs for spe-cific populations.

  8. Psoriasis and dyslipidaemia: a population-based study.

    PubMed

    Dreiher, Jacob; Weitzman, Dahlia; Davidovici, Batya; Shapiro, Jonathan; Cohen, Arnon D

    2008-01-01

    Previous reports demonstrated an association between psoriasis and the metabolic syndrome. The aim of this study was to elucidate the association between psoriasis and dyslipidaemia. A cross-sectional study was performed utilizing a population-based database. Psoriasis patients were compared with enrollees without psoriasis regarding the prevalence of dyslipidaemia and lipid levels. Comparison of lipid levels was performed on a "low-risk" subset of subjects without diabetes, hypertension and cardiovascular disease. The study included 10,669 psoriasis patients and 22,996 subjects without psoriasis. The prevalence of dyslipidaemia was significantly higher in psoriasis patients (odds ratio (OR) = 1.48, 95% confidence interval (CI) 1.40-1.55). The association remained significant after controlling for confounders (OR = 1.19, 95% CI 1.12-1.26, p < 0.001). In multivariate analysis of the "low-risk" subset, triglyceride levels were higher in psoriasis patients and high-density lipoprotein cholesterol levels were lower. This study supports previous reports of an association between psoriasis and lipid abnormalities.

  9. Stress and dysmenorrhoea: a population based prospective study

    PubMed Central

    Wang, L; Wang, X; Wang, W; Chen, C; Ronnennberg, A; Guang, W; Huang, A; Fang, Z; Zang, T; Wang, L; Xu, X

    2004-01-01

    Background: Dysmenorrhoea is the most common gynaecological disorder in women of reproductive age. Despite the association between stress and pregnancy outcomes, few studies have examined the possible link between stress and dysmenorrhoea. Aims and Methods: Using a population based cohort of Chinese women, the independent effect of women's perceived stress in the preceding menstrual cycle on the incidence of dysmenorrhoea in the subsequent cycle was investigated prospectively. The analysis included 1160 prospectively observed menstrual cycles from 388 healthy, nulliparous, newly married women who intended to conceive. The perception of stress and the occurrence of dysmenorrhoea in each menstrual cycle were determined from daily diaries recorded by the women. Results: After adjustment for important covariates, the risk of dysmenorrhoea was more than twice as great among women with high stress compared to those with low stress in the preceding cycle (OR = 2.4; 95% CI 1.4 to 4.3). The risk of dysmenorrhoea was greatest among women with both high stress and a history of dysmenorrhoea compared to women with low stress and no history of dysmenorrhoea (OR = 10.4, 95% CI 4.9 to 22.3). Stress in the follicular phase of the preceding cycles had a stronger association with dysmenorrhoea than stress in the luteal phase of the preceding cycles. Conclusion: This study shows a significant association between stress and the incidence of dysmenorrhoea, which is even stronger among women with a history of dysmenorrhoea. PMID:15550609

  10. Genetic analysis reveals demographic fragmentation of grizzly bears yielding vulnerably small populations.

    PubMed

    Proctor, Michael F; McLellan, Bruce N; Strobeck, Curtis; Barclay, Robert M R

    2005-11-22

    Ecosystem conservation requires the presence of native carnivores, yet in North America, the distributions of many larger carnivores have contracted. Large carnivores live at low densities and require large areas to thrive at the population level. Therefore, if human-dominated landscapes fragment remaining carnivore populations, small and demographically vulnerable populations may result. Grizzly bear range contraction in the conterminous USA has left four fragmented populations, three of which remain along the Canada-USA border. A tenet of grizzly bear conservation is that the viability of these populations requires demographic linkage (i.e. inter-population movement of both sexes) to Canadian bears. Using individual-based genetic analysis, our results suggest this demographic connection has been severed across their entire range in southern Canada by a highway and associated settlements, limiting female and reducing male movement. Two resulting populations are vulnerably small (< or =100 animals) and one of these is completely isolated. Our results suggest that these trans-border bear populations may be more threatened than previously thought and that conservation efforts must expand to include international connectivity management. They also demonstrate the ability of genetic analysis to detect gender-specific demographic population fragmentation in recently disturbed systems, a traditionally intractable yet increasingly important ecological measurement worldwide.

  11. Projectile Base Flow Analysis

    DTIC Science & Technology

    2007-11-02

    S) AND ADDRESS(ES) DCW Industries, Inc. 5354 Palm Drive La Canada, CA 91011 8. PERFORMING ORGANIZATION...REPORT NUMBER DCW -38-R-05 9. SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES) U. S. Army Research Office...Turbulence Modeling for CFD, Second Edition, DCW Industries, Inc., La Cañada, CA. Wilcox, D. C. (2001), “Projectile Base Flow Analysis,” DCW

  12. Evidenced-Based Treatment of Depression in the College Population

    ERIC Educational Resources Information Center

    Lee, Carolyn L.

    2005-01-01

    This review explores evidence-based treatment for depression within the college and university population. Treatments for depression in adults are among the most rigorous studied treatment modalities in the psychotherapy literature, providing consistent evidence for the efficacy of at least two treatments, cognitive behavioral therapy and…

  13. Graphical analysis of the interrelationships among waterborne asbestos, digestive system cancer and population density

    SciTech Connect

    Tarter, M.E.; Cooper, R.C.; Freeman, W.R.

    1983-11-01

    Five statistical procedures were used to partial the correlation between waterborne asbestos and digestive site cancer for the putative effects of population density. These include: analysis based on a data subset with roughly homogeneous population density; standard residual analysis (partial correlation); conditional probability integral transformation; analysis based upon ranked data, and use of logarithmic transformation. To examine the nature or shape of the asbestos-cancer dose-response curve, nonparametric regression graphical techniques are applied. There appears to be a considerable difference between analyses involving non-high-density tracts and non-San Francisco tracts. Evidence is also presented that the modal-type nonparametric regression curve forks or bifurcates when adjustment is made for population density. 24 references, 25 figures.

  14. Genetic analysis in the Collaborative Cross breeding population

    SciTech Connect

    Philip, Vivek; Sokoloff, Greta; Ackert-Bicknell, Cheryl; Striz, Martin; Branstetter, Lisa R; Beckmann, Melissa; Spence, Jason S; Jackson, Barbara L; Galloway, Leslie D; Barker, Gene; Wymore, Ann M; Hunsicker, Patricia R; Durtschi, David W; Shaw, Ginger S; Shinpock, Sarah G; Manly, Kenneth F; Miller, Darla R; Donahue, Kevin; Culiat, Cymbeline T; Churchill, Gary A; Lariviere, William R; Palmer, Abraham; O'Hara, Bruce; Voy, Brynn H; Chesler, Elissa J

    2011-01-01

    Genetic reference populations in model organisms are critical resources for systems genetic analysis of disease related phenotypes. The breeding history of these inbred panels may influence detectable allelic and phenotypic diversity. The existing panel of common inbred strains reflects historical selection biases, and existing recombinant inbred panels have low allelic diversity. All such populations may be subject to consequences of inbreeding depression. The Collaborative Cross (CC) is a mouse reference population with high allelic diversity that is being constructed using a randomized breeding design that systematically outcrosses eight founder strains, followed by inbreeding to obtain new recombinant inbred strains. Five of the eight founders are common laboratory strains, and three are wild-derived. Since its inception, the partially inbred CC has been characterized for physiological, morphological, and behavioral traits. The construction of this population provided a unique opportunity to observe phenotypic variation as new allelic combinations arose through intercrossing and inbreeding to create new stable genetic combinations. Processes including inbreeding depression and its impact on allelic and phenotypic diversity were assessed. Phenotypic variation in the CC breeding population exceeds that of existing mouse genetic reference populations due to both high founder genetic diversity and novel epistatic combinations. However, some focal evidence of allele purging was detected including a suggestive QTL for litter size in a location of changing allele frequency. Despite these inescapable pressures, high diversity and precision for genetic mapping remain. These results demonstrate the potential of the CC population once completed and highlight implications for development of related populations. Supplementary material consists of Supplementary Table 1 Phenotypic means, variances, ranges and heritabilities for all traits and generations, Supplementary Table

  15. Methods for the survey and genetic analysis of populations

    DOEpatents

    Ashby, Matthew

    2003-09-02

    The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

  16. QTL mapping for combining ability in different population-based NCII designs: a simulation study.

    PubMed

    Li, Lanzhi; Sun, Congwei; Chen, Yuan; Dai, Zhijun; Qu, Zhen; Zheng, Xingfei; Yu, Sibin; Mou, Tongmin; Xu, Chenwu; Hu, Zhongli

    2013-12-01

    The NCII design (North Carolina mating design II) has been widely applied in studies of combining ability and heterosis. The objective of our research was to estimate how different base populations, sample sizes, testcross numbers and heritability influence QTL analyses of combining ability and heterosis. A series of Monte Carlo simulation experiments with QTL mapping were then conducted for the base population performance, testcross population phenotypic values and the general combining ability (GCA), specific combining ability (SCA) and Hmp (midparental heterosis) datasets. The results indicated that: (i) increasing the number of testers did not necessarily enhance the QTL detection power for GCA, but it was significantly related to the QTL effect. (ii) The QTLs identified in the base population may be different from those from GCA dataset. Similar phenomena can be seen from QTL detected in SCA and Hmp datasets. (iii) The QTL detection power for GCA ranked in the order of DH(RIL) based > F2 based > BC based NCII design, when the heritability was low. The recombinant inbred lines (RILs) (or DHs) allows more recombination and offers higher mapping resolution than other populations. Further, their testcross progeny can be repeatedly generated and phenotyped. Thus, RIL based (or DH based) NCII design was highly recommend for combining ability QTL analysis. Our results expect to facilitate selecting elite parental lines with high combining ability and for geneticists to research the genetic basis of combining ability.

  17. [The actual approaches to the analysis of the decrease of population mortality on the territorial level].

    PubMed

    Krasnenkov, V L; Kamruzzaman, Saĭed

    2010-01-01

    The article deals with one of the major medical demographic problems of Tver region's higher population mortality, including mortality of able-bodied population. The prevalence of main causes of death and their structure are analyzed. The prospective forecast of death rate indicators based on extrapolation technique is proposed. The main strategic approaches to the development of target programs of decreasing premature population mortality in Tverskaya oblast on the basis of the expertise of hospital lethality and analysis of demographic situation is presented. The proposed approaches can promote the study of optimal management and organization decision-making by administrations of different levels.

  18. Sleep Apnea and Cancer: Analysis of a Nationwide Population Sample

    PubMed Central

    Gozal, David; Ham, Sandra A.; Mokhlesi, Babak

    2016-01-01

    Study Objectives: Epidemiological evidence from relatively small cohorts suggests that obstructive sleep apnea (OSA) is associated with higher cancer incidence and mortality. Here we aimed to determine whether cancer incidence for major cancer types and risk of metastases or mortality from cancer are increased in the presence of OSA. Methods: All OSA diagnoses included in an employee-sponsored health insurance database spanning the years 2003–2012 were identified and 1:1 matched demographically based on age, gender, and state of residence, or alternatively matched by comorbidities. The incidence of 12 types of cancer was assessed. In addition, another cohort of patients with a primary diagnosis of cancer was retrieved, and the risk of metastatic disease or cancer mortality was determined as a function of the presence or absence of OSA. Multivariate Cox proportional hazards regression models were fitted to assess the independent associations between OSA and outcomes of interest. Results: Based on a cohort of ∼5.6 million individuals, the incidence of all cancer diagnoses combined was similar in OSA and retrospectively matched cases. However, the adjusted risk of pancreatic and kidney cancer and melanoma were significantly higher in patients with OSA, while the risk of colorectal, breast, and prostate cancers appeared to be lower. Among individuals with a diagnosis of cancer, the presence of OSA was not associated with an increased risk for metastasis or death. Conclusions: In a large nationally representative health insurance database, OSA appears to increase the risk for only a very selective number of cancer types, and does not appear to be associated with an increased risk of metastatic cancer or cancer-related deaths. Citation: Gozal D, Ham SA, Mokhlesi B. Sleep apnea and cancer: analysis of a nationwide population sample. SLEEP 2016;39(8):1493–1500. PMID:27166241

  19. An Individual-Based Model of Zebrafish Population Dynamics Accounting for Energy Dynamics

    PubMed Central

    Beaudouin, Rémy; Goussen, Benoit; Piccini, Benjamin; Augustine, Starrlight; Devillers, James; Brion, François; Péry, Alexandre R. R.

    2015-01-01

    Developing population dynamics models for zebrafish is crucial in order to extrapolate from toxicity data measured at the organism level to biological levels relevant to support and enhance ecological risk assessment. To achieve this, a dynamic energy budget for individual zebrafish (DEB model) was coupled to an individual based model of zebrafish population dynamics (IBM model). Next, we fitted the DEB model to new experimental data on zebrafish growth and reproduction thus improving existing models. We further analysed the DEB-model and DEB-IBM using a sensitivity analysis. Finally, the predictions of the DEB-IBM were compared to existing observations on natural zebrafish populations and the predicted population dynamics are realistic. While our zebrafish DEB-IBM model can still be improved by acquiring new experimental data on the most uncertain processes (e.g. survival or feeding), it can already serve to predict the impact of compounds at the population level. PMID:25938409

  20. Addendum to "Population-Based Prevention of Child Maltreatment: The U.S. Triple P System Population Trial".

    PubMed

    Prinz, Ronald J; Sanders, Matthew R; Shapiro, Cheri J; Whitaker, Daniel J; Lutzker, John R

    2016-04-01

    A previous article published several years ago (Prinz et al. Prevention Science, 10, 1-12, 2009) described the main results of a place-randomized-design study focused on the prevention of child-maltreatment-related outcomes at a population level through the implementation of a multilevel system of parenting and family support (the Triple P-Positive Parenting Program). The current report, prepared at the encouragement of the journal, provides additional details about procedures, measures, and design-related decisions, presents an additional analysis of the main outcome variables, and poses questions about the study and its implications. We also offer guidance about how the field can move forward to build on this line of research. From the outset, the three designated primary child maltreatment outcomes were county-wide rates for substantiated child maltreatment cases, out-of-home placements, and hospital-treated child maltreatment injuries, derived from independent data sources available through administrative archival records. Baseline equivalence between the two intervention conditions was reaffirmed. The additional analysis, which made use of a 5-year baseline (replacing a 1-year baseline) and ANCOVA, yielded large effect sizes for all three outcomes that converged with those from the original analyses. Overall, the study underscored the potential for community-wide parenting and family support to produce population-level preventive impact on child maltreatment. Issues addressed included (1) the need for replication of population-oriented maltreatment prevention strategies like the one tested in this randomized experiment, (2) the need to demonstrate that a parenting-based population approach to maltreatment prevention can also impact children's adjustment apart from child abuse, and (3) the role of implementation science for achieving greater population reach and maintenance over time.

  1. Molecular population genetic analysis of emerged bacterial pathogens: selected insights.

    PubMed Central

    Musser, J. M.

    1996-01-01

    Research in bacterial population genetics has increased in the last 10 years. Population genetic theory and tools and related strategies have been used to investigate bacterial pathogens that have contributed to recent episodes of temporal variation in disease frequency and severity. A common theme demonstrated by these analyses is that distinct bacterial clones are responsible for disease outbreaks and increases in infection frequency. Many of these clones are characterized by unique combinations of virulence genes or alleles of virulence genes. Because substantial interclonal variance exists in relative virulence, molecular population genetic studies have led to the concept that the unit of bacterial pathogenicity is the clone or cell line. Continued new insights into host parasite interactions at the molecular level will be achieved by combining clonal analysis of bacterial pathogens with large-scale comparative sequencing of virulence genes. PMID:8903193

  2. Collection of pedigree data for genetic analysis in isolate populations.

    PubMed

    Williams-Blangero, Sarah; Blangero, John

    2006-02-01

    Pedigree data are useful for a wealth of research purposes in human population biology and genetics. The collection of extended pedigrees represents the most powerful sampling design for quantitative genetic and linkage studies of both normal and disease-related quantitative traits. In this paper we outline an approach for collecting pedigree data in stable isolate populations. As an example, the pedigree for the Jirel population, which was obtained using the methods presented, is described. The Jirel pedigree contains 2,000 study participants and more than 62,000 pairwise relationships that are informative for genetic analysis. Once such pedigrees are genetically characterized by a genome scan for a given trait, they become an invaluable resource for future genetic studies of any quantitative trait.

  3. Characterization of population exposure to organochlorines: a cluster analysis application.

    PubMed

    Guimarães, Raphael Mendonça; Asmus, Carmen Ildes Rodrigues Fróes; Burdorf, Alex

    2013-06-01

    This study aimed to show the results from a cluster analysis application in the characterization of population exposure to organochlorines through variables related to time and exposure dose. Characteristics of 354 subjects in a population exposed to organochlorine pesticides residues related to time and exposure dose were subjected to cluster analysis to separate them into subgroups. We performed hierarchical cluster analysis. To evaluate the classification accuracy, compared to intra-group and inter-group variability by ANOVA for each dimension. The aggregation strategy was accomplished by the method of Ward. It was, for the creation of clusters, variables associated with exposure and routes of contamination. The information on the estimated intake doses of compound were used to weight the values of exposure time at each of the routes, so as to obtain values proxy exposure intensity. The results showed three clusters: cluster 1 (n = 45), characteristics of greatest exposure, the cluster 2 (n = 103), intermediate exposure, and cluster 3 (n = 206), less exposure. The bivariate analyzes performed with groups that are groups showed a statistically significant difference. This study demonstrated the applicability of cluster analysis to categorize populations exposed to organochlorines and also points to the relevance of typological studies that may contribute to a better classification of subjects exposed to chemical agents, which is typical of environmental epidemiology studies to a wider understanding of etiological, preventive and therapeutic contamination.

  4. Sexually Transmitted Diseases and Risk Behaviors among California Farmworkers: Results from a Population-Based Survey

    ERIC Educational Resources Information Center

    Brammeier, Monique; Chow, Joan M.; Samuel, Michael C.; Organista, Kurt C.; Miller, Jamie; Bolan, Gail

    2008-01-01

    Context: The prevalence of sexually transmitted diseases and associated risk behaviors among California farmworkers is not well described. Purpose: To estimate the prevalence of sexually transmitted diseases (STDs) and associated risk behaviors among California farmworkers. Methods: Cross-sectional analysis of population-based survey data from 6…

  5. Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds.

    PubMed

    Edea, Z; Bhuiyan, M S A; Dessie, T; Rothschild, M F; Dadi, H; Kim, K S

    2015-02-01

    Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69,903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.

  6. A theoretical analysis of optimum consumer population and its control.

    PubMed

    Jiang, Z; Mao, Z; Wang, H

    1994-01-01

    consumption structure elasticity. This model was used in the correlation analysis of the coordinated healthy development of optimum consumer population and the economy.

  7. Population.

    ERIC Educational Resources Information Center

    King, Pat; Landahl, John

    This pamphlet has been prepared in response to a new problem, a rapidly increasing population, and a new need, population education. It is designed to help teachers provide their students with some basic population concepts with stress placed on the elements of decision making. In the first section of the pamphlet, some of the basic concepts of…

  8. [Population].

    PubMed

    1979-01-01

    Data on the population of Venezuela between 1975 and 1977 are presented in descriptive tables and graphs. Information is included on the employed population according to category, sex, and type of economic activity, and by sex, age, and area on the employment rate and the total, the economically active, and the unemployed population.

  9. Adjustment for population stratification via principal components in association analysis of rare variants.

    PubMed

    Zhang, Yiwei; Guan, Weihua; Pan, Wei

    2013-01-01

    For unrelated samples, principal component (PC) analysis has been established as a simple and effective approach to adjusting for population stratification in association analysis of common variants (CVs, with minor allele frequencies MAF > 5%). However, it is less clear how it would perform in analysis of low-frequency variants (LFVs, MAF between 1% and 5%), or of rare variants (RVs, MAF < 5%). Furthermore, with next-generation sequencing data, it is unknown whether PCs should be constructed based on CVs, LFVs, or RVs. In this study, we used the 1000 Genomes Project sequence data to explore the construction of PCs and their use in association analysis of LFVs or RVs for unrelated samples. It is shown that a few top PCs based on either CVs or LFVs could separate two continental groups, European and African samples, but those based on only RVs performed less well. When applied to several association tests in simulated data with population stratification, using PCs based on either CVs or LFVs was effective in controlling Type I error rates, while nonadjustment led to inflated Type I error rates. Perhaps the most interesting observation is that, although the PCs based on LFVs could better separate the two continental groups than those based on CVs, the use of the former could lead to overadjustment in the sense of substantial power loss in the absence of population stratification; in contrast, we did not see any problem with the use of the PCs based on CVs in all our examples.

