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Sample records for population based analysis

  1. Likelihood-based population independent component analysis

    PubMed Central

    Eloyan, Ani; Crainiceanu, Ciprian M.; Caffo, Brian S.

    2013-01-01

    Independent component analysis (ICA) is a widely used technique for blind source separation, used heavily in several scientific research areas including acoustics, electrophysiology, and functional neuroimaging. We propose a scalable two-stage iterative true group ICA methodology for analyzing population level functional magnetic resonance imaging (fMRI) data where the number of subjects is very large. The method is based on likelihood estimators of the underlying source densities and the mixing matrix. As opposed to many commonly used group ICA algorithms, the proposed method does not require significant data reduction by a 2-fold singular value decomposition. In addition, the method can be applied to a large group of subjects since the memory requirements are not restrictive. The performance of our approach is compared with a commonly used group ICA algorithm via simulation studies. Furthermore, the proposed method is applied to a large collection of resting state fMRI datasets. The results show that established brain networks are well recovered by the proposed algorithm. PMID:23314416

  2. 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.

  3. Older people's use of ambulance services: a population based analysis.

    PubMed Central

    Clark, M J; FitzGerald, G

    1999-01-01

    OBJECTIVE: To investigate the use of emergency and non-urgent ambulance transport services by people aged 65 years and over. SETTING: The study was undertaken in Queensland where the Queensland Ambulance Services (QAS) is the sole provider of emergency pre-hospital and non-urgent ambulance services for the entire state. METHODS: The age and sex of 351,000 emergency and non-urgent cases treated and transported by the QAS from July 1995 to June 1996 were analysed. RESULTS: People aged 65 years and over who comprise 12% of the population utilise approximately one third of the emergency and two thirds of the non-urgent ambulance resources provided in Queensland. While the absolute number of occasions of service for females for emergency services is higher than for males, when the data are stratified for age and sex, males have higher rates of emergency ambulance service utilisation than females across every age group, and particularly in older age groups. Gender differences are also found for non-urgent ambulance usage. The absolute number of occasions of service for older females aged 65 and over using non-urgent ambulance transport is high, but utilisation patterns on stratified data reveal similar gender usage patterns across most age groupings, except at the older age groupings where male usage greatly exceeds female usage. CONCLUSIONS: As the aged are disproportionately high users of ambulance services, it will become increasingly important for ambulance services to plan for the projected increase in the aged population. Emergency pre-hospital care is one of the few health services along the continuum of care where male usage patterns are higher than those of females. More information needs to be obtained on the age and presenting characteristics of those people who are multiple users of the ambulance service. Such information will assist service planners. PMID:10191443

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites

    PubMed Central

    Samad, Hanif; Coll, Francesc; Preston, Mark D.; Ocholla, Harold; Fairhurst, Rick M.; Clark, Taane G.

    2015-01-01

    Whole-genome sequencing technologies are being increasingly applied to Plasmodium falciparum clinical isolates to identify genetic determinants of malaria pathogenesis. However, genome-wide discovery methods, such as haplotype scans for signatures of natural selection, are hindered by missing genotypes in sequence data. Poor correlation between single nucleotide polymorphisms (SNPs) in the P. falciparum genome complicates efforts to apply established missing-genotype imputation methods that leverage off patterns of linkage disequilibrium (LD). The accuracy of state-of-the-art, LD-based imputation methods (IMPUTE, Beagle) was assessed by measuring allelic r2 for 459 P. falciparum samples from malaria patients in 4 countries: Thailand, Cambodia, Gambia, and Malawi. In restricting our analysis to 86k high-quality SNPs across the populations, we found that the complete-case analysis was restricted to 21k SNPs (24.5%), despite no single SNP having more than 10% missing genotypes. The accuracy of Beagle in filling in missing genotypes was consistently high across all populations (allelic r2, 0.87-0.96), but the performance of IMPUTE was mixed (allelic r2, 0.34-0.99) depending on reference haplotypes and population. Positive selection analysis using Beagle-imputed haplotypes identified loci involved in resistance to chloroquine (crt) in Thailand, Cambodia, and Gambia, sulfadoxine-pyrimethamine (dhfr, dhps) in Cambodia, and artemisinin (kelch13) in Cambodia. Tajima’s D-based analysis identified genes under balancing selection that encode well-characterized vaccine candidates: apical merozoite antigen 1 (ama1) and merozoite surface protein 1 (msp1). In contrast, the complete-case analysis failed to identify any well-validated drug resistance or candidate vaccine loci, except kelch13. In a setting of low LD and modest levels of missing genotypes, using Beagle to impute P. falciparum genotypes is a viable strategy for conducting accurate large-scale population genetics and

  9. Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites.

    PubMed

    Samad, Hanif; Coll, Francesc; Preston, Mark D; Ocholla, Harold; Fairhurst, Rick M; Clark, Taane G

    2015-04-01

    Whole-genome sequencing technologies are being increasingly applied to Plasmodium falciparum clinical isolates to identify genetic determinants of malaria pathogenesis. However, genome-wide discovery methods, such as haplotype scans for signatures of natural selection, are hindered by missing genotypes in sequence data. Poor correlation between single nucleotide polymorphisms (SNPs) in the P. falciparum genome complicates efforts to apply established missing-genotype imputation methods that leverage off patterns of linkage disequilibrium (LD). The accuracy of state-of-the-art, LD-based imputation methods (IMPUTE, Beagle) was assessed by measuring allelic r2 for 459 P. falciparum samples from malaria patients in 4 countries: Thailand, Cambodia, Gambia, and Malawi. In restricting our analysis to 86 k high-quality SNPs across the populations, we found that the complete-case analysis was restricted to 21k SNPs (24.5%), despite no single SNP having more than 10% missing genotypes. The accuracy of Beagle in filling in missing genotypes was consistently high across all populations (allelic r2, 0.87-0.96), but the performance of IMPUTE was mixed (allelic r2, 0.34-0.99) depending on reference haplotypes and population. Positive selection analysis using Beagle-imputed haplotypes identified loci involved in resistance to chloroquine (crt) in Thailand, Cambodia, and Gambia, sulfadoxine-pyrimethamine (dhfr, dhps) in Cambodia, and artemisinin (kelch13) in Cambodia. Tajima's D-based analysis identified genes under balancing selection that encode well-characterized vaccine candidates: apical merozoite antigen 1 (ama1) and merozoite surface protein 1 (msp1). In contrast, the complete-case analysis failed to identify any well-validated drug resistance or candidate vaccine loci, except kelch13. In a setting of low LD and modest levels of missing genotypes, using Beagle to impute P. falciparum genotypes is a viable strategy for conducting accurate large-scale population genetics and

  10. Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites.

    PubMed

    Samad, Hanif; Coll, Francesc; Preston, Mark D; Ocholla, Harold; Fairhurst, Rick M; Clark, Taane G

    2015-04-01

    Whole-genome sequencing technologies are being increasingly applied to Plasmodium falciparum clinical isolates to identify genetic determinants of malaria pathogenesis. However, genome-wide discovery methods, such as haplotype scans for signatures of natural selection, are hindered by missing genotypes in sequence data. Poor correlation between single nucleotide polymorphisms (SNPs) in the P. falciparum genome complicates efforts to apply established missing-genotype imputation methods that leverage off patterns of linkage disequilibrium (LD). The accuracy of state-of-the-art, LD-based imputation methods (IMPUTE, Beagle) was assessed by measuring allelic r2 for 459 P. falciparum samples from malaria patients in 4 countries: Thailand, Cambodia, Gambia, and Malawi. In restricting our analysis to 86 k high-quality SNPs across the populations, we found that the complete-case analysis was restricted to 21k SNPs (24.5%), despite no single SNP having more than 10% missing genotypes. The accuracy of Beagle in filling in missing genotypes was consistently high across all populations (allelic r2, 0.87-0.96), but the performance of IMPUTE was mixed (allelic r2, 0.34-0.99) depending on reference haplotypes and population. Positive selection analysis using Beagle-imputed haplotypes identified loci involved in resistance to chloroquine (crt) in Thailand, Cambodia, and Gambia, sulfadoxine-pyrimethamine (dhfr, dhps) in Cambodia, and artemisinin (kelch13) in Cambodia. Tajima's D-based analysis identified genes under balancing selection that encode well-characterized vaccine candidates: apical merozoite antigen 1 (ama1) and merozoite surface protein 1 (msp1). In contrast, the complete-case analysis failed to identify any well-validated drug resistance or candidate vaccine loci, except kelch13. In a setting of low LD and modest levels of missing genotypes, using Beagle to impute P. falciparum genotypes is a viable strategy for conducting accurate large-scale population genetics and

  11. [Genetic structure of wild Macrobrachium nipponense populations in Taihu Lake based on microsatellite analysis].

    PubMed

    Feng, Jian-Bin; Wu, Chun-Lin; Ma, Ke-Yi; Ding, Huai-Yu; Hua, Xue-Ming; Li, Jia-Le

    2011-06-01

    By using eight highly polymorphic microsatellite DNA loci, this paper analyzed the genetic structure of wild Macrobrachium nipponense populations in Taihu Lake. For the 15 M. nipponense populations in the Lake, there were at least three of the loci presenting heterozygosity deficiency and obvious deviation from Hardy-Weinberg equilibrium after Bonferroni correction. The observed heterozygosity values of the 15 populations were all above 0. 683, displaying a high genetic diversity, but the diversity varied obviously with site. For example, the genetic diversity of the eastern and southern populations at Dukou and Luxiang was higher than that of the western and northern populations at Huazhuang and Yangzhu. For the 15 populations, parts of the loci showed heterozygote excess and departure from mutation-drift equilibrium, suggesting that the population structure had experienced bottleneck effect and the population amount had declined. The AMOVA analysis across all the populations and loci showed that the genetic divergence among the 15 populations was at a lower level (F(ST) = 0.011 ). 98.9% of the genetic variation came from intra-population, and 1.1% came from inter-population, suggesting that all the M. nipponense populations in the Lake could be protected and managed as a single unit in genetic resource. However, the genetic distance between Huazhuang and Wutangmen populations reached 0.206, being close to the delimitation of species identification. Further studies would be needed for the sustainable utilization of the genetic resource of M. nipponense in Taihu Lake.

  12. 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

  13. Non-linear analysis indicates chaotic dynamics and reduced resilience in model-based Daphnia populations exposed to environmental stress.

    PubMed

    Ottermanns, Richard; Szonn, Kerstin; Preuβ, Thomas G; Roβ-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. Mixture models for cancer survival analysis: application to population-based data with covariates.

    PubMed

    De Angelis, R; Capocaccia, R; Hakulinen, T; Soderman, B; Verdecchia, A

    1999-02-28

    The interest in estimating the probability of cure has been increasing in cancer survival analysis as the curability of many cancer diseases is becoming a reality. Mixture survival models provide a way of modelling time to death when cure is possible, simultaneously estimating death hazard of fatal cases and the proportion of cured case. In this paper we propose an application of a parametric mixture model to relative survival rates of colon cancer patients from the Finnish population-based cancer registry, and including major survival determinants as explicative covariates. Disentangling survival into two different components greatly facilitates the analysis and the interpretation of the role of prognostic factors on survival patterns. For example, age plays a different role in determining, from one side, the probability of cure, and, from the other side, the life expectancy of fatal cases. The results support the hypothesis that observed survival trends are really due to a real prognostic gain for more recently diagnosed patients.

  15. Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis

    NASA Astrophysics Data System (ADS)

    Qiao, Hongjin; Liu, Xiangquan; Zhang, Xijia; Jiang, Haibin; Wang, Jiying; Zhang, Limin

    2013-03-01

    Amplified fragment length polymorphisms (AFLP) markers were developed to assess the genetic variation of populations and clones of Rhopilema esculentum Kishinouye (Scyphozoa, Rhizostomatidae). One hundred and seventy-nine loci from 56 individuals of two hatchery populations and two wild populations were genotyped with five primer combinations. The polymorphic ratio, Shannon's diversity index and average heterozygosity were 70.3%, 0.346 and 0.228 for the white hatchery population, 74.3%, 0.313, and 0.201 for the red hatchery population, 79.3%, 0.349, and 0.224 for the Jiangsu wild population, and 74.9%, 0.328 and 0.210 for the Penglai wild population, respectively. Thus, all populations had a relatively high level of genetic diversity. A specific band was identified that could separate the white from the red hatchery population. There was 84.85% genetic differentiation within populations. Individual cluster analysis using unweighted pair-group method with arithmetic mean (UPGMA) suggested that hatchery populations and wild populations could be divided. For the hatchery populations, the white and red populations clustered separately; however, for the wild populations, Penglai and Jiangsu populations clustered together. The genetic diversity at the clone level was also determined. Our data suggest that there are relatively high genetic diversities within populations but low genetic differentiation between populations, which may be related to the long-term use of germplasm resources from Jiangsu Province for artificial seeding and releasing. These findings will benefit the artificial seeding and conservation of the germplasm resources.

  16. Exploratory factor analysis of self-reported symptoms in a large, population-based military cohort

    PubMed Central

    2010-01-01

    Background US military engagements have consistently raised concern over the array of health outcomes experienced by service members postdeployment. Exploratory factor analysis has been used in studies of 1991 Gulf War-related illnesses, and may increase understanding of symptoms and health outcomes associated with current military conflicts in Iraq and Afghanistan. The objective of this study was to use exploratory factor analysis to describe the correlations among numerous physical and psychological symptoms in terms of a smaller number of unobserved variables or factors. Methods The Millennium Cohort Study collects extensive self-reported health data from a large, population-based military cohort, providing a unique opportunity to investigate the interrelationships of numerous physical and psychological symptoms among US military personnel. This study used data from the Millennium Cohort Study, a large, population-based military cohort. Exploratory factor analysis was used to examine the covariance structure of symptoms reported by approximately 50,000 cohort members during 2004-2006. Analyses incorporated 89 symptoms, including responses to several validated instruments embedded in the questionnaire. Techniques accommodated the categorical and sometimes incomplete nature of the survey data. Results A 14-factor model accounted for 60 percent of the total variance in symptoms data and included factors related to several physical, psychological, and behavioral constructs. A notable finding was that many factors appeared to load in accordance with symptom co-location within the survey instrument, highlighting the difficulty in disassociating the effects of question content, location, and response format on factor structure. Conclusions This study demonstrates the potential strengths and weaknesses of exploratory factor analysis to heighten understanding of the complex associations among symptoms. Further research is needed to investigate the relationship between

  17. Bayesian population analysis of a harmonized physiologically based pharmacokinetic model of trichloroethylene and its metabolites.

    PubMed

    Hack, C Eric; Chiu, Weihsueh A; Jay Zhao, Q; Clewell, Harvey J

    2006-10-01

    Bayesian population analysis of a harmonized physiologically based pharmacokinetic (PBPK) model for trichloroethylene (TCE) and its metabolites was performed. In the Bayesian framework, prior information about the PBPK model parameters is updated using experimental kinetic data to obtain posterior parameter estimates. Experimental kinetic data measured in mice, rats, and humans were available for this analysis, and the resulting posterior model predictions were in better agreement with the kinetic data than prior model predictions. Uncertainty in the prediction of the kinetics of TCE, trichloroacetic acid (TCA), and trichloroethanol (TCOH) was reduced, while the kinetics of other key metabolites dichloroacetic acid (DCA), chloral hydrate (CHL), and dichlorovinyl mercaptan (DCVSH) remain relatively uncertain due to sparse kinetic data for use in this analysis. To help focus future research to further reduce uncertainty in model predictions, a sensitivity analysis was conducted to help identify the parameters that have the greatest impact on various internal dose metric predictions. For application to a risk assessment for TCE, the model provides accurate estimates of TCE, TCA, and TCOH kinetics. This analysis provides an important step toward estimating uncertainty of dose-response relationships in noncancer and cancer risk assessment, improving the extrapolation of toxic TCE doses from experimental animals to humans.

  18. Does geography influence the treatment and outcomes of colorectal cancer? A population-based analysis

    PubMed Central

    2013-01-01

    Background The Canadian province of Manitoba covers a large geographical area but only has one major urban center, Winnipeg. We sought to determine if regional differences existed in the quality of colorectal cancer care in a publicly funded health care system. Methods This was a population-based historical cohort analysis of the treatment and outcomes of Manitobans diagnosed with colorectal cancer between 2004 and 2006. Administrative databases were utilized to assess quality of care using published quality indicators. Results A total of 2,086 patients were diagnosed with stage I to IV colorectal cancer and 42.2% lived outside of Winnipeg. Patients from North Manitoba had a lower odds of undergoing major surgery after controlling for other confounders (odds ratio (OR): 0.48, 95% confidence interval (CI): 0.26 to 0.90). No geographic differences existed in the quality measures of 30-day operative mortality, consultations with oncologists, surveillance colonoscopy, and 5-year survival. However, there was a trend towards lower survival in North Manitoba. Conclusion We found minimal differences by geography. However, overall compliance with quality measures is low and there are concerning trends in North Manitoba. This study is one of the few to evaluate population-based benchmarks for colorectal cancer therapy in Canada. PMID:23773619

  19. Recipe for uncovering predictive genes using support vector machines based on model population analysis.

    PubMed

    Li, Hong-Dong; Liang, Yi-Zeng; Xu, Qing-Song; Cao, Dong-Sheng; Tan, Bin-Bin; Deng, Bai-Chuan; Lin, Chen-Chen

    2011-01-01

    Selecting a small number of informative genes for microarray-based tumor classification is central to cancer prediction and treatment. Based on model population analysis, here we present a new approach, called Margin Influence Analysis (MIA), designed to work with support vector machines (SVM) for selecting informative genes. The rationale for performing margin influence analysis lies in the fact that the margin of support vector machines is an important factor which underlies the generalization performance of SVM models. Briefly, MIA could reveal genes which have statistically significant influence on the margin by using Mann-Whitney U test. The reason for using the Mann-Whitney U test rather than two-sample t test is that Mann-Whitney U test is a nonparametric test method without any distribution-related assumptions and is also a robust method. Using two publicly available cancerous microarray data sets, it is demonstrated that MIA could typically select a small number of margin-influencing genes and further achieves comparable classification accuracy compared to those reported in the literature. The distinguished features and outstanding performance may make MIA a good alternative for gene selection of high dimensional microarray data. (The source code in MATLAB with GNU General Public License Version 2.0 is freely available at http://code.google.com/p/mia2009/). PMID:21339535

  20. 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.

  1. 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.

  2. A quantitative meta-analysis of population-based studies of premorbid intelligence and schizophrenia

    PubMed Central

    Khandaker, Golam M.; Barnett, Jennifer H.; White, Ian R.; Jones, Peter B.

    2011-01-01

    Objective A premorbid IQ deficit supports a developmental dimension to schizophrenia and its cognitive aspects that are crucial to functional outcome. Better characterisation of the association between premorbid IQ and the disorder may provide further insight into its origin and etiology. We aimed to quantify premorbid cognitive function in schizophrenia through systematic review and meta-analysis of longitudinal, population-based studies, and to characterize the risk of schizophrenia across the entire range of premorbid IQ. Method Electronic and manual searches identified general population-based cohort or nested case–control studies that measured intelligence before onset of schizophrenic psychosis using standard psychometric tests, and that defined cases using contemporaneous ICD or DSM. Meta-analyses explored dose–response relationships between premorbid cognitive deficit (using full-scale, verbal and performance IQ) and risk of schizophrenia. Meta-regression analyses explored relationships with age of illness onset, change in premorbid intelligence over time and gender differences. Results Meta-analysis of 4396 cases and over 745 000 controls from 12 independent studies confirmed significant decrements in premorbid IQ (effect size − 0.43) among future cases. Risk of schizophrenia operated as a consistent dose–response effect, increasing by 3.7% for every point decrease in IQ (p < 0.0001). Verbal and nonverbal measures were equally affected. Greater premorbid IQ decrement was associated with earlier illness onset (p < 0.0001). There was no evidence of a progressively increasing deficit during the premorbid period toward illness onset. Conclusions Strong associations between premorbid IQ and risk for schizophrenia, and age of illness onset argue for a widespread neurodevelopmental contribution to schizophrenia that operates across the entire range of intellectual ability. This also suggests higher IQ may be protective in schizophrenia, perhaps by

  3. 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

  4. How are population-based funding formulae for healthcare composed? A comparative analysis of seven models

    PubMed Central

    2013-01-01

    Background Population-based funding formulae act as an important means of promoting equitable health funding structures. To evaluate how policy makers in different jurisdictions construct health funding formulae and build an understanding of contextual influences underpinning formula construction we carried out a comparative analysis of key components of funding formulae across seven high-income and predominantly publically financed health systems: New Zealand, England, Scotland, the Netherlands, the state of New South Wales in Australia, the Canadian province of Ontario, and the city of Stockholm, Sweden. Methods Core components from each formula were summarised and key similarities and differences evaluated from a compositional perspective. We categorised approaches to constructing funding formulae under three main themes: identifying factors which predict differential need amongst populations; adjusting for cost factors outside of needs factors; and engaging in normative correction of allocations for ‘unmet’ need. Results We found significant congruence in the factors used to guide need and cost adjustments. However, there is considerable variation in interpretation and implementation of these factors. Conclusion Despite broadly similar frameworks, there are distinct differences in the composition of the formulae across the seven health systems. Ultimately, the development of funding formulae is a dynamic process, subject to availability of data reflecting health needs, the influence of wider socio-political objectives and health system determinants. PMID:24209410

  5. Epilepsy in Onchocerciasis Endemic Areas: Systematic Review and Meta-analysis of Population-Based Surveys

    PubMed Central

    Pion, Sébastien D. S.; Kaiser, Christoph; Boutros-Toni, Fernand; Cournil, Amandine; Taylor, Melanie M.; Meredith, Stefanie E. O.; Stufe, Ansgar; Bertocchi, Ione; Kipp, Walter; Preux, Pierre-Marie; Boussinesq, Michel

    2009-01-01

    Objective We sought to evaluate the relationship between onchocerciasis prevalence and that of epilepsy using available data collected at community level. Design We conducted a systematic review and meta-regression of available data. Data Sources Electronic and paper records on subject area ever produced up to February 2008. Review Methods We searched for population-based studies reporting on the prevalence of epilepsy in communities for which onchocerciasis prevalence was available or could be estimated. Two authors independently assessed eligibility and study quality and extracted data. The estimation of point prevalence of onchocerciasis was standardized across studies using appropriate correction factors. Variation in epilepsy prevalence was then analyzed as a function of onchocerciasis endemicity using random-effect logistic models. Results Eight studies from west (Benin and Nigeria), central (Cameroon and Central African Republic) and east Africa (Uganda, Tanzania and Burundi) met the criteria for inclusion and analysis. Ninety-one communities with a total population of 79,270 individuals screened for epilepsy were included in the analysis. The prevalence of epilepsy ranged from 0 to 8.7% whereas that of onchocerciasis ranged from 5.2 to 100%. Variation in epilepsy prevalence was consistent with a logistic function of onchocerciasis prevalence, with epilepsy prevalence being increased, on average, by 0.4% for each 10% increase in onchocerciasis prevalence. Conclusion These results give further evidence that onchocerciasis is associated with epilepsy and that the disease burden of onchocerciasis might have to be re-estimated by taking into account this relationship. PMID:19529767

  6. Mutation scanning-based analysis of Theileria orientalis populations in cattle following an outbreak.

    PubMed

    Cufos, Nadia; Jabbar, Abdul; de Carvalho, Luís M; Gasser, Robin B

    2012-07-01

    Bovine theileriosis is a tick-borne disease caused by one or more hemoprotozoan parasites of the genus Theileria. In the past, Theileria infection in cattle in Australia was largely asymptomatic and recognized to be associated with Theileria buffeli. However, outbreaks of theileriosis have occurred in beef and dairy cattle in subtropical climatic regions (New South Wales) of Australia. There is also one published report of a recent theileriosis outbreak in a beef farm near Seymour in the southeastern state of Victoria. In order to gain an improved insight into the genetic composition of Theileria populations following this outbreak, we undertook herein an integrated PCR-coupled mutation scanning-sequencing-phylogenetic analysis of sequence variation in part of the major piroplasm surface protein (MPSP) gene within and among samples from cattle involved in the outbreak. Theileria DNA was detected in 89.4% of 94 cattle in the Seymour farm; the genetic analysis showed that the ikeda and chitose genotypes representing the Theileria orientalis complex were detected in 75 and 4.8% of 84 infected cattle, respectively, and that mixed populations of these two genotypes were found in 20.2% of infected cattle. Given unpublished reports of a significant increase in the number of outbreaks in Victoria, future investigations should focus sharply on elucidating the epidemiology of Theileria to subvert the economic impact on the cattle industry in this state. Although used here to explore genetic variation within the T. orientalis complex in Australia, a mutation scanning-based approach has broad applicability to other species of Theileria in other countries.

  7. Impact of the Massachusetts tobacco control programme: population based trend analysis

    PubMed Central

    Biener, Lois; Harris, Jeffrey E; Hamilton, William

    2000-01-01

    Objective To assess the impact of the Massachusetts tobacco control programme, which, since its start in January 1993, has spent over $200m—“the highest per capita expenditure for tobacco control in the world”—funded by an extra tax of 25 cents per pack of cigarettes. Design Population based trend analysis with comparison group. Subjects Adult residents of Massachusetts and other US states excluding California. Main outcome measures Per capita consumption of cigarettes as measured by states' sales tax records; prevalence of smoking in adults as measured by several population-based telephone surveys. Results From 1988 to 1992, decline in per capita consumption of cigarettes in Massachusetts (15%) was similar to that in the comparison states (14%), corresponding to an annual decline of 3-4% for both groups. During 1992-3, consumption continued to decline by 4% in the comparison states but dropped 12% in Massachusetts in response to the tax increase. From 1993 onward, consumption in Massachusetts showed a consistent annual decline of more than 4%, whereas in the comparison states it levelled off, decreasing by less than 1% a year. From 1992, the prevalence of adult smoking in Massachusetts has declined annually by 0.43% (95% confidence interval 0.21% to 0.66%) compared with an increase of 0.03% (-0.06% to 0.12%) in the comparison states (P<0.001). Conclusions These findings show that a strongly implemented, comprehensive tobacco control programme can significantly reduce tobacco use. PMID:10926595

  8. Sub-population analysis based on temporal features of high content images

    PubMed Central

    2009-01-01

    Background High content screening techniques are increasingly used to understand the regulation and progression of cell motility. The demand of new platforms, coupled with availability of terabytes of data has challenged the traditional technique of identifying cell populations by manual methods and resulted in development of high-dimensional analytical methods. Results In this paper, we present sub-populations analysis of cells at the tissue level by using dynamic features of the cells. We used active contour without edges for segmentation of cells, which preserves the cell morphology, and autoregressive modeling to model cell trajectories. The sub-populations were obtained by clustering static, dynamic and a combination of both features. We were able to identify three unique sub-populations in combined clustering. Conclusion We report a novel method to identify sub-populations using kinetic features and demonstrate that these features improve sub-population analysis at the tissue level. These advances will facilitate the application of high content screening data analysis to new and complex biological problems. PMID:19958514

  9. 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

  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. PMID:24209380

  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. Bayesian population analysis of a washin-washout physiologically based pharmacokinetic model for acetone

    SciTech Connect

    Moerk, Anna-Karin; Jonsson, Fredrik; Johanson, Gunnar

    2009-11-01

    The aim of this study was to derive improved estimates of population variability and uncertainty of physiologically based pharmacokinetic (PBPK) model parameters, especially of those related to the washin-washout behavior of polar volatile substances. This was done by optimizing a previously published washin-washout PBPK model for acetone in a Bayesian framework using Markov chain Monte Carlo simulation. The sensitivity of the model parameters was investigated by creating four different prior sets, where the uncertainty surrounding the population variability of the physiological model parameters was given values corresponding to coefficients of variation of 1%, 25%, 50%, and 100%, respectively. The PBPK model was calibrated to toxicokinetic data from 2 previous studies where 18 volunteers were exposed to 250-550 ppm of acetone at various levels of workload. The updated PBPK model provided a good description of the concentrations in arterial, venous, and exhaled air. The precision of most of the model parameter estimates was improved. New information was particularly gained on the population distribution of the parameters governing the washin-washout effect. The results presented herein provide a good starting point to estimate the target dose of acetone in the working and general populations for risk assessment purposes.

  14. The uptake of active surveillance for the management of prostate cancer: A population-based analysis

    PubMed Central

    Richard, Patrick O.; Alibhai, Shabbir M.H.; Panzarella, Tony; Klotz, Laurence; Komisarenko, Maria; Fleshner, Neil E.; Urbach, David; Finelli, Antonio

    2016-01-01

    Introduction: Active surveillance (AS) is a strategy for the management of low-risk prostate cancer (PCa). However, few studies have assessed the uptake of AS at a population level and none of these were based on a Canadian population. Therefore, our objectives were to estimate the proportion of men being managed by AS in Ontario and to assess the factors associated with its uptake. Methods: This was a retrospective, population-based study using administrative databases from the province of Ontario to identify men ≤75 years diagnosed with localized PCa between 2002 and 2010. Descriptive statistics were used to estimate the proportion of men managed by AS, whereas mixed models were used to assess the factors associated with the uptake of AS. Results: 45 691 men met our inclusion criteria. Of these, 18% were managed by AS. Over time, the rates of AS increased significantly from 11% to 21% (p<0.001). Older age, residing in an urban centre, being diagnosed in the later years of the study period, having a neighborhood income in the highest quintile, and being managed by urologists were all associated with greater odds of receiving AS. Conclusions: There has been a steady increase in the uptake of AS between 2002 and 2010. However, only 18% of men diagnosed with localized PCa were managed by AS during the study period. The decisions to adopt AS were influenced by several individual and physician characteristics. The data suggest that there is significant opportunity for more widespread adoption of AS. PMID:27800055

  15. Individual-based analysis opens new insights into understanding population structure and animal behaviour.

    PubMed

    Planes, Serge; Lemer, Sarah

    2011-01-01

    Studying the movement of individuals in the wild has always been a challenge in ecology. However, estimating such movement is essential in life sciences as it is the base-line for evaluating connectivity, a major component in developing management and conservation plans. Furthermore, movement, or migration, is an essential parameter in population genetics, as it directly affects genetic differentiation. The development of highly variable markers has allowed genetic discrimination between individuals within populations and at larger scales, and the availability of high-throughput technologies means that many samples and hence many individuals can be screened. These advances mean that we can now use genetic identification for tracking individuals, and hence follow both survival and reproductive output through the life cycle. The paper by Morrissey & Ferguson (2011, this issue) is a demonstration of this new capability, as authors were able to infer the movement of salmonid fish initially captured as juveniles, and later as reproductively mature adults.

  16. 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. PMID:26031410

  17. 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

  18. Core genome conservation of Staphylococcus haemolyticus limits sequence based population structure analysis.

    PubMed

    Cavanagh, Jorunn Pauline; Klingenberg, Claus; Hanssen, Anne-Merethe; Fredheim, Elizabeth Aarag; Francois, Patrice; Schrenzel, Jacques; Flægstad, Trond; Sollid, Johanna Ericson

    2012-06-01

    The notoriously multi-resistant Staphylococcus haemolyticus is an emerging pathogen causing serious infections in immunocompromised patients. Defining the population structure is important to detect outbreaks and spread of antimicrobial resistant clones. Currently, the standard typing technique is pulsed-field gel electrophoresis (PFGE). In this study we describe novel molecular typing schemes for S. haemolyticus using multi locus sequence typing (MLST) and multi locus variable number of tandem repeats (VNTR) analysis. Seven housekeeping genes (MLST) and five VNTR loci (MLVF) were selected for the novel typing schemes. A panel of 45 human and veterinary S. haemolyticus isolates was investigated. The collection had diverse PFGE patterns (38 PFGE types) and was sampled over a 20 year-period from eight countries. MLST resolved 17 sequence types (Simpsons index of diversity [SID]=0.877) and MLVF resolved 14 repeat types (SID=0.831). We found a low sequence diversity. Phylogenetic analysis clustered the isolates in three (MLST) and one (MLVF) clonal complexes, respectively. Taken together, neither the MLST nor the MLVF scheme was suitable to resolve the population structure of this S. haemolyticus collection. Future MLVF and MLST schemes will benefit from addition of more variable core genome sequences identified by comparing different fully sequenced S. haemolyticus genomes. PMID:22484086

  19. A new method for studying population genetics of cyst nematodes based on Pool-Seq and genomewide allele frequency analysis.

    PubMed

    Mimee, Benjamin; Duceppe, Marc-Olivier; Véronneau, Pierre-Yves; Lafond-Lapalme, Joël; Jean, Martine; Belzile, François; Bélair, Guy

    2015-11-01

    Cyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time-consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping-by-sequencing and Pool-Seq. This method yielded thousands of SNPs and allowed us to study the relationships between populations of different origins or pathotypes. Validation of the method on well-characterized populations also demonstrated that it was a powerful and accurate tool for population genetics. The genomewide allele frequencies of 23 populations of golden nematode, from nine countries and representing the five known pathotypes, were compared. A clear separation of the pathotypes and fine genetic relationships between and among global populations were obtained using this method. In addition to being powerful, this tool has proven to be very time- and cost-efficient and could be applied to other cyst nematode species.

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

    PubMed Central

    KATSAROU, MARTHA-SPYRIDOULA; LATSI, ROSANA; PAPASAVVA, MARIA; DEMERTZIS, NIKOLAOS; KALOGRIDIS, THODORIS; TSATSAKIS, ARISTIDES M.; SPANDIDOS, DEMETRIOS A.; DRAKOULIS, NIKOLAOS

    2016-01-01

    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, due to influences from

  1. 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…

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

    PubMed Central

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

    2015-01-01

    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. PMID:26687035

  3. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.

    PubMed

    Zhernakova, Alexandra; Kurilshikov, Alexander; Bonder, Marc Jan; Tigchelaar, Ettje F; Schirmer, Melanie; Vatanen, Tommi; Mujagic, Zlatan; Vila, Arnau Vich; Falony, Gwen; Vieira-Silva, Sara; Wang, Jun; Imhann, Floris; Brandsma, Eelke; Jankipersadsing, Soesma A; Joossens, Marie; Cenit, Maria Carmen; Deelen, Patrick; Swertz, Morris A; Weersma, Rinse K; Feskens, Edith J M; Netea, Mihai G; Gevers, Dirk; Jonkers, Daisy; Franke, Lude; Aulchenko, Yurii S; Huttenhower, Curtis; Raes, Jeroen; Hofker, Marten H; Xavier, Ramnik J; Wijmenga, Cisca; Fu, Jingyuan

    2016-04-29

    Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These factors collectively explain 18.7% of the variation seen in the interindividual distance of microbial composition. We could associate 110 factors to 125 species and observed that fecal chromogranin A (CgA), a protein secreted by enteroendocrine cells, was exclusively associated with 61 microbial species whose abundance collectively accounted for 53% of microbial composition. Low CgA concentrations were seen in individuals with a more diverse microbiome. These results are an important step toward a better understanding of environment-diet-microbe-host interactions. PMID:27126040

  4. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.

    PubMed

    Zhernakova, Alexandra; Kurilshikov, Alexander; Bonder, Marc Jan; Tigchelaar, Ettje F; Schirmer, Melanie; Vatanen, Tommi; Mujagic, Zlatan; Vila, Arnau Vich; Falony, Gwen; Vieira-Silva, Sara; Wang, Jun; Imhann, Floris; Brandsma, Eelke; Jankipersadsing, Soesma A; Joossens, Marie; Cenit, Maria Carmen; Deelen, Patrick; Swertz, Morris A; Weersma, Rinse K; Feskens, Edith J M; Netea, Mihai G; Gevers, Dirk; Jonkers, Daisy; Franke, Lude; Aulchenko, Yurii S; Huttenhower, Curtis; Raes, Jeroen; Hofker, Marten H; Xavier, Ramnik J; Wijmenga, Cisca; Fu, Jingyuan

    2016-04-29

    Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These factors collectively explain 18.7% of the variation seen in the interindividual distance of microbial composition. We could associate 110 factors to 125 species and observed that fecal chromogranin A (CgA), a protein secreted by enteroendocrine cells, was exclusively associated with 61 microbial species whose abundance collectively accounted for 53% of microbial composition. Low CgA concentrations were seen in individuals with a more diverse microbiome. These results are an important step toward a better understanding of environment-diet-microbe-host interactions.

  5. Association between gastroesophageal reflux disease and coronary heart disease: A nationwide population-based analysis.

    PubMed

    Chen, Chien-Hua; Lin, Cheng-Li; Kao, Chia-Hung

    2016-07-01

    In this study, we aimed to determine the association between gastroesophageal reflux disease (GERD) and subsequent coronary heart disease (CHD) development, if any, and to evaluate whether longer use of proton pump inhibitors (PPIs) increases the risk of CHD.Patients diagnosed with GERD between 2000 and 2011 were identified as the study cohort (n = 12,960). Patients without GERD were randomly selected from the general population, frequency-matched with the study group according to age, sex, and index year, and evaluated as the comparison cohort (n = 51,840). Both cohorts were followed up until the end of 2011 to determine the incidence of CHD. The risk of CHD was evaluated in both groups by using Cox proportional hazards regression models.The GERD patients had a greater probability of CHD than the cohort without GERD did (log-rank test, P < 0.001 and 11.8 vs 6.5 per 1000 person-years). The GERD cohort had a higher risk of CHD than the comparison cohort did after adjustment for age, sex, hypertension, diabetes, hyperlipidemia, alcohol-related illness, stroke, chronic obstructive pulmonary disease, asthma, biliary stone, anxiety, depression, chronic kidney disease, and cirrhosis (adjusted hazard ratio [aHR]: 1.49, 95% confidence interval [CI]: 1.34-1.66). The risk of CHD was greater for the patients treated with PPIs for more than 1 year (aHR = 1.67, 95% CI = 1.34-2.08) than for those treated with PPIs for <1 year (aHR = 1.56, 95% CI = 1.39-1.74).Our population-based cohort study results indicate that GERD was associated with an increased risk of developing CHD, and that PPI use for more than 1 year might increase the risk of CHD. PMID:27399102

  6. 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

  7. 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

  8. Multilocus sequence-based analysis delineates a clonal population of Agrobacterium (Rhizobium) radiobacter (Agrobacterium tumefaciens) of human origin.

