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Sample records for population based analysis

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

    NASA Astrophysics Data System (ADS)

    Cui, Jing; Wang, Yingjie; Yan, Hong

    2009-07-01

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

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

    PubMed

    Player, Candice T

    2014-01-01

    In Populations, Public Health and the Law, legal scholar Wendy Parmet urges courts to embrace population-based legal analysis, a public health inspired approach to legal reasoning. Parmet contends that population-based legal analysis offers a way to analyze legal issues--not unlike law and economics--as well as a set of values from which to critique contemporary legal discourse. Population-based analysis has been warmly embraced by the health law community as a bold new way of analyzing legal issues. Still, population-based analysis is not without its problems. At times, Parmet claims too much territory for the population perspective. Moreover, Parmet urges courts to recognize population health as an important norm in legal reasoning. What should we do when the insights of public health and conventional legal reasoning conflict? Still in its infancy, population-based analysis offers little in the way of answers to these questions. This Article applies population-based legal analysis to the constitutional problems that arise when states condition public assistance benefits on passing a drug test, thereby highlighting the strengths of the population perspective and exposing its weaknesses. PMID:24844042

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

    USGS Publications Warehouse

    Pine, William Pine, III; 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.

  4. A Patient-Based Analysis of Drug Disorder Diagnoses in the Medicare Population

    PubMed Central

    Cartwright, William S.; Ingster, Lillian M.

    1993-01-01

    This article utilizes the Part A Medicare provider analysis and review (MEDPAR) file for fiscal year (FY) 1987. The discharge records were organized into a patient-based record that included alcohol, drug, and mental (ADM) disorder diagnoses as well as measures of resource use. The authors find that there are substantially higher costs of health care incurred by the drug disorder diagnosed population. Those of the Medicare population diagnosed with drug disorders had longer lengths of stay (LOSs), higher hospital charges, and more discharges. Costs increased monotonically as the number of drug diagnoses increased. Overlap of mental and alcohol problems is presented for the drug disorder diagnosed population. PMID:10171899

  5. 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

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

    PubMed Central

    Matuszewski, Damian J.; Wählby, Carolina

    2016-01-01

    Image-based screening typically produces quantitative measurements of cell appearance. Large-scale screens involving tens of thousands of images, each containing hundreds of cells described by hundreds of measurements, result in overwhelming amounts of data. Reducing per-cell measurements to the averages across the image(s) for each treatment leads to loss of potentially valuable information on population variability. We present PopulationProfiler—a new software tool that reduces per-cell measurements to population statistics. The software imports measurements from a simple text file, visualizes population distributions in a compact and comprehensive way, and can create gates for subpopulation classes based on control samples. We validate the tool by showing how PopulationProfiler can be used to analyze the effect of drugs that disturb the cell cycle, and compare the results to those obtained with flow cytometry. PMID:26987120

  7. Population based analysis of directional information in serial deformation tensor morphometry.

    PubMed

    Studholme, Colin; Cardenas, Valerie

    2007-01-01

    Deformation morphometry provides a sensitive approach to detecting and mapping subtle volume changes in the brain. Population based analyses of this data have been used successfully to detect characteristic changes in different neurodegenerative conditions. However, most studies have been limited to statistical mapping of the scalar volume change at each point in the brain, by evaluating the determinant of the Jacobian of the deformation field. In this paper we describe an approach to spatial normalisation and analysis of the full deformation tensor. The approach employs a spatial relocation and reorientation of tensors of each subject. Using the assumption of small changes, we use a linear modeling of effects of clinical variables on each deformation tensor component across a population. We illustrate the use of this approach by examining the pattern of significance and orientation of the volume change effects in recovery from alcohol abuse. Results show new local structure which was not apparent in the analysis of scalar volume changes. PMID:18044583

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

    PubMed

    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

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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

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

    PubMed Central

    2013-01-01

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

  15. 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

  16. 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

  17. Prison tobacco control policies and deaths from smoking in United States prisons: population based retrospective analysis

    PubMed Central

    Carson, E Ann; Krueger, Patrick M; Mueller, Shane R; Steiner, John F; Sabol, William J

    2014-01-01

    Objective To determine the mortality attributable to smoking and years of potential life lost from smoking among people in prison and whether bans on smoking in prison are associated with reductions in smoking related deaths. Design Analysis of cross sectional survey data with the smoking attributable mortality, morbidity, and economic costs system; population based time series analysis. Setting All state prisons in the United States. Main outcome measures Prevalence of smoking from cross sectional survey of inmates in state correctional facilities. Data on state prison tobacco policies from web based searches of state policies and legislation. Deaths and causes of death in US state prisons from the deaths in custody reporting program of the Bureau of Justice Statistics for 2001-11. Smoking attributable mortality and years of potential life lost was assessed from the smoking attributable mortality, morbidity, and economic costs system of the Centers for Disease Control and Prevention. Multivariate Poisson models quantified the association between bans and smoking related cancer, cardiovascular and pulmonary deaths. Results The most common causes of deaths related to smoking among people in prison were lung cancer, ischemic heart disease, other heart disease, cerebrovascular disease, and chronic airways obstruction. The age adjusted smoking attributable mortality and years of potential life lost rates were 360 and 5149 per 100 000, respectively; these figures are higher than rates in the general US population (248 and 3501, respectively). The number of states with any smoking ban increased from 25 in 2001 to 48 by 2011. In prisons the mortality rate from smoking related causes was lower during years with a ban than during years without a ban (110.4/100 000 v 128.9/100 000). Prisons that implemented smoking bans had a 9% reduction (adjusted incidence rate ratio 0.91, 95% confidence interval 0.88 to 0.95) in smoking related deaths. Bans in place for longer than

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

    PubMed Central

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

    2013-01-01

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

  19. 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

  20. [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. PMID:17393796

  1. Population-based survival analysis of colorectal cancer patients in Singapore, 1968-1992.

    PubMed

    Du, Wen-Bo; Chia, Kee-Seng; Sankaranarayanan, Rengaswamy; Sankila, Risto; Seow, Adeline; Lee, Hin-Peng

    2002-05-20

    Since the 1980s, colorectal cancer incidence in Singapore has ranked second to lung in males and females. We describe a population-based analysis of survival of colorectal cancer patients diagnosed from 1968 to 1992 in Singapore. Data of colorectal cancer patients diagnosed during 1968-1992 were retrieved from the Singapore Cancer Registry. Patients were passively followed up for death to the end of 1997. The final dataset consisted of 10,114 subjects. Observed and relative survival rates were calculated by stage (localized, regional metastases and distant metastases), age, ethnicity and calendar period for both genders. Over the study period, a significant progress in survival of colorectal cancer patients was observed. For localized cancer of the colon, the 5-year age-standardized relative survival (ASRS) increased from 36% in 1968-1972 to 66% in 1988-1992 for males and from 32 to 71% for females. For localized rectal cancer, the 5-year ASRS improved from 25 to 66% for males and from 23 to 66% in females. Similarly, improvement was observed in colorectal cancer patients with regional metastases, but not in those with distant metastases. Calendar year period and clinical stage of disease were identified as major significant prognostic factors of survival for colorectal cancer. The substantially improved colorectal cancer survival rates reflected the interplay of cancer control activities in various areas, such as health promotion, early diagnosis and treatment. Our study shows a unique changing pattern of survival experience for colorectal patients from a country undergoing rapid economic development. PMID:11992418

  2. Profiling the different needs and expectations of patients for population-based medicine: a case study using segmentation analysis

    PubMed Central

    2012-01-01

    Background This study illustrates an evidence-based method for the segmentation analysis of patients that could greatly improve the approach to population-based medicine, by filling a gap in the empirical analysis of this topic. Segmentation facilitates individual patient care in the context of the culture, health status, and the health needs of the entire population to which that patient belongs. Because many health systems are engaged in developing better chronic care management initiatives, patient profiles are critical to understanding whether some patients can move toward effective self-management and can play a central role in determining their own care, which fosters a sense of responsibility for their own health. A review of the literature on patient segmentation provided the background for this research. Method First, we conducted a literature review on patient satisfaction and segmentation to build a survey. Then, we performed 3,461 surveys of outpatient services users. The key structures on which the subjects’ perception of outpatient services was based were extrapolated using principal component factor analysis with varimax rotation. After the factor analysis, segmentation was performed through cluster analysis to better analyze the influence of individual attitudes on the results. Results Four segments were identified through factor and cluster analysis: the “unpretentious,” the “informed and supported,” the “experts” and the “advanced” patients. Their policies and managerial implications are outlined. Conclusions With this research, we provide the following: – a method for profiling patients based on common patient satisfaction surveys that is easily replicable in all health systems and contexts; – a proposal for segments based on the results of a broad-based analysis conducted in the Italian National Health System (INHS). Segments represent profiles of patients requiring different strategies for delivering health services. Their

  3. 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. PMID:21265063

  4. 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

  5. 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. PMID:25846829

  6. 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

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

    PubMed

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

    2015-01-01

    Previous case reports and small studies have suggested that 3-hydroxy-3-methylglutaryl-CoA reductase inhibitors (HMG-CoA-Is) may increase the risk of tendon rupture. We conducted a population-based retrospective cohort evaluation to better assess this relationship. From approximately 800,000 enrollees of a private insurance database, those who were aged ≤64 years with at least 1 year of continuous enrollment were selected. Exposure was defined as initiation of HMG-CoA-I after the beginning of the study period. Each exposed person was matched with 2 controls of similar age and gender. Baseline characteristics, including known risk factors for tendon rupture, were compared between exposed and control cohorts with fidelity to the study's matched design. After adjusting for differences in follow-up and baseline characteristics, incidence rate ratios for tendon rupture was assessed in HMG-CoA-I users and nonusers. A total of 34,749 exposed patients were matched with 69,498 controls. There was no difference in the occurrence of tendon ruptures in HMG-CoA-I users versus nonusers. The results remained unchanged after adjustment for age and gender. In conclusion, this population-based retrospective cohort evaluation suggests that use of HMG-CoA-Is as a group are not associated with tendon rupture. PMID:24451300

  8. 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…

  9. 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

  10. 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

  11. Risk of Parkinson Disease in Diabetes Mellitus: An Updated Meta-Analysis of Population-Based Cohort Studies

    PubMed Central

    Yue, Xuejing; Li, Hehua; Yan, Haiqing; Zhang, Ping; Chang, Li; Li, Tong

    2016-01-01

    Abstract Previous meta-analysis has identified the associations between diabetes mellitus (DM) and the risk of Parkinson disease (PD). However, the results are still debatable. The purpose of this study is to perform an updated meta-analysis to investigate the up-to-date pooling evidence based on published population-based cohort studies and assess the association between DM and the risk of PD. Electronic database including Pubmed and Embase were searched to identify cohort studies published before October, 2015. Studies were selected if they reported the risk estimates for PD associated with DM. We pooled the adjusted effect estimates using random-effects meta-analysis. Funnel plot, Begg, or Egger test as well as Duval and Tweedie trim-and-fill approach were applied to assess publication bias. A total of 7 population-based cohort studies, representing 1,761,632 individuals were included in the meta-analysis. The pooled adjusted relative risk (RR) of PD associated with DM was 1.38 (95% CI 1.18–1.62, P < 0.001). An effect was consistent in female (RR 1.50 95% CI 1.07–2.11, P = 0.019) and in male (RR 1.40, 95% CI 1.17–1.67). The association was similar when stratified by study quality, research region, study design, sample size, published year, diabetes duration, and baseline age. The trim-and-fill approach confirmed the robutness of the result (RR 1.31, 95% CI 1.09–1.57, P = 0.015). Our findings based on population-based cohort studies indicate that diabetes is associated with increased PD risk by about 38%. More large-scale prospective studies are warranted to further clarify this association and its mechanism. PMID:27149468

  12. Risk of Parkinson Disease in Diabetes Mellitus: An Updated Meta-Analysis of Population-Based Cohort Studies.

    PubMed

    Yue, Xuejing; Li, Hehua; Yan, Haiqing; Zhang, Ping; Chang, Li; Li, Tong

    2016-05-01

    Previous meta-analysis has identified the associations between diabetes mellitus (DM) and the risk of Parkinson disease (PD). However, the results are still debatable. The purpose of this study is to perform an updated meta-analysis to investigate the up-to-date pooling evidence based on published population-based cohort studies and assess the association between DM and the risk of PD.Electronic database including Pubmed and Embase were searched to identify cohort studies published before October, 2015. Studies were selected if they reported the risk estimates for PD associated with DM. We pooled the adjusted effect estimates using random-effects meta-analysis. Funnel plot, Begg, or Egger test as well as Duval and Tweedie trim-and-fill approach were applied to assess publication bias.A total of 7 population-based cohort studies, representing 1,761,632 individuals were included in the meta-analysis. The pooled adjusted relative risk (RR) of PD associated with DM was 1.38 (95% CI 1.18-1.62, P < 0.001). An effect was consistent in female (RR 1.50 95% CI 1.07-2.11, P = 0.019) and in male (RR 1.40, 95% CI 1.17-1.67). The association was similar when stratified by study quality, research region, study design, sample size, published year, diabetes duration, and baseline age. The trim-and-fill approach confirmed the robutness of the result (RR 1.31, 95% CI 1.09-1.57, P = 0.015).Our findings based on population-based cohort studies indicate that diabetes is associated with increased PD risk by about 38%. More large-scale prospective studies are warranted to further clarify this association and its mechanism. PMID:27149468

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

    PubMed

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

    2016-09-01

    Knowledge on the characteristics of infectious disease propagation in metropolises plays a critical role in guiding public health intervention strategies to reduce death tolls, disease incidence, and possible economic losses. Based on the SIR model, we established a comprehensive spatiotemporal risk assessment model to compute infectious disease propagation within an urban setting using Beijing, China as a case study. The model was developed for a dynamic population distribution using actual data on location, density of residences and offices, and means of public transportation (e.g., subways, buses and taxis). We evaluated four influencing factors including biological, behavioral, environmental parameters and infectious sources. The model output resulted in a set of maps showing how the four influencing factors affected the trend and characteristics of airborne infectious disease propagation in Beijing. We compared the scenarios for the long-term dynamic propagation of infectious disease without governmental interventions versus scenarios with government intervention and hospital coordinated emergency responses. Lastly, the sensitivity of the average number of people at different location in spreading infections is analyzed. Based on our results, we provide valuable recommendations to governmental agencies and the public in order to minimize the disease propagation. PMID:27107973

  14. Sex estimation based on scapula analysis in a Japanese population using multidetector computed tomography.

    PubMed

    Torimitsu, Suguru; Makino, Yohsuke; Saitoh, Hisako; Sakuma, Ayaka; Ishii, Namiko; Yajima, Daisuke; Inokuchi, Go; Motomura, Ayumi; Chiba, Fumiko; Yamaguchi, Rutsuko; Hashimoto, Mari; Hoshioka, Yumi; Iwase, Hirotaro

    2016-05-01

    Accurate sex estimation based on measurements of dimorphic dimensions in human unknown remains is important as the first step toward making individual identification. The purpose of this study was to assess the sexual dimorphism of the scapula and to quantify the accuracy of sex estimation in a contemporary Japanese forensic sample using scapular measurements based on three-dimensional (3D) computed tomographic (CT) images. A total of 218 cadavers (109 males, 109 females) that underwent postmortem CT and subsequent forensic autopsy were used. Ten scapular measurements were performed on 3D CT reconstructed images that extracted only bone data, and were analyzed using descriptive statistics and discriminant function analyses (DFA). All measurements were dimorphic in terms of sex differences. Univariate DFA provided sex classification accuracy rates of 75.7-91.3%. Stepwise DFA yielded sex prediction accuracy rates of 93.1-94.5%. In conclusion, the scapular measurements using 3D CT images of a contemporary Japanese population may be useful for the estimation of skeletal sex in the field of forensic anthropology. PMID:26965402

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

    PubMed Central

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

    2013-01-01

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

  16. 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

  17. 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

  18. 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

  19. 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.

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

    PubMed

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

    2013-04-21

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

  1. Utilization of blood cultures in Danish hospitals: a population-based descriptive analysis.

    PubMed

    Gubbels, S; Nielsen, J; Voldstedlund, M; Kristensen, B; Schønheyder, H C; Vandenbroucke-Grauls, C M J E; Arpi, M; Björnsdóttir, M K; Knudsen, J Dahl; Dessau, R B; Jensen, T Gorm; Kjældgaard, P; Lemming, L; Møller, J K; Hansen, D Schrøder; Mølbak, K

    2015-04-01

    This national population-based study was conducted as part of the development of a national automated surveillance system for hospital-acquired bacteraemia and ascertains the utilization of blood cultures (BCs). A primary objective was to understand how local differences may affect interpretation of nationwide surveillance for bacteraemia. From the Danish Microbiology Database, we retrieved all BCs taken between 2010 and 2013 and linked these to admission data from the National Patient Registry. In total, 4 587 295 admissions were registered, and in 11%, at least one BC was taken. Almost 50% of BCs were taken at admission. The chance of having a BC taken declined over the next days but increased after 4 days of admission. Data linkage identified 876 290 days on which at least one BC was taken; 6.4% yielded positive results. Ten species, Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Enterococcus faecium, Enterococcus faecalis, Pseudomonas aeruginosa, Candida albicans, Enterobacter cloacae and Klebsiella oxytoca, accounted for 74.7% of agents for this purpose classified as pathogenic. An increase in BCs and positive BCs was observed over time, particularly among older patients. BCs showed a seasonal pattern overall and for S. pneumoniae particularly. A predominance of male patients was seen for bacteraemias due to S. aureus, E. faecium and K. pneumoniae. Minor differences in BCs and positive BCs between departments of clinical microbiology underpin the rationale of a future automated surveillance for bacteraemia. The study also provides important knowledge for interpretation of surveillance of invasive infections more generally. PMID:25658520

  2. 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

  3. Changing population structure and commuting situation in Tokyo Megalopolis: a municipality-based analysis.

    PubMed

    Ohtsuka, R; Umezaki, M

    1993-06-01

    Census data was analyzed for 20 municipalities along the Tohoku Line in Tokyo Megalopolis to elucidate the changes in the population structure and the commuting situation in the last two decades. The major findings were: (1) the changing pattern of population structure markedly varied among the municipalities, and (2) the long-distance commuting workers have increased particularly among those 50 km or more from central Tokyo. PMID:8064153

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

    PubMed

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

    2016-07-01

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

  5. Viability analysis of reef fish populations based on limited demographic information.

    PubMed

    Wielgus, Jeffrey; Ballantyne, Ford; Sala, Enric; Gerber, Leah R

    2007-04-01

    Marine protected areas (MPAs) that allow some degree of artisanal fishing have been proposed to control the overexploitation of marine resources while allowing extraction by local communities. Nevertheless, the management of MPAs is often impaired by the absence of data on the status of their resources. We devised a method to estimate population growth rates with the type of data that are usually available for reef fishes. We used 7 years of spatially explicit abundance data on the leopard grouper (Mycteroperca rosacea) in an MPA in the Gulf of California, Mexico, to construct a matrix population model that incorporated the effects of El Niño/La Niña Southern Oscillation on population dynamics. An environmental model that estimated different demographic estimates for El Niño and La Niña periods performed better than a single-environment model, and a single-habitat model performed better than a model that considered different depths as different habitats. Our results suggest that the population of the leopard grouper off the main island of the MPA is not viable under present conditions. Although the impact of fishing on leopard grouper populations in the MPA has not yet been established, fishing should be closed as a precautionary measure at this island if a priority of the MPA is to ensure the sustainability of its fish populations. PMID:17391194

  6. 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

  7. 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,…

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

    ERIC Educational Resources Information Center

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

    2011-01-01

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

  9. Harms associated with single unit perioperative transfusion: retrospective population based analysis

    PubMed Central

    Kim, Helen; Auerbach, Andrew D

    2015-01-01

    Objective To determine whether perioperative transfusion of as little as one unit of packed red blood cells in the operating room or the day after surgery is associated with measurably increased odds for perioperative ischemic stroke and myocardial infarction. Design Retrospective cohort study of hospital administrative data. Setting 346 hospitals in the United States participating in the claims based Premier Perspective database from 1 January 2009 to 31 March 2012. Participants 1 583 819 adults who underwent non-cardiac, non-intracranial, non-vascular surgery and required a stay of at least one night in hospital and did not receive packed red blood cells on days two to seven after surgery. Intervention Transfusion of packed red blood cells on the day of surgery or one day after by exposure categories (none or one, two, three or four or more units). Main outcome measures The composite outcome of stroke/myocardial infarction was defined as ischemic stroke, ST elevation myocardial infarction, ventricular tachycardia, or ventricular fibrillation during index admission or as a primary diagnosis for readmission within 30 days. Ventricular tachycardia/ventricular fibrillation were included as a surrogate for myocardial infarction. Results 41 421 (2.6%) patients received at least one unit of packed red blood cells within 48 hours of surgery, and 8044 (0.51%) experienced the composite outcome of stroke/myocardial infarction. Patients who were transfused were older, more likely to be women, and had more comorbid disease. Hierarchical logistic regression adjusted for comorbidities and demographics with random effects by hospital showed that transfusion of as little as one unit was associated with an odds ratio of 2.33 (95% confidence interval 1.90 to 2.86) for perioperative stroke/myocardial infarction, and the odds of stroke/myocardial infarction markedly increased with transfusion of four or more units. Subgroup analysis limiting the cohort to one of several common