  10. Population genetic analysis and sub-structuring in Babesia bovis.

    PubMed

    Simuunza, Martin; Bilgic, Huseyin; Karagenc, Tulin; Syakalima, Michelo; Shiels, Brian; Tait, Andy; Weir, William

    2011-06-01

    The tick-borne protozoan parasite, Babesia bovis is one of the causes of bovine babesiosis, an economically important disease of cattle in tropical and sub-tropical countries. Using the recently published genome sequence of the parasite, we developed a panel of eight mini- and micro-satellite markers and used these to investigate the role of genetic exchange in the population structure and diversity of the parasite using isolates from Zambia and Turkey. This population genetic analysis showed that genetic exchange occurs and that there are high levels of genetic diversity, with geographical sub-structuring quantified using Wright's F Index. Linkage disequilibrium was observed when isolates from both countries were treated as one population, but when isolates from Zambia were analysed separately linkage equilibrium was observed. The Turkish isolates were sub-structured, containing two genetically distinct sub-groups, both of which appeared to be in linkage equilibrium. The results of the Zambian study suggest that a sub-set of the parasite population is responsible for the westward spread of babesiosis into the previously disease-free central region of the country. The Zambian isolates had a significantly higher number of genotypes per sample than those from Turkey and age was found to be a significant predictor of the multiplicity of infection. The high levels of diversity seen in the Zambian and Turkish B. bovis populations have implications in the development of subunit vaccines against the disease and the spread of drug resistance.

  11. A Comparison of Four Estimators of a Population Measure of Model Fit in Covariance Structure Analysis

    ERIC Educational Resources Information Center

    Zhang, Wei

    2008-01-01

    A major issue in the utilization of covariance structure analysis is model fit evaluation. Recent years have witnessed increasing interest in various test statistics and so-called fit indexes, most of which are actually based on or closely related to F[subscript 0], a measure of model fit in the population. This study aims to provide a systematic…

  12. A Bibliometric Analysis on Cancer Population Science with Topic Modeling.

    PubMed

    Li, Ding-Cheng; Rastegar-Mojarad, Majid; Okamoto, Janet; Liu, Hongfang; Leichow, Scott

    2015-01-01

    Bibliometric analysis is a research method used in library and information science to evaluate research performance. It applies quantitative and statistical analyses to describe patterns observed in a set of publications and can help identify previous, current, and future research trends or focus. To better guide our institutional strategic plan in cancer population science, we conducted bibliometric analysis on publications of investigators currently funded by either Division of Cancer Preventions (DCP) or Division of Cancer Control and Population Science (DCCPS) at National Cancer Institute. We applied two topic modeling techniques: author topic modeling (AT) and dynamic topic modeling (DTM). Our initial results show that AT can address reasonably the issues related to investigators' research interests, research topic distributions and popularities. In compensation, DTM can address the evolving trend of each topic by displaying the proportion changes of key words, which is consistent with the changes of MeSH headings.

  13. The genetics of amphibian decline: population substructure and molecular differentiation in the Yosemite toad, Bufo canorus (Anura, Bufonidae) based on single-strand conformation polymorphism analysis (SSCP) and mitochondrial DNA sequence data

    USGS Publications Warehouse

    Shaffer, H. Bradley; Fellers, Gary M.; Magee, Allison; Voss, S. Randal

    2000-01-01

    We present a comprehensive survey of genetic variation across the range of the narrowly distributed endemic Yosemite toad Bufo canorus, a declining amphibian restricted to the Sierra Nevada of California. Based on 322 bp of mitochondrial cytochrome b sequence data, we found limited support for the monophyly of B. canorus and its closely related congener B. exsul to the exclusion of the widespread western toad B. boreas. However, B. exsul was always phylogenetically nested within B. canorus, suggesting that the latter may not be monophyletic. SSCP (single-strand conformation polymorphism) analysis of 372 individual B. canorus from 28 localities in Yosemite and Kings Canyon National Parks revealed no shared haplotypes among these two regions and lead us to interpret these two parks as distinct management units for B. canorus. Within Yosemite, we found significant genetic substructure both at the level of major drainages and among breeding ponds. Kings Canyon samples show a different pattern, with substantial variation among breeding sites, but no substructure among drainages. Across the range of B. canorus as well as among Yosemite ponds, we found an isolation-by-distance pattern suggestive of a stepping stone model of migration. However, in Kings Canyon we found no hint of such a pattern, suggesting that movement patterns of toads may be quite different in these nearby parklands. Our data imply that management for B. canorus should focus at the individual pond level, and effective management may necessitate reintroductions if local extirpations occur. A brief review of other pond-breeding anurans suggests that highly structured populations are often the case, and thus that our results for B. canorus may be general for other species of frogs and toads.

  14. What affects response rates in primary healthcare-based programmes? An analysis of individual and unit-related factors associated with increased odds of non-response based on HCV screening in the general population in Poland

    PubMed Central

    Parda, Natalia; Stępień, Małgorzata; Zakrzewska, Karolina; Madaliński, Kazimierz; Kołakowska, Agnieszka; Godzik, Paulina; Rosińska, Magdalena

    2016-01-01

    Objectives Response rate in public health programmes may be a limiting factor. It is important to first consider their delivery and acceptability for the target. This study aimed at determining individual and unit-related factors associated with increased odds of non-response based on hepatitis C virus screening in primary healthcare. Design Primary healthcare units (PHCUs) were extracted from the Register of Health Care Centres. Each of the PHCUs was to enrol adult patients selected on a random basis. Data on the recruitment of PHCUs and patients were analysed. Multilevel modelling was applied to investigate individual and unit-related factors associated with non-response. Multilevel logistic model was developed with fixed effects and only a random intercept for the unit. Preliminary analysis included a random effect for unit and each of the individual or PHCU covariates separately. For each of the PHCU covariates, we applied a two-level model with individual covariates, unit random effect and a single fixed effect of this unit covariate. Setting This study was conducted in primary care units in selected provinces in Poland. Participants A total of 242 PHCUs and 24 480 adults were invited. Of them, 44 PHCUs and 20 939 patients agreed to participate. Both PHCUs and patients were randomly selected. Results Data on 44 PHCUs and 24 480 patients were analysed. PHCU-level factors and recruitment strategies were important predictors of non-response. Unit random effect was significant in all models. Larger and private units reported higher non-response rates, while for those with a history of running public health programmes the odds of non-response was lower. Proactive recruitment, more working hours devoted to the project and patient resulted in higher acceptance of the project. Higher number of personnel had no such effect. Conclusions Prior to the implementation of public health programme, several factors that could hinder its execution should be addressed. PMID

  15. Analysis of genetic diversity in Bolivian llama populations using microsatellites.

    PubMed

    Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

    2013-08-01

    South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations.

  16. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

    PubMed Central

    De la Rúa, Pilar; Galián, José; Serrano, José; Moritz, Robin FA

    2003-01-01

    The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain) was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca) and Pitiusas (Ibiza and Formentera), which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees. PMID:12729553

  17. A stage-based model of manatee population dynamics

    USGS Publications Warehouse

    Runge, M.C.; Langtimm, C.A.; Kendall, W.L.

    2004-01-01

    A stage-structured population model for the Florida manatee (Trichechus manatus latirostris) was developed that explicitly incorporates uncertainty in parameter estimates. The growth rates calculated with this model reflect the status of the regional populations over the most recent 10-yr period. The Northwest and Upper St. Johns River regions have growth rates (8) of 1.037 (95% interval, 1.016?1.056) and 1.062 (1.037?1.081), respectively. The Southwest region has a growth rate of 0.989 (0.946?1.024), suggesting this population has been declining at about 1.1% per year. The estimated growth rate in the Atlantic region is 1.010 (0.988?1.029), but there is some uncertainty about whether adult survival rates have been constant over the last 10 yr; using the mean survival rates from the most recent 5-yr period, the estimated growth rate in this region is 0.970 (0.938?0.998). Elasticity analysis indicates that the most effective management actions should seek to increase adult survival rates. Decomposition of the uncertainty in the growth rates indicates that uncertainty about population status can best be reduced through increased monitoring of adult survival rate.

  18. Population genetic analysis and origin discrimination of snow crab (Chionoecetes opilio) using microsatellite markers.

    PubMed

    Kang, Jung-Ha; Park, Jung-Youn; Kim, Eun-Mi; Ko, Hyun-Sook

    2013-10-01

    Major habitats for the snow crab Chionoecetes opilio are mostly found within the northwest Atlantic and North Pacific Oceans. However, the East Sea populations of C. opilio, along with its relative the red snow crab (C. japonicas), are two of the most important commercial crustacean species for fisheries on the east coast of the Korean Peninsula. The East Sea populations of C. opilio are facing declining resources due to overfishing and global climate change. Thus, an analysis of population structure is necessary for future management. Five Korean and one Russian group of C. opilio were analyzed using nine microsatellite markers that were recently developed using next-generation sequencing. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The number of alleles per locus varied from 4 to 18 with a mean of 12, and allelic richness per locus ranged from 4.0 to 17.1 across all populations with a mean of 9.7. The Hardy-Weinberg equilibrium test revealed significant deviation in three out of nine loci in some populations after sequential Bonferroni correction and all of them had higher expected heterozygosity than observed heterozygosity. Null alleles were presumed in four loci, which explained the homozygosity in three loci. The pairwise fixation index (F ST ) values among the five Korean snow crab populations did not differ significantly, but all of the pairwise F ST values between each of the Korean snow crab populations and the Russian snow crab population differed significantly. An UPGMA dendrogram revealed clear separation of the Russian snow crab population from the Korean snow crab populations. Assignment tests based on the allele distribution discriminated between Korean and Russian origins with 93 % accuracy. Therefore, the snow crab populations around the Korean Peninsula need to be managed separately from the populations in Bering Sea in global scale resource management. Also, this information can be

  19. Health Literacy in Taiwan: A Population-Based Study.

    PubMed

    Duong, Van Tuyen; Lin, I-Feng; Sorensen, Kristine; Pelikan, Jürgen M; Van Den Broucke, Stephan; Lin, Ying-Chin; Chang, Peter Wushou

    2015-11-01

    Data on health literacy (HL) in the population is limited for Asian countries. This study aimed to test the validity of the Mandarin version of the European Health Literacy Survey Questionnaire (HLS-EU-Q) for use in the general public in Taiwan. Multistage stratification random sampling resulted in a sample of 2989 people aged 15 years and above. The HLS-EU-Q was validated by confirmatory factor analysis with excellent model data fit indices. The general HL of the Taiwanese population was 34.4 ± 6.6 on a scale of 50. Multivariate regression analysis showed that higher general HL is significantly associated with the higher ability to pay for medication, higher self-perceived social status, higher frequency of watching health-related TV, and community involvement but associated with younger age. HL is also associated with health status, health behaviors, and health care accessibility and use. The HLS-EU-Q was found to be a useful tool to assess HL and its associated factors in the general population.

  20. Climate change threatens polar bear populations: a stochastic demographic analysis.

    PubMed

    Hunter, Christine M; Caswell, Hal; Runge, Michael C; Regehr, Eric V; Amstrup, Steve C; Stirling, Ian

    2010-10-01

    The polar bear (Ursus maritimus) depends on sea ice for feeding, breeding, and movement. Significant reductions in Arctic sea ice are forecast to continue because of climate warming. We evaluated the impacts of climate change on polar bears in the southern Beaufort Sea by means of a demographic analysis, combining deterministic, stochastic, environment-dependent matrix population models with forecasts of future sea ice conditions from IPCC general circulation models (GCMs). The matrix population models classified individuals by age and breeding status; mothers and dependent cubs were treated as units. Parameter estimates were obtained from a capture-recapture study conducted from 2001 to 2006. Candidate statistical models allowed vital rates to vary with time and as functions of a sea ice covariate. Model averaging was used to produce the vital rate estimates, and a parametric bootstrap procedure was used to quantify model selection and parameter estimation uncertainty. Deterministic models projected population growth in years with more extensive ice coverage (2001-2003) and population decline in years with less ice coverage (2004-2005). LTRE (life table response experiment) analysis showed that the reduction in lambda in years with low sea ice was due primarily to reduced adult female survival, and secondarily to reduced breeding. A stochastic model with two environmental states, good and poor sea ice conditions, projected a declining stochastic growth rate, log lambdas, as the frequency of poor ice years increased. The observed frequency of poor ice years since 1979 would imply log lambdas approximately - 0.01, which agrees with available (albeit crude) observations of population size. The stochastic model was linked to a set of 10 GCMs compiled by the IPCC; the models were chosen for their ability to reproduce historical observations of sea ice and were forced with "business as usual" (A1B) greenhouse gas emissions. The resulting stochastic population

  1. Climate change threatens polar bear populations: A stochastic demographic analysis

    USGS Publications Warehouse

    Hunter, C.M.; Caswell, H.; Runge, M.C.; Regehr, E.V.; Amstrup, Steven C.; Stirling, I.

    2010-01-01

    The polar bear (Ursus maritimus) depends on sea ice for feeding, breeding, and movement. Significant reductions in Arctic sea ice are forecast to continue because of climate warming. We evaluated the impacts of climate change on polar bears in the southern Beaufort Sea by means of a demographic analysis, combining deterministic, stochastic, environment-dependent matrix population models with forecasts of future sea ice conditions from IPCC general circulation models (GCMs). The matrix population models classified individuals by age and breeding status; mothers and dependent cubs were treated as units. Parameter estimates were obtained from a capture-recapture study conducted from 2001 to 2006. Candidate statistical models allowed vital rates to vary with time and as functions of a sea ice covariate. Model averaging was used to produce the vital rate estimates, and a parametric bootstrap procedure was used to quantify model selection and parameter estimation uncertainty. Deterministic models projected population growth in years with more extensive ice coverage (2001-2003) and population decline in years with less ice coverage (2004-2005). LTRE (life table response experiment) analysis showed that the reduction in ?? in years with low sea ice was due primarily to reduced adult female survival, and secondarily to reduced breeding. A stochastic model with two environmental states, good and poor sea ice conditions, projected a declining stochastic growth rate, log ??s, as the frequency of poor ice years increased. The observed frequency of poor ice years since 1979 would imply log ??s ' - 0.01, which agrees with available (albeit crude) observations of population size. The stochastic model was linked to a set of 10 GCMs compiled by the IPCC; the models were chosen for their ability to reproduce historical observations of sea ice and were forced with "business as usual" (A1B) greenhouse gas emissions. The resulting stochastic population projections showed drastic

  2. Population viability analysis with species occurrence data from museum collections.

    PubMed

    Skarpaas, Olav; Stabbetorp, Odd E

    2011-06-01

    The most comprehensive data on many species come from scientific collections. Thus, we developed a method of population viability analysis (PVA) in which this type of occurrence data can be used. In contrast to classical PVA, our approach accounts for the inherent observation error in occurrence data and allows the estimation of the population parameters needed for viability analysis. We tested the sensitivity of the approach to spatial resolution of the data, length of the time series, sampling effort, and detection probability with simulated data and conducted PVAs for common, rare, and threatened species. We compared the results of these PVAs with results of standard method PVAs in which observation error is ignored. Our method provided realistic estimates of population growth terms and quasi-extinction risk in cases in which the standard method without observation error could not. For low values of any of the sampling variables we tested, precision decreased, and in some cases biased estimates resulted. The results of our PVAs with the example species were consistent with information in the literature on these species. Our approach may facilitate PVA for a wide range of species of conservation concern for which demographic data are lacking but occurrence data are readily available.

  3. Aspects of Ancient Mitochondrial DNA Analysis in Different Populations for Understanding Human Evolution

    PubMed Central

    Nesheva, DV

    2014-01-01

    The evolution of modern humans is a long and difficult process which started from their first appearance and continues to the present day. The study of the genetic origin of populations can help to determine population kinship and to better understand the gradual changes of the gene pool in space and time. Mitochondrial DNA (mtDNA) is a proper tool for the determination of the origin of populations due to its high evolutionary importance. Ancient mitochondrial DNA retrieved from museum specimens, archaeological finds and fossil remains can provide direct evidence for population origins and migration processes. Despite the problems with contaminations and authenticity of ancient mitochondrial DNA, there is a developed set of criteria and platforms for obtaining authentic ancient DNA. During the last two decades, the application of different methods and techniques for analysis of ancient mitochondrial DNA gave promising results. Still, the literature is relatively poor with information for the origin of human populations. Using comprehensive phylogeographic and population analyses we can observe the development and formation of the contemporary populations. The aim of this study was to shed light on human migratory processes and the formation of populations based on available ancient mtDNA data. PMID:25741209

  4. Population.

    ERIC Educational Resources Information Center

    International Planned Parenthood Federation, London (England).

    In an effort to help meet the growing interest and concern about the problems created by the rapid growth of population, The International Planned Parenthood Federation has prepared this booklet with the aim of assisting the study of the history and future trends of population growth and its impact on individual and family welfare, national,…

  5. Changing roles of population-based cancer registries in Australia.

    PubMed

    Roder, David; Creighton, Nicola; Baker, Deborah; Walton, Richard; Aranda, Sanchia; Currow, David

    2015-09-01

    Registries have key roles in cancer incidence, mortality and survival monitoring and in showing disparities across the population. Incidence monitoring began in New South Wales in 1972 and other jurisdictions soon followed. Registry data are used to evaluate outcomes of preventive, screening, treatment and support services. They have shown decreases in cancer incidence following interventions and have been used for workforce and other infrastructure planning. Crude markers of optimal radiotherapy and chemotherapy exist and registry data are used to show shortfalls against these markers. The data are also used to investigate cancer clusters and environmental concerns. Survival data are used to assess service performance and interval cancer data are used in screening accreditation. Registries enable determination of risk of multiple primary cancers. Clinical quality registries are used for clinical quality improvement. Population-based cancer registries and linked administrative data complement clinical registries by providing high-level system-wide data. The USA Commission on Cancer has long used registries for quality assurance and service accreditation. Increasingly population-based registry data in Australia are linked with administrative data on service delivery to assess system performance. Addition oftumour stage and otherprognostic indicators is important forthese analyses and is facilitated by the roll-out of structured pathology reporting. Data linkage with administrative data, following checks on the quality of these data, enables assessment of patterns of care and other performance indicators for health-system monitoring. Australian cancer registries have evolved and increasingly are contributing to broader information networks for health system management.

  6. Incorporating parametric uncertainty into population viability analysis models

    USGS Publications Warehouse

    McGowan, Conor P.; Runge, Michael C.; Larson, Michael A.

    2011-01-01

    Uncertainty in parameter estimates from sampling variation or expert judgment can introduce substantial uncertainty into ecological predictions based on those estimates. However, in standard population viability analyses, one of the most widely used tools for managing plant, fish and wildlife populations, parametric uncertainty is often ignored in or discarded from model projections. We present a method for explicitly incorporating this source of uncertainty into population models to fully account for risk in management and decision contexts. Our method involves a two-step simulation process where parametric uncertainty is incorporated into the replication loop of the model and temporal variance is incorporated into the loop for time steps in the model. Using the piping plover, a federally threatened shorebird in the USA and Canada, as an example, we compare abundance projections and extinction probabilities from simulations that exclude and include parametric uncertainty. Although final abundance was very low for all sets of simulations, estimated extinction risk was much greater for the simulation that incorporated parametric uncertainty in the replication loop. Decisions about species conservation (e.g., listing, delisting, and jeopardy) might differ greatly depending on the treatment of parametric uncertainty in population models.

  7. Qualifications and Competencies for Population Health Management Positions: A Content Analysis of Job Postings.

    PubMed

    Meyer, Melanie

    2017-04-06

    The need for population health management expertise has increased as the health care industry shifts toward value-based care. However, many organizations report hiring gaps as they seek to fill positions. The purpose of this study was to analyze the types of population health management positions for which health care organizations are hiring, including qualifications and competencies required for these positions. A content analysis was conducted on 271 job postings collected during a 2-month period. A typology of qualifications and competencies was developed based on the content analysis. Profiles were generated for the top 5 job title classifications: directors, coordinators, care managers, analysts, and specialists. This study highlights the investment health care organizations are making in population health management and the prominent role these positions are playing in the health care environment today. Many organizations are building out population health management teams resulting in multiple positions at different levels being added. As the market demands competent candidates who are equipped with specialized population health expertise as well as practical experience in program development, technology applications, care management, and analytics, professional education programs will need to adapt curricula to address the required areas. Competencies for specific job title classifications may need further evaluation and refinement over time. Study results can be used by organizations for strategic planning, by educators to target needed qualifications and competencies, and by researchers and policy advisors to assess progress toward value-based care.

  8. Efficient population assignment and outlier detection in human populations using biallelic markers chosen by principal component-based rankings.