    PubMed

    Aujoulat, Fabien; Jumas-Bilak, Estelle; Masnou, Agnès; Sallé, Fanny; Faure, Denis; Segonds, Christine; Marchandin, Hélène; Teyssier, Corinne

    2011-05-01

    The genus Agrobacterium includes plant-associated bacteria and opportunistic human pathogens. Taxonomy and nomenclature within the genus remain controversial. In particular, isolates of human origin were all affiliated with the species Agrobacterium (Rhizobium) radiobacter, while phytopathogenic strains were designated under the synonym denomination Agrobacterium tumefaciens. In order to study the relative distribution of Agrobacterium strains according to their origins, we performed a multilocus sequence-based analysis (MLSA) on a large collection of 89 clinical and environmental strains from various origins. We proposed an MLSA scheme based on the partial sequence of 7 housekeeping genes (atpD, zwf, trpE, groEL, dnaK, glnA, and rpoB) present on the circular chromosome of A. tumefaciens C58. Multilocus phylogeny revealed that 88% of the clinical strains belong to genovar A7, which formed a homogeneous population with linkage disequilibrium, suggesting a low rate of recombination. Comparison of genomic fingerprints obtained by pulsed-field gel electrophoresis (PFGE) showed that the strains of genovar A7 were epidemiologically unrelated. We present genetic evidence that genovar A7 may constitute a human-associated population distinct from the environmental population. Also, phenotypic characteristics, such as culture at 42°C, agree with this statement. This human-associated population might represent a potential novel species in the genus Agrobacterium.

  9. 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

  10. 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.

  11. 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.

  12. Statin use and risk of glioma: population-based case-control analysis.

    PubMed

    Seliger, Corinna; Meier, Christoph Rudolf; Becker, Claudia; Jick, Susan Sara; Bogdahn, Ulrich; Hau, Peter; Leitzmann, Michael Fred

    2016-09-01

    Statins have been reported to decrease the incidence of cancer, but the risk of glioma among statin users has been investigated in only two prior observational studies, both of them suggesting a modest protective effect of statins. We conducted a matched case-control study using data from the UK-based Clinical Practice Research Datalink to analyse use of statins among 2469 cases with glioma and 24,690 controls. We performed conditional logistic regression analysis to calculate relative risks, estimated as odds ratios (ORs) with 95 % confidence intervals (CIs) adjusting for multiple confounding factors. As compared with non-use of statins, use of statins was not associated with risk of glioma (OR for ≥90 prescriptions=0.75; 95 % CI 0.48-1.17). Our findings do not support previous sparse evidence of a possible inverse association between statin use and glioma risk. PMID:27041698

  13. A population-based analysis of clustering identifies a strong genetic contribution to lethal prostate cancer

    PubMed Central

    Nelson, Quentin; Agarwal, Neeraj; Stephenson, Robert; Cannon-Albright, Lisa A.

    2013-01-01

    Background: Prostate cancer is a common and often deadly cancer. Decades of study have yet to identify genes that explain much familial prostate cancer. Traditional linkage analysis of pedigrees has yielded results that are rarely validated. We hypothesize that there are rare segregating variants responsible for high-risk prostate cancer pedigrees, but recognize that within-pedigree heterogeneity is responsible for significant noise that overwhelms signal. Here we introduce a method to identify homogeneous subsets of prostate cancer, based on cancer characteristics, which show the best evidence for an inherited contribution. Methods: We have modified an existing method, the Genealogical Index of Familiality (GIF) used to show evidence for significant familial clustering. The modification allows a test for excess familial clustering of a subset of prostate cancer cases when compared to all prostate cancer cases. Results: Consideration of the familial clustering of eight clinical subsets of prostate cancer cases compared to the expected familial clustering of all prostate cancer cases identified three subsets of prostate cancer cases with evidence for familial clustering significantly in excess of expected. These subsets include prostate cancer cases diagnosed before age 50 years, prostate cancer cases with body mass index (BMI) greater than or equal to 30, and prostate cancer cases for whom prostate cancer contributed to death. Conclusions: This analysis identified several subsets of prostate cancer cases that cluster significantly more than expected when compared to all prostate cancer familial clustering. A focus on high-risk prostate cancer cases or pedigrees with these characteristics will reduce noise and could allow identification of the rare predisposition genes or variants responsible. PMID:23970893

  14. 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

  15. 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,…

  16. A population-based analysis of pneumococcal disease mortality in California, 1989-1998.

    PubMed Central

    Redelings, Matthew D.; Sorvillo, Frank; Simon, Paul

    2005-01-01

    OBJECTIVES: Pneumococcal disease is an important cause of vaccine-preventable mortality. It is important to understand the burden and distribution of mortality so that prevention efforts can be targeted appropriately. This study evaluated pneumococcal disease mortality and its demographic correlates in California from 1989 to 1998. METHODS: Deaths due to pneumococcal disease were identified from statewide vital records data using multiple cause-coded information. Denominator data were obtained from estimates from the California Department of Finance. Crude and age-adjusted mortality rates and 95% confidence intervals were calculated for each age, gender, and racial/ethnic group. RESULTS: The age-adjusted pneumococcal disease mortality rate was 2.05 deaths per 100,000 population. Mortality was highest in elderly individuals (reaching 38.29 deaths per 100,000 population in individuals older than age 85). Age-adjusted mortality rates were elevated in the African American race/ethnicity group (2.96 deaths per 100,000 population) and males (2.67 deaths per 100,000 population). The majority of individuals who died of pneumococcal disease (78.9%) fell into at-risk groups indicated for vaccination. The majority of all pneumococcal deaths were caused by pneumococcal pneumonia. Mortality was seasonal, reaching a peak in the winter months. A decreasing trend in mortality was observed over the 10-year period examined. CONCLUSIONS: Pneumococcal disease remains a significant cause of vaccine-preventable mortality in the California population. Greater efforts must be made to vaccinate at-risk individuals, especially those in demographic groups at highest risk of death. PMID:15842117

  17. Switching from body surface area-based to fixed dosing for the investigational proteasome inhibitor ixazomib: a population pharmacokinetic analysis

    PubMed Central

    Gupta, Neeraj; Zhao, Yuan; Hui, Ai-Min; Esseltine, Dixie-Lee; Venkatakrishnan, Karthik

    2015-01-01

    Aims This population pharmacokinetic analysis of the investigational oral proteasome inhibitor ixazomib assessed the feasibility of switching from body surface area (BSA)-based to fixed dosing, and the impact of baseline covariates on ixazomib pharmacokinetics. Methods Data were pooled from 226 adult patients with multiple myeloma, lymphoma or solid tumours in four phase 1 studies, in which ixazomib dosing (oral/intravenous, once/twice weekly) was based on BSA. Population pharmacokinetic modelling was undertaken using nonmem version 7.2. Results Ixazomib pharmacokinetics were well described by a three compartment model with first order absorption and linear elimination. Ixazomib was absorbed rapidly (Ka 0.5 h−1), with dose- and time-independent pharmacokinetics. Estimated absolute bioavailability and clearance were 60% and 2 l h−1, respectively. Although a small effect of BSA (range 1.3–2.6 m2) was observed on the peripheral volume of distribution (V4), reducing the corresponding inter-individual variability by 12.9%, there was no relationship between BSA and ixazomib clearance (the parameter that dictates total systemic exposure following fixed dosing). Consistently, based on simulations (n = 1000), median AUCs (including interquartile range) were similar after BSA-based (2.23 mg m−2) and fixed (4 mg) oral dosing with no trend in simulated AUC vs. BSA for fixed dosing (P = 0.42). No other covariates, including creatinine clearance (22–213.7 ml min−1) and age (23–86 years), influenced ixazomib pharmacokinetics. Conclusions This analysis supports a switch from BSA-based to fixed dosing, without dose modification for mild/moderate renal impairment or age, in future adult studies of ixazomib, simplifying dosing guidance and clinical development. PMID:25377318

  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. [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. PMID:25715463

  20. Prostate-Specific Antigen (PSA)–Based Population Screening for Prostate Cancer: An Evidence-Based Analysis

    PubMed Central

    Pron, G

    2015-01-01

    Background Prostate cancer (PC) is the most commonly diagnosed non-cutaneous cancer in men and their second or third leading cause of cancer death. Prostate-specific antigen (PSA) testing for PC has been in common practice for more than 20 years. Objectives A systematic review of the scientific literature was conducted to determine the effectiveness of PSA-based population screening programs for PC to inform policy decisions in a publicly funded health care system. Data Sources A systematic review of bibliographic databases was performed for systematic reviews or randomized controlled trials (RCT) of PSA-based population screening programs for PC. Review Methods A broad search strategy was employed to identify studies reporting on key outcomes of PC mortality and all-cause mortality. Results The search identified 5 systematic reviews and 6 RCTs. None of the systematic reviews found a statistically significant reduction in relative risk (RR) of PC mortality or overall mortality with PSA-based screening. PC mortality reductions were found to vary by country, by screening program, and by age of men at study entry. The European Randomized Study of Screening for Prostate Cancer found a statistically significant reduction in RR in PC mortality at 11-year follow-up (0.79; 95% CI, 0.67–0.92), although the absolute risk reduction was small (1.0/10,000 person-years). However, the primary treatment for PCs differed significantly between countries and between trial arms. The American Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) found a statistically non-significant increase in RR for PC mortality with 13-year follow-up (1.09; 95% CI, 0.87–1.36). The degree of opportunistic screening in the control arm of the PLCO trial, however, was high. None of the RCTs found a reduction in all-cause mortality and all found a statistically significant increase in the detection of mainly low-risk, organ-confined PCs in the screening arm. Conclusions There was no

  1. [Analysis of cytogenetic stability in natural populations of terrestrial mollusks (based on DNA comet assay)].

    PubMed

    Snegin, É A

    2014-01-01

    Abstract-Alkaline gel electrophoresis of isolated cells (comet assay) was used to assess degree of nuclear DNA damage in populations of terrestrial mollusks Bradybaenafruticum Müll., Chondrula tridens Müll., Cepaea vindobonensis Fer., and Stenomphalia ravergieri Fer. living in the forest-steppe landscape of the southern part of the Mid-Russian Upland. Evidence of differences in the parameters studied was found. The age dynamics of the degree of damage of the genetic apparatus was observed. Possible causes of the identified differences are discussed.

  2. 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

  3. Population-level impact of shorter-course regimens for tuberculosis: a model-based analysis.

    PubMed

    Fofana, Mariam O; Knight, Gwenan M; Gomez, Gabriela B; White, Richard G; Dowdy, David W

    2014-01-01

    Despite current control efforts, global tuberculosis (TB) incidence is decreasing slowly. New regimens that can shorten treatment hold promise for improving treatment completion and success, but their impact on population-level transmission remains unclear. Earlier models projected that a four-month regimen could reduce TB incidence by 10% but assumed that an entire course of therapy must be completed to derive any benefit. We constructed a dynamic transmission model of TB disease calibrated to global estimates of incidence, prevalence, mortality, and treatment success. To account for the efficacy of partial treatment, we used data from clinical trials of early short-course regimens to estimate relapse rates among TB patients who completed one-third, one-half, two-thirds, and all of their first-line treatment regimens. We projected population-level incidence and mortality over 10 years, comparing standard six-month therapy to hypothetical shorter-course regimens with equivalent treatment success but fewer defaults. The impact of hypothetical four-month regimens on TB incidence after 10 years was smaller than estimated in previous modeling analyses (1.9% [95% uncertainty range 0.6-3.1%] vs. 10%). Impact on TB mortality was larger (3.5% at 10 years) but still modest. Transmission impact was most sensitive to the proportion of patients completing therapy: four-month therapy led to greater incidence reductions in settings where 25% of patients leave care ("default") over six months. Our findings remained robust under one-way variation of model parameters. These findings suggest that novel regimens that shorten treatment duration may have only a modest effect on TB transmission except in settings of very low treatment completion.

  4. A Population Based Analysis of Subclinical Psychosis and Help-Seeking Behavior

    PubMed Central

    Murphy, Jamie; Shevlin, Mark; Houston, James; Adamson, Gary

    2012-01-01

    Clinically defined psychosis is recognizable and distinguishable from nonclinical or subclinical psychosis by virtue of its clinical relevance (ie, its associated distress and its need for care and/or treatment). According to the continuum hypothesis, subclinical psychosis is merely quantitatively different from more extreme phenotypic expressions and as such should also be indicative of distress and help-seeking behavior but to a lesser extent. Using data from the Adult Psychiatric Morbidity Survey, the current study focused on self-reported psychosis and help-seeking experiences in a general population sample free from clinically defined psychosis (N = 7266). After statistically controlling for the effects of a series of potential help-seeking correlates the findings showed that subclinical psychosis symptom experience was significantly associated with various forms of help-seeking behavior. Individuals who reported subclinical experiences of thought control, paranoia, and strange experiences were on average 2 times more likely to attend their general practitioner for emotional problems compared with those individuals who reported no psychosis. Individuals who reported subclinical experiences of paranoia were 3 times more likely to be in receipt of counseling/therapy compared with those with no experience of paranoia. Multiple subclinical psychotic experiences also predicted elevated help-seeking behavior. These findings may have a positive impact on the detection of individuals who are at increased risk of psychological distress and aid in the design and implementation of more effective treatments at both clinical and subclinical levels. PMID:20709763

  5. 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.

  6. 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

  7. 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...

  8. Preventing young children's injuries: analysis of data from a population-based surveillance.

    PubMed

    Toblin, Robin L; Brenner, Ruth A; Taneja, Gitanjali S; Rossi, Maryann W; Collins, Millicent; Mickalide, Angela D; Overpeck, Mary D; Clinton-Reid, Yvette; Dever, Jill A; Boyle, Kerrie; Trumble, Ann C; Scheidt, Peter C

    2011-12-01

    The objective of this study is to determine prevention strategies for potentially serious injury events among children younger than 3 years of age based upon circumstances surrounding injury events. Surveillance was conducted on all injuries to District of Columbia (DC) residents less than 3 years old that resulted in an Emergency Department (ED) visit, hospitalization, or death for 1 year. Data were collected through abstraction of medical records and interviews with a subset of parents of injured children. Investigators coded injury-related events for the potential for death or disability. Potential prevention strategies were then determined for all injury events that had at least a moderate potential for death or disability and sufficient detail for coding (n = 425). Injury-related events included 10 deaths, 163 hospitalizations, and 2,868 ED visits (3,041 events in total). Of the hospitalizations, 88% were coded as moderate or high potential for disability or death, versus only 21% of the coded ED visits. For potentially serious events, environmental change strategies were identified for 47%, behavior change strategies for 77%, and policy change strategies for 24%. For 46% of the events more than one type of prevention strategy was identified. Only 8% had no identifiable prevention strategy. Prevention strategies varied by specific cause of injury. Potential prevention strategies were identifiable for nearly all potentially serious injury events, with multiple potential prevention strategies identified for a large fraction of the events. These findings support developing multifaceted prevention approaches informed by community-based injury surveillance.

  9. Preventing young children's injuries: analysis of data from a population-based surveillance.

    PubMed

    Toblin, Robin L; Brenner, Ruth A; Taneja, Gitanjali S; Rossi, Maryann W; Collins, Millicent; Mickalide, Angela D; Overpeck, Mary D; Clinton-Reid, Yvette; Dever, Jill A; Boyle, Kerrie; Trumble, Ann C; Scheidt, Peter C

    2011-12-01

    The objective of this study is to determine prevention strategies for potentially serious injury events among children younger than 3 years of age based upon circumstances surrounding injury events. Surveillance was conducted on all injuries to District of Columbia (DC) residents less than 3 years old that resulted in an Emergency Department (ED) visit, hospitalization, or death for 1 year. Data were collected through abstraction of medical records and interviews with a subset of parents of injured children. Investigators coded injury-related events for the potential for death or disability. Potential prevention strategies were then determined for all injury events that had at least a moderate potential for death or disability and sufficient detail for coding (n = 425). Injury-related events included 10 deaths, 163 hospitalizations, and 2,868 ED visits (3,041 events in total). Of the hospitalizations, 88% were coded as moderate or high potential for disability or death, versus only 21% of the coded ED visits. For potentially serious events, environmental change strategies were identified for 47%, behavior change strategies for 77%, and policy change strategies for 24%. For 46% of the events more than one type of prevention strategy was identified. Only 8% had no identifiable prevention strategy. Prevention strategies varied by specific cause of injury. Potential prevention strategies were identifiable for nearly all potentially serious injury events, with multiple potential prevention strategies identified for a large fraction of the events. These findings support developing multifaceted prevention approaches informed by community-based injury surveillance. PMID:21904860

  10. Risk analysis of carotid stent from a population-based database in Taiwan

    PubMed Central

    Cheng, Chun-An; Chien, Wu-Chien; Hsu, Chien-Yeh; Lin, Hui-Chen; Chiu, Hung-Wen

    2016-01-01

    Abstract Because stroke is the third leading disease that causes mortality in the world, the prevention of stroke from advanced carotid stenosis is an important issue. The carotid stent (CAS) is a less invasive to treat advanced carotid stenosis, but for high-risk patients it may cause some events after the procedure that reduces the benefit of stroke prevention. Because patients and their families have less information about risk of events after CAS and are easy concerned, this study calculates the individual probability of major adverse cardiovascular events including any stroke, myocardial infarction, or death after procedure. The analyzed dataset was composed of patients undergoing CAS from the longitudinal National Health Insurance claim database in Taiwan. The validation dataset was composed of patients undergoing CAS from the Tri-Service General Hospital. We excluded patients under 18 years of age. The prediction model was constructed with a multivariable Cox proportional hazard regression and performed with forward stepwise selection. The nomogram construction was based on the multivariable Cox model. The risk factors were determined as follows: age with a hazard ratio (HR) of 1.027 (95% confidence interval [CI]: 1.002–1.053) for every 1 year older, congestive heart failure with a HR of 2.196 (95% CI: 1.368–3.524), malignant disease with a HR of 1.724 (95% CI: 1.009–2.944), diabetes mellitus with a HR of 1.722 (95% CI: 1.109–2.674), and symptomatic status with a HR of 1.604 (95% CI: 1.027–2.507). The model showed good discrimination with a P < 0.001 (concordance index, 0.681; bootstrap corrected, 0.661) in the derivation data. The concordance index of external validation was 0.66 (P = 0.048), which indicates acceptable performance. We developed a nomogram with a visual scale method and prognostic information, and it is easy to use in clinical practice. The integer-base method may support communication between clinicians and patients before CAS to

  11. Risk analysis of carotid stent from a population-based database in Taiwan.

    PubMed

    Cheng, Chun-An; Chien, Wu-Chien; Hsu, Chien-Yeh; Lin, Hui-Chen; Chiu, Hung-Wen

    2016-08-01

    Because stroke is the third leading disease that causes mortality in the world, the prevention of stroke from advanced carotid stenosis is an important issue. The carotid stent (CAS) is a less invasive to treat advanced carotid stenosis, but for high-risk patients it may cause some events after the procedure that reduces the benefit of stroke prevention. Because patients and their families have less information about risk of events after CAS and are easy concerned, this study calculates the individual probability of major adverse cardiovascular events including any stroke, myocardial infarction, or death after procedure.The analyzed dataset was composed of patients undergoing CAS from the longitudinal National Health Insurance claim database in Taiwan. The validation dataset was composed of patients undergoing CAS from the Tri-Service General Hospital. We excluded patients under 18 years of age. The prediction model was constructed with a multivariable Cox proportional hazard regression and performed with forward stepwise selection. The nomogram construction was based on the multivariable Cox model.The risk factors were determined as follows: age with a hazard ratio (HR) of 1.027 (95% confidence interval [CI]: 1.002-1.053) for every 1 year older, congestive heart failure with a HR of 2.196 (95% CI: 1.368-3.524), malignant disease with a HR of 1.724 (95% CI: 1.009-2.944), diabetes mellitus with a HR of 1.722 (95% CI: 1.109-2.674), and symptomatic status with a HR of 1.604 (95% CI: 1.027-2.507). The model showed good discrimination with a P < 0.001 (concordance index, 0.681; bootstrap corrected, 0.661) in the derivation data. The concordance index of external validation was 0.66 (P = 0.048), which indicates acceptable performance.We developed a nomogram with a visual scale method and prognostic information, and it is easy to use in clinical practice. The integer-base method may support communication between clinicians and patients before CAS to reduce the anxiety

  12. Frequency and predictors of tablet splitting in statin prescriptions: a population-based analysis

    PubMed Central

    Dormuth, Colin R; Schneeweiss, Sebastian; Brookhart, Alan M; Carney, Greg; Bassett, Ken; Adams, Stephen; Wright, James M

    2008-01-01

    Background The price per milligram for most statin medications decreases at higher strengths, which provides an economic incentive to split tablets. We sought to determine the frequency with which statin tablets are split, and to evaluate factors associated with this practice. Methods We obtained prescription claims data for statins from the BC Ministry of Health for the period Jan. 1, 1996, to Dec. 31, 2006. We estimated the number of tablets per day, based on the ratio of the number of tablets to days-supply in each prescription, to estimate the frequency with which splitting occurred with each statin. We used multivariable logistic regression to assess patient and physician characteristics and the level of public drug plan coverage associated with tablet splitting. To estimate related cost savings, we used information on drug costs and quantities of dispensed statins reported by pharmacies. Results During the 11-year study period, we estimated that tablet splitting occurred in 2.6% of 7.2 million statin prescriptions. There was an increasing trend in the practice over time, to 4.5% of prescriptions in 2006. Lovastatin was the only scored tablet and was the most likely to be split, followed by rosuvastatin and atorvastatin. Fifty percent of the prescriptions in which tablet splitting occurred were prescribed by only 7.9% of the routine statin prescribers (i.e., > 10 statin prescriptions over the study period). Specialists were less likely than general practitioners to prescribe statins that were subsequently split (odds ratio [OR] 0.43, 95% confidence interval [CI] 0.40–0.46). Statin prescriptions that were fully covered by the public drug plan were half as likely as those with no such coverage to involve tablet splitting (OR 0.48, 95% CI 0.44–0.92). Having no public drug coverage, having a low annual household income and being female were patient factors found to be positively associated with tablet splitting. In 2006, the cost savings associated with

  13. 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

  14. Implementation of a routine genetic evaluation for longevity based on survival analysis techniques in dairy cattle populations in Switzerland.

    PubMed

    Vukasinovic, N; Moll, J; Casanova, L

    2001-09-01

    Genetic evaluation of sires for functional longevity of their daughters based on survival analysis has been implemented in the populations of Braunvieh, Simmental, and Holstein cattle in Switzerland. A Weibull mixed sire-maternal grandsire survival model was used to estimate breeding values of sires with data on cows that calved since April 1, 1980. Data on Braunvieh and Simmental cows included about 1.1 million records, data on Holstein cows comprised about 220,000 records. Data contained approximately 20 to 24% right-censored records and 6 to 9% left-truncated records. Besides the random sire and maternal grandsire effects, the model included effects of herd-year-season, age at first calving, parity, stage of lactation, alpine pasturing (Braunvieh and Simmental), and relative milk yield and relative fat and protein percentage within herd to account for culling for production. Heritability of functional longevity, estimated on a subset of data including approximately 150,000 animals, were 0.181, 0.198, and 0.184 for Braunvieh, Simmental, and Holstein, respectively. Breeding values were estimated for all sires with at least six daughters or three granddaughters in the data. Breeding values of sires are expressed in months of functional productive life and published in sire catalogs along with breeding values for production traits.

  15. 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

  16. 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...

  17. 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.

  18. A population-based analysis of emergent versus elective paraesophageal hernia repair using the Nationwide Inpatient Sample

    PubMed Central

    Jassim, Hassanain; Seligman, Johnathan T.; Frelich, Matthew; Goldblatt, Matthew; Kastenmeier, Andrew; Wallace, James; Zhao, Heather S.; Szabo, Aniko; Gould, Jon C.

    2015-01-01

    Background As the life expectancy in the United States continues to increase, more elderly, sometimes frail patients present with sub-acute surgical conditions such as a symptomatic paraesophageal hernia (PEH). While the outcomes of PEH repair have improved largely due to the proliferation of laparoscopic surgery, there is still a defined rate of morbidity and mortality. We sought to characterize the outcomes of both elective and emergent PEH repair using a large population-based data set. Methods The Nationwide Inpatient Sample was queried for primary ICD-9 codes associated with PEH repair (years 2006–2008). Outcomes were in-hospital mortality and the occurrence of a pre-identified complication. Multivariate analysis was performed to determine the risk factors for complications and mortality following both elective and emergent PEH repair. Results A total of 8,462 records in the data, representing 41,723 patients in the US undergoing PEH repair in the study interval, were identified. Of these procedures, 74.2 % was elective and 42.4 % was laparoscopic. The overall complication and mortality rates were 20.8 and 1.1 %, respectively. Emergent repair was associated with a higher rate of morbidity (33.4 vs. 16.5 %, p > 0.001) and mortality (3.2 vs. 0.37 %, p > 0.001) than elective repair. Emergent repair patients were more likely to be male, were older, and more likely to be minority. Logistic modeling revealed that younger age, elective case status, and a laparoscopic approach were independently associated with a lower probability of complications and mortality. Conclusions Patients undergoing emergent PEH repair in the United States tend to be older, more likely a racial minority, and less likely to undergo laparoscopic repair. Elective repair, younger age, and a laparoscopic approach are associated with improved outcomes. Considering all of the above, we recommend that patients consider elective repair with a surgeon experienced in the laparoscopic approach

  19. 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.

  20. Population- and individual-based approaches to the design and analysis of epidemiologic studies of sexually transmitted disease transmission.

    PubMed

    Shiboski, S; Padian, N S

    1996-10-01

    Epidemiologic studies of sexually transmitted disease (STD) transmission present a number of unique challenges in design and analysis. These arise both from the social nature of STD transmission and from inherent difficulties in collecting accurate and informative data on exposure and infection. Risk of acquiring an STD depends on both individual-level factors and the behavior and infectiousness of others. Consequently, study designs and analysis methods developed for studying chronic disease risk in individuals or groups may not apply directly. Simple models of STD transmission were used to investigate these issues, focusing on how the interplay between individual- and population-level factors influences design and interpretation of epidemiologic studies, with particular attention to interpretation of common measures of association and to common sources of bias in epidemiologic data. Existing methods for investigating risk factors can be modified such that these issues may be addressed directly. PMID:8843249

  1. Web based health surveys: Using a Two Step Heckman model to examine their potential for population health analysis.

    PubMed

    Morrissey, Karyn; Kinderman, Peter; Pontin, Eleanor; Tai, Sara; Schwannauer, Mathias

    2016-08-01

    In June 2011 the BBC Lab UK carried out a web-based survey on the causes of mental distress. The 'Stress Test' was launched on 'All in the Mind' a BBC Radio 4 programme and the test's URL was publicised on radio and TV broadcasts, and made available via BBC web pages and social media. Given the large amount of data created, over 32,800 participants, with corresponding diagnosis, demographic and socioeconomic characteristics; the dataset are potentially an important source of data for population based research on depression and anxiety. However, as respondents self-selected to participate in the online survey, the survey may comprise a non-random sample. It may be only individuals that listen to BBC Radio 4 and/or use their website that participated in the survey. In this instance using the Stress Test data for wider population based research may create sample selection bias. Focusing on the depression component of the Stress Test, this paper presents an easy-to-use method, the Two Step Probit Selection Model, to detect and statistically correct selection bias in the Stress Test. Using a Two Step Probit Selection Model; this paper did not find a statistically significant selection on unobserved factors for participants of the Stress Test. That is, survey participants who accessed and completed an online survey are not systematically different from non-participants on the variables of substantive interest. PMID:27394193

  2. 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.

  3. Deciphering diversity in populations of various linguistic and ethnic affiliations of different geographical regions of India: analysis based on 15 microsatellite markers.

    PubMed

    Kashyap, V K; Ashma, Richa; Gaikwad, Sonali; Sarkar, B N; Trivedi, R

    2004-04-01

    The extent of genetic polymorphism at fifteen autosomal microsatellite markers in 54 ethnically, linguistically and geographically diverse human populations of India was studied to decipher intrapopulation diversity. The parameters used to quantify intrapopulation diversity were average allele diversity, average heterozygosity, allele range (base pairs), and number of alleles. Multilocus genotype frequencies calculated for selected populations were utilized for testing conformity with the assumption of Hardy-Weinberg equilibrium. The exact test values, after Bonferroni correction, showed significant deviation amongst Gowda (vWA, Penta E); Dhangar, Satnami and Gounder (D8S1179); Hmar (FGA); Kuki and Balti (vWA) groups. Relatively low number of alleles and allelic diversity (base-pairs size) had been observed in populations of central India as compared with southern and northern regions of the country. The communities of Indo-Caucasoid ethnic origin and Indo-European linguistic family (Kshatriya of Uttar Pradesh) showed highest allelic diversity, as well as rare alleles, not reported in any other Indian populations. Analysis based on average heterozygosity was also found to be lowest among the populations of central India (0.729) and highest among the populations from north (0.777) and west (0.784) regions of the country, having Indo-Caucasoid ethnic origin and Austro-Asiatic linguistic affiliation. The maximum power of discrimination (85%-89%) had been observed at loci FGA, Penta E, D18S51 and D21S11, suggested high intrapopulation diversity in India. Genetic diversity revealed by STR markers was consistent with the known demographic histories of populations. Thus, the present study clearly demonstrated that the intrapopulation diversity is not only present at the national level, but also within smaller geographical regions of the country. This is the first attempt to understand the extent of diversity within populations of India at such a large scale at genomic

  4. 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

  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. Evidences for multiple maternal lineages of Caryocar brasiliense populations in the Brazilian Cerrado based on the analysis of chloroplast DNA sequences and microsatellite haplotype variation.

    PubMed

    Collevatti, Rosane G; Grattapaglia, Dario; Hay, John D

    2003-01-01

    In this work we report on the phylogeography of the endangered tree species Caryocar brasiliense based on variability in two classes of maternally inherited chloroplast DNA sequences with different rates of molecular evolution. Eleven sequence haplotypes of a noncoding region between the genes trnT and trnF and 21 distinct 10-locus microsatellite haplotypes could be identified in a total of 160 individuals, collected in 10 widespread populations of C. brasiliense. An amova indicated that most of the variation can be attributed to differences among populations, both for DNA sequence (87.51%) and microsatellites (84.38%). Phylogeography based on a median-joining network analysis of the noncoding region showed a sharp difference from the analysis of microsatellite haplotypes. Nevertheless, both analyses indicated that multiple lineages may have contributed to the origin of C. brasiliense populations in Brazilian Cerrado. Incongruences in the microsatellite haplotypes network suggest that homoplasy, which emerged from recurrent and independent mutations, greatly influenced the evolution of the C. brasiliense chloroplast genome. We hypothesize that our results may show the outcome of the restriction of ancient relic populations to moist refugias during extended droughts coinciding with glaciation in the northern hemisphere. The subsequent spread to favourable areas throughout Central Brazil may have caused contact between different lineages during the interglacial periods. The extinction of megafauna dispersers in the last glaciation may have caused a restriction in seed movement and currently, gene flow has been occurring mainly by pollen movement.

  8. 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

  9. Identifying Distinct Geographic Health Service Environments in British Columbia, Canada: Cluster Analysis of Population-Based Administrative Data.

    PubMed

    Lavergne, M Ruth

    2016-08-01

    Definitions of "urban" and "rural" developed for general purposes may not reflect the organization and delivery of healthcare. This research used cluster analysis to group Local Health Areas based on the distribution of healthcare spending across service categories. Though total spending was similar, the metropolitan areas of Vancouver and Victoria were identified as distinct from non-metropolitan and remote communities, based on the distribution of healthcare spending alone. Non-metropolitan communities with large community hospitals and greater physician supply were further distinguished from those with fewer healthcare resources. This approach may be useful to other researchers and service planners. PMID:27585025

  10. Identifying Distinct Geographic Health Service Environments in British Columbia, Canada: Cluster Analysis of Population-Based Administrative Data.

    PubMed

    Lavergne, M Ruth

    2016-08-01

    Definitions of "urban" and "rural" developed for general purposes may not reflect the organization and delivery of healthcare. This research used cluster analysis to group Local Health Areas based on the distribution of healthcare spending across service categories. Though total spending was similar, the metropolitan areas of Vancouver and Victoria were identified as distinct from non-metropolitan and remote communities, based on the distribution of healthcare spending alone. Non-metropolitan communities with large community hospitals and greater physician supply were further distinguished from those with fewer healthcare resources. This approach may be useful to other researchers and service planners.

  11. 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

  12. Incidence, Surgical Treatment, and Prognosis of Anorectal Melanoma From 1973 to 2011: A Population-Based SEER Analysis.

    PubMed

    Chen, Haiyan; Cai, Yibo; Liu, Yue; He, Jinjie; Hu, Yeting; Xiao, Qian; Hu, Wangxiong; Ding, Kefeng

    2016-02-01

    Anorectal melanoma (AM) is a rare type of melanoma that accounts for 0.4% to 1.6% of total malignant melanomas. The incidence of AM increases over time, and it remains highly lethal, with a 5-year survival rate of 6% to 22%. Considering the rare nature of this disease, most studies on AM comprise isolated case reports and single-center trials, which could not provide comprehensive assessment of the disease. Therefore, we conducted a population-based study by using the Surveillance, Epidemiology, and End Results (SEER) program to provide the latest and best available evidence of AM.We extracted all cases of AM registered in the SEER database from 1973 to 2011 (April 2014 release) and calculated age-adjusted incidence. Only cases with active follow-up were included to predict factors associated with prognosis. Survival outcomes were also compared among different types of surgery.We identified 640 AM cases, which consisted of 265 rectal melanoma and 375 anal melanoma. The estimated annual incidence rates of AM per 1 million population were 0.259 in males and 0.407 in females, and it increased with advanced age and over time. Tumor stage and surgical treatment were independent predictors of survival. Results implied that surgery improved the prognosis of patients with local- and regional-stage AM but could not prolong the survival of patients with distant-stage AM. Moreover, the outcome of less extensive excision was not statistically different from that of more extensive excision.This study provides an up-to-date estimation of the incidence and prognosis of AM by using SEER data. The incidence of AM continuously increases over time, despite its rarity. This disease also exhibits poor prognosis. Thus, AM must be further investigated in future studies. We also recommend surgery as the optimal treatment for local- and regional-stage AM patients but not for those with distant metastasis.

  13. Incidence, Surgical Treatment, and Prognosis of Anorectal Melanoma From 1973 to 2011: A Population-Based SEER Analysis.

    PubMed

    Chen, Haiyan; Cai, Yibo; Liu, Yue; He, Jinjie; Hu, Yeting; Xiao, Qian; Hu, Wangxiong; Ding, Kefeng

    2016-02-01

    Anorectal melanoma (AM) is a rare type of melanoma that accounts for 0.4% to 1.6% of total malignant melanomas. The incidence of AM increases over time, and it remains highly lethal, with a 5-year survival rate of 6% to 22%. Considering the rare nature of this disease, most studies on AM comprise isolated case reports and single-center trials, which could not provide comprehensive assessment of the disease. Therefore, we conducted a population-based study by using the Surveillance, Epidemiology, and End Results (SEER) program to provide the latest and best available evidence of AM.We extracted all cases of AM registered in the SEER database from 1973 to 2011 (April 2014 release) and calculated age-adjusted incidence. Only cases with active follow-up were included to predict factors associated with prognosis. Survival outcomes were also compared among different types of surgery.We identified 640 AM cases, which consisted of 265 rectal melanoma and 375 anal melanoma. The estimated annual incidence rates of AM per 1 million population were 0.259 in males and 0.407 in females, and it increased with advanced age and over time. Tumor stage and surgical treatment were independent predictors of survival. Results implied that surgery improved the prognosis of patients with local- and regional-stage AM but could not prolong the survival of patients with distant-stage AM. Moreover, the outcome of less extensive excision was not statistically different from that of more extensive excision.This study provides an up-to-date estimation of the incidence and prognosis of AM by using SEER data. The incidence of AM continuously increases over time, despite its rarity. This disease also exhibits poor prognosis. Thus, AM must be further investigated in future studies. We also recommend surgery as the optimal treatment for local- and regional-stage AM patients but not for those with distant metastasis. PMID:26886623

  14. 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

  15. 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

  16. 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

  17. 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

  18. Genetic distances between popcorn populations based on molecular markers and correlations with heterosis estimates made by diallel analysis of hybrids.

    PubMed

    Munhoz, R E F; Prioli, A J; Amaral, A T; Scapim, C A; Simon, G A

    2009-01-01

    Diallel analysis was used to obtain information on combining ability, heterosis, estimates of genetic distances by random amplified polymorphic DNA (RAPD) and on their correlations with heterosis, for the popcorn varieties RS 20, UNB2, CMS 43, CMS 42, Zélia, UEM J1, UEM M2, Beija-Flor, and Viçosa, which were crossed to obtain all possible combinations, without reciprocals. The genitors and the 36 F(1) hybrids were evaluated in field trials in Maringá during two growing seasons in a randomized complete block design with three replications. Based on the results, strategies for further studies were developed, including the construction of composites by joining varieties with high general combining ability for grain yield (UNB2 and CMS 42) with those with high general combining ability for popping expansion (Zélia, RS 20 and UEM M2). Based on the RAPD markers, UEM J1 and Zélia were the most genetically distant and RS 20 and UNB2 were the most similar. The low correlation between heterosis and genetic distances may be explained by the random dispersion of the RAPD markers, which were insufficient for the exploitation of the popcorn genome. We concluded that an association between genetic dissimilarity and heterosis based only on genetic distance is not expected without considering the effect of dominant loci. PMID:19731196

  19. 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

  20. 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

  1. 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

  2. Conditional survival estimates improve over time for patients with advanced melanoma: results from a population-based analysis

    PubMed Central

    Xing, Yan; Chang, George J.; Hu, Chung-Yuan; Askew, Robert L.; Ross, Merrick I.; Gershenwald, Jeffrey E.; Lee, Jeffrey E.; Mansfield, Paul F.; Lucci, Anthony; Cormier, Janice N.