  10. Systemic Hypertension as a Risk Factor for Open-Angle Glaucoma: A Meta-Analysis of Population-Based Studies

    PubMed Central

    Bae, Hyoung Won; Lee, Naeun; Lee, Hye Sun; Hong, Samin; Seong, Gong Je; Kim, Chan Yun

    2014-01-01

    Background/Aims Systemic hypertension is thought to increase the risk for developing open-angle glaucoma (OAG) through several mechanisms. However, previous epidemiological studies have shown conflicting results regarding this potential association. We systematically evaluated this issue by conducting a meta-analysis of population-based studies. Methods A comprehensive search for articles published before 31 March 2014 was performed using PubMed, Embase, and reference lists. The pooled odds ratio (OR) was calculated using the fixed- and random-effects models, and meta-regression was performed according to age. Subgroup analyses were also conducted, and publication bias was assessed using a funnel plot and Egger’s regression test. Results This meta-analysis included 16 studies involving 60,084 individuals, with substantial homogeneity among the studies. The pooled OR for OAG was 1.22 (95% confidence interval, CI: 1.09–1.36) using the fixed-effects model and 1.22 (95% CI: 1.08–1.37) using the random-effects model in all included studies. For subgroup analyses, the pooled OR for high-tension glaucoma (HTG) was higher than that for normal-tension glaucoma (NTG) (OR = 1.92 and 0.94, respectively). No significant difference was detected between Asian and Western populations, and no publication bias was detected in either analysis. Conclusions Systemic hypertension increases the risk for developing OAG, especially in those with HTG. PMID:25254373

  11. 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

  12. A population-based analysis of the health experience of African Nova Scotians

    PubMed Central

    Kisely, Steve; Terashima, Mikiko; Langille, Don

    2008-01-01

    Background People of African descent living in Britain and the United States have higher rates of morbidity from chronic disease than among the general population. We investigated whether the same applied to people of African descent living in a Canadian province. Methods We used administrative data to calculate 10-year cumulative incidence rate ratios for the period 1996–2005 for treated circulatory disease, diabetes mellitus and psychiatric disorders in Preston (population 2425), a community of predominantly African Nova Scotians. We used data for the province of Nova Scotia as a whole as the population reference standard. We also calculated 10-year incidence rate ratios for visits to family physicians and specialists and for admissions to hospital. We compared these findings with those in 7 predominantly white communities in Nova Scotia with otherwise similar socio-economic characteristics. Results In the province as a whole, we identified 787 787 incident cases for the 3 disease groups over the 10-year period. Incidence rate ratios for the community of interest relative to the provincial population were significantly elevated for the 3 diseases: circulatory disease (1.19, 95% CI 1.08–1.29), diabetes (1.43, 95% CI 1.21–1.64) and psychiatric disorders (1.13, 95% CI 1.06–1.20). Incidence rate ratios in the community of interest were also higher than those in the comparison communities. Visits to family physicians and specialists for circulatory disease and diabetes were similarly elevated, but the pattern was less clear for visits for psychiatric disorders and hospital admissions. Interpretation African Nova Scotians had higher morbidity levels associated with treated disease, which could not be explained by socio-economic characteristics, recent immigration or language. Apart from psychiatric disorders, use of specialist services was consistent with morbidity. Further study is needed to investigate the relative contribution of genetic, biological

  13. 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

  14. [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

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

    PubMed

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

    2014-09-01

    We evaluated the population structure of the bog and dry land populations of the Siberian pine Pinus sibirica (P. sibrica) in Western Siberia using nuclear genome markers. Six pairs of nuclear microsatellite loci were used for this analysis. We detected 30 allelic variants in 120 individuals of four populations of P. Sibirica. We established that the studied populations differ by genetic structure. The most essential differences were identified between the Siberian pine population from oligotrophic bog and the group of populations from dry land within eutrophic bogs and near settlements P. sibirica forest (F(ST) = 0.019; D(N) = 0.053). We estimated that diversification of the West Siberian populations of P. sibirica exceeded 2.4% (F(ST) = 0.024), based on an analysis of SSR markers. PMID:25735136

  16. 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

  17. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    USGS Publications Warehouse

    Coggins, L.G., Jr.; Pine, William E., III; 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.

  20. 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...

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

    PubMed Central

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

    2010-01-01

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

  2. 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

  3. Cancer of unknown primary: a population-based analysis of temporal change and socioeconomic disparities

    PubMed Central

    Urban, D; Rao, A; Bressel, M; Lawrence, Y R; Mileshkin, L

    2013-01-01

    Background: Cancer of unknown primary (CUP) is the fourth most common cause of cancer death. With advanced diagnostics and treatments, we investigated the proportion of cancers diagnosed as CUP, treatment outcomes and association with socioeconomic disparities. Methods: We analysed trends in CUP diagnosis and outcome within the Surveillance, Epidemiology, and End Results registry between 1973 and 2008. Results: The percentage of all cancers diagnosed as CUP has decreased over time comprising <2% of cancers since 2007. A higher proportion of CUP was diagnosed in the elderly, females, blacks and residents of less affluent or less educated counties. Median survival of all CUP patients was 3 months, with no improvement over time. The 5-year survival significantly improved in those with squamous histology (squamous cell carcinoma; SCC) but only marginally in non-SCC. Factors associated with a longer survival on multivariate analysis included white race; female; <65 years old; most recent decade at diagnosis; SCC; married; a histological diagnosis; and treatment with radiotherapy (all P<0.001). Despite the improvement in survival with radiotherapy, its use was less frequent in females and blacks. Conclusion: The percentage of cancers diagnosed as CUP is decreasing but prognosis remains poor, particularly in non-SCC CUP. However, significant socioeconomic disparities exist in diagnosis and survival, suggesting inequalities in access to diagnostic investigations and treatment. PMID:23860528

  4. 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

  5. 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

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

    PubMed Central

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

    2013-01-01

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

  7. GIS based analysis on the population migration of main nationalities in Gansu province since the founding of China

    NASA Astrophysics Data System (ADS)

    Fu, Haiyue; Li, Manchun; Zhao, Jun; Gao, Zhonghua

    2007-06-01

    This paper sets up 5 Census database in 1953,1964,1983,1990,2000 based on GIS. The population gravity centers of main nationalities were calculated using gravity model in 1953, 1964,1983,1990,2000. Then, the characteristics and the influence factors of the moving of the minority population are analyzed. Study results show that population gravity center move to capitals are obvious. The move velocities of minorities' population gravity centers are slowdown, while the move velocities of HAN is Accelerated. Movement distances of east-west direction are generally greater than that of the north-south direction. The population gravity center are continued moving to southeast all the while. Finally, the factors of Natural conditions, Economic development, Policies as the mainly reasons were discussed.

  8. Acceptance of Internet-Based Health Care Services Among Households in Poland: Secondary Analysis of a Population-Based Survey

    PubMed Central

    2012-01-01

    Background Polish society is benefiting from growing access to the Internet, but the use of advanced e-services is still limited. The provision of Internet-based health services depends not only on the penetration of the Internet into society, but also on the acceptance of this technology by potential users. Objective The main objective of this study was focused on the assessment of predictors of acceptance of Internet use for provision of health services (eg, sociodemographic status, the use of information technologies, and consumption of health care services) among households in Poland. Methods The study was based on a secondary analysis of the dataset from the 2011 Social Diagnosis survey (a biannual survey conducted since 2001 about economic and non-economic aspects of household and individual living conditions in Poland). Analysis of the questionnaire results focused on the situations of the households included in the study. The predictors for 2 outcome variables describing the acceptance of households for Internet use for provision of a full health care service, or at least access to information and download of required forms, were assessed using multivariate logistic regression. Results After excluding those households that would not consider the use of health care services or for which predictor variables assumed missing values, the final analyses were conducted on data from 8915 households. Acceptance of the use of the Internet for provision of full health care services in Polish households was significantly higher among households in urban locations with ≥ 200,000 inhabitants than among households in rural areas; it was also higher with salaried employment as the source of income than with self-employment in agriculture (odds ratio [OR] = 0.53, 95% CI 0.40 - 0.70), retirement pension (OR = 0.46, 95% CI 0.39 - 0.54), disability pension (OR = 0.48, 95% CI 0.34 - 0.68), or with several simultaneous income sources (OR = 0.66; 95% CI 0.57 - 0

  9. 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

  10. Gender and socioeconomic disparities in BMI trajectories in the Seychelles: a cohort analysis based on serial population-based surveys

    PubMed Central

    2011-01-01

    Background The relationship between body mass index (BMI) and socioeconomic status (SES) tends to change over time and across populations. In this study, we examined, separately in men and women, whether the association between BMI and SES changed over successive birth cohorts in the Seychelles (Indian Ocean, African region). Methods We used data from all participants in three surveys conducted in 1989, 1994 and 2004 in independent random samples of the population aged 25-64 years in the Seychelles (N = 3'403). We used linear regression to model mean BMI according to age, cohort, SES and smoking status, allowing for a quadratic term for age to account for a curvilinear relation between BMI and age and interactions between SES and age and between SES and cohorts to test whether the relation between SES and BMI changed across subsequent cohorts. All analyses were performed separately in men and women. Results BMI increased with age in all birth cohorts. BMI was lower in men of low SES than high SES but was higher in women of low SES than high SES. In all SES categories, BMI increased over successive cohorts (1.24 kg/m2 in men and 1.51 kg/m2 for a 10-year increase in birth cohorts, p < 0.001). The difference in BMI between men or women of high vs. low SES did not change significantly across successive cohorts (the interaction between SES and year of birth of cohort was statistically not significant). Smoking was associated with lower BMI in men and women (respectively -1.55 kg/m2 and 2.46 kg/m2, p < 0.001). Conclusions Although large differences exist between men and women, social patterning of BMI did not change significantly over successive cohorts in this population of a middle-income country in the African region. PMID:22152035

  11. Role of Adjuvant Radiotherapy in Left-Sided Pancreatic Cancer-Population-Based Analysis with Propensity Score Matching.

    PubMed

    Lim, Yu Jin; Kim, Kyubo; Chie, Eui Kyu; Kim, BoKyong; Ha, Sung W

    2015-12-01

    This population-based study evaluated the survival impact of postoperative radiotherapy (PORT) in left-sided pancreatic cancer. The Surveillance, Epidemiology, and End Results (SEER) database was used to identify patients with surgically resected left-sided pancreatic adenocarcinoma from 2004 to 2010. Propensity score matching was conducted to compare PORT and non-PORT groups. A total of 445 patients were identified, and PORT was performed in 180 (40 %) patients. In the unmatched population, there were no significant differences in overall survival (OS) (P = 0.197) and cause-specific survival (CSS) (P = 0.379) between the PORT and non-PORT groups. After propensity score matching, the patients treated with PORT had longer median OS (P = 0.012) and CSS (P = 0.039) than the non-PORT group. In propensity-adjusted multivariate analysis, non-receipt of PORT was a poor prognostic factor in OS (hazard ratio [HR] 1.39, 95 % confidence interval [CI] 1.08-1.79), and CSS (HR 1.31, 95 % CI 1.01-1.71). The log odds of positive lymph nodes (LOODS) (≥-0.73) was also associated with worse OS (P = 0.003) and CSS (P = 0.001). In left-sided pancreatic cancer, considering the addition of PORT is a reasonable option as in pancreatic head cancer. The LOODS was suggested as a strong predictive indicator of the patients' prognoses. PMID:26376994

  12. 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

  13. 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...

  14. Latent class analysis identifies three subtypes of aggressive end-of-life care: a population-based study in Taiwan.

    PubMed

    Chen, Mei-Ling; Chen, Yun-Yi; Tang, Siew Tzuh

    2013-10-01

    The aggressiveness of end-of-life (EOL) cancer care has often been analysed by the occurrence of several indicators, separately or aggregately. Whether aggressive EOL cancer care has different subtypes is unknown. This study sought to identify distinct subtypes of aggressive EOL care based on usage patterns of aggressive EOL-care indicators and to explore demographic, disease and treatment factors associated with the identified subtypes. This retrospective study linked data from 2001 to 2006 from three Taiwanese databases: National Registration of Death Database, Cancer Registration System and National Health Insurance claims database. Adult cancer patients (N=203,642) who died in 2001-2006 were selected. For these cancer patients' last month of life, we analysed eight indicators of aggressive EOL care: receiving chemotherapy, >1 emergency room visit, >1 hospitalisation, hospitalisation for >14 days, intensive care unit admission, received cardiopulmonary resuscitation, received intubation and received mechanical ventilation. Subtypes of aggressive EOL care were identified by latent class analysis. Among the study population, only 22.3% were treated by medical oncologists. Based on their profiles of EOL care, deceased cancer patients were classified into three subgroups: 'not aggressive' (45%), 'intent to sustain life' (33%) and 'symptom crisis' group (22%). Patients assigned to the 'intent to sustain life' group were less likely to have metastatic disease and to receive hospice care in the last year of life, but more likely to be cared for by non-medical oncologists, to die within 2 months after diagnosis and to die in hospital. EOL cancer care may be improved by understanding factors related to different subtypes of aggressive EOL care. PMID:23756054

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

    PubMed Central

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

    2012-01-01

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

  16. Community patterns of stigma towards persons living with HIV: A population-based latent class analysis from rural Vietnam

    PubMed Central

    2011-01-01

    Background The negative effects of stigma on persons living with HIV (PLHIV) have been documented in many settings and it is thought that stigma against PLHIV leads to more difficulties for those who need to access HIV testing, treatment and care, as well as to limited community uptake of HIV prevention and testing messages. In order to understand and prevent stigma towards PLHIV, it is important to be able to measure stigma within communities and to understand which factors are associated with higher stigma. Methods To analyze patterns of community stigma and determinants to stigma toward PLHIV, we performed an exploratory population-based survey with 1874 randomly sampled adults within a demographic surveillance site (DSS) in rural Vietnam. Participants were interviewed regarding knowledge of HIV and attitudes towards persons living with HIV. Data were linked to socioeconomic and migration data from the DSS and latent class analysis and multinomial logistic regression were conducted to examine stigma group sub-types and factors associated with stigma group membership. Results We found unexpectedly high and complex patterns of stigma against PLHIV in this rural setting. Women had the greatest odds of belong to the highest stigma group (OR 1.84, 95% CI 1.42-2.37), while those with more education had lower odds of highest stigma group membership (OR 0.45, 95% CI 0.32-0.62 for secondary education; OR 0.19, 95% CI 0.10-0.35 for tertiary education). Long-term migration out of the district (OR 0.61, 95% CI 0.4-0.91), feeling at-risk for HIV (OR 0.42, 95% CI 0.27-0.66), having heard of HIV from more sources (OR 0.44, 95% CI 0.3-0.66), and knowing someone with HIV (OR 0.76, 95% CI 0.58-0.99) were all associated with lower odds of highest stigma group membership. Nearly 20% of the population was highly unsure of their attitudes towards PLHIV and persons in this group had significantly lower odds of feeling at-risk for HIV (OR 0.54, 95% CI 0.33-0.90) or of knowing someone

  17. Power analysis to detect time trends on population-based cancer registries data: When size really matters.

    PubMed

    Zanetti, Roberto; Sera, Francesco; Sacchetto, Lidia; Coebergh, Jan Willem; Rosso, Stefano

    2015-06-01

    Detecting statistically significant trends in incidence with cancer registries data not only depends on the size of their covered population but also on the levels of incidence rates, duration of diagnostic period and type of temporal variation. We simulated sample sizes of newly diagnosed cases based on a variety of plausible levels of cancer rates and scenarios of changing trends over a period of about 30 years. Each simulated set of cases was then analysed with joinpoint regression models. The power was derived as the relative frequency of the simulation runs where the p-value of the coefficient was less than 0.05 under the alternative model. In case of a decreasing trend with no change of direction (join), an Annual Percentage Change (APC) of 1% for an average rate of 10 per 100,000 is detectable in populations of half a million inhabitants or more with a nominal power of 80%. In a model with one joinpoint followed by an increasing trend, the minimum detectable APC increases, and an APC of about 2%, can be detected only with populations of at least 2 million. For analyses requiring a larger sample size than the actual covered population, alternative organisational strategies should be considered, such as an extension of population coverage or data pooling and merging from registries with comparable data. (i.e. when heterogeneity across merging registries is low or acceptable for the specific study question). PMID:24239127

  18. 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.

  19. Principal Components Analysis of Population Admixture

    PubMed Central

    Ma, Jianzhong; Amos, Christopher I.

    2012-01-01

    With the availability of high-density genotype information, principal components analysis (PCA) is now routinely used to detect and quantify the genetic structure of populations in both population genetics and genetic epidemiology. An important issue is how to make appropriate and correct inferences about population relationships from the results of PCA, especially when admixed individuals are included in the analysis. We extend our recently developed theoretical formulation of PCA to allow for admixed populations. Because the sampled individuals are treated as features, our generalized formulation of PCA directly relates the pattern of the scatter plot of the top eigenvectors to the admixture proportions and parameters reflecting the population relationships, and thus can provide valuable guidance on how to properly interpret the results of PCA in practice. Using our formulation, we theoretically justify the diagnostic of two-way admixture. More importantly, our theoretical investigations based on the proposed formulation yield a diagnostic of multi-way admixture. For instance, we found that admixed individuals with three parental populations are distributed inside the triangle formed by their parental populations and divide the triangle into three smaller triangles whose areas have the same proportions in the big triangle as the corresponding admixture proportions. We tested and illustrated these findings using simulated data and data from HapMap III and the Human Genome Diversity Project. PMID:22808102

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

    PubMed Central

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

    2016-01-01

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

  2. 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

  3. 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. PMID:25685706

  4. 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

  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. PMID:17505264

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

    PubMed Central

    2013-01-01

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

  7. Impact of Population Stratification on Family-Based Association in an Admixed Population.

    PubMed

    Mersha, T B; Ding, L; He, H; Alexander, E S; Zhang, X; Kurowski, B G; Pilipenko, V; Kottyan, L; Martin, L J; Fardo, D W

    2015-01-01

    Population substructure is a well-known confounder in population-based case-control genetic studies, but its impact in family-based studies is unclear. We performed population substructure analysis using extended families of admixed population to evaluate power and Type I error in an association study framework. Our analysis shows that power was improved by 1.5% after principal components adjustment. Type I error was also reduced by 2.2% after adjusting for family substratification. The presence of population substructure was underscored by discriminant analysis, in which over 92% of individuals were correctly assigned to their actual family using only 100 principal components. This study demonstrates the importance of adjusting for population substructure in family-based studies of admixed populations. PMID:26064873

  8. [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

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

    PubMed

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

    2016-04-01

    Analysis of the genetic diversity and population structure of crops is very important for use in breeding programs and for genetic resources conservation. We analyzed the genetic diversity and population structure of 47 rice genotypes from diverse origins using amplified fragment length polymorphism (AFLP) markers and morphological characters. The 47 genotypes, which were composed of four populations: Iranian native varieties, Iranian improved varieties, International Rice Research Institute (IRRI) rice varieties, and world rice collections, were analyzed using ten primer combinations. A total of 221 scorable bands were produced with an average of 22.1 alleles per pair of primers, of which 120 (54.30%) were polymorphic. The polymorphism information content (PIC) values varied from 0.32 to 0.41 with an average of 0.35. The high percentage of polymorphic bands (%PB) was found to be 64.71 and the resolving power (R p) collections were 63.36. UPGMA clustering based on numerical data from AFLP patterns clustered all 47 genotypes into three large groups. The genetic similarity between individuals ranged from 0.54 to 0.94 with an average of 0.74. Population genetic tree showed that Iranian native cultivars formed far distant cluster from the other populations, which may indicate that these varieties had minimal genetic change over time. Analysis of molecular variance (AMOVA) revealed that the largest proportion of the variation (84%) to be within populations showing the inbreeding nature of rice. Therefore, Iranian native varieties (landraces) may have unique genes, which can be used for future breeding programs and there is a need to conserve this unique diversity. Furthermore, crossing of Iranian genotypes with the genetically distant genotypes in the other three populations may result in useful combinations, which can be used as varieties and/or lines for future rice breeding programs. PMID:26762294

  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. PMID:27585025

  11. Power Analysis for Population-Based Longitudinal Studies Investigating Gene-Environment Interactions in Chronic Diseases: A Simulation Study

    PubMed Central

    Ma, Jinhui; Thabane, Lehana; Beyene, Joseph; Raina, Parminder

    2016-01-01

    Conventional methods for sample size calculation for population-based longitudinal studies tend to overestimate the statistical power by overlooking important determinants of the required sample size, such as the measurement errors and unmeasured etiological determinants, etc. In contrast, a simulation-based sample size calculation, if designed properly, allows these determinants to be taken into account and offers flexibility in accommodating complex study design features. The Canadian Longitudinal Study on Aging (CLSA) is a Canada-wide, 20-year follow-up study of 30,000 people between the ages of 45 and 85 years, with in-depth information collected every 3 years. A simulation study, based on an illness-death model, was conducted to: (1) investigate the statistical power profile of the CLSA to detect the effect of environmental and genetic risk factors, and their interaction on age-related chronic diseases; and (2) explore the design alternatives and implementation strategies for increasing the statistical power of population-based longitudinal studies in general. The results showed that the statistical power to identify the effect of environmental and genetic risk exposures, and their interaction on a disease was boosted when: (1) the prevalence of the risk exposures increased; (2) the disease of interest is relatively common in the population; and (3) risk exposures were measured accurately. In addition, the frequency of data collection every three years in the CLSA led to a slightly lower statistical power compared to the design assuming that participants underwent health monitoring continuously. The CLSA had sufficient power to detect a small (1

  12. 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

  13. Antibiotics in fetal and early life and subsequent childhood asthma: nationwide population based study with sibling analysis

    PubMed Central

    Lundholm, Cecilia; Kieler, Helle; Ludvigsson, Jonas F; Fall, Tove; Ye, Weimin; Almqvist, Catarina

    2014-01-01

    Objective To investigate the association between exposure to antibiotics in fetal and early life and asthma in childhood, with adjustment for confounding factors. Design Nationwide prospective population based cohort study, including sibling control design. Setting Swedish population identified from national demographic and health registers. Participants 493 785 children born 2006-10; 180 894 of these were eligible for sibling analyses. Main outcome measure Asthma defined as having both an asthma diagnosis and dispensed asthma drugs. The association between antibiotic exposure and asthma was investigated in the whole cohort with Cox proportional hazard regression. A stratified proportional hazards model conditional on sibling group was used to adjust for shared factors within families. Confounding by respiratory infections was assessed by investigating whether specific groups of antibiotics were associated with asthma. Results Antibiotic exposure in fetal life was associated with an increased risk of asthma in cohort analyses (hazard ratio 1.28, 95% confidence interval 1.25 to 1.32), but not in sibling analyses (0.99, 0.92 to 1.07). In cohort analyses, antibiotics used to treat respiratory infections in childhood were associated with a more pronounced increased risk of asthma (4.12, 3.78 to 4.50) than antibiotics used for urinary tract and skin infections (1.54, 1.24 to 1.92). In sibling analyses, the excess risks after exposure to antibiotics for respiratory infections decreased (2.36, 1.78 to 3.13) and disappeared for antibiotics for urinary tract and skin (0.85, 0.47 to 1.55). Conclusions Previous positive associations between exposure to antibiotics in fetal and early life and subsequent childhood asthma could have been caused by confounding by shared familial factors, in addition to confounding by respiratory infections. PMID:25432937

  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. Genetic variability in geographical populations of Culex quinquefasciatus Say (Diptera: Culicidae) from India based on random amplified polymorphic DNA analysis.