    PubMed

    Raaum, Ryan L; Wang, Alex B; Al-Meeri, Ali M; Mulligan, Connie J

    2010-06-01

    Whole-genome studies of genetic variation are now performed routinely and have accelerated the identification of disease-associated allelic variants, positive selection, recombination, and structural variation. However, these studies are sensitive to the presence of outlier data from individuals of different ancestry than the rest of the sample. Currently, the most common method of excluding outlier individuals is to collect a population sample and exclude outliers after genome-wide data have been collected. Here we show that a small collection of 20-27 polymorphic Alu insertions, selected using a principal component-based method with genetic ancestry estimates, may be used to easily assign Africans, East Asians, and Europeans to their population of origin. In addition, we show that samples from a geographically and genetically intermediate population (in our study, samples from India) can be identified within the original sample of Africans, East Asians, and Europeans. Finally, we show that outlier individuals from neighboring geographic regions (in our study, Yemen and sub-Saharan Africa) can be identified. These results will be of value in preselection of samples for more in-depth analysis as well as customized identification of maximally informative polymorphic markers for regional studies.

  9. Evaluating Nicotine Replacement Therapy and Stage-Based Therapies in a Population-Based Effectiveness Trial

    ERIC Educational Resources Information Center

    Velicer, Wayne F.; Friedman, Robert H.; Fava, Joseph L.; Gulliver, Suzy B.; Keller, Stefan; Sun, Xiaowu; Ramelson, Harley; Prochaska, James O.

    2006-01-01

    Pharmacological interventions for smoking cessation are typically evaluated using volunteer samples (efficacy trials) but should also be evaluated in population-based trials (effectiveness trials). Nicotine replacement therapy (NRT) alone and in combination with behavioral interventions was evaluated on a population of smokers from a New England…

  10. Variogram Analysis of the Spatial Genetic Structure of Continuous Populations Using Multilocus Microsatellite Data

    PubMed Central

    Wagner, Helene H.; Holderegger, Rolf; Werth, Silke; Gugerli, Felix; Hoebee, Susan E.; Scheidegger, Christoph

    2005-01-01

    A geostatistical perspective on spatial genetic structure may explain methodological issues of quantifying spatial genetic structure and suggest new approaches to addressing them. We use a variogram approach to (i) derive a spatial partitioning of molecular variance, gene diversity, and genotypic diversity for microsatellite data under the infinite allele model (IAM) and the stepwise mutation model (SMM), (ii) develop a weighting of sampling units to reflect ploidy levels or multiple sampling of genets, and (iii) show how variograms summarize the spatial genetic structure within a population under isolation-by-distance. The methods are illustrated with data from a population of the epiphytic lichen Lobaria pulmonaria, using six microsatellite markers. Variogram-based analysis not only avoids bias due to the underestimation of population variance in the presence of spatial autocorrelation, but also provides estimates of population genetic diversity and the degree and extent of spatial genetic structure accounting for autocorrelation. PMID:15654102

  11. Identification of geographically distributed sub-populations of Leishmania (Leishmania) major by microsatellite analysis

    PubMed Central

    2008-01-01

    Background Leishmania (Leishmania) major, one of the agents causing cutaneous leishmaniasis (CL) in humans, is widely distributed in the Old World where different species of wild rodent and phlebotomine sand fly serve as animal reservoir hosts and vectors, respectively. Despite this, strains of L. (L.) major isolated from many different sources over many years have proved to be relatively uniform. To investigate the population structure of the species highly polymorphic microsatellite markers were employed for greater discrimination among it's otherwise closely related strains, an approach applied successfully to other species of Leishmania. Results Multilocus Microsatellite Typing (MLMT) based on 10 different microsatellite markers was applied to 106 strains of L. (L.) major from different regions where it is endemic. On applying a Bayesian model-based approach, three main populations were identified, corresponding to three separate geographical regions: Central Asia (CA); the Middle East (ME); and Africa (AF). This was congruent with phylogenetic reconstructions based on genetic distances. Re-analysis separated each of the populations into two sub-populations. The two African sub-populations did not correlate well with strains' geographical origin. Strains falling into the sub-populations CA and ME did mostly group according to their place of isolation although some anomalies were seen, probably, owing to human migration. Conclusion The model- and distance-based analyses of the microsatellite data exposed three main populations of L. (L.) major, Central Asia, the Middle East and Africa, each of which separated into two sub-populations. This probably correlates with the different species of rodent host. PMID:18577226

  12. Mosquito population dynamics from cellular automata-based simulation

    NASA Astrophysics Data System (ADS)

    Syafarina, Inna; Sadikin, Rifki; Nuraini, Nuning

    2016-02-01

    In this paper we present an innovative model for simulating mosquito-vector population dynamics. The simulation consist of two stages: demography and dispersal dynamics. For demography simulation, we follow the existing model for modeling a mosquito life cycles. Moreover, we use cellular automata-based model for simulating dispersal of the vector. In simulation, each individual vector is able to move to other grid based on a random walk. Our model is also capable to represent immunity factor for each grid. We simulate the model to evaluate its correctness. Based on the simulations, we can conclude that our model is correct. However, our model need to be improved to find a realistic parameters to match real data.

  13. Using Christmas Bird Count data in analysis of population change

    USGS Publications Warehouse

    Sauer, J.R.; Link, W.A.

    2002-01-01

    The scientific credibility of Christmas Bird Count (CBC) results depend on the development and implementation of appropriate methods of statistical analysis. The key to any successful analysis of CBC data is to begin with a careful review of how the limitations of the data are likely to influence the results of the analysis, then to choose methods of analysis that accommodate as much as possible the limitations of the survey. For our analyses of CBC data, we develop a flexible model for effort adjustment and use information from the data to guide the selection of the best model. We include geographic structuring to accommodate the regional variation in number of samples, use a model that allows for overdispersed poisson data appropriate for counts, and employ empirical Bayes procedures to accommodate differences in quality of information in regional summaries. This generalized linear model approach is very flexible, and can be applied to a variety of studies focused on factors influencing wintering bird populations. In particular, the model can be easily modified to contain covariates, allowing for assessment of associations between CBC counts and winter weather, disturbance, and a variety of other environmental factors. These new survey analysis methods have added value in that they provide insights into changes in survey design that can enhance the value of the information. The CBC has been extremely successful as a tool for increasing public interest in birding and bird conservation. Use of the information for bird conservation creates new demands on quality of information, and it is important to maintain a dialogue between users of the information, information needs for the analyses, and survey coordinators and participants. Our work as survey analysts emphasizes the value and limitations of existing data, and provides some indications of what features of the survey could be modified to make the survey a more reliable source of bird population data. Surveys

  14. Genome-wide analysis in endangered populations: a case study in Barbaresca sheep.

    PubMed

    Mastrangelo, S; Portolano, B; Di Gerlando, R; Ciampolini, R; Tolone, M; Sardina, M T

    2017-01-12

    Analysis of genomic data is becoming increasingly common in the livestock industry and the findings have been an invaluable resource for effective management of breeding programs in small and endangered populations. In this paper, with the goal of highlighting the potential of genomic analysis for small and endangered populations, genome-wide levels of linkage disequilibrium, measured as the squared correlation coefficient of allele frequencies at a pair of loci, effective population size, runs of homozygosity (ROH) and genetic diversity parameters, were estimated in Barbaresca sheep using Illumina OvineSNP50K array data. Moreover, the breed's genetic structure and its relationship with other breeds were investigated. Levels of pairwise linkage disequilibrium decreased with increasing distance between single nucleotide polymorphisms. An average correlation coefficient <0.25 was found for markers located up to 50 kb apart. Therefore, these results support the need to use denser single nucleotide polymorphism panels for high power association mapping and genomic selection efficiency in future breeding programs. The estimate of past effective population size ranged from 747 animals 250 generations ago to 28 animals five generations ago, whereas the contemporary effective population size was 25 animals. A total of 637 ROH were identified, most of which were short (67%) and ranged from 1 to 10 Mb. The genetic analyses revealed that the Barbaresca breed tended to display lower variability than other Sicilian breeds. Recent inbreeding was evident, according to the ROH analysis. All the investigated parameters showed a comparatively narrow genetic base and indicated an endangered status for Barbaresca. Multidimensional scaling, model-based clustering, measurement of population differentiation, neighbor networks and haplotype sharing distinguished Barbaresca from other breeds, showed a low level of admixture with the other breeds considered in this study, and indicated

  15. The simcyp population based simulator: architecture, implementation, and quality assurance.

    PubMed

    Jamei, Masoud; Marciniak, Steve; Edwards, Duncan; Wragg, Kris; Feng, Kairui; Barnett, Adrian; Rostami-Hodjegan, Amin

    2013-01-01

    Developing a user-friendly platform that can handle a vast number of complex physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) models both for conventional small molecules and larger biologic drugs is a substantial challenge. Over the last decade the Simcyp Population Based Simulator has gained popularity in major pharmaceutical companies (70% of top 40 - in term of R&D spending). Under the Simcyp Consortium guidance, it has evolved from a simple drug-drug interaction tool to a sophisticated and comprehensive Model Based Drug Development (MBDD) platform that covers a broad range of applications spanning from early drug discovery to late drug development. This article provides an update on the latest architectural and implementation developments within the Simulator. Interconnection between peripheral modules, the dynamic model building process and compound and population data handling are all described. The Simcyp Data Management (SDM) system, which contains the system and drug databases, can help with implementing quality standards by seamless integration and tracking of any changes. This also helps with internal approval procedures, validation and auto-testing of the new implemented models and algorithms, an area of high interest to regulatory bodies.

  16. Demixed principal component analysis of neural population data

    PubMed Central

    Kobak, Dmitry; Brendel, Wieland; Constantinidis, Christos; Feierstein, Claudia E; Kepecs, Adam; Mainen, Zachary F; Qi, Xue-Lian; Romo, Ranulfo; Uchida, Naoshige; Machens, Christian K

    2016-01-01

    Neurons in higher cortical areas, such as the prefrontal cortex, are often tuned to a variety of sensory and motor variables, and are therefore said to display mixed selectivity. This complexity of single neuron responses can obscure what information these areas represent and how it is represented. Here we demonstrate the advantages of a new dimensionality reduction technique, demixed principal component analysis (dPCA), that decomposes population activity into a few components. In addition to systematically capturing the majority of the variance of the data, dPCA also exposes the dependence of the neural representation on task parameters such as stimuli, decisions, or rewards. To illustrate our method we reanalyze population data from four datasets comprising different species, different cortical areas and different experimental tasks. In each case, dPCA provides a concise way of visualizing the data that summarizes the task-dependent features of the population response in a single figure. DOI: http://dx.doi.org/10.7554/eLife.10989.001 PMID:27067378

  17. Using Bayesian Population Viability Analysis to Define Relevant Conservation Objectives

    PubMed Central

    Green, Adam W.; Bailey, Larissa L.

    2015-01-01

    Adaptive management provides a useful framework for managing natural resources in the face of uncertainty. An important component of adaptive management is identifying clear, measurable conservation objectives that reflect the desired outcomes of stakeholders. A common objective is to have a sustainable population, or metapopulation, but it can be difficult to quantify a threshold above which such a population is likely to persist. We performed a Bayesian metapopulation viability analysis (BMPVA) using a dynamic occupancy model to quantify the characteristics of two wood frog (Lithobates sylvatica) metapopulations resulting in sustainable populations, and we demonstrate how the results could be used to define meaningful objectives that serve as the basis of adaptive management. We explored scenarios involving metapopulations with different numbers of patches (pools) using estimates of breeding occurrence and successful metamorphosis from two study areas to estimate the probability of quasi-extinction and calculate the proportion of vernal pools producing metamorphs. Our results suggest that ≥50 pools are required to ensure long-term persistence with approximately 16% of pools producing metamorphs in stable metapopulations. We demonstrate one way to incorporate the BMPVA results into a utility function that balances the trade-offs between ecological and financial objectives, which can be used in an adaptive management framework to make optimal, transparent decisions. Our approach provides a framework for using a standard method (i.e., PVA) and available information to inform a formal decision process to determine optimal and timely management policies. PMID:26658734

  18. Atomic clock based on transient coherent population trapping

    SciTech Connect

    Guo Tao; Deng Ke; Chen Xuzong; Wang Zhong

    2009-04-13

    We proposed a scheme to implement coherent population trapping (CPT) atomic clock based on the transient CPT phenomenon. We proved that the transient transmitted laser power in a typical {lambda} system near CPT resonance features as a damping oscillation. Also, the oscillating frequency is exactly equal to the frequency detuning from the atomic hyperfine splitting. Therefore, we can directly measure the frequency detuning and then compensated to the output frequency of microwave oscillator to get the standard frequency. By this method, we can further simplify the structure of CPT atomic clock, and make it easier to be digitized and miniaturized.

  19. Graphic analysis of population structure on genome-wide rheumatoid arthritis data.

    PubMed

    Zhang, Jun; Weng, Chunhua; Niyogi, Partha

    2009-12-15

    Principal-component analysis (PCA) has been used for decades to summarize the human genetic variation across geographic regions and to infer population migration history. Reduction of spurious associations due to population structure is crucial for the success of disease association studies. Recently, PCA has also become a popular method for detecting population structure and correction of population stratification in disease association studies. Inspired by manifold learning, we propose a novel method based on spectral graph theory. Regarding each study subject as a node with suitably defined weights for its edges to close neighbors, one can form a weighted graph. We suggest using the spectrum of the associated graph Laplacian operator, namely, Laplacian eigenfunctions, to infer population structures instead of principal components (PCs). For the whole genome-wide association data for the North American Rheumatoid Arthritis Consortium (NARAC) provided by Genetic Workshop Analysis 16, Laplacian eigenfunctions revealed more meaningful structures of the underlying population than PCA. The proposed method has connection to PCA, and it naturally includes PCA as a special case. Our simple method is computationally fast and is suitable for disease studies at the genome-wide scale.

  20. Estimating glomerular filtration rate in a population-based study

    PubMed Central

    Shankar, Anoop; Lee, Kristine E; Klein, Barbara EK; Muntner, Paul; Brazy, Peter C; Cruickshanks, Karen J; Nieto, F Javier; Danforth, Lorraine G; Schubert, Carla R; Tsai, Michael Y; Klein, Ronald

    2010-01-01

    Background: Glomerular filtration rate (GFR)-estimating equations are used to determine the prevalence of chronic kidney disease (CKD) in population-based studies. However, it has been suggested that since the commonly used GFR equations were originally developed from samples of patients with CKD, they underestimate GFR in healthy populations. Few studies have made side-by-side comparisons of the effect of various estimating equations on the prevalence estimates of CKD in a general population sample. Patients and methods: We examined a population-based sample comprising adults from Wisconsin (age, 43–86 years; 56% women). We compared the prevalence of CKD, defined as a GFR of <60 mL/min per 1.73 m2 estimated from serum creatinine, by applying various commonly used equations including the modification of diet in renal disease (MDRD) equation, Cockcroft–Gault (CG) equation, and the Mayo equation. We compared the performance of these equations against the CKD definition of cystatin C >1.23 mg/L. Results: We found that the prevalence of CKD varied widely among different GFR equations. Although the prevalence of CKD was 17.2% with the MDRD equation and 16.5% with the CG equation, it was only 4.8% with the Mayo equation. Only 24% of those identified to have GFR in the range of 50–59 mL/min per 1.73 m2 by the MDRD equation had cystatin C levels >1.23 mg/L; their mean cystatin C level was only 1 mg/L (interquartile range, 0.9–1.2 mg/L). This finding was similar for the CG equation. For the Mayo equation, 62.8% of those patients with GFR in the range of 50–59 mL/min per 1.73 m2 had cystatin C levels >1.23 mg/L; their mean cystatin C level was 1.3 mg/L (interquartile range, 1.2–1.5 mg/L). The MDRD and CG equations showed a false-positive rate of >10%. Discussion: We found that the MDRD and CG equations, the current standard to estimate GFR, appeared to overestimate the prevalence of CKD in a general population sample. PMID:20730018

  1. Ion-beam amorphization of semiconductors: A physical model based on the amorphous pocket population

    SciTech Connect

    Mok, K.R.C.; Jaraiz, M.; Martin-Bragado, I.; Rubio, J.E.; Castrillo, P.; Pinacho, R.; Barbolla, J.; Srinivasan, M.P.

    2005-08-15

    We introduce a model for damage accumulation up to amorphization, based on the ion-implant damage structures commonly known as amorphous pockets. The model is able to reproduce the silicon amorphous-crystalline transition temperature for C, Si, and Ge ion implants. Its use as an analysis tool reveals an unexpected bimodal distribution of the defect population around a characteristic size, which is larger for heavier ions. The defect population is split in both size and composition, with small, pure interstitial and vacancy clusters below the characteristic size, and amorphous pockets with a balanced mixture of interstitials and vacancies beyond that size.

  2. Morphological analysis of palatal rugae pattern in central Indian population

    PubMed Central

    Dwivedi, Neha; Nagarajappa, Anil Kumar

    2016-01-01

    Aim: The aim of this study was to analyze the morphological study of palatal rugae pattern in a central Indian population and to determine sex differentiation. Objectives: To investigate the distinctive rugae patterns of the study population and determine the contribution of rugae patterns in gender identification. Material and Methods: The present cross-sectional study was conducted among a Central Indian population with a sample size of 500 participants. The study involved 250 males and 250 females who were randomly selected from the outpatient department of Oral Medicine Diagnosis and Radiology, Hitkarini Dental College and Hospital, Jabalpur, Madhya Pradesh. After collection of impression, casts were made and analyzed to evaluate the palatal rugae pattern in a central Indian population by using Thomas and Kotze classification (1983) for number, shape, direction, and unification of palatal rugae pattern. The statistical analysis was carried out using Mann–Whitney test and Chi-square (χ2) tests for categorical variables. Result: Males showed more number of rugae than females [P = 0.00 (≤0.001)]. Males had more number of wavy rugae pattern whereas females showed more number of straight rugae patterns [P = 0.00 (≤0.001)]. Males showed more backwardly directed rugae whereas females showed more forwardly directed rugae [P = 0.00 (≤0.001)]. The unification did not show any significant difference. Conclusion: This study showed that there was a significant relationship between palatoscopy, human identification, and sex determination. Thus, palatoscopy can be considered as a cost effective, easy, unique, and stable method for human identification. PMID:27891307

  3. Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula

    PubMed Central

    2013-01-01

    Background Inbreeding is among the major concerns in management of local livestock populations. The effective population size of these populations tends to be small, which enhances the risk of fitness reduction and extinction. High-density SNP data make it possible to undertake novel approaches in conservation genetics of endangered breeds and wild populations. A total of 97 representative samples of domestic and wild pig populations from the Iberian Peninsula, subjected to different levels of threat with extinction, were genotyped with a 60 K SNP panel. Data analyses based on: (i) allele frequency differences; (ii) linkage disequilibrium and (iii) runs of homozygosity were integrated to study population relationships, inbreeding and demographic history. Results The domestic pigs analyzed belonged to local Spanish and Portuguese breeds: Iberian ─ including the variants Retinto Iberian, Negro Iberian and Manchado de Jabugo ─, Bisaro and Chato Murciano. The population structure and persistence of phase analysis suggested high genetic relations between Iberian variants, with recent crossbreeding of Manchado de Jabugo with other pig populations. Chato Murciano showed a high frequency of long runs of homozygosity indicating recent inbreeding and reflecting the recent bottleneck reported by historical records. The Chato Murciano and the Manchado de Jabugo breeds presented the lowest effective population sizes in accordance with their status of highly inbred breeds. The Iberian wild boar presented a high frequency of short runs of homozygosity indicating past small population size but no signs of recent inbreeding. The Iberian breed showed higher genetic similarities with Iberian wild boar than the other domestic breeds. Conclusions High-density SNP data provided a consistent overview of population structure, demographic history and inbreeding of minority breeds and wild pig populations from the Iberian Peninsula. Despite the very different background of the

  4. Contrasting results from molecular and pedigree-based population diversity measures in captive zebra highlight challenges facing genetic management of zoo populations.

    PubMed

    Ito, Hideyuki; Ogden, Rob; Langenhorst, Tanya; Inoue-Murayama, Miho

    2017-01-01

    Zoo conservation breeding programs manage the retention of population genetic diversity through analysis of pedigree records. The range of demographic and genetic indices determined through pedigree analysis programs allows the conservation of diversity to be monitored relative to the particular founder population for a species. Such approaches are based on a number of well-documented founder assumptions, however without knowledge of actual molecular genetic diversity there is a risk that pedigree-based measures will be misinterpreted and population genetic diversity misunderstood. We examined the genetic diversity of the captive populations of Grevy's zebra, Hartmann's mountain zebra and plains zebra in Japan and the United Kingdom through analysis of mitochondrial DNA sequences. Very low nucleotide variability was observed in Grevy's zebra. The results were evaluated with respect to current and historic diversity in the wild, and indicate that low genetic diversity in the captive population is likely a result of low founder diversity, which in turn suggests relatively low wild genetic diversity prior to recent population declines. Comparison of molecular genetic diversity measures with analogous diversity indices generated from the studbook data for Grevy's zebra and Hartmann's mountain zebra show contrasting patterns, with Grevy's zebra displaying markedly less molecular diversity than mountain zebra, despite studbook analysis indicating that the Grevy's zebra population has substantially more founders, greater effective population size, lower mean kinship, and has suffered less loss of gene diversity. These findings emphasize the need to validate theoretical estimates of genetic diversity in captive breeding programs with empirical molecular genetic data. Zoo Biol. 36:87-94, 2017. © 2016 Wiley Periodicals, Inc.