    2009-01-01

    Background Conditional survival (CS) has emerged as a clinically relevant measure of prognosis for cancer survivors. The objective of this analysis was to provide melanoma-specific CS estimates to help clinicians promote more informed patient decision-making. Methods Patients with melanoma and at least 5 years of follow-up were identified from the Surveillance Epidemiology and End Results (SEER) registry (1988–2000). Using the methods of Kaplan and Meier, stage-specific 5-year CS estimates were independently calculated for survivors for each year following diagnosis. Stage-specific multivariate Cox regression models including baseline survivor functions were used to calculate adjusted melanoma-specific CS for different subgroups of patients further stratified by age, gender, race, marital status, anatomic tumor location, and tumor histology. Results Five-year CS estimates for stage I patients remained constant at 97% annually, while for patients with stages II, III and IV disease, 5-year CS estimates from time 0 (diagnosis) to 5 years improved from 72% to 86%, 51% to 87%, and 19% to 84%, respectively. Multivariate CS analysis revealed that differences in stages II through IV CS based on age, gender and race decreased over time. Conclusions Five-year melanoma-specific CS estimates improve dramatically over time for survivors with advanced stages of disease. These prognostic data are critical to patients for both treatment and non-treatment related life decisions. PMID:20187100

  3. 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

  4. The association of GSTT1 deletion polymorphism with lung cancer risk among Chinese population: evidence based on a cumulative meta-analysis

    PubMed Central

    Wang, Yadong; Yang, Haiyan; Wang, Haiyu

    2015-01-01

    Objective Previous studies investigating the relationship between glutathione S-transferase T1 (GSTT1) gene deletion polymorphism and lung cancer risk among Chinese population produced inconsistent results. To obtain a precise conclusion, we performed this meta-analysis to evaluate the association between GSTT1 deletion polymorphism and lung cancer risk among Chinese population. Methods The databases of Medline/PubMed, Embase, Web of Science, Wanfang Med Online, and Chinese National Knowledge Infrastructure were searched. The strength of the association was assessed by odds ratio (OR) with 95% confidence intervals (95% CI). Results Overall, we found an increased lung cancer risk among subjects carrying GSTT1 null genotype compared with those carrying present genotype (OR =1.31, 95% CI: 1.12–1.52) on the basis of 20 studies with 3,351 cases and 4,683 controls. We also observed an increased risk of lung cancer among subjects carrying GSTT1 null genotype compared with those carrying present genotype in stratified analyses (OR =1.31, 95% CI: 1.11–1.55 for healthy subjects-based control; OR =2.29, 95% CI: 1.84–2.85 for squamous cell carcinoma and OR =1.47, 95% CI: 1.22–1.77 for adenocarcinoma, respectively). Conclusion This meta-analysis suggested that GSTT1 deletion polymorphism might contribute to lung cancer risk among Chinese population. PMID:26491361

  5. 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

  6. Price of pain: population-based cohort burden of disease analysis of medication cost of herpes zoster and postherpetic neuralgia

    PubMed Central

    Friesen, Kevin J; Falk, Jamie; Alessi-Severini, Silvia; Chateau, Dan; Bugden, Shawn

    2016-01-01

    Background Pain is a main symptom of herpes zoster (HZ), and postherpetic neuralgia (PHN) is a frequent complication occurring in 5% to 15% of cases, causing moderate to severe neuropathic pain. A population-based observational study was conducted to evaluate the treatment patterns and economic burden of prescription drug treatment of HZ and PHN pain in the province of Manitoba (Canada) over a period of 15 years. Methods Administrative health care data, including medical and hospital separation records, were examined to identify episodes of HZ using International Classification of Diseases-9/10 codes between April 1, 1997 and March 31, 2014. Episodes of PHN were identified using medical and prescription claims. Incident use of analgesic, antidepressant, or anticonvulsant drugs was used to determine prescription pain costs. Results The age-adjusted incidence of HZ increased from 4.7 episodes/1,000 person-years in 1997/98 to 5.7/1,000 person-years in 2013/14. PHN occurred in 9.2% of HZ cases, a rate that did not change over the study period (P=0.57). The annual cost to treat HZ pain rose by 174% from 1997/98, reaching CAD $332,981 in 2011/12, 82.8% (95% confidence interval [CI] 81.2%, 84.3%) of which was related to PHN. The per episode cost of HZ rose by 111% from $31.59 (95% CI $25.35, $37.84) to $66.81 (95% CI $56.84, $76.78) and by 94% for PHN from $292 (95% CI $225, $358) to $566 (95% CI $478, $655). These increases were driven by increasing use of anticonvulsants, primarily gabapentin, which accounted for 57% of the increase in cost. Conclusion There has been an increase in the incidence of HZ and PHN and in the average cost associated with the prescription treatment of their resultant neuropathic pain. The primary driver of the increased episodic cost is the increased use of gabapentin. These changes have resulted in a substantial increase in the economic burden associated with HZ and PHN. PMID:27536159

  7. 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.

  8. 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

  9. 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.

  10. Population databases in development analysis.

    PubMed

    Chamie, J

    1994-01-01

    Population databases are very important in formulating analyses of social and economic change and development. Since such analyses are often the basis for policy making and program formulation, it is important to have a sound understanding of their strengths and limitations. This paper focuses upon databases which deal with population size, life expectancy at birth, and infant mortality. Considerable progress has been made in producing population databases over the last several decades, but many problems remain with regard to their comparability, completeness of coverage, and accuracy. Governmental and political circumstances greatly influence the availability and quality of population databases. Globally, the comparability of data remains a serious concern due to deviations from standard definitions. The completeness of coverage of databases among less developed countries varies widely by region, while the data for preparing estimates and assessing demographic trends are deficient and problematic. Technological advances and the repackaging of population databases have greatly advanced their production and availability, but confusion and ignorance have become widespread regarding the original source and nature of the data. Database users therefore too often undertake faulty analyses which lead to false conclusions.

  11. 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.

  12. An image-based automatic mesh generation and numerical simulation for a population-based analysis of aerosol delivery in the human lungs

    NASA Astrophysics Data System (ADS)

    Miyawaki, Shinjiro; Tawhai, Merryn H.; Hoffman, Eric A.; Lin, Ching-Long

    2013-11-01

    The authors propose a method to automatically generate three-dimensional subject-specific airway geometries and meshes for computational fluid dynamics (CFD) studies of aerosol delivery in the human lungs. The proposed method automatically expands computed tomography (CT)-based airway skeleton to generate the centerline (CL)-based model, and then fits it to the CT-segmented geometry to generate the hybrid CL-CT-based model. To produce a turbulent laryngeal jet known to affect aerosol transport, we developed a physiologically-consistent laryngeal model that can be attached to the trachea of the above models. We used Gmsh to automatically generate the mesh for the above models. To assess the quality of the models, we compared the regional aerosol distributions in a human lung predicted by the hybrid model and the manually generated CT-based model. The aerosol distribution predicted by the hybrid model was consistent with the prediction by the CT-based model. We applied the hybrid model to 8 healthy and 16 severe asthmatic subjects, and average geometric error was 3.8% of the branch radius. The proposed method can be potentially applied to the branch-by-branch analyses of a large population of healthy and diseased lungs. NIH Grants R01-HL-094315 and S10-RR-022421, CT data provided by SARP, and computer time provided by XSEDE.

  13. Does heavy physical exertion trigger myocardial infarction? A case-crossover analysis nested in a population-based case-referent study.

    PubMed

    Hallqvist, J; Möller, J; Ahlbom, A; Diderichsen, F; Reuterwall, C; de Faire, U

    2000-03-01

    To study possible triggering of first events of acute myocardial infarction by heavy physical exertion, the authors conducted a case-crossover analysis (1993-1994) within a population-based case-referent study in Stockholm County, Sweden (the Stockholm Heart Epidemiology Program). Interviews were carried out with 699 myocardial infarction patients after onset of the disease. These cases represented 47 percent of all cases in the study base, and 70 percent of all nonfatal cases. The relative risk from vigorous exertion was 6.1 (95% confidence interval: 4.2, 9.0). The rate difference was 1.5 per million person-hours, and the attributable proportion was 5.7 percent. The risk was modified by physical fitness, with an increased risk being seen among sedentary subjects as in earlier studies, but the data also suggested a U-shaped association. In addition, the trigger effect was modified by socioeconomic status. Premonitory symptoms were common, and this implies risks of reverse causation bias and misclassification of case exposure information that require methodological consideration. Different techniques (the use of the usual-frequency type of control information, a pair-matched analysis, and a standard case-referent analysis) were applied to overcome the threat of misclassification of control exposure information. A case-crossover analysis in a random sample of healthy subjects resulted in a relative risk close to unity, as expected.

  14. 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.

  15. 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

    2015-01-01

    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. PMID:26662418

  16. 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.

  17. 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).

  18. [Genetic analysis of feather color and shank color traits based on F-2 resource population in Tibetan chicken].

    PubMed

    Wang, Cun-Fang; Li, Ning; Wu, Chang-Xin

    2006-07-01

    Tibetan chickens were crossed reciprocally with White Leghorn and Shou-Guang chicken respectively, and inter se matings in F1 were carried out to generate the F2 population. Feather color and shank color appearance and segregation ratio in F1 and F2 were observed. Results indicate that white feather of White Leghorn chicken and black feather of Shou-Guang chicken exhibit complete dominant heredity to hemp feather of Tibetan chicken. Hemp feather is determined by two or more alleles. Only when these two or more alleles are concurrently present, will hemp feather then be displayed. The Id/id allele that determines shank color demonstrates sex-linked inheritance, and the recessive id is expressed gradually in the homozygotes. We confirm that genotype of shank color in White Leghorn rooster used in this study is the dominant homozygote. PMID:16825167

  19. Sex prevalence of major congenital anomalies in the United Kingdom: A national population-based study and international comparison meta-analysis

    PubMed Central

    Sokal, Rachel; Tata, Laila J; Fleming, Kate M

    2014-01-01

    Background The aim of this study was to assess sex differences in major congenital anomaly (CA) diagnoses within a national population sample; to examine the influence of sociodemographic and maternal factors on these risks; and to conduct a meta-analysis using estimates from other population-based studies. Methods We conducted a population-based study in a United Kingdom research database of prospectively collected primary care data (The Health Improvement Network) including children born 1990 to 2009 (n = 794,169) and identified major CA diagnoses using EUROCAT (European Surveillance of Congenital Anomalies) classification. Prevalence ratios (PR) were used to estimate the risk of CA in males compared with females for any CA, system-specific subgroups and specific CA diagnoses. In a subpopulation of children whose medical records were linked to their mothers', we assessed the effect of adjusting for sociodemographic and maternal factors on sex odds ratios. PRs were pooled with measures from previously published studies. Results The prevalence of any CA was 307/10,000 in males (95% CI, 302–313) and 243/10,000 in females (95% CI, 238–248). Overall the risk of any CA was 26% greater in males (PR (male: female) 1.26, 95% CI, 1.23–1.30) however there was considerable variation across specific diagnoses. The magnitude and direction of risk did not change for any specific CA upon adjustment for sociodemographic and maternal factors. Our PRs were highly consistent with those from previous studies. Conclusion The overall risk of CA is greater in males than females, although this masked substantial variation by specific diagnoses. Sociodemographic and maternal factors do not appear to affect these risks. Birth Defects Research (Part A) 100:79–91, 2014. © 2014 Wiley Periodicals, Inc. PMID:24523198

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

    NASA Astrophysics Data System (ADS)

    Garcia, Ricardo A. C.; Oliveira, Sergio C.; Zezere, Jose L.

    2015-04-01

    Exposed Population is a major topic that needs to be taken into account in a full landslide risk analysis. Usually, risk analysis is based on an accounting of inhabitants number or inhabitants density, applied over statistical or administrative terrain units, such as NUTS or parishes. However, this kind of approach may skew the obtained results underestimating the importance of population, mainly in territorial units with predominance of rural occupation. Furthermore, the landslide susceptibility scores calculated for each terrain unit are frequently more detailed and accurate than the location of the exposed population inside each territorial unit based on Census data. These drawbacks are not the ideal setting when landslide risk analysis is performed for urban management and emergency planning. Dasymetric cartography, which uses a parameter or set of parameters to restrict the spatial distribution of a particular phenomenon, is a methodology that may help to enhance the resolution of Census data and therefore to give a more realistic representation of the population distribution. Therefore, this work aims to map and to compare the population distribution based on a traditional approach (population per administrative terrain units) and based on dasymetric cartography (population by building). The study is developed in the Region North of Lisbon using 2011 population data and following three main steps: i) the landslide susceptibility assessment based on statistical models independently validated; ii) the evaluation of population distribution (absolute and density) for different administrative territorial units (Parishes and BGRI - the basic statistical unit in the Portuguese Census); and iii) the dasymetric population's cartography based on building areal weighting. Preliminary results show that in sparsely populated administrative units, population density differs more than two times depending on the application of the traditional approach or the dasymetric

  1. 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.

  2. 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

  3. 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. PMID:25181553

  4. 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

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

    PubMed

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

    2016-06-01

    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.

  6. 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 ...

  7. Post-Acute Care Services Received by Older Adults Following a Cardiac Event: A Population-Based Analysis

    PubMed Central

    Xu, Fang; Zullo, Melissa; Shishehbor, Mehdi; Moore, Shirley M.; Rimm, Alfred A.

    2010-01-01

    Background Post-acute care (PAC) is available for older adults who need additional services after hospitalization for acute cardiac events. With the aging population and an increase in the prevalence of cardiac disease, it is important to determine current PAC use for cardiac patients to assist health care workers to meet the needs of older cardiac patients. The purpose of this study was to determine the current PAC use and factors associated with PAC use for older adults following hospitalization for a cardiac event that includes coronary artery bypass graph (CABG) and valve surgeries, myocardial infarction (MI), percutaneous coronary intervention (PCI), and heart failure (HF). Methods and Results A cross-sectional design and the 2003 Medicare Part A database were used for this study. The sample (n=1,493,521) consisted of patients aged 65 years and older discharged after their first cardiac event. Multinomial logistic regression was used to examine factors associated with PAC use. Overall, PAC use was 55% for cardiac valve surgery, 50% for MI, 45% for HF, 44% for CABG, and 5% for PCI. Medical patients use more skilled nursing facility care and surgical patients use more home health care. Only 0.1–3.4% of the cardiac patients use intermediate rehabilitation facilities. Compared to those who do not use PAC, those who use home health care and skilled nursing facility care are older, female, have a longer hospital length of stay, and more comorbidity. Asians, Hispanics and Native Americans were less likely to use PAC after hospitalization for an MI or HF. Conclusions The current rate of PAC use indicates that almost half of non-disabled Medicare patients discharged from the hospital following a cardiac event use one of these services. Healthcare professionals can increase PAC use for Asians, Hispanics and Native Americans by including culturally targeted communication. Optimizing recovery for cardiac patients who use PAC may require focused cardiac rehabilitation

  8. 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

    2015-01-01

    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.

  9. 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

  10. A general semi-parametric approach to the analysis of genetic association studies in population-based designs

    PubMed Central

    2013-01-01

    Background For genetic association studies in designs of unrelated individuals, current statistical methodology typically models the phenotype of interest as a function of the genotype and assumes a known statistical model for the phenotype. In the analysis of complex phenotypes, especially in the presence of ascertainment conditions, the specification of such model assumptions is not straight-forward and is error-prone, potentially causing misleading results. Results In this paper, we propose an alternative approach that treats the genotype as the random variable and conditions upon the phenotype. Thereby, the validity of the approach does not depend on the correctness of assumptions about the phenotypic model. Misspecification of the phenotypic model may lead to reduced statistical power. Theoretical derivations and simulation studies demonstrate both the validity and the advantages of the approach over existing methodology. In the COPDGene study (a GWAS for Chronic Obstructive Pulmonary Disease (COPD)), we apply the approach to a secondary, quantitative phenotype, the Fagerstrom nicotine dependence score, that is correlated with COPD affection status. The software package that implements this method is available. Conclusions The flexibility of this approach enables the straight-forward application to quantitative phenotypes and binary traits in ascertained and unascertained samples. In addition to its robustness features, our method provides the platform for the construction of complex statistical models for longitudinal data, multivariate data, multi-marker tests, rare-variant analysis, and others. PMID:23448186

  11. 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

  12. The United Nations manuals for population analysis.

    PubMed

    Isupov, A

    1986-01-01

    Between 1952 and 1983 the United Nations Secretariat, acting on the recommendations of the Population Commission, published 10 manuals on population analysis, evaluation and forecasting. The importance and utility of the manuals has been recognized by demographers and statisticians in a wide range of countries, especially those in the developing regions which do not yet have complete population statistics or a fully developed capability for evaluating demographic information. The manuals continue to be extensively used in both research and applied work on population. Research is being expanded and improvements are being made in population statistics and the technics of data calculation, in accordance with decisions made at the 1974 World Population Conference and the World Population Plan of Action adopted there, and with recommendations of the 1984 International Conference on Population. As a result, there is a growing need for the manuals to be updated and to present methods of conducting a more through analysis of demographic processes in association with economic and social factors, and for the subsequent derivation of, if possible, more realistic assumptions about future trends in population growth.

  13. 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.

  14. Widening access to medical education for under-represented socioeconomic groups: population based cross sectional analysis of UK data, 2002-6

    PubMed Central

    Mathers, Jonathan; Sitch, Alice; Marsh, Jennifer L

    2011-01-01

    Objective To determine whether new programmes developed to widen access to medicine in the United Kingdom have produced more diverse student populations. Design Population based cross sectional analysis. Setting 31 UK universities that offer medical degrees. Participants 34 407 UK medical students admitted to university in 2002-6. Main outcome measures Age, sex, socioeconomic status, and ethnicity of students admitted to traditional courses and newer courses (graduate entry courses (GEC) and foundation) designed to widen access and increase diversity. Results The demographics of students admitted to foundation courses were markedly different from traditional, graduate entry, and pre-medical courses. They were less likely to be white and to define their background as higher managerial and professional. Students on the graduate entry programme were older than students on traditional courses (25.5 v 19.2 years) and more likely to be white (odds ratio 3.74, 95% confidence interval 3.27 to 4.28; P<0.001) than those on traditional courses, but there was no difference in the ratio of men. Students on traditional courses at newer schools were significantly older by an average of 2.53 (2.41 to 2.65; P<0.001) years, more likely to be white (1.55, 1.41 to 1.71; P<0.001), and significantly less likely to have higher managerial and professional backgrounds than those at established schools (0.67, 0.61 to 0.73; P<0.001). There were marked differences in demographics across individual established schools offering both graduate entry and traditional courses. Conclusions The graduate entry programmes do not seem to have led to significant changes to the socioeconomic profile of the UK medical student population. Foundation programmes have increased the proportion of students from under-represented groups but numbers entering these courses are small. PMID:21343208

  15. Methyl coenzyme M reductase (mcrA) gene based phylogenetic analysis of methanogens population in Murrah buffaloes (Bubalus bubalis).

    PubMed

    Chaudhary, Prem Prashant; Sirohi, Sunil Kumar; Singh, Dheer; Saxena, Jyoti

    2011-08-01

    The aim of the present study was to decipher the diversity of methanogens in rumen of Murrah buffaloes so that effective strategies can be made in order to mitigate methane emission from these methanogens. In the present study diversity of rumen methanogens in Murrah buffaloes (Bubalus bubalis) from North India was evaluated by using mcr-A gene library obtained from the pooled PCR product from four animals and by using MEGA4 software. A total of 104 clones were examined, revealing 26 different mcr-A gene sequences or phylotypes. Of the 26 phylotypes, 16 (64 of 104 clones) were less than 97% similar to any of the cultured strain of methanogens. Seven clone sequences were clustered with Methanomicrobium mobile and three clone sequences were clustered with Methanobrevibacter gottschalkii during the phylogenetic analysis. Uncultured group of methanogens comes out to be the major component of the methanogens community structure in Murrah buffaloes. Methanomicrobium phylotype comes out to be major phylotype among cultured methanogens followed by Methanobrevibacter phylotype. These results help in making effective strategies to check the growth of dominant communities in the rumen of this animal which in turn help in the reduction of methane emission in the environment and ultimately helps us in fighting with the problem of global warming.

  16. Regional inequalities in under-5 mortality in Nigeria: a population-based analysis of individual- and community-level determinants

    PubMed Central

    2011-01-01

    Background Regions with geographically diverse ecology and socioeconomic circumstances may have different disease exposures and child health outcomes. This study assessed variations in the risks of death in children under age 5 across regions of Nigeria and determined characteristics at the individual and community levels that explain possible variations among regions. Methods Multilevel Cox proportional hazards analysis was performed using a nationally representative sample of 6,029 children from 2,735 mothers aged 15-49 years and nested within 365 communities from the 2003 Nigeria Demographic and Health Survey. Hazard ratios (HR) with 95% confidence intervals (CI) were used to express measures of association among the characteristics. Variance partition coefficients and Wald statistic were used to express measures of variation. Results Patterns of under-5 mortality cluster within families and communities. The risks of under-5 deaths were significantly higher for children of mothers residing in the South South (Niger Delta) region (HR: 1.30; 95% CI: 1.76-2.20) and children of mothers residing in communities with a low proportion of mothers attending prenatal care by a doctor (HR: 1.36; 95% CI: 1.15-1.86). In addition, the cross-level interaction between mothers' education and community prenatal care by a doctor was associated with a more than 40% higher risk of dying (HR: 1.41; 95% CI: 1.21-1.78). Conclusion The findings suggest the need to differentially focus on community-level interventions aimed at increasing maternal and child health care utilization and improving the socioeconomic position of mothers, especially in disadvantaged regions such as the South South (Niger Delta) region. Further studies on community-levels determinants of under-5 mortality are needed. PMID:21388522

  17. Bayesian analysis of genetic differentiation between populations.

    PubMed Central

    Corander, Jukka; Waldmann, Patrik; Sillanpää, Mikko J

    2003-01-01

    We introduce a Bayesian method for estimating hidden population substructure using multilocus molecular markers and geographical information provided by the sampling design. The joint posterior distribution of the substructure and allele frequencies of the respective populations is available in an analytical form when the number of populations is small, whereas an approximation based on a Markov chain Monte Carlo simulation approach can be obtained for a moderate or large number of populations. Using the joint posterior distribution, posteriors can also be derived for any evolutionary population parameters, such as the traditional fixation indices. A major advantage compared to most earlier methods is that the number of populations is treated here as an unknown parameter. What is traditionally considered as two genetically distinct populations, either recently founded or connected by considerable gene flow, is here considered as one panmictic population with a certain probability based on marker data and prior information. Analyses of previously published data on the Moroccan argan tree (Argania spinosa) and of simulated data sets suggest that our method is capable of estimating a population substructure, while not artificially enforcing a substructure when it does not exist. The software (BAPS) used for the computations is freely available from http://www.rni.helsinki.fi/~mjs. PMID:12586722

  18. 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.

  19. 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.

  20. 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

  1. A Cluster Analysis of Reported Sleeping Patterns of 9-Month Old Infants and the Association with Maternal Health: Results from a Population Based Cohort Study.

    PubMed

    Hughes, Aoife; Gallagher, Stephen; Hannigan, Ailish

    2015-08-01

    The aim of this study was to identify, using cluster analysis, novel sleep phenotypes in a population based cohort of infants, and to explore the associations between infant sleep profiles and their mothers' health and well-being. 11,134 mothers of 9-month old infants were interviewed as part of the Growing Up in Ireland National Longitudinal study and reported on their health and infant's sleep patterns. 16 infant sleep variables were recorded together with measures of parental stress, depression, health and well-being. Multiple iterations of a two-step hierarchical cluster analysis were carried out to identify the optimum number of clusters and the subset of parental-reported sleep variables required to identify distinct sleep profiles. Four distinct sleep profiles were identified based on the following variables; (1) infant sleep duration at night, (2) parental sleep duration, (3) does baby wake during night (yes, no)? (4) Usual sleep location for most of the night and, (5) parental reporting of problem infant sleep patterns. This identified two less favorable profiles with both infants and mothers sleeping less and where mothers are more likely to report their infants' sleep patterns as problematic. Mothers of infants belonging to these sleep profiles were more likely to have higher levels of stress, depressive symptoms, and poorer self-reported health than other sleep profiles. Breastfeeding was associated with both groups and rates were highest in a group of infants that were more likely to co-sleep with their parents and have diverse ethnic backgrounds. This study demonstrates, for the first time, two infant sleep profiles with distinct phenotypical frameworks that are significantly associated with maternal stress, depression, and poorer self-report of health.

  2. Variations in patient-reported physical health between cardiac and musculoskeletal diseases: systematic review and meta-analysis of population-based studies.

    PubMed

    Prior, James A; Jordan, Kelvin P; Kadam, Umesh T

    2015-01-01

    Population-based assessments of physical health are important to evaluate healthcare resource allocation. Normative data on the level of physical impairments attributable to specific diseases and severity levels within these diseases is critical to interpreting such data. Our objective, by means of a systematic review and meta-analysis, was to test the hypothesis that specific diseases which form cardiovascular and musculoskeletal disease spectra are associated with gradients of physical impairments. We examined a cardiovascular disease spectrum which consisted of hypertension, ischaemic heart disease and heart failure, and a musculoskeletal disease spectrum of lower back pain, osteoarthritis and rheumatoid arthritis. Using Medline, EMBASE and CINAHL databases, articles which had examined these morbidities and used either the SF-12 or SF-36 in general or primary care populations were selected; data was extracted independently by three reviewers. Study characteristics were described and the mean physical component summary scores of the SF-12 or SF-36 was analysed by disease, using random-effects meta-analysis. The association between disease and physical health (mean physical component summary scores) was assessed using multilevel meta-regression analysis, adjusting for age, health setting, country, disease definition and SF-12 or 36 format. From this search, 26 articles were identified, yielding 70 separate estimates of mean physical component summary scores across the morbidities from 14 different countries. For the selected conditions, pooled unadjusted mean physical component summary scores were: 44.4 for hypertension, 38.9 for ischaemic heart disease, 35.9 for heart failure, 39.5 for lower back pain, 36.0 for osteoarthritis and 36.5 for rheumatoid arthritis. The adjusted meta-regression showed mean physical component summary score difference for ischaemic heart disease of -4.6 (95 % confidence interval -6.0 to -3.2) and heart failure -7.5 (-9.1 to -5

  3. A statewide, population-based time-series analysis of the increasing frequency of nonoperative management of abdominal solid organ injury.

    PubMed Central

    Rutledge, R; Hunt, J P; Lentz, C W; Fakhry, S M; Meyer, A A; Baker, C C; Sheldon, G F

    1995-01-01

    Emergency operative intervention has been one of the cornerstones of the care of the injured patient. Over the past several years, nonoperative management has increasing been recommended for the care of selected blunt abdominal solid organ injuries. The purpose of this study was to utilize a large statewide, population-based data set to perform a time-series analysis of the practice of physicians caring for blunt solid organ injury of the abdomen. The study was designed to assess the changing frequency and the outcomes of operative and nonoperative treatments for blunt hepatic and splenic injuries. METHODS: Data were obtained from the state hospital discharge data base, which tracks information on all hospitalized patients from each of the 157 hospitals in the state of North Carolina. All trauma patients who had sustained injury to a solid abdominal organ (kidney, liver, or spleen) were selected for initial analysis. RESULTS: During the 5 years of the study, 210,256 trauma patients were admitted to the state's hospitals (42,051 +/- 7802 per year). The frequency of nonoperative interventions for hepatic and splenic injuries increased over the period studied. The frequency of nonoperative management of hepatic injuries increased from 55% in 1988 to 79% in 1992 in patients with hepatic injuries and from 34% to 46% in patients with splenic injuries. The rate of nonoperative management of hepatic injuries increased from 54% to 64% in nontrauma centers compared with an increase from 56% to 74% in trauma centers (p = 0.01). In patients with splenic injuries, the rate of nonoperative management increased from 35% to 44% in nontrauma centers compared with an increase from 33% to 49% in trauma centers (p < 0.05). The rate of nonoperative management was associated with the organ injury severity, ranging from 90% for minor injuries to 19%-40% for severe injuries. Finally, in an attempt to compare blood use in operatively and nonoperatively treated patients, the total charges

  4. 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.

  5. 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.

  6. 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. PMID:21481213

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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. PMID:26517499

  12. 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

    2016-10-01

    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. PMID:27435388

  13. 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

    2016-10-01

    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.

  14. Association of folate-pathway gene polymorphisms with the risk of prostate cancer: a population-based nested case-control study, systematic review, and meta-analysis.

    PubMed

    Collin, Simon M; Metcalfe, Chris; Zuccolo, Luisa; Lewis, Sarah J; Chen, Lina; Cox, Angela; Davis, Michael; Lane, J Athene; Donovan, Jenny; Smith, George Davey; Neal, David E; Hamdy, Freddie C; Gudmundsson, Julius; Sulem, Patrick; Rafnar, Thorunn; Benediktsdottir, Kristrun R; Eeles, Rosalind A; Guy, Michelle; Kote-Jarai, Zsofia; Morrison, Jonathan; Al Olama, Ali Amin; Stefansson, Kari; Easton, Douglas F; Martin, Richard M

    2009-09-01

    Folate-pathway gene polymorphisms have been implicated in several cancers and investigated inconclusively in relation to prostate cancer. We conducted a systematic review, which identified nine case-control studies (eight included, one excluded). We also included data from four genome-wide association studies and from a case-control study nested within the UK population-based Prostate Testing for Cancer and Treatment study. We investigated by meta-analysis the effects of eight polymorphisms: MTHFR C677T (rs1801133; 12 studies; 10,745 cases; 40,158 controls), MTHFR A1298C (rs1801131; 5 studies; 3,176 cases; 4,829 controls), MTR A2756G (rs1805087; 8 studies; 7,810 cases; 37,543 controls), MTRR A66G (rs1801394; 4 studies; 3,032 cases; 4,515 controls), MTHFD1 G1958A (rs2236225; 6 studies; 7,493 cases; 36,941 controls), SLC19A1/RFC1 G80A (rs1051266; 4 studies; 6,222 cases; 35,821 controls), SHMT1 C1420T (rs1979277; 2 studies; 2,689 cases; 4,110 controls), and FOLH1 T1561C (rs202676; 5 studies; 6,314 cases; 35,190 controls). The majority (10 of 13) of eligible studies had 100% Caucasian subjects; only one study had <90% Caucasian subjects. We found weak evidence of dominant effects of two alleles: MTR 2756A>G [random effects pooled odds ratio, 1.06 (1.00-1.12); P = 0.06 (P = 0.59 for heterogeneity across studies)] and SHMT1 1420C>T [random effects pooled odds ratio, 1.11 (1.00-1.22); P = 0.05 (P = 0.38 for heterogeneity across studies)]. We found no effect of MTHFR 677C>T or any of the other alleles in dominant, recessive or additive models, or in comparing a/a versus A/A homozygous. Neither did we find any difference in effects on advanced or localized cancers. Our meta-analysis suggests that known common folate-pathway single nucleotide polymorphisms do not have significant effects on susceptibility to prostate cancer. PMID:19706844

  15. Spatial uncertainty analysis of population models

    SciTech Connect

    Jager, Yetta; King, Anthony Wayne; Schumaker, Nathan; Ashwood, Tom L; Jackson, Barbara L

    2004-01-01

    This paper describes an approach for conducting spatial uncertainty analysis of spatial population models, and illustrates the ecological consequences of spatial uncertainty for landscapes with different properties. Spatial population models typically simulate birth, death, and migration on an input map that describes habitat. Typically, only a single reference map is available, but we can imagine that a collection of other, slightly different, maps could be drawn to represent a particular species' habitat. As a first approximation, our approach assumes that spatial uncertainty (i.e., the variation among values assigned to a location by such a collection of maps) is constrained by characteristics of the reference map, regardless of how the map was produced. Our approach produces lower levels of uncertainty than alternative methods used in landscape ecology because we condition our alternative landscapes on local properties of the reference map. Simulated spatial uncertainty was higher near the borders of patches. Consequently, average uncertainty was highest for reference maps with equal proportions of suitable and unsuitable habitat, and no spatial autocorrelation. We used two population viability models to evaluate the ecological consequences of spatial uncertainty for landscapes with different properties. Spatial uncertainty produced larger variation among predictions of a spatially explicit model than those of a spatially implicit model. Spatially explicit model predictions of final female population size varied most among landscapes with enough clustered habitat to allow persistence. In contrast, predictions of population growth rate varied most among landscapes with only enough clustered habitat to support a small population, i.e., near a spatially mediated extinction threshold. We conclude that spatial uncertainty has the greatest effect on persistence when the amount and arrangement of suitable habitat are such that habitat capacity is near the minimum

  16. 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

  17. MTHFR gene A1298C polymorphisms are associated with breast cancer risk among Chinese population: evidence based on an updated cumulative meta-analysis

    PubMed Central

    Wang, Yadong; Yang, Haiyan; Duan, Guangcai

    2015-01-01

    Objectives: Published studies on the association between methylenetetrahydrofolate reductase (MTHFR) gene A1298C polymorphisms and breast cancer risk among Chinese population have yielded conflicting results. The purpose of this study was to clarify the association between MTHFR gene A1298C polymorphisms and breast cancer risk among Chinese population. Methods: Systematic searches were performed through the database of Medline/PubMed, Science Direct, Elsevier, CNKI and Wanfang Medical Online. Results: Overall, a significantly increased risk of breast cancer was observed among the subjects carrying MTHFR gene A1298C AC+CC genotype (odds ratio [OR]=1.05 with 95% confidence interval [CI]: 1.01-1.10) as compared to those carrying AA genotype among total Chinese population. We did not observe any significant association between MTHFR gene A1298C polymorphisms and the risk of breast cancer under the additional genetic models of AC vs. AA, CC vs. AA and C-allele vs. A-allele (OR=1.00 with 95% CI: 0.97-1.02, OR=1.01 with 95% CI: 1.00-1.02 and OR=1.00 with 95% CI: 0.99-1.02, respectively). The cumulative meta-analysis showed similar results. In subgroup analysis, we observed subjects carrying AC+CC genotype had an increased breast cancer risk compared with those carrying AA genotype among the studies of sample size less than 1000. We did not observe any significant association between MTHFR gene A1298C polymorphisms and breast cancer risk in additional subgroup analyses. Conclusions: Our results suggest that MTHFR gene A1298C AC+CC genotype may be a risk factor for the development of breast cancer among Chinese population. Well-designed studies with a large sample size are needed to further confirm our findings. PMID:26884927

  18. 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

  19. 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.

  20. 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. PMID:26699457

  1. 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

    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.

  2. 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

  3. Racial Disparities in Treatment Rates for Chronic Hepatitis C: Analysis of a Population-Based Cohort of 73,665 Patients in the United States.

    PubMed

    Vutien, Philip; Hoang, Joseph; Brooks, Louis; Nguyen, Nghia H; Nguyen, Mindie H

    2016-05-01

    Chronic hepatitis C (CHC) disproportionately affects racial minorities in the United States (US). Although prior studies have reported lower treatment rates in Blacks than in Caucasians, the rates of other minorities remain understudied. We aimed to examine antiviral treatment rates by race and to evaluate the effect of other demographic, medical, and psychiatric factors on treatment rates. We performed a population-based study of adult CHC patients identified via ICD-9CM query from OptumInsight's Data Mart from January 2009 to December 2013. Antiviral treatment was defined by pharmaceutical claims for interferon and/or pegylated-interferon. A total of 73,665 insured patients were included: 51,282 Caucasians, 10,493 Blacks, 8679 Hispanics, and 3211 Asians. Caucasians had the highest treatment rate (10.7%) followed by Blacks (8.8%), Hispanics (8.8%), and Asians (7.9%, P < .001). Hispanics had the highest cirrhosis rates compared with Caucasians, Blacks, and Asians (20.7% vs 18.3%, 17.1%, and 14.3%, respectively). Caucasians were the most likely to have a psychiatric comorbidity (20.1%) and Blacks the most likely to have a medical comorbidity (44%). Asians were the least likely to have a psychiatric (6.4%) or medical comorbidity (26.9%). On multivariate analysis, racial minority was a significant predictor of nontreatment with odds ratios of 0.82 [confidence interval (CI): 0.74-0.90] for Blacks, 0.87 (CI: 0.78-0.96) for Hispanics, and 0.73 (CI: 0.62-0.86) for Asians versus Caucasians. Racial minorities had lower treatment rates than Caucasians. Despite fewer medical and psychiatric comorbidities and higher incomes and educational levels, Asians had the lowest treatment rates. Hispanics also had lower treatment rates than Caucasians despite having higher rates of cirrhosis. Future studies should aim to identify underlying racial-related barriers to hepatitis C virus treatment besides socioeconomic status and medical or psychiatric comorbidities. PMID:27258498

  4. 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

  5. A microsatellite-based analysis for the detection of selection on BTA1 and BTA20 in northern Eurasian cattle (Bos taurus) populations

    PubMed Central

    2010-01-01

    Hitchhiking due to tight linkage with alleles at candidate genes, e.g. the POLL gene, is a possible explanation for this pattern. The potential impact of selective breeding by man on cattle populations is discussed in the context of selection effects. Our results also suggest that a practical approach to detect loci under selection is to simultaneously apply multiple neutrality tests based on different assumptions and estimations. PMID:20691068

  6. 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 Central

    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. PMID:24971357

  7. Oral Sex and HPV: Population Based Indications.

    PubMed

    Mishra, Anupam; Verma, Veerendra

    2015-03-01

    Human pappilloma virus (HPV) is well established in etiology of uterine cervical cancers, but its role in head and neck cancer is strongly suggested through many epidemiological and laboratory studies. Although HPV-16 induced oropharyngeal cancer is a distinct molecular entity, its role at other sub-sites (oral cavity, larynx, nasopharynx, hypopharynx) is less well established. Oral sex is supposedly the most commonly practiced unnatural sex across the globe and may prove to be a potential transmitting link between cancers of the uterine cervix and the oropharynx in males particularly in those 10-15% non-smokers. In India with the second largest population (higher population density than China) the oral sex is likely to be a common 'recreation-tool' amongst the majority (poor) and with the concurrent highly prevalent bad cervical/oral hygiene the HPV is likely to synergize other carcinogens. Hence in accordance (or coincidently), in India the cervical cancer happens to be the commonest cancer amongst females while oral/oropharyngeal cancer amongst males. Oral sex as a link between these two cancer types, can largely be argued considering a poor level of evidence in the existing literature. The modern world has even commercialized oral sex in the form of flavored condoms. The inadequate world literature currently is of a low level of evidence to conclude such a relationship because no such specific prospective study has been carried out and also due to wide (and unpredictable) variety of sexual practices, such a relationship can only be speculated. This article briefly reviews the existing literature on various modes and population based indications for HPV to be implicated in head and neck cancer with reference to oral sexual practice.