    PubMed

    Sharma, A K; Mendki, M J; Tikar, S N; Chandel, K; Sukumaran, D; Parashar, B D; Veer, Vijay; Agarwal, O P; Prakash, Shri

    2009-10-01

    Genetic variability and environmental factors may influence the refractiveness, propagation of pathogen and transmission of disease. Random amplified polymorphic DNA (RAPD) is one of the widely used molecular markers for population genetic diversity studies. In present study, RAPD is used to ascertain the genetic variability in Culex quinquefasciatus populations collected from various Indian geographical locations. Out of 50 RAPD primers screened, 14 primers exhibited clear, concrete and distinct banding pattern showing up to 100% polymorphism. Primer OPBD3 was tested with DNA of 14 geographical populations from India (including one laboratory population) showed 21 loci representing 14 populations with 100% polymorphism. The genetic diversity among the populations indicated the Shannon index (I) and gene diversity index (H(ST)), 0.48 and 0.31, respectively among the population, displaying rich genetic variation among the Cx. quinquefasciatus populations. Consensus tree showed two clusters indicating the genetic variation among the various geographical populations. The findings of this study may be useful to understand the population variation under different ecological conditions and development of effective vector management strategies. PMID:19577531

  17. 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

  18. PopTract: Population-Based Tractography

    PubMed Central

    Yap, Pew-Thian; Gilmore, John H.; Lin, Weili

    2016-01-01

    White matter fiber tractography plays a key role in the in vivo understanding of brain circuitry. For tract-based comparison of a population of images, a common approach is to first generate an atlas by averaging, after spatial normalization, all images in the population, and then perform tractography using the constructed atlas. The reconstructed fiber trajectories form a common geometry onto which diffusion properties of each individual subject can be projected based on the corresponding locations in the subject native space. However, in the case of high angular resolution diffusion imaging (HARDI), where modeling fiber crossings is an important goal, the above-mentioned averaging method for generating an atlas results in significant error in the estimation of local fiber orientations and causes a major loss of fiber crossings. These limitatitons have significant impact on the accuracy of the reconstructed fiber trajectories and jeopardize subsequent tract-based analysis. As a remedy, we present in this paper a more effective means of performing tractography at a population level. Our method entails determining a bipolar Watson distribution at each voxel location based on information given by all images in the population, giving us not only the local principal orientations of the fiber pathways, but also confidence levels of how reliable these orientations are across subjects. The distribution field is then fed as an input to a probabilistic tractography framework for reconstructing a set of fiber trajectories that are consistent across all images in the population. We observe that the proposed method, called PopTract, results in significantly better preservation of fiber crossings, and hence yields better trajectory reconstruction in the atlas space. PMID:21571607

  19. 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

  20. Risk of venous thromboembolism in women with polycystic ovary syndrome: a population-based matched cohort analysis

    PubMed Central

    Bird, Steven T.; Hartzema, Abraham G.; Brophy, James M.; Etminan, Mahyar; Delaney, Joseph A.C.

    2013-01-01

    Background: There is an increased risk of venous thromboembolism among women taking oral contraceptives. However, whether there is an additional risk among women with polycystic ovary syndrome (PCOS) is unknown. Methods: We developed a population-based cohort from the IMS LifeLink Health Plan Claims Database, which includes managed care organizations in the United States. Women aged 18–46 years taking combined oral contraceptives and who had a claim for PCOS (n = 43 506) were matched, based on a propensity score, to control women (n = 43 506) taking oral contraceptives. Venous thromboembolism was defined using administrative coding and use of anticoagulation. We used Cox proportional hazards models to assess the relative risk (RR) of venous thromboembolism among users of combined oral contraceptives with and without PCOS. Results: The incidence of venous thromboembolism among women with PCOS was 23.7/10 000 person-years, while that for matched controls was 10.9/10 000 person-years. Women with PCOS taking combined oral contraceptives had an RR for venous thromboembolism of 2.14 (95% confidence interval [CI] 1.41–3.24) compared with other contraceptive users. The incidence of venous thromboembolism was 6.3/10 000 person-years among women with PCOS not taking oral contraceptives; the incidence was 4.1/10 000 person-years among matched controls. The RR of venous thromboembolism among women with PCOS not taking oral contraceptives was 1.55 (95% CI 1.10–2.19). Interpretation: We found a 2-fold increased risk of venous thromboembolism among women with PCOS who were taking combined oral contraceptives and a 1.5-fold increased risk among women with PCOS not taking oral contraceptives. Physicians should consider the increased risk of venous thromboembolism when prescribing contraceptive therapy to women with PCOS. PMID:23209115

  1. Mutational analysis of 33 autosomal short tandem repeat (STR) loci in southwest Chinese Han population based on trio parentage testing.

    PubMed

    Jin, Bo; Su, Qin; Luo, Haibo; Li, Yingbi; Wu, Jin; Yan, Jing; Hou, Yiping; Liang, Weibo; Zhang, Lin

    2016-07-01

    Mutation rates and 95% CI of 33 short tandem repeat (STR) loci (D1S2142, D2S1338, D2S441, D3S1358, D3S1754, D5S818, D6S1043, D7S3048, D7S820, D8S1132, D8S1179, D10S1248, D11S2368, D12S391, D13S1492, D13S317, D13S325, D14S306, D15S659, D16S539, D18S1364, D18S51, D19S433, D20S161, D21S11, D22GATA198B05, CSF1PO, FGA, Penta D, Penta E, TH01, TPOX, and vWA) were investigated through more than 424,000 parent-child meiotic transfers obtained from 10636 trios parentage testing cases in southwest Chinese Han population. Overall, 297, including 292 single-step, 4 double-step and 1 triple-step mutation events were observed. The average mutation rate was 0.70×10(-3). Most of the locus-specific mutation rates (varied from 0.20×10(-3) to 1.96×10(-3)) were lower than the other datasets (p<0.05). Mutations of 7 loci are reported for the first time. Mutation rates varied with population from different ethnicities and geographical regions. There was no significant difference between mutation expansion and contraction (∼1.04:1). Paternal origin mutations occurred more frequently than maternal origin ones (∼5.02:1). In addition, mutation rates indicated positive correlation with the expected heterozygosity (He) and geometric mean of longest run of perfect repeats (LRPR), respectively. Short alleles showed a trend toward mutation gain while long alleles trended toward mutation loss. A credible forensic dataset for locus-specific mutation rates of 33 loci has been established based upon strict inclusion criteria of large-sized parents/child-trio cases. PMID:27045978

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

    PubMed Central

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

    2014-01-01

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

  3. 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

  4. Breast cancer incidence after hormonal treatments for infertility: systematic review and meta-analysis of population-based studies.

    PubMed

    Gennari, Alessandra; Costa, Mauro; Puntoni, Matteo; Paleari, Laura; De Censi, Andrea; Sormani, Maria Pia; Provinciali, Nicoletta; Bruzzi, Paolo

    2015-04-01

    The increasing practice of hormonal infertility treatments (HITs) raised concerns about their effects on breast cancer (BC) risk. Available evidence reported conflicting results. The aim of this study was to assess the potential association between HITs and BC risk. The literature was searched through November 2014. Eligible studies included cohort studies reporting BC incidence in women undergone HITs. Data were analyzed with standard meta-analytic techniques. Subgroup analyses were performed by type of intervention (IVF vs. NO IVF), follow-up duration (<10 vs. >10 years), and type of control (population vs. infertile). 20 eligible studies (207.914 women, 2347 BC) were retrieved: no increased risk was detected (SRR = 1.05, 95 % CI 0.96-1.14), with a significant heterogeneity (I (2) = 59 %, p = 0.001) among studies. In the seven studies with the in vitro fertilization (IVF) procedure, no increase in BC risk was observed (SRR = 0.96, 95 % CI 0.80-1.14); in the three NO IVF studies, an increased BC risk was identified (SRR = 1.26, 95 %CI 1.06-1.50). A borderline interaction between type of intervention (IVF vs. NO IVF) and BC risk was observed (p = 0.06). An increased risk with longer follow-up (≥10 vs. <10 years) was detected (SRR = 1.13, 95 % CI 1.02-1.26 vs. SRR = 0.95, 95 % CI 0.85-1.06). Overall, HITs are not associated with an increased BC risk. In particular, no increased risk was observed in women undergoing IVF. Conversely, an increased in BC risk cannot be ruled out with older treatment protocols based on clomiphene. The long-term administration of clomiphene outside the current indications should be discouraged because of a possible increase in BC risk. PMID:25744295

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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

  10. Cancer by industry: analysis of a population-based cancer registry with an emphasis on blue-collar workers.

    PubMed

    Hall, N E; Rosenman, K D

    1991-01-01

    This paper uses information on occupation and industry routinely collected in a state-based cancer registry to assess potential associations between work place exposures and cancer incidence. Industry-specific proportional cancer incidence ratios (PCIR) were calculated by race and sex for all individuals and for white males with blue-collar occupations. Expected numbers of cancers were derived both from cancers occurring among all occupations and just among blue-collar occupations. This latter analysis was done as a control for differences in the prevalence of life-style habits between blue- and white-collar workers. Increased lung cancer PCIR were seen in most industries previously reported to be associated with lung cancer risk. The effects of socioeconomic status on these results are discussed. Other results include an increased ratio of melanoma in blue-collar white male rubber and plastic product workers, an increased ratio of non-Hodgkin's lymphomas in motor vehicle manufacture workers, and an increased PCIR of chronic lymphocytic leukemia in general construction workers. Uterine cancer was increased in proportion in white females for a number of industries including rubber and plastic product manufacture, apparel manufacture, and electrical equipment manufacture. PMID:1992675

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

    PubMed Central

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

    2016-01-01

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

  12. Comparison of population- and family-based methods for genetic association analysis in the presence of interacting loci.

    PubMed

    Howson, Joanna M M; Barratt, Bryan J; Todd, John A; Cordell, Heather J

    2005-07-01

    We compared different ascertainment schemes for genetic association analysis: affected sib-pairs (ASPs), case-parent trios, and unrelated cases and controls. We found, with empirical type 1 diabetes data at four known disease loci, that studies based on case-parent trios and on unmatched cases and controls often gave higher odds ratio estimates and stronger significance test values than ASP designs. We used simulations and a simplified disease model involving two interacting loci, one of large effect and one smaller, to examine interaction models that could cause such an effect. The different ascertainment schemes were compared for power to detect an effect when only the locus of smaller effect was genotyped. ASPs showed the greatest power for association testing under most models of interaction except under additive and certain epistatic crossover models, for which case/controls and case-parent trios did better. All ascertainment schemes gave an unbiased estimation of log genotype relative risks (GRRs) under a multiplicative model. Under nonmultiplicative interactions, GRRs at the minor locus as estimated from ASPs could be biased upwards or downwards, resulting in either an increase or decrease in power compared to the case/control or trio design. For the four known type 1 diabetes loci, we observed decreased risks with ASPs, which could be due to additive interactions with the remaining susceptibility loci. Thus, the optimal ascertainment strategy in genetic association studies depends on the unknown underlying multilocus genetic model, and on whether the goal of the study is to detect an effect or to accurately estimate the resulting disease risks. PMID:15892093

  13. 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.

  14. Breastfeeding: population-based perspectives.

    PubMed

    Labbok, Miriam H

    2013-02-01

    From a population perspective, the achievement of the goals of exclusive breastfeeding throughout the first 6 months of life and continued breastfeeding with the introduction of age-appropriate complementary feeding for infant feeding, women and families must be inspired and empowered to overcome health system, sociocultural, and economic/political barriers. This article discusses trends in breastfeeding, influences on the reacceptance of a breastfeeding norm, and breastfeeding as a social and public health issue. The goal is to create an enabling environment for optimal breastfeeding in health care and social norms, and to adjust the social and political realities to support an economic milieu that favors breastfeeding. PMID:23178058

  15. Family-based analysis identified CD2 as a susceptibility gene for primary open angle glaucoma in Chinese Han population

    PubMed Central

    Liu, Ting; Xie, Lin; Ye, Jian; He, Xiangge

    2014-01-01

    Primary open angle glaucoma (POAG) is characterized by optic disc cupping and irreversible loss of retinal ganglion cells. Few genes have been detected that influence POAG susceptibility and little is known about its genetic architecture. In this study, we employed exome sequencing on three members from a high frequency POAG family to identify the risk factors of POAG in Chinese population. Text-mining method was applied to identify genes associated with glaucoma in literature, and protein–protein interaction networks were constructed. Furthermore, reverse transcription PCR and Western blot were performed to confirm the differential gene expression. Six genes, baculoviral inhibitors of apoptosis protein repeat containing 6 (BIRC6), CD2, luteinizing hormone/choriogonadotropin receptor (LHCGR), polycystic kidney and hepatic disease gene 1 (PKHD1), phenylalanine hydroxylase (PAH) and fucosyltransferase 7 (FUT7), which might be associated with POAG, were identified. Both the mRNA expression levels and protein expression levels of HSP27 were increased in astrocytes from POAG patients compared with those from normal control, suggesting that mutation in CD2 might pose a risk for POAG in Chinese population. In conclusion, novel rare variants detected by exome sequencing may hold the key to unravelling the remaining contribution of genetics to complex diseases such as POAG. PMID:24597656

  16. 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.

  17. A general methodology for population analysis

    NASA Astrophysics Data System (ADS)

    Lazov, Petar; Lazov, Igor

    2014-12-01

    For a given population with N - current and M - maximum number of entities, modeled by a Birth-Death Process (BDP) with size M+1, we introduce utilization parameter ρ, ratio of the primary birth and death rates in that BDP, which, physically, determines (equilibrium) macrostates of the population, and information parameter ν, which has an interpretation as population information stiffness. The BDP, modeling the population, is in the state n, n=0,1,…,M, if N=n. In presence of these two key metrics, applying continuity law, equilibrium balance equations concerning the probability distribution pn, n=0,1,…,M, of the quantity N, pn=Prob{N=n}, in equilibrium, and conservation law, and relying on the fundamental concepts population information and population entropy, we develop a general methodology for population analysis; thereto, by definition, population entropy is uncertainty, related to the population. In this approach, what is its essential contribution, the population information consists of three basic parts: elastic (Hooke's) or absorption/emission part, synchronization or inelastic part and null part; the first two parts, which determine uniquely the null part (the null part connects them), are the two basic components of the Information Spectrum of the population. Population entropy, as mean value of population information, follows this division of the information. A given population can function in information elastic, antielastic and inelastic regime. In an information linear population, the synchronization part of the information and entropy is absent. The population size, M+1, is the third key metric in this methodology. Namely, right supposing a population with infinite size, the most of the key quantities and results for populations with finite size, emerged in this methodology, vanish.

  18. 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

  19. [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

  20. 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).

  1. 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

  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. 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

  6. 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

  7. Is Traumatic Brain Injury A Risk Factor for Schizophrenia? A Meta-Analysis of Case-Controlled Population-Based Studies

    PubMed Central

    Molloy, Charlene; Conroy, Ronan M.; Cotter, David R.; Cannon, Mary

    2011-01-01

    Traumatic brain injury (TBI) is known to lead to a range of adverse psychiatric sequelae but the question of whether TBI is a risk factor for psychosis and, in particular, schizophrenia remains unclear. Studies examining this issue have yielded conflicting results. We carried out a systematic review of the literature on TBI and psychosis in order to identify all population-based controlled studies which provide estimates of risk for schizophrenia following TBI. Odds ratios (ORs) were combined using random effects meta-analysis. Our literature search yielded 172 studies which were considered to be potentially relevant. From these, we identified 9 studies that could provide estimates of risk in the form of ORs. The pooled analysis revealed a significant association between TBI and schizophrenia (OR = 1.65; 95% CI = 1.17–2.32), with significant heterogeneity between the studies. Estimates from the family studies (OR = 2.8: 95% CI =1.76–4.47) were higher than those from the cohort/nested case-control studies (OR = 1.42: 95% CI = 1.02–1.97) by a factor of almost 2. There did not appear to be a dose-response relationship between severity of head injury and subsequent risk of schizophrenia. This meta-analysis supports an increased risk of schizophrenia following TBI, with a larger effect in those with a genetic predisposition to psychosis. Further epidemiological and neuroscientific studies to elucidate the mechanisms underlying this association are warranted. PMID:21813439

  8. 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.

  9. 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.

  10. Modification of breast cancer risk according to age and menopausal status: A combined analysis of five population-based case-control studies

    PubMed Central

    Trentham-Dietz, Amy; Sprague, Brian L.; Hampton, John M.; Miglioretti, Diana L.; Nelson, Heidi D.; Titus, Linda J.; Egan, Kathleen M.; Remington, Patrick L.; Newcomb, Polly A.

    2014-01-01

    Purpose While several risk factors for breast cancer have been identified, studies have not consistently shown whether these factors operate more strongly at certain ages or for just pre- or postmenopausal women. We evaluated whether risk factors for breast cancer differ according to age or menopausal status. Methods Data from five population-based case-control studies conducted during 1988-2008 were combined and analyzed. Cases (N=23,959) and population controls (N=28,304) completed telephone interviews. Logistic regression was used to estimate adjusted odds ratios and 95% confidence intervals and tests for interaction by age and menopausal status. Results Odds ratios for first-degree family history of breast cancer were strongest for younger women—reaching two-fold elevations—but were still statistically significantly elevated by 58-69% among older women. Obesity was inversely associated with breast cancer among younger women and positively associated with risk for older women (interaction P<0.0001). Recent alcohol intake was more strongly related to breast cancer risk among older women, although consumption of 3 or more drinks/day among younger women also was associated with elevated odd ratios (P<0.0001). Associations with benign breast disease and most reproductive/menstrual factors did not vary by age. Repeating analysis stratifying by menopausal status produced similar results. Conclusions With few exceptions, menstrual and lifestyle factors are associated with breast cancer risk regardless of age or menopausal status. Variation in the association of family history, obesity, and alcohol use with breast cancer risk by age and menopausal status may need to be considered when determining individual risk for breast cancer. PMID:24647890

  11. 16S rDNA-based analysis of dominant bacterial populations associated with early life stages of coho salmon (Oncorhynchus kisutch).