  5. Choice of population database for forensic DNA profile analysis.

    PubMed

    Steele, Christopher D; Balding, David J

    2014-12-01

    When evaluating the weight of evidence (WoE) for an individual to be a contributor to a DNA sample, an allele frequency database is required. The allele frequencies are needed to inform about genotype probabilities for unknown contributors of DNA to the sample. Typically databases are available from several populations, and a common practice is to evaluate the WoE using each available database for each unknown contributor. Often the most conservative WoE (most favourable to the defence) is the one reported to the court. However the number of human populations that could be considered is essentially unlimited and the number of contributors to a sample can be large, making it impractical to perform every possible WoE calculation, particularly for complex crime scene profiles. We propose instead the use of only the database that best matches the ancestry of the queried contributor, together with a substantial FST adjustment. To investigate the degree of conservativeness of this approach, we performed extensive simulations of one- and two-contributor crime scene profiles, in the latter case with, and without, the profile of the second contributor available for the analysis. The genotypes were simulated using five population databases, which were also available for the analysis, and evaluations of WoE using our heuristic rule were compared with several alternative calculations using different databases. Using FST=0.03, we found that our heuristic gave WoE more favourable to the defence than alternative calculations in well over 99% of the comparisons we considered; on average the difference in WoE was just under 0.2 bans (orders of magnitude) per locus. The degree of conservativeness of the heuristic rule can be adjusted through the FST value. We propose the use of this heuristic for DNA profile WoE calculations, due to its ease of implementation, and efficient use of the evidence while allowing a flexible degree of conservativeness.

  6. Allozyme and RAPD analysis of the genetic diversity and geographic variation in wild populations of the American chestnut (Fagaceae).

    PubMed

    Huang, H; Dane, F; Kubisiak, T

    1998-07-01

    Genetic variation among 12 populations of the American chestnut (Castanea dentata) was investigated. Population genetic parameters estimated from allozyme variation suggest that C. dentata at both the population and species level has narrow genetic diversity as compared to other species in the genus. Average expected heterozygosity was relatively low for the population collected in the Black Rock Mountain State Park, Georgia (He = 0.096 +/- 0.035), and high for the population in east central Alabama (He = 0.196 +/- 0.048). Partitioning of the genetic diversity based on 18 isozyme loci showed that ~10% of the allozyme diversity resided among populations. Cluster analysis using unweighted pair-group method using arithmetric averages of Rogers' genetic distance and principal components analysis based on allele frequencies of both isozyme and RAPD loci revealed four groups: the southernmost population, south-central Appalachian populations, north-central Appalachian populations, and northern Appalachian populations. Based on results presented in this study, a conservation strategy and several recommendations related to the backcross breeding aimed at restoring C. dentata are discussed.

  7. On the accuracy of population analyses based on fitted densities().

    PubMed

    de la Lande, Aurélien; Clavaguéra, Carine; Köster, Andreas

    2017-04-01

    Population analyses are part of the theoretical chemist's toolbox. They provide means to extract information about the repartition of the electronic density among molecules or solids. The values of atomic multipoles in a molecule can shed light on its electrostatic properties and may help to predict how different molecules could interact or to rationalize chemical reactivity for instance. Not being physical observables to which a quantum mechanical operator can be associated, atomic charges and higher order atomic multipoles cannot be defined unambiguously in a molecule, and therefore, several population schemes (PS) have been devised in the last decades. In the context of density functional theory (DFT), PS based on the electron density seem to be best grounded. In particular, some groups have proposed various iterative schemes the outcomes of which are very encouraging. Modern implementations of DFT that are for example based on density fitting techniques permit the investigation of molecular systems comprising of hundreds of atoms. However, population analyses following iterative schemes may become very CPU time consuming for such large systems. In this article, we investigate if the computationally less expensive analyses of the variationally fitted electronic densities can be safely carried out instead of the Kohn-Sham density. It is shown that as long as flexible auxiliary function sets including f and g functions are used, the multipoles extracted from the fitted densities are extremely close to those obtained from the KS density. We further assess if the multipoles obtained through the Hirshfeld's approach, in its standard or iterative form, can be a useful approach to calculate interaction energies in non-covalent complexes. Relative energies computed with the AMOEBA polarizable forced field combined to iterative Hirshfeld multipoles are encouraging.

  8. Geographic population structure analysis of worldwide human populations infers their biogeographical origins.

    PubMed

    Elhaik, Eran; Tatarinova, Tatiana; Chebotarev, Dmitri; Piras, Ignazio S; Maria Calò, Carla; De Montis, Antonella; Atzori, Manuela; Marini, Monica; Tofanelli, Sergio; Francalacci, Paolo; Pagani, Luca; Tyler-Smith, Chris; Xue, Yali; Cucca, Francesco; Schurr, Theodore G; Gaieski, Jill B; Melendez, Carlalynne; Vilar, Miguel G; Owings, Amanda C; Gómez, Rocío; Fujita, Ricardo; Santos, Fabrício R; Comas, David; Balanovsky, Oleg; Balanovska, Elena; Zalloua, Pierre; Soodyall, Himla; Pitchappan, Ramasamy; Ganeshprasad, Arunkumar; Hammer, Michael; Matisoo-Smith, Lisa; Wells, R Spencer

    2014-04-29

    The search for a method that utilizes biological information to predict humans' place of origin has occupied scientists for millennia. Over the past four decades, scientists have employed genetic data in an effort to achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing data have achieved an accuracy of 700 km in Europe, they were inaccurate elsewhere. Here we describe the Geographic Population Structure (GPS) algorithm and demonstrate its accuracy with three data sets using 40,000-130,000 SNPs. GPS placed 83% of worldwide individuals in their country of origin. Applied to over 200 Sardinians villagers, GPS placed a quarter of them in their villages and most of the rest within 50 km of their villages. GPS's accuracy and power to infer the biogeography of worldwide individuals down to their country or, in some cases, village, of origin, underscores the promise of admixture-based methods for biogeography and has ramifications for genetic ancestry testing.

  9. Optimal inverse functions created via population-based optimization.

    PubMed

    Jennings, Alan L; Ordóñez, Raúl

    2014-06-01

    Finding optimal inputs for a multiple-input, single-output system is taxing for a system operator. Population-based optimization is used to create sets of functions that produce a locally optimal input based on a desired output. An operator or higher level planner could use one of the functions in real time. For the optimization, each agent in the population uses the cost and output gradients to take steps lowering the cost while maintaining their current output. When an agent reaches an optimal input for its current output, additional agents are generated in the output gradient directions. The new agents then settle to the local optima for the new output values. The set of associated optimal points forms an inverse function, via spline interpolation, from a desired output to an optimal input. In this manner, multiple locally optimal functions can be created. These functions are naturally clustered in input and output spaces allowing for a continuous inverse function. The operator selects the best cluster over the anticipated range of desired outputs and adjusts the set point (desired output) while maintaining optimality. This reduces the demand from controlling multiple inputs, to controlling a single set point with no loss in performance. Results are demonstrated on a sample set of functions and on a robot control problem.

  10. Copula-Based Approach to Synthetic Population Generation

    PubMed Central

    Kim, Deok-Soo

    2016-01-01

    Generating synthetic baseline populations is a fundamental step of agent-based modeling and simulation, which is growing fast in a wide range of socio-economic areas including transportation planning research. Traditionally, in many commercial and non-commercial microsimulation systems, the iterative proportional fitting (IPF) procedure has been used for creating the joint distribution of individuals when combining a reference joint distribution with target marginal distributions. Although IPF is simple, computationally efficient, and rigorously founded, it is unclear whether IPF well preserves the dependence structure of the reference joint table sufficiently when fitting it to target margins. In this paper, a novel method is proposed based on the copula concept in order to provide an alternative approach to the problem that IPF resolves. The dependency characteristic measures were computed and the results from the proposed method and IPF were compared. In most test cases, the proposed method outperformed IPF in preserving the dependence structure of the reference joint distribution. PMID:27490692

  11. Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation.

    PubMed

    Kuroda, Y; Kaga, A; Tomooka, N; Vaughan, D A

    2006-04-01

    The research objectives were to determine aspects of the population dynamics relevant to effective monitoring of gene flow in the soybean crop complex in Japan. Using 20 microsatellite primers, 616 individuals from 77 wild soybean (Glycine soja) populations were analysed. All samples were of small seed size (< 0.03 g), were directly collected in the field and came from all parts of Japan where wild soybeans grow, except Hokkaido. Japanese wild soybean showed significant reduction in observed heterozygosity, low outcrossing rate (mean 3.4%) and strong genetic differentiation among populations. However, the individual assignment test revealed evidence of rare long-distance seed dispersal (> 10 km) events among populations, and spatial autocorrelation analysis revealed that populations within a radius of 100 km showed a close genetic relationship to one another. When analysis of graphical ordination was applied to compare the microsatellite variation of wild soybean with that of 53 widely grown Japanese varieties of cultivated soybean (Glycine max), the primary factor of genetic differentiation was based on differences between wild and cultivated soybeans and the secondary factor was geographical differentiation of wild soybean populations. Admixture analysis revealed that 6.8% of individuals appear to show introgression from cultivated soybeans. These results indicated that population genetic structure of Japanese wild soybean is (i) strongly affected by the founder effect due to seed dispersal and inbreeding strategy, (ii) generally well differentiated from cultivated soybean, but (iii) introgression from cultivated soybean occurs. The implications of the results for the release of transgenic soybeans where wild soybeans grow are discussed.

  12. Adélie Penguin Population Diet Monitoring by Analysis of Food DNA in Scats

    PubMed Central

    Jarman, Simon N.; McInnes, Julie C.; Faux, Cassandra; Polanowski, Andrea M.; Marthick, James; Deagle, Bruce E.; Southwell, Colin; Emmerson, Louise

    2013-01-01

    The Adélie penguin is the most important animal currently used for ecosystem monitoring in the Southern Ocean. The diet of this species is generally studied by visual analysis of stomach contents; or ratios of isotopes of carbon and nitrogen incorporated into the penguin from its food. There are significant limitations to the information that can be gained from these methods. We evaluated population diet assessment by analysis of food DNA in scats as an alternative method for ecosystem monitoring with Adélie penguins as an indicator species. Scats were collected at four locations, three phases of the breeding cycle, and in four different years. A novel molecular diet assay and bioinformatics pipeline based on nuclear small subunit ribosomal RNA gene (SSU rDNA) sequencing was used to identify prey DNA in 389 scats. Analysis of the twelve population sample sets identified spatial and temporal dietary change in Adélie penguin population diet. Prey diversity was found to be greater than previously thought. Krill, fish, copepods and amphipods were the most important food groups, in general agreement with other Adélie penguin dietary studies based on hard part or stable isotope analysis. However, our DNA analysis estimated that a substantial portion of the diet was gelatinous groups such as jellyfish and comb jellies. A range of other prey not previously identified in the diet of this species were also discovered. The diverse prey identified by this DNA-based scat analysis confirms that the generalist feeding of Adélie penguins makes them a useful indicator species for prey community composition in the coastal zone of the Southern Ocean. Scat collection is a simple and non-invasive field sampling method that allows DNA-based estimation of prey community differences at many temporal and spatial scales and provides significant advantages over alternative diet analysis approaches. PMID:24358158

  13. Adélie penguin population diet monitoring by analysis of food DNA in scats.

    PubMed

    Jarman, Simon N; McInnes, Julie C; Faux, Cassandra; Polanowski, Andrea M; Marthick, James; Deagle, Bruce E; Southwell, Colin; Emmerson, Louise

    2013-01-01

    The Adélie penguin is the most important animal currently used for ecosystem monitoring in the Southern Ocean. The diet of this species is generally studied by visual analysis of stomach contents; or ratios of isotopes of carbon and nitrogen incorporated into the penguin from its food. There are significant limitations to the information that can be gained from these methods. We evaluated population diet assessment by analysis of food DNA in scats as an alternative method for ecosystem monitoring with Adélie penguins as an indicator species. Scats were collected at four locations, three phases of the breeding cycle, and in four different years. A novel molecular diet assay and bioinformatics pipeline based on nuclear small subunit ribosomal RNA gene (SSU rDNA) sequencing was used to identify prey DNA in 389 scats. Analysis of the twelve population sample sets identified spatial and temporal dietary change in Adélie penguin population diet. Prey diversity was found to be greater than previously thought. Krill, fish, copepods and amphipods were the most important food groups, in general agreement with other Adélie penguin dietary studies based on hard part or stable isotope analysis. However, our DNA analysis estimated that a substantial portion of the diet was gelatinous groups such as jellyfish and comb jellies. A range of other prey not previously identified in the diet of this species were also discovered. The diverse prey identified by this DNA-based scat analysis confirms that the generalist feeding of Adélie penguins makes them a useful indicator species for prey community composition in the coastal zone of the Southern Ocean. Scat collection is a simple and non-invasive field sampling method that allows DNA-based estimation of prey community differences at many temporal and spatial scales and provides significant advantages over alternative diet analysis approaches.

  14. Validation of population-based disease simulation models: a review of concepts and methods

    PubMed Central

    2010-01-01

    Background Computer simulation models are used increasingly to support public health research and policy, but questions about their quality persist. The purpose of this article is to review the principles and methods for validation of population-based disease simulation models. Methods We developed a comprehensive framework for validating population-based chronic disease simulation models and used this framework in a review of published model validation guidelines. Based on the review, we formulated a set of recommendations for gathering evidence of model credibility. Results Evidence of model credibility derives from examining: 1) the process of model development, 2) the performance of a model, and 3) the quality of decisions based on the model. Many important issues in model validation are insufficiently addressed by current guidelines. These issues include a detailed evaluation of different data sources, graphical representation of models, computer programming, model calibration, between-model comparisons, sensitivity analysis, and predictive validity. The role of external data in model validation depends on the purpose of the model (e.g., decision analysis versus prediction). More research is needed on the methods of comparing the quality of decisions based on different models. Conclusion As the role of simulation modeling in population health is increasing and models are becoming more complex, there is a need for further improvements in model validation methodology and common standards for evaluating model credibility. PMID:21087466

  15. An analysis of the basic population structure of Shanghai Municipality.

    PubMed

    Shen, A

    1984-01-01

    This paper analyzes the changes in Shanghai's population structure over the last 30 years in the 4 aspects of age structure, sex composition, urban and rural composition, and labor and employment structure. In 1953 those of the 0 to 6 age group accounted for 21.2% of the total population; in 1957 the group represented a proportion of 24.6%. Since the 1960s, especially after the 1970s, the family planning program gradually took effect, and the birthrate of the entire municipality fell drastically. The number of school-age children in 1979 was 1 1/2 times more than the same age group in 1953; there should be no worry that population control may result in a shortage of manpower to meet the needs of the work force and the armed forces either toward the end of this century or at the beginning of the next. The economy in China is underdeveloped, production and technology remain at a low level, average wages for employees are low, and for a long time the low living standard of the people has shown little sign of improvement. The problem is mainly manifest in the following areas: 1) distribution of the work force in heavy and light industries is not sufficiently rational, 2) the distribution of the work force between captial construction and transport and communications on the 1 hand and the national economy on the other is out of proportion, 3) the distribution of the work force between commerce, service trades, and public utilities on the 1 hand and the national economy on the other is disproportionated, and 4) the distribution of the work force between undertakings of culture, education, scientific research, health, and medical care on the 1 hand and economic construction on the other is improper. How to control population growth and adjust parts of the population structure to suit the national economic development poses a problem that calls for further in-depth study and analysis to resolve it step by step.

  16. Controlling for non-independence in comparative analysis of patterns across populations within species

    PubMed Central

    Stone, Graham N.; Nee, Sean; Felsenstein, Joseph

    2011-01-01

    How do we quantify patterns (such as responses to local selection) sampled across multiple populations within a single species? Key to this question is the extent to which populations within species represent statistically independent data points in our analysis. Comparative analyses across species and higher taxa have long recognized the need to control for the non-independence of species data that arises through patterns of shared common ancestry among them (phylogenetic non-independence), as have quantitative genetic studies of individuals linked by a pedigree. Analyses across populations lacking pedigree information fall in the middle, and not only have to deal with shared common ancestry, but also the impact of exchange of migrants between populations (gene flow). As a result, phenotypes measured in one population are influenced by processes acting on others, and may not be a good guide to either the strength or direction of local selection. Although many studies examine patterns across populations within species, few consider such non-independence. Here, we discuss the sources of non-independence in comparative analysis, and show why the phylogeny-based approaches widely used in cross-species analyses are unlikely to be useful in analyses across populations within species. We outline the approaches (intraspecific contrasts, generalized least squares, generalized linear mixed models and autoregression) that have been used in this context, and explain their specific assumptions. We highlight the power of ‘mixed models’ in many contexts where problems of non-independence arise, and show that these allow incorporation of both shared common ancestry and gene flow. We suggest what can be done when ideal solutions are inaccessible, highlight the need for incorporation of a wider range of population models in intraspecific comparative methods and call for simulation studies of the error rates associated with alternative approaches. PMID:21444315

  17. Controlling for non-independence in comparative analysis of patterns across populations within species.

    PubMed

    Stone, Graham N; Nee, Sean; Felsenstein, Joseph

    2011-05-12

    How do we quantify patterns (such as responses to local selection) sampled across multiple populations within a single species? Key to this question is the extent to which populations within species represent statistically independent data points in our analysis. Comparative analyses across species and higher taxa have long recognized the need to control for the non-independence of species data that arises through patterns of shared common ancestry among them (phylogenetic non-independence), as have quantitative genetic studies of individuals linked by a pedigree. Analyses across populations lacking pedigree information fall in the middle, and not only have to deal with shared common ancestry, but also the impact of exchange of migrants between populations (gene flow). As a result, phenotypes measured in one population are influenced by processes acting on others, and may not be a good guide to either the strength or direction of local selection. Although many studies examine patterns across populations within species, few consider such non-independence. Here, we discuss the sources of non-independence in comparative analysis, and show why the phylogeny-based approaches widely used in cross-species analyses are unlikely to be useful in analyses across populations within species. We outline the approaches (intraspecific contrasts, generalized least squares, generalized linear mixed models and autoregression) that have been used in this context, and explain their specific assumptions. We highlight the power of 'mixed models' in many contexts where problems of non-independence arise, and show that these allow incorporation of both shared common ancestry and gene flow. We suggest what can be done when ideal solutions are inaccessible, highlight the need for incorporation of a wider range of population models in intraspecific comparative methods and call for simulation studies of the error rates associated with alternative approaches.

  18. Spike-Based Population Coding and Working Memory

    PubMed Central

    Boerlin, Martin; Denève, Sophie

    2011-01-01

    Compelling behavioral evidence suggests that humans can make optimal decisions despite the uncertainty inherent in perceptual or motor tasks. A key question in neuroscience is how populations of spiking neurons can implement such probabilistic computations. In this article, we develop a comprehensive framework for optimal, spike-based sensory integration and working memory in a dynamic environment. We propose that probability distributions are inferred spike-per-spike in recurrently connected networks of integrate-and-fire neurons. As a result, these networks can combine sensory cues optimally, track the state of a time-varying stimulus and memorize accumulated evidence over periods much longer than the time constant of single neurons. Importantly, we propose that population responses and persistent working memory states represent entire probability distributions and not only single stimulus values. These memories are reflected by sustained, asynchronous patterns of activity which make relevant information available to downstream neurons within their short time window of integration. Model neurons act as predictive encoders, only firing spikes which account for new information that has not yet been signaled. Thus, spike times signal deterministically a prediction error, contrary to rate codes in which spike times are considered to be random samples of an underlying firing rate. As a consequence of this coding scheme, a multitude of spike patterns can reliably encode the same information. This results in weakly correlated, Poisson-like spike trains that are sensitive to initial conditions but robust to even high levels of external neural noise. This spike train variability reproduces the one observed in cortical sensory spike trains, but cannot be equated to noise. On the contrary, it is a consequence of optimal spike-based inference. In contrast, we show that rate-based models perform poorly when implemented with stochastically spiking neurons. PMID:21379319

  19. Increasing incidence of cataract surgery: Population-based study

    PubMed Central

    Gollogly, Heidrun E.; Hodge, David O.; St. Sauver, Jennifer L.; Erie, Jay C.