  8. Characteristics and analysis of simple sequence repeats in the cotton genome based on a linkage map constructed from a BC1 population between Gossypium hirsutum and G. barbadense.

    PubMed

    Zhang, Yanxin; Lin, Zhongxu; Xia, Qizhong; Zhang, Mingju; Zhang, Xianlong

    2008-07-01

    In the past decade, several molecular maps of cotton have been constructed using diverse DNA molecular markers and mapping populations. In this study, an interspecific linkage map of allotetraploid cotton was developed using a BC1 population ((Gossypium hirsutum x G. barbadense) x G. hirsutum). This map was genome-wide and was based entirely on simple sequence repeat (SSR) markers. Forty-four linkage groups were assigned to 26 chromosomes, with 917 loci spanning 5452.2 cM of the genome. The average distance between loci was 5.9 cM, providing uniform coverage of the A subgenome and D subgenome. Characteristics of this map were analyzed in detail, including the distributions of genomic SSRs, expressed sequence tag (EST)-SSRs, and distorted markers. Furthermore, the relationships between motif characteristics (size, type, length) and the level of polymorphism in EST-SSRs were also surveyed. The results showed that tetranucleotide and dinucleotide repeats had similar levels of polymorphism, and ACAT, AC, and ACT repeats had the highest polymorphism rates. Loci with lengths of 27 bp, 33 bp, and 24 bp were more likely to be polymorphic. This work will provide information to assist in designing future EST-SSRs.

  9. Collaborations in Population-Based Health Research

    PubMed Central

    Lieu, Tracy A.; Hinrichsen, Virginia L.; Moreira, Andrea; Platt, Richard

    2011-01-01

    The HMO Research Network (HMORN) is a consortium of 16 health care systems with integrated research centers. Approximately 475 people participated in its 17th annual conference, hosted by the Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School. The theme, “Collaborations in Population-Based Health Research,” reflected the network’s emphasis on collaborative studies both among its members and with external investigators. Plenary talks highlighted the initial phase of the HMORN’s work to establish the NIH-HMO Collaboratory, opportunities for public health collaborations, the work of early career investigators, and the state of the network. Platform and poster presentations showcased a broad spectrum of innovative public domain research in areas including disease epidemiology and treatment, health economics, and information technology. Special interest group sessions and ancillary meetings provided venues for informal conversation and structured work among ongoing groups, including networks in cancer, cardiovascular diseases, lung diseases, medical product safety, and mental health. PMID:22090515

  10. Analysis of a Population-Based Pneumocystis carinii Pneumonia Index as an Outcome Measure of Access and Quality of Care for the Treatment of HIV Disease

    PubMed Central

    Arno, Peter S.; Gourevitch, Marc N.; Drucker, Ernest; Fang, Jing; Goldberg, Clara; Memmott, Margaret; Bonuck, Karen; Deb, Nandini; Schoenbaum, Ellie

    2002-01-01

    Objectives. A population-based Pneumocystis carinii pneumonia (PCP) Index was developed in New York City to identify geographic areas and subpopulations at increased risk for PCP. Methods. A zip code–level PCP Index was created from AIDS surveillance and hospital discharge records and defined as (number of PCP-related hospitalizations)/(number of persons living with AIDS). Results. In 1997, there were 2262 hospitalizations for PCP among 39 740 persons living with AIDS in New York City (PCP Index = .05691). PCP Index values varied widely across neighborhoods with high AIDS prevalence (West Village = .02532 vs Central Harlem = .08696). Some neighborhoods with moderate AIDS prevalence had strikingly high rates (Staten Island = .14035; northern Manhattan = .08756). Conclusions. The PCP Index highlights communities in particular need of public health interventions to improve HIV-related service delivery. (Am J Public Health. 2002;92:395–398) PMID:11867318

  11. 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

  12. 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.

  13. Educational level, prevalence of hysterectomy, and age at amenorrhoea: a cross-sectional analysis of 9536 women from six population-based cohort studies in Germany

    PubMed Central

    2014-01-01

    Background Hysterectomy prevalence has been shown to vary by education level. Hysterectomy influences age at amenorrhoea. The aim of this study was to examine these associations in Germany within population-based data sets. Methods Baseline assessments in six population-based cohorts took place from 1997 through 2006 and included 9,548 women aged 20–84 years. All studies assessed hysterectomy history, school and professional degrees. Degrees were categorized into three levels each. Adjusted prevalence ratios and 95% confidence intervals (95% CI) were estimated. Results Prevalences were higher in West Germany than East Germany, increased by age, and leveled off starting at 55–64 years. The age- and study-adjusted prevalence ratio (lowest versus highest school level) was 2.61 (95% CI: 1.28-5.30), 1.48 (95% CI: 1.21-1.81), and 1.01 (95% CI: 0.80-1.28) for women aged 20–45, 45–64, and 65 and more years respectively. The estimated adjusted prevalence ratios per one unit decrement of the educational qualification score (range 1 = lowest, 8 = highest) were 1.29 (95% CI: 1.02-1.64), 1.08 (95% CI: 1.04-1.12), and 0.98 (95% CI: 0.93-1.03) for women aged 20–44, 45–64, and 65–84 years respectively. Age at amenorrhoea was on average 6.2 years lower (43.5 years versus 49.7 years) among women with a history of hysterectomy than those without. Conclusions Lower educational level was associated with a higher hysterectomy prevalence among women aged 20–64 years. Several mediators associated with educational level and hysterectomy including women’s disease risk, women’s treatment preference, and women’s access to uterus-preserving treatment may explain this association. At population level, hysterectomy decreases the age of amenorrhoea on average by 6.2 years. PMID:24433474

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

    PubMed

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

    2014-05-01

    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

  15. 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

  16. The fatty acid binding protein 2 (FABP2) polymorphism Ala54Thr and obesity in Pakistan: A population based study and a systematic meta-analysis.

    PubMed

    Shabana; Hasnain, Shahida

    2015-12-10

    The prevalence of obesity has increased worldwide and it has been designated as a global epidemic by WHO. In Pakistan, recent decades have seen an explosion of obesity, but the research in the field of obesity genetics is limited. We aimed to determine the allele/genotype frequencies of Ala54Thr polymorphism of the FABP2 gene that affects fatty acid metabolism and look for its association on serum biochemical parameters in the Pakistani population. A total of 569 obese and 446 non obese controls were genotyped by PCR-RFLP method. Serum parameters were determined by commercially available kits. Results showed a higher allele frequency of Thr54 allele in cases (0.424) as well as controls (0.331) than Caucasians (0.271). The risk allele was significantly associated with obesity (p=0.002) and there was a significant difference in allele and genotype frequencies among cases and controls (p=0.002). The risk allele is significantly associated with serum total cholesterol and LDL-c but not triglycerides, HDL-c, leptin, systolic/diastolic blood pressure and insulin. The Ala54Thr polymorphism has a high prevalence in the Pakistani population and may play a considerable role in the development of obesity. The effect on obesity may be in part mediated through changing serum cholesterol levels. We then performed a systematic search for any previous reports on the association of the variant with obesity. We identified 5 studies for Ala54Thr association with obesity in Asian subjects. The meta-analysis revealed a significant association of the variant with obesity (Thr allele: OR=1.15, CI=1.02-1.30 and p-value=0.02).

  17. 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

  18. 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

  19. Is Emmetropia the Natural Endpoint for Human Refractive Development? An Analysis of Population-based Data from the Refractive Error Study in Children (RESC)

    PubMed Central

    Morgan, Ian G.; Rose, Kathryn A.; Ellwein, Leon B.

    2009-01-01

    Purpose To determine the natural end-point for refractive development during childhood. Methods Cycloplegic (1% cyclopentolate) autorefraction was performed on 38,811 children aged 5 and 15 in population-based samples at eight sites in the Refractive Error Study in Children (RESC). Refractions (right eye) were categorized as myopic (≤ −0.5D), emmetropic (> −0.5D to ≤ +0.5D), mildly hyperopic (> +0.5D to ≤ +2.0D and hyperopic (> +2.0D). Results At 5 sites (Jhapa – rural Nepal, New Delhi -urban India, Mahabubnagar - rural India, Durban - semi-urban South Africa, and La Florida – urban Chile), there was <20% myopia by age 15. Mild hyperopia was the most prevalent category at all ages, except for Mahabubnagar where emmetropia became the marginally most prevalent category at ages 14 and 15. At the other sites (Gombak – semi-urban Malaysia, Shunyi – semi-rural China, and Guangzhou - urban China) there was substantial (>35%) myopia by age 15. At these sites, mild hyperopia was the most prevalent category during early childhood, and myopia became the predominant category later. In Gombak district and Guangzhou, emmetropia was a minor category at all ages, with myopia increasing as mild hyperopia decreased. In Shunyi district, emmetropia was the most prevalent category over the ages 11-14. Conclusion Emmetropia was not the predominant outcome for refractive development in children. Instead, populations were either predominantly mildly hyperopic, or substantial amounts of myopia appeared. This suggests that mild hyperopia is the natural state of refractive development in children, and that emmetropia during childhood carries the risk of subsequent progression to myopia. PMID:19958289

  20. 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.

  1. 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.

  2. 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. PMID:23450090

  3. 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

    2016-01-01

    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. PMID:27525883

  4. 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.

  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. 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.

  7. 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

  8. 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

  9. Spoligotype-based comparative population structure analysis of multidrug-resistant and isoniazid-monoresistant Mycobacterium tuberculosis complex clinical isolates in Poland.

    PubMed

    Jagielski, Tomasz; Augustynowicz-Kopec, Ewa; Zozio, Thierry; Rastogi, Nalin; Zwolska, Zofia

    2010-11-01

    The spoligotyping-based population structure of multidrug-resistant (MDR) Mycobacterium tuberculosis strains isolated in Poland (n = 46), representing all culture-positive MDR tuberculosis (MDR-TB) cases, was compared to that of isoniazid (INH)-monoresistant strains (n = 71) isolated in 2004. The latter data set from a previous study (E. Augustynowicz-Kopeć, T. Jagielski, and Z. Zwolska, J. Clin. Microbiol. 2008, 46:4041-4044) represented 87% of all INH-monoresistant strains. The clustering rates and genotypic-diversity indexes for the 2 subpopulations were not significantly different (P = 0.05). The results were entered in the SITVIT2 database to assign specific shared type designations, corresponding genotypic lineages, and geographical distributions and compared to available data from neighboring countries (Germany, n = 704; Czech Republic, n = 530; Sweden, n = 379; Kaliningrad, Russia, n = 90) and strains from previous studies in Poland (n = 317). MDR strains resulted in 27 patterns (20 unique strains within the study and 7 clusters containing 2 to 6 isolates per cluster with a clustering rate of 56.5%) and belonged to the following genotypic lineages: ill-defined T family (28.3%), Haarlem (17.4%), Latin American and Mediterranean (LAM) (13%), Beijing (8.7%), S family (4.35%), and the X clade (2.17%). Comparison of the genetic structure of the MDR strains with that of INH-monoresistant strains showed that a total of 9 patterns were shared by both groups; these represented 1/3 of the MDR strains and 2/3 of the INH-monoresistant strains. Interestingly, 76.1% of the MDR isolates and 71.8% of the INH-resistant isolates yielded spoligotypes that were previously reported from Poland. The observation that nearly half of the spoligotypes identified among both MDR (48.1%) and INH-monoresistant (43.3%) M. tuberculosis isolates were present in Poland's neighboring countries suggested that a significant proportion of MDR and INH-resistant TB cases in Poland were caused by

  10. Multi-site time series analysis of acute effects of multiple air pollutants on respiratory mortality: a population-based study in Beijing, China.

    PubMed

    Yang, Yang; Cao, Yang; Li, Wenjing; Li, Runkui; Wang, Meng; Wu, Zhenglai; Xu, Qun

    2015-03-01

    In large cities in China, the traffic-related air pollution has become the focus of attention, and its adverse effects on health have raised public concerns. We conducted a study to quantify the association between exposure to three major traffic-related pollutants - particulate matter < 10 μm in aerodynamic diameter (PM10), carbon monoxide (CO) and nitrogen dioxide (NO2) and the risk of respiratory mortality in Beijing, China at a daily spatiotemporal resolution. We used the generalized additive models (GAM) with natural splines and principal component regression method to associate air pollutants with daily respiratory mortality, covariates and confounders. The GAM analysis adjusting for the collinearity among pollutants indicated that PM10, CO and NO2 had significant effects on daily respiratory mortality in Beijing. An interquartile range increase in 2-day moving averages concentrations of day 0 and day 1 of PM10, CO and NO2 corresponded to 0.99 [95% confidence interval (CI): 0.30, 1.67], 0.89 (95% CI: 0.27, 1.51) and 0.95 (95% CI: 0.29, 1.61) percent increase in daily respiratory mortality, respectively. The effects were varied across the districts. The strongest effects were found in two rural districts and one suburban district but significant in only one district. In conclusion, high level of several traffic-related air pollutants is associated with an increased risk of respiratory mortality in Beijing over a short-time period. The high risk found in rural areas suggests a potential susceptible sub-population with undiagnosed respiratory diseases in these areas. Although the rural areas have relatively lower air pollution levels, they deserve more attention to respiratory disease prevention and air pollution reduction.

  11. Serum 25-hydroxyvitamin D levels and incident diabetes mellitus type 2: a competing risk analysis in a large population-based cohort of older adults.

    PubMed

    Schöttker, Ben; Herder, Christian; Rothenbacher, Dietrich; Perna, Laura; Müller, Heiko; Brenner, Hermann

    2013-03-01

    Plausible mechanisms of how vitamin D deficiency may contribute to the development of diabetes mellitus have been proposed but longitudinal cohort studies have yielded heterogeneous results. In 7,791 initially diabetes-free participants of a German population-based cohort, aged 50-74 years, adjusted Cox regression models were employed to estimate hazard ratios (HR) with 95 % confidence intervals (CI) for the association of serum 25-hydroxyvitamin D (25(OH)D) quintiles and incident diabetes. Dose-response relationships were assessed with restricted cubic spline curves. Additionally, analyses accounting for the competing risks of diabetes and death were performed. During 8 years of follow-up, 829 study participants developed diabetes. In women, diabetes risk was significantly increased in the lowest 25(OH)D quintile (HR, 1.38; 1.09-1.75) and non-significantly increased in the 2nd quintile (HR, 1.24; 0.98-1.55) compared to women in 25(OH)D quintiles 3-5. The dose-response relationship showed a non-linear inverse association with risk starting to increase at 25(OH)D levels below 70 nmol/L (statistically significant: below 40 nmol/L). In men, 25(OH)D levels were not associated with diabetes incidence. Renal dysfunction was an effect modifier with a more than doubled diabetes risk in 25(OH)D quintile 1 and an about 1.5-fold risk in quintile 2 compared to quintiles 3-5 if subjects had renal dysfunction. The observed associations were not influenced by the competing risk of death. In this large cohort study of older adults, serum 25(OH)D levels were inversely associated with incident diabetes in women but not in men. The association was particularly strong in subjects with renal dysfunction.

  12. 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.

  13. Population and Economics: A Bioeconomic Analysis.

    ERIC Educational Resources Information Center

    Daly, Herman E.

    1992-01-01

    The notion of optimal population is recast as a problem of optimal scale (population times per capita resource use). Considers bioeconomic limits to scale. Discusses the choice between many people at low resource use per capita versus fewer people at higher resource per capita and suggests a policy that serves both efficiency and sufficiency.…

  14. 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

  15. 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. PMID:26816162

  16. 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.

  17. 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

    2015-10-01

    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. PMID:26492258

  18. 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.

  19. 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

  20. 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

  1. 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

  2. Role of radiation therapy in primary mediastinal large B-cell lymphoma in rituximab era: A US population-based analysis.

    PubMed

    Giri, Smith; Bhatt, Vijaya Raj; Pathak, Ranjan; Bociek, R Gregory; Vose, Julie M; Armitage, James O

    2015-11-01

    The use of radiation (RT) in primary mediastinal large B-cell lymphoma (PMBCL) may predispose young patients to the risk of cardiopulmonary toxicities and secondary malignancies. We used Surveillance, Epidemiology and End Results (SEER) 18 database to compare the overall survival (OS) differences among adult patients treated with and without RT after rituximab approval in the US. Multivariate analyses were performed using Cox proportional hazards regression to compare OS based on the use of RT while adjusting for age, year of diagnosis, race, stage and gender. PMBCL patients (n = 258), who received RT (48%), were similar in terms of age, gender, race, and stage at diagnosis to patients who did not receive RT. The five year OS was similar between patients treated with versus without RT (82.5% vs. 78.6%, P = 0.47). In a multivariate analysis, the use of RT did not influence OS in the rituximab era (HR 0.83; 95% CI 0.43-1.59; P = 0.56). Rituximab may reduce the benefit of RT in select patients such as those who achieve a metabolic complete remission at the end of chemotherapy. PMID:26270899

  3. 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.

  4. Human hair neutron activation analysis: Analysis on population level, mapping

    NASA Astrophysics Data System (ADS)

    Zhuk, L. I.; Kist, A. A.

    1999-01-01

    Neutron activation analysis is an outstanding analytical method having very wide applications in various fields. Analysis of human hair within last decades mostly based on neutron activation analysis is a very attractive illustration of the application of nuclear analytical techniques. Very interesting question is how the elemental composition differs in different areas or cities. In this connection the present paper gives average data and maps of various localities in the vicinity of drying-out Aral Sea and of various industrial cities in Central Asia.

  5. A population-based study of large granular lymphocyte leukemia

    PubMed Central

    Shah, M V; Hook, C C; Call, T G; Go, R S

    2016-01-01

    Large granular lymphocyte (LGL) leukemia is a lymphoproliferative disorder of cytotoxic cells. T-cell LGL (T-LGL) leukemia is characterized by accumulation of cytotoxic T cells in blood and infiltration of the bone marrow, liver or spleen. Population-based studies have not been reported in LGL leukemia. We present clinical characteristics, natural history and risk factors for poor survival in patients with LGL leukemia using the Surveillance, Epidemiology, and End Results Program (SEER) and the United States National Cancer Data Base (NCDB). LGL leukemia is an extremely rare disease with the incidence of 0.2 cases per 1 000 000 individuals. The median age at diagnosis was 66.5 years with females likely to be diagnosed at 3 years earlier compared with males. Analysis of patient-level data using NCDB (n=978) showed that 45% patients with T-LGL leukemia required some form of systemic treatment at the time of diagnosis. T-LGL leukemia patients have reduced survival compared with general population, with a median overall survival of 9 years. Multivariate analysis showed that age >60 years at the time of diagnosis and the presence of significant comorbidities were independent predictors of poor survival. PMID:27494824

  6. Motor Phenotype of Decline in Cognitive Performance among Community-Dwellers without Dementia: Population-Based Study and Meta-Analysis

    PubMed Central

    Beauchet, Olivier; Allali, Gilles; Montero-Odasso, Manuel; Sejdić, Ervin; Fantino, Bruno; Annweiler, Cédric

    2014-01-01

    Background Decline in cognitive performance is associated with gait deterioration. Our objectives were: 1) to determine, from an original study in older community-dwellers without diagnosis of dementia, which gait parameters, among slower gait speed, higher stride time variability (STV) and Timed Up & Go test (TUG) delta time, were most strongly associated with lower performance in two cognitive domains (i.e., episodic memory and executive function); and 2) to quantitatively synthesize, with a systematic review and meta-analysis, the association between gait performance and cognitive decline (i.e., mild cognitive impairment (MCI) and dementia). Methods Based on a cross-sectional design, 934 older community-dwellers without dementia (mean±standard deviation, 70.3±4.9years; 52.1% female) were recruited. A score at 5 on the Short Mini-Mental State Examination defined low episodic memory performance. Low executive performance was defined by clock-drawing test errors. STV and gait speed were measured using GAITRite system. TUG delta time was calculated as the difference between the times needed to perform and to imagine the TUG. Then, a systematic Medline search was conducted in November 2013 using the Medical Subject Heading terms “Delirium,” “Dementia,” “Amnestic,” “Cognitive disorders” combined with “Gait” OR “Gait disorders, Neurologic” and “Variability.” Findings A total of 294 (31.5%) participants presented decline in cognitive performance. Higher STV, higher TUG delta time, and slower gait speed were associated with decline in episodic memory and executive performances (all P-values <0.001). The highest magnitude of association was found for higher STV (effect size  =  −0.74 [95% Confidence Interval (CI): −1.05;−0.43], among participants combining of decline in episodic memory and in executive performances). Meta-analysis underscored that higher STV represented a gait biomarker in patients with MCI (effect size  =  0

  7. 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

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

    USGS Publications Warehouse

    Link, W.A.; Royle, J. Andrew; Hatfield, J.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.

  9. 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

  10. Endometrial cancer and antidepressants: A nationwide population-based study.

    PubMed

    Lin, Chiao-Fan; Chan, Hsiang-Lin; Hsieh, Yi-Hsuan; Liang, Hsin-Yi; Chiu, Wei-Che; Huang, Kuo-You; Lee, Yena; McIntyre, Roger S; Chen, Vincent Chin-Hung

    2016-07-01

    To our knowledge, the association between antidepressant exposure and endometrial cancer has not been previously explored. Herein, we aim to investigate the association between antidepressant prescription, including novel antidepressants, and the risk for endometrial cancer in a population-based study.Data for the analysis were derived from National Health Insurance Research Database. We identified 8392 cases with a diagnosis of endometrial cancer and 82,432 matched controls. A conditional logistic regression model was used, with adjusting for potentially confounding variables (e.g., comorbid psychiatric diseases, comorbid physical diseases, and other medications). Risk for endometrial cancer in the population-based study sample was categorized by, and assessed as a function of, antidepressant prescription and cumulative dosage.We report no association between endometrial cancer incidence and antidepressant prescription, including those prescribed either selective serotonin reuptake inhibitors (adjusted odds ratio [OR] = 0.98; 95% confidence interval [CI], 0.84-1.15) or serotonin norepinephrine reuptake inhibitors (adjusted OR = 1.14; 95% CI, 0.76-1.71). We also did not identify an association between higher cumulative doses of antidepressant prescription and endometrial cancer.There was no association between antidepressant prescription and endometrial cancer. PMID:27442640

  11. Age- and Gender-Based Populations

    MedlinePlus

    ... societal benefits of prevention, treatment, and recovery for mental and substance use disorders. Popular Programs, Campaigns, & Initiatives National Registry of Evidence-based Programs and Practices (NREPP) Medication-Assisted Treatment (MAT) Too Smart To ...

  12. 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.

  13. 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.

  14. 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. PMID:23899430

  15. 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.

  16. Family-based analysis of tumor necrosis factor and lymphotoxin-α tag polymorphisms with type 1 diabetes in the population of South Croatia

    PubMed Central

    Boraska, Vesna; Zeggini, Eleftheria; Groves, Christopher J.; Rayner, Nigel W.; Škrabić, Veselin; Diakite, Mahamadou; Rockett, Kirk A.; Kwiatkowski, Dominic; McCarthy, Mark I.; Zemunik, Tatijana

    2009-01-01

    Tumor necrosis factor (TNF) and lymphotoxin-α (LTA) are cytokines with a wide range of inflammatory and immunomodulatory activities. Type 1 diabetes is an autoimmune disease characterized by destruction of insulin-producing pancreatic β cells. The aim of the present study was to evaluate the association of polymorphisms in the TNF/LTA gene region with susceptibility to type 1 diabetes. We investigated 11 TNF/LTA tag polymorphisms, designed to capture the majority of common variation in the region, in 160 trio families from South Croatia. We observed overtransmission of alleles from parents to affected child at five variants: (rs909253, allele C, p = 1.2×10−4; rs1041981, allele A, p = 1.1×10−4; rs1800629 (G-308A), allele A, p = 1.2×10−4; rs361525(G-238A), allele G, p = 8.2×10−3 and rs3093668, allele G, p = 0.014). We also identified overtransmission of the rs 1800629(G-308A)-rs361525(G-238A) A-G haplotype, p = 2.384×10−5. The present study found an association of the TNF/LTA gene region with type 1 diabetes. A careful assessment of TNF/LTA variants adjusted for linkage disequilibrium with HLA loci is needed to further clarify the role of these genes in type 1 diabetes susceptibility in the population of South Croatia. PMID:19167443

  17. 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.

  18. 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.

  19. Comparative Analysis of State Fish Consumption Advisories Targeting Sensitive Populations

    PubMed Central

    Scherer, Alison C.; Tsuchiya, Ami; Younglove, Lisa R.; Burbacher, Thomas M.; Faustman, Elaine M.

    2008-01-01

    Objective Fish consumption advisories are issued to warn the public of possible toxicological threats from consuming certain fish species. Although developing fetuses and children are particularly susceptible to toxicants in fish, fish also contain valuable nutrients. Hence, formulating advice for sensitive populations poses challenges. We conducted a comparative analysis of advisory Web sites issued by states to assess health messages that sensitive populations might access. Data sources We evaluated state advisories accessed via the National Listing of Fish Advisories issued by the U.S. Environmental Protection Agency. Data extraction We created criteria to evaluate advisory attributes such as risk and benefit message clarity. Data synthesis All 48 state advisories issued at the time of this analysis targeted children, 90% (43) targeted pregnant women, and 58% (28) targeted women of childbearing age. Only six advisories addressed single contaminants, while the remainder based advice on 2–12 contaminants. Results revealed that advisories associated a dozen contaminants with specific adverse health effects. Beneficial health effects of any kind were specifically associated only with omega-3 fatty acids found in fish. Conclusions These findings highlight the complexity of assessing and communicating information about multiple contaminant exposure from fish consumption. Communication regarding potential health benefits conferred by specific fish nutrients was minimal and focused primarily on omega-3 fatty acids. This overview suggests some lessons learned and highlights a lack of both clarity and consistency in providing the breadth of information that sensitive populations such as pregnant women need to make public health decisions about fish consumption during pregnancy. PMID:19079708

  20. 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.

  1. Big Data for Population-Based Cancer Research

    PubMed Central

    Meyer, Anne-Marie; Olshan, Andrew F.; Green, Laura; Meyer, Adrian; Wheeler, Stephanie B.; Basch, Ethan; Carpenter, William R.

    2016-01-01

    The Integrated Cancer Information and Surveillance System (ICISS) facilitates population-based cancer research by developing extensive information technology systems that can link and manage large data sets. Taking an interdisciplinary “team science” approach, ICISS has developed data, systems, and methods that allow researchers to better leverage the power of big data to improve population health. PMID:25046092

  2. 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...

  3. Time Trend Analysis of Cancer‏ Incidence in Caspian Sea, 2004 – 2009: A Population-based Cancer Registries Study (northern Iran)

    PubMed Central

    Salehiniya, Hamid; Ghobadi Dashdebi, Sakineh; Rafiemanesh, Hosein; Mohammadian-Hafshejani, Abdollah; Enayatrad, Mostafa

    2016-01-01

    Background: Cancer is a major public health problem in the world. In Iran especially after a transition to a dynamic and urban community, the pattern of cancer has changed significantly. An important change occurred regarding the incidence of cancer at the southern shores of the Caspian Sea, including Gilan, Mazandaran and Golestan province. This study was designed it investigate the epidemiology and changes in trend of cancer incidence in the geographic region of the Caspian Sea (North of Iran). Methods: Data were collected from Cancer Registry Center report of Iran health deputy. Trends of incidence were analyzed by joinpoint regression analysis. Results: During the study period year (2004-2009), 33,807 cases of cancer had been recorded in three provinces of Gilan, Mazandran and Golstan. Joinpoint analysis indicated a significant increase in age-standardized incidence rates (ASR) with an average annual percentage change (AAPC) 10.3, 8.5 and 5.2 in Gilan, Mazandaran and Golestan, respectively. The most common cancer in these provinces were correspondingly cancer of stomach, breast, skin, colorectal and bladder, respectively. Conclusion: The incidence of cancer tends to be increasing in North of Iran. These findings warrant the epidemiologic studies are helpful in planning preventive programs and recognition of risk factors. PMID:26958329

  4. A Lifetime Prevalence of Comorbidity Between Bipolar Affective Disorder and Anxiety Disorders: A Meta-analysis of 52 Interview-based Studies of Psychiatric Population

    PubMed Central

    Nabavi, Behrouz; Mitchell, Alex J.; Nutt, David

    2015-01-01

    Background Bipolar affective disorder has a high rate of comorbidity with a multitude of psychiatric disorders and medical conditions. Among all the potential comorbidities, co-existing anxiety disorders stand out due to their high prevalence. Aims To determine the lifetime prevalence of comorbid anxiety disorders in bipolar affective disorder under the care of psychiatric services through systematic review and meta-analysis. Method Random effects meta-analyses were used to calculate the lifetime prevalence of comorbid generalised anxiety disorder, panic disorder, social anxiety disorder, specific phobia, agoraphobia, obsessive compulsive disorder and posttraumatic stress disorder in bipolar affective disorder. Results 52 studies were included in the meta-analysis. The rate of lifetime comorbidity was as follows: panic disorder 16.8% (95% CI 13.7–20.1), generalised anxiety disorder 14.4% (95% CI 10.8–18.3), social anxiety disorder13.3% (95% CI 10.1–16.9), post-traumatic stress disorder 10.8% (95% CI 7.3–14.9), specific phobia 10.8% (95% CI 8.2–13.7), obsessive compulsive disorder 10.7% (95% CI 8.7–13.0) and agoraphobia 7.8% (95% CI 5.2–11.0). The lifetime prevalence of any anxiety disorders in bipolar disorder was 42.7%. Conclusions Our results suggest a high rate of lifetime concurrent anxiety disorders in bipolar disorder. The diagnostic issues at the interface are particularly difficult because of the substantial symptom overlap. The treatment of co-existing conditions has clinically remained challenging. PMID:26629535

  5. Dynamic analysis of a parasite population model

    NASA Astrophysics Data System (ADS)

    Sibona, G. J.; Condat, C. A.

    2002-03-01

    We study the dynamics of a model that describes the competitive interaction between an invading species (a parasite) and its antibodies in an living being. This model was recently used to examine the dynamical competition between Tripanosoma cruzi and its antibodies during the acute phase of Chagas' disease. Depending on the antibody properties, the model yields three types of outcomes, corresponding, respectively, to healing, chronic disease, and host death. Here, we study the dynamics of the parasite-antibody interaction with the help of simulations, obtaining phase trajectories and phase diagrams for the system. We show that, under certain conditions, the size of the parasite inoculation can be crucial for the infection outcome and that a retardation in the stimulated production of an antibody species may result in the parasite gaining a definitive advantage. We also find a criterion for the relative sizes of the parameters that are required if parasite-generated decoys are indeed to help the invasion. Decoys may also induce a qualitatively different outcome: a limit cycle for the antibody-parasite population phase trajectories.

  6. Genetic analysis of population differentiation and adaptation in Leuciscus waleckii.

    PubMed

    Chang, Yumei; Tang, Ran; Sun, Xiaowen; Liang, Liqun; Chen, Jinping; Huang, Jinfeng; Dou, Xinjie; Tao, Ran

    2013-12-01

    Demographic events and natural selection both influence animal phenotypic and genetic variation; exploring the effects of demography and selection on population divergence is of great significance in evolutionary biology. To uncover the causes behind the patterns of genetic differentiation and adaptation among six populations of Leuciscus waleckii from Dali Basin (two populations, alkaline vs. freshwater) and Amur Basin (four populations, freshwater rivers vs. alkaline lake), a set of 21 unlinked polymorphic microsatellite markers and two mitochondrial DNA sequences (Cytb and D-loop) were applied to examine whether populations from different environments or habitats have distinct genetic differentiation and whether alkalinity is the major factor that caused population divergence. Bayesian analysis and principal component analysis as well as haplotype network analysis showed that these populations are primarily divided into two groups, which are congruent with geographic separation but not inconsistent with the habitat environment (alkalinity). Using three different approaches, outlier detection indicated that one locus, HLJYL017, may be under directional selection and involved in local adaptation processes. Overall, this study suggested that demographic events and selection of local environmental conditions including of alkalinity are jointly responsible for population divergence. These findings constitute an important step towards the understanding of the genetic basis of differentiation and adaptation, as well as towards the conservation of L. waleckii.

  7. Trends and prognoses of dental status in the Swedish population: analysis based on interviews in 1975 to 1997 by Statistics Sweden.

    PubMed

    Osterberg, T; Carlsson, G E; Sundh, V

    2000-08-01

    The aims of this study were to describe changes in dental status over the 22-year period from 1975 to 1997, and to make a prognosis of dental status based on these data for the years 2005 and 2015. The study is based on regular investigations of the living conditions performed by Statistics Sweden of samples varying between 11,582 and 14,964 participants and a response rate from 78% to 86%. The questions of the interview used in this study were focused on dental status and utilization of dental services. The prevalence of edentulism in the age group 25-74 years decreased from 19% in 1975 to 3% in 1996/97. The proportion of dentate persons increased from 75% in 1975 to 97% in 1996/97 in age group 45-64 years with similar trends in the other age groups. In 1996/97, 2.1% of the whole sample (16-84 years) reported that they had received implant-supported restorations. The rate was higher among the elderly and the edentulous subjects. The great regional differences in dental status found in the first part of the observation period remained only in the oldest age group in 1996/97. The prognosis predicts that 95% of the subjects in age group 65-74 years and 90% in age group 75-84 years will be dentate in the year 2015. The substantial increase of dentate subjects among the elderly that has occurred during the past few decades and its expected continuation in the coming years implies a great change in need and demand for dental care services.

  8. Prevalence and risk factors for erectile dysfunction and lower urinary tract symptoms in Russian Federation men: analysis from a national population-based multicenter study.

    PubMed

    Korneyev, I A; Alexeeva, T A; Al-Shukri, S H; Bernikov, A N; Erkovich, A A; Kamalov, A A; Kogan, M I; Pavlov, V N; Zhuravlev, V N; Pushkar, D Y

    2016-01-01

    An analysis of prevalence and associated common risk factors of ED and lower urinary tract symptoms (LUTS) was performed in Russian Federation by cross-sectional multicenter survey. International Index of Erectile Function (IIEF) score and International Prostate Symptom Score (IPSS) were used for data collection in 1225 men between 20 and 77 years interviewed in six regions of Russian Federation. In addition, each participant's social, demographic, lifestyle, sexual and medical history was taken with special emphasis on risk factors for ED. Upon the basis of IIEF erectile domain score interpretation, ED was found in 530 (48.9%) men, consisting of mild and mild to moderate, moderate and severe ED in 375 (34.6%), 78 (7.2%) and 77 (7.1%) respondents, respectively. According to IPSS assessment, LUTSs were present in 649 (59.9%) responders; inclusive 370 (34.2%), 216 (19.9%) and 63 (5.8%) men with mild, moderate and severe LUTS, respectively. Men with both ED and LUTS shared common co-morbidities and lifestyle risk factors with age-adjusted odds ratio between 1.2 and 5.2. In logistic regression model (R(2)=0.361), the strongest associated with ED factor found was IPSS symptom score, followed by hypertension, IPSS-related quality of life, age, diabetes mellitus, obesity and unmotivated fatigue. PMID:26865104

  9. Prevalence and risk factors for erectile dysfunction and lower urinary tract symptoms in Russian Federation men: analysis from a national population-based multicenter study.

    PubMed

    Korneyev, I A; Alexeeva, T A; Al-Shukri, S H; Bernikov, A N; Erkovich, A A; Kamalov, A A; Kogan, M I; Pavlov, V N; Zhuravlev, V N; Pushkar, D Y

    2016-01-01

    An analysis of prevalence and associated common risk factors of ED and lower urinary tract symptoms (LUTS) was performed in Russian Federation by cross-sectional multicenter survey. International Index of Erectile Function (IIEF) score and International Prostate Symptom Score (IPSS) were used for data collection in 1225 men between 20 and 77 years interviewed in six regions of Russian Federation. In addition, each participant's social, demographic, lifestyle, sexual and medical history was taken with special emphasis on risk factors for ED. Upon the basis of IIEF erectile domain score interpretation, ED was found in 530 (48.9%) men, consisting of mild and mild to moderate, moderate and severe ED in 375 (34.6%), 78 (7.2%) and 77 (7.1%) respondents, respectively. According to IPSS assessment, LUTSs were present in 649 (59.9%) responders; inclusive 370 (34.2%), 216 (19.9%) and 63 (5.8%) men with mild, moderate and severe LUTS, respectively. Men with both ED and LUTS shared common co-morbidities and lifestyle risk factors with age-adjusted odds ratio between 1.2 and 5.2. In logistic regression model (R(2)=0.361), the strongest associated with ED factor found was IPSS symptom score, followed by hypertension, IPSS-related quality of life, age, diabetes mellitus, obesity and unmotivated fatigue.