    PubMed

    Romero, Jaime; Navarrete, Paola

    2006-05-01

    In this study, we used a 16S rDNA-based approach to determine bacterial populations associated with coho salmon (Oncorhynchus kisutch) in its early life stages, highlighting dominant bacteria in the gastrointestinal tract during growth in freshwater. The present article is the first molecular analysis of bacterial communities of coho salmon. Cultivability of the salmon gastrointestinal microbiota was estimated by comparison of direct microscopic counts (using acridine orange) with colony counts (in tryptone soy agar). In general, a low fraction (about 1%) of the microbiota could be recovered as cultivable bacteria. Using DNA extracted directly from individuals belonging to the same lot, bacterial communities present in eggs and gastrointestinal tract of first-feeding fries and juveniles were monitored by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The DGGE profiles revealed simple communities in all stages and exposed changes in bacterial community during growth. Sequencing and phylogenetic analysis of excised DGGE bands revealed the nature of the main bacteria found in each stage. In eggs, the dominant bacteria belonged to beta-Proteobacteria (Janthinobacterium and Rhodoferax). During the first feeding stage, the most abundant bacteria in the gastrointestinal tract clustered with gamma-Proteobacteria (Shewanella and Aeromonas). In juveniles ranging from 2 to 15 g, prevailing bacteria were Pseudomonas and Aeromonas. To determine the putative origin of dominant Pseudomonas and Aeromonas found in juvenile gastrointestinal tracts, primers for these groups were designed based on sequences retrieved from DGGE gel. Subsequently, samples of the water influent, pelletized feed, and eggs were analyzed by PCR amplification. Only those amplicons obtained from samples of eggs and the water influent presented identical sequences to the dominant bands of DGGE. Overall, our results suggest that a stable microbiota is established after the first

  12. Defining Prolonged Length of Acute Care Stay for Surgically and Conservatively Treated Patients with Spontaneous Intracerebral Hemorrhage: A Population-Based Analysis

    PubMed Central

    Stein, Marco; Misselwitz, Björn; Hamann, Gerhard F.; Kolodziej, Malgorzata A.; Reinges, Marcus H. T.; Uhl, Eberhard

    2016-01-01

    Background. The definition of prolonged length of stay (LOS) during acute care remains unclear among surgically and conservatively treated patients with intracerebral hemorrhage (ICH). Methods. Using a population-based quality assessment registry, we calculated change points in LOS for surgically and conservatively treated patients with ICH. The influence of comorbidities, baseline characteristics at admission, and in-hospital complications on prolonged LOS was evaluated in a multivariate model. Results. Overall, 13272 patients with ICH were included in the analysis. Surgical therapy of the hematoma was documented in 1405 (10.6%) patients. Change points for LOS were 22 days (CI: 8, 22; CL 98%) for surgically treated patients and 16 days (CI: 16, 16; CL: 99%) for conservatively treated patients. Ventilation therapy was related to prolonged LOS in surgically (OR: 2.2, 95% CI: 1.5–3.1; P < 0.001) and conservatively treated patients (OR: 2.5, 95% CI: 2.2–2.9; P < 0.001). Two or more in-hospital complications in surgical patients (OR: 2.7, 95% CI: 2.1–3.5) and ≥1 in conservative patients (OR: 3.0, 95% CI: 2.7–3.3) were predictors of prolonged LOS. Conclusion. The definition of prolonged LOS after ICH could be useful for several aspects of quality management and research. Preventing in-hospital complications could decrease the number of patients with prolonged LOS. PMID:27110572

  13. 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

  14. 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

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

    PubMed

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

    2011-01-01

    The yeast Saccharomyces cerevisiae has a limited replicative lifespan. The cell mass at division is partitioned unequally between a larger, old parent cell and a smaller, new daughter cell. Industrial beer fermentations maintain and reuse yeast. At the end of fermentation a portion of the yeast is 'cropped' from the vessel for 'serial repitching'. Harvesting yeast may select a population with an imbalance of young and aged individuals, but the output of any bioprocess is dependent on the physiology of each single cell in the population. Unlike continuous models, individual-based modelling is an approach that considers each microbe as an individual, a unique and discrete entity, with characteristics that change throughout its life. The aim of this contribution is to explore, by means of individual-based simulations, the effects of inoculum size and cell genealogical age on the dynamics of virtual yeast fermentation, focussing on: (1) the first stages of population growth, (2) the mean biomass evolution of the population, (3) the rate of glucose uptake and ethanol production, and (4) the biomass and genealogical age distributions. The ultimate goal is to integrate these results in order to make progress in the understanding of the composition of yeast populations and their temporal evolution in beer fermentations. Simulation results show that there is a clear influence of these initial features of the inocula on the subsequent growth dynamics. By contrasting both the individual and global properties of yeast cells and populations, we gain insight into the interrelation between these two types of data, which helps us to deal with the macroscopic behaviour observed in experimental research. PMID:20811925

  16. 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.

  17. 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

  18. 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

  19. T2 relaxation time alterations underlying neurocognitive deficits in alcohol-use disorders (AUD) in an Indian population: A combined conventional ROI and voxel-based relaxometry analysis.

    PubMed

    Bagga, Deepika; Modi, Shilpi; Poonia, Mahesh; Kaur, Prabhjot; Bhattacharya, D; Garg, M L; Khushu, Subash; Singh, Namita

    2015-11-01

    Long-term heavy alcohol consumption has traditionally been associated with impaired cognitive abilities, such as deficits in abstract reasoning, problem solving, verbal fluency, memory, attention, and visuospatial processing. The present study aimed at exploring these neuropsychological deficits in alcohol-use disorders (AUD) in an Indian population using the Postgraduate Institute Battery of Brain Dysfunction (PGIBBD) and their possible correlation with alterations in T2 relaxation times (T2-RT), using whole-brain voxel-based relaxometry (VBR) and conventional region of interest (ROI) approach. Multi-echo T2 mapping sequence was performed on 25 subjects with AUD and 25 healthy controls matched for age, education, and socioeconomic status. Whole-brain T2-RT measurements were conducted using VBR and conventional ROI approach. The study was carried out on a 3T whole-body MR scanner. Post processing for VBR and ROI analysis was performed using SPM 8 software and vendor-provided software, respectively. A PGIBBD test battery was conducted on all subjects to assess their cognitive abilities, and the results were reported as raw scores. VBR and ROI results revealed that AUD subjects showed prolonged T2-RTs in cerebellum bilaterally, parahippocampal gyrus bilaterally, right anterior cingulate cortex, left superior temporal gyrus, left middle frontal gyrus, and left calcarine gyrus. A significant correlation was also observed between the neuropsychological test raw scores and alterations in T2-RT in AUD subjects. Our results are consistent with previous studies suggesting tissue disruption or gliosis or demyelination as a possible reason for prolonged T2-RTs. This damage to brain tissue, which is evident as prolonged T2-RT, could possibly be associated with impaired cognitive abilities noticeable in AUD subjects. PMID:26537482

  20. Incidence Patterns and Temporal Trends of Invasive Nonmelanotic Vulvar Tumors in Germany 1999-2011. A Population-Based Cancer Registry Analysis

    PubMed Central

    Buttmann-Schweiger, Nina; Klug, Stefanie J.; Luyten, Alexander; Holleczek, Bernd; Heitz, Florian; du Bois, Andreas; Kraywinkel, Klaus

    2015-01-01

    Objectives Time trends on the incidence and characteristics of invasive vulvar cancer in Germany have so far been studied in few local population- and hospital based tumor registries. We aimed to provide an overview on recent developments of vulvar cancer in Germany, using population-based cancer registry data. Methods We analyzed the data on vulvar cancer of eight population-based German cancer registries for the period 1999-2011. ICD-10 codes and ICD-O-3 morphology codes were used to select site and histologic types. The annual percentage change was calculated on age-adjusted incidence rates with a joinpoint regression model. Results A total of 12,711 registered cases of invasive carcinoma of the vulva were included in the analyses, hereof were 12,205 of squamous cell origin. Age-standardized incidence rates of vulvar cancer annually increased by 6.7% (95% confidence limits: 5.6-7.9) from 1.7 per 100,000 women in 1999 to 3.6 per 100,000 women in 2011. An increase was observed among women of all ages, and especially between 30 and 69 years of age. Conclusion The annual incidence of invasive carcinoma of the vulva nearly doubled in the past decade in Germany, considerably exceeding the rates observed in other Western European countries. A combination of changes in risk factors, and documentation practice might have contributed to the observed substantial increase in vulvar cancer incidence. PMID:26020540

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

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

    SciTech Connect

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

    1999-03-04

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

  9. Regular inhaled corticosteroids in adult-onset asthma and the risk for future cancer: a population-based cohort study with proper person-time analysis

    PubMed Central

    Kok, Victor C; Horng, Jorng-Tzong; Huang, Hsu-Kai; Chao, Tsung-Ming; Hong, Ya-Fang

    2015-01-01

    Background Recent studies have shown that inhaled corticosteroids (ICS) can exert anti-inflammatory effects for chronic airway diseases, and several observational studies suggest that they play a role as cancer chemopreventive agents, particularly against lung cancer. We aimed to examine whether regular ICS use was associated with a reduced risk for future malignancy in patients with newly diagnosed adult-onset asthma. Methods We used a population-based cohort study between 2001 and 2008 with appropriate person-time analysis. Participants were followed up until the first incident of cancer, death, or to the end of 2008. The Cox model was used to derive an adjusted hazard ratio (aHR) for cancer development. Kaplan–Meier cancer-free survival curves of two groups were compared. Results The exposed group of 2,117 regular ICS users and the nonexposed group of 17,732 non-ICS users were assembled. After 7,365 (mean, 3.5 years; standard deviation 2.1) and 73,789 (mean, 4.1 years; standard deviation 2.4) person-years of follow-up for the ICS users and the comparator group of non-ICS users, respectively, the aHR for overall cancer was nonsignificantly elevated at 1.33 with 95% confidence interval (CI), 1.00–1.76, P=0.0501. The Kaplan–Meier curves for overall cancer-free proportions of both groups were not significant (log-rank, P=0.065). Synergistic interaction of concurrent presence of regular ICS use was conducted using “ICS-negative and chronic obstructive pulmonary disease (COPD)-negative” as the reference. The aHR for the group of “ICS-positive, COPD-negative” did not reach statistically significant levels with aHR at 1.38 (95% CI, 0.53–3.56). There was a statistically significant synergistic interaction of concurrent presence of regular ICS use and COPD with aHR at 3.78 (95% CI, 2.10–6.81). Conclusion The protective effect of regular ICS use in the studied East Asian patients with adult-onset asthma was not detectable, contrary to reports of previous

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

    PubMed Central

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

    2015-01-01

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

  11. 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

  12. Body composition analysis in the pediatric population.

    PubMed

    Weber, David R; Leonard, Mary B; Zemel, Babette S

    2012-11-01

    Body composition analysis has become a useful tool in both clinical and research settings. Its use in the pediatric population is complicated by the rapid periods of growth and physical development that are characteristic of infancy, childhood, and adolescence. A thorough understanding of the changing nature of body composition during this time is essential for choosing the most appropriate measurement technique for a given individual, population, or clinical question. Growing evidence suggests that tissues such as fat, muscle, and bone are intimately involved in the regulation of whole body energy metabolism. This knowledge, when coupled with advancements in imaging techniques such as MRI and PET-CT, offers the possibility of developing new models of "functional" body composition. These models may prove to be especially important when assessing malnutrition and metabolic risk in patients with chronic disease. PMID:23469390

  13. 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

  14. Cost effectiveness analysis of population-based serology screening and 13C-Urea breath test for Helicobacter pylori to prevent gastric cancer: A markov model

    PubMed Central

    Xie, Feng; Luo, Nan; Lee, Hin-Peng

    2008-01-01

    AIM: To compare the costs and effectiveness of no screening and no eradication therapy, the population-based Helicobacter pylori (H pylori) serology screening with eradication therapy and 13C-Urea breath test (UBT) with eradication therapy. METHODS: A Markov model simulation was carried out in all 237 900 Chinese males with age between 35 and 44 from the perspective of the public healthcare provider in Singapore. The main outcome measures were the costs, number of gastric cancer cases prevented, life years saved, and quality-adjusted life years (QALYs) gained from screening age to death. The uncertainty surrounding the cost-effectiveness ratio was addressed by one-way sensitivity analyses. RESULTS: Compared to no screening, the incremental cost-effectiveness ratio (ICER) was $16 166 per life year saved or $13 571 per QALY gained for the serology screening, and $38 792 per life year saved and $32 525 per QALY gained for the UBT. The ICER was $477 079 per life year saved or $390 337 per QALY gained for the UBT compared to the serology screening. The cost-effectiveness of serology screening over the UBT was robust to most parameters in the model. CONCLUSION: The population-based serology screening for H pylori was more cost-effective than the UBT in prevention of gastric cancer in Singapore Chinese males. PMID:18494053

  15. 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

  16. Soft tissue cephalometric analysis applied to regional Indian population

    PubMed Central

    Upadhyay, Jay S.; Maheshwari, Sandhya; Verma, Sanjeev K.; Zahid, Syed Naved

    2013-01-01

    Introduction: Importance of soft tissue consideration in establishing treatment goals for orthodontics and orthognathic surgery has been recognized and various cephalometric analysis incorporating soft tissue parameters have evolved. The great variance in soft tissue drape of the human face and perception of esthetics exists and normative data based on one population group cannot be applied to all. The study was conducted to compare the standard soft tissue cephalometric analysis (STCA) norms with norms derived for population of western Uttar Pradesh region of India. Materials and Methods: The sample consisted of lateral cephalograms taken in natural head position of 33 normal subjects (16 males, 17 females). The cephalograms were analyzed with soft tissue cephalometric analysis for orthodontic diagnosis and treatment planning, and the Student's t test was used to compare the difference in means between study population and standard STCA norms. Results: Compared with established STCA norms, females in our study had steeper maxillary occlusal plane, more proclined mandibular incisors, and less protrusive lips. Both males and females showed an overall decrease in facial lengths, less prominent midface and mandibular structures and more convex profile compared with established norms for the White population. Conclusions: Statistically significant differences were found in certain key parameters of STCA for western Uttar Pradesh population when compared with established norms. PMID:24665169

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

    PubMed Central

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

    2014-01-01

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

  18. Symptom factor analysis, clinical findings, and functional status in a population-based case control study of Gulf War unexplained illness.

    PubMed

    Bourdette, D N; McCauley, L A; Barkhuizen, A; Johnston, W; Wynn, M; Joos, S K; Storzbach, D; Shuell, T; Sticker, D

    2001-12-01

    Few epidemiological studies have been conducted that have incorporated clinical evaluations of Gulf War veterans with unexplained health symptoms and healthy controls. We conducted a mail survey of 2022 Gulf War veterans residing in the northwest United States and clinical examinations on a subset of 443 responders who seemed to have unexplained health symptoms or were healthy. Few clinical differences were found between cases and controls. The most frequent unexplained symptoms were cognitive/psychological, but significant overlap existed with musculoskeletal and fatigue symptoms. Over half of the veterans with unexplained musculoskeletal pain met the criteria for fibromyalgia, and a significant portion of the veterans with unexplained fatigue met the criteria for chronic fatigue syndrome. Similarities were found in the clinical interpretation of unexplained illness in this population and statistical factor analysis performed by this study group and others. PMID:11765674

  19. 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

  20. 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

  1. 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. PMID:23056922

  2. Continuous probabilistic analysis to evolutionary game dynamics in finite populations.

    PubMed

    Gao, Meng

    2009-07-01

    Evolutionary game dynamics of two strategies in finite population is studied by continuous probabilistic approach. Besides frequency dependent selection, mutation was also included in this study. The equilibrium probability density functions of abundance, expected time to extinction or fixation were derived and their numerical solutions are calculated as illustrations. Meanwhile, individual-based computer simulations are also done. A comparison reveals the consistency between theoretical analysis and simulations. PMID:19219510

  3. 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

  4. Population genetic analysis of Enterocytozoon bieneusi in humans.

    PubMed

    Li, Wei; Cama, Vitaliano; Feng, Yaoyu; Gilman, Robert H; Bern, Caryn; Zhang, Xichen; Xiao, Lihua

    2012-01-01

    Genotyping based on sequence analysis of the ribosomal internal transcribed spacer has revealed significant genetic diversity in Enterocytozoonbieneusi. Thus far, the population genetics of E. bieneusi and its significance in the epidemiology of microsporidiosis have not been examined. In this study, a multilocus sequence typing of E. bieneusi in AIDS patients in Lima, Peru was conducted, using 72 specimens previously genotyped as A, D, IV, EbpC, WL11, Peru7, Peru8, Peru10 and Peru11 at the internal transcribed spacer locus. Altogether, 39 multilocus genotypes were identified among the 72 specimens. The observation of strong intragenic linkage disequilibria and limited genetic recombination among markers were indicative of an overall clonal population structure of E. bieneusi. Measures of pair-wise intergenic linkage disequilibria and a standardised index of association (IAS) based on allelic profile data further supported this conclusion. Both sequence-based and allelic profile-based phylogenetic analyses showed the presence of two genetically isolated groups in the study population, one (group 1) containing isolates of the anthroponotic internal transcribed spacer genotype A, and the other (group 2) containing isolates of multiple internal transcribed spacer genotypes (mainly genotypes D and IV) with zoonotic potential. The measurement of linkage disequilibria and recombination indicated group 2 had a clonal population structure, whereas group 1 had an epidemic population structure. The formation of the two sub-populations was confirmed by STRUCTURE and Wright's fixation index (FST) analyses. The data highlight the power of MLST in understanding the epidemiology of E. bieneusi. PMID:22534008

  5. The Incidence and Prevalence of Thromboangiitis Obliterans in Taiwan: A Nationwide, Population-based Analysis of Data Collected from 2002 to 2011

    PubMed Central

    Zheng, Jie-Fu; Chen, Yi-Ming; Chen, Der-Yuan; Lin, Ching-Heng; Chen, Hsin-Hua

    2016-01-01

    OBJECTIVE: To estimate the incidence and prevalence of thromboangiitis obliterans in Taiwan in the period spanning from 2002 to 2011. METHODS: We identified all incident and prevalent cases with a diagnosis of thromboangiitis obliterans (International Classification of Diseases, Ninth Revision code 443.1) in the period spanning from 2002 to 2011 using Taiwan’s National Health Insurance Research Database. We calculated the age- and sex-specific incidence and prevalence rates of thromboangiitis obliterans during the study period. RESULTS: From 2002 to 2011, 158 patients were diagnosed with thromboangiitis obliterans; of these, 76% were men. Most (63%) of the patients were <50 years old when they were first diagnosed. After reaching 20 years of age, the incidence rate increased with age and peaked among those aged ≥60 years. The average incidence rate of thromboangiitis obliterans during the 2002–2011 period was 0.068 per 105 years. The incidence of thromboangiitis obliterans decreased with time, from 0.10 per 105 years in 2002 to 0.04 per 105 years in 2011. The prevalence increased from 0.26 × 10−5 in 2002 to 0.65 × 10−5 in 2011. CONCLUSION: This is the first epidemiologic study of thromboangiitis obliterans using claims data from a general population in Taiwan. This nationwide, population-based study found that the incidence and prevalence of thromboangiitis obliterans in Taiwan in the 2002–2011 period were lower than those in other countries before 2000. This study also revealed a trend of decreasing incidence with simultaneous increasing prevalence of thromboangiitis obliterans in Taiwan from 2002 to 2011. PMID:27464297

  6. 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

  7. 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

  8. 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.

  9. 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

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

    SciTech Connect

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

    2012-05-01

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

  11. 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

  12. Use of perioperative hydroxyethyl starch 6% and albumin 5% in elective joint arthroplasty and association with adverse outcomes: a retrospective population based analysis

    PubMed Central

    Opperer, Mathias; Poeran, Jashvant; Rasul, Rehana; Mazumdar, Madhu

    2015-01-01

    Objective To determine whether the perioperative use of hydroxyethyl starch 6% and albumin 5% in elective joint arthroplasties are associated with an increased risk for perioperative complications. Design Retrospective cohort study of population based data between 2006 and 2013. Setting Data from 510 different hospitals across the United States participating in the Premier Perspective database. Participants 1 051 441 patients undergoing elective total hip and knee arthroplasties. Exposures Perioperative fluid resuscitation with hydroxyethyl starch 6% or albumin 5%, or neither. Main outcome measures Acute renal failure and thromboembolic, cardiac, and pulmonary complications. Results Compared with patients who received neither colloid, perioperative fluid resuscitation with hydroxyethyl starch 6% or albumin 5% was associated with an increased risk of acute renal failure (odds ratios 1.23 (95% confidence interval 1.13 to 1.34) and 1.56 (1.36 to 1.78), respectively) and most other complications. A recent decrease in hydroxyethyl starch 6% use was noted, whereas that of albumin 5% increased. Conclusions Similar to studies in critically ill patients, we showed that use of hydroxyethyl starch 6% was associated with an increased risk of acute renal failure and other complications in the elective perioperative orthopedic setting. This increased risk also applied to albumin 5%. These findings raise questions regarding the widespread use of these colloids in elective joint arthroplasty procedures. PMID:25817299

  13. An item response theory analysis of the DSM-IV borderline personality disorder criteria in a population-based sample of 11- to 12-year-old children.