    2015-01-01

    PURPOSE To estimate the incidence of cataract surgery in a defined population and to determine longitudinal cataract surgery patterns. SETTING Mayo Clinic, Rochester, Minnesota, USA. DESIGN Cohort study. METHODS Rochester Epidemiology Project (REP) databases were used to identify all incident cataract surgeries in Olmsted County, Minnesota, between January 1, 2005, and December 31, 2011. Age-specific and sex-specific incidence rates were calculated and adjusted to the 2010 United States white population. Data were merged with previous REP data (1980 to 2004) to assess temporal trends in cataract surgery. Change in the incidence over time was assessed by fitting generalized linear models assuming a Poisson error structure. The probability of second-eye cataract surgery was calculated using the Kaplan-Meier method. RESULTS Included were 8012 cataract surgeries from 2005 through 2011. During this time, incident cataract surgery significantly increased (P < .001), peaking in 2011 with a rate of 1100 per 100 000 (95% confidence interval, 1050–1160). The probability of second-eye surgery 3, 12, and 24 months after first-eye surgery was 60%, 76%, and 86%, respectively, a significant increase compared with the same intervals in the previous 7 years (1998 to 2004) (P < .001). When merged with 1980 to 2004 REP data, incident cataract surgery steadily increased over the past 3 decades (P < .001). CONCLUSION Incident cataract surgery steadily increased over the past 32 years and has not leveled off, as reported in Swedish population-based series. Second-eye surgery was performed sooner and more frequently, with 60% of residents having second-eye surgery within 3-months of first-eye surgery. PMID:23820302

  20. Challenges in analysis and interpretation of microsatellite data for population genetic studies

    PubMed Central

    Putman, Alexander I; Carbone, Ignazio

    2014-01-01

    Advancing technologies have facilitated the ever-widening application of genetic markers such as microsatellites into new systems and research questions in biology. In light of the data and experience accumulated from several years of using microsatellites, we present here a literature review that synthesizes the limitations of microsatellites in population genetic studies. With a focus on population structure, we review the widely used fixation (FST) statistics and Bayesian clustering algorithms and find that the former can be confusing and problematic for microsatellites and that the latter may be confounded by complex population models and lack power in certain cases. Clustering, multivariate analyses, and diversity-based statistics are increasingly being applied to infer population structure, but in some instances these methods lack formalization with microsatellites. Migration-specific methods perform well only under narrow constraints. We also examine the use of microsatellites for inferring effective population size, changes in population size, and deeper demographic history, and find that these methods are untested and/or highly context-dependent. Overall, each method possesses important weaknesses for use with microsatellites, and there are significant constraints on inferences commonly made using microsatellite markers in the areas of population structure, admixture, and effective population size. To ameliorate and better understand these constraints, researchers are encouraged to analyze simulated datasets both prior to and following data collection and analysis, the latter of which is formalized within the approximate Bayesian computation framework. We also examine trends in the literature and show that microsatellites continue to be widely used, especially in non-human subject areas. This review assists with study design and molecular marker selection, facilitates sound interpretation of microsatellite data while fostering respect for their practical

  1. Population and genomic analysis of the genus Halorubrum

    PubMed Central

    Fullmer, Matthew S.; Soucy, Shannon M.; Swithers, Kristen S.; Makkay, Andrea M.; Wheeler, Ryan; Ventosa, Antonio; Gogarten, J. Peter; Papke, R. Thane

    2014-01-01

    The Halobacteria are known to engage in frequent gene transfer and homologous recombination. For stably diverged lineages to persist some checks on the rate of between lineage recombination must exist. We surveyed a group of isolates from the Aran-Bidgol endorheic lake in Iran and sequenced a selection of them. Multilocus Sequence Analysis (MLSA) and Average Nucleotide Identity (ANI) revealed multiple clusters (phylogroups) of organisms present in the lake. Patterns of intein and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) presence/absence and their sequence similarity, GC usage along with the ANI and the identities of the genes used in the MLSA revealed that two of these clusters share an exchange bias toward others in their phylogroup while showing reduced rates of exchange with other organisms in the environment. However, a third cluster, composed in part of named species from other areas of central Asia, displayed many indications of variability in exchange partners, from within the lake as well as outside the lake. We conclude that barriers to gene exchange exist between the two purely Aran-Bidgol phylogroups, and that the third cluster with members from other regions is not a single population and likely reflects an amalgamation of several populations. PMID:24782836

  2. Population and genomic analysis of the genus Halorubrum.

    PubMed

    Fullmer, Matthew S; Soucy, Shannon M; Swithers, Kristen S; Makkay, Andrea M; Wheeler, Ryan; Ventosa, Antonio; Gogarten, J Peter; Papke, R Thane

    2014-01-01

    The Halobacteria are known to engage in frequent gene transfer and homologous recombination. For stably diverged lineages to persist some checks on the rate of between lineage recombination must exist. We surveyed a group of isolates from the Aran-Bidgol endorheic lake in Iran and sequenced a selection of them. Multilocus Sequence Analysis (MLSA) and Average Nucleotide Identity (ANI) revealed multiple clusters (phylogroups) of organisms present in the lake. Patterns of intein and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) presence/absence and their sequence similarity, GC usage along with the ANI and the identities of the genes used in the MLSA revealed that two of these clusters share an exchange bias toward others in their phylogroup while showing reduced rates of exchange with other organisms in the environment. However, a third cluster, composed in part of named species from other areas of central Asia, displayed many indications of variability in exchange partners, from within the lake as well as outside the lake. We conclude that barriers to gene exchange exist between the two purely Aran-Bidgol phylogroups, and that the third cluster with members from other regions is not a single population and likely reflects an amalgamation of several populations.

  3. Quantitative analysis of the heterogeneous population of endocytic vesicles.

    PubMed

    Kozlov, Konstantin; Kosheverova, Vera; Kamentseva, Rimma; Kharchenko, Marianna; Sokolkova, Alena; Kornilova, Elena; Samsonova, Maria

    2017-03-07

    The quantitative characterization of endocytic vesicles in images acquired with microscope is critically important for deciphering of endocytosis mechanisms. Image segmentation is the most important step of quantitative image analysis. In spite of availability of many segmentation methods, the accurate segmentation is challenging when the images are heterogeneous with respect to object shapes and signal intensities what is typical for images of endocytic vesicles. We present a Morphological reconstruction and Contrast mapping segmentation method (MrComas) for the segmentation of the endocytic vesicle population that copes with the heterogeneity in their shape and intensity. The method uses morphological opening and closing by reconstruction in the vicinity of local minima and maxima respectively thus creating the strong contrast between their basins of attraction. As a consequence, the intensity is flattened within the objects and their edges are enhanced. The method accurately recovered quantitative characteristics of synthetic images that preserve characteristic features of the endocytic vesicle population. In benchmarks and quantitative comparisons with two other popular segmentation methods, namely manual thresholding and Squash plugin, MrComas shows the best segmentation results on real biological images of EGFR (Epidermal Growth Factor Receptor) endocytosis. As a proof of feasibility, the method was applied to quantify the dynamical behavior of Early Endosomal Autoantigen 1 (EEA1)-positive endosome subpopulations during EGF-stimulated endocytosis.

  4. Portable atomic frequency standard based on coherent population trapping

    NASA Astrophysics Data System (ADS)

    Shi, Fan; Yang, Renfu; Nian, Feng; Zhang, Zhenwei; Cui, Yongshun; Zhao, Huan; Wang, Nuanrang; Feng, Keming

    2015-05-01

    In this work, a portable atomic frequency standard based on coherent population trapping is designed and demonstrated. To achieve a portable prototype, in the system, a single transverse mode 795nm VCSEL modulated by a 3.4GHz RF source is used as a pump laser which generates coherent light fields. The pump beams pass through a vapor cell containing atom gas and buffer gas. This vapor cell is surrounded by a magnetic shield and placed inside a solenoid which applies a longitudinal magnetic field to lift the Zeeman energy levels' degeneracy and to separate the resonance signal, which has no first-order magnetic field dependence, from the field-dependent resonances. The electrical control system comprises two control loops. The first one locks the laser wavelength to the minimum of the absorption spectrum; the second one locks the modulation frequency and output standard frequency. Furthermore, we designed the micro physical package and realized the locking of a coherent population trapping atomic frequency standard portable prototype successfully. The short-term frequency stability of the whole system is measured to be 6×10-11 for averaging times of 1s, and reaches 5×10-12 at an averaging time of 1000s.

  5. A population-based study of the stratum corneum moisture

    PubMed Central

    de Farias Pires, Thiago; Azambuja, Ana Paula; Horimoto, Andrea Roseli Vançan Russo; Nakamura, Mary Sanae; de Oliveira Alvim, Rafael; Krieger, José Eduardo; Pereira, Alexandre Costa

    2016-01-01

    Background The stratum corneum (SC) has important functions as a bound-water modulator and a primary barrier of the human skin from the external environment. However, no large epidemiological study has quantified the relative importance of different exposures with regard to these functional properties. In this study, we have studied a large sample of individuals from the Brazilian population in order to understand the different relationships between the properties of SC and a number of demographic and self-perceived variables. Methods One thousand three hundred and thirty-nine individuals from a rural Brazilian population, who were participants of a family-based study, were submitted to a cross-sectional examination of the SC moisture by capacitance using the Corneometer® CM820 and investigated regarding environmental exposures, cosmetic use, and other physiological and epidemiological measurements. Self-perception-scaled questions about skin conditions were also applied. Results We found significant associations between SC moisture and sex, age, high sun exposure, and sunscreen use frequency (P<0.025). In specific studied sites, self-reported race and obesity were also found to show significant effects. Dry skin self-perception was also found to be highly correlated with the objective measurement of the skin. Other environmental effects on SC moisture are also reported. PMID:27143945

  6. Central poststroke pain: a population-based study.

    PubMed

    Klit, Henriette; Finnerup, Nanna Brix; Andersen, Grethe; Jensen, Troels Staehelin

    2011-04-01

    Central poststroke pain (CPSP) is a specific pain condition arising as a direct consequence of a cerebrovascular lesion. There is limited knowledge about the epidemiology and clinical characteristics of this often neglected but important consequence of stroke. In this population-based study, a questionnaire was sent out to all (n=964) stroke patients identified through the Danish National Indicator Project Stroke Database in Aarhus County, Denmark, between March 2004 and February 2005. All surviving patients who fulfilled 4 questionnaire criteria for possible CPSP (n=51) were selected for further clinical examination, and their pain was classified by using stringent and well-defined criteria and a detailed, standardized clinical examination. The minimum prevalence of definite or probable CPSP in this population is 7.3% and the prevalence of CPSP-like dysesthesia or pain is 8.6%. Pinprick hyperalgesia was present in 57%, cold allodynia in 40%, and brush-evoked dysesthesia in 51% of patients with CPSP. Because of its negative impact on quality of life and rehabilitation, pain is an important symptom to assess in stroke survivors.

  7. Genetic diversity analysis of Capparis spinosa L. populations by using ISSR markers.

    PubMed

    Liu, C; Xue, G P; Cheng, B; Wang, X; He, J; Liu, G H; Yang, W J

    2015-12-09

    Capparis spinosa L. is an important medicinal species in the Xinjiang Province of China. Ten natural populations of C. spinosa from 3 locations in North, Central, and South Xinjiang were studied using morphological trait inter simple sequence repeat (ISSR) molecular markers to assess the genetic diversity and population structure. In this study, the 10 ISSR primers produced 313 amplified DNA fragments, with 52% of fragments being polymorphic. Unweighted pair-group method with arithmetic average (UPGMA) cluster analysis indicated that 10 C. spinosa populations were clustered into 3 geographically distinct groups. The Nei gene of C. spinosa populations in different regions had Diversity and Shannon's information index ranges of 0.1312-0.2001 and 0.1004-0.1875, respectively. The 362 markers were used to construct the dendrogram based on the UPGMA cluster analysis. The dendrogram indicated that 10 populations of C. spinosa were clustered into 3 geographically distinct groups. The results showed these genotypes have high genetic diversity, and can be used for an alternative breeding program.

  8. Transformation of a cadaver population: Analysis of a South African cadaver program, 1921-2013.

    PubMed

    Kramer, Beverley; Hutchinson, Erin F

    2015-01-01

    Anatomy has served as a cornerstone in the training of various allied and clinical disciplines and has traditionally been based on dissection of the human body. Thus, to pursue this method of teaching and learning, access to cadavers is of continuing importance. Over a significant period of time unclaimed cadavers have performed an essential role in the teaching of anatomy in South Africa and in Africa. As recent cadaver numbers were declining at the School of Anatomical Sciences, University of the Witwatersrand, Johannesburg and difficulty in procurement was being experienced, the purpose of this study was to critically evaluate the composition of our cadaver population over time so as to provide possible strategies to arrest the decline. A retrospective, quantitative analysis of cadaver records from the School of Anatomical Sciences between 1921 and 2013 was undertaken. Analysis included a comparison of Poisson counts and Fischer's exact test. A significant decrease in the number of cadavers received during the period 2000-2013 and a slow bequest program over the same period of time has led to concerns about the sustainability of teaching anatomy through dissection. Decreases in the numbers of males and cadavers of the black population group occurred between 1990 and 2013, and of bequests from 2000 to 2013. An influence on the cadaver population from a changing political climate and change in socioeconomic status of part of the population was perceived. Changes in sex and population group of the cadavers may have a long-term effect on teaching and research.

  9. 3D Regression Heat Map Analysis of Population Study Data.

    PubMed

    Klemm, Paul; Lawonn, Kai; Glaßer, Sylvia; Niemann, Uli; Hegenscheid, Katrin; Völzke, Henry; Preim, Bernhard

    2016-01-01

    Epidemiological studies comprise heterogeneous data about a subject group to define disease-specific risk factors. These data contain information (features) about a subject's lifestyle, medical status as well as medical image data. Statistical regression analysis is used to evaluate these features and to identify feature combinations indicating a disease (the target feature). We propose an analysis approach of epidemiological data sets by incorporating all features in an exhaustive regression-based analysis. This approach combines all independent features w.r.t. a target feature. It provides a visualization that reveals insights into the data by highlighting relationships. The 3D Regression Heat Map, a novel 3D visual encoding, acts as an overview of the whole data set. It shows all combinations of two to three independent features with a specific target disease. Slicing through the 3D Regression Heat Map allows for the detailed analysis of the underlying relationships. Expert knowledge about disease-specific hypotheses can be included into the analysis by adjusting the regression model formulas. Furthermore, the influences of features can be assessed using a difference view comparing different calculation results. We applied our 3D Regression Heat Map method to a hepatic steatosis data set to reproduce results from a data mining-driven analysis. A qualitative analysis was conducted on a breast density data set. We were able to derive new hypotheses about relations between breast density and breast lesions with breast cancer. With the 3D Regression Heat Map, we present a visual overview of epidemiological data that allows for the first time an interactive regression-based analysis of large feature sets with respect to a disease.

  10. Constructing linkage map based on a four-way cross population

    PubMed Central

    Beibei, Jiang; Shizhou, Yu; Bingguang, Xiao; Xiangyang, Lou; Haiming, Xu

    2014-01-01

    Summary Currently, developing genetic linkage map mostly use the derived-populations from crossing of two homogenous parents, which only covers limited genetic diversity and is inappropriate for some species, such as tobacco with lower diversity in genome. It is very general that there are no sufficient polymorphic markers to construct linkage map and ineffective to conduct marker-assisted selection (MAS) and quantitative trait locus (QTL) mapping based on lower density linkage map. This study proposed a method for developing genetic linkage map based on a four-way cross population. Computer simulation was conducted to investigate the feasibility and effectiveness of the method and a supporting program was designed. The main procedures and features of the proposed method were summarized as follows: 1) estimating genetic distance of any paired markers based on maximum likelihood method; 2) splitting all markers into different groups (linkage group) by cluster analysis based on genetic distance of markers; 3) for each linkage group, two end markers were first determined, then the marker order could be determined by inserting other markers in appropriate position by distance analysis of any three neighboring markers. Monte Carlo simulation showed that the proposed method is feasible, effective, and applicable in other derived populations from crossing of two homogenous parents. PMID:25541573

  11. Population pharmacokinetic analysis of axitinib in healthy volunteers

    PubMed Central

    Garrett, May; Poland, Bill; Brennan, Meghan; Hee, Brian; Pithavala, Yazdi K; Amantea, Michael A

    2014-01-01

    AIMS Axitinib is a potent and selective second generation inhibitor of vascular endothelial growth factor receptors 1, 2 and 3 approved for second line treatment of advanced renal cell carcinoma. The objectives of this analysis were to assess plasma pharmacokinetics and identify covariates that may explain variability in axitinib disposition following single dose administration in healthy volunteers. METHODS Plasma concentration–time data from 337 healthy volunteers in 10 phase I studies were analyzed, using non-linear mixed effects modelling (nonmem) to estimate population pharmacokinetic parameters and evaluate relationships between parameters and food, formulation, demographic factors, measures of renal and hepatic function and metabolic genotypes (UGT1A1*28 and CYP2C19). RESULTS A two compartment structural model with first order absorption and lag time best described axitinib pharmacokinetics. Population estimates for systemic clearance (CL), central volume of distribution (Vc), absorption rate constant (ka) and absolute bioavailability (F) were 17.0 l h−1, 45.3 l, 0.523 h−1 and 46.5%, respectively. With axitinib Form IV, ka and F increased in the fasted state by 207% and 33.8%, respectively. For Form XLI (marketed formulation), F was 15% lower compared with Form IV. CL was not significantly influenced by any of the covariates studied. Body weight significantly affected Vc, but the effect was within the estimated interindividual variability for Vc. CONCLUSIONS The analysis established a model that adequately characterizes axitinib pharmacokinetics in healthy volunteers. Vc was found to increase with body weight. However, no change in plasma exposures is expected with change in body weight; hence no dose adjustment is warranted. PMID:23834452

  12. Predictors of Childhood Anxiety: A Population-Based Cohort Study

    PubMed Central

    2015-01-01

    Background Few studies have explored predictors of early childhood anxiety. Objective To determine the prenatal, postnatal, and early life predictors of childhood anxiety by age 5. Methods Population-based, provincial administrative data (N = 19,316) from Manitoba, Canada were used to determine the association between demographic, obstetrical, psychosocial, medical, behavioral, and infant factors on childhood anxiety. Results Risk factors for childhood anxiety by age 5 included maternal psychological distress from birth to 12 months and 13 months to 5 years post-delivery and an infant 5-minute Apgar score of ≤7. Factors associated with decreased risk included maternal age < 20 years, multiparity, and preterm birth. Conclusion Identifying predictors of childhood anxiety is a key step to early detection and prevention. Maternal psychological distress is an early, modifiable risk factor. Future research should aim to disentangle early life influences on childhood anxiety occurring in the prenatal, postnatal, and early childhood periods. PMID:26158268

  13. Knowledge-Based Image Analysis.

    DTIC Science & Technology

    1981-04-01

    UNCLASSIF1 ED ETL-025s N IIp ETL-0258 AL Ai01319 S"Knowledge-based image analysis u George C. Stockman Barbara A. Lambird I David Lavine Laveen N. Kanal...extraction, verification, region classification, pattern recognition, image analysis . 3 20. A. CT (Continue on rever.. d. It necessary and Identify by...UNCLgSTFTF n In f SECURITY CLASSIFICATION OF THIS PAGE (When Date Entered) .L1 - I Table of Contents Knowledge Based Image Analysis I Preface

  14. Evolving effective behaviours to interact with tag-based populations

    NASA Astrophysics Data System (ADS)

    Yucel, Osman; Crawford, Chad; Sen, Sandip

    2015-07-01

    Tags and other characteristics, externally perceptible features that are consistent among groups of animals or humans, can be used by others to determine appropriate response strategies in societies. This usage of tags can be extended to artificial environments, where agents can significantly reduce cognitive effort spent on appropriate strategy choice and behaviour selection by reusing strategies for interacting with new partners based on their tags. Strategy selection mechanisms developed based on this idea have successfully evolved stable cooperation in games such as the Prisoner's Dilemma game but relies upon payoff sharing and matching methods that limit the applicability of the tag framework. Our goal is to develop a general classification and behaviour selection approach based on the tag framework. We propose and evaluate alternative tag matching and adaptation schemes for a new, incoming individual to select appropriate behaviour against any population member of an existing, stable society. Our proposed approach allows agents to evolve both the optimal tag for the environment as well as appropriate strategies for existing agent groups. We show that these mechanisms will allow for robust selection of optimal strategies by agents entering a stable society and analyse the various environments where this approach is effective.