  10. A population genetic analysis of chloroplast DNA in wild populations of Prunus avium L. in Europe.

    PubMed

    Mohanty, A; Martín, J P; Aguinagalde, I

    2001-10-01

    A population genetic study of chloroplast DNA was carried out in 23 wild populations of Prunus avium sampled from several European deciduous forests. An analysis of approx. 9% of the chloroplast genome detected mostly insertion-deletion mutations and one point mutation. In all, 16 haplotypes were detected. Six haplotypes were shared by two or more populations and 10 were unique. One haplotype was present in 21 of the 23 populations and 161 of 211 individuals, which probably indicates its ancient origin. The level of population subdivision, using unordered and ordered alleles, was low, GSTC=0.29 and NSTC=0.33, respectively. The difference between GSTC and NSTC is nonsignificant, indicating an absence of correlation between haplotype phylogeny and geographical distribution. The absence of phylogeographic structure in wild cherry may be attributed to long distance gene flow among populations by birds, animals and anthropogenic activities. The minimum-length spanning tree depicting the phylogenetic relationships between the haplotypes indicates the possible existence of two lineages represented by the haplotypes H3 and H4. The information about homogeneity or heterogeneity of populations in terms of haplotype constitution and detection of rare haplotypes in some populations will be useful for formulation of conservation and management strategies of wild cherry.

  11. 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

  12. The influence of neighborhood socioeconomic status and race on survival from ovarian cancer: a population-based analysis of Cook County, Illinois

    PubMed Central

    Brewer, Katherine C.; Peterson, Caryn E.; Davis, Faith G.; Hoskins, Kent; Pauls, Heather; Joslin, Charlotte E.

    2015-01-01

    Purpose Despite significant improvements in treatment for ovarian cancer, survival is poorer for non-Hispanic black (NHB) women compared to non-Hispanic white (NHW) women. Neighborhood socioeconomic status (SES) has been implicated in racial disparities across a variety of health outcomes and may similarly contribute to racial disparities in ovarian cancer survival. The purpose of this analysis is to assess the influence of neighborhood SES on NHB-NHW survival differences after accounting for differences in tumor characteristics and in treatment. Methods Data were obtained from 2432 women (443 NHB and 1989 NHW) diagnosed with epithelial ovarian cancer in Cook County, Illinois between 1998 and 2007. Neighborhood (i.e., census tract) SES at the time of diagnosis was calculated for each woman using two well-established composite measures of affluence and disadvantage. Cox proportional hazard models measured the association between NHB race and survival after adjusting for age, tumor characteristics, treatment, year of diagnosis, and neighborhood SES. Results There was a strong association between ovarian cancer survival and both measures of neighborhood SES (P < .0001 for both affluence and disadvantage). After adjusting for age, tumor characteristics, treatment, and year of diagnosis, NHB were more likely than NHW to die of ovarian cancer (hazard ratio [HR] = 1.47, 95% confidence interval [CI]: 1.28–1.68). The inclusion of neighborhood affluence and disadvantage into models separately and together attenuated this risk (HRaffluence = 1.37, 95% CI: 1.18 –1.58; HRdisadvantage = 1.28, 95% CI: 1.08–1.52; and HRaffluence + disadvantage = 1.28, 95% CI: 1.08–1.52. Conclusions Neighborhood SES, as measured by composite measures of affluence and disadvantage, is a predictor of survival in women diagnosed with ovarian cancer in Cook County, Illinois and may contribute to the racial disparity in survival. PMID:25986734

  13. 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

  14. 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.

  15. Resolving discrepancies between deterministic population models and individual-based simulations.

    PubMed

    Wilson, W G

    1998-02-01

    This work ties together two distinct modeling frameworks for population dynamics: an individual-based simulation and a set of coupled integrodifferential equations involving population densities. The simulation model represents an idealized predator-prey system formulated at the scale of discrete individuals, explicitly incorporating their mutual interactions, whereas the population-level framework is a generalized version of reaction-diffusion models that incorporate population densities coupled to one another by interaction rates. Here I use various combinations of long-range dispersal for both the offspring and adult stages of both prey and predator species, providing a broad range of spatial and temporal dynamics, to compare and contrast the two model frameworks. Taking the individual-based modeling results as given, two examinations of the reaction-dispersal model are made: linear stability analysis of the deterministic equations and direct numerical solution of the model equations. I also modify the numerical solution in two ways to account for the stochastic nature of individual-based processes, which include independent, local perturbations in population density and a minimum population density within integration cells, below which the population is set to zero. These modifications introduce new parameters into the population-level model, which I adjust to reproduce the individual-based model results. The individual-based model is then modified to minimize the effects of stochasticity, producing a match of the predictions from the numerical integration of the population-level model without stochasticity. PMID:18811412

  16. 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

  17. 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

  18. 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

    2016-01-01

    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

  19. Localization of specialized intestinal metaplasia and the molecular alterations in Barrett esophagus in a Japanese population: an analysis of biopsy samples based on the "Seattle" biopsy protocol.

    PubMed

    Fukui, Shota; Watari, Jiro; Tomita, Toshihiko; Yamasaki, Takahisa; Okugawa, Takuya; Kondo, Takashi; Kono, Tomoaki; Tozawa, Katsuyuki; Ikehara, Hisatomo; Ohda, Yoshio; Oshima, Tadayuki; Fukui, Hirokazu; Das, Kiron M; Miwa, Hiroto

    2016-05-01

    It remains unclear why Barrett esophagus (BE)-associated adenocarcinoma (EAC) frequently occurs in the 0 to 3 o'clock area of the BE. The aims of this study were to clarify the localization of specialized intestinal metaplasia (SIM) as a precancerous lesion and of molecular alterations among different locations using 4-quadrant biopsies based on the "Seattle" protocol. We prospectively evaluated microsatellite instability; methylation status at the APC, CDKN2A, hMLH1, RUNX3, and MGMT genes; the immunoreactivity of the monoclonal antibody Das-1 for the colonic phenotype; and Ki-67 staining in 10 early EACs and 128 biopsy samples from 32 BE patients. Among the molecular changes, only APC gene hypermethylation was an independent predictive marker of EAC (odds ratio, 24.4; P = .01). SIM was more frequently identified in the 0 to 3 o'clock quadrant than in the 6 to 9 o'clock quadrant (P = .08). The Ki-67 index was higher in SIM than in the columnar-lined epithelium (CLE) without goblet cells (P < .0001) and in both SIM and CLE with Das-1 reactivity than in those without (P = .04 and P = .06, respectively). Furthermore, the index was relatively higher in the 0 to 3 o'clock quadrant than in the 6 to 9 o'clock quadrant in cases with Das-1 reactivity. RUNX3 methylation was more frequently found in SIM than in CLE (P = .04), whereas the incidence of the other biomarkers did not show a significant difference between the 0 to 3 o'clock and 6 to 9 o'clock areas, nor between SIM and CLE. SIM with Das-1 reactivity, but not molecular alterations, in the 0 to 3 o'clock quadrant may have higher proliferative activity compared to the other areas of the BE. PMID:27067780

  20. Global analysis of population growth and river water quality

    NASA Astrophysics Data System (ADS)

    Wen, Yingrong; Schoups, Gerrit; van de Giesen, Nick

    2014-05-01

    Human-related pressures on river water quality are a concern of global proportions.. However, little is known about the more specific impact of increasing population on river water quality and how it provides a vital environmental reference for water management. Combining global gridded data on population and river discharge with digitized river networks, we conduct numerical simulations to demonstrate the direct impact of population growth on river water quality. Our model traces the transport, dilution, and degradation of anthropogenic organic matter (BOD) emissions into rivers. Spanning the period from the early 20th century to the present, our analysis indicates that the pressure on downstream river networks markedly increased since the population explosion starting in 1950, especially in developing countries. The ratio of population to river discharge reveals the link between impact severity and dilution capacity. In addition, a denser population is found to be correlated with higher impact severity. Consideration of direct population influences on global river water quality becomes limited as society develops and should be studied as a fundamental reference for human-related river water management. Keywords: Population growth, River water quality, Space-time analysis, Human activities, Water Management

  1. 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

  2. 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. PMID:26383256

  3. 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

  4. A clinically based prognostic index for diffuse large B-cell lymphoma with a cut-off at 70 years of age significantly improves prognostic stratification: population-based analysis from the Danish Lymphoma Registry.

    PubMed

    Gang, Anne O; Pedersen, Michael; d'Amore, Francesco; Pedersen, Lars M; Jensen, Bo A; Jensen, Paw; Møller, Michael B; Mourits-Andersen, Hans T; Pedersen, Robert S; Klausen, Tobias W; de N Brown, Peter

    2015-01-01

    The introduction of rituximab and generally improved health among elderly patients have increased the survival of patients with diffuse large B-cell lymphoma (DLBCL). The International Prognostic Index (IPI) from 1992 is based on pre-rituximab data from clinical trials including several lymphoma subtypes. We applied IPI factors to a population-based rituximab-treated cohort of 1990 patients diagnosed 2000-2010 and explored new factors and the optimal prognostic age cut-off for DLBCL. Multivariate-analyses (MVA) confirmed the prognostic value of all IPI factors except the presence of > 1 extranodal lesion. The optimal age cut-off was 70 years. In a MVA of albumin, lymphocyte count, sex, immunoglobulin G, bulky disease, hemoglobin and B-symptoms, only albumin was prognostic. We propose: (1) a modified DLBCL prognostic index (DLBCL-PI) including: age (70 years), performance status (PS), lactate dehydrogenase (LDH), stage and albumin level, and (2) a separate age-adjusted DLBCL-PI for patients ≤ 70 years including PS, LDH, albumin level and > 1 extranodal lesion, however excluding stage.

  5. 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.

  6. The genetic structure of Oreochromis spp. (Tilapia) populations in Malaysia as revealed by microsatellite DNA analysis.

    PubMed

    Bhassu, S; Yusoff, K; Panandam, J M; Embong, W K; Oyyan, S; Tan, S G

    2004-08-01

    The genetic make-up of five populations of Oreochromis spp. was examined by microsatellite analysis. Eleven polymorphic microsatellite loci showed significant departures from the Hardy-Weinberg equilibrium. The mean heterozygosity ranged from 0.6280 to 0.7040 for each population. The genetic distance values showed a clear separation between O. niloticus and O. mossambicus. The differentiation of the O. niloticus populations was then tested with various genetic measures, which are based on both the Infinite Allele and the Stepwise Mutation models. All these measures grouped the populations similarly. PMID:15487586

  7. The relationship between the cranial base and jaw base in a Chinese population

    PubMed Central

    2014-01-01

    Introduction The cranial base plays an important role in determining how the mandible and maxilla relate to each other. This study assessed the relationship between the cranial base and jaw base in a Chinese population. Methods This study involved 83 subjects (male: 27; female: 56; age: 18.4 ± 4.2 SD years) from Hong Kong, who were classified into 3 sagittal discrepancy groups on the basis of their ANB angle. A cephalometric analysis of the angular and linear measurements of their cranial and jaw bases was carried out. The morphological characteristics of the cranial and jaw bases in the three groups were compared and assessments were made as to whether a relationship existed between the cranial base and the jaw base discrepancy. Results Significant differences were found in the cranial base angles of the three groups. Skeletal Class II cases presented with a larger NSBa, whereas skeletal Class III cases presented with a smaller NSBa (P < 0.001). In the linear measurement, skeletal Class III cases presented with a shorter NBa than skeletal Class I and II cases (P < 0.01). There was a correlation between the cranial base angle NSBa and the SNB for the whole sample, (r = -0.523, P < 0.001). Furthermore, correlations between SBaFH and Wits (r = -0.594, P < 0.001) and SBaFH and maxillary length (r = -0.616, P < 0.001) were more obvious in the skeletal Class III cases. Conclusions The cranial base appears to have a certain correlation with the jaw base relationship in a southern Chinese population. The correlation between cranial base and jaw base tends to be closer in skeletal Class III cases. PMID:25129070

  8. 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

  9. 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

  10. Population based mortality surveillance in carbon products manufacturing plants.

    PubMed Central

    Teta, M J; Ott, M G; Schnatter, A R

    1987-01-01

    The utility of a population based, corporate wide mortality surveillance system was evaluated after a 10 year observation period of one of the company's divisions. The subject population, 2219 white male, long term employees from Union Carbide Corporation's carbon based electrode and specialty products operations, was followed up for mortality from 1974 to 1983. External comparisons with the United States male population were supplemented with internal comparisons among subgroups of the study population, defined by broad job categories and time related variables, adjusting for important correlates of the healthy worker effect. Significant deficits of deaths were observed for all causes and the major non-cancer causes of death. The numbers of deaths due to malignant neoplasms and respiratory cancer were less than, but not statistically different from, expected. There was a non-significant excess of deaths from lymphopoietic cancer, occurring predominantly among salaried employees. When specific locations were examined, operations with potential exposure to coal tar products exhibited a mortality pattern similar to that of the total cohort. The risk for lung cancer was significantly raised (five observed, 1.4 expected) in one small, but older, location which did not involve coal tar products during the period of employment of these individuals, but which historically used asbestos materials for several unique applications. Although these findings are limited by small numbers and a short observation period, the population based surveillance strategy has provided valuable information regarding the mortality experience of the population, directions for future research, and the allocation of epidemiological resources. PMID:3593661

  11. 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.

  12. 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.

  13. Preliminary assessment of aerial photography techniques for canvasback population analysis

    USGS Publications Warehouse

    Munro, R.E.; Trauger, D.L.

    1976-01-01

    Recent intensive research on the canvasback has focused attention on the need for more precise estimates of population parameters. During the 1972-75 period, various types of aerial photographing equipment were evaluated to determine the problems and potentials for employing these techniques in appraisals of canvasback populations. The equipment and procedures available for automated analysis of aerial photographic imagery were also investigated. Serious technical problems remain to be resolved, but some promising results were obtained. Final conclusions about the feasibility of operational implementation await a more rigorous analysis of the data collected.

  14. 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. PMID:22653866

  15. 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.

  16. Nested cladistic analysis of Brazilian populations of Drosophila serido.

    PubMed

    de Brito, Reinaldo A; Manfrin, Maura H; Sene, Fabio M

    2002-01-01

    The effects of Quaternary climatic cycles were investigated in Drosophila serido, a Brazilian cactophilic fly widely distributed outside the Amazonian region. Previous studies have indicated this species displays remarkable karyotypic, male genitalia, and mtDNA variation, so much so that it has been described as a species complex, or superspecies. In the present study we expand the analysis of the mtDNA COI gene on D. serido populations, particularly in central Brazil, by obtaining DNA sequences from 248 individuals distributed across 47 localities. This allowed us to perform a nested clade analysis to discriminate historical from recurrent forces shaping the evolution of D. serido populations. The nested analysis indicates one event of past fragmentation separating populations from south and central Brazil (referred to as type B) from populations in central and northeast Brazil (type D) and 15 other significant events. The most common outcome of our analysis was contiguous range expansion and we discuss why this was expected in D. serido. Our data indicate that D. serido has been distributed across Brazil at least since the Mid-Pleistocene, which contradicts the hypothesis of current distribution being determined by last glaciation cycle. Nonetheless, we present evidence that climatic cycles during the Quaternary and before have had a significant impact on the differentiation of D. serido in Brazil. Our study confirms the usefulness of the nested clade analysis for disentangling the effects of historical and present-day forces shaping the evolution and distribution of a taxon.

  17. Microsatellite analysis of genetic variation in black bear populations.

    PubMed

    Paetkau, D; Strobeck, C

    1994-10-01

    Measuring levels of genetic variation is an important aspect of conservation genetics. The informativeness of such measurements is related to the variability of the genetic markers used; a particular concern in species, such as bears, which are characterized by low levels of genetic variation resulting from low population densities and small effective population sizes. We describe the development of microsatellite analysis in bears and its use in assessing interpopulation differences in genetic variation in black bears from three Canadian National Parks. These markers are highly variable and allowed identification of dramatic differences in both distribution and amount of variation between populations. Low levels of variation were observed in a population from the Island of Newfoundland. The significance of interpopulation differences in variability was tested using a likelihood ratio test of estimates of theta = 4Ne mu.

  18. Image-driven population analysis through mixture modeling.

    PubMed

    Sabuncu, Mert R; Balci, Serdar K; Shenton, Martha E; Golland, Polina

    2009-09-01

    We present iCluster, a fast and efficient algorithm that clusters a set of images while co-registering them using a parameterized, nonlinear transformation model. The output of the algorithm is a small number of template images that represent different modes in a population. This is in contrast with traditional, hypothesis-driven computational anatomy approaches that assume a single template to construct an atlas. We derive the algorithm based on a generative model of an image population as a mixture of deformable template images. We validate and explore our method in four experiments. In the first experiment, we use synthetic data to explore the behavior of the algorithm and inform a design choice on parameter settings. In the second experiment, we demonstrate the utility of having multiple atlases for the application of localizing temporal lobe brain structures in a pool of subjects that contains healthy controls and schizophrenia patients. Next, we employ iCluster to partition a data set of 415 whole brain MR volumes of subjects aged 18 through 96 years into three anatomical subgroups. Our analysis suggests that these subgroups mainly correspond to age groups. The templates reveal significant structural differences across these age groups that confirm previous findings in aging research. In the final experiment, we run iCluster on a group of 15 patients with dementia and 15 age-matched healthy controls. The algorithm produces two modes, one of which contains dementia patients only. These results suggest that the algorithm can be used to discover subpopulations that correspond to interesting structural or functional "modes."

  19. Linkage and association analysis in pedigrees from different populations.

    PubMed

    Beyene, Joseph; Yan, Jun; Greenwood, Celia M T

    2005-01-01

    Using the Genetic Analysis Workshop 14 simulated datasets we carried out nonparametric linkage analyses and applied a log-linear method for analysis of case-parent-triad data with stratification on parental mating type. We proposed and applied a random effect modelling approach to explore the impact of population heterogeneity on tests of association between genetic markers and disease status. The estimated genetic effect may appear to be strongly significant in one population but nonsignificant in another population, leading to confusion about interpretation. However, when results are interpreted in the light of a random effects model, both studies may be making similar statements about a genetic effect that varies depending on environment and background. PMID:16451671

  20. Stacks: an analysis tool set for population genomics

    PubMed Central

    CATCHEN, JULIAN; HOHENLOHE, PAUL A.; BASSHAM, SUSAN; AMORES, ANGEL; CRESKO, WILLIAM A.

    2014-01-01

    Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics. PMID:23701397

  1. [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.

  2. [Phenetic analysis of populations of Porcellionides pruinosus (Brandt, 1833) (Crustacea, Isopoda, Oniscidea)].

    PubMed

    Achouri, Mohamed Sghaïer; Charfi-Cheikhrouha, Faouzia

    2008-03-01

    The cosmopolitan species, Porcellionides pruinosus (Brandt, 1833), exhibited a geographical variation of its morphological features and its reproduction pattern. In fact, some Tunisian populations had a seasonal reproductive period and other ones showed a reproductive activity. A phenetic analysis has been performed to compare populations belonging to P. pruinosus from different geographical localities. For this, nineteen quantitative characters in 800 specimens of P. pruinosus issued from nine populations located in the North, the Centre, and the South of Tunisia, and one population from Athens (Greece) were studied. These populations were characterized by different reproductive behaviours. The populations of Tabarka, Korba, and Tamerza showed reproductive activity, whereas those of Garat Nâam, Raccada, Sahline, Gafsa, Rdayef, Gabès, and Athens exhibited a seasonal reproductive period. The variability of the first three axes of the principal components analysis (PCA) and their significance showed an intraspecific variability structure. The graphical representation of the population's dispersion generated by the two first axes (63.55% of the total variability) revealed a great heterogeneity among females of the different populations of P. pruinosus. The Garat Nâam population was set apart from the other ones by its cephalic width and length and also by its apophysis length. Furthermore, cephalic and uropod length separated the Garat Nâam and Tabarka populations. The dendrogram, based on Euclidean coordinates, confirms an isolation of the populations of Tabarka and Garat Nâam, exhibiting respectively reproductive activity and seasonal reproduction. However, the other populations do not show any relationship with the reproduction behaviour. They were clustered in two groups. The first one is represented by the populations of the Southeast and the West of Tunisia. The second pooled the populations of the Northeast and the Centre of Tunisia with the population of

  3. Introducing Dynamic Analysis Using Malthus's Principle of Population.

    ERIC Educational Resources Information Center

    Pingle, Mark

    2003-01-01

    Declares the use of dynamic models is increasing in macroeconomics. Explains how to introduce dynamic models to students whose technical skills are modest or varied. Chooses Malthus's Principle of Population as a natural context for introducing dynamic analysis because it provides a method for reviewing the mathematical tools and theoretical…

  4. [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.

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

    PubMed Central

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

    2005-01-01

    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 (≤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. PMID:16243699

  6. 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.

  7. 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…

  8. 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

  9. 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.

  10. 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

  11. 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. PMID:26780665

  12. Probability bounds analysis for nonlinear population ecology models.

    PubMed

    Enszer, Joshua A; Andrei Măceș, D; Stadtherr, Mark A

    2015-09-01

    Mathematical models in population ecology often involve parameters that are empirically determined and inherently uncertain, with probability distributions for the uncertainties not known precisely. Propagating such imprecise uncertainties rigorously through a model to determine their effect on model outputs can be a challenging problem. We illustrate here a method for the direct propagation of uncertainties represented by probability bounds though nonlinear, continuous-time, dynamic models in population ecology. This makes it possible to determine rigorous bounds on the probability that some specified outcome for a population is achieved, which can be a core problem in ecosystem modeling for risk assessment and management. Results can be obtained at a computational cost that is considerably less than that required by statistical sampling methods such as Monte Carlo analysis. The method is demonstrated using three example systems, with focus on a model of an experimental aquatic food web subject to the effects of contamination by ionic liquids, a new class of potentially important industrial chemicals.

  13. 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

  14. 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…

  15. The genetics of amphibian declines: 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.

    PubMed

    Shaffer, H B; Fellers, G M; Magee, A; Voss, S R

    2000-03-01

    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.

  16. 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.

  17. The genetics of amphibian declines: 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

    Bradley, Shaffer H.; Fellers, G.M.; Magee, A.; Randal, Voss S.

    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.

  18. 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…

  19. [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.

  20. Individual organisms as units of analysis: Bayesian-clustering alternatives in population genetics.

    PubMed

    Mank, Judith E; Avise, John C

    2004-12-01

    Population genetic analyses traditionally focus on the frequencies of alleles or genotypes in 'populations' that are delimited a priori. However, there are potential drawbacks of amalgamating genetic data into such composite attributes of assemblages of specimens: genetic information on individual specimens is lost or submerged as an inherent part of the analysis. A potential also exists for circular reasoning when a population's initial identification and subsequent genetic characterization are coupled. In principle, these problems are circumvented by some newer methods of population identification and individual assignment based on statistical clustering of specimen genotypes. Here we evaluate a recent method in this genre--Bayesian clustering--using four genotypic data sets involving different types of molecular markers in non-model organisms from nature. As expected, measures of population genetic structure (F(ST) and phiST) tended to be significantly greater in Bayesian a posteriori data treatments than in analyses where populations were delimited a priori. In the four biological contexts examined, which involved both geographic population structures and hybrid zones, Bayesian clustering was able to recover differentiated populations, and Bayesian assignments were able to identify likely population sources of specific individuals.

  1. Assessment of military population-based psychological resilience programs.

    PubMed

    Morgan, Brenda J; Bibb, Sandra C Garmon

    2011-09-01

    Active duty service members' (ADSMs) seemingly poor adaptability to traumatic stressors is a risk to force health. Enhancing the psychological resilience of ADSMs has become a key focus of Department of Defense (DoD) leaders and the numbers of military programs for enhancing psychological resilience have increased. The purpose of this article is to describe the results of an assessment conducted to determine comprehensiveness of current psychological resilience building programs that target ADSMs. A modified six-step, population-based needs assessment was used to evaluate resilience programs designed to meet the psychological needs of the ADSM population. The assessment results revealed a gap in published literature regarding program outcomes. DoD leaders may benefit from targeted predictive research that assesses program effectiveness outcomes. The necessity of including preventive, evidence-based interventions in new programs, such as positive emotion interventions shown to enhance psychological resilience in civilian samples, is also recommended.

  2. 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.

  3. 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

  4. The prevalence of ADHD in a population-based sample

    PubMed Central

    Rowland, Andrew S.; Skipper, Betty J.; Umbach, David M.; Rabiner, David L.; Campbell, Richard A.; Naftel, A. Jack; Sandler, Dale P.

    2014-01-01

    Objective Few studies of ADHD prevalence have used population-based samples, multiple informants, and DSM-IV criteria. In addition, children who are asymptomatic while receiving ADHD mediction often have been misclassified. Therefore, we conducted a population-based study to estimate the prevalence of ADHD in elementary school children using DSM-IV critera. Methods We screened 7587 children for ADHD. Teachers of 81% of the children completed a DSM-IV checklist. We then interviewed parents using a structured interview (DISC). Of these, 72% participated. Parent and teacher ratings were combined to determine ADHD status. We also estimated the proportion of cases attributable to other conditions. Results Overall, 15.5% of our sample (95% confidence interval (C.I.) 14.6%-16.4%) met DSM-IV-TR criteria for ADHD. Over 40% of cases reported no previous diagnosis. With additional information, other conditions explained about 9% of cases. Conclusions The prevalence of ADHD in this population-based sample was higher than the 3-7% commonly reported. To compare study results, the methods used to implement the DSM criteria need to be standardized. PMID:24336124

  5. 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. PMID:26419635

  6. 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

  7. 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

  8. 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

  9. 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

  10. Human immunodeficiency virus testing for patient-based and population-based diagnosis.

    PubMed

    Albritton, W L; Vittinghoff, E; Padian, N S

    1996-10-01

    Laboratory testing for human immunodeficiency virus (HIV) has been introduced for individual patient-based diagnosis as well as high-risk and low-risk population-based screening. The choice of test, confirmatory algorithm, and interpretative criteria used depend on the clinical setting. In the context of general population-based testing, factors affecting test performance will have to be considered carefully in the development of testing policy. PMID:8843247

  11. [Population life process and spectral analysis of rare and endangered plant Alsophila spinulosa].

    PubMed

    Song, Ping; Hong, Wei; Wu, Cheng-zhen; Feng, Lei; Fan, Hai-lan

    2008-12-01

    According to population life table and survival analysis theory, the time-specific life table and the survival function curve of Alsophila spinulosa population were established and drawn based on height class, and the life process of the population was analyzed. The results revealed that the population structure of A. spinulosa was of the type ascending at early stage and stable at late stage. The peak of expected life appeared at the 4th age class, indicating the relative good survival quality at this phase, and the survival curve belonged to the typical form of Deevey-III. There existed three death peak phases in the population life process, i.e., the growth stages from 2nd to 3rd age class, from 10th to 11th age class, and from 12th to 13th age class. With the increase of age class, the population survivability dropped down monotonously, and ow nosy, a the accumulative mortality rose up correspondently. The variation extent was high in early phase and low in anaphase. The death density function curve displayed the characteristics of descent in early phase and stabilization in anaphase, and the concave point occurred at 4th age class. Spectral analysis showed that the quantitative fluctuation of A. spinulosa population was multi-harmonic superposition with large cycles containing small cycles. The influences of these cycles dropped with the diminishment of cycle length, and the effect of fundamental wave was most prominent. PMID:19288706

  12. Genetic analysis of Indian tasar silkmoth (Antheraea mylitta) populations.

    PubMed

    Chakraborty, Saikat; Muthulakshmi, M; Vardhini, Deena; Jayaprakash, P; Nagaraju, J; Arunkumar, K P

    2015-01-01

    Indian tasar silkmoth, Antheraea mylitta is an economically important wild silkmoth species distributed across India. A number of morphologically and ethologically well-defined ecotypes are known for this species that differ in their primary food plant specificity. Most of these ecotypes do not interbreed in nature, but are able to produce offspring under captive conditions. Microsatellite markers were developed for A. mylitta, and out of these, ten well-behaved microsatellite loci were used to analyze the population structure of different ecoraces. A total of 154 individual moths belonging to eight different ecoraces, were screened at each locus. Hierarchical analysis of population structure using Analysis of MOlecular VAriance (AMOVA) revealed significant structuring (FST = 0.154) and considerable inbreeding (FIS = 0.505). A significant isolation by distance was also observed. The number of possible population clusters was investigated using distance method, Bayesian algorithm and self organization maps (SOM). The first two methods revealed two distinct clusters, whereas the SOM showed the different ecoraces not to be clearly differentiated. These results suggest that although there is a large degree of phenotypic variation among the different ecoraces of A. mylitta, genetically they are not very different, and the phenotypic differences may largely be a result of their respective ecology. PMID:26510465

  13. Genetic analysis of Indian tasar silkmoth (Antheraea mylitta) populations

    PubMed Central

    Chakraborty, Saikat; Muthulakshmi, M; Vardhini, Deena; Jayaprakash, P; Nagaraju, J; Arunkumar, K. P.

    2015-01-01

    Indian tasar silkmoth, Antheraea mylitta is an economically important wild silkmoth species distributed across India. A number of morphologically and ethologically well-defined ecotypes are known for this species that differ in their primary food plant specificity. Most of these ecotypes do not interbreed in nature, but are able to produce offspring under captive conditions. Microsatellite markers were developed for A. mylitta, and out of these, ten well-behaved microsatellite loci were used to analyze the population structure of different ecoraces. A total of 154 individual moths belonging to eight different ecoraces, were screened at each locus. Hierarchical analysis of population structure using Analysis of MOlecular VAriance (AMOVA) revealed significant structuring (FST = 0.154) and considerable inbreeding (FIS = 0.505). A significant isolation by distance was also observed. The number of possible population clusters was investigated using distance method, Bayesian algorithm and self organization maps (SOM). The first two methods revealed two distinct clusters, whereas the SOM showed the different ecoraces not to be clearly differentiated. These results suggest that although there is a large degree of phenotypic variation among the different ecoraces of A. mylitta, genetically they are not very different, and the phenotypic differences may largely be a result of their respective ecology. PMID:26510465

  14. Conformity cannot be identified based on population-level signatures

    PubMed Central

    Acerbi, Alberto; van Leeuwen, Edwin J. C.; Haun, Daniel B. M.; Tennie, Claudio

    2016-01-01

    Conformist transmission, defined as a disproportionate likelihood to copy the majority, is considered a potent mechanism underlying the emergence and stabilization of cultural diversity. However, ambiguity within and across disciplines remains as to how to identify conformist transmission empirically. In most studies, a population level outcome has been taken as the benchmark to evidence conformist transmission: a sigmoidal relation between individuals’ probability to copy the majority and the proportional majority size. Using an individual-based model, we show that, under ecologically plausible conditions, this sigmoidal relation can also be detected without equipping individuals with a conformist bias. Situations in which individuals copy randomly from a fixed subset of demonstrators in the population, or in which they have a preference for one of the possible variants, yield similar sigmoidal patterns as a conformist bias would. Our findings warrant a revisiting of studies that base their conformist transmission conclusions solely on the sigmoidal curve. More generally, our results indicate that population level outcomes interpreted as conformist transmission could potentially be explained by other individual-level strategies, and that more empirical support is needed to prove the existence of an individual-level conformist bias in human and other animals. PMID:27796373

  15. Population-based incidence and prevalence of facioscapulohumeral dystrophy

    PubMed Central

    Arnts, Hisse; van der Maarel, Silvère M.; Padberg, George W.; Verschuuren, Jan J.G.M.; Bakker, Egbert; Weinreich, Stephanie S.; Verbeek, André L.M.; van Engelen, Baziel G.M.

    2014-01-01

    Objective: To determine the incidence and prevalence of facioscapulohumeral muscular dystrophy (FSHD) in the Netherlands. Methods: Using 3-source capture-recapture methodology, we estimated the total yearly number of newly found symptomatic individuals with FSHD, including those not registered in any of the 3 sources. To this end, symptomatic individuals with FSHD were available from 3 large population-based registries in the Netherlands if diagnosed within a 10-year period (January 1, 2001 to December 31, 2010). Multiplication of the incidence and disease duration delivered the prevalence estimate. Results: On average, 52 people are newly diagnosed with FSHD every year. This results in an incidence rate of 0.3/100,000 person-years in the Netherlands. The prevalence rate was 12/100,000, equivalent to 2,000 affected individuals. Conclusions: We present population-based incidence and prevalence estimates regarding symptomatic individuals with FSHD, including an estimation of the number of symptomatic individuals not present in any of the 3 used registries. This study shows that the total number of symptomatic persons with FSHD in the population may well be underestimated and a considerable number of affected individuals remain undiagnosed. This suggests that FSHD is one of the most prevalent neuromuscular disorders. PMID:25122204

  16. 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

  17. Hungarian population data on seven PCR-based loci.

    PubMed

    Budowle, B; Woller, J; Koons, B W; Furedi, S; Errera, J D; Padar, Z

    1996-07-01

    Hungarian population data for the loci LDLR, GYPA, HBGG, D7S8, Gc, HLA-DQA1, and D1S80 were generated. The genotype frequency distributions for the loci do not deviate from Hardy Weinberg expectations. Furthermore, there was little evidence for departures from expectations of independence between the loci. Using a test for homogeneity all the loci were similar between two Hungarian population samples and only the HLA-DQA1 locus was statistically different between Hungarians and US Caucasians. There generally would be little forensic differences, whether a Hungarian or a US Caucasian database was used, for estimating multiple locus profile frequencies for the seven PCR-based loci. PMID:8754580

  18. Genetic analysis of Kashmiri Muslim population living in Pakistan.

    PubMed

    Rakha, Allah; Yu, Bing; Hadi, S; Li, Shengbin

    2008-07-01

    The PowerPlex 16 amplification kit was used for the analysis of allele frequencies for the 15 STR loci (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX and FGA) in unrelated, autochthonous healthy adults from Kashmiri refugee population in Pakistani Punjab (n=125). The allelic distributions were in Hardy-Weinberg equilibrium in all of loci examined except for the vWA locus. Forensic parameters were calculated and a comparison was made with geographically nearby populations. PMID:18328763

  19. 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.

  20. Increasing incidence of Barrett's oesophagus: a population-based study.

    PubMed

    Coleman, Helen G; Bhat, Shivaram; Murray, Liam J; McManus, Damian; Gavin, Anna T; Johnston, Brian T

    2011-09-01

    Oesophageal adenocarcinoma, a highly fatal cancer, has risen in incidence in Western societies, but it is unclear whether this is due to increasing incidence of its pre-cursor condition, Barrett's oesophagus (BO) or whether the proportion of BO patients undergoing malignant progression has increased in the face of unchanged BO incidence. Data from population-based studies of BO incidence is limited, with equivocal results to date difficult to distinguish from changes in endoscopic practices. The aim of this study was to assess population trends in Barrett's oesophagus (BO) diagnoses in relation to endoscopy and biopsy rates over a 13 year period. The Northern Ireland Barrett's oesophagus Register (NIBR) is a population-based register of all 9,329 adults diagnosed with columnar epithelium of the oesophagus in Northern Ireland between 1993 and 2005, of whom 58.3% were male. European age-standardised annual BO incidence rates were calculated per 100,000 of the population, per 100 endoscopies and per 100 endoscopies including an oesophageal biopsy. Average annual BO incidence rates rose by 159% during the study period, increasing from 23.9/100,000 during 1993-1997 to 62.0/100,000 during 2002-2005. This elevation far exceeded corresponding increases in rates of endoscopies and oesophageal biopsies being conducted. BO incidence increased most markedly in individuals aged < 60 years, and most notably amongst males aged < 40 years. This study points towards a true increase in the incidence of BO which would appear to be most marked in young males. These findings have significant implications for future rates of oesophageal adenocarcinoma and surveillance programmes.

  1. 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…

  2. 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,…

  3. Anthropometric markers and their association with incident type 2 diabetes mellitus: which marker is best for prediction? Pooled analysis of four German population-based cohort studies and comparison with a nationwide cohort study

    PubMed Central

    Hartwig, Saskia; Kluttig, Alexander; Tiller, Daniel; Fricke, Julia; Müller, Grit; Schipf, Sabine; Völzke, Henry; Schunk, Michaela; Meisinger, Christa; Schienkiewitz, Anja; Heidemann, Christin; Moebus, Susanne; Pechlivanis, Sonali; Werdan, Karl; Kuss, Oliver; Tamayo, Teresa; Haerting, Johannes; Greiser, Karin Halina

    2016-01-01

    Objective To compare the association between different anthropometric measurements and incident type 2 diabetes mellitus (T2DM) and to assess their predictive ability in different regions of Germany. Methods Data of 10 258 participants from 4 prospective population-based cohorts were pooled to assess the association of body weight, body mass index (BMI), waist circumference (WC), waist-to-hip-ratio (WHR) and waist-to-height-ratio (WHtR) with incident T2DM by calculating HRs of the crude, adjusted and standardised markers, as well as providing receiver operator characteristic (ROC) curves. Differences between HRs and ROCs for the different anthropometric markers were calculated to compare their predictive ability. In addition, data of 3105 participants from the nationwide survey were analysed separately using the same methods to provide a nationally representative comparison. Results Strong associations were found for each anthropometric marker and incidence of T2DM. Among the standardised anthropometric measures, we found the strongest effect on incident T2DM for WC and WHtR in the pooled sample (HR for 1 SD difference in WC 1.97, 95% CI 1.75 to 2.22, HR for WHtR 1.93, 95% CI 1.71 to 2.17 in women) and in female DEGS participants (HR for WC 2.24, 95% CI 1.91 to 2.63, HR for WHtR 2.10, 95% CI 1.81 to 2.44), whereas the strongest association in men was found for WHR among DEGS participants (HR 2.29, 95% CI 1.89 to 2.78). ROC analysis showed WHtR to be the strongest predictor for incident T2DM. Differences in HR and ROCs between the different markers confirmed WC and WHtR to be the best predictors of incident T2DM. Findings were consistent across study regions and age groups (<65 vs ≥65 years). Conclusions We found stronger associations between anthropometric markers that reflect abdominal obesity (ie, WC and WHtR) and incident T2DM than for BMI and weight. The use of these measurements in risk prediction should be encouraged. PMID:26792214

  4. 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.