    PubMed

    Michonski, Jared D; Sharp, Carla; Steinberg, Lynne; Zanarini, Mary C

    2013-01-01

    Although a growing body of empirical literature provides some support for the diagnosis of borderline personality disorder (BPD) in youth, little is known about the internal structure of BPD and the performance of the individual diagnostic criteria, especially in younger samples. We used item response theory (IRT) methods to investigate the psychometric properties of the Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV) BPD criteria in a large, population-based sample (n = 6,339) of young adolescents from the United Kingdom (ages 11 to 12). BPD was assessed using the Childhood Interview for DSM-IV Borderline Personality Disorder (CI-BPD; Zanarini, Horwood, Waylen, & Wolke, 2004). A single underlying dimension adequately accounted for covariation among the BPD criteria. Each criterion was found to be discriminating to a degree comparable to what has been reported in adult studies. BPD criteria were most informative within a range of severity of BPD pathology between +1 and +3 standard units. Five criteria were found to exhibit differential item functioning (DIF) between boys and girls. However, DIF balanced out for the total interview score. Despite the controversy associated with applying the borderline construct to youth, the current findings provide psychometric evidence in favor of doing so. PMID:22642465

  14. 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

  15. 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

  16. 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. PMID:25478654

  17. Automated Analysis of a Diverse Synapse Population

    PubMed Central

    Busse, Brad; Smith, Stephen

    2013-01-01

    Synapses of the mammalian central nervous system are highly diverse in function and molecular composition. Synapse diversity per se may be critical to brain function, since memory and homeostatic mechanisms are thought to be rooted primarily in activity-dependent plastic changes in specific subsets of individual synapses. Unfortunately, the measurement of synapse diversity has been restricted by the limitations of methods capable of measuring synapse properties at the level of individual synapses. Array tomography is a new high-resolution, high-throughput proteomic imaging method that has the potential to advance the measurement of unit-level synapse diversity across large and diverse synapse populations. Here we present an automated feature extraction and classification algorithm designed to quantify synapses from high-dimensional array tomographic data too voluminous for manual analysis. We demonstrate the use of this method to quantify laminar distributions of synapses in mouse somatosensory cortex and validate the classification process by detecting the presence of known but uncommon proteomic profiles. Such classification and quantification will be highly useful in identifying specific subpopulations of synapses exhibiting plasticity in response to perturbations from the environment or the sensory periphery. PMID:23555213

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2016-01-01

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

  20. 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.

  1. Awareness Levels about Breast Cancer Risk Factors, Early Warning Signs, and Screening and Therapeutic Approaches among Iranian Adult Women: A large Population Based Study Using Latent Class Analysis

    PubMed Central

    Tazhibi, Mahdi

    2014-01-01

    Background and Objective. Breast cancer (BC) continues to be a major cause of morbidity and mortality among women throughout the world and in Iran. Lack of awareness and early detection program in developing country is a main reason for escalating the mortality. The present research was conducted to assess the Iranian women's level of knowledge about breast cancer risk factors, early warning signs, and therapeutic and screening approaches, and their correlated determinants. Methods. In a cross-sectional study, 2250 women before participating at a community based screening and public educational program in an institute of cancer research in Isfahan, Iran, in 2012 were investigated using a self-administered questionnaire about risk factors, early warning signs, and therapeutic and screening approaches of BC. Latent class regression as a comprehensive statistical method was used for evaluating the level of knowledge and its correlated determinants. Results. Only 33.2%, 31.9%, 26.7%, and 35.8% of study participants had high awareness levels about screening approaches, risk factors, early warning signs and therapeutic modalities of breast cancer, respectively, and majority had poor to moderate knowledge levels. Most effective predictors of high level of awareness were higher educational qualifications, attending in screening and public educational programs, personal problem, and family history of BC, respectively. Conclusion. Results of current study indicated that the levels of awareness among study population about key elements of BC are low. These findings reenforce the continuing need for more BC education through conducting public and professional programs that are intended to raise awareness among younger, single women and those with low educational attainments and without family history. PMID:25295257

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

    PubMed Central

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

    2007-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  4. 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

  5. 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

  6. 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

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

    PubMed Central

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

    2015-01-01

    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

  8. Above and beyond state-of-the-art approaches to investigate sequence data: summary of methods and results from the population-based association group at the Genetic Analysis Workshop 19.

    PubMed

    Lorenzo Bermejo, Justo

    2016-01-01

    This paper summarizes the contributions from the Population-Based Association group at the Genetic Analysis Workshop 19. It provides an overview of the new statistical approaches tried out by group members in order to take best advantage of population-based sequence data.Although contributions were highly heterogeneous regarding the applied quality control criteria and the number of investigated variants, several technical issues were identified, leading to practical recommendations. Preliminary analyses revealed that Hurdle-negative binomial regression is a promising approach to investigate the distribution of allele counts instead of called genotypes from sequence data. Convergence problems, however, limited the use of this approach, creating a technical challenge shared by environment-stratified models used to investigate rare variant-environment interactions, as well as by rare variant haplotype analyses using well-established public software. Estimates of relatedness and population structure strongly depended on the allele frequency of selected variants for inference. Another practical recommendation was that dissenting probability values from standard and small-sample tests of a particular hypothesis may reflect a lack of validity of large-sample approximations. Novel statistical approaches that integrate evolutionary information showed some advantage to detect weak genetic signals, and Bayesian adjustment for confounding was able to efficiently estimate causal genetic effects. Haplotype association methods may constitute a valuable complement of collapsing approaches for sequence data. This paper reports on the experience of members of the Population-Based Association group with several novel, promising approaches to preprocessing and analyzing sequence data, and to following up identified association signals. PMID:26866664

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-08-01

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

  11. Part I. A look at population-based medical care.

    PubMed

    Weiss, K

    1998-08-01

    Recent trends toward managed health care have generated interest in developing strategies to manage the health care of a population as a whole. Population-based medicine places the individual patient within the context of the larger community, which is composed of both sick and well individuals; when viewed in these terms, only a small proportion of the people who consult a primary care physician are at risk for substantial morbidity. However, the physician serves as the central figure for delivering population-based health care to the entire community. Many strategies for population-based care contain the following 4 basic elements: 1. Identifying the health and disease states that are likely to be responsive to population-based care, 2. Applying principles of epidemiology to define the population-of-interest, 3. Assembling a multidisciplinary team, and 4. Building information systems to support ongoing surveillance of population-based care. To date, most of the published examples of population-based management have been conducted in managed care environments, but population-based management may also be used by a single physician practice or a small group practice. Programs aimed at health promotion or disease prevention are among the easiest to implement. By examining the results of an entire population with a given condition, physicians and their teams may begin to identify ways to improve the overall delivery of care, either by establishing new procedures or improving old ones. PMID:9735940

  12. 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

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

    PubMed

    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

  14. A mathematical analysis of small mammal populations.

    PubMed

    Hoppensteadt, F C; Murphy, L

    1987-01-01

    Populations of Microtus montanus, the montane vole, have been extensively studied. It is known that their reproductive activity is closely linked to the availability of the chemicals in growing plants. We use a mathematical model here to study how the length of the vegetative season and the natural reproduction rhythm of voles are involved in the long term dynamics of the population numbers. In particular, we use data obtained from Timpie Springs, Utah, and from Jackson Hole, Wyoming, to formulate a model. The novelty of this model is its use of littering curves that highlight the temporally discrete nature of vole reproduction. The model shows how the timing of the vegetative season can influence vole population sizes. PMID:3305751

  15. 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.

  16. Predictive accuracy of population viability analysis in conservation biology.

    PubMed

    Brook, B W; O'Grady, J J; Chapman, A P; Burgman, M A; Akçakaya, H R; Frankham, R

    2000-03-23

    Population viability analysis (PVA) is widely applied in conservation biology to predict extinction risks for threatened species and to compare alternative options for their management. It can also be used as a basis for listing species as endangered under World Conservation Union criteria. However, there is considerable scepticism regarding the predictive accuracy of PVA, mainly because of a lack of validation in real systems. Here we conducted a retrospective test of PVA based on 21 long-term ecological studies--the first comprehensive and replicated evaluation of the predictive powers of PVA. Parameters were estimated from the first half of each data set and the second half was used to evaluate the performance of the model. Contrary to recent criticisms, we found that PVA predictions were surprisingly accurate. The risk of population decline closely matched observed outcomes, there was no significant bias, and population size projections did not differ significantly from reality. Furthermore, the predictions of the five PVA software packages were highly concordant. We conclude that PVA is a valid and sufficiently accurate tool for categorizing and managing endangered species. PMID:10746724

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

    PubMed

    Elouafi, I; Nachit, M M

    2004-02-01

    Durum wheat ( Triticum turgidum L. var durum) is mainly produced and consumed in the Mediterranean region; it is used to produce several specific end-products; such as local pasta, couscous and burghul. To study the genetics of grain-milling quality traits, chromosomal locations, and interaction with the environment, a genetic linkage map of durum was constructed and the quantitative trait loci QTLs for the milling-related traits, test weight (TW) and thousand-kernel weight (TKW), were identified. The population constituted 114 recombinant inbred lines derived from the cross: Omrabi 5 /Triticum dicoccoides 600545// Omrabi 5. TW and TKW were analyzed over 18 environments (sites x years). Single-sequence-repeat markers (SSRs), Amplified-fragment-length-polymorphism markers (AFLPs), and seed storage proteins (SSPs) showed a high level of polymorphism (>60%). The map was constructed with 124 SSRs, 149 AFLPs and 6 SSPs; its length covered 2,288.8 cM (8.2 cM/marker). The map showed high synteny with previous wheat maps, and both SSRs and AFLPs mapped evenly across the genome, with more markers in the B genome. However, some rearrangements were observed. For TW, a high genotypic effect was detected and two QTLs with epistasic effect were identified on 7AS and 6BS, explaining 30% of the total variation. The TKW showed a significant transgressive inheritance and five QTLs were identified, explaining 32% of the total variation, out of which 25% was of a genetic nature, and showing QTLxE interaction. The major TKW-QTLs were around the centromere region of 6B. For both traits, Omrabi 5 alleles had a significant positive effect. This population will be used to determine other QTLs of interest, as its parents are likely to harbor different genes for diseases and drought tolerance. PMID:14676946

  18. Advance and stagnation in the treatment of patients with lymphoma and myeloma: Analysis using population-based cancer registry data in Japan from 1993 to 2006.

    PubMed

    Chihara, Dai; Ito, Hidemi; Izutsu, Koji; Hattori, Masakazu; Nishino, Yoshikazu; Ioka, Akiko; Matsuda, Tomohiro; Ito, Yuri

    2015-09-01

    There have been significant advances in the treatment of patients with lymphoma and myeloma. Although the improvements in survival outcome have been clearly addressed by clinical trials, these studies includes patients who are otherwise healthy and would be eligible for trials that the actual improvement in survival in the general patient population over time is yet to be elucidated. Therefore, we reviewed the cancer-registry data of patients with lymphoma and myeloma in Japan from 1993 to 2006 and estimated relative survival (adjusted for competing causes of death in same-age members of the general population) according to three periods of diagnosis (1993-1997, 1998-2002 and 2003-2006). We also estimated conditional 5-year relative survival (5-year survival rate of patients who have survived 5 years). A total of 26,141 patients were reviewed and analyzed. Relative survival improved in Hodgkin lymphoma (HL, N = 853, +20% improvement), diffuse large B-cell lymphoma (DLBCL, N = 4,919, +14% improvement) and follicular lymphoma (FL, N = 1,333, +13% improvement). In contrast, we found no significant improvement in survival since 1993 in peripheral T-cell lymphoma (PTCL, N = 667, +4% improvement), adult T-cell leukemia/lymphoma (ATLL, N = 2,166, -5% improvement) or multiple myeloma (MM, N = 4,914, -2% improvement). Conditional 5-year survival of HL, DLBCL, FL, PTCL, ATLL and MM was 88, 87, 79, 63, 53 and 45%, respectively. Relative survival of patients with HL, DLBCL and FL significantly improved from 1993 to 2006 in Japan; in contrast, no improvement was seen in other diseases, suggesting unmet need of novel treatment strategies. PMID:25694231

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

    USGS Publications Warehouse

    Bell, T.J.; Bowles, M.L.; McEachern, A.K.

    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

  20. 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

  1. 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 ...

  2. Simultaneous genotyping of CYP2D6*3, *4, *5 and *6 polymorphisms in a Spanish population through multiplex long polymerase chain reaction and minisequencing multiplex single base extension analysis.

    PubMed

    Crescenti, A; Mas, S; Gassó, P; Baiget, M; Bernardo, M; Lafuente, A

    2007-10-01

    1. The aim of the present study was to perform a descriptive study of the prevalence of the four major CYP2D6 poor metaboliser (PM) alleles (*3, *4, *5 and *6) in a Spanish population (n = 290) using a method based on a new combination of multiplex long polymerase chain reaction (PCR) and minisequencing through multiplex single base extension (SBE) analysis. 2. The method was validated using different strategies, such as allelic discrimination assay and PCR-restriction fragment length polymorphism (RFLP). 3. The allele frequencies were similar to those described for other Spanish populations, namely 0.9% (95% confidence interval (CI) 0.5-1.3), 16.4% (95% CI 14.9-18.0), 2.7% (95% CI 2.0-3.4) and 0.7% (95% CI 0.3-1.0) for the *3, *4, *5 and *6 alleles, respectively. The results were satisfactory and left little doubt as to the genotypes, which were confirmed either by allelic discrimination assay (*4 and *6) or PCR-RFLP (*3) with 100% concordance. 4. The present study corroborates the low prevalence of the most frequent polymorphism (CYP2D6*4) that leads to null CYP2D6 activity in Spain and the allelic geographical gradient between Caucasian populations in the north and south. The present study reports a technique for the detection of four polymorphisms that account for 98% of the CYP2D6 defect alleles. This multiplex long PCR-SBE technique is a combination of several known methods to genotype CYP2D6 alleles (*3, *4, *5 and*6). Given the importance of CYP2D6 in drug metabolism and the need to genotype a large number of samples, we believe that this method will find broad application. PMID:17714084

  3. 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

  4. 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 Central

    Bochicchio, Mario Alessandro

    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. PMID:25028648

  5. 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. PMID:25028648

  6. GRAPHICAL ANALYSIS OF THE INTERRELATIONSHIPS AMONG WATERBORNE ASBESTOS, DIGESTIVE SYSTEM CANCER AND POPULATION DENSITY

    EPA Science Inventory

    Five statistical procedures were used to partial the correlation between water-borne asbestos and digestive site cancer for the putative effects of population density. These include: analysis based on a data subset with roughly homogeneous population density; standard residual an...

  7. Analysis of genetic data on Jewish populations. I. Historical background, demographic features, and genetic markers.

    PubMed Central

    Bonné-Tamir, B; Karlin, S; Kenett, R

    1979-01-01

    Part I describes the data sets on which the analysis of Part II is based. This covers the nature of the populations sampled, the extent to which the samples are representative, and a brief review of historical and demographic facts on the populations involved. PMID:380329

  8. Population pharmacokinetic and pharmacodynamic analysis in allergic diseases.

    PubMed

    Lovern, Mark; Sargentini-Maier, Maria-Laura; Otoul, Christian; Watelet, Jean-Baptiste

    2009-01-01

    In this chapter, we introduce the concepts and methodologies of population analysis as applied to analyzing pharmacokinetic and pharmacodynamic data. One of the key determining characteristics of the population approach is that through it, one seeks not only to characterize deterministic trends in the data, but also to identify and estimate the magnitudes of the important sources of variability within the data. The first section of this chapter provides an introduction to the primary concepts of, and motivation for, population modeling by way of a hypothetical case study. Then, the various methodologies that have been employed throughout the history of population analysis are described in further detail. Of these, the most commonly employed today is nonlinear mixed-effects (NLME) modeling. Finally, notable examples of the application of population PK and PK/PD modeling to treatments for allergies and asthma are discussed. Population PK models have frequently been used to extrapolate exposures to special populations, such as pediatrics, as well as to optimize treatment regimens and trial designs for these populations. Population PK/PD models have most frequently been applied to analyzing and interpreting data from wheal and flare trials, but are also becoming increasingly important in the analysis of PD data from monoclonal antibodies. PMID:19601723

  9. 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.

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

    PubMed Central

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

    2015-01-01

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

  11. 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...

  12. 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

  13. 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.

  14. 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

  15. Burden of vaccine-preventable disease in adult Medicaid and commercially insured populations: analysis of claims-based databases, 2006–2010.

    PubMed

    Krishnarajah, Girishanthy; Carroll, Charlotte; Priest, Julie; Arondekar, Bhakti; Burstin, Stuart; Levin, Myron

    2014-01-01

    Vaccination rates among United States (US) adults are suboptimal, resulting in morbidity, mortality, and financial burden attributable to potentially vaccine-preventable diseases (VPDs). Unadjusted annual incidence proportions of VPDs were estimated for Medicaid and commercially insured adults aged 19-64 years using 2006-2010 claims, along with age/gender-adjusted incidence proportions for 2010. In 2010, 1.6 million Medicaid adults (mean age 34 ± 12 years; 73.4% female) and 33 million commercially insured (mean age 42 ± 13 years; 52.2% female) were included. Age/gender-adjusted incidence proportions (per 100 000) in 2010 among Medicaid vs commercially insured adults for meningococcal disease were 26.2 (95% CI 22.9-29.8) vs 2.0 (1.9-2.2) (P < 0.001); hepatitis B 88.9 (82.6-95.6) vs 17.5 (17.0-17.9) (P < 0.001); pneumococcal disease 98.2 (91.7-105.1) vs 21.1 (20.7-21.6) (P < 0.001); hepatitis A 19.8 (16.9-23.1) vs 4.5 (4.3-4.7) (P < 0.001); mumps 2.1 (1.3-3.3) vs 1.4 (1.3-1.6) (P = 0.14); measles 0.3 (0.1-1.0) vs 0.3 (0.2-0.3) (P = 0.38); herpes zoster (60- to 64-year-olds only) 459 (408-515) vs 473 (466-481) (P = 0.35); varicella (19- to 39-year-olds only) 6.5 (4.8-8.5) vs 8.0 (7.5-8.5) (P = 0.12); influenza 586 (573-598) vs 633 (631-636) (P < 0.001); and pertussis 1.8 (1.1-2.8) vs 3.2 (3.0-3.4) (P < 0.001). Research is needed to fully understand the causes of the disparity of the coded incidence of some VPDs in adult Medicaid population than commercially insured adults in the US. PMID:25424956

  16. 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

  17. Estimation of statistical binding properties of ligand population during in vitro selection based on population dynamics theory.

    PubMed

    Aita, Takuyo; Nishigaki, Koichi; Husimi, Yuzuru

    2014-01-01

    During in vitro selection process, it is very valuable to monitor the binding properties of the ligand population in real time, particularly the population average of the association constant in the population. If this monitoring can be realized, the selection process can be controlled in a rational way. In this paper, we present a simple method to estimate the binding properties of the ligand population during in vitro selection. The framework of the method is as follows. First, the number of all the collected ligand molecules, which are eluted after incubation and washing, is measured. Ideally, this number corresponds to the number of all the ligand molecules bound with the target-receptor or other materials in a test tube. This measurement is performed through several successive rounds of selection. Second, the measured numbers of molecules are subjected to a theoretical analysis, based on the mathematical theory of population dynamics in the selection process. Then, we can estimate the probability density of the binding free energy in the ligand population. The validity of our method was confirmed by several computer simulations based on a physicochemical model. PMID:24239675

  18. Mixed dentition analysis in a Moroccan population.

    PubMed

    Diagne, F; Diop-Ba, K; Ngom, P I; El Boury, O

    2004-12-01

    The aims of this study were to produce odontometric data for a Moroccan population, to test Tanaka and Johnston and Moyers methods, to derive regression equations and elaborate a specific orthodontic prediction table for Moroccan children. 50 dental casts of Moroccan students (25 males, 25 females, mean age 22.6 years sd 1.35) were used to perform measurements of the greatest mesiodistal widths of all mandibular and maxillary canines and premolars and mandibular incisors with an orthodontic calliper. Significant sexual dimorphism was found in tooth sizes (p = .001). The study revealed close relationships between the total mesiodistal widths of the mandibular permanent incisors and that of the maxillary and mandibular canines and premolars. The correlation coefficients (r) and the coefficient of determination (R2) were better sexes combined for the maxilla (r = 0.60 ; R2 = 0.36 ) and for the mandible (r = 0.61 ; R2= 0.37). The regression equations elaborated for males and females were used as a basis for establishing an orthodontic prediction table for Moroccan children. PMID:15853270

  19. 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.