  15. Varying total population enhances disease persistence: Qualitative analysis on a diffusive SIS epidemic model

    NASA Astrophysics Data System (ADS)

    Li, Huicong; Peng, Rui; Wang, Feng-Bin

    2017-01-01

    This paper performs qualitative analysis on an SIS epidemic reaction-diffusion system with a linear source in spatially heterogeneous environment. The main feature of our model lies in that its total population number varies, compared to its counterpart proposed by Allen et al. [2]. The uniform bounds of solutions are derived, based on which, the threshold dynamics in terms of the basic reproduction number is established and the global stability of the unique endemic equilibrium is discussed when spatial environment is homogeneous. In particular, the asymptotic profile of endemic equilibria is determined if the diffusion rate of the susceptible or infected population is small or large. The theoretical results show that a varying total population can enhance persistence of infectious disease, and therefore the disease becomes more threatening and harder to control.

  16. Sex determination by discriminant function analysis of palatal rugae from a population of coastal Andhra

    PubMed Central

    Bharath, Sreenivasa T; Kumar, Govind Raj; Dhanapal, Raghu; Saraswathi, TR

    2011-01-01

    Objective: The aim of the study was to investigate differences in the palatal rugae patterns in males and females of a cross-sectional hospital-based coastal Andhra population and application of discriminant function analysis in sex identification. Materials and Methods: One hundred pre-orthodontic plaster casts, equally distributed between males and females belonging to an age range of 15-30 years, were examined for different rugae patterns. Thomas classification was adopted for analysis. Association between rugae patterns and sexual dimorphism were tested using Unpaired t test, Chi square test and discriminant function analysis developed using SAS package. Results: Difference in unification pattern among males and females was found to be statistically significant. The total number of the rugae was not statistically significant between the sexes. Association between rugae length and shape with sex determination was computed using discriminant analysis which enabled sex differentiation in this population with an accuracy of 78%. Conclusion: Palatal rugae revealed a specific pattern in unification among males and females of the coastal Andhra population. Discriminant function analysis enabled sex determination of individuals. However, these interpretations were precluded by the small sample size and further research work on larger samples and use of different classification systems is required to validate its use in forensic science. PMID:22408321

  17. Study of Electron Delocalization in 1,2-, 1,3-, and 1,4-Azaborines Based on the Canonical Molecular Orbital Contributions to the Induced Magnetic Field and Polyelectron Population Analysis.

    PubMed

    Papadopoulos, Anastasios G; Charistos, Nickolas D; Kyriakidou, Katerina; Sigalas, Michael P

    2015-10-01

    The electron delocalization in 1,2-azaborine, 1,3-azaborine, and 1,4-azaborine is studied using canonical molecular orbital contributions to the induced magnetic field (CMO-IMF) method and polyelectron population analysis (PEPA). Contour maps of the out-of-plane component of the induced magnetic field (Bz(ind)) of the π system show that the three azaborines, in contrast with borazine, sustain much of benzene's π-aromatic character. Among them, 1,3-azaborine exhibits the strongest π delocalization, while 1,4-azaborine is the weakest. Contour maps of Bz(ind) for individual π orbitals reveal that the differentiation of the magnetic response among the three isomers originates from the π-HOMO orbitals, whose magnetic response is governed by rotational allowed transitions to unoccupied orbitals. The low symmetry of azaborines enables a paratropic response from HOMO to unoccupied orbitals excitations, with their magnitude depending on the shape of interacting orbitals. 1,3-Azaborine presents negligible paratropic contributions to Bz(ind) from HOMO to unoccupied orbitals transitions, where 1,2- and 1,4-azaborine present substantial paratropic contributions, which lead to reduced diatropic response. Natural bond orbital (NBO) analysis employing PEPA shows that only the 1,3-azaborine contains π-electron fully delocalized resonance structures.

  18. Normalizing for individual cell population context in the analysis of high-content cellular screens

    PubMed Central

    2011-01-01

    Background High-content, high-throughput RNA interference (RNAi) offers unprecedented possibilities to elucidate gene function and involvement in biological processes. Microscopy based screening allows phenotypic observations at the level of individual cells. It was recently shown that a cell's population context significantly influences results. However, standard analysis methods for cellular screens do not currently take individual cell data into account unless this is important for the phenotype of interest, i.e. when studying cell morphology. Results We present a method that normalizes and statistically scores microscopy based RNAi screens, exploiting individual cell information of hundreds of cells per knockdown. Each cell's individual population context is employed in normalization. We present results on two infection screens for hepatitis C and dengue virus, both showing considerable effects on observed phenotypes due to population context. In addition, we show on a non-virus screen that these effects can be found also in RNAi data in the absence of any virus. Using our approach to normalize against these effects we achieve improved performance in comparison to an analysis without this normalization and hit scoring strategy. Furthermore, our approach results in the identification of considerably more significantly enriched pathways in hepatitis C virus replication than using a standard analysis approach. Conclusions Using a cell-based analysis and normalization for population context, we achieve improved sensitivity and specificity not only on a individual protein level, but especially also on a pathway level. This leads to the identification of new host dependency factors of the hepatitis C and dengue viruses and higher reproducibility of results. PMID:22185194

  19. Geographic population structure analysis of worldwide human populations infers their biogeographical origins

    PubMed Central

    Elhaik, Eran; Tatarinova, Tatiana; Chebotarev, Dmitri; Piras, Ignazio S.; Maria Calò, Carla; De Montis, Antonella; Atzori, Manuela; Marini, Monica; Tofanelli, Sergio; Francalacci, Paolo; Pagani, Luca; Tyler-Smith, Chris; Xue, Yali; Cucca, Francesco; Schurr, Theodore G.; Gaieski, Jill B.; Melendez, Carlalynne; Vilar, Miguel G.; Owings, Amanda C.; Gómez, Rocío; Fujita, Ricardo; Santos, Fabrício R.; Comas, David; Balanovsky, Oleg; Balanovska, Elena; Zalloua, Pierre; Soodyall, Himla; Pitchappan, Ramasamy; GaneshPrasad, ArunKumar; Hammer, Michael; Matisoo-Smith, Lisa; Wells, R. Spencer; Acosta, Oscar; Adhikarla, Syama; Adler, Christina J.; Bertranpetit, Jaume; Clarke, Andrew C.; Cooper, Alan; Der Sarkissian, Clio S. I.; Haak, Wolfgang; Haber, Marc; Jin, Li; Kaplan, Matthew E.; Li, Hui; Li, Shilin; Martínez-Cruz, Begoña; Merchant, Nirav C.; Mitchell, John R.; Parida, Laxmi; Platt, Daniel E.; Quintana-Murci, Lluis; Renfrew, Colin; Lacerda, Daniela R.; Royyuru, Ajay K.; Sandoval, Jose Raul; Santhakumari, Arun Varatharajan; Soria Hernanz, David F.; Swamikrishnan, Pandikumar; Ziegle, Janet S.

    2014-01-01

    The search for a method that utilizes biological information to predict humans’ place of origin has occupied scientists for millennia. Over the past four decades, scientists have employed genetic data in an effort to achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing data have achieved an accuracy of 700 km in Europe, they were inaccurate elsewhere. Here we describe the Geographic Population Structure (GPS) algorithm and demonstrate its accuracy with three data sets using 40,000–130,000 SNPs. GPS placed 83% of worldwide individuals in their country of origin. Applied to over 200 Sardinians villagers, GPS placed a quarter of them in their villages and most of the rest within 50 km of their villages. GPS’s accuracy and power to infer the biogeography of worldwide individuals down to their country or, in some cases, village, of origin, underscores the promise of admixture-based methods for biogeography and has ramifications for genetic ancestry testing. PMID:24781250

  20. Population structure and admixture in Cerro Largo, Uruguay, based on blood markers and mitochondrial DNA polymorphisms.

    PubMed

    Sans, Mónica; Merriwether, D Andrew; Hidalgo, Pedro C; Bentancor, Nilo; Weimer, Tania A; Franco, Maria Helena L P; Alvarez, Inés; Kemp, Brian M; Salzano, Francisco M

    2006-01-01

    Recent studies of the Uruguayan population revealed different amounts of Amerindian and African genetic contributions. Our previous analysis of Afro-Uruguayans from the capital city of the Department of Cerro Largo showed a high proportion of African genes, and the effects of directional mating involving Amerindian women. In this paper, we extended the analysis to a sample of more than 100 individuals representing a random sample of the population of the whole Department. Based on 18 autosomal markers and one X-linked marker, we estimated 82% European, 8% Amerindian, and 10% African contributions to their ancestry, while from seven mitochondrial DNA site-specific polymorphic markers and sequences of hypervariable segment I, we determined 49% European, 30% Amerindian, and 21% African maternal contributions. Directional matings between Amerindian women and European men were detected, but differences involving Africans were not significant. Data about the specific origins of maternal lineages were also provided, and placed in a historical context.

  1. Estimating marbofloxacin withdrawal time in broiler chickens using a population physiologically based pharmacokinetics model.

    PubMed

    Yang, F; Yang, Y R; Wang, L; Huang, X H; Qiao, G; Zeng, Z L

    2014-12-01

    Residue depletion of marbofloxacin in broiler chicken after oral administration at 5 mg/kg/day for three consecutive days was studied in this study. The areas under the concentration-time curve from 0 h to ∞ (AUC0-∞ s) of marbofloxacin in tissues and plasma were used to calculate tissue/plasma partition coefficients (PX s). Based on PX s and the other parameters derived from published studies, a flow-limited physiologically based pharmacokinetics (PBPK) model was developed to predict marbofloxacin concentrations, which were then compared with those derived from the residue depletion study so as to validate this model. Considering individual difference in drug disposition, a Monte Carlo simulation included 1000 iterations was further incorporated into the validated model to generate a population PBPK model and to estimate the marbofloxacin residue withdrawal times in edible tissues. The withdrawal periods were compared to those derived from linear regression analysis. The PBPK model presented here successfully predicted the measured concentrations in all tissues. The withdrawal times in all edible tissues derived from the population PBPK model were longer than those from linear regression analysis, and based on the residues in kidney, a withdrawal time of 4 days was estimated for marbofloxacin after oral administration at 5 mg/kg/day for three consecutive days. It was shown that population PBPK model could be used to accurately predict marbofloxacin residue withdrawal time in edible tissues in broiler chickens.

  2. A Class of Population Covariance Matrices in the Bootstrap Approach to Covariance Structure Analysis.

    PubMed

    Yuan, Ke-Hai; Hayashi, Kentaro; Yanagihara, Hirokazu

    2007-01-01

    Model evaluation in covariance structure analysis is critical before the results can be trusted. Due to finite sample sizes and unknown distributions of real data, existing conclusions regarding a particular statistic may not be applicable in practice. The bootstrap procedure automatically takes care of the unknown distribution and, for a given sample size, also provides more accurate results than those based on standard asymptotics. But the procedure needs a matrix to play the role of the population covariance matrix. The closer the matrix is to the true population covariance matrix, the more valid the bootstrap inference is. The current paper proposes a class of covariance matrices by combining theory and data. Thus, a proper matrix from this class is closer to the true population covariance matrix than those constructed by any existing methods. Each of the covariance matrices is easy to generate and also satisfies several desired properties. An example with nine cognitive variables and a confirmatory factor model illustrates the details for creating population covariance matrices with different misspecifications. When evaluating the substantive model, bootstrap or simulation procedures based on these matrices will lead to more accurate conclusion than that based on artificial covariance matrices.

  3. Real-time real-world analysis of seasonal influenza vaccine effectiveness: method development and assessment of a population-based cohort in Stockholm County, Sweden, seasons 2011/12 to 2014/15

    PubMed Central

    Leval, Amy; Hergens, Maria Pia; Persson, Karin; Örtqvist, Åke

    2016-01-01

    Real-world estimates of seasonal influenza vaccine effectiveness (VE) are important for early detection of vaccine failure. We developed a method for evaluating real-time in-season vaccine effectiveness (IVE) and overall seasonal VE. In a retrospective, register-based, cohort study including all two million individuals in Stockholm County, Sweden, during the influenza seasons from 2011/12 to 2014/15, vaccination status was obtained from Stockholm’s vaccine register. Main outcomes were hospitalisation or primary care visits for influenza (International Classification of Disease (ICD)-10 codes J09-J11). VE was assessed using Cox multivariate stratified and non-stratified analyses adjusting for age, sex, socioeconomic status, comorbidities and previous influenza vaccinations. Stratified analyses showed moderate VE in prevention of influenza hospitalisations among chronically ill adults ≥ 65 years in two of four seasons, and lower but still significant VE in one season; 53% (95% confidence interval (CI): 33–67) in 2012/13, 55% (95% CI: 25–73) in 2013/14 and 18% (95% CI: 3–31) in 2014/15. In conclusion, seasonal influenza vaccination was associated with substantial reductions in influenza-specific hospitalisation, particularly in adults ≥ 65 years with underlying chronic conditions. With the use of population-based patient register data on influenza-specific outcomes it will be possible to obtain real-time estimates of seasonal influenza VE. PMID:27813473

  4. Real-time real-world analysis of seasonal influenza vaccine effectiveness: method development and assessment of a population-based cohort in Stockholm County, Sweden, seasons 2011/12 to 2014/15.

    PubMed

    Leval, Amy; Hergens, Maria Pia; Persson, Karin; Örtqvist, Åke

    2016-10-27

    Real-world estimates of seasonal influenza vaccine effectiveness (VE) are important for early detection of vaccine failure. We developed a method for evaluating real-time in-season vaccine effectiveness (IVE) and overall seasonal VE. In a retrospective, register-based, cohort study including all two million individuals in Stockholm County, Sweden, during the influenza seasons from 2011/12 to 2014/15, vaccination status was obtained from Stockholm's vaccine register. Main outcomes were hospitalisation or primary care visits for influenza (International Classification of Disease (ICD)-10 codes J09-J11). VE was assessed using Cox multivariate stratified and non-stratified analyses adjusting for age, sex, socioeconomic status, comorbidities and previous influenza vaccinations. Stratified analyses showed moderate VE in prevention of influenza hospitalisations among chronically ill adults ≥ 65 years in two of four seasons, and lower but still significant VE in one season; 53% (95% confidence interval (CI): 33-67) in 2012/13, 55% (95% CI: 25-73) in 2013/14 and 18% (95% CI: 3-31) in 2014/15. In conclusion, seasonal influenza vaccination was associated with substantial reductions in influenza-specific hospitalisation, particularly in adults ≥ 65 years with underlying chronic conditions. With the use of population-based patient register data on influenza-specific outcomes it will be possible to obtain real-time estimates of seasonal influenza VE.

  5. Analysis of bipolar and amacrine populations in marmoset retina.

    PubMed

    Weltzien, Felix; Percival, Kumiko A; Martin, Paul R; Grünert, Ulrike

    2015-02-01

    About 15 parallel ganglion cell pathways transmit visual signals to the brain, but the interneuron (bipolar and amacrine) populations providing input to ganglion cells remain poorly understood in primate retina. We carried out a quantitative analysis of the inner nuclear layer in the retina of the marmoset (Callithrix jacchus). Vertical Vibratome sections along the horizontal meridian were processed with immunohistochemical markers. Image stacks were taken with a confocal microscope, and densities of cell populations were determined. The density of flat midget bipolar cells fell from 15,746 cells/mm(2) at 1 mm (8 deg) to 7,827 cells/mm(2) at 3 mm (25 deg). The rod bipolar cell density fell from 8,640 cells/mm(2) at 1 mm to 4,278 cells/mm(2) at 3 mm, but the ratio of the two bipolar cell types did not change with eccentricity. The amacrine cell density ranged from 30,000 cells/mm(2) at 8 deg to less than 15,000 cells/mm(2) at 25 deg, but throughout the retina, the ratio of glycinergic to γ-aminobutyric acid (GABA)ergic to amacrine cells remained relatively constant. The fractions of rod bipolar, cone bipolar, amacrine, Müller, and horizontal cells of all cells in the inner nuclear layer were comparable in central and peripheral retina. Marmosets had lower proportions of midget bipolar and rod bipolar in comparison with macaque. These differences were correlated with differences in rod and cone densities between the two species and did not reflect fundamental differences in the wiring between the two species.

  6. Population analysis of the cingulum bundle using the tubular surface model for schizophrenia detection

    NASA Astrophysics Data System (ADS)

    Mohan, Vandana; Sundaramoorthi, Ganesh; Kubicki, Marek; Terry, Douglas; Tannenbaum, Allen

    2010-03-01

    We propose a novel framework for population analysis of DW-MRI data using the Tubular Surface Model. We focus on the Cingulum Bundle (CB) - a major tract for the Limbic System and the main connection of the Cingulate Gyrus, which has been associated with several aspects of Schizophrenia symptomatology. The Tubular Surface Model represents a tubular surface as a center-line with an associated radius function. It provides a natural way to sample statistics along the length of the fiber bundle and reduces the registration of fiber bundle surfaces to that of 4D curves. We apply our framework to a population of 20 subjects (10 normal, 10 schizophrenic) and obtain excellent results with neural network based classification (90% sensitivity, 95% specificity) as well as unsupervised clustering (k-means). Further, we apply statistical analysis to the feature data and characterize the discrimination ability of local regions of the CB, as a step towards localizing CB regions most relevant to Schizophrenia.

  7. A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies.

    PubMed

    Huyghe, Jeroen R; Fransen, Erik; Hannula, Samuli; Van Laer, Lut; Van Eyken, Els; Mäki-Torkko, Elina; Aikio, Pekka; Sorri, Martti; Huentelman, Matthew J; Van Camp, Guy

    2011-03-01

    The understanding of patterns of genetic variation within and among human populations is a prerequisite for successful genetic association mapping studies of complex diseases and traits. Some populations are more favorable for association mapping studies than others. The Saami from northern Scandinavia and the Kola Peninsula represent a population isolate that, among European populations, has been less extensively sampled, despite some early interest for association mapping studies. In this paper, we report the results of a first genome-wide SNP-based study of genetic population structure in the Finnish Saami. Using data from the HapMap and the human genome diversity project (HGDP-CEPH) and recently developed statistical methods, we studied individual genetic ancestry. We quantified genetic differentiation between the Saami population and the HGDP-CEPH populations by calculating pair-wise F(ST) statistics and by characterizing identity-by-state sharing for pair-wise population comparisons. This study affirms an east Asian contribution to the predominantly European-derived Saami gene pool. Using model-based individual ancestry analysis, the median estimated percentage of the genome with east Asian ancestry was 6% (first and third quartiles: 5 and 8%, respectively). We found that genetic similarity between population pairs roughly correlated with geographic distance. Among the European HGDP-CEPH populations, F(ST) was smallest for the comparison with the Russians (F(ST)=0.0098), and estimates for the other population comparisons ranged from 0.0129 to 0.0263. Our analysis also revealed fine-scale substructure within the Finnish Saami and warns against the confounding effects of both hidden population structure and undocumented relatedness in genetic association studies of isolated populations.

  8. A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies

    PubMed Central

    Huyghe, Jeroen R; Fransen, Erik; Hannula, Samuli; Van Laer, Lut; Van Eyken, Els; Mäki-Torkko, Elina; Aikio, Pekka; Sorri, Martti; Huentelman, Matthew J; Camp, Guy Van

    2011-01-01

    The understanding of patterns of genetic variation within and among human populations is a prerequisite for successful genetic association mapping studies of complex diseases and traits. Some populations are more favorable for association mapping studies than others. The Saami from northern Scandinavia and the Kola Peninsula represent a population isolate that, among European populations, has been less extensively sampled, despite some early interest for association mapping studies. In this paper, we report the results of a first genome-wide SNP-based study of genetic population structure in the Finnish Saami. Using data from the HapMap and the human genome diversity project (HGDP-CEPH) and recently developed statistical methods, we studied individual genetic ancestry. We quantified genetic differentiation between the Saami population and the HGDP-CEPH populations by calculating pair-wise FST statistics and by characterizing identity-by-state sharing for pair-wise population comparisons. This study affirms an east Asian contribution to the predominantly European-derived Saami gene pool. Using model-based individual ancestry analysis, the median estimated percentage of the genome with east Asian ancestry was 6% (first and third quartiles: 5 and 8%, respectively). We found that genetic similarity between population pairs roughly correlated with geographic distance. Among the European HGDP-CEPH populations, FST was smallest for the comparison with the Russians (FST=0.0098), and estimates for the other population comparisons ranged from 0.0129 to 0.0263. Our analysis also revealed fine-scale substructure within the Finnish Saami and warns against the confounding effects of both hidden population structure and undocumented relatedness in genetic association studies of isolated populations. PMID:21150888

  9. Population-Based Assessment of Exposure to Risk Behaviors in Motion Pictures.

    PubMed

    Sargent, James D; Worth, Keilah A; Beach, Michael; Gerrard, Meg; Heatherton, Todd F

    2008-01-01

    The aim of most population-based studies of media is to relate a specific exposure to an outcome of interest. A research program has been developed that evaluates exposure to different components of movies in an attempt of assess the association of such exposure with the adoption of substance use during adolescence. To assess exposure to movie substance use, one must measure both viewing time and content. In developing the exposure measure, the study team was interested in circumventing a common problem in exposure measurement, where measures often conflate exposure to media with attention to media. Our aim in this paper is to present a validated measure of exposure to entertainment media, the Beach method, which combines recognition of a movie title with content analysis of the movie for substance use, to generate population based measures of exposure to substance use in this form of entertainment.