  5. Systematics and population level analysis of Anopheles darlingi.

    PubMed

    Conn, J E

    1998-01-01

    A new phylogenetic analysis of the Nyssorhynchus subgenus (Danoff-Burg and Conn, unpub. data) using six data sets morphological (all life stages); scanning electron micrographs of eggs; nuclear ITS2 sequences; mitochondrial COII, ND2 and ND6 sequences¿ revealed different topologies when each data set was analyzed separately but no heterogeneity between the data sets using the arn test. Consequently, the most accurate estimate of the phylogeny was obtained when all the data were combined. This new phylogeny supports a monophyletic Nyssorhynchus subgenus but both previously recognized sections in the subgenus (Albimanus and Argyritarsis) were demonstrated to be paraphyletic relative to each other and four of the seven clades included species previously placed in both sections. One of these clades includes both Anopheles darlingi and An. albimanus, suggesting that the ability to vector malaria effectively may have originated once in this subgenus. Both a conserved (315 bp) and a variable (425 bp) region of the mitochondrial COI gene from 15 populations of An. darlingi from Belize, Bolivia, Brazil, French Guiana, Peru and Venezuela were used to examine the evolutionary history of this species and to test several analytical assumptions. Results demonstrated (1) parsimony analysis is equally informative compared to distance analysis using NJ; (2) clades or clusters are more strongly supported when these two regions are combined compared to either region separately; (3) evidence (in the form of remnants of older haplotype lineages) for two colonization events; and (4) significant genetic divergence within the population from Peixoto de Azevedo (State of Mato Grosso, Brazil). The oldest lineage includes populations from Peixoto, Boa Vista (State of Roraima) and Dourado (State of São Paulo).

  6. 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

  7. Population-Based Analysis of Hematologic Malignancy Referrals to a Comprehensive Cancer Center, Referrals for Blood and Marrow Transplantation, and Participation in Clinical Trial, Survey, and Biospecimen Research by Race.

    PubMed

    Clay, Alyssa; Peoples, Brittany; Zhang, Yali; Moysich, Kirsten; Ross, Levi; McCarthy, Philip; Hahn, Theresa

    2015-08-01

    Racial and ethnic disparities have been reported in clinical trial/research participation, utilization of autologous and allogeneic blood and marrow transplantation (BMT), and availability of allogeneic donors. We performed a population-based cohort study to investigate adult hematologic malignancy referrals to a US tertiary cancer center, utilization of BMT, and participation in clinical trial, survey, and biospecimen research by race. US Census Data and the New York State Public Access Cancer Epidemiology Database identified the racial distribution of the general population and new hematologic malignancy cases in the primary catchment area. From 2005 to 2011, 1106 patients aged 18 to 75 years were referred for BMT consultation; although the rate of BMT among hematologic malignancy referrals did not differ by race, the reasons for not receiving a BMT did. Participation in biospecimen research did not vary by race; however, African Americans and other minorities were significantly less likely to participate in survey research than European Americans. Although rates of hematologic malignancy referrals and use of BMT for minorities appear to be low (<10%), they closely reflect the race distribution of all hematologic malignancy cases and the western New York population. African Americans are equally likely as other races to participate in biospecimen banking, but further study is needed to understand reasons for lower participation in survey research.

  8. 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

  9. Macrolide-induced digoxin toxicity: a population-based study.

    PubMed

    Gomes, T; Mamdani, M M; Juurlink, D N

    2009-10-01

    In this 15-year, population-based, nested case-control study, we investigated the association between hospitalization for digoxin toxicity and recent exposure to individual macrolide antibiotics. Clarithromycin was associated with the highest risk of digoxin toxicity (adjusted odds ratio (OR) 14.8; 95% confidence interval (CI) 7.9-27.9), whereas erythromycin and azithromycin were associated with much lower risk (adjusted OR 3.7; 95% CI 1.7-7.9; and adjusted OR 3.7; 95% CI 1.1-12.5, respectively). We found no increased risk with a neutral comparator, cefuroxime (adjusted OR 0.8; 95% CI 0.2-3.4).

  10. 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.

  11. Microsatellite-based genetic diversity patterns in disjunct populations of a rare orchid.

    PubMed

    Pandey, Madhav; Richards, Matt; Sharma, Jyotsna

    2015-12-01

    We investigated the patterns of genetic diversity and structure in seven disjunct populations of a rare North American orchid, Cypripedium kentuckiense by including populations that represented the periphery and the center of the its range. Eight nuclear and two chloroplast microsatellites were used. Genetic diversity was low across the sampled populations of C. kentuckiense based on both nuclear (average An = 4.0, Ho = 0.436, He = 0.448) and cpDNA microsatellites (average An = 1.57, Nh = 1.57 and H = 0.133). The number of private alleles ranged from one to four per population with a total of 17 private alleles detected at five nuclear microsatellites. One private allele at one cpDNA microsatellite was also observed. Although the absolute values for nuclear microsatellite based population differentiation were low (Fst = 0.075; ϕPT = 0.24), they were statistically significant. Pairwise Fst values ranged from 0.038 to 0.123 and each comparison was significant. We also detected isolation by distance with nDNA microsatellites based on the Mantel test (r(2) = 0.209, P = 0.05). STRUCTURE analysis and the neighbor joining trees grouped the populations similarly whereby the geographically proximal populations were genetically similar. Our data indicate that the species is genetically depauperate but the diversity is distributed more or less equally across its range. Population differentiation and isolation by distance were detectable, which indicates that genetic isolation is beginning to manifest itself across the range in this rare species.

  12. Using Bayesian Population Viability Analysis to Define Relevant Conservation Objectives.

    PubMed

    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.

  13. 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

  14. Using Bayesian Population Viability Analysis to Define Relevant Conservation Objectives.

    PubMed

    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

  15. Applicability of Bolton's Analysis: A Study on Jaipur Population.

    PubMed

    Trehan, Mridula; Agarwal, Sonahita; Sharma, Sunil

    2012-05-01

    This study was undertaken to compare the Bolton's anterior and overall ratios among males and females in Jaipur population. One hundred study models (50 males and 50 females) of orthodontic patients were randomly selected from the Department of Orthodontics, Mahatma Gandhi Dental College, Jaipur. The normative data for the mesiodistal widths of males and females were established and the anterior and overall ratios were obtained for both males and females. It was observed that were no significant differences in both the ratios in males and females. Hence, both the ratios were obtained for the sample as a whole. These ratios were found to be similar to the Boltons standard with no significant differences. Therefore, it can be concluded that Boltons standards can be applied to this population irrespective of sex or ethnic background. How to cite this article: Trehan M, Agarwal S, Sharma S. Applicability of Bolton's Analysis: A Study on Jaipur Population. Int J Clin Pediatr Dent 2012;5(2):113-117.

  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. 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

  18. An analysis of the social space structure of population in the Shanghai municipality.

    PubMed

    Zhu, J

    1996-01-01

    This article constructs a typology of the spatial distribution of urban population in Shanghai municipality in China. Chinese research follows in the traditions of Western ecological and social spatial theories of urban population distribution. Xu Wei and Yu Wei discovered that Shanghai's social space was affected by population clustering and the structure of population culture and occupation. Xu Xueqiang analyzed the social space structure of Guangzhou City using 67 variables. Data for this analysis were obtained from the neighborhood census area for 1982 and 1990 in Shanghai. Land utility data pertained to 1988. The geological information system techniques of Zhu Junming were used to establish the 119 spatial units. Urban social space structure is characterized by 14 factors generated from 113 variables: degree of population density, household registration structure, natural and mechanical changes of population, zoning, sex, age, education, employment, occupation, marital status, land utility, residential conditions, and housing typology. Principal components factor analysis, which was based on the principal components factor score matrix, and systematic cluster analysis were used to categorize spatial units and assign typologies. Ward statistics for distance coefficients were used to determine appropriate categorization. Findings indicate that 69.4% of the total variance in spatial units could be characterized by six principal components: educational structure (26.1%), degree of population density (17.11%), gender and occupational structure (11.3%), immigrant population (6.1%), living conditions (5.23%), and marital status (3.5%). Five social region typologies were constructed: a high density commercial residential area, a medium density cultural residential area, an industrial mixed residential area, newly erected residential areas, and outlying science and technology, cultural, and educational areas. The Shanghai social space structure was affected by history

  19. 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.

  20. The population genetics of familial mediterranean fever: a meta-analysis study.

    PubMed

    Papadopoulos, V P; Giaglis, S; Mitroulis, I; Ritis, K

    2008-11-01

    Our aim was to construct a Familial Mediterranean Fever (FMF) cumulative database and to propose a MEFV based phylogenetic tree. Data were collected from published studies. A meta-analysis based on 16,756 chromosomes from FMF patients and normal individuals from 14 affected populations was performed. Arlequin 2.0 and Phylip 3.2 software were used for population genetics analysis and phylogenetic tree construction. We have shown that MEFV mutations are distributed non-uniformly along the Mediterranean Sea area. The most frequent mutations detected in FMF patients are M694V (39.6%), V726A (13.9%), M680I (11.4%), E148Q (3.4%), and M694I (2.9%), while 28.8% of chromosomes carry unidentified or no mutations, especially in Western Europeans. The mean overall carrier rate is 0.186 with peak values in Arabs, Armenians, Jews, and Turks. Only V726A obeys the Hardy-Weinberg law in FMF patients implying that this mutation is the most ancient. Jews present the most intense genetic isolation and drift; thus they might have nested de novo mutations and accelerated evolution. Besides Jews, three population groups might follow distinct evolutionary lines (Asia Minor, Eastern European, and Western European). In conclusion, the MEFV mutation pattern is non-uniform regarding distribution, phenotypic expression, neutrality and population genetics characteristics. Jews are the candidate population for founder effects in MEFV. PMID:18691160

  1. Improved Statistical Analysis of Low Abundance Phenomena in Bimodal Bacterial Populations

    PubMed Central

    Reinhard, Friedrich; van der Meer, Jan Roelof

    2013-01-01

    Accurate detection of subpopulation size determinations in bimodal populations remains problematic yet it represents a powerful way by which cellular heterogeneity under different environmental conditions can be compared. So far, most studies have relied on qualitative descriptions of population distribution patterns, on population-independent descriptors, or on arbitrary placement of thresholds distinguishing biological ON from OFF states. We found that all these methods fall short of accurately describing small population sizes in bimodal populations. Here we propose a simple, statistics-based method for the analysis of small subpopulation sizes for use in the free software environment R and test this method on real as well as simulated data. Four so-called population splitting methods were designed with different algorithms that can estimate subpopulation sizes from bimodal populations. All four methods proved more precise than previously used methods when analyzing subpopulation sizes of transfer competent cells arising in populations of the bacterium Pseudomonas knackmussii B13. The methods’ resolving powers were further explored by bootstrapping and simulations. Two of the methods were not severely limited by the proportions of subpopulations they could estimate correctly, but the two others only allowed accurate subpopulation quantification when this amounted to less than 25% of the total population. In contrast, only one method was still sufficiently accurate with subpopulations smaller than 1% of the total population. This study proposes a number of rational approximations to quantifying small subpopulations and offers an easy-to-use protocol for their implementation in the open source statistical software environment R. PMID:24205184

  2. Adjustment for local ancestry in genetic association analysis of admixed populations

    PubMed Central

    Wang, Xuexia; Zhu, Xiaofeng; Qin, Huaizhen; Cooper, Richard S.; Ewens, Warren J.; Li, Chun; Li, Mingyao

    2011-01-01

    Motivation: Admixed populations offer a unique opportunity for mapping diseases that have large disease allele frequency differences between ancestral populations. However, association analysis in such populations is challenging because population stratification may lead to association with loci unlinked to the disease locus. Methods and results: We show that local ancestry at a test single nucleotide polymorphism (SNP) may confound with the association signal and ignoring it can lead to spurious association. We demonstrate theoretically that adjustment for local ancestry at the test SNP is sufficient to remove the spurious association regardless of the mechanism of population stratification, whether due to local or global ancestry differences among study subjects; however, global ancestry adjustment procedures may not be effective. We further develop two novel association tests that adjust for local ancestry. Our first test is based on a conditional likelihood framework which models the distribution of the test SNP given disease status and flanking marker genotypes. A key advantage of this test lies in its ability to incorporate different directions of association in the ancestral populations. Our second test, which is computationally simpler, is based on logistic regression, with adjustment for local ancestry proportion. We conducted extensive simulations and found that the Type I error rates of our tests are under control; however, the global adjustment procedures yielded inflated Type I error rates when stratification is due to local ancestry difference. Contact: mingyao@upenn.edu; chun.li@vanderbilt.edu. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21169375

  3. 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. PMID:24235281

  4. Histocompatibility antigens in a population based silicosis series.

    PubMed Central

    Kreiss, K; Danilovs, J A; Newman, L S

    1989-01-01

    Individual susceptibility to silicosis is suggested by the lack of a uniform dose response relation and by the presence of immunological epiphenomena, such as increased antibody levels and associated diseases that reflect altered immune regulation. Human leucocyte antigens (HLA) are linked with immune response capability and might indicate a possible genetic susceptibility to silicosis. Forty nine silicotic subjects were identified from chest radiographs in a population based study in Leadville, Colorado. They were interviewed for symptoms and occupational history and gave a blood specimen for HLA-A, -B, -DR, and -DQ typing and for antinuclear antibody, immune complexes, immunoglobulins, and rheumatoid factor. Silicotic subjects had twice the prevalence of B44 (45%) of the reference population and had triple the prevalence of A29 (20%), both of which were statistically significant when corrected for the number of comparisons made. No perturbations in D-region antigen frequencies were detected. B44-positive subjects were older at diagnosis and had less dyspnoea than other subjects. A29-positive subjects were more likely to have abnormal levels of IgA and had higher levels of immune complexes. This study is the first to find significant HLA antigen excesses among a series of silicotic cases and extends earlier reported hypotheses that were based on groups of antigens of which B44 and A29 are components. PMID:2818968

  5. 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.

  6. Copula-Based Approach to Synthetic Population Generation.

    PubMed

    Jeong, Byungduk; Lee, Wonjoon; Kim, Deok-Soo; Shin, Hayong

    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

  7. 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

  8. 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.

  9. 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.

  10. Automatic clustering and population analysis of white matter tracts using maximum density paths.

    PubMed

    Prasad, Gautam; Joshi, Shantanu H; Jahanshad, Neda; Villalon-Reina, Julio; Aganj, Iman; Lenglet, Christophe; Sapiro, Guillermo; McMahon, Katie L; de Zubicaray, Greig I; Martin, Nicholas G; Wright, Margaret J; Toga, Arthur W; Thompson, Paul M

    2014-08-15

    We introduce a framework for population analysis of white matter tracts based on diffusion-weighted images of the brain. The framework enables extraction of fibers from high angular resolution diffusion images (HARDI); clustering of the fibers based partly on prior knowledge from an atlas; representation of the fiber bundles compactly using a path following points of highest density (maximum density path; MDP); and registration of these paths together using geodesic curve matching to find local correspondences across a population. We demonstrate our method on 4-Tesla HARDI scans from 565 young adults to compute localized statistics across 50 white matter tracts based on fractional anisotropy (FA). Experimental results show increased sensitivity in the determination of genetic influences on principal fiber tracts compared to the tract-based spatial statistics (TBSS) method. Our results show that the MDP representation reveals important parts of the white matter structure and considerably reduces the dimensionality over comparable fiber matching approaches. PMID:24747738

  11. Automatic Clustering and Population Analysis of White Matter Tracts using Maximum Density Paths

    PubMed Central

    Prasad, Gautam; Joshi, Shantanu H.; Jahanshad, Neda; Villalon-Reina, Julio; Aganj, Iman; Lenglet, Christophe; Sapiro, Guillermo; McMahon, Katie L.; de Zubicaray, Greig I.; Martin, Nicholas G.; Wright, Margaret J.; Toga, Arthur W.; Thompson, Paul M.

    2014-01-01

    We introduce a framework for population analysis of white matter tracts based on diffusion-weighted images of the brain. The framework enables extraction of fibers from high angular resolution diffusion images (HARDI); clustering of the fibers based partly on prior knowledge from an atlas; representation of the fiber bundles compactly using a path following points of highest density (maximum density path; MDP); and registration of these paths together using geodesic curve matching to find local correspondences across a population. We demonstrate our method on 4-Tesla HARDI scans from 565 young adults to compute localized statistics across 50 white matter tracts based on fractional anisotropy (FA). Experimental results show increased sensitivity in the determination of genetic influences on principal fiber tracts compared to the tract-based spatial statistics (TBSS) method. Our results show that the MDP representation reveals important parts of the white matter structure and considerably reduces the dimensionality over comparable fiber matching approaches. PMID:24747738

  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. 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.

  15. 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

  16. The CKD enigma with misleading statistics and myths about CKD, and conflicting ESRD and death rates in the literature: results of a 2008 U.S. population-based cross-sectional CKD outcomes analysis.

    PubMed

    Onuigbo, Macaulay A C

    2013-01-01

    The just released (August 2012) U.S. Preventive Services Task Force (USPSTF) report on chronic kidney disease (CKD) screening concluded that we know surprisingly little about whether screening adults with no signs or symptoms of CKD will improve health outcomes and that clinicians and patients deserve better information on CKD. The implications of the recently introduced CKD staging paradigm versus long-term renal outcomes remain uncertain. Furthermore, the natural history of CKD remains unclear. We completed a comparison of US population-wide CKD to projected annual incidence of end stage renal disease (ESRD) for 2008 based on current evidence in the literature . Projections for new ESRD resulted in an estimated 840,000 new ESRD cases in 2008, whereas the actual reported new ESRD incidence in 2008, according to the 2010 USRDS Annual Data Report, was in fact only 112,476, a gross overestimation by about 650%. We conclude that we as nephrologists in particular, and physicians in general, still do not understand the true natural history of CKD. We further discussed the limitations of current National Kidney Foundation Disease Outcomes Quality Initiative (NKF KDOQI) CKD staging paradigms. Moreover, we have raised questions regarding the CKD patients who need to be seen by nephrologists, and have further highlighted the limitations and intricacies of the individual patient prognostication among CKD populations when followed overtime, and the implications of these in relation to future planning of CKD care in general. Finally, the clear heterogeneity of the so-called CKD patient is brought into prominence as we review the very misleading concept of classifying and prognosticating all CKD patients as one homogenous patient population.

  17. Physiologically based modeling of lead kinetics: a pilot study using data from a Canadian population.

    PubMed

    MacMillan, John W; Behinaein, Sepideh; Chettle, David R; Inskip, Mike; McNeill, Fiona E; Manton, William I; Healey, Norm; Fisher, Mandy; Arbuckle, Tye E; Fleming, David E B

    2015-12-01

    The Canadian population is currently subject to low, chronic lead exposure and an understanding of its effects is of great significance to the population's health. Such low exposure is difficult to measure directly; approximation by physiologically based modeling may provide a preferable approach to population analysis. The O'Flaherty model of lead kinetics is based on an age-dependent approach to human growth and development and devotes special attention to bone turnover rates. Because lead is a bone-seeking element, the model was deemed ideal for such an analysis. Sample from 263 individuals of various ages from the Greater Toronto Area were selected to evaluate the applicability of the current version of the O'Flaherty model to populations with low lead exposure. For each individual, the input value of lead exposure was calibrated to match the output value of cortical bone lead to the individual's measured tibia lead concentration; the outputs for trabecular bone, blood, and plasma lead concentrations obtained from these calibrations were then compared with the subjects' measured calcaneus, blood, and serum lead concentrations, respectively. This indicated a need for revision of the model parameters; those for lead binding in blood and lead clearance from blood to bone were adjusted and new outputs were obtained in the same fashion as before. Model predictions of trabecular lead concentration did not agree with measurements in the calcaneus. The outputs for blood and plasma lead concentrations were highly scattered and, on an individual level, inconsistent with corresponding measurements; however, the general trends of the outputs matched those of the measurements reasonably well, which indicates that the revised blood lead binding and lead clearance parameters may be useful in future studies. Overall, the analysis showed that with the revisions to the model discussed here, the model should be a useful tool in the analysis of human lead kinetics and body burden

  18. Physiologically based modeling of lead kinetics: a pilot study using data from a Canadian population.

    PubMed

    MacMillan, John W; Behinaein, Sepideh; Chettle, David R; Inskip, Mike; McNeill, Fiona E; Manton, William I; Healey, Norm; Fisher, Mandy; Arbuckle, Tye E; Fleming, David E B

    2015-12-01

    The Canadian population is currently subject to low, chronic lead exposure and an understanding of its effects is of great significance to the population's health. Such low exposure is difficult to measure directly; approximation by physiologically based modeling may provide a preferable approach to population analysis. The O'Flaherty model of lead kinetics is based on an age-dependent approach to human growth and development and devotes special attention to bone turnover rates. Because lead is a bone-seeking element, the model was deemed ideal for such an analysis. Sample from 263 individuals of various ages from the Greater Toronto Area were selected to evaluate the applicability of the current version of the O'Flaherty model to populations with low lead exposure. For each individual, the input value of lead exposure was calibrated to match the output value of cortical bone lead to the individual's measured tibia lead concentration; the outputs for trabecular bone, blood, and plasma lead concentrations obtained from these calibrations were then compared with the subjects' measured calcaneus, blood, and serum lead concentrations, respectively. This indicated a need for revision of the model parameters; those for lead binding in blood and lead clearance from blood to bone were adjusted and new outputs were obtained in the same fashion as before. Model predictions of trabecular lead concentration did not agree with measurements in the calcaneus. The outputs for blood and plasma lead concentrations were highly scattered and, on an individual level, inconsistent with corresponding measurements; however, the general trends of the outputs matched those of the measurements reasonably well, which indicates that the revised blood lead binding and lead clearance parameters may be useful in future studies. Overall, the analysis showed that with the revisions to the model discussed here, the model should be a useful tool in the analysis of human lead kinetics and body burden

  19. The Costs of Skull Base Surgery in the Pediatric Population

    PubMed Central

    Stapleton, A. L.; Tyler-Kabara, E. C.; Gardner, P. A.; Snyderman, C. H.

    2014-01-01

    Objectives To determine the costs of endoscopic endonasal surgery (EES) for pediatric skull base lesions. Methods Retrospective chart review of pediatric patients (ages 1 month to 19 years) treated for skull base lesions with EES from 1999 to 2013. Demographic and operative data were recorded. The cost of care for the surgical day, intensive care unit (ICU), floor, and total overall cost of inpatient stay were acquired from the finance department. Results A total of 160 pediatric patients undergoing EES for skull base lesions were identified. Of these, 55 patients had complete financial data available. The average total inpatient and surgical costs of care were $34, 056 per patient. Angiofibromas were the most costly: $59,051 per patient. Fibro-osseous lesions had the lowest costs: $10,931 per patient. The average ICU stay was 1.8 days at $4,577 per ICU day. The average acute care stay was 3.4 days at $1,961 per day. Overall length of stay was 4.5 days. Three cerebrospinal fluid leaks (4%) and two cases of meningitis (3%) occurred. One tracheostomy was required (1.5%). Conclusions EES is a cost-effective model for removal of skull base lesions in the pediatric population. Costs of care vary according to pathology, staged surgeries, length of ICU stay, and need for second operations. PMID:25685648

  20. 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

  1. Stellar population models based on new generation stellar library

    NASA Astrophysics Data System (ADS)

    Koleva, M.; Vazdekis, A.

    The spectral predictions of stellar population models are not as accurate in the ultra-violet (UV) as in the optical wavelength domain. One of the reasons is the lack of high-quality stellar libraries. The New Generation Stellar Library (NGSL), recently released, represents a significant step towards the improvement of this situation. To prepare NGSL for population synthesis, we determined the atmospheric parameters of its stars, we assessed the precision of the wavelength calibration and characterised its intrinsic resolution. We also measured the Galactic extinction for each of the NGSL stars. For our analyses we used Ulyss, a full spectrum fitting package, fitting the NGSL spectra against the MILES interpolator. As a second step we build preliminary single stellar population models using Vazdekis (2003) synthesis code. We find that the wavelength calibration is precise up to 0.1 px, after correcting a systematic effect in the optical range. The spectral resolution varies from 3 Å in the UV to 10 Å in the near-infrared (NIR), corresponding to a roughly constant reciprocal resolution R=λ/δλ ≈1000 and an instrumental velocity dispersion σ_{ins} ≈ 130 kms. We derived the atmospheric parameters homogeneously. The precision for the FGK stars is 42 K, 0.24 and 0.09 dex for teff, logg and feh, respectively. The corresponding mean errors are 150 K, 0.50 and 0.48 dex for the M stars, and for the OBA stars they are 4.5 percent, 0.44 and 0.18 dex. The comparison with the literature shows that our results are not biased. Our first version of models compares well with models based on optical libraries, having the advantages to be free from artifacts due to the atmosphere. In future we will fine-tune our models by comparing to different models and observations of globular clusters.

  2. An analysis of the composite stellar population in M32

    NASA Astrophysics Data System (ADS)

    Coelho, P.; Mendes de Oliveira, C.; Cid Fernandes, R.

    2009-06-01

    We obtained long-slit spectra of high signal-to-noise ratio of the galaxy M32 with the Gemini Multi-Object Spectrograph at the Gemini-North telescope. We analysed the integrated spectra by means of full spectral fitting in order to extract the mixture of stellar populations that best represents its composite nature. Three different galactic radii were analysed, from the nuclear region out to 2arcmin from the centre. This allows us to compare, for the first time, the results of integrated light spectroscopy with those of resolved colour-magnitude diagrams from the literature. As a main result we propose that an ancient and an intermediate-age population co-exist in M32, and that the balance between these two populations change between the nucleus and outside one effective radius (1reff) in the sense that the contribution from the intermediate population is larger at the nuclear region. We retrieve a smaller signal of a young population at all radii whose origin is unclear and may be a contamination from horizontal branch stars, such as the ones identified by Brown et al. in the nuclear region. We compare our metallicity distribution function for a region 1 to 2arcmin from the centre to the one obtained with photometric data by Grillmair et al. Both distributions are broad, but our spectroscopically derived distribution has a significant component with [Z/Zsolar] <= -1, which is not found by Grillmair et al. Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the NSF on behalf of the Gemini partnership: the National Science Foundation (United States), the Particle Physics and Astronomy Research Council (United Kingdom), the National Research Council (Canada), CONICYT (Chile), the Australian Research Council (Australia), CNPq (Brazil) and CONICET (Argentina) (observing run ID: GN-2004B-Q-74). E-mail: pcoelho@iap.fr (PC); oliveira

  3. 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

  4. Men's health: a population-based study on social inequalities.

    PubMed

    Bastos, Tássia Fraga; Alves, Maria Cecília Goi Porto; Barros, Marilisa Berti de Azevedo; Cesar, Chester Luiz Galvão

    2012-11-01

    This study evaluates social inequalities in health according to level of schooling in the male population. This was a cross-sectional, population-based study with a sample of 449 men ranging from 20 to 59 years of age and living in Campinas, São Paulo State, Brazil. The chi-square test was used to verify associations, and a Poisson regression model was used to estimate crude and adjusted prevalence ratios. Men with less schooling showed higher rates of alcohol consumption and dependence, smoking, sedentary lifestyle during leisure time, and less healthy eating habits, in addition to higher prevalence of bad or very bad self-rated health, at least one chronic disease, hypertension, and other health problems. No differences were detected between the two schooling strata in terms of use of health services, except for dental services. The findings point to social inequality in health-related behaviors and in some health status indicators. However, possible equity was observed in the use of nearly all types of health services.

  5. 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

  6. 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

  7. Validity of moyers mixed dentition analysis for Saudi population

    PubMed Central

    Al-Dlaigan, Yousef H.; Alqahtani, Nasser D.; Almoammar, Khalid; Al-Jewair, Thikriat; Salamah, Fahad Bin; Alswilem, Mohamme; Albarakati, Sahar F.

    2015-01-01

    Objectives: To evaluate the applicability of Moyers probability tables and to formulate more accurate mixed dentition prediction tables in the Saudi population. Methods: A cross-sectional study was conducted at the College of Dentistry, Kind Saud University, Saudi Arabia. The data were collected from 410 (203 males and 207 females) orthodontic study models, which had erupted mandibular permanent incisors, maxillary, mandibular canines and premolars. The mesiodistal widths were measured using a digital caliper with an accuracy of 0.01 mm. Student’s paired t-test was used to compare the mean width values derived from this study with the values derived using the Moyers table. Simple linear regression was used to evaluate the linear relationship between the combined mesiodistal widths of the mandibular permanent incisors and the canine-premolar segments in each dental arch. Results: The regression equations for the maxillary canine-premolar segment (males: Y=10.27+0.48X; females: Y=11.71 + 0.39X) and the mandibular canine-premolar segment (males: Y=9.71 + 0.40X; females: 11.28 + 0.39X) were used to formulate new probability tables on the Moyers pattern. Statistically significant differences were observed between predicted widths in our subjects and the widths obtained using Moyers tables. Conclusions: The new prediction tables derived in this study provided a more precise mixed dentition space analysis than Moyers prediction tables in estimating tooth dimensions in the Saudi population. PMID:26870104

  8. Populations at Increased Risk for HIV Infection in Kenya: Results From a National Population-Based Household Survey, 2012

    PubMed Central

    Githuka, George; Hladik, Wolfgang; Mwalili, Samuel; Cherutich, Peter; Muthui, Mercy; Gitonga, Joshua; Maina, William K.; Kim, Andrea A.

    2016-01-01

    Background Populations with higher risks for HIV exposure contribute to the HIV epidemic in Kenya. We present data from the second Kenya AIDS Indicator Survey to estimate the size and HIV prevalence of populations with high-risk characteristics. Methods The Kenya AIDS Indicator Survey 2012 was a national survey of Kenyans aged 18 months to 64 years which linked demographic and behavioral information with HIV results. Data were weighted to account for sampling probability. This analysis was restricted to adults aged 18 years and older. Results Of 5088 men and 6745 women, 0.1% [95% confidence interval (CI): 0.03 to 0.14] were persons who inject drugs (PWID). Among men, 0.6% (CI: 0.3 to 0.8) had ever had sex with other men, and 3.1% (CI: 2.4 to 3.7) were males who had ever engaged in transactional sex work (MTSW). Among women, 1.9% (CI: 1.3 to 2.5) had ever had anal sex, and 4.1% (CI: 3.5 to 4.8) were women who had ever engaged in transactional sex work (FTSW). Among men, 17.6% (CI: 15.7 to 19.6) had been male clients of transactional sex workers (TSW). HIV prevalence was 0% among men who have sex with men, 6.3% (CI: 0 to 18.1) among persons who injected drugs, 7.1% (CI: 4.8 to 9.4) among male clients of TSW, 7.6% (CI: 1.8 to 13.4) among MTSW, 12.1% (CI: 7.1 to 17.1) among FTSW, and 12.1% (CI: 5.0 to 19.2) among females who ever had engaged in anal sex. Conclusions Population-based data on high-risk populations can be used to set realistic targets for HIV prevention, care, and treatment for these groups. These data should inform priorities for high-risk populations in the upcoming Kenyan strategic plan on HIV/AIDS. PMID:24732821

  9. A space-based mission to characterize the IEO population

    NASA Astrophysics Data System (ADS)

    Findlay, Ross; Eßmann, Olaf; Grundmann, Jan Thimo; Hoffmann, Harald; Kührt, Ekkehard; Messina, Gabriele; Michaelis, Harald; Mottola, Stefano; Müller, Hartmut; Pedersen, Jakob Fromm

    2013-09-01

    In 2007 the German Space Agency (DLR) initiated the Kompaktsatellit series of small satellites. With growing scientific interest in the threat of future asteroid impacts on Earth, the first mission selected for the Kompaktsatellit programme was AsteroidFinder, a mission to characterise the unknown Inner Earth Object (IEO) population. The mission is based around the AsteroidFinder Instrument (AFI), a high-performance optical telescope, with asteroids identified on-ground via their apparent motion against the fixed star background. Such a challenging mission implies significant demands on the Kompaktsatellit bus platform required to support the AFI. The tight constraints of small satellite design, namely time, finance and available mass, require innovative solutions to problems. With a launch scheduled for 2014 and the project due to enter Phase C in 2011, the challenges of achieving high science with a small satellite are already apparent.

  10. 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

  11. 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. PMID:26529689

  12. 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.

  13. Prevalence and Incidence of Hypoglycaemia in 532,542 People with Type 2 Diabetes on Oral Therapies and Insulin: A Systematic Review and Meta-Analysis of Population Based Studies

    PubMed Central

    Edridge, Chloe L.; Dunkley, Alison J.; Bodicoat, Danielle H.; Rose, Tanith C.; Gray, Laura J.; Davies, Melanie J.; Khunti, Kamlesh

    2015-01-01

    Objective To collate and evaluate the current literature reporting the prevalence and incidence of hypoglycaemia in population based studies of type 2 diabetes. Research Design and Methods Medline, Embase and Cochrane were searched up to February 2014 to identify population based studies reporting the proportion of people with type 2 diabetes experiencing hypoglycaemia or rate of events experienced. Two reviewers independently screened studies for eligibility and extracted data for included studies. Random effects meta-analyses were carried out to calculate the prevalence and incidence of hypoglycaemia. Results 46 studies (n = 532,542) met the inclusion criteria. Prevalence of hypoglycaemia was 45% (95%CI 0.34,0.57) for mild/moderate and 6% (95%CI, 0.05,0.07) for severe. Incidence of hypoglycaemic episodes per person-year for mild/moderate and for severe was 19 (95%CI 0.00, 51.08) and 0.80 (95%CI 0.00,2.15), respectively. Hypoglycaemia was prevalent amongst those on insulin; for mild/moderate episodes the prevalence was 50% and incidence 23 events per person-year, and for severe episodes the prevalence was 21% and incidence 1 event per person-year. For treatment regimes that included a sulphonylurea, mild/moderate prevalence was 30% and incidence 2 events per person-year, and severe prevalence was 5% and incidence 0.01 events per person-year. A similar prevalence of 5% was found for treatment regimes that did not include sulphonylureas. Conclusions Current evidence shows hypoglycaemia is considerably prevalent amongst people with type 2 diabetes, particularly for those on insulin, yet still fairly common for other treatment regimens. This highlights the subsequent need for educational interventions and individualisation of therapies to reduce the risk of hypoglycaemia. PMID:26061690

  14. Liver abscesses in adult patients with and without diabetes mellitus: an analysis of the clinical characteristics, features of the causative pathogens, outcomes and predictors of fatality: a report based on a large population, retrospective study in China.

    PubMed

    Tian, L-T; Yao, K; Zhang, X-Y; Zhang, Z-D; Liang, Y-J; Yin, D-L; Lee, L; Jiang, H-C; Liu, L-X

    2012-09-01

    In China, there are four types of liver abscesses (LAs) that meet the clinical criteria. Pyogenic liver abscesses (PLAs) and amoebic liver abscesses (ALAs) are two of the most common types of abscesses, followed by fungal liver abscesses (FLAs) and hydatid secondary liver abscesses (HsLAs). Diabetes mellitus (DM) is associated with the development of PLAs. However, there is a lack of population-based studies that have evaluated the underlying relationship between LAs (mainly PLAs and FLAs) and DM. We conducted a retrospective study based on a large population to identify the potential differences and factors that affect the mortality of PLA patients in DM and non-DM groups. Our results revealed that the prevalence of DM is 44.3% (158/357) in PLA patients and 35.3% (18/51) in FLA patients. Compared with the non-DM patients, statistically significant differences were found in DM patients according to symptomatology, clinical manifestations, laboratory findings, microbiological characteristics, antimicrobial resistance, clinical treatments and outcomes in relation to mortality. In addition, the status of antibiotic resistance to E. coli and K. pneumoniae, which were isolated from the patient samples, is severe in the area in which the study was conducted. Regarding the treatment of PLAs, our study indicated that broad-spectrum antimicrobial therapy and drug combinations should be recommended and initiated before the pathogens are cultured and identified. In the clinic, therapies that combine percutaneous drainage with antibiotics and surgery with antibiotics are the two most useful strategies for treating an LA. These two combined treatments resulted in satisfactory cure rates. In the DM and non-DM groups, the cure rates for percutaneous drainage with antibiotics were 90.3% and 92.0%, respectively, and the cure rates for surgery with antibiotics were 93.9% and 95.2%, respectively.

  15. Guiding principles and checklist for population-based quality metrics.

    PubMed

    Krishnan, Mahesh; Brunelli, Steven M; Maddux, Franklin W; Parker, Thomas F; Johnson, Douglas; Nissenson, Allen R; Collins, Allan; Lacson, Eduardo

    2014-06-01

    The Centers for Medicare and Medicaid Services oversees the ESRD Quality Incentive Program to ensure that the highest quality of health care is provided by outpatient dialysis facilities that treat patients with ESRD. To that end, Centers for Medicare and Medicaid Services uses clinical performance measures to evaluate quality of care under a pay-for-performance or value-based purchasing model. Now more than ever, the ESRD therapeutic area serves as the vanguard of health care delivery. By translating medical evidence into clinical performance measures, the ESRD Prospective Payment System became the first disease-specific sector using the pay-for-performance model. A major challenge for the creation and implementation of clinical performance measures is the adjustments that are necessary to transition from taking care of individual patients to managing the care of patient populations. The National Quality Forum and others have developed effective and appropriate population-based clinical performance measures quality metrics that can be aggregated at the physician, hospital, dialysis facility, nursing home, or surgery center level. Clinical performance measures considered for endorsement by the National Quality Forum are evaluated using five key criteria: evidence, performance gap, and priority (impact); reliability; validity; feasibility; and usability and use. We have developed a checklist of special considerations for clinical performance measure development according to these National Quality Forum criteria. Although the checklist is focused on ESRD, it could also have broad application to chronic disease states, where health care delivery organizations seek to enhance quality, safety, and efficiency of their services. Clinical performance measures are likely to become the norm for tracking performance for health care insurers. Thus, it is critical that the methodologies used to develop such metrics serve the payer and the provider and most importantly, reflect

  16. 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.