  20. 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

  1. Effect of radiotherapy on survival of women with locally excised ductal carcinoma in situ of the breast: a Surveillance, Epidemiology, and End Results population-based analysis

    PubMed Central

    Qian, Guo-Wei; Ni, Xiao-Jian; Wang, Zheng; Jiang, Yi-Zhou; Yu, Ke-Da; Shao, Zhi-Ming

    2015-01-01

    Background Although it has been previously reported that radiotherapy (RT) effectively reduced the incidence of local recurrence of ductal carcinoma in situ (DCIS) following breast-conserving surgery (BCS), little is known about the effect of RT on survival of patients with locally excised DCIS. Patients and methods Using Surveillance, Epidemiology, and End Results registry data, we selected 56,968 female DCIS patients treated with BCS between 1998 and 2007. Overall survival (OS) and breast cancer-specific survival (BCSS) were compared among patients who received RT or no RT using the Kaplan–Meier methods and Cox proportional hazards regression models. Results Median follow-up was 91 months. In the multivariable model, patients receiving postoperative RT had better OS than those undergoing BCS alone (hazard ratio [HR] 0.59, 95% confidence interval [CI] 0.53–0.67, P<0.001). This pattern remained after stratification by estrogen receptor (ER) status and age. In contrast, RT delivery was not significantly associated with improved BCSS (HR 0.71, 95% CI 0.48–1.03, P=0.073). However, after stratifying by the above two variables, RT contributed to better BCSS in ER-negative/borderline patients (HR 0.41, 95% CI 0.19–0.88, P=0.023) and younger patients (≤50 years old; HR 0.37, 95% CI 0.15–0.91, P=0.030). Conclusion Our analysis confirms the beneficial effect of RT on OS in women with locally excised DCIS and reveals the specific protective effect of RT on BCSS in ER-negative/borderline and younger patients. PMID:26089689

  2. Association of neighborhood context with offspring risk of preterm birth and low birthweight: A systematic review and meta-analysis of population-based studies.

    PubMed

    Ncube, Collette N; Enquobahrie, Daniel A; Albert, Steven M; Herrick, Amy L; Burke, Jessica G

    2016-03-01

    Findings from studies investigating associations of residential environment with poor birth outcomes have been inconsistent. In a systematic review and meta-analysis, we examined associations of neighborhood disadvantage with preterm birth (PTB) and low birthweight (LBW), and explored differences in relationships among racial groups. Two reviewers searched English language articles in electronic databases of published literature. We used random effects logistic regression to calculate odds ratios (and 95% confidence intervals) relating neighborhood disadvantage with PTB and LBW. Neighborhood disadvantage, most disadvantaged versus least disadvantaged neighborhoods, was defined by researchers of included studies, and comprised of poverty, deprivation, racial residential segregation or racial composition, and crime. We identified 1314 citations in the systematic review. The meta-analyses included 7 PTB and 14 LBW cross-sectional studies conducted in the United States (U.S.). Overall, we found 27% [95%CI: 1.16, 1.39] and 11% [95%CI: 1.07, 1.14] higher risk for PTB and LBW among the most disadvantaged compared with least disadvantaged neighborhoods. No statistically significant association was found in meta-analyses of studies that adjusted for race. In race-stratified meta-analyses models, we found 48% [95%CI: 1.25, 1.75] and 61% [95%CI: 1.30, 2.00] higher odds of PTB and LBW among non-Hispanic white mothers living in most disadvantaged neighborhoods compared with those living in least disadvantaged neighborhoods. Similar, but less strong, associations were observed for PTB (15% [95%CI: 1.09, 1.21]) and LBW (17% [95%CI: 1.10, 1.25]) among non-Hispanic black mothers. Neighborhood disadvantage is associated with PTB and LBW, however, associations may differ by race. Future studies evaluating causal mechanisms underlying the associations, and racial/ethnic differences in associations, are warranted. PMID:26900890

  3. 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

  4. The demographic features, clinicopathologic characteristics, treatment outcome and disease-specific prognostic factors of solitary fibrous tumor: a population-based analysis

    PubMed Central

    Wushou, Alimujiang; Jiang, Yi-Zhou; Liu, Yi-Rong; Shao, Zhi-Ming

    2015-01-01

    Background Solitary fibrous tumor's (SFT) demographic features, clinicopathologic characteristics, treatment outcome and disease-specific prognostic factors were unexplored comprehensively. Methods SEER program was used to identify patients diagnosed with SFT from 1973 to 2012. Overall collected data were analyzed by using the SPSS 18.0. Results In total, 804 cases were found including 613 cases with SFT-specific mortality and 801 patients were analyzed for overall survival (OS). The 3-year disease specific survival (DSS), 5-year DSS and 10-year DSS were 73.3%, 65.7% and 53.3%. The 3-year OS, 5-year OS and 10-year OS were 71.9%, 63.3% and 47.3%. In the multivariate survival analysis, the age > 51 years (hazard ratio [HR] = 1.851 for DSS, P = 0.024 and HR = 1.652 for OS, P = 0.033; Reference [Ref] ≤ 51 years for DSS and ≤ 53 years for OS), SEER stage metastasized tumor (HR = 4.269 for DSS, P = 0.000 and HR = 2.905 for OS, P = 0.028, Ref - localized + regional tumor), pathologic grade III + IV (HR = 2.734 for DSS, P = 0.001 and HR = 2.585 for OS, P = 0.000, Ref - grade I + II) were adversely associated with DSS and OS. In addition, surgery was favorably associated with DSS (HR = 0.217, P = 0.045, Ref - surgery + radiotherapy). Conclusions The surgery was an independent prognostic factor for DSS. The patient's age, SEER stage and pathologic grade were SFT-specific independent prognostic indicators for DSS and OS. PMID:26496033

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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

  11. Population genomic analysis of outcrossing and recombination in yeast.

    PubMed

    Ruderfer, Douglas M; Pratt, Stephen C; Seidel, Hannah S; Kruglyak, Leonid

    2006-09-01

    The budding yeast Saccharomyces cerevisiae has been used by humans for millennia to make wine, beer and bread. More recently, it became a key model organism for studies of eukaryotic biology and for genomic analysis. However, relatively little is known about the natural lifestyle and population genetics of yeast. One major question is whether genetically diverse yeast strains mate and recombine in the wild. We developed a method to infer the evolutionary history of a species from genome sequences of multiple individuals and applied it to whole-genome sequence data from three strains of Saccharomyces cerevisiae and the sister species Saccharomyces paradoxus. We observed a pattern of sequence variation among yeast strains in which ancestral recombination events lead to a mosaic of segments with shared genealogy. Based on sequence divergence and the inferred median size of shared segments (approximately 2,000 bp), we estimated that although any two strains have undergone approximately 16 million cell divisions since their last common ancestor, only 314 outcrossing events have occurred during this time (roughly one every 50,000 divisions). Local correlations in polymorphism rates indicate that linkage disequilibrium in yeast should extend over kilobases. Our results provide the initial foundation for population studies of association between genotype and phenotype in S. cerevisiae. PMID:16892060

  12. 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

  13. 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

  14. Sensitivity analysis of periodic matrix population models.

    PubMed

    Caswell, Hal; Shyu, Esther

    2012-12-01

    Periodic matrix models are frequently used to describe cyclic temporal variation (seasonal or interannual) and to account for the operation of multiple processes (e.g., demography and dispersal) within a single projection interval. In either case, the models take the form of periodic matrix products. The perturbation analysis of periodic models must trace the effects of parameter changes, at each phase of the cycle, on output variables that are calculated over the entire cycle. Here, we apply matrix calculus to obtain the sensitivity and elasticity of scalar-, vector-, or matrix-valued output variables. We apply the method to linear models for periodic environments (including seasonal harvest models), to vec-permutation models in which individuals are classified by multiple criteria, and to nonlinear models including both immediate and delayed density dependence. The results can be used to evaluate management strategies and to study selection gradients in periodic environments. PMID:23316494

  15. 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

  16. 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

  17. 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

  18. Analysis of population substructure in two sympatric populations of Gran Chaco, Argentina.

    PubMed

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

    2013-01-01

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

  19. Fixed point sensitivity analysis of interacting structured populations.

    PubMed

    Barabás, György; Meszéna, Géza; Ostling, Annette

    2014-03-01

    Sensitivity analysis of structured populations is a useful tool in population ecology. Historically, methodological development of sensitivity analysis has focused on the sensitivity of eigenvalues in linear matrix models, and on single populations. More recently there have been extensions to the sensitivity of nonlinear models, and to communities of interacting populations. Here we derive a fully general mathematical expression for the sensitivity of equilibrium abundances in communities of interacting structured populations. Our method yields the response of an arbitrary function of the stage class abundances to perturbations of any model parameters. As a demonstration, we apply this sensitivity analysis to a two-species model of ontogenetic niche shift where each species has two stage classes, juveniles and adults. In the context of this model, we demonstrate that our theory is quite robust to violating two of its technical assumptions: the assumption that the community is at a point equilibrium and the assumption of infinitesimally small parameter perturbations. Our results on the sensitivity of a community are also interpreted in a niche theoretical context: we determine how the niche of a structured population is composed of the niches of the individual states, and how the sensitivity of the community depends on niche segregation. PMID:24368160

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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

    2009-03-01

    The prevention of child maltreatment necessitates a public health approach. In the U.S. Triple P System Population Trial, 18 counties were randomly assigned to either dissemination of the Triple P-Positive Parenting Program system or to the services-as-usual control condition. Dissemination involved Triple P professional training for the existing workforce (over 600 service providers), as well as universal media and communication strategies. Large effect sizes were found for three independently derived population indicators: substantiated child maltreatment, child out-of-home placements, and child maltreatment injuries. This study is the first to randomize geographical areas and show preventive impact on child maltreatment at a population level using evidence-based parenting interventions. PMID:19160053

  6. Inbreeding effective population size and parentage analysis without parents.

    PubMed

    Waples, Robin S; Waples, Ryan K

    2011-03-01

    An important use of genetic parentage analysis is the ability to directly calculate the number of offspring produced by each parent (k(i)) and hence effective population size, N(e). But what if parental genotypes are not available? In theory, given enough markers, it should be possible to reconstruct parental genotypes based entirely on a sample of progeny, and if so the vector of parental k(i) values. However, this would provide information only about parents that actually contributed offspring to the sample. How would ignoring the 'null' parents (those that produced no offspring) affect an estimate of N(e)? The surprising answer is that null parents have no effect at all. We show that: (i) The standard formula for inbreeding N(e) can be rewritten so that it is a function only of sample size and ∑(k(2)(i)); it is not necessary to know the total number of parents (N). This same relationship does not hold for variance N(e). (ii) This novel formula provides an unbiased estimate of N(e) even if only a subset of progeny is available, provided the parental contributions are accurately determined, in which case precision is also high compared to other single-sample estimators of N(e). (iii) It is not necessary to actually reconstruct parental genotypes; from a matrix of pairwise relationships (as can be estimated by some current software programs), it is possible to construct the vector of k(i) values and estimate N(e). The new method based on parentage analysis without parents (PwoP) can potentially be useful as a single-sample estimator of contemporary N(e), provided that either (i) relationships can be accurately determined, or (ii) ∑(k(2)(i)) can be estimated directly. PMID:21429172

  7. Modified electronic population analysis for transition-metal complexes

    SciTech Connect

    Noell, J.O.

    1982-01-01

    A modification to the Mulliken electronic population analysis designed primarily for use on transition-metal systems is presented. All terms arising from the metal basis functions including diagonal terms are repartioned between the metal and the ligands. This reapportionment is an attempt to reflect more accurately the actual electron density in well-defined areas of space, which characterize the metal and the ligand. This modified analysis appears to yield more reasonable charge assignments than a conventional Mulliken analysis. The cost of the analysis is negligible in comparison with that of calculating the wave function.

  8. 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

  9. 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

  10. 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…

  11. Microsatellite analysis reveals genetically distinct populations of red pine (Pinus resinosa, Pinaceae).

    PubMed

    Boys, Jacquelyn; Cherry, Marilyn; Dayanandan, Selvadurai

    2005-05-01

    Red pine (Pinus resinosa Ait.) is an ecologically and economically important forest tree species of northeastern North America and is considered one of the most genetically depauperate conifer species in the region. We have isolated and characterized 13 nuclear microsatellite loci by screening a partial genomic library with di-, tri-, and tetranucleotide repeat oligonucleotide probes. In an analysis of over 500 individuals representing 17 red pine populations from Manitoba through Newfoundland, five polymorphic microsatellite loci with an average of nine alleles per locus were identified. The mean expected and observed heterozygosity values were 0.508 and 0.185, respectively. Significant departures from Hardy-Weinberg equilibrium with excess homozygosity indicating high levels of inbreeding were evident in all populations studied. The population differentiation was high with 28-35% of genetic variation partitioned among populations. The genetic distance analysis showed that three northeastern (two Newfoundland and one New Brunswick) populations are genetically distinct from the remaining populations. The coalescence-based analysis suggests that "northeastern" and "main" populations likely became isolated during the most recent Pleistocene glacial period, and severe population bottlenecks may have led to the evolution of a highly selfing mating system in red pine. PMID:21652464

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

    ERIC Educational Resources Information Center

    Lee, Carolyn L.

    2005-01-01

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

  13. 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

  14. 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.

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

    PubMed

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

    2013-12-01

    The NCII design (North Carolina mating design II) has been widely applied in studies of combining ability and heterosis. The objective of our research was to estimate how different base populations, sample sizes, testcross numbers and heritability influence QTL analyses of combining ability and heterosis. A series of Monte Carlo simulation experiments with QTL mapping were then conducted for the base population performance, testcross population phenotypic values and the general combining ability (GCA), specific combining ability (SCA) and Hmp (midparental heterosis) datasets. The results indicated that: (i) increasing the number of testers did not necessarily enhance the QTL detection power for GCA, but it was significantly related to the QTL effect. (ii) The QTLs identified in the base population may be different from those from GCA dataset. Similar phenomena can be seen from QTL detected in SCA and Hmp datasets. (iii) The QTL detection power for GCA ranked in the order of DH(RIL) based > F2 based > BC based NCII design, when the heritability was low. The recombinant inbred lines (RILs) (or DHs) allows more recombination and offers higher mapping resolution than other populations. Further, their testcross progeny can be repeatedly generated and phenotyped. Thus, RIL based (or DH based) NCII design was highly recommend for combining ability QTL analysis. Our results expect to facilitate selecting elite parental lines with high combining ability and for geneticists to research the genetic basis of combining ability. PMID:24371174

  16. 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

  17. 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

  18. 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

  19. 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…

  20. A theoretical analysis of optimum consumer population and its control.

    PubMed

    Jiang, Z; Mao, Z; Wang, H

    1994-01-01

    consumption structure elasticity. This model was used in the correlation analysis of the coordinated healthy development of optimum consumer population and the economy. PMID:12288173

  1. 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.

  2. Population-based register of stroke: manual of operations.

    PubMed

    Giampaoli, Simona; Hammar, Niklas; Adany, Roza; De Peretti, Christine

    2007-12-01

    Cardiovascular disease is the leading cause of death and hospitalization in both sexes in nearly all countries of Europe. The main forms of cardiovascular disease are ischaemic heart disease and stroke. Stroke by itself is the second leading cause of death in the European Union, and the annual number of cases of stroke is expected to increase within the next few decades, mainly owing to a growth in the proportion of older people. Stroke is an expensive disease because of the large number of premature deaths, ongoing disability in survivors, and the impact on families or caregivers and on health services (treatment and rehabilitation). Therefore, there is a pressing need to make stroke prevention and treatment a priority, to reduce the growing health burden and lessen its socioeconomic impact. The magnitude of the problem contrasts with the shortage, weak quality, and comparability of data available in most European countries. A stepwise surveillance procedure based on standardized data collection, appropriate record linkage, and validation methods was set up by the EUROCISS project (EUROpean Cardiovascular Indicators Surveillance Set), to build up comparable and reliable indicators for the surveillance of stroke at the population level.This manual of operations is intended for health professionals and policy makers. It provides a standardized and simple model for the implementation of a population-based register, which can provide estimates of attack rate and case fatality. The manual recommends starting from a minimum data set. Before implementing a population-based register, it is important to identify the target population under surveillance, which should preferably cover a well defined geographical and administrative area or region representative of the whole country, where population data and vital statistics (mortality and hospital discharge records at least) are routinely collected and easily available each year. All cases among residents should be recorded

  3. 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…

  4. 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.

  5. Population.

    ERIC Educational Resources Information Center

    King, Pat; Landahl, John

    This pamphlet has been prepared in response to a new problem, a rapidly increasing population, and a new need, population education. It is designed to help teachers provide their students with some basic population concepts with stress placed on the elements of decision making. In the first section of the pamphlet, some of the basic concepts of…

  6. Importance of population-based studies in clinical practice

    PubMed Central

    Ronnie, George; Ve, Ramesh Sathyamangalam; Velumuri, Lokapavani; Asokan, Rashima; Vijaya, Lingam

    2011-01-01

    In the last decade, there have been reports on the prevalence of glaucoma from the Vellore Eye Survey, Andhra Pradesh Eye Diseases Survey, Aravind Comprehensive Eye Survey, Chennai Glaucoma Study and West Bengal Glaucoma Study. Population-based studies provide important information regarding the prevalence and risk factors for glaucoma. They also highlight regional differences in the prevalence of various types of glaucoma. It is possible to gather important insights regarding the number of persons affected with glaucoma and the proportion with undiagnosed disease. We reviewed the different population-based studies from India and compare their findings. The lacunae in ophthalmic care that can be inferred from these studies are identified and possible reasons and solutions are discussed. We also discuss the clinical relevance of the various findings, and how it reflects on clinical practice in the country. Since India has a significantly high disease burden, we examine the possibility of population-based screening for disease in the Indian context. PMID:21150021

  7. Perturbation theory analysis of competition in a heterogeneous population

    NASA Astrophysics Data System (ADS)

    Utzny, C.; Burroughs, N. J.

    2003-01-01

    A physiologically structured population model of T cell populations at the end of an immune response is proposed and analysed. The proposed model describes a T cell population with a structured death rate mediated by cytokine receptor surface expression. This provides a structuring that determines the ability of a T cell to compete for survival cytokines. Homogeneous differentiation into memory combined with heterogeneous survival abilities leads to a system of nonlinear first-order integro differential equations. The mathematical model is studied analytically by a perturbation approach which agrees well with numerical integrations. We find that the structured death rate leads to selection of T cells expressing high cytokine receptor levels. Selection in this model is independent of the initial T cell distribution which allows us to define a universal selection curve, a property lost under receptor downregulation (i.e. loss of cytokine receptors from the surface). Furthermore, we examine the effects of a population dependent memory differentiation rate and of cytokine receptor downregulation on selection. A population dependent memory differentiation rate increases selection significantly while putting an upper bound on the number of T cells differentiating into memory. Under receptor downregulation a dramatic change of the memory T cell distribution is induced. We find that there exists a critical ratio of the receptor downregulation rate to the average T cell death rate for which selection becomes maximal. Our analysis reveals that this maximum property is the result of an interplay between single cell dynamics and population dynamics. We propose that the selection studied in this paper plays an important role in the selection of optimal T cells for the memory pool.

  8. 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

  9. 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

  10. 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

  11. 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

  12. A Detailed Analysis of Stellar Populations in Galaxies During Reionization

    NASA Astrophysics Data System (ADS)

    Finkelstein, Steven

    2010-09-01

    We request archival funds to complete a robust study of galaxies in the z > 7 Universe using a new set of unprecedentedly deep data from HST WFC3/IR. These data probe an epoch when the Universe was only 500 - 800 Myr old, placing constraints on the earliest phases of galaxy formation. We recently completed a thorough study of the HUDF with WFC3. Using robust analysis techniques to study the stellar populations in these galaxies, we improved upon early release papers to provide a valuable analysis to the community. We will continue this work, combining the HUDF, HUDF-01 and HUDF-02 datasets to compile a sample ~ 3X larger. We will search for galaxies at z = 7 - 9 within this dataset by computing photometric redshifts, which offers a smaller redshift uncertainty than typical Lyman break color-criteria selection, as well as allowing a more complete census of the galaxy population at z > 7. We will run bootstrap Monte Carlo simulations on our sample, which place strong constraints on the presence of primordial stellar populations in these galaxies - this is more physically accurate than other studies, which have only reported the standard error on the mean, which does not give information on how well one can rule out certain scenarios. Lastly, we will fit the full spectral energy distributions of these objects to a suite of stellar population models, computing confidence ranges on each property. As we found in our previous work, although the age and dust are difficult to constrain, the stellar mass is well constrained with only rest-UV detections due to the old age of the Universe. A 3X increase in sample size nearly doubles the accuracy with which we can pin down the stellar populations in these galaxies.At such high redshifts, large samples of galaxies are expensive and extremely hard to come by. The opportunity to examine a sample of ~ 100 z > 7 galaxies is a unique one, and by applying our robust techniques, we will present the most complete analysis of the galaxy

  13. [Analysis of mitochondrial DNA haplotypes in yakut population].