  10. Statistical genetics with application to population-based study design: a primer for clinicians.

    PubMed

    Beyene, Joseph; Pare, Guillaume

    2014-02-01

    With the completion of the entire human genome sequence and remarkable advances in genotyping technologies, there has been an increased interest in the application of genetics and genomics in biomedical research over the last decade. Large-scale population-based genetic association studies have now become routine and their application to several multifactorial diseases such as cardiovascular disorders has led to the identification of a number of novel susceptibility genes. However, to be able to interpret results from such studies, clinicians need to have a basic understanding of unique concepts and issues related to this fast-moving area of research. In this primer, we provide a broad overview of design, analysis, and methodological issues with a focus on population-based study design.

  11. Exact hybrid particle/population simulation of rule-based models of biochemical systems.

    PubMed

    Hogg, Justin S; Harris, Leonard A; Stover, Lori J; Nair, Niketh S; Faeder, James R

    2014-04-01

    Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational modifications. Rule-based modeling overcomes this problem by representing molecules as structured objects and encoding their interactions as pattern-based rules. This greatly simplifies the process of model specification, avoiding the tedious and error prone task of manually enumerating all species and reactions that can potentially exist in a system. From a simulation perspective, rule-based models can be expanded algorithmically into fully-enumerated reaction networks and simulated using a variety of network-based simulation methods, such as ordinary differential equations or Gillespie's algorithm, provided that the network is not exceedingly large. Alternatively, rule-based models can be simulated directly using particle-based kinetic Monte Carlo methods. This "network-free" approach produces exact stochastic trajectories with a computational cost that is independent of network size. However, memory and run time costs increase with the number of particles, limiting the size of system that can be feasibly simulated. Here, we present a hybrid particle/population simulation method that combines the best attributes of both the network-based and network-free approaches. The method takes as input a rule-based model and a user-specified subset of species to treat as population variables rather than as particles. The model is then transformed by a process of "partial network expansion" into a dynamically equivalent form that can be simulated using a population-adapted network-free simulator. The transformation method has been implemented within the open-source rule-based modeling platform BioNetGen, and resulting hybrid models can be simulated using the particle-based simulator NFsim. Performance tests show that significant memory savings

  12. A Framework for Image-Based Classification of Mitotic Cells in Asynchronous Populations

    PubMed Central

    Slattery, Scott D.; Newberg, Justin Y.; Szafran, Adam T.; Hall, Rebecca M.; Brinkley, Bill R.

    2012-01-01

    Abstract High content screening (HCS) has emerged an important tool for drug discovery because it combines rich readouts of cellular responses in a single experiment. Inclusion of cell cycle analysis into HCS is essential to identify clinically suitable anticancer drugs that disrupt the aberrant mitotic activity of cells. One challenge for integration of cell cycle analysis into HCS is that cells must be chemically synchronized to specific phases, adding experimental complexity to high content screens. To address this issue, we have developed a rules-based method that utilizes mitotic phosphoprotein monoclonal 2 (MPM-2) marker and works consistently in different experimental conditions and in asynchronous populations. Further, the performance of the rules-based method is comparable to established machine learning approaches for classifying cell cycle data, indicating the robustness of the features we use in the framework. As such, we suggest the use of MPM-2 analysis and its associated expressive features for integration into HCS approaches. PMID:22084958

  13. Population-based public health interventions: practice-based and evidence-supported. Part I.

    PubMed

    Keller, Linda Olson; Strohschein, Susan; Lia-Hoagberg, Betty; Schaffer, Marjorie A

    2004-01-01

    The Intervention Wheel is a population-based practice model that encompasses three levels of practice (community, systems, and individual/family) and 17 public health interventions. Each intervention and practice level contributes to improving population health. The Intervention Wheel, previously known as the Public Health Intervention Model, was originally introduced in 1998 by the Minnesota Department of Health, Section of Public Health Nursing. The model has been widely disseminated and used throughout the United States since that time. The evidence supporting the Intervention Wheel was recently subjected to a rigorous critique by regional and national experts. This critical process, which involved hundreds of public health nurses, resulted in a more robust Intervention Wheel and established the validity of the model. The critique also produced basic steps and best practices for each of the 17 interventions. Part I describes the Intervention Wheel, defines population-based practice, and details the recommended modifications and validation process. Part II provides examples of the innovative ways that the Intervention Wheel is being used in public health/public health nursing practice, education, and administration. The two articles provide a foundation and vision for population-based public health nursing practice and direction for improving population health.

  14. Machine Learning Based Classification of Microsatellite Variation: An Effective Approach for Phylogeographic Characterization of Olive Populations.

    PubMed

    Torkzaban, Bahareh; Kayvanjoo, Amir Hossein; Ardalan, Arman; Mousavi, Soraya; Mariotti, Roberto; Baldoni, Luciana; Ebrahimie, Esmaeil; Ebrahimi, Mansour; Hosseini-Mazinani, Mehdi

    2015-01-01

    Finding efficient analytical techniques is overwhelmingly turning into a bottleneck for the effectiveness of large biological data. Machine learning offers a novel and powerful tool to advance classification and modeling solutions in molecular biology. However, these methods have been less frequently used with empirical population genetics data. In this study, we developed a new combined approach of data analysis using microsatellite marker data from our previous studies of olive populations using machine learning algorithms. Herein, 267 olive accessions of various origins including 21 reference cultivars, 132 local ecotypes, and 37 wild olive specimens from the Iranian plateau, together with 77 of the most represented Mediterranean varieties were investigated using a finely selected panel of 11 microsatellite markers. We organized data in two '4-targeted' and '16-targeted' experiments. A strategy of assaying different machine based analyses (i.e. data cleaning, feature selection, and machine learning classification) was devised to identify the most informative loci and the most diagnostic alleles to represent the population and the geography of each olive accession. These analyses revealed microsatellite markers with the highest differentiating capacity and proved efficiency for our method of clustering olive accessions to reflect upon their regions of origin. A distinguished highlight of this study was the discovery of the best combination of markers for better differentiating of populations via machine learning models, which can be exploited to distinguish among other biological populations.

  15. Machine Learning Based Classification of Microsatellite Variation: An Effective Approach for Phylogeographic Characterization of Olive Populations

    PubMed Central

    Mousavi, Soraya; Mariotti, Roberto; Baldoni, Luciana; Ebrahimie, Esmaeil; Ebrahimi, Mansour; Hosseini-Mazinani, Mehdi

    2015-01-01

    Finding efficient analytical techniques is overwhelmingly turning into a bottleneck for the effectiveness of large biological data. Machine learning offers a novel and powerful tool to advance classification and modeling solutions in molecular biology. However, these methods have been less frequently used with empirical population genetics data. In this study, we developed a new combined approach of data analysis using microsatellite marker data from our previous studies of olive populations using machine learning algorithms. Herein, 267 olive accessions of various origins including 21 reference cultivars, 132 local ecotypes, and 37 wild olive specimens from the Iranian plateau, together with 77 of the most represented Mediterranean varieties were investigated using a finely selected panel of 11 microsatellite markers. We organized data in two ‘4-targeted’ and ‘16-targeted’ experiments. A strategy of assaying different machine based analyses (i.e. data cleaning, feature selection, and machine learning classification) was devised to identify the most informative loci and the most diagnostic alleles to represent the population and the geography of each olive accession. These analyses revealed microsatellite markers with the highest differentiating capacity and proved efficiency for our method of clustering olive accessions to reflect upon their regions of origin. A distinguished highlight of this study was the discovery of the best combination of markers for better differentiating of populations via machine learning models, which can be exploited to distinguish among other biological populations. PMID:26599001

  16. Internal Transcribed Spacer 1 (ITS1) based sequence typing reveals phylogenetically distinct Ascaris population.

    PubMed

    Das, Koushik; Chowdhury, Punam; Ganguly, Sandipan

    2015-01-01

    Taxonomic differentiation among morphologically identical Ascaris species is a debatable scientific issue in the context of Ascariasis epidemiology. To explain the disease epidemiology and also the taxonomic position of different Ascaris species, genome information of infecting strains from endemic areas throughout the world is certainly crucial. Ascaris population from human has been genetically characterized based on the widely used genetic marker, internal transcribed spacer1 (ITS1). Along with previously reported and prevalent genotype G1, 8 new sequence variants of ITS1 have been identified. Genotype G1 was significantly present among female patients aged between 10 to 15 years. Intragenic linkage disequilibrium (LD) analysis at target locus within our study population has identified an incomplete LD value with potential recombination events. A separate cluster of Indian isolates with high bootstrap value indicate their distinct phylogenetic position in comparison to the global Ascaris population. Genetic shuffling through recombination could be a possible reason for high population diversity and frequent emergence of new sequence variants, identified in present and other previous studies. This study explores the genetic organization of Indian Ascaris population for the first time which certainly includes some fundamental information on the molecular epidemiology of Ascariasis.

  17. Diffusion-based population statistics using tract probability maps.

    PubMed

    Wassermann, Demian; Kanterakis, Efstathios; Gur, Ruben C; Deriche, Rachid; Verma, Ragini

    2010-01-01

    We present a novel technique for the tract-based statistical analysis of diffusion imaging data. In our technique, we represent each white matter (WM) tract as a tract probability map (TPM): a function mapping a point to its probability of belonging to the tract. We start by automatically clustering the tracts identified in the brain via tractography into TPMs using a novel Gaussian process framework. Then, each tract is modeled by the skeleton of its TPM, a medial representation with a tubular or sheet-like geometry. The appropriate geometry for each tract is implicitly inferred from the data instead of being selected a priori, as is done by current tract-specific approaches. The TPM representation makes it possible to average diffusion imaging based features along directions locally perpendicular to the skeleton of each WM tract, increasing the sensitivity and specificity of statistical analyses on the WM. Our framework therefore facilitates the automated analysis of WM tract bundles, and enables the quantification and visualization of tract-based statistical differences between groups. We have demonstrated the applicability of our framework by studying WM differences between 34 schizophrenia patients and 24 healthy controls.

  18. Understanding exoplanet populations with simulation-based methods

    NASA Astrophysics Data System (ADS)

    Morehead, Robert Charles

    The Kepler candidate catalog represents an unprecedented sample of exoplanet host stars. This dataset is ideal for probing the populations of exoplanet systems and exploring their architectures. Confirming transiting exoplanets candidates through traditional follow-up methods is challenging, especially for faint host stars. Most of Kepler's validated planets relied on statistical methods to separate true planets from false-positives. Multiple transiting planet systems (MTPS) have been previously shown to have low false-positive rates and over 850 planets in MTPSs have been statistically validated so far. We show that the period-normalized transit duration ratio (xi) offers additional information that can be used to establish the planetary nature of these systems. We briefly discuss the observed distribution of xi for the Q1-Q17 Kepler Candidate Search. We also use xi to develop a Bayesian statistical framework combined with Monte Carlo methods to determine which pairs of planet candidates in an MTPS are consistent with the planet hypothesis for a sample of 862 MTPSs that include candidate planets, confirmed planets, and known false-positives. This analysis proves to be efficient and advantageous in that it only requires catalog-level bulk candidate properties and galactic population modeling to compute the probabilities of a myriad of feasible scenarios composed of background and companion stellar blends in the photometric aperture, without needing additional observational follow-up. Our results agree with the previous results of a low false-positive rate in the Kepler MTPSs. This implies, independently of any other estimates, that most of the MTPSs detected by Kepler are planetary in nature, but that a substantial fraction could be orbiting stars other than then the putative target star, and therefore may be subject to significant error in the inferred planet parameters resulting from unknown or mismeasured stellar host attributes. We also apply approximate

  19. TRUS Biopsy Yield in Indian Population: A Retrospective Analysis

    PubMed Central

    Pawar, Prakash Wamanrao; Sawant, Ajit Somaji; Patil, Akshay Vijay; Narwade, Sayalee Suryabhan; Mundhe, Shankar Tanaji; Savalia, Abhishek Jaysukhbhai; Tamhankar, Ashwin Sunil

    2017-01-01

    Introduction The reported cancer detection rate of Trans-Rectal Ultrasonography (TRUS) biopsies (TRUS biopsy yield) has been around 30 percent in western countries. However it is much lower in Asian countries, including India. Hence a larger proportion of patients in India undergo unnecessary biopsies. Aims To find out the cancer detection rate of TRUS biopsy (TRUS biopsy yield) in contemporary Indian population. Also, to study the positive predictive values at different serum Prostate-Specific Antigen (PSA)/PSA Density (PSAD) cut off levels and suspicious Digital Rectal Examination (DRE) findings. Materials and Methods This retrospective study was carried out in a tertiary care institute. All symptomatic patients who underwent TRUS guided biopsy for indication of raised serum PSA level (>4 ng/ml) or suspicious DRE findings (nodule, irregularity, hard consistency, immobile rectal mucosa) from January 2012 to December 2014 were included. For serum PSA range (4-10) ng/ml, TRUS guided biopsy was done in patients with percent free/total PSA < 25. Statistical analysis used were Chi-square test, Mann-Whitney U-test, Spearman’s rank correlation analysis and Receiver-Operating Characteristic (ROC) curve. Results Out of the 235 patients included, 60 patients had malignancy (overall cancer detection rate= 25.53%). The cancer detection rate for PSA ranges of (4-10) and (10-20) ng/ml was as low as 5.95% and 13.16% respectively. Patients with malignant disease had significantly smaller prostate gland size than patients with benign disease (53.89 vs 63.06; p-value <0.05). On the other hand, cancer detection rate was 100% for PSA greater than 50ng/ml. The cancer detection rates were only upto 10% for PSA density ranges upto 0.25 ng/ml/cm3. The Area Under the Curve (AUC) for PSA and PSAD was 0.876 and 0.884 respectively. Only one patient (0.43%) had post-biopsy complication (acute bacterial prostatitis) requiring hospital admission. Conclusion The current serum PSA and PSAD cut

  20. Population pharmacokinetic analysis of colistin in burn patients.

    PubMed

    Lee, Jongtae; Han, Seunghoon; Jeon, Sangil; Hong, Taegon; Song, Wonkeun; Woo, Heungjeong; Yim, Dong-Seok

    2013-05-01

    Colistin is increasingly used as a salvage therapy for nosocomial infections caused by multidrug-resistant Gram-negative bacteria such as Pseudomonas aeruginosa and Acinetobacter baumannii. However, the available pharmacokinetic (PK) data for colistin are limited to guide dosing. The aim of this study was to develop a population PK model of colistin and to identify the optimal dosage regimens for burn patients. Fifty patients with burns ranging from 4% to 85% of total body surface area who had been treated with colistimethate sodium (CMS) were studied. CMS, which is hydrolyzed in vivo to an active metabolite, was intravenously administered every 12 h. Blood samples were collected at 0, 1, 2, 4, 6, and 8 h after more than five infusions to measure the colistin concentration using a liquid chromatography-tandem mass spectrometry (LC-MS/MS) system. The population PK model was developed using nonlinear mixed effect modeling (NONMEM, v. 6.2). A one-compartment linear PK model for colistin best described the data. The covariates included in the final model were creatinine clearance for the relative fraction of CMS converted into colistin and the presence of edema for the turnover rate constant of CMS converted into colistin. A steady-state 24-h area under the concentration-time curve was simulated from 1,000 virtual patients receiving 150 mg colistin base activity every 12 h using the final model. Relative to previous studies with critically ill patients, the elimination half-life of colistin (6.6 h) was much shorter, and continuous renal replacement therapy was not a significant covariate for any PK parameters.

  1. Birth order and mortality: a population-based cohort study.

    PubMed

    Barclay, Kieron; Kolk, Martin

    2015-04-01

    This study uses Swedish population register data to investigate the relationship between birth order and mortality at ages 30 to 69 for Swedish cohorts born between 1938 and 1960, using a within-family comparison. The main analyses are conducted with discrete-time survival analysis using a within-family comparison, and the estimates are adjusted for age, mother's age at the time of birth, and cohort. Focusing on sibships ranging in size from two to six, we find that mortality risk in adulthood increases with later birth order. The results show that the relative effect of birth order is greater among women than among men. This pattern is consistent for all the major causes of death but is particularly pronounced for mortality attributable to cancers of the respiratory system and to external causes. Further analyses in which we adjust for adult socioeconomic status and adult educational attainment suggest that social pathways only mediate the relationship between birth order and mortality risk in adulthood to a limited degree.

  2. Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia

    PubMed Central

    2010-01-01

    Background Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation. Results Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity. Conclusions During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success. PMID:20698974

  3. Estimating future global per capita water availability based on changes in climate and population

    SciTech Connect

    Parish, Esther S; Kodra, Evan; Ganguly, Auroop R; Steinhaeuser, Karsten

    2012-01-01

    Human populations are profoundly affected by water stress, or the lack of sufficient per capita available freshwater. Water stress can result from overuse of available freshwater resources or from a reduction in the amount of available water due to decreases in rainfall and stored water supplies. Analyzing the interrelationship between human populations and water availability is complicated by the uncertainties associated with climate change projections and population projections. We present a simple methodology developed to integrate disparate climate and population data sources and develop first-order per capita water availability projections at the global scale. Simulations from the coupled land-ocean-atmosphere Community Climate System Model version 3 (CCSM3) forced with a range of hypothetical greenhouse gas emissions scenarios are used to project grid-based changes in precipitation minus evapotranspiration as proxies for changes in runoff, or fresh water supply. Population growth changes according to several Intergovernmental Panel on Climate Change (IPCC) storylines are used as proxies for changes in fresh water demand by 2025, 2050 and 2100. These freshwater supply and demand projections are then combined to yield estimates of per capita water availability aggregated by watershed and political unit. Results suggest that important insights might be extracted from the use of the process developed here, notably including the identification of the globe s most vulnerable regions in need of more detailed analysis and the relative importance of population growth versus climate change in in altering future freshwater supplies. However, these are only exemplary insights and, as such, could be considered hypotheses that should be rigorously tested with multiple climate models, multiple observational climate datasets, and more comprehensive population change storylines.

  4. Estimating future global per capita water availability based on changes in climate and population

    NASA Astrophysics Data System (ADS)

    Parish, Esther S.; Kodra, Evan; Steinhaeuser, Karsten; Ganguly, Auroop R.

    2012-05-01

    Human populations are profoundly affected by water stress, or the lack of sufficient per capita available freshwater. Water stress can result from overuse of available freshwater resources or from a reduction in the amount of available water due to decreases in rainfall and stored water supplies. Analyzing the interrelationship between human populations and water availability is complicated by the uncertainties associated with climate change projections and population projections. We present a simple methodology developed to integrate disparate climate and population data sources and develop first-order per capita water availability projections at the global scale. Simulations from the coupled land-ocean-atmosphere Community Climate System Model version 3 (CCSM3) forced with a range of hypothetical greenhouse gas emissions scenarios are used to project grid-based changes in precipitation minus evapotranspiration as proxies for changes in runoff, or fresh water supply. Population growth changes, according to Intergovernmental Panel on Climate Change (IPCC) storylines, are used as proxies for changes in fresh water demand by 2025, 2050 and 2100. These freshwater supply and demand projections are then combined to yield estimates of per capita water availability aggregated by watershed and political unit. Results suggest that important insights might be extracted from the use of the process developed here, notably including the identification of the globe's most vulnerable regions in need of more detailed analysis and the relative importance of population growth versus climate change in altering future freshwater supplies. However, these are only exemplary insights and, as such, could be considered hypotheses that should be rigorously tested with multiple climate models, multiple observational climate datasets, and more comprehensive population change storylines.

  5. Genetic comparison of lake sturgeon populations: Differentiation based on allelic frequencies at seven microsatellite loci

    USGS Publications Warehouse

    McQuown, E.; Krueger, C.C.; Kincaid, H.L.; Gall, G.A.E.; May, B.

    2003-01-01

    The lake sturgeon (Acipenser fulvescens) has recently become a high priority for restoration management because of the near extinction of the species from many areas of North America. The identification of the level of population differentiation that naturally exists among lake sturgeon populations will be useful in the development of management plans to conserve and restore diversity, and in the choice of donor populations to use for re-introduction. Genetic variation among and within 210 lake sturgeon collected from seven locations (St. Lawrence River, Des Prairies River (tributary to the St. Lawrence River), Mattagami River (Hudson Bay drainage), Menominee River (Lake Michigan drainage), Wolf River (Lake Michigan drainage), Niagara River, and Lake Erie) was examined based on allelic variation at seven microsatellite loci (four disomic and three putative tetrasomic). High levels of variability were detected at these loci. Analyses revealed an average of 8.6 alleles per locus (range 5 to 12 alleles per locus) and heterozygosity values at the four disomic loci ranging from 0.46 to 0.66. Multivariate factor analysis of Nei's genetic distance values produced three distinct population groups that were organized by geography: 1) Mattagami (northern Quebec), 2) Menominee/ Wolf (Lake Michigan - Wisconsin), and 3) St. Lawrence/ Des Prairies/ Niagara/ Erie (lower Great Lakes). Differences based on G-tests summed over all loci occurred between all possible paired comparisons of the collections (P < 0.01). These analyses indicated that lake sturgeon populations are differentiated within the Great Lakes basin. Managers of this species will need to identify individual populations in their jurisdictions and provide separate consideration for their conservation and rehabilitation.