  17. 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

    2015-01-01

    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.

  18. Rapid increase of health care utilization and cost due to benign prostatic hyperplasia in Korean men: retrospective population-based analysis using the Health Insurance Review and Assessment service data.

    PubMed

    Son, Hwancheol; Park, Juhyun; Song, Sang Hoon; Kang, Jung Yoon; Hong, Sung Kyu; Lee, Hyun Moo; Kim, Sun-Hee; Park, Byung-Joo; Lee, Hyung-Lae; Lee, Kyung Seop

    2015-02-01

    Using the Korean public health insurance database, we analyzed patients diagnosed as benign prostatic hyperplasia (BPH) from 2004 to 2008. Age and year-specific amount and seasonal variation of hospital visits (HV), duration of treatment (DT), the total and per capita amount of insurance payment (TAIP, PCIP) were evaluated. A total of 12,088,995 HV were studied. Total HV increased 1.7 times and DT almost doubled in 2008 compared to those in 2004. HV, DT, and TAIP showed linearly increasing patterns year by year. In a time series analysis, HV increased in winter and demonstrated seasonality in a 12-month cycle. In a Poisson regression analysis, the annual variations of HV, DT, TAIP, and PCIP were different by age groups. In patients older than 40 yr, HV significantly increased 1.10-1.16 times compared to that of the previous year. DT markedly increased in their 60s and 80s patients. The rate of increase in PCIP was steeper in patients 50 yr and older than in the others.Health care utilization due to BPH was rapidly increasing in Korea and it was remarkable in the elderly population. Seasonal variation of HV demonstrated that health care utilization increased in winter.

  19. 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.

  20. Genetic diversity of wild soybean populations in Dongying, China, by simple sequence repeat analysis.

    PubMed

    Wang, Y H; Zhang, X J; Fan, S J

    2015-09-28

    Annual wild soybean (Glycine soja Sieb. et Zucc.), the ancestor of cultivated soybean (G. max), is believed to be a potential gene source for further improvement of soybean to cope with environmental stress. In this study, 10 simple sequence repeat (SSR) markers were used to evaluate the genetic diversity and population genetic structure in five wild soybean populations using 195 accessions collected from Dongying, China. Ten SSR markers yielded 90 bands, with an average of nine bands per marker. The percentage of polymorphic loci (P) was 97.78%, the distribution of expected heterozygosity (HE) was 0.1994-0.4460 with an average of 0.3262, and the distribution from Shannon's information index (I) was 0.3595-0.6506 with an average of 0.5386. The results showed that wild soybean had a high degree of genetic diversity at the species level. Nei's differentiation coefficient (FST) was 0.1533, and gene flow (Nm) was 1.3805, which indicated that genetic variation mainly existed within populations and that there was a certain level of gene exchange between populations. Some genetic differentiation occurred among populations, although this was not significant. Cluster analysis indicated that there was no significant correlation between the genetic structure of wild soybean populations and their geographic distribution, and the clustering results may be relatively consistent with the habitats of the accessions. In the present study, the genetic diversity of wild soybeans showed a broad genetic base and enables suggestions for the conservation of this plant to be made.

  1. 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

  2. Population-level analysis of gut microbiome variation.

    PubMed

    Falony, Gwen; Joossens, Marie; Vieira-Silva, Sara; Wang, Jun; Darzi, Youssef; Faust, Karoline; Kurilshikov, Alexander; Bonder, Marc Jan; Valles-Colomer, Mireia; Vandeputte, Doris; Tito, Raul Y; Chaffron, Samuel; Rymenans, Leen; Verspecht, Chloë; De Sutter, Lise; Lima-Mendez, Gipsi; D'hoe, Kevin; Jonckheere, Karl; Homola, Daniel; Garcia, Roberto; Tigchelaar, Ettje F; Eeckhaudt, Linda; Fu, Jingyuan; Henckaerts, Liesbet; Zhernakova, Alexandra; Wijmenga, Cisca; Raes, Jeroen

    2016-04-29

    Fecal microbiome variation in the average, healthy population has remained under-investigated. Here, we analyzed two independent, extensively phenotyped cohorts: the Belgian Flemish Gut Flora Project (FGFP; discovery cohort; N = 1106) and the Dutch LifeLines-DEEP study (LLDeep; replication; N = 1135). Integration with global data sets (N combined = 3948) revealed a 14-genera core microbiota, but the 664 identified genera still underexplore total gut diversity. Sixty-nine clinical and questionnaire-based covariates were found associated to microbiota compositional variation with a 92% replication rate. Stool consistency showed the largest effect size, whereas medication explained largest total variance and interacted with other covariate-microbiota associations. Early-life events such as birth mode were not reflected in adult microbiota composition. Finally, we found that proposed disease marker genera associated to host covariates, urging inclusion of the latter in study design. PMID:27126039

  3. A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum interspecific populations and Gossypium hirsutum x Gossypium barbadense populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent Meta-analysis of quantitative trait loci (QTL) in tetraploid cotton (Gossypium spp.) has identified regions of the genome with high concentrations of various trait QTL called clusters, and specific trait QTL called hotspots. The Meta-analysis included all population types of Gossypium mixing ...

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. Association of the FABP2 Ala54Thr polymorphism with type 2 diabetes, obesity, and metabolic syndrome: a population-based case-control study and a systematic meta-analysis.

    PubMed

    Liu, Y; Wu, G; Han, L; Zhao, K; Qu, Y; Xu, A; Huang, Q

    2015-02-06

    Previous studies have reported associations between the functional FABP2 Ala54Thr (rs1799883) polymorphism and type 2 diabetes mellitus (T2DM), obesity, and metabolic syndrome in different populations with conflicting results. We investigated the association between the FABP2 Ala54Thr polymorphism and T2DM (235 cases, 431 controls), obesity (377 cases, 431 controls), and metabolic syndrome (315 cases, 323 controls) by logistic regression analysis in a Chinese study cohort recruited from Yichang, Hubei Province. We then comprehensively reviewed the association of the FABP2 Ala54Thr polymorphism with T2DM, obesity, and metabolic syndrome via meta-analysis. The strength of association was assessed by odds ratios (ORs) with 95% confidence intervals (CIs). The FABP2 Ala54Thr polymorphism was significantly associated with obesity (AT vs AA: OR = 2.633, 95%CI = 1.065-6.663, P = 0.036; TT vs AA: OR = 4.160, 95%CI = 1.609-10.757, P = 0.003) and metabolic syndrome (TT vs AA: OR = 2.273, 95%CI = 1.242-4.156, P = 0.008) by logistic regression with adjustment for covariates. However, no significant association was found between T2DM and the FABP2 Ala54Thr polymorphism. We identified 24 studies on T2DM (4517 cases, 5224 controls), 9 studies on obesity (949 cases, 2002 controls), and 6 studies on metabolic syndrome (2194 cases, 3282 controls) by literature search. The meta-analyses revealed significant associations for metabolic syndrome (T allele: OR = 1.179, 95%CI = 1.015-1.362, P = 0.031) and T2DM (T allele: OR = 1.160, 95%CI = 1.08-1.24, P < 0.001), but no association for obesity (T allele: OR = 1.069, 95%CI = 0.925-1.235, P = 0.367).

  9. Analysis of microsatellite DNA markers reveals no genetic differentiation between wild and hatchery populations of Pacific threadfin in Hawaii.

    PubMed

    Pan, Gang; Yang, Jinzeng

    2010-01-01

    Pacific threadfin, Polydactylus sexfilis, is popular fish in recreational fishing, as well as aquaculture in Hawaii. Its natural population has been continuously declining in the past several decades. Microsatellite DNA markers are useful DNA-based tool for monitoring Pacific threadfin populations. In this study, fifteen Microsatellite (MS) DNA markers were identified from a partial genomic Pacific threadfin DNA library enriched in CA repeats, and six highly-polymorphic microsatellite loci were employed to analyze genetic similarity and differences between the wild population and hatchery population in Oahu Island. A total of 37 alleles were detected at the six MS loci in the two populations. Statistical analysis of fixation index (F(ST)) and analysis of molecular variance (AMOVA) showed no genetic differentiation between the wild and hatchery populations (F(ST) = 0.001, CI(95%) = -0.01-0.021). Both high genetic diversity (H(o) = 0.664-0.674 and H(e) = 0.710-0.715) and Hardy-Weinberg equilibrium were observed in the wild and hatchery populations. Results of genetic bottleneck analysis indicated that the hatchery was founded with sufficient numbers of brooders as inbreeding coefficient is very low (F(IS) = 0.052-0.072) in both wild and hatchery populations. Further studies are needed for comprehensive determinations of genetic varieties of primary founder broodstocks and successive offspring of the hatchery and wild populations with increased number of Pacific threadfin sample collections.

  10. 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.

  11. 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.

  12. Internal Transcribed Spacer 1 (ITS1) based sequence typing reveals phylogenetically distinct Ascaris population

    PubMed Central

    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. PMID:26504510

  13. 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.

  14. 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

  15. Cancer incidence in Ghana, 2012: evidence from a population-based cancer registry

    PubMed Central

    2014-01-01

    Background Data on cancers is a challenge in most developing countries. Population-based cancer registries are also not common in developing countries despite the usefulness of such registries in informing cancer prevention and control programmes. The availability of population-based data on cancers in Africa varies across different countries. In Ghana, data and research on cancer have focussed on specific cancers and have been hospital-based with no reference population. The Kumasi Cancer Registry was established as the first population-based cancer registry in Ghana in 2012 to provide information on cancer cases seen in the city of Kumasi. Methods This paper reviews data from the Kumasi Cancer Registry for the year 2012. The reference geographic area for the registry is the city of Kumasi as designated by the 2010 Ghana Population and Housing Census. Data was from all clinical departments of the Komfo Anokye Teaching Hospital, Pathology Laboratory Results, Death Certificates and the Kumasi South Regional Hospital. Data was abstracted and entered into Canreg 5 database. Analysis was conducted using Canreg 5, Microsoft Excel and Epi Info Version 7.1.2.0. Results The majority of cancers were recorded among females accounting for 69.6% of all cases. The mean age at diagnosis for all cases was 51.6 years. Among males, the mean age at diagnosis was 48.4 compared with 53.0 years for females. The commonest cancers among males were cancers of the Liver (21.1%), Prostate (13.2%), Lung (5.3%) and Stomach (5.3%). Among females, the commonest cancers were cancers of the Breast (33.9%), Cervix (29.4%), Ovary (11.3%) and Endometrium (4.5%). Histology of the primary tumour was the basis of diagnosis in 74% of cases with clinical and other investigations accounting for 17% and 9% respectively. The estimated cancer incidence Age Adjusted Standardised Rate for males was 10.9/100,000 and 22.4/100, 000 for females. Conclusion This first attempt at population-based cancer

  16. Estimation of the Genetic Diversity in Tetraploid Alfalfa Populations Based on RAPD Markers for Breeding Purposes

    PubMed Central

    Nagl, Nevena; Taski-Ajdukovic, Ksenija; Barac, Goran; Baburski, Aleksandar; Seccareccia, Ivana; Milic, Dragan; Katic, Slobodan

    2011-01-01

    Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm. PMID:21954370

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. Microsatellite analysis of North American wapiti (Cervus elaphus) populations.

    PubMed

    Polziehn, R O; Hamr, J; Mallory, F F; Strobeck, C

    2000-10-01

    Eleven populations of wapiti (Cervus elaphus) were analysed for genetic diversity using 12 microsatellite loci. Samples were taken from Vancouver Island, British Columbia; Burwash and French River herds in Ontario; Ya Ha Tinda Ranch, Alberta; and Banff, Elk Island, Jasper, Kootenay, Riding Mountain, Yellowstone and Yoho National Parks. Overall, wapiti populations have on average three to four alleles per locus and an average expected heterozygosity that ranged from 25.75 to 52.85%. The greatest genetic distances were observed between the Vancouver population and all other populations. Using the assignment test, Roosevelt wapiti (C. e. roosevelti Merriam 1897) assigned only to the Vancouver Island population. The distance and assignment values suggest a divergence of the Roosevelt wapiti from other populations and support the subspecific status for the Vancouver Island population. No evidence was found for the existence of unique Eastern wapiti (C. e. canadensis Erxleben 1777) in the Burwash or French River herds in Ontario. The overlapping distribution of genotypes from indigenous populations from Riding Mountain, Elk Island and Yellowstone National Parks suggests that wapiti were once a continuous population before settlers decimated their numbers. The lack of differentiation between these populations raises questions about the status of Manitoban (C. e.manitobensis Millais 1915) and Rocky Mountain (C. e.nelsoni Bailey 1935) subspecies.

  2. Epidemiology of Rett syndrome: a population-based registry.

    PubMed

    Kozinetz, C A; Skender, M L; MacNaughton, N; Almes, M J; Schultz, R J; Percy, A K; Glaze, D G

    1993-02-01

    The Texas Rett Syndrome Registry maintains the largest population-based registry of cases and potential cases of Rett syndrome in the world. The most precise estimate of the prevalence of Rett syndrome of 1 per 22800 (0.44/10000) females aged 2 through 18 years of age was generated from this Registry. In addition, the first prevalence figures for black and Hispanic female cases were estimated. Registry cases are actively ascertained from multiple sources. Registry staff identify presumptive cases from review of information provided to the Registry by the parent or guardian. Preliminary diagnostic evaluation includes standardized review of medical records and videotape of key behaviors. Diagnosis is confirmed at clinical evaluation. The active surveillance system is monitored with the two-source capture-recapture methodology and case ascertainment is projected. The 1990 prevalence estimate of Rett syndrome indicates that the syndrome occurs less frequently than previously estimated. Until a biologic marker for Rett syndrome is identified or a standard definition for an incident case of Rett syndrome is designated, the prevalence of Rett syndrome will remain a major investigative issue of its epidemiology, and the Registry will be an important, systematic mean to gather case material for clinical and laboratory studies providing the foundation for the development of preventive interventions.

  3. 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.

  4. 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.

  5. Generalized Laminar Population Analysis (gLPA) for Interpretation of Multielectrode Data from Cortex.

    PubMed

    Głąbska, Helena T; Norheim, Eivind; Devor, Anna; Dale, Anders M; Einevoll, Gaute T; Wójcik, Daniel K

    2016-01-01

    Laminar population analysis (LPA) is a method for analysis of electrical data recorded by linear multielectrodes passing through all lamina of cortex. Like principal components analysis (PCA) and independent components analysis (ICA), LPA offers a way to decompose the data into contributions from separate cortical populations. However, instead of using purely mathematical assumptions in the decomposition, LPA is based on physiological constraints, i.e., that the observed LFP (low-frequency part of signal) is driven by action-potential firing as observed in the MUA (multi-unit activity; high-frequency part of the signal). In the presently developed generalized laminar population analysis (gLPA) the set of basis functions accounting for the LFP data is extended compared to the original LPA, thus allowing for a better fit of the model to experimental data. This enhances the risk for overfitting, however, and we therefore tested various versions of gLPA on virtual LFP data in which we knew the ground truth. These synthetic data were generated by biophysical forward-modeling of electrical signals from network activity in the comprehensive, and well-known, thalamocortical network model developed by Traub and coworkers. The results for the Traub model imply that while the laminar components extracted by the original LPA method overall are in fair agreement with the ground-truth laminar components, the results may be improved by use of gLPA method with two (gLPA-2) or even three (gLPA-3) postsynaptic LFP kernels per laminar population. PMID:26834620

  6. Generalized Laminar Population Analysis (gLPA) for Interpretation of Multielectrode Data from Cortex.

    PubMed

    Głąbska, Helena T; Norheim, Eivind; Devor, Anna; Dale, Anders M; Einevoll, Gaute T; Wójcik, Daniel K

    2016-01-01

    Laminar population analysis (LPA) is a method for analysis of electrical data recorded by linear multielectrodes passing through all lamina of cortex. Like principal components analysis (PCA) and independent components analysis (ICA), LPA offers a way to decompose the data into contributions from separate cortical populations. However, instead of using purely mathematical assumptions in the decomposition, LPA is based on physiological constraints, i.e., that the observed LFP (low-frequency part of signal) is driven by action-potential firing as observed in the MUA (multi-unit activity; high-frequency part of the signal). In the presently developed generalized laminar population analysis (gLPA) the set of basis functions accounting for the LFP data is extended compared to the original LPA, thus allowing for a better fit of the model to experimental data. This enhances the risk for overfitting, however, and we therefore tested various versions of gLPA on virtual LFP data in which we knew the ground truth. These synthetic data were generated by biophysical forward-modeling of electrical signals from network activity in the comprehensive, and well-known, thalamocortical network model developed by Traub and coworkers. The results for the Traub model imply that while the laminar components extracted by the original LPA method overall are in fair agreement with the ground-truth laminar components, the results may be improved by use of gLPA method with two (gLPA-2) or even three (gLPA-3) postsynaptic LFP kernels per laminar population.

  7. Generalized Laminar Population Analysis (gLPA) for Interpretation of Multielectrode Data from Cortex

    PubMed Central

    Głąbska, Helena T.; Norheim, Eivind; Devor, Anna; Dale, Anders M.; Einevoll, Gaute T.; Wójcik, Daniel K.

    2016-01-01

    Laminar population analysis (LPA) is a method for analysis of electrical data recorded by linear multielectrodes passing through all lamina of cortex. Like principal components analysis (PCA) and independent components analysis (ICA), LPA offers a way to decompose the data into contributions from separate cortical populations. However, instead of using purely mathematical assumptions in the decomposition, LPA is based on physiological constraints, i.e., that the observed LFP (low-frequency part of signal) is driven by action-potential firing as observed in the MUA (multi-unit activity; high-frequency part of the signal). In the presently developed generalized laminar population analysis (gLPA) the set of basis functions accounting for the LFP data is extended compared to the original LPA, thus allowing for a better fit of the model to experimental data. This enhances the risk for overfitting, however, and we therefore tested various versions of gLPA on virtual LFP data in which we knew the ground truth. These synthetic data were generated by biophysical forward-modeling of electrical signals from network activity in the comprehensive, and well-known, thalamocortical network model developed by Traub and coworkers. The results for the Traub model imply that while the laminar components extracted by the original LPA method overall are in fair agreement with the ground-truth laminar components, the results may be improved by use of gLPA method with two (gLPA-2) or even three (gLPA-3) postsynaptic LFP kernels per laminar population. PMID:26834620

  8. Population pharmacokinetic analysis of Ibuprofen enantiomers in preterm newborn infants.

    PubMed

    Gregoire, Nicolas; Desfrere, Luc; Roze, Jean-Christophe; Kibleur, Yves; Koehne, Petra

    2008-12-01

    The aim of this pharmacokinetic analysis was to develop and validate a population pharmacokinetic model for R- and S-ibuprofen from samples obtained after 3 successive administrations of ibuprofen (10-5-5 mg/kg) at 24-hour intervals to preterm newborn infants aged from <6 hours to 8 days of life. A model including unilateral bioconversion of R-ibuprofen into S-ibuprofen was developed using the software NONMEM. R- and S-ibuprofen plasma concentrations were adequately fitted by this model. Estimated clearance and volume of distribution were 3.5 mL/h/kg and 173 mL/kg, respectively, with a calculated half-life (t((1/2))) of 34.3 hours for S-ibuprofen. Estimated clearance at birth and volume of distribution were 25.5 mL/h/kg and 306 mL/kg with a t((1/2)) at birth of 8.3 hours for R-ibuprofen. R-ibuprofen elimination increased during the first week of life, whereas S-ibuprofen pharmacokinetics were weakly modified. Therefore, because the activity of the 2 enantiomers differs, it is important that subsequent studies consider R- and S-enantiomers separately. Mean simulated ibuprofen concentrations at various dose regimens were in agreement with observed concentrations. The present analysis allows a more accurate estimation of the ibuprofen pharmacokinetics as parameters could be estimated separately for each enantiomer and the effect of postnatal age on the elimination of R-ibuprofen was elicited. PMID:18796580

  9. [Methods and applications of population viability analysis (PVA): a review].

    PubMed

    Tian, Yu; Wu, Jian-Guo; Kou, Xiao-Jun; Wang, Tian-Ming; Smith, Andrew T; Ge, Jian-Ping

    2011-01-01

    With the accelerating human consumption of natural resources, the problems associated with endangered species caused by habitat loss and fragmentation have become greater and more urgent than ever. Conceptually associated with the theories of island biogeography, population viability analysis (PVA) has been one of the most important approaches in studying and protecting endangered species, and this methodology has occupied a central place in conservation biology and ecology in the past several decades. PVA has been widely used and proven effective in many cases, but its predictive ability and accuracy are still in question. Also, its application needs expand. To overcome some of the problems, we believe that PVA needs to incorporate some principles and methods from other fields, particularly landscape ecology and sustainability science. Integrating landscape pattern and socioeconomic factors into PVA will make the approach theoretically more comprehensive and practically more useful. Here, we reviewed the history, basic conception, research methods, and modeling applications and their accuracies of PVA, and proposed the perspective in this field. PMID:21548317

  10. Chromosomal aberrations analysis in a Brazilian population exposed to pesticides.

    PubMed

    Antonucci, G A; de Syllos Cólus, I M

    2000-01-01

    In spite of being harmful, pesticides are widely used in Brazil. Their genotoxic effects might be studied through population monitoring by means of the analysis of chromosomal aberrations in occupationally exposed individuals. The aim of this study was to evaluate the chromosomal aberration frequencies in temporary cultures of lymphocytes from periferic blood of 23 workers professionally exposed to a mixture of pesticides. The workers were employed by the Agronomic Institute of Parana (Brazil) and used all of the prevention measures provided. A detailed history of pesticide use, as well as personal data, smoking habits, and history of recent illnesses and medical treatment were collected through a standardized questionnaire administered to each subject. Nonexposed subjects, matched for age, sex, and smoking habits, served as the negative control. A total of 100 cells were analyzed from each individual. A significant increase in chromosomal aberration frequencies was observed in exposed individuals when compared to the control group. Some individual characteristics such as age, sex, time of exposure to the pesticides, and smoking habits showed no correlation with chromosomal aberrations. Therefore, the positive results may be considered true effects of pesticides on human somatic cells. PMID:10992273

  11. Analysis of Geographic and Pairwise Distances among Chinese Cashmere Goat Populations

    PubMed Central

    Liu, Jian-Bin; Wang, Fan; Lang, Xia; Zha, Xi; Sun, Xiao-Ping; Yue, Yao-Jing; Feng, Rui-Lin; Yang, Bo-Hui; Guo, Jian

    2013-01-01

    This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism information content of loci ranged from 0.5213 to 0.7582; the number of effective alleles ranged from 4.0484 to 4.6178; the observed heterozygosity was from 0.5023 to 0.5602 for the practical sample; the expected heterozygosity ranged from 0.5783 to 0.6464; and Allelic richness ranged from 4.7551 to 8.0693. These results indicated that Chinese Cashmere goat populations exhibited rich genetic diversity. Further, the Wright’s F-statistics of subpopulation within total (FST) was 0.1184; the genetic differentiation coefficient (GST) was 0.0940; and the average gene flow (Nm) was 2.0415. All pairwise FST values among the populations were highly significant (p<0.01 or p<0.001), suggesting that the populations studied should all be considered to be separate breeds. Finally, the clustering analysis divided the Chinese Cashmere goat populations into at least four clusters, with the Hexi and Yashan goat populations alone in one cluster. These results have provided useful, practical, and important information for the future of Chinese Cashmere goat breeding. PMID:25049794

  12. Community Based Cardiovascular Health Interventions in Vulnerable Populations: A Systematic Review

    PubMed Central

    Walton-Moss, Benita; Samuel, Laura; Nguyen, Tam H; Commodore-Mensah, Yvonne; Hayat, Matthew J.; Szanton, Sarah L.

    2013-01-01

    Background Although cardiovascular health has been improving for many Americans, this is not true of those in “vulnerable populations.” To address this growing disparity communities and researchers have worked for decades, and as a result of their work a growing body of literature supports the use of community engagement as a component of successful interventions. However, little literature synthesizes community-based interventions that address this disparity among a wide range of vulnerable populations. Objective This paper provides a critical review of community-based cardiovascular disease (CVD) interventions to improve cardiovascular health behaviors and factors among vulnerable populations based on the American Heart Association’s 7 metrics of ideal cardiovascular health. Methods In February 2011, four databases (PubMed, PsychInfo, CINAHL, and Scopus) were searched using the following keywords: vulnerable populations OR healthcare disparities AND cardiovascular disease AND clinical trials OR public health practice AND English. Results This search strategy resulted in the retrieval of 7,120 abstracts. Each abstract was reviewed by at least two authors and eligibility for the systematic review was confirmed after reading the full article. Thirty two studies met eligibility criteria. Education was the most common intervention (41%), followed by counseling or support (38%), and exercise classes (28%). Half of the interventions were multi-component. Health care providers were the most frequent interventionists. Interventions aimed at decreasing blood pressure were the most promising while behavior change interventions were the most challenging. Almost all of the interventions were at the individual level, and were proof of concept or efficacy trials. Conclusions This analysis provides a step towards understanding the current literature on cardiovascular interventions for vulnerable population. The next step should be integrating the identified successful

  13. Model-Based Safety Analysis

    NASA Technical Reports Server (NTRS)

    Joshi, Anjali; Heimdahl, Mats P. E.; Miller, Steven P.; Whalen, Mike W.

    2006-01-01

    System safety analysis techniques are well established and are used extensively during the design of safety-critical systems. Despite this, most of the techniques are highly subjective and dependent on the skill of the practitioner. Since these analyses are usually based on an informal system model, it is unlikely that they will be complete, consistent, and error free. In fact, the lack of precise models of the system architecture and its failure modes often forces the safety analysts to devote much of their effort to gathering architectural details about the system behavior from several sources and embedding this information in the safety artifacts such as the fault trees. This report describes Model-Based Safety Analysis, an approach in which the system and safety engineers share a common system model created using a model-based development process. By extending the system model with a fault model as well as relevant portions of the physical system to be controlled, automated support can be provided for much of the safety analysis. We believe that by using a common model for both system and safety engineering and automating parts of the safety analysis, we can both reduce the cost and improve the quality of the safety analysis. Here we present our vision of model-based safety analysis and discuss the advantages and challenges in making this approach practical.

  14. A microarray analysis of two distinct lymphatic endothelial cell populations.

    PubMed

    Schweighofer, Bernhard; Rohringer, Sabrina; Pröll, Johannes; Holnthoner, Wolfgang

    2015-06-01

    We have recently identified lymphatic endothelial cells (LECs) to form two morphologically different populations, exhibiting significantly different surface protein expression levels of podoplanin, a major surface marker for this cell type. In vitro shockwave treatment (IVSWT) of LECs resulted in enrichment of the podoplanin(high) cell population and was accompanied by markedly increased cell proliferation, as well as 2D and 3D migration. Gene expression profiles of these distinct populations were established using Affymetrix microarray analyses. Here we provide additional details about our dataset (NCBI GEO accession number GSE62510) and describe how we analyzed the data to identify differently expressed genes in these two LEC populations.

  15. 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

  16. Genetic diversity, population structure and association analysis in cut chrysanthemum (Chrysanthemum morifolium Ramat.).

    PubMed

    Li, Pirui; Zhang, Fei; Chen, Sumei; Jiang, Jiafu; Wang, Haibin; Su, Jiangshuo; Fang, Weimin; Guan, Zhiyong; Chen, Fadi

    2016-06-01

    Characterizing the genetic diversity present in a working set of plant germplasm can contribute to its effective management and genetic improvement. The cut flower chrysanthemum (Chrysanthemum morifolium Ramat.) is an economically important ornamental species. With the repeated germplasm exchange and intensive breeding activities, it remains a major task in genetic research. The purpose of the present study was to characterize the genetic diversity and the population structure of a worldwide collection of 159 varieties, and to apply an association mapping approach to identify DNA-based markers linked to five plant architecture traits and six inflorescence traits. The genotyping demonstrated that there was no lack of genetic diversity in the collection and that pair-wise kinship values were relatively low. The clustering based on a Bayesian model of population structure did not reflect known variation in either provenance or inflorescence type. A principal coordinate analysis was, however, able to discriminate most of the varieties according to both of these criteria. About 1 in 100 marker pairs exhibited a degree of linkage disequilibrium. The association analysis identified a number of markers putatively linked to one or more of the traits. Some of these associations were robust over two seasons. The findings provide an in-depth understanding of genetic diversity and population structure present in cut flower chrysanthemum varieties, and an insight into the genetic control of plant architecture and inflorescence-related traits. PMID:26780102

  17. 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.

  18. [Analysis of population status in the People's Republic of Mongolia].

    PubMed

    Bater

    1991-02-01

    The population of the People's Republic of Mongolia increased 2.1 times in 70 years from 0.65 million in 1981 to 2.02 million in 1987. 1918-1956 was a pre-transitional period of low population growth. A substantial growth was experienced during the period of 1956-1987, since economic and technological development increased living standards and reduced mortality. The Mongolian government adopted a pro-natal policy in which incentives are given to have large families. Nevertheless, fertility started to decline in the 1980s. Promoting education had been an important achievement of Mongolia since its independence in 1921. 54% of the current population received more than 8 years of education, and 7.32% had college or vocational school education. Over a quarter of the population was in school. The rapid increase in the level of education attained by the population can be attributed to the priority status given to education by the government. The expenditure in education and health in 1987 was 7.7% of the total national economic investment. Education at all levels including kindergarten is free. The occupational composition of the population had undergone considerable changes since 1960. Those engaged in farming and animal husbandry decreased from 60.8% of the working population in 1960 to 31.5% in 1987. while the proportion of industrial workers increased from 12% of the working population in 1960 to 19% in 1987. The population in the service industry, research, and education increased to 5.5, 3.5, and 1.8 times the 1960 figure, respectively, in 1987. The rural population decreased from 78.4% in 1959 to 47.9% in 1987. These population changes reflects the socio-economic development of Mongolia.

  19. Population structure and genetic analysis of narrow-clawed crayfish (Astacus leptodactylus) populations in Turkey.

    PubMed

    Akhan, Suleyman; Bektas, Yusuf; Berber, Selcuk; Kalayci, Gokhan

    2014-10-01

    The genetic differentiation among Turkish populations of the narrow-clawed crayfish was investigated using a partial sequence of cytochrome oxidase subunit I gene (585 bp) of 183 specimens from 17 different crayfish populations. Median joining network and all phylogenetic analyses disclosed a strong haplotype structure with three prominent clades diverged by a range between 20 and 50 mutations and substantial inter-group pairwise sequence divergence (5.19-6.95 %), suggesting the presence of three distinct clades within the Anatolian populations of Astacus leptodactylus. The divergence times among the three clades of Turkish A. leptodactylus are estimated to be 4.96-3.70 Mya using a molecular clock of 1.4 % sequence divergence per million years, pointing to a lower Pliocene separation. The high level of genetic variability (H d = 95.8 %, π = 4.17 %) and numerous private haplotypes suggest the presence of refugial populations in Anatolia unaffected by Pleistocene habitat restrictions. The pattern of genetic variation among Turkish A. leptodactylus populations, therefore, suggests that the unrevealed intraspecific genetic structure is independent of geographic tendency and congruent with the previously reported geographic distribution and number of subspecies (A. l. leptodactylus and A. l. salinus) of A. leptodactylus.

  20. 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.

  1. Scalable Entity-Based Modeling of Population-Based Systems, Final LDRD Report

    SciTech Connect

    Cleary, A J; Smith, S G; Vassilevska, T K; Jefferson, D R

    2005-01-27

    The goal of this project has been to develop tools, capabilities and expertise in the modeling of complex population-based systems via scalable entity-based modeling (EBM). Our initial focal application domain has been the dynamics of large populations exposed to disease-causing agents, a topic of interest to the Department of Homeland Security in the context of bioterrorism. In the academic community, discrete simulation technology based on individual entities has shown initial success, but the technology has not been scaled to the problem sizes or computational resources of LLNL. Our developmental emphasis has been on the extension of this technology to parallel computers and maturation of the technology from an academic to a lab setting.

  2. 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

  3. The measurement and analysis of leaf spectral reflectance of two stands of loblolly pine populations

    NASA Technical Reports Server (NTRS)

    Paul, Anthony D.

    1993-01-01

    My research was conducted under the mentorship of Dr. Jeff Luvall. I worked at Marshall from June 1 through August 6, 1993. My proposal is titled 'The Measurement and Analysis of Leaf Spectral Reflectance of Two Stands of Loblolly Pine Populations.' The populations for this study were chosen from a larger population of 31 families managed by the International Forest Seed Company, Odenville, Alabama. The technology for mobile ground base spectral detecting is new and therefore the majority of time, June 2 through July 9, was spent on learning the techniques of the Spectrometer 2 spectroradiometer used in the gathering of spectra information. The activities included in the learning process were as follows: calibration of the equipment, programming the associated computer for data management, operation of the spectral devices, and input and output of data. From July 12 through August 3 the time was spent on learning the 'STATGRAP' computer software. This software will be used in the analysis of the data retrieved by the Spectrometer 2 spectroradiometer. Dr. Greg Carter, at Stennis, a colleague of Dr. Luvall, has been conducting similar work with different instruments and procedures and has agreed to host us for a training session on data gathering and analysis. This visit, which has previously planned for July 9, 1993, but had to be postponed because of schedule conflicts, is now confirmed for August 18-22, 1993. This trip to Stennis will provide the knowledge for conducting the field operations in my study, i.e., gathering of data and file conversions.

  4. Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition

    PubMed Central

    Saeed, Isaam; Tang, Sen-Lin; Halgamuge, Saman K.

    2012-01-01

    An approach to infer the unknown microbial population structure within a metagenome is to cluster nucleotide sequences based on common patterns in base composition, otherwise referred to as binning. When functional roles are assigned to the identified populations, a deeper understanding of microbial communities can be attained, more so than gene-centric approaches that explore overall functionality. In this study, we propose an unsupervised, model-based binning method with two clustering tiers, which uses a novel transformation of the oligonucleotide frequency-derived error gradient and GC content to generate coarse groups at the first tier of clustering; and tetranucleotide frequency to refine these groups at the secondary clustering tier. The proposed method has a demonstrated improvement over PhyloPythia, S-GSOM, TACOA and TaxSOM on all three benchmarks that were used for evaluation in this study. The proposed method is then applied to a pyrosequenced metagenomic library of mud volcano sediment sampled in southwestern Taiwan, with the inferred population structure validated against complementary sequencing of 16S ribosomal RNA marker genes. Finally, the proposed method was further validated against four publicly available metagenomes, including a highly complex Antarctic whale-fall bone sample, which was previously assumed to be too complex for binning prior to functional analysis. PMID:22180538

  5. Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia.

    PubMed

    Moges, Asmare D; Admassu, Belayneh; Belew, Derbew; Yesuf, Mohammed; Njuguna, Joyce; Kyalo, Martina; Ghimire, Sita R

    2016-01-01

    Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (FST = 0.049) as evidenced by high level of gene flow estimate (Nm = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia.

  6. Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia.

    PubMed

    Moges, Asmare D; Admassu, Belayneh; Belew, Derbew; Yesuf, Mohammed; Njuguna, Joyce; Kyalo, Martina; Ghimire, Sita R

    2016-01-01

    Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (FST = 0.049) as evidenced by high level of gene flow estimate (Nm = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia. PMID:26978654

  7. Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia

    PubMed Central

    Moges, Asmare D.; Admassu, Belayneh; Belew, Derbew; Yesuf, Mohammed; Njuguna, Joyce; Kyalo, Martina; Ghimire, Sita R.

    2016-01-01

    Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (FST = 0.049) as evidenced by high level of gene flow estimate (Nm = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia. PMID:26978654

  8. Accounting for linkage disequilibrium in association analysis of diverse populations.

    PubMed

    Charles, Bashira A; Shriner, Daniel; Rotimi, Charles N

    2014-04-01

    The National Human Genome Research Institute's catalog of published genome-wide association studies (GWAS) lists over 10,000 genetic variants collectively associated with over 800 human diseases or traits. Most of these GWAS have been conducted in European-ancestry populations. Findings gleaned from these studies have led to identification of disease-associated loci and biologic pathways involved in disease etiology. In multiple instances, these genomic findings have led to the development of novel medical therapies or evidence for prescribing a given drug as the appropriate treatment for a given individual beyond phenotypic appearances or socially defined constructs of race or ethnicity. Such findings have implications for populations throughout the globe and GWAS are increasingly being conducted in more diverse populations. A major challenge for investigators seeking to follow up genomic findings between diverse populations is discordant patterns of linkage disequilibrium (LD). We provide an overview of common measures of LD and opportunities for their use in novel methods designed to address challenges associated with following up GWAS conducted in European-ancestry populations in African-ancestry populations or, more generally, between populations with discordant LD patterns. We detail the strengths and weaknesses associated with different approaches. We also describe application of these strategies in follow-up studies of populations with concordant LD patterns (replication) or discordant LD patterns (transferability) as well as fine-mapping studies. We review application of these methods to a variety of traits and diseases.

  9. Population models for passerine birds: structure, parameterization, and analysis

    USGS Publications Warehouse

    Noon, B.R.; Sauer, J.R.; McCullough, D.R.; Barrett, R.H.