    PubMed

    Fedorova, S A; Bermisheva, M A; Villems, R; Maksimova, N R; Khusnutdinova, E K

    2003-01-01

    To study the mitochondrial gene pool structure in Yakuts, polymorphism of mtDNA hypervariable segment I (16,024-16,390) was analyzed in 191 people sampled from the indigenous population of the Sakha Republic. In total, 67 haplotypes of 14 haplogroups were detected. Most (91.6%) haplotypes belonged to haplogroups A, B, C, D, F, G, M*, and Y, which are specific for East Eurasian ethnic groups; 8.4% haplotypes represented Caucasian haplogroups H, HV1, J, T, U, and W. A high frequency of mtDNA types belonging to Asian supercluster M was peculiar for Yakuts: mtDNA types belonging to haplogroup C, D, or G and undifferentiated mtDNA types of haplogroup M (M*) accounted for 81% of all haplotypes. The highest diversity was observed for haplogroups C and D, which comprised respectively 22 (44%) and 18 (30%) haplotypes. Yakuts showed the lowest genetic diversity (H = 0.964) among all Turkic ethnic groups. Phylogenetic analysis testified to a common genetic substrate of Yakuts, Mongols, and Central Asian (Kazakh, Kyrgyz, Uigur) populations. Yakuts proved to share 21 (55.5%) mtDNA haplogroups with the Central Asian ethnic groups and Mongols. Comparisons with modern paleo-Asian populations (Chukcha, Itelmen, Koryaks) revealed three (8.9%) haplotypes common for Yakuts and Koryaks. The results of mtDNA analysis disagree with the hypothesis of an appreciable paleo-Asian contribution to the modern Yakut gene pool. PMID:12942638

  14. 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

  15. 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

  16. 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

  17. 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

  18. Population pharmacokinetic analysis of meloxicam in rheumatoid arthritis patients

    PubMed Central

    Meineke, Ingolf; Türck, Dietrich

    2003-01-01

    Aim To perform a nonlinear mixed effect modelling (NONMEM) population pharmacokinetic analysis of meloxicam plasma concentrations in rheumatoid arthritis (RA) patients participating in three clinical trials, and to evaluate the effects of age, weight, gender and concomitant medications on meloxicam pharmacokinetics. Methods Meloxicam was administered to RA patients once daily for 3 weeks or 6 months at doses between 7.5 and 60 mg. Plasma samples were obtained at least 7 days after the first dose and meloxicam plasma concentrations were quantified by h.p.l.c.. Results NONMEM analysis was conducted on plasma samples derived from 586 patients. A one-compartmental model was found to describe the data adequately. For a typical subject in the population, a clearance of 0.377 l h−1 (95% confidence interval (CI) 0.0304–0.449) in males and 0.347 l h−1 (95% CI 0.274-0.419) in females was obtained. The volume of distribution was estimated to be 14.9 l. The findings were corroborated by subsequent analysis using WinBUGS. Analysis of covariates showed that age and gender both significantly (P < 0.005) affected clearance. The effect of age was relatively small and a dose adjustment of <10% was deemed unnecessary. Differences between males and females were attributed to differences in weight. No clinically relevant drug-drug interactions were found, although sulphasalazine and glucocorticoids both significantly (P < 0.005) affected meloxicam clearance (+19% and −12%, respectively). The mechanisms by which these agents affect meloxicam clearance remain to be elucidated. Conclusions The population pharmacokinetic meloxicam data from patients with RA gave similar results to those obtained from phase I trials. However, uncommon drug interactions may not be detected in phase I trials because of the small number of observations made. PMID:12534638

  19. 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…

  20. 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.

  1. 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

  2. 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.

  3. Population pharmacokinetic analysis of sorafenib in patients with solid tumours

    PubMed Central

    Jain, Lokesh; Woo, Sukyung; Gardner, Erin R; Dahut, William L; Kohn, Elise C; Kummar, Shivaani; Mould, Diane R; Giaccone, Giuseppe; Yarchoan, Robert; Venitz, Jürgen; Figg, William D

    2011-01-01

    AIMS To characterize the pharmacokinetics (PK) of sorafenib in patients with solid tumours and to evaluate the possible effects of demographic, clinical and pharmacogenetic (CYP3A4*1B, CYP3A5*3C, UGT1A9*3 and UGT1A9*5) covariates on the disposition of sorafenib. METHODS PK were assessed in 111 patients enrolled in five phase I and II clinical trials, where sorafenib 200 or 400 mg was administered twice daily as a single agent or in combination therapy. All patients were genotyped for polymorphisms in metabolic enzymes for sorafenib. Population PK analysis was performed by using nonlinear mixed effects modelling (NONMEM). The final model was validated using visual predictive checks and nonparametric bootstrap analysis. RESULTS A one compartment model with four transit absorption compartments and enterohepatic circulation (EHC) adequately described sorafenib disposition. Baseline bodyweight was a statistically significant covariate for distributional volume, accounting for 4% of inter-individual variability (IIV). PK model parameter estimates (range) for an 80 kg patient were clearance 8.13 l h−1 (3.6–22.3 l h−1), volume 213 l (50–1000 l), mean absorption transit time 1.98 h (0.5–13 h), fraction undergoing EHC 50% and average time to gall bladder emptying 6.13 h. CONCLUSIONS Overall, population PK analysis was consistent with known biopharmaceutical/PK characteristics of oral sorafenib. No clinically important PK covariates were identified. PMID:21392074

  4. 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. PMID:25899454

  5. 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

  6. The simcyp population based simulator: architecture, implementation, and quality assurance.

    PubMed

    Jamei, Masoud; Marciniak, Steve; Edwards, Duncan; Wragg, Kris; Feng, Kairui; Barnett, Adrian; Rostami-Hodjegan, Amin

    2013-01-01

    Developing a user-friendly platform that can handle a vast number of complex physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) models both for conventional small molecules and larger biologic drugs is a substantial challenge. Over the last decade the Simcyp Population Based Simulator has gained popularity in major pharmaceutical companies (70% of top 40 - in term of R&D spending). Under the Simcyp Consortium guidance, it has evolved from a simple drug-drug interaction tool to a sophisticated and comprehensive Model Based Drug Development (MBDD) platform that covers a broad range of applications spanning from early drug discovery to late drug development. This article provides an update on the latest architectural and implementation developments within the Simulator. Interconnection between peripheral modules, the dynamic model building process and compound and population data handling are all described. The Simcyp Data Management (SDM) system, which contains the system and drug databases, can help with implementing quality standards by seamless integration and tracking of any changes. This also helps with internal approval procedures, validation and auto-testing of the new implemented models and algorithms, an area of high interest to regulatory bodies. PMID:25505654

  7. 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.

  8. Successes and challenges in population-based cancer screening.

    PubMed

    Spayne, Mary; Rabeneck, Linda; Guerriero, Lynn

    2015-01-01

    Cancer Care Ontario's (CCO's) organized breast, colorectal and cervical cancer screening programs are in different stages of development and maturity. Headed by clinical and scientific leads, the programs reflect a deep understanding of how to design, evaluate and report on programs based on evidence and best practice. Guided by a CCO-Ministry of Health and Long-Term Care ("the Ministry") joint committee and supported by recent investments in information technology infrastructure, the programs provide high-quality cancer screening to Ontario's eligible population. PMID:25562129

  9. 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. PMID:26481007

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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.

  15. A population-based study of birth defects in Malaysia.

    PubMed

    Thong, M K; Ho, J J; Khatijah, N N

    2005-01-01

    Birth defects are one of the leading causes of paediatric disability and mortality in developed and developing countries. Data on birth defects from population-based studies originating from developing countries are lacking. One of the objectives of this study was to determine the epidemiology of major birth defects in births during the perinatal period in Kinta district, Perak, Malaysia over a 14-month period, using a population-based birth defect register. There were 253 babies with major birth defects in 17,720 births, giving an incidence of 14.3/1000 births, a birth prevalence of 1 in 70. There were 80 babies with multiple birth defects and 173 with isolated birth defects. The exact syndromic diagnosis of the babies with multiple birth defects could not be identified in 18 (22.5%) babies. The main organ systems involved in the isolated birth defects were cardiovascular (13.8%), cleft lip and palate (11.9%), clubfeet (9.1%), central nervous system (CNS) (including neural tube defects) (7.9%), musculoskeletal (5.5%) and gastrointestinal systems (4.7%), and hydrops fetalis (4.3%). The babies with major birth defects were associated with lower birth weights, premature deliveries, higher Caesarean section rates, prolonged hospitalization and increased specialist care. Among the cohort of babies with major birth defects, the mortality rate was 25.2% during the perinatal period. Mothers with affected babies were associated with advanced maternal age, birth defects themselves or their relatives but not in their other offspring, and significantly higher rates of previous abortions. The consanguinity rate of 2.4% was twice that of the control population. It is concluded that a birth defects register is needed to monitor these developments and future interventional trials are needed to reduce birth defects in Malaysia. PMID:16096215

  16. 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

  17. Independent component analysis of neural populations from multielectrode field potential measurements.

    PubMed

    Tanskanen, Jarno M A; Mikkonen, Jarno E; Penttonen, Markku

    2005-06-30

    Independent component analysis (ICA) is proposed for analysis of neural population activity from multichannel electrophysiological field potential measurements. The proposed analysis method provides information on spatial extents of active neural populations, locations of the populations with respect to each other, population evolution, including merging and splitting of populations in time, and on time lag differences between the populations. In some cases, results of the proposed analysis may also be interpreted as independent information flows carried by neurons and neural populations. In this paper, a detailed description of the analysis method is given. The proposed analysis is demonstrated with an illustrative simulation, and with an exemplary analysis of an in vivo multichannel recording from rat hippocampus. The proposed method can be applied in analysis of any recordings of neural networks in which contributions from a number of neural populations or information flows are simultaneously recorded via a number of measurement points, as well in vivo as in vitro. PMID:15922038

  18. Population-based absolute risk estimation with survey data.

    PubMed

    Kovalchik, Stephanie A; Pfeiffer, Ruth M

    2014-04-01

    Absolute risk is the probability that a cause-specific event occurs in a given time interval in the presence of competing events. We present methods to estimate population-based absolute risk from a complex survey cohort that can accommodate multiple exposure-specific competing risks. The hazard function for each event type consists of an individualized relative risk multiplied by a baseline hazard function, which is modeled nonparametrically or parametrically with a piecewise exponential model. An influence method is used to derive a Taylor-linearized variance estimate for the absolute risk estimates. We introduce novel measures of the cause-specific influences that can guide modeling choices for the competing event components of the model. To illustrate our methodology, we build and validate cause-specific absolute risk models for cardiovascular and cancer deaths using data from the National Health and Nutrition Examination Survey. Our applications demonstrate the usefulness of survey-based risk prediction models for predicting health outcomes and quantifying the potential impact of disease prevention programs at the population level. PMID:23686614

  19. 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

  20. mtDNA analysis of 174 Eurasian populations using a new iterative rank correlation method.

    PubMed

    Juhász, Zoltán; Fehér, Tibor; Németh, Endre; Pamjav, Horolma

    2016-02-01

    In this study, we analyse 27-dimensional mtDNA haplogroup distributions of 174 Eurasian, North-African and American populations, including numerous ancient data as well. The main contribution of this work was the description of the haplogroup distribution of recent and ancient populations as compounds of certain hypothetic ancient core populations immediately or indirectly determining the migration processes in Eurasia for a long time. To identify these core populations, we developed a new iterative algorithm determining clusters of the 27 mtDNA haplogroups studied having strong rank correlation among each other within a definite subset of the populations. Based on this study, the current Eurasian populations can be considered as compounds of three early core populations regarding to maternal lineages. We wanted to show that a simultaneous analysis of ancient and recent data using a new iterative rank correlation algorithm and the weighted SOC learning technique may reveal the most important and deterministic migration processes in the past. This technique allowed us to determine geographically, historically and linguistically well-interpretable clusters of our dataset having a very specific, hardly classifiable structure. The method was validated using a 2-dimensional stepping stone model. PMID:26142878

  1. Improved statistical analysis of low abundance phenomena in bimodal bacterial populations.

    PubMed

    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. 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

  3. 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

  4. Choice of population database for forensic DNA profile analysis.

    PubMed

    Steele, Christopher D; Balding, David J

    2014-12-01

    When evaluating the weight of evidence (WoE) for an individual to be a contributor to a DNA sample, an allele frequency database is required. The allele frequencies are needed to inform about genotype probabilities for unknown contributors of DNA to the sample. Typically databases are available from several populations, and a common practice is to evaluate the WoE using each available database for each unknown contributor. Often the most conservative WoE (most favourable to the defence) is the one reported to the court. However the number of human populations that could be considered is essentially unlimited and the number of contributors to a sample can be large, making it impractical to perform every possible WoE calculation, particularly for complex crime scene profiles. We propose instead the use of only the database that best matches the ancestry of the queried contributor, together with a substantial FST adjustment. To investigate the degree of conservativeness of this approach, we performed extensive simulations of one- and two-contributor crime scene profiles, in the latter case with, and without, the profile of the second contributor available for the analysis. The genotypes were simulated using five population databases, which were also available for the analysis, and evaluations of WoE using our heuristic rule were compared with several alternative calculations using different databases. Using FST=0.03, we found that our heuristic gave WoE more favourable to the defence than alternative calculations in well over 99% of the comparisons we considered; on average the difference in WoE was just under 0.2 bans (orders of magnitude) per locus. The degree of conservativeness of the heuristic rule can be adjusted through the FST value. We propose the use of this heuristic for DNA profile WoE calculations, due to its ease of implementation, and efficient use of the evidence while allowing a flexible degree of conservativeness. PMID:25498938

  5. Validation of population-based disease simulation models: a review of concepts and methods

    PubMed Central

    2010-01-01

    Background Computer simulation models are used increasingly to support public health research and policy, but questions about their quality persist. The purpose of this article is to review the principles and methods for validation of population-based disease simulation models. Methods We developed a comprehensive framework for validating population-based chronic disease simulation models and used this framework in a review of published model validation guidelines. Based on the review, we formulated a set of recommendations for gathering evidence of model credibility. Results Evidence of model credibility derives from examining: 1) the process of model development, 2) the performance of a model, and 3) the quality of decisions based on the model. Many important issues in model validation are insufficiently addressed by current guidelines. These issues include a detailed evaluation of different data sources, graphical representation of models, computer programming, model calibration, between-model comparisons, sensitivity analysis, and predictive validity. The role of external data in model validation depends on the purpose of the model (e.g., decision analysis versus prediction). More research is needed on the methods of comparing the quality of decisions based on different models. Conclusion As the role of simulation modeling in population health is increasing and models are becoming more complex, there is a need for further improvements in model validation methodology and common standards for evaluating model credibility. PMID:21087466

  6. 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

  7. 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. PMID:12314770

  8. 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

  9. Portable atomic frequency standard based on coherent population trapping

    NASA Astrophysics Data System (ADS)

    Shi, Fan; Yang, Renfu; Nian, Feng; Zhang, Zhenwei; Cui, Yongshun; Zhao, Huan; Wang, Nuanrang; Feng, Keming

    2015-05-01

    In this work, a portable atomic frequency standard based on coherent population trapping is designed and demonstrated. To achieve a portable prototype, in the system, a single transverse mode 795nm VCSEL modulated by a 3.4GHz RF source is used as a pump laser which generates coherent light fields. The pump beams pass through a vapor cell containing atom gas and buffer gas. This vapor cell is surrounded by a magnetic shield and placed inside a solenoid which applies a longitudinal magnetic field to lift the Zeeman energy levels' degeneracy and to separate the resonance signal, which has no first-order magnetic field dependence, from the field-dependent resonances. The electrical control system comprises two control loops. The first one locks the laser wavelength to the minimum of the absorption spectrum; the second one locks the modulation frequency and output standard frequency. Furthermore, we designed the micro physical package and realized the locking of a coherent population trapping atomic frequency standard portable prototype successfully. The short-term frequency stability of the whole system is measured to be 6×10-11 for averaging times of 1s, and reaches 5×10-12 at an averaging time of 1000s.

  10. 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

  11. 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

  12. 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

  13. 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.

  14. 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

  15. Mixed dentition space analysis in a Thai population.

    PubMed

    Jaroontham, J; Godfrey, K

    2000-04-01

    This study produced simple linear regression equations to be used for mixed dentition space analysis for males and females, and sexes pooled in a population living in northeastern Thailand. Measurements of teeth were made to within 0.01 mm on the dental casts of 215 boys and 215 girls (mean age 15.7 years). All dentitions were required to be free of any signs of dental pathology or anomalies. It was found that males had significantly larger teeth than females as represented by summations of mandibular incisor, canine, and premolar widths. ANOVA of regression indicated a close relationship between mandibular incisor summation and corresponding summations of canine and premolars. The low coefficients of determination (r2) of the regressions ranged between 0.29 and 0.42, and were higher for females than males, which might be attributable to the ethnic diversity of the sampled population. The regression equations produced predictions of mesio-distal width summations for maxillary and mandibular canine, and premolar arch segments that were slightly different from other reported Asian studies. Moyers' prediction tables at the 50th percentile were found to under-estimate tooth size summation compared with the present investigation. The predictions from simplified regression equations matched well with those of this study for sexes pooled, and for males and females separately. PMID:10822885

  16. 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

  17. 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

  18. 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

  19. Birth Prevalence of Cerebral Palsy: A Population-Based Study

    PubMed Central

    Van Naarden Braun, Kim; Doernberg, Nancy; Schieve, Laura; Christensen, Deborah; Goodman, Alyson; Yeargin-Allsopp, Marshalyn

    2015-01-01

    OBJECTIVE Population-based data in the United States on trends in cerebral palsy (CP) birth prevalence are limited. The objective of this study was to examine trends in the birth prevalence of congenital spastic CP by birth weight, gestational age, and race/ethnicity in a heterogeneous US metropolitan area. METHODS Children with CP were identified by a population-based surveillance system for developmental disabilities (DDs). Children with CP were included if they were born in metropolitan Atlanta, Georgia, from 1985 to 2002, resided there at age 8 years, and did not have a postneonatal etiology (n = 766). Birth weight, gestational age, and race/ethnicity subanalyses were restricted to children with spastic CP (n = 640). Trends were examined by CP subtype, gender, race/ethnicity, co-occurring DDs, birth weight, and gestational age. RESULTS Birth prevalence of spastic CP per 1000 1-year survivors was stable from 1985 to 2002 (1.9 in 1985 to 1.8 in 2002; 0.3% annual average prevalence; 95% confidence interval [CI] −1.1 to 1.8). Whereas no significant trends were observed by gender, subtype, birth weight, or gestational age overall, CP prevalence with co-occurring moderate to severe intellectual disability significantly decreased (−2.6% [95% CI −4.3 to −0.8]). Racial disparities persisted over time between non-Hispanic black and non-Hispanic white children (prevalence ratio 1.8 [95% CI 1.5 to 2.1]). Different patterns emerged for non-Hispanic white and non-Hispanic black children by birth weight and gestational age. CONCLUSIONS Given improvements in neonatal survival, evidence of stability of CP prevalence is encouraging. Yet lack of overall decreases supports continued monitoring of trends and increased research and prevention efforts. Racial/ethnic disparities, in particular, warrant further study. PMID:26659459

  20. 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. PMID:25653490

  1. HIV-1 Transmission Patterns in Antiretroviral Therapy-Naïve, HIV-Infected North Americans Based on Phylogenetic Analysis by Population Level and Ultra-Deep DNA Sequencing

    PubMed Central

    Ross, Lisa L.; Horton, Joseph; Hasan, Samiul; Brown, James R.; Murphy, Daniel; DeJesus, Edwin; Potter, Martin; LaMarca, Anthony; Melendez-Rivera, Ivan; Ward, Douglas; Uy, Jonathon; Shaefer, Mark S.