  6. Declining scaup populations: A retrospective analysis of long-term population and harvest survey data

    USGS Publications Warehouse

    Afton, A.D.; Anderson, M.G.

    2001-01-01

    We examined long-term databases concerning population status of scaup (lesser [Aythya affinis] and greater scaup [A. marila] combined) and harvest statistics of lesser scaup to identify factors potentially limiting population growth. Specifically, we explored evidence for and against the general hypotheses that scaup populations have declined in association with declining recruitment and/or female survival. We examined geographic heterogeneity in scaup demographic patterns that could yield evidence about potential limiting factors. Several biases exist in survey methodology used to estimate scaup populations and harvest statistics; however, none of these biases likely accounted for our major findings that (1) the continental scaup breeding population has declined over the last 20 years, with widespread and consistent declines within surveyed areas of the Canadian western boreal forest where most lesser scaup breed; (2) sex ratios of lesser scaup in the U.S. harvest have increased (more males now relative to females); and (3) age ratios of lesser scaup in the U.S. harvest have declined (fewer immatures now relative to adults), especially in the midcontinent region. We interpreted these major findings as evidence that (1) recruitment of lesser scaup has declined over the last 20 years, particularly in the Canadian western boreal forest; and (2) survival of female lesser scaup has declined relative to that of males. We found little evidence that harvest was associated with the scaup population decline. Our findings underscore the need for both improvements and changes to population survey procedures and new research to discriminate among various hypotheses explaining the recent scaup population decline.

  7. Bayesian data analysis in population ecology: motivations, methods, and benefits

    USGS Publications Warehouse

    Dorazio, Robert

    2016-01-01

    During the 20th century ecologists largely relied on the frequentist system of inference for the analysis of their data. However, in the past few decades ecologists have become increasingly interested in the use of Bayesian methods of data analysis. In this article I provide guidance to ecologists who would like to decide whether Bayesian methods can be used to improve their conclusions and predictions. I begin by providing a concise summary of Bayesian methods of analysis, including a comparison of differences between Bayesian and frequentist approaches to inference when using hierarchical models. Next I provide a list of problems where Bayesian methods of analysis may arguably be preferred over frequentist methods. These problems are usually encountered in analyses based on hierarchical models of data. I describe the essentials required for applying modern methods of Bayesian computation, and I use real-world examples to illustrate these methods. I conclude by summarizing what I perceive to be the main strengths and weaknesses of using Bayesian methods to solve ecological inference problems.

  8. Dynamic analysis of grinding using the population balance model

    SciTech Connect

    Williams, M.C. |

    1995-12-31

    The dynamic behavior of batch mill, CSTR mill, and a closed grinding network consisting of a mill, sump, and cyclone was analyzed using the dynamic population balance model (PBM). The dynamic solution of the PBM of a batch, CSTR and a closed grinding network consisting of a mill, sump, and cyclone forms the basis of the dynamic analysis presented here. Two numerical dynamic solution approaches were used. These are: (1) providing additional constraints on breakage selection functions or (2) performing the Arbiter-Bhrany (or other) normalization of the selection functions. Actual experimental anthracite batch grinding data was used to obtain the functionality of the batch dynamic mill selection and breakage functions for a real physical system. The Levenberg-Marquardt algorithm for systems of constrained non-linear equations is used to solve the batch dynamic PBM grinding equations to obtain the grinding selection and breakage rate functions. The mill, sump and hydrocyclone were modeled as a CSTR operating at various retention times. Batch dynamic PBM data was used to provide the mill kinetic and breakage selection function data. Different dynamic solutions were obtained depending on the numerical approach used. Each solution approach to a dynamic PBM with transport, while giving the same prediction for a single batch grinding time, gives different solutions or predictions for mill composition for other grinding times. This fact makes dynamic nodal analysis and control problematic. The fact that the constraint solution approach gives a solution may suggest that normalization for closed networks is not necessary. Differences in solutions to the PBM cannot be excused away by inaccuracies in the data used to model the grinding phenomenon.

  9. Provider communication on perinatal depression: a population-based study.

    PubMed

    Farr, Sherry L; Ko, Jean Y; Burley, Kim; Gupta, Seema

    2016-02-01

    Women's lack of knowledge on symptoms of perinatal depression and treatment resources is a barrier to receiving care. We sought to estimate the prevalence and predictors of discussing depression with a prenatal care provider. We used the 2011 population-based data from 24 sites participating in the Pregnancy Risk Assessment Monitoring System (n = 32,827 women with recent live births) to examine associations between maternal characteristics and report that a prenatal care provider discussed with her what to do if feeling depressed during or after pregnancy. Overall, 71.9 % of women reported discussing perinatal depression with their prenatal care provider (range 60.7 % in New York City to 85.6 % in Maine). Women were more likely to report a discussion on perinatal depression with their provider if they they were 18-29 years of age than over 35 years of age compared to older (adjusted prevalence ratio [aPR] 18 to 19 y = 1.08, 20 to 24 y = 1.10, 25 to 29 y = 1.09), unmarried (aPR = 1.07) compared to married, had <12 years of education (aPR = 1.05) compared to > 12 years, and had no previous live births (aPR = 1.03) compared to ≥ 1 live births. Research is needed on effective ways to educate women about perinatal depression and whether increased knowledge on perinatal depression results in higher rates of treatment and shorter duration of symptoms.

  10. Risk of Peripheral Artery Occlusive Disease in Patients with Vertigo, Tinnitus, or Sudden Deafness: A Secondary Case-Control Analysis of a Nationwide, Population-Based Health Claims Database

    PubMed Central

    Hwang, Juen-Haur

    2016-01-01

    Background Cochleovestibular symptoms, such as vertigo, tinnitus, and sudden deafness, are common manifestations of microvascular diseases. However, it is unclear whether these symptoms occurred preceding the diagnosis of peripheral artery occlusive disease (PAOD). Therefore, the aim of this case-control study was to investigate the risk of PAOD among patients with vertigo, tinnitus, and sudden deafness using a nationwide, population-based health claim database in Taiwan. Methods We identified 5,340 adult patients with PAOD diagnosed between January 1, 2006 and December 31, 2010 and 16,020 controls, frequency matched on age interval, sex, and year of index date, from the Taiwan National Health Insurance Research Database. Risks of PAOD in patients with vertigo, tinnitus, or sudden deafness were separately evaluated with multivariate logistic regression analyses. Results Of the 5,340 patients with PAOD, 12.7%, 6.7%, and 0.3% were diagnosed with vertigo, tinnitus, and sudden deafness, respectively. In the controls, 10.6%, 6.1%, and 0.3% were diagnosed with vertigo (P < 0.001), tinnitus (P = 0.161), and sudden deafness (P = 0.774), respectively. Results from the multivariate logistic regression analyses showed that the risk of PAOD was significantly increased in patients with vertigo (adjusted odds ratio = 1.12, P = 0.027) but not in those with tinnitus or sudden deafness. Conclusions A modest increase in the risk of PAOD was observed among Taiwanese patients with vertigo, after adjustment for comorbidities. PMID:27631630

  11. Population-Based Incidence and Prevalence of Systemic Lupus Erythematosus

    PubMed Central

    Somers, Emily C.; Marder, Wendy; Cagnoli, Patricia; Lewis, Emily E.; DeGuire, Peter; Gordon, Caroline; Helmick, Charles G.; Wang, Lu; Wing, Jeffrey J.; Dhar, J. Patricia; Leisen, James; Shaltis, Diane; McCune, W. Joseph

    2014-01-01

    Objective To estimate the incidence and prevalence of systemic lupus erythematosus (SLE) in a sociodemographically diverse southeastern Michigan source population of 2.4 million people. Methods SLE cases fulfilling the American College of Rheumatology classification criteria (primary case definition) or meeting rheumatologist-judged SLE criteria (secondary definition) and residing in Wayne or Washtenaw Counties during 2002–2004 were included. Case finding was performed from 6 source types, including hospitals and private specialists. Age-standardized rates were computed, and capture–recapture was performed to estimate underascertainment of cases. Results The overall age-adjusted incidence and prevalence (ACR definition) per 100,000 persons were 5.5 (95% confidence interval [95% CI] 5.0–6.1) and 72.8 (95% CI 70.8–74.8). Among females, the incidence was 9.3 per 100,000 persons and the prevalence was 128.7 per 100,000 persons. Only 7 cases were estimated to have been missed by capture–recapture, adjustment for which did not materially affect the rates. SLE prevalence was 2.3-fold higher in black persons than in white persons, and 10-fold higher in females than in males. Among incident cases, the mean ± SD age at diagnosis was 39.3 ± 16.6 years. Black SLE patients had a higher proportion of renal disease and end-stage renal disease (ESRD) (40.5% and 15.3%, respectively) as compared to white SLE patients (18.8% and 4.5%, respectively). Black patients with renal disease were diagnosed as having SLE at younger age than white patients with renal disease (mean ± SD 34.4 ± 14.9 years versus 41.9 ± 21.3 years; P = 0.05). Conclusion SLE prevalence was higher than has been described in most other population-based studies and reached 1 in 537 among black female persons. There were substantial racial disparities in the burden of SLE, with black patients experiencing earlier age at diagnosis, >2-fold increases in SLE incidence and prevalence, and increased

  12. Ophthalmic manifestations of tuberous sclerosis: a population based study

    PubMed Central

    Rowley, S; O'Callaghan, F; Osborne, J

    2001-01-01

    BACKGROUND/AIMS—Tuberous sclerosis complex (TSC) has retinal and non-retinal ophthalmic manifestations. This study was designed to determine the prevalence of the ophthalmic manifestations and of refractive errors in a population of patients with TSC.
METHODS—179 patients identified were in a prevalence study of TSC in the south of England and 107 of these agreed to full ophthalmic examination which was successful in 100. Ophthalmic examination included examination of the eyelids, cover test, examination of the irides, dilation funduscopy using both direct and indirect ophthalmoscopy, and refraction using retinoscopy. Myopia was defined as a spherical equivalent <−0.5D and hyperopia as a spherical equivalent >+0.5D.
RESULTS—Retinal hamartomas were seen in 44 of the 100 patients. The commonest morphological type of hamartoma seen was the flat, translucent lesion in 31 of the 44 patients (70%). The multinodular "mulberry" lesion was seen in 24 of the 44 patients (55%) and the transitional type lesion was seen in four of the 44 patients (9%). Punched out areas of retinal depigmentation were seen in 39 of the 100 patients but only six of 100 controls. 27% of eyes were myopic, 22% were hyperopic, and 27% had astigmatism >0.75D. Of the non-retinal findings, 39 patients had angiofibromas of the eyelids, five had non-paralytic strabismus, and three had colobomas.
CONCLUSION—Apart from the higher prevalence of flat retinal hamartomas, the findings of this study compare closely with previous large clinic based series of TSC patients. Refractive findings were similar to previous studies of a similarly aged non-TSC population. This is the first series to document the statistically significant association of punched out chorioretinal depigmentation with TSC and the authors believe that it should be looked for as an aid to diagnosis.

 PMID:11264130

  13. Metatranscriptomic Analysis of Groundwater Reveals an Active Anammox Bacterial Population

    NASA Astrophysics Data System (ADS)

    Jewell, T. N. M.; Karaoz, U.; Thomas, B. C.; Banfield, J. F.; Brodie, E.; Williams, K. H.; Beller, H. R.

    2014-12-01

    Groundwater is a major natural resource, yet little is known about the contribution of microbial anaerobic ammonium oxidation (anammox) activity to subsurface nitrogen cycling. During anammox, energy is generated as ammonium is oxidized under anaerobic conditions to dinitrogen gas, using nitrite as the final electron acceptor. This process is a global sink for fixed nitrogen. Only a narrow range of monophyletic bacteria within the Planctomycetes carries out anammox, and the full extent of their metabolism, and subsequent impact on nitrogen cycling and microbial community structure, is still unknown. Here, we employ a metatranscriptomic analysis on enriched mRNA to identify the abundance and activity of a population of anammox bacteria within an aquifer at Rifle, CO. Planktonic biomass was collected over a two-month period after injection of up to 1.5 mM nitrate. Illumina-generated sequences were mapped to a phylogenetically binned Rifle metagenome database. We identified transcripts for genes with high protein sequence identities (81-98%) to those of anammox strain KSU-1 and to two of the five anammox bacteria genera, Brocadia and Kuenenia, suggesting an active, if not diverse, anammox population. Many of the most abundant anammox transcripts mapped to a single scaffold, indicative of a single dominant anammox species. Transcripts of the genes necessary for the anammox pathway were present, including an ammonium transporter (amtB), nitrite/formate transporter, nitrite reductase (nirK), and hydrazine oxidoreductase (hzoB). The form of nitrite reductase encoded by anammox is species-dependent, and we only identified nirK, with no evidence of anammox nirS. In addition to the anammox pathway we saw evidence of the anammox bacterial dissimilatory nitrate reduction to ammonium pathway (narH, putative nrfA, and nrfB), which provides an alternate means of generating substrates for anammox from nitrate, rather than relying on an external pool. Transcripts for hydroxylamine

  14. Proactive Population Health Management in the Context of a Regional Health Information Exchange Using Standards-Based Decision Support

    PubMed Central

    Lobach, David F.; Kawamoto, Kensaku; Anstrom, Kevin J.; Kooy, Kevin R.; Eisenstein, Eric L.; Silvey, Garry M.; Willis, Janese M.; Johnson, Frederick; Simo, Jessica

    2007-01-01

    The clinic-based healthcare model does not deliver high quality, cost-effective care to populations of patients. Despite public perception that aggressive investment in information technology will lead to improvements in the safety and quality of healthcare delivery, there is little evidence that health information technology can be used to promote population-based health management. This paper describes the use of a standards-based clinical decision support system to facilitate proactive population health management using data from a regional health information exchange (HIE) network. The initial release of this system was designed to detect ten sentinel health events related to hospitalization, emergency department (ED) utilization, and care coordination in a population of 36,000 individuals. In an analysis of 11,899 continuously enrolled patients from a single county over a six-month period, 2,285 unique patients experienced 7,226 sentinel health events. The most common events were ED utilization for low severity conditions (2,546), two or more missed appointments within a 60-day period (1,728), ED encounters for patients with asthma (1,220), and three or more ED encounters within 90 days (731). Logistic regression analysis identified patients aged 19–64 as the population most likely to have sentinel health events. In addition to presenting data demonstrating the feasibility of population health management in the context of an HIE, this paper also includes lessons learned from the development, implementation, and operational support of the population health management system. PMID:18693881

  15. Novel Analysis of Stellar Populations and Constraints on Galaxy Evolution

    NASA Astrophysics Data System (ADS)

    Zaritsky, Dennis

    2006-07-01

    We propose to utilize HST archival data to develop a new method for the reconstruction of star formation histories of galaxies at all redshifts. In particular, using ground-based and HST archival data we will develop a method that is based on the distribution of pixel values rather than stellar photometry. This new conceptual appropach accesses data below an image's limiting magnitude and does not introduce many of the uncertainties inherrent in crowded-field photometry. Both will lead to significantly tighter constraints on the ancient star formation history. Comparing the results of this technique applied to the ground-based images with the results of the standard method on HST color-magnitude diagrams will validate {or not} the specific algorithms we develop. Once we have developed a succcessful technique it can be applied to HST data of galaxies in the nearby universe {for example, HST images of M 33 are comparable to our ground-based images of the LMC}. By varying the angular pixel scale in the analysis we will be able to produce internally self-consistent analyses of star formation histories at all redshifts. For the nearby universe this technique maximizes the information extracted from the existing imaging - for the distant universe in enables direct comparison to the local star formation histories. We will make the algorithm{s} public, as we have done with our more classical star formation reconstruction code, StarFISH.

  16. Secondary Data Analysis of National Surveys in Japan Toward Improving Population Health.

    PubMed

    Ikeda, Nayu

    2016-01-01

    Secondary data analysis of national health surveys of the general population is a standard methodology for health metrics and evaluation; it is used to monitor trends in population health over time and benchmark the performance of health systems. In Japan, the government has established electronic databases of individual records from national surveys of the population's health. However, the number of publications based on these datasets is small considering the scale and coverage of the surveys. There appear to be two major obstacles to the secondary use of Japanese national health survey data: strict data access control under the Statistics Act and an inadequate interdisciplinary research environment for resolving methodological difficulties encountered when dealing with secondary data. The usefulness of secondary analysis of survey data is evident with examples from the author's previous studies based on vital records and the National Health and Nutrition Surveys, which showed that (i) tobacco smoking and high blood pressure are the major risk factors for adult mortality from non-communicable diseases in Japan; (ii) the decrease in mean blood pressure in Japan from the late 1980s to the early 2000s was partly attributable to the increased use of antihypertensive medication and reduced dietary salt intake; and (iii) progress in treatment coverage and control of high blood pressure is slower in Japan than in the United States and Britain. National health surveys in Japan are an invaluable asset, and findings from secondary analyses of these surveys would provide important suggestions for improving health in people around the world.

  17. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice

    PubMed Central

    Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai

    2016-01-01

    Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright’s F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance. PMID:27494320

  18. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

    PubMed

    Pradhan, Sharat Kumar; Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai; Pandit, Elssa

    2016-01-01

    Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright's F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.

  19. Population genetic analysis among five Indian population groups using six microsatellite markers.

    PubMed

    Ghosh, Anu; Das, Birajalaxmi; Seshadri, M

    2003-04-01

    Genetic variation at six tetranucleotide microsatellites (HUMTHO1, HUMVWA, F13A01, D3S1359, D12S66, and D12S67) has heen determined in five endogamous ethnic population groups of India belonging to two major linguistic families. The populations analyzed were Konkanastha Brahmins and Marathas (Maharashtra state) from the Indo-Aryan linguistic family and Nairs, Ezhavas, and Muslims (Kerala state) from the Dravidian family. All six loci show high gene diversity, ranging from 0.63 +/- 0.04 to 0.84 +/- 0.02. The average GST value observed was 1.7%, indicating that the differences between the populations account for less than 2% of the diversity, while the genetic variation is high within the five population groups studied (>98%). The phylogenetic tree fails to show any clear cluster. The absence of any cluster along with low average GST is suggestive of substantial genetic similarity among the studied populations, in spite of clear geographical, linguistic, and cultural barriers. This similarity indicates either a greater gene flow between these groups or, alternatively, may reflect a recent evolution for them, considering that the Indian caste system evolved only about 3000 years ago.

  20. [Analysis on age structure and dynamics of Kindonia uniflora populations].

    PubMed

    Zhang, Wenhui; Li, Jingxia; Li, Hong; Liu, Xiangjun

    2004-04-01

    Kindonia uniflora is a perennial clone herbaceous plant, and also, a native endangered plant in China. This paper studied its age structure, life table and survivorship curve in different habitats in Taibai mountain area. The results indicated that the age structure and dynamics of K. uniflora populations in the Betula utilis forest at altitude 2500-2700 m, in the Abies fargesii forest at altitude 2700-2900 m, and in the Larix chinensis forest at altitude 2900-3100 m had the similar pattern and developing tendency. The number of younger ramets at 1-2 years old or older than 5 years was less, and the number of ramets at 3-5 years old was the highest in the age structures. The negative values of dx (dead number), qx (mortality rate) and Kx (Killing rate) in the life table showed the increasing rate of the population sizes during the age stage. The survivorship curve of K. uniflora populations in different habitats belonged to Deevey C after 3-5 years old. The mortality rate of populations during 5-10 years stage was higher, and was stable after 10 years old. As for the characters of asexual propagation and clone growth, the rhizomes of the populations were in humus of soil, and developed and expanded as guerilla line style. During growth season, only one leaf grew above ground at every inter-node, and the population growth and development were rarely influenced by external factors. The forest communities, such as Betula utilis, Abies fargesii and Larix chinensis forest, in which K. uniflora populations lived, were at middle or higher mountain, where there were rarely disturbance from human being. Therefore, the habitats for K. uniflora populations to live were relatively stable. As the altitude increased, the disturbances from human being became less, the density of K. uniflora populations increased, the life cycle expanded, the peak of population death delayed, and the population living strategy changed to adapt to the habitats. K. uniflora populations preferred to