    1992-01-01

    Population models have great potential as management tools, as they use infonnation about the life history of a species to summarize estimates of fecundity and survival into a description of population change. Models provide a framework for projecting future populations, determining the effects of management decisions on future population dynamics, evaluating extinction probabilities, and addressing a variety of questions of ecological and evolutionary interest. Even when insufficient information exists to allow complete identification of the model, the modelling procedure is useful because it forces the investigator to consider the life history of the species when determining what parameters should be estimated from field studies and provides a context for evaluating the relative importance of demographic parameters. Models have been little used in the study of the population dynamics of passerine birds because of: (1) widespread misunderstandings of the model structures and parameterizations, (2) a lack of knowledge of life histories of many species, (3) difficulties in obtaining statistically reliable estimates of demographic parameters for most passerine species, and (4) confusion about functional relationships among demographic parameters. As a result, studies of passerine demography are often designed inappropriately and fail to provide essential data. We review appropriate models for passerine bird populations and illustrate their possible uses in evaluating the effects of management or other environmental influences on population dynamics. We identify environmental influences on population dynamics. We identify parameters that must be estimated from field data, briefly review existing statistical methods for obtaining valid estimates, and evaluate the present status of knowledge of these parameters.

  10. Molecular genetic analysis of populations of Wohlfahrt's wound myiasis fly, Wohlfahrtia magnifica, in outbreak populations from Greece and Morocco.

    PubMed

    Hall, M J R; Testa, J M; Smith, L; Adams, Z J O; Khallaayoune, K; Sotiraki, S; Stefanakis, A; Farkas, R; Ready, P D

    2009-06-01

    Wohlfahrt's wound myiasis fly, Wohlfahrtia magnifica (Schiner) (Diptera: Sarcophagidae), is the most important cause of traumatic myiasis in the southern Palaearctic region. Larval stages are obligate parasites and the wounds caused by infestations are very similar to those caused by Old and New World screwworm flies. During the last decade, W. magnifica appears to have expanded its range to parts of northern and central Morocco, and to Crete, Greece. Specimens of W. magnifica were collected in Morocco and Crete either as larvae (preserved in 80% ethanol) or as adults (dry-pinned). Comparison specimens were collected in Spain, Hungary and mainland Greece. A DNA fragment containing the 3' 715 base pairs of the mitochondrial cytochrome b gene was amplified by polymerase chain reaction from each of 132 larvae or adults of W. magnifica and the amplicons were directly sequenced and analysed phylogeographically. Twelve cytochrome b haplotypes were detected. All haplotypes from Morocco belonged to a lineage that included specimens from the Iberian peninsula, and restricted mixing of central and northern populations in Morocco was demonstrated. Cytochrome b haplotyping combined with an analysis of larval size provided clear evidence of multiple infestations of hosts in all geographical areas, with one quarter of wounds containing larvae from two to at least four females. More than 80% of specimens from Crete contained a haplotype predominating in mainland Greece and Hungary. Our survey indicated that wohlfahrtiosis was more widespread in northern and central Morocco than previously recorded by government veterinarians. However, the prevalence of wohlfahrtiosis was low (< 1%). The high genetic diversity of Moroccan populations is consistent with longterm endemicity, rather than recent introduction. Crete showed a higher prevalence of wohlfahrtiosis (< or = 15%) and less genetic diversity of W. magnifica, which is consistent with a recent introduction. The western and

  11. Impact of 13-Valent Pneumococcal Conjugate Vaccine Used in Children on Invasive Pneumococcal Disease in Children and Adults in the United States: Analysis of Multisite, Population-based Surveillance

    PubMed Central

    Moore, Matthew R.; Link-Gelles, Ruth; Schaffner, William; Lynfield, Ruth; Lexau, Catherine; Bennett, Nancy M.; Petit, Susan; Zansky, Shelley M.; Harrison, Lee H.; Reingold, Arthur; Miller, Lisa; Scherzinger, Karen; Thomas, Ann; Farley, Monica M.; Zell, Elizabeth R.; Taylor, Thomas H.; Pondo, Tracy; Rodgers, Loren; McGee, Lesley; Beall, Bernard; Jorgensen, James H.; Whitney, Cynthia G.

    2016-01-01

    SUMMARY Background In 2000, 7-valent pneumococcal conjugate vaccine (PCV7) was introduced in the U.S. and resulted in dramatic reductions in invasive pneumococcal disease (IPD) and modest increases in non-PCV7-type IPD. In 2010, a 13-valent pneumococcal conjugate vaccine (PCV13) replaced PCV7 in the U.S. immunization schedule. We evaluated the effect of PCV13 use in children on IPD in children and adults in the U.S. Methods We used laboratory- and population-based data on incidence of IPD from CDC’s Emerging Infections Program / Active Bacterial Core surveillance in a time-series model to estimate the impact of vaccination. Cases of IPD during July 2004–June 2013 were classified as being caused by the PCV13 serotypes against which PCV7 has no effect (PCV13/nonPCV7). Findings Compared with incidence expected among children <5 years old if PCV7 alone had been continued, incidence of IPD overall and IPD caused by PCV13/nonPCV7 serotypes declined by 64% (95% interval estimate [IE] 59–68 %) and 93% (95%IE 91–94), respectively, by July 2012–June 2013. Among adults, incidence of IPD overall and PCV13/nonPCV7-type IPD also declined by 12–32% and 58–72%, respectively, depending on age. In all age groups, reductions were driven principally by changes in incidence of serotypes 19A and 7F. We estimate that over 30,000 cases of IPD and 3,000 deaths were averted in the first 3 years following PCV13 introduction. Interpretation PCV13 has reduced IPD among all ages when used routinely in children in the U.S. Serotypes 19A and 7F, which emerged after PCV7 introduction, have been effectively controlled. PMID:25656600

  12. Delineating outcomes of patients with diffuse large b cell lymphoma using the national comprehensive cancer network-international prognostic index and positron emission tomography-defined remission status; a population-based analysis.

    PubMed

    Bishton, Mark J; Hughes, Simon; Richardson, Faith; James, Eleanor; Bessell, Eric; Sovani, Vishakha; Ganatra, Rakesh; Haynes, Andrew P; McMillan, Andrew K; Fox, Christopher P

    2016-01-01

    The recently devised National Comprehensive Cancer Network International Prognostic Index (NCCN-IPI) appears superior to the revised IPI (R-IPI) in delineating outcome in diffuse large B-cell lymphoma. We examined the outcome of a population-based cohort of 223 consecutive patients treated with R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, prednisolone) or R-CHOP-like immuno-chemotherapy between January 2005 and December 2011 by both the NCCN-IPI and R-IPI, and further stratified outcome by the achievement of both computerized tomography (CT) and positron emission tomography (PET)-CT complete remission (CR), with the latter reassessed using blinded central review by an independent nuclear medicine and radiology specialist. The NCCN-IPI was superior to the R-IPI in identifying patients at very high risk of systemic and/or central nervous system relapse. Notably, both the NCCN-IPI and the R-IPI remained strongly predictive of relapse irrespective of CT or PET-defined remission status following R-CHOP. Patients with high-risk NCCN-IPI scores (≥6) have a dismal outcome following R-CHOP therapy regardless of PET-defined response to R-CHOP. Moreover, such patients appear refractory to salvage chemotherapy and thus require alternative therapeutic approaches, although age and performance status may, for many patients, preclude the safe delivery of a primary intensified regimen. By contrast, patients with NCCN-IPI 1-5 who achieve PET-CR following R-CHOP have excellent outcomes and may merit reduced follow up frequency. PMID:26577576

  13. MtDNA analysis of global populations support that major population expansions began before Neolithic Time

    NASA Astrophysics Data System (ADS)

    Zheng, Hong-Xiang; Yan, Shi; Qin, Zhen-Dong; Jin, Li

    2012-10-01

    Agriculture resulted in extensive population growths and human activities. However, whether major human expansions started after Neolithic Time still remained controversial. With the benefit of 1000 Genome Project, we were able to analyze a total of 910 samples from 11 populations in Africa, Europe and Americas. From these random samples, we identified the expansion lineages and reconstructed the historical demographic variations. In all the three continents, we found that most major lineage expansions (11 out of 15 star lineages in Africa, all autochthonous lineages in Europe and America) coalesced before the first appearance of agriculture. Furthermore, major population expansions were estimated after Last Glacial Maximum but before Neolithic Time, also corresponding to the result of major lineage expansions. Considering results in current and previous study, global mtDNA evidence showed that rising temperature after Last Glacial Maximum offered amiable environments and might be the most important factor for prehistorical human expansions.

  14. Effects of climate change on an emperor penguin population: analysis of coupled demographic and climate models.

    PubMed

    Jenouvrier, Stéphanie; Holland, Marika; Stroeve, Julienne; Barbraud, Christophe; Weimerskirch, Henri; Serreze, Mark; Caswell, Hal

    2012-09-01

    Sea ice conditions in the Antarctic affect the life cycle of the emperor penguin (Aptenodytes forsteri). We present a population projection for the emperor penguin population of Terre Adélie, Antarctica, by linking demographic models (stage-structured, seasonal, nonlinear, two-sex matrix population models) to sea ice forecasts from an ensemble of IPCC climate models. Based on maximum likelihood capture-mark-recapture analysis, we find that seasonal sea ice concentration anomalies (SICa ) affect adult survival and breeding success. Demographic models show that both deterministic and stochastic population growth rates are maximized at intermediate values of annual SICa , because neither the complete absence of sea ice, nor heavy and persistent sea ice, would provide satisfactory conditions for the emperor penguin. We show that under some conditions the stochastic growth rate is positively affected by the variance in SICa . We identify an ensemble of five general circulation climate models whose output closely matches the historical record of sea ice concentration in Terre Adélie. The output of this ensemble is used to produce stochastic forecasts of SICa , which in turn drive the population model. Uncertainty is included by incorporating multiple climate models and by a parametric bootstrap procedure that includes parameter uncertainty due to both model selection and estimation error. The median of these simulations predicts a decline of the Terre Adélie emperor penguin population of 81% by the year 2100. We find a 43% chance of an even greater decline, of 90% or more. The uncertainty in population projections reflects large differences among climate models in their forecasts of future sea ice conditions. One such model predicts population increases over much of the century, but overall, the ensemble of models predicts that population declines are far more likely than population increases. We conclude that climate change is a significant risk for the emperor

  15. Nuisance Source Population Modeling for Radiation Detection System Analysis

    SciTech Connect

    Sokkappa, P; Lange, D; Nelson, K; Wheeler, R

    2009-10-05

    A major challenge facing the prospective deployment of radiation detection systems for homeland security applications is the discrimination of radiological or nuclear 'threat sources' from radioactive, but benign, 'nuisance sources'. Common examples of such nuisance sources include naturally occurring radioactive material (NORM), medical patients who have received radioactive drugs for either diagnostics or treatment, and industrial sources. A sensitive detector that cannot distinguish between 'threat' and 'benign' classes will generate false positives which, if sufficiently frequent, will preclude it from being operationally deployed. In this report, we describe a first-principles physics-based modeling approach that is used to approximate the physical properties and corresponding gamma ray spectral signatures of real nuisance sources. Specific models are proposed for the three nuisance source classes - NORM, medical and industrial. The models can be validated against measured data - that is, energy spectra generated with the model can be compared to actual nuisance source data. We show by example how this is done for NORM and medical sources, using data sets obtained from spectroscopic detector deployments for cargo container screening and urban area traffic screening, respectively. In addition to capturing the range of radioactive signatures of individual nuisance sources, a nuisance source population model must generate sources with a frequency of occurrence consistent with that found in actual movement of goods and people. Measured radiation detection data can indicate these frequencies, but, at present, such data are available only for a very limited set of locations and time periods. In this report, we make more general estimates of frequencies for NORM and medical sources using a range of data sources such as shipping manifests and medical treatment statistics. We also identify potential data sources for industrial source frequencies, but leave the task of

  16. Recurrent Wheezing in Infants: A Population-Based Study.

    PubMed

    Belhassen, Manon; De Blic, Jacques; Laforest, Laurent; Laigle, Valérie; Chanut-Vogel, Céline; Lamezec, Liliane; Brouard, Jacques; Fauroux, Brigitte; de Pouvourville, Gérard; Ginoux, Marine; Van Ganse, Eric

    2016-04-01

    Recurrent wheezing (RW) has a significant impact on infants, caregivers, and society, but morbidity and related medical resource utilization (MRU) have not been thoroughly explored. The burden of RW needs to be documented with population-based data. The objective was to assess the characteristics, medical management, and MRU of RW infants identified from national claims data. Infants aged from 6 to 24 months, receiving ≥2 dispensations of respiratory drugs within 3 months, and presenting a marker of poor control (index date), were selected. During the 6 months after index date, MRU was described in the cohort and among 3 subgroups with more severe RW, defined as ≥4 dispensations of respiratory drugs, ≥3 dispensations of oral corticosteroids (OCS), or ≥1 hospitalization for respiratory symptoms. A total of 115,489 infants had RW, corresponding to 8.2% of subjects in this age group. During follow-up, 68.7% of infants received inhaled corticosteroids, but only 1.8 U (unit) were dispensed over 6 months, suggesting discontinuous use. Control was mostly inadequate: 61.7% of subjects received OCS, 80.2% antibiotics, and 71.2% short-acting beta-agonists, and medical/paramedical visits were numerous, particularly for physiotherapy. Severe RW concerned 39.0% of the cohort; 32.8% and 11.7% of infants had repeated use of respiratory drugs and OCS, respectively, and 5.5% were hospitalized for respiratory symptoms. In this real-life nation-wide study, RW was common and infants had poor control and high MRU. Interventions are needed to support adequate use of controller therapy, and to improve medical care. PMID:27082618

  17. Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle.

    PubMed

    Mészáros, Gábor; Boison, Solomon A; Pérez O'Brien, Ana M; Ferenčaković, Maja; Curik, Ino; Da Silva, Marcos V Barbosa; Utsunomiya, Yuri T; Garcia, Jose F; Sölkner, Johann

    2015-01-01

    Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (F ROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in Ne

  18. Predictive Performance of Physiologically Based Pharmacokinetic and Population Pharmacokinetic Modeling of Renally Cleared Drugs in Children

    PubMed Central

    Zhou, W; Johnson, TN; Xu, H; Cheung, SYA; Bui, KH; Li, J; Al‐Huniti, N

    2016-01-01

    Predictive performance of physiologically based pharmacokinetic (PBPK) and population pharmacokinetic (PopPK) models of drugs predominantly eliminated through kidney in the pediatric population was evaluated. After optimization using adult clinical data, the verified PBPK models can predict 33 of 34 drug clearance within twofold of the observed values in children 1 month and older. More specifically, 10 of 11 of predicted clearance values were within 1.5‐fold of those observed in children between 1 month and 2 years old. The PopPK approach also predicted 19 of 21 drug clearance within twofold of the observed values in children. In summary, our analysis demonstrated both PBPK and PopPK adult models, after verification with additional adult pharmacokinetic (PK) studies and incorporation of known ontogeny of renal filtration, could be applied for dosing regimen recommendation in children 1 month and older for renally eliminated drugs in a first‐in‐pediatric study. PMID:27566992

  19. [Obesity in adults: a population based study in a small town in South of Brazil, 2005].

    PubMed

    Sarturi, Juliana Barbosa; das Neves, Janaina; Peres, Karen Glazer

    2010-01-01

    Changes in nutritional pattern in Brazilian population have been observed mainly in relation to obesity increase. This study aims to estimate the prevalence of obesity and associated factors in adult population in Santo Angelo, Rio Grande do Sul State, 2005. A cross sectional study was carried out involving adult subjects from 20 to 59 years old (n=434), of both sexes. People with Body Mass Index equal to or higher than 30 kg/m(2) were considered obese. A questionnaire was applied to collect data related to socioeconomic, demographic, and behavioral conditions. The multiple logistic regression analysis was performed to identify the associated factors. The response rate was 95.0% and the prevalence of obesity was equal to 16.6% (CI 95% 13.120.1). Presence of obesity was positively associated with lack of physical activity, none feeding habits care, and some individuals that mentioned current health problems regardless of sex. The prevalence of obesity found was similar to other Brazilian population based studies. The results may support planning and implementing prevention actions as well as obesity control in adult population taking into account the relevant details of a small size town.

  20. A Population- and Hospital-based Cross-sectional Study of Renal Function in Hidradenitis Suppurativa.

    PubMed

    Miller, Iben M; Carlson, Nicholas; Mogensen, Ulla B; Ellervik, Christina; Jemec, Gregor B E

    2016-01-01

    The chronic inflammatory skin diseases hidradenitis suppurativa (HS) and psoriasis have been linked to cardiovascular risk factors and the latter has also been linked to possible renal dysfunction. Since basement membrane thinning in the skin of HS patients has been described, we speculated whether similar basement membrane defects might occur in renal tissue. Our objective was to investigate a possible association between HS and renal dysfunction. We performed a hospital and population-based cross-sectional study using estimated Glomerular-Filtration-Rate (eGFR) to assess renal function. Thirty-two hospital individuals with HS, 430 population individuals with HS, and 20,780 population individuals without HS were (controls) identified. The age-, sex-, smoking-, BMI-, hypertension- and diabetes-adjusted analysis revealed a statistically significant higher eGFR for the hospital group with HS and a mean difference in eGFR of 6.81 (1.27-12.35) ml/min/1.73 m2 between the hospital group with HS and the population group without HS. The observed higher eGFR in the hospital group with HS indicates a possible association of HS and renal dysfunction.

  1. Analysis of genetic diversity in red clover (Trifolium pratense L.) breeding populations as revealed by RAPD genetic markers.

    PubMed

    Ulloa, Odeth; Ortega, Fernando; Campos, Hugo

    2003-08-01

    Red clover is an important forage legume species for temperate regions and very little is known about the genetic organization of its breeding populations. We used random amplified polymorphic DNA (RAPD) genetic markers to address the genetic diversity and the distribution of variation in 20 breeding populations and cultivars from Chile, Argentina, Uruguay, and Switzerland. Genetic distances were calculated for all possible pairwise combinations. A high level of polymorphism was found and the proportion of polymorphic loci across populations was 74.2%. A population derived from a non-certified seedlot displayed a higher proportion of polymorphic loci than its respective certified seedlot. Gene diversity values and population genetics parameters suggest that the populations analyzed are diverse. An analysis of molecular variance (AMOVA) revealed that the largest proportion of variation (80.4%) resides at the within population level. RAPD markers are a useful tool for red clover breeding programs. A dendrogram based on genetic distances divided the breeding populations analyzed into three distinct groups. The amount and partition of diversity observed can be of value in identifying the populations that parents of synthetic cultivars are derived from and to exploit the variation available in the populations analyzed. PMID:12897860

  2. Understanding Crystal Populations; Looking Towards 3D Quantitative Analysis

    NASA Astrophysics Data System (ADS)

    Jerram, D. A.; Morgan, D. J.

    2010-12-01

    In order to understand volcanic systems, the potential record held within crystal populations needs to be revealed. It is becoming increasingly clear, however, that the crystal populations that arrive at the surface in volcanic eruptions are commonly mixtures of crystals, which may be representative of simple crystallization, recycling of crystals and incorporation of alien crystals. If we can quantify the true 3D population within a sample then we will be able to separate crystals with different histories and begin to interrogate the true and complex plumbing within the volcanic system. Modeling crystal populations is one area where we can investigate the best methodologies to use when dealing with sections through 3D populations. By producing known 3D shapes and sizes with virtual textures and looking at the statistics of shape and size when such populations are sectioned, we are able to gain confidence about what our 2D information is telling us about the population. We can also use this approach to test the size of population we need to analyze. 3D imaging through serial sectioning or x-ray CT, provides a complete 3D quantification of a rocks texture. Individual phases can be identified and in principle the true 3D statistics of the population can be interrogated. In practice we need to develop strategies (as with 2D-3D transformations), that enable a true characterization of the 3D data, and an understanding of the errors and pitfalls that exist. Ultimately, the reproduction of true 3D textures and the wealth of information they hold, is now within our reach.

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

    PubMed Central

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

    2015-01-01

    Copy number variations (CNVs) can be used as significant bio-markers and next generation sequencing (NGS) provides a high resolution detection of these CNVs. But how to extract features from CNVs and further apply them to genomic studies such as population clustering have become a big challenge. In this paper, we propose a novel method for population clustering based on CNVs from NGS. First, CNVs are extracted from each sample to form a feature matrix. Then, this feature matrix is decomposed into the source matrix and weight matrix with non-negative matrix factorization (NMF). The source matrix consists of common CNVs that are shared by all the samples from the same group, and the weight matrix indicates the corresponding level of CNVs from each sample. Therefore, using NMF of CNVs one can differentiate samples from different ethnic groups, i.e. population clustering. To validate the approach, we applied it to the analysis of both simulation data and two real data set from the 1000 Genomes Project. The results on simulation data demonstrate that the proposed method can recover the true common CNVs with high quality. The results on the first real data analysis show that the proposed method can cluster two family trio with different ancestries into two ethnic groups and the results on the second real data analysis show that the proposed method can be applied to the whole-genome with large sample size consisting of multiple groups. Both results demonstrate the potential of the proposed method for population clustering. PMID:25152046

  4. Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing

    PubMed Central

    Rocher, Solen; Jean, Martine; Castonguay, Yves; Belzile, François

    2015-01-01

    Genotyping-by-sequencing (GBS) is a relatively low-cost high throughput genotyping technology based on next generation sequencing and is applicable to orphan species with no reference genome. A combination of genome complexity reduction and multiplexing with DNA barcoding provides a simple and affordable way to resolve allelic variation between plant samples or populations. GBS was performed on ApeKI libraries using DNA from 48 genotypes each of two heterogeneous populations of tetraploid alfalfa (Medicago sativa spp. sativa): the synthetic cultivar Apica (ATF0) and a derived population (ATF5) obtained after five cycles of recurrent selection for superior tolerance to freezing (TF). Nearly 400 million reads were obtained from two lanes of an Illumina HiSeq 2000 sequencer and analyzed with the Universal Network-Enabled Analysis Kit (UNEAK) pipeline designed for species with no reference genome. Following the application of whole dataset-level filters, 11,694 single nucleotide polymorphism (SNP) loci were obtained. About 60% had a significant match on the Medicago truncatula syntenic genome. The accuracy of allelic ratios and genotype calls based on GBS data was directly assessed using 454 sequencing on a subset of SNP loci scored in eight plant samples. Sequencing depth in this study was not sufficient for accurate tetraploid allelic dosage, but reliable genotype calls based on diploid allelic dosage were obtained when using additional quality filtering. Principal Component Analysis of SNP loci in plant samples revealed that a small proportion (<5%) of the genetic variability assessed by GBS is able to differentiate ATF0 and ATF5. Our results confirm that analysis of GBS data using UNEAK is a reliable approach for genome-wide discovery of SNP loci in outcrossed polyploids. PMID:26115486

  5. Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing.

    PubMed

    Rocher, Solen; Jean, Martine; Castonguay, Yves; Belzile, François

    2015-01-01

    Genotyping-by-sequencing (GBS) is a relatively low-cost high throughput genotyping technology based on next generation sequencing and is applicable to orphan species with no reference genome. A combination of genome complexity reduction and multiplexing with DNA barcoding provides a simple and affordable way to resolve allelic variation between plant samples or populations. GBS was performed on ApeKI libraries using DNA from 48 genotypes each of two heterogeneous populations of tetraploid alfalfa (Medicago sativa spp. sativa): the synthetic cultivar Apica (ATF0) and a derived population (ATF5) obtained after five cycles of recurrent selection for superior tolerance to freezing (TF). Nearly 400 million reads were obtained from two lanes of an Illumina HiSeq 2000 sequencer and analyzed with the Universal Network-Enabled Analysis Kit (UNEAK) pipeline designed for species with no reference genome. Following the application of whole dataset-level filters, 11,694 single nucleotide polymorphism (SNP) loci were obtained. About 60% had a significant match on the Medicago truncatula syntenic genome. The accuracy of allelic ratios and genotype calls based on GBS data was directly assessed using 454 sequencing on a subset of SNP loci scored in eight plant samples. Sequencing depth in this study was not sufficient for accurate tetraploid allelic dosage, but reliable genotype calls based on diploid allelic dosage were obtained when using additional quality filtering. Principal Component Analysis of SNP loci in plant samples revealed that a small proportion (<5%) of the genetic variability assessed by GBS is able to differentiate ATF0 and ATF5. Our results confirm that analysis of GBS data using UNEAK is a reliable approach for genome-wide discovery of SNP loci in outcrossed polyploids.

  6. [Population genetic variation and structure analysis on five populations of mirror carp Cyprinus carpio L. using microsatellites].

    PubMed

    Quan, Ying-Chun; Li, Da-Yu; Cao, Ding-Chen; Sun, Xiao-Wen; Liang, Li-Qun

    2006-12-01

    In this paper, population genetic variability and genetic structure of five populations of an important cultivation species, mirror carp (Cyprinus carpio L.) were analyzed using 30 microsatellite loci. The observed (Ho) and expected (He) heterozygosity values, polymorphic information content (PIC) and number of effective alleles (Ae) were all determined. The genetic similarity coefficient and Nei's standard genetic distance were computed based on the allele frequencies. The Hardy-Weinberg equilibrium was checked by chi2 test. Genetic differentiation and hierarchical partition of genetic diversity were evaluated by FST and Nm. A dendrogram was constructed based on UPGMA methods using PHYLIP software package supported by a bootstrap value of 91.0%. Totally 7,083 fragments were procured. Their lengths were from 102 bp to 446 bp. For each locus, 1-16 alleles were amplified, adding up to 356 alleles in all the 5 populations. We found the genetic variability level was relatively high in all five populations, as shown by Ae = 1.07-2.30, He= 0.70-0.78 and PIC=0.69-0.75, respectively. The genetic similarity coefficients were all above 0.52, indicating their close genetic relationships. The UPGMA phylogenetic tree showed mirror carps sampled from Donggang, Fengcheng and Liaozhong were clustered into one group and the other two populations, both collected from Songpu, were grouped together. There were obvious relations between genetic distances and geographical distributions of the five populations. No fragments were amplified from some loci of EST-SSRs, which may suggest the loss of these loci in mirror carp genome or sequence divergence at the primer binding sites. These null alleles may result from selection because functional genes are under more selection pressure than non-encoding loci. Overall, population genetic variation is high for each of the five mirror carp, and the differentiations are also significant among populations. PMID:17138540

  7. New evidence of risk factors for community-acquired pneumonia: a population-based study.

    PubMed

    Almirall, J; Bolíbar, I; Serra-Prat, M; Roig, J; Hospital, I; Carandell, E; Agustí, M; Ayuso, P; Estela, A; Torres, A

    2008-06-01

    The aim of the present study was to identify risk factors for community-acquired pneumonia (CAP), with special emphasis on modifiable risk factors and those applicable to the general population. A population-based, case-control study was conducted, with a target population of 859,033 inhabitants aged >14 yrs. A total of 1,336 patients with confirmed CAP were matched to control subjects by age, sex and primary centre over 1 yr. In the univariate analysis, outstanding risk factors were passive smoking in never-smokers aged >65 yrs, heavy alcohol intake, contact with pets, households with >10 people, contact with children, interventions on the upper airways and poor dental health. Risky treatments included amiodarone, N-acetylcysteine and oral steroids. Influenza and pneumococcal vaccine, and visiting the dentist were protective factors. Multivariable analysis confirmed cigarette smoking, usual contact with children, sudden changes of temperature at work, inhalation therapy (particularly containing steroids and using plastic pear-spacers), oxygen therapy, asthma and chronic bronchitis as independent risk factors. Interventions for reducing community-acquired pneumonia should integrate health habits and lifestyle factors related to household, work and community, together with individual clinical conditions, comorbidities and oral or inhaled regular treatments. Prevention would include vaccination, dental hygiene and avoidance of upper respiratory colonisation.

  8. Single-cell Migration Chip for Chemotaxis-based Microfluidic Selection of Heterogeneous Cell Populations

    NASA Astrophysics Data System (ADS)

    Chen, Yu-Chih; Allen, Steven G.; Ingram, Patrick N.; Buckanovich, Ronald; Merajver, Sofia D.; Yoon, Euisik

    2015-05-01

    Tumor cell migration toward and intravasation into capillaries is an early and key event in cancer metastasis, yet not all cancer cells are imbued with the same capability to do so. This heterogeneity within a tumor is a fundamental property of cancer. Tools to help us understand what molecular characteristics allow a certain subpopulation of cells to spread from the primary tumor are thus critical for overcoming metastasis. Conventional in vitro migration platforms treat populations in aggregate, which leads to a masking of intrinsic differences among cells. Some migration assays reported recently have single-cell resolution, but these platforms do not provide for selective retrieval of the distinct migrating and non-migrating cell populations for further analysis. Thus, to study the intrinsic differences in cells responsible for chemotactic heterogeneity, we developed a single-cell migration platform so that individual cells’ migration behavior can be studied and the heterogeneous population sorted based upon chemotactic phenotype. Furthermore, after migration, the highly chemotactic and non-chemotactic cells were retrieved and proved viable for later molecular analysis of their differences. Moreover, we modified the migration channel to resemble lymphatic capillaries to better understand how certain cancer cells are able to move through geometrically confining spaces.

  9. Genetic diversity of wild soybean populations in Dongying, China, by simple sequence repeat analysis.

    PubMed

    Wang, Y H; Zhang, X J; Fan, S J

    2015-01-01

    Annual wild soybean (Glycine soja Sieb. et Zucc.), the ancestor of cultivated soybean (G. max), is believed to be a potential gene source for further improvement of soybean to cope with environmental stress. In this study, 10 simple sequence repeat (SSR) markers were used to evaluate the genetic diversity and population genetic structure in five wild soybean populations using 195 accessions collected from Dongying, China. Ten SSR markers yielded 90 bands, with an average of nine bands per marker. The percentage of polymorphic loci (P) was 97.78%, the distribution of expected heterozygosity (HE) was 0.1994-0.4460 with an average of 0.3262, and the distribution from Shannon's information index (I) was 0.3595-0.6506 with an average of 0.5386. The results showed that wild soybean had a high degree of genetic diversity at the species level. Nei's differentiation coefficient (FST) was 0.1533, and gene flow (Nm) was 1.3805, which indicated that genetic variation mainly existed within populations and that there was a certain level of gene exchange between populations. Some genetic differentiation occurred among populations, although this was not significant. Cluster analysis indicated that there was no significant correlation between the genetic structure of wild soybean populations and their geographic distribution, and the clustering results may be relatively consistent with the habitats of the accessions. In the present study, the genetic diversity of wild soybeans showed a broad genetic base and enables suggestions for the conservation of this plant to be made. PMID:26436402

  10. Genetic diversity and population structure analysis of European hexaploid bread wheat (Triticum aestivum L.) varieties.

    PubMed

    Nielsen, Nanna Hellum; Backes, Gunter; Stougaard, Jens; Andersen, Stig Uggerhøj; Jahoor, Ahmed

    2014-01-01

    Progress in plant breeding is facilitated by accurate information about genetic structure and diversity. Here, Diversity Array Technology (DArT) was used to characterize a population of 94 bread wheat (Triticum aestivum L.) varieties of mainly European origin. In total, 1,849 of 7,000 tested markers were polymorphic and could be used for population structure analysis. Two major subgroups of wheat varieties, GrI and GrII, were identified using the program STRUCTURE, and confirmed by principal component analysis (PCA). These subgroups were largely separated according to origin; GrI comprised varieties from Southern and Eastern Europe, whereas GrII contained mostly modern varieties from Western and Northern Europe. A large proportion of the markers contributing most to the genetic separation of the subgroups were located on chromosome 2D near the Reduced height 8 (Rht8) locus, and PCR-based genotyping suggested that breeding for the Rht8 allele had a major impact on subgroup separation. Consistently, analysis of linkage disequilibrium (LD) suggested that different selective pressures had acted on chromosome 2D in the two subgroups. Our data provides an overview of the allele composition of bread wheat varieties anchored to DArT markers, which will facilitate targeted combination of alleles following DArT-based QTL studies. In addition, the genetic diversity and distance data combined with specific Rht8 genotypes can now be used by breeders to guide selection of crossing parents.

  11. Genetic Diversity and Population Structure Analysis of European Hexaploid Bread Wheat (Triticum aestivum L.) Varieties

    PubMed Central

    Nielsen, Nanna Hellum; Backes, Gunter; Stougaard, Jens; Andersen, Stig Uggerhøj; Jahoor, Ahmed

    2014-01-01

    Progress in plant breeding is facilitated by accurate information about genetic structure and diversity. Here, Diversity Array Technology (DArT) was used to characterize a population of 94 bread wheat (Triticum aestivum L.) varieties of mainly European origin. In total, 1,849 of 7,000 tested markers were polymorphic and could be used for population structure analysis. Two major subgroups of wheat varieties, GrI and GrII, were identified using the program STRUCTURE, and confirmed by principal component analysis (PCA). These subgroups were largely separated according to origin; GrI comprised varieties from Southern and Eastern Europe, whereas GrII contained mostly modern varieties from Western and Northern Europe. A large proportion of the markers contributing most to the genetic separation of the subgroups were located on chromosome 2D near the Reduced height 8 (Rht8) locus, and PCR-based genotyping suggested that breeding for the Rht8 allele had a major impact on subgroup separation. Consistently, analysis of linkage disequilibrium (LD) suggested that different selective pressures had acted on chromosome 2D in the two subgroups. Our data provides an overview of the allele composition of bread wheat varieties anchored to DArT markers, which will facilitate targeted combination of alleles following DArT-based QTL studies. In addition, the genetic diversity and distance data combined with specific Rht8 genotypes can now be used by breeders to guide selection of crossing parents. PMID:24718292

  12. Agent-based forward analysis

    SciTech Connect

    Kerekes, Ryan A.; Jiao, Yu; Shankar, Mallikarjun; Potok, Thomas E.; Lusk, Rick M.

    2008-01-01

    We propose software agent-based "forward analysis" for efficient information retrieval in a network of sensing devices. In our approach, processing is pushed to the data at the edge of the network via intelligent software agents rather than pulling data to a central facility for processing. The agents are deployed with a specific query and perform varying levels of analysis of the data, communicating with each other and sending only relevant information back across the network. We demonstrate our concept in the context of face recognition using a wireless test bed comprised of PDA cell phones and laptops. We show that agent-based forward analysis can provide a significant increase in retrieval speed while decreasing bandwidth usage and information overload at the central facility. n

  13. Hand-Based Biometric Analysis

    NASA Technical Reports Server (NTRS)

    Bebis, George

    2013-01-01

    Hand-based biometric analysis systems and techniques provide robust hand-based identification and verification. An image of a hand is obtained, which is then segmented into a palm region and separate finger regions. Acquisition of the image is performed without requiring particular orientation or placement restrictions. Segmentation is performed without the use of reference points on the images. Each segment is analyzed by calculating a set of Zernike moment descriptors for the segment. The feature parameters thus obtained are then fused and compared to stored sets of descriptors in enrollment templates to arrive at an identity decision. By using Zernike moments, and through additional manipulation, the biometric analysis is invariant to rotation, scale, or translation or an input image. Additionally, the analysis uses re-use of commonly seen terms in Zernike calculations to achieve additional efficiencies over traditional Zernike moment calculation.

  14. Hand-Based Biometric Analysis

    NASA Technical Reports Server (NTRS)

    Bebis, George (Inventor); Amayeh, Gholamreza (Inventor)

    2015-01-01

    Hand-based biometric analysis systems and techniques are described which provide robust hand-based identification and verification. An image of a hand is obtained, which is then segmented into a palm region and separate finger regions. Acquisition of the image is performed without requiring particular orientation or placement restrictions. Segmentation is performed without the use of reference points on the images. Each segment is analyzed by calculating a set of Zernike moment descriptors for the segment. The feature parameters thus obtained are then fused and compared to stored sets of descriptors in enrollment templates to arrive at an identity decision. By using Zernike moments, and through additional manipulation, the biometric analysis is invariant to rotation, scale, or translation or an in put image. Additionally, the analysis utilizes re-use of commonly-seen terms in Zernike calculations to achieve additional efficiencies over traditional Zernike moment calculation.

  15. Population viability analysis: using a modeling tool to assess the viability of tapir populations in fragmented landscapes.

    PubMed

    Medici, Emília Patrícia; Desbiez, Arnaud Leonard Jean

    2012-12-01

    A population viability analysis (PVA) was conducted of the lowland tapir populations in the Atlantic Forest of the Pontal do Paranapanema region, Brazil, including Morro do Diabo State Park (MDSP) and surrounding forest fragments. Results from the model projected that the population of 126 tapirs in MDSP is likely to persist over the next 100 years; however, 200 tapirs would be required to maintain a viable population. Sensitivity analysis showed that sub-adult mortality and adult mortality have the strongest influence on the dynamics of lowland tapir populations. High road-kill has a major impact on the MDSP tapir population and can lead to population extinction. Metapopulation modeling showed that dispersal of tapirs from MDSP to the surrounding fragments can be detrimental to the overall metapopulation, as fragments act as sinks. Nevertheless, the model showed that under certain conditions the maintenance of the metapopulation dynamics might be determinant for the persistence of tapirs in the region, particularly in the smaller fragments. The establishment of corridors connecting MDSP to the forest fragments models resulted in an increase in the stochastic growth rate, making tapirs more resilient to threats and catastrophes, but only if rates of mortality were not increased when using corridors. The PVA showed that the conservation of tapirs in the Pontal region depends on: the effective protection of MDSP; maintenance and, whenever possible, enhancement of the functional connectivity of the landscape, reducing mortality during dispersal and threats in the unprotected forest fragments; and neutralization of all threats affecting tapirs in the smaller forest fragments. PMID:23253367

  16. Population viability analysis: using a modeling tool to assess the viability of tapir populations in fragmented landscapes.