    2014-01-01

    Factors that contribute to the transmission of human immunodeficiency virus type 1 (HIV-1), especially drug-resistant HIV-1 variants remain a significant public health concern. In-depth phylogenetic analyses of viral sequences obtained in the screening phase from antiretroviral-naïve HIV-infected patients seeking enrollment in EPZ108859, a large open-label study in the USA, Canada and Puerto Rico (ClinicalTrials.gov NCT00440947) were examined for insights into the roles of drug resistance and epidemiological factors that could impact disease dissemination. Viral transmission clusters (VTCs) were initially predicted from a phylogenetic analysis of population level HIV-1 pol sequences obtained from 690 antiretroviral-naïve subjects in 2007. Subsequently, the predicted VTCs were tested for robustness by ultra deep sequencing (UDS) using pyrosequencing technology and further phylogenetic analyses. The demographic characteristics of clustered and non-clustered subjects were then compared. From 690 subjects, 69 were assigned to 1 of 30 VTCs, each containing 2 to 5 subjects. Race composition of VTCs were significantly more likely to be white (72% vs. 60%; p = 0.04). VTCs had fewer reverse transcriptase and major PI resistance mutations (9% vs. 24%; p = 0.002) than non-clustered sequences. Both men-who-have-sex-with-men (MSM) (68% vs. 48%; p = 0.001) and Canadians (29% vs. 14%; p = 0.03) were significantly more frequent in VTCs than non-clustered sequences. Of the 515 subjects who initiated antiretroviral therapy, 33 experienced confirmed virologic failure through 144 weeks while only 3/33 were from VTCs. Fewer VTCs subjects (as compared to those with non-clustering virus) had HIV-1 with resistance-associated mutations or experienced virologic failure during the course of the study. Our analysis shows specific geographical and drug resistance trends that correlate well with transmission clusters defined by HIV sequences of similarity. Furthermore, our

  2. 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.

  3. 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. PMID:25475681

  4. 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. PMID:26662446

  5. Comparing G: multivariate analysis of genetic variation in multiple populations.

    PubMed

    Aguirre, J D; Hine, E; McGuigan, K; Blows, M W

    2014-01-01

    The additive genetic variance-covariance matrix (G) summarizes the multivariate genetic relationships among a set of traits. The geometry of G describes the distribution of multivariate genetic variance, and generates genetic constraints that bias the direction of evolution. Determining if and how the multivariate genetic variance evolves has been limited by a number of analytical challenges in comparing G-matrices. Current methods for the comparison of G typically share several drawbacks: metrics that lack a direct relationship to evolutionary theory, the inability to be applied in conjunction with complex experimental designs, difficulties with determining statistical confidence in inferred differences and an inherently pair-wise focus. Here, we present a cohesive and general analytical framework for the comparative analysis of G that addresses these issues, and that incorporates and extends current methods with a strong geometrical basis. We describe the application of random skewers, common subspace analysis, the 4th-order genetic covariance tensor and the decomposition of the multivariate breeders equation, all within a Bayesian framework. We illustrate these methods using data from an artificial selection experiment on eight traits in Drosophila serrata, where a multi-generational pedigree was available to estimate G in each of six populations. One method, the tensor, elegantly captures all of the variation in genetic variance among populations, and allows the identification of the trait combinations that differ most in genetic variance. The tensor approach is likely to be the most generally applicable method to the comparison of G-matrices from any sampling or experimental design. PMID:23486079

  6. Mitochondrial DNA Analysis of Mongolian Populations and Implications for the Origin of New World Founders

    PubMed Central

    Kolman, C. J.; Sambuughin, N.; Bermingham, E.

    1996-01-01

    High levels of mitochondrial DNA (mtDNA) diversity were determined for Mongolian populations, represented by the Mongol-speaking Khalkha and Dariganga. Although 103 samples were collected across Mongolia, low levels of genetic substructuring were detected, reflecting the nomadic lifestyle and relatively recent ethnic differentiation of Mongolian populations. mtDNA control region I sequence and seven additional mtDNA polymorphisms were assayed to allow extensive comparison with previous human population studies. Based on a comparative analysis, we propose that indigenous populations in east Central Asia represent the closest genetic link between Old and New World populations. Utilizing restriction/deletion polymorphisms, Mongolian populations were found to carry all four New World founding haplogroups as defined by WALLACE and coworkers. The ubiquitous presence of the four New World haplogroups in the Americas but narrow distribution across Asia weakens support for GREENBERG and coworkers' theory of New World colonization via three independent migrations. The statistical and geographic scarcity of New World haplogroups in Asia makes it improbable that the same four haplotypes would be drawn from one geographic region three independent times. Instead, it is likely that founder effects manifest throughout Asia and the Americas are responsible for differences in mtDNA haplotype frequencies observed in these regions. PMID:8846908

  7. 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

  8. The utility of population-based surveys to describe the continuum of HIV services for key and general populations.

    PubMed

    Hladik, Wolfgang; Benech, Irene; Bateganya, Moses; Hakim, Avi J

    2016-01-01

    Monitoring the cascade or continuum of HIV services - ranging from outreach services to anti-retroviral treatment - has become increasingly important as the focus in prevention moves toward biomedical interventions, in particular, 'Treatment as Prevention.' The HIV continuum typically utilises clinic-based care and treatment monitoring data and helps identify gaps and inform programme improvements. This paper discusses the merits of a population-based survey-informed continuum of services. Surveys provide individual-level, population-based data by sampling persons both in and outside the continuum, which facilitate the estimation of population fractions, such as the proportion of people living with HIV in care, as well as the examination of determinants for being in or outside the continuum. Survey-informed cascades of services may especially benefit key populations at increased risk for HIV infection for who social marginalisation, criminalisation, and stigma result in barriers to access and retention in services, a low social visibility, mobility, and outreach-based services can compromise clinic-based monitoring. Adding CD4+ T-cell count and viral load measurements to such surveys may provide population-level information on viral load suppression, stage of disease, treatment needs, and population-level transmission potential. While routine clinic-based reporting will remain the mainstay of monitoring, a survey-informed service cascade can address some of its limitations and offer additional insights. PMID:25907348

  9. Prevalence and distribution of cognitive impairment no dementia (CIND) among the aged population and the analysis of socio-demographic characteristics: the community-based cross-sectional study.

    PubMed

    Fei, Ma; Qu, Yi Cheng; Wang, Ting; Yin, Jiong; Bai, Jing Xu; Ding, Qi Han

    2009-01-01

    The epidemiology on "cognitive impairment no dementia" (CIND) and its natural history are of great importance for understanding the transition from normal aging to dementia. Epidemiologic studies of CIND, however, are limited in China. The goal of our study was to determine the prevalence and distribution of CIND in the aged population and analyze socio-demographic factors. To accomplish this, we performed cluster random sampling of 6192 people aged over 65 years in Taiyuan, a metropolitan city located in northern China. Socio-demographic factors were surveyed by self-administered questionnaires. Neuropsychologic testing consisting of the Mini-Mental State Examination, Boston Naming Test, Trail Making Tests A and B, Block Design, Rey Auditory Verbal Learning Test, Visual Reproduction, Logical Memory, letter and category fluency, the National Adult Reading Test, the Geriatric Depression Scale, and the "state" section of the State-Trait Anxiety Inventory was also obtained. Pearson chi statistics and odds ratio with 95% confidence intervals were used to identify the relationship between CIND and socio-demographic factors. Logistic regression modeling was undertaken to identify potential risk factors. Results showed that an overall prevalence of CIND was 9.70% (95% confidence intervals: 9.62%-9.77%). Univariate analyses showed that the prevalence of CIND differed significantly according to age, sex, education level, monthly household income, and marital status (P<0.01), but not by occupational achievement (P>0.05). In a multiple logistic regression analysis, age, sex, marital status, educational level, and occupation were significantly associated with increased risk for CIND (P<0.01). This study confirms the high prevalence of CIND among the elderly population of China, similar to previous epidemiologic studies in other countries. Nearly all socio-demographic characteristics are associated with CIND. The putative risk factors identified merit further study. PMID

  10. 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

  11. Variation and genetic structure of Tunisian Festuca arundinacea populations based on inter-simple sequence repeat pattern.

    PubMed

    Chtourou-Ghorbel, N; Elazreg, H; Ghariani, S; Ben Mheni, N; Sekmani, M; Chakroun, M; Trifi-Farah, N

    2015-01-01

    Tunisian tall fescue (Festuca arundinacea Schreb.) is an important grass for forages or soil conservation, particularly in marginal sites. Inter-simple sequence repeats were used to estimate genetic diversity within and among 8 natural populations and 1 cultivar from Northern Tunisia. A total of 181 polymorphic inter-simple sequence repeat markers were generated using 7 primers. Shannon's index and analysis of molecular variance evidenced a high molecular polymorphism at intra-specific levels for wild and cultivated accessions, showing that Tunisian tall fescue germplasm constitutes an important pool of diversity. Within-population variation accounted for 39.42% of the total variation, but no regional differentiation was discernible to designate close relationships between regions. Most of the variation (GST = 67%) occurred between populations, rather than within populations. The ɸST (0.60) revealed high population structuring. Additionally, the population structure was independent of the geographic origin and was not affected by environmental factors. The unweighted pair group method with arithmetic mean tree based on genetic similarity and principal coordinate analysis based on coefficient similarity illustrated that continental populations from the proximate localities of Beja and Jendouba were genetically closely related, while the wild Skalba population from the littoral Tunisian locality was the most diverse from the others. Moreover, great molecular similarity of the spontaneous population Sedjnane originated from the mountain areas was revealed with the local cultivar Mornag. The observed genetic diversity can be used to implement conservation strategies and breeding programs for improving forage crops in Tunisia. PMID:25966071

  12. 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

  13. Clinician Use and Acceptance of Population-Based Data about Respiratory Pathogens: Implications for Enhancing Population-Based Clinical Practice

    PubMed Central

    Gesteland, Per H; Allison, Mandy A; Staes, Catherine J; Samore, Matthew H; Rubin, Michael A; Carter, Marjorie E; Wuthrich, Amyanne; Kinney, Anita Y; Mottice, Susan; Byington, Carrie L

    2008-01-01

    Front line health care providers (HCPs) play a central role in endemic (e.g., pertussis), epidemic (e.g., influenza) and pandemic (e.g., avian influenza) infectious disease outbreaks. Effective preparedness for this role requires access to and awareness of population-based data (PBD). We investigated the degree to which this is currently achieved among HCPs in Utah by surveying a sample about access, awareness and attitudes concerning PBD in clinical practice. We found variability in the number and nature (national vs. local, pushed vs. pulled) of PBD sources accessed by HCPs, with a subset using multiple sources and using them frequently. We found that HCPs believe PBD improves their clinical performance and that they cannot rely on their own practice to remain informed. These findings suggest that an integrated system, which interprets PBD from multiple sources and optimizes the delivery of PBD, may facilitate preparedness of HCPs through the application of PBD in routine clinical practice. PMID:18999305

  14. Compact atomic clock prototype based on coherent population trapping

    NASA Astrophysics Data System (ADS)

    Danet, Jean-Marie; Kozlova, Olga; Yun, Peter; Guérande, Stéphane; de Clercq, Emeric

    2014-08-01

    Toward the next generations of compact atomic clocks, clocks based on coherent population trapping (CPT) offer a very interesting alternative. Thanks to CPT, a quantum interfering process, this technology has made a decisive step in the miniaturization direction. Fractional frequency stability of 1.5x10-10 at 1 s has been demonstrated in commercial devices of a few cm3. The laboratory prototype presented here intends to explore what could be the ultimate stability of a CPT based device. To do so, an original double-Λ optical scheme and a pulsed interrogation have been implemented in order to get a good compromise between contrast and linewidth. A study of two main sources of noise, the relative intensity and the local oscillator (LO) noise, has been performed. By designing simple solutions, it led to a new fractional frequency limitation lower than 4x10-13 at 1 s integration. Such a performance proves that such a technology could rival with classical ones as double resonance clocks.

  15. 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. PMID:24903645

  16. 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

  17. Geographic population structure analysis of worldwide human populations infers their biogeographical origins.

    PubMed

    Elhaik, Eran; Tatarinova, Tatiana; Chebotarev, Dmitri; Piras, Ignazio S; Maria Calò, Carla; De Montis, Antonella; Atzori, Manuela; Marini, Monica; Tofanelli, Sergio; Francalacci, Paolo; Pagani, Luca; Tyler-Smith, Chris; Xue, Yali; Cucca, Francesco; Schurr, Theodore G; Gaieski, Jill B; Melendez, Carlalynne; Vilar, Miguel G; Owings, Amanda C; Gómez, Rocío; Fujita, Ricardo; Santos, Fabrício R; Comas, David; Balanovsky, Oleg; Balanovska, Elena; Zalloua, Pierre; Soodyall, Himla; Pitchappan, Ramasamy; Ganeshprasad, Arunkumar; Hammer, Michael; Matisoo-Smith, Lisa; Wells, R Spencer

    2014-01-01

    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

  18. 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. PMID:26599001

  19. 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

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

    PubMed

    Das, Koushik; Chowdhury, Punam; Ganguly, Sandipan

    2015-01-01

    Taxonomic differentiation among morphologically identical Ascaris species is a debatable scientific issue in the context of Ascariasis epidemiology. To explain the disease epidemiology and also the taxonomic position of different Ascaris species, genome information of infecting strains from endemic areas throughout the world is certainly crucial. Ascaris population from human has been genetically characterized based on the widely used genetic marker, internal transcribed spacer1 (ITS1). Along with previously reported and prevalent genotype G1, 8 new sequence variants of ITS1 have been identified. Genotype G1 was significantly present among female patients aged between 10 to 15 years. Intragenic linkage disequilibrium (LD) analysis at target locus within our study population has identified an incomplete LD value with potential recombination events. A separate cluster of Indian isolates with high bootstrap value indicate their distinct phylogenetic position in comparison to the global Ascaris population. Genetic shuffling through recombination could be a possible reason for high population diversity and frequent emergence of new sequence variants, identified in present and other previous studies. This study explores the genetic organization of Indian Ascaris population for the first time which certainly includes some fundamental information on the molecular epidemiology of Ascariasis. PMID:26504510

  1. Machine Learning Based Classification of Microsatellite Variation: An Effective Approach for Phylogeographic Characterization of Olive Populations

    PubMed Central

    Mousavi, Soraya; Mariotti, Roberto; Baldoni, Luciana; Ebrahimie, Esmaeil; Ebrahimi, Mansour; Hosseini-Mazinani, Mehdi

    2015-01-01

    Finding efficient analytical techniques is overwhelmingly turning into a bottleneck for the effectiveness of large biological data. Machine learning offers a novel and powerful tool to advance classification and modeling solutions in molecular biology. However, these methods have been less frequently used with empirical population genetics data. In this study, we developed a new combined approach of data analysis using microsatellite marker data from our previous studies of olive populations using machine learning algorithms. Herein, 267 olive accessions of various origins including 21 reference cultivars, 132 local ecotypes, and 37 wild olive specimens from the Iranian plateau, together with 77 of the most represented Mediterranean varieties were investigated using a finely selected panel of 11 microsatellite markers. We organized data in two ‘4-targeted’ and ‘16-targeted’ experiments. A strategy of assaying different machine based analyses (i.e. data cleaning, feature selection, and machine learning classification) was devised to identify the most informative loci and the most diagnostic alleles to represent the population and the geography of each olive accession. These analyses revealed microsatellite markers with the highest differentiating capacity and proved efficiency for our method of clustering olive accessions to reflect upon their regions of origin. A distinguished highlight of this study was the discovery of the best combination of markers for better differentiating of populations via machine learning models, which can be exploited to distinguish among other biological populations. PMID:26599001

  2. Birth order and mortality: a population-based cohort study.

    PubMed

    Barclay, Kieron; Kolk, Martin

    2015-04-01

    This study uses Swedish population register data to investigate the relationship between birth order and mortality at ages 30 to 69 for Swedish cohorts born between 1938 and 1960, using a within-family comparison. The main analyses are conducted with discrete-time survival analysis using a within-family comparison, and the estimates are adjusted for age, mother's age at the time of birth, and cohort. Focusing on sibships ranging in size from two to six, we find that mortality risk in adulthood increases with later birth order. The results show that the relative effect of birth order is greater among women than among men. This pattern is consistent for all the major causes of death but is particularly pronounced for mortality attributable to cancers of the respiratory system and to external causes. Further analyses in which we adjust for adult socioeconomic status and adult educational attainment suggest that social pathways only mediate the relationship between birth order and mortality risk in adulthood to a limited degree. PMID:25777302

  3. A Framework for Image-Based Classification of Mitotic Cells in Asynchronous Populations

    PubMed Central

    Slattery, Scott D.; Newberg, Justin Y.; Szafran, Adam T.; Hall, Rebecca M.; Brinkley, Bill R.

    2012-01-01

    Abstract High content screening (HCS) has emerged an important tool for drug discovery because it combines rich readouts of cellular responses in a single experiment. Inclusion of cell cycle analysis into HCS is essential to identify clinically suitable anticancer drugs that disrupt the aberrant mitotic activity of cells. One challenge for integration of cell cycle analysis into HCS is that cells must be chemically synchronized to specific phases, adding experimental complexity to high content screens. To address this issue, we have developed a rules-based method that utilizes mitotic phosphoprotein monoclonal 2 (MPM-2) marker and works consistently in different experimental conditions and in asynchronous populations. Further, the performance of the rules-based method is comparable to established machine learning approaches for classifying cell cycle data, indicating the robustness of the features we use in the framework. As such, we suggest the use of MPM-2 analysis and its associated expressive features for integration into HCS approaches. PMID:22084958

  4. 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

  5. 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

  6. Population analysis of the cingulum bundle using the tubular surface model for schizophrenia detection

    NASA Astrophysics Data System (ADS)

    Mohan, Vandana; Sundaramoorthi, Ganesh; Kubicki, Marek; Terry, Douglas; Tannenbaum, Allen

    2010-03-01

    We propose a novel framework for population analysis of DW-MRI data using the Tubular Surface Model. We focus on the Cingulum Bundle (CB) - a major tract for the Limbic System and the main connection of the Cingulate Gyrus, which has been associated with several aspects of Schizophrenia symptomatology. The Tubular Surface Model represents a tubular surface as a center-line with an associated radius function. It provides a natural way to sample statistics along the length of the fiber bundle and reduces the registration of fiber bundle surfaces to that of 4D curves. We apply our framework to a population of 20 subjects (10 normal, 10 schizophrenic) and obtain excellent results with neural network based classification (90% sensitivity, 95% specificity) as well as unsupervised clustering (k-means). Further, we apply statistical analysis to the feature data and characterize the discrimination ability of local regions of the CB, as a step towards localizing CB regions most relevant to Schizophrenia.

  7. Analysis of Rare, Exonic Variation amongst Subjects with Autism Spectrum Disorders and Population Controls

    PubMed Central

    Liu, Li; Sabo, Aniko; Neale, Benjamin M.; Nagaswamy, Uma; Stevens, Christine; Lim, Elaine; Bodea, Corneliu A.; Muzny, Donna; Reid, Jeffrey G.; Banks, Eric; Coon, Hillary; DePristo, Mark; Dinh, Huyen; Fennel, Tim; Flannick, Jason; Gabriel, Stacey; Garimella, Kiran; Gross, Shannon; Hawes, Alicia; Lewis, Lora; Makarov, Vladimir; Maguire, Jared; Newsham, Irene; Poplin, Ryan; Ripke, Stephan; Shakir, Khalid; Samocha, Kaitlin E.; Wu, Yuanqing; Boerwinkle, Eric; Buxbaum, Joseph D.; Cook, Edwin H.; Devlin, Bernie; Schellenberg, Gerard D.; Sutcliffe, James S.; Daly, Mark J.; Gibbs, Richard A.; Roeder, Kathryn

    2013-01-01

    We report on results from whole-exome sequencing (WES) of 1,039 subjects diagnosed with autism spectrum disorders (ASD) and 870 controls selected from the NIMH repository to be of similar ancestry to cases. The WES data came from two centers using different methods to produce sequence and to call variants from it. Therefore, an initial goal was to ensure the distribution of rare variation was similar for data from different centers. This proved straightforward by filtering called variants by fraction of missing data, read depth, and balance of alternative to reference reads. Results were evaluated using seven samples sequenced at both centers and by results from the association study. Next we addressed how the data and/or results from the centers should be combined. Gene-based analyses of association was an obvious choice, but should statistics for association be combined across centers (meta-analysis) or should data be combined and then analyzed (mega-analysis)? Because of the nature of many gene-based tests, we showed by theory and simulations that mega-analysis has better power than meta-analysis. Finally, before analyzing the data for association, we explored the impact of population structure on rare variant analysis in these data. Like other recent studies, we found evidence that population structure can confound case-control studies by the clustering of rare variants in ancestry space; yet, unlike some recent studies, for these data we found that principal component-based analyses were sufficient to control for ancestry and produce test statistics with appropriate distributions. After using a variety of gene-based tests and both meta- and mega-analysis, we found no new risk genes for ASD in this sample. Our results suggest that standard gene-based tests will require much larger samples of cases and controls before being effective for gene discovery, even for a disorder like ASD. PMID:23593035

  8. Population-based analysis of non-steroidal anti-inflammatory drug use among children in four European countries in the SOS project: what size of data platforms and which study designs do we need to assess safety issues?

    PubMed Central

    2013-01-01

    Background Data on utilization patterns and safety of non-steroidal anti-inflammatory drugs (NSAIDs) in children are scarce. The purpose of this study was to investigate the utilization of NSAIDs among children in four European countries as part of the Safety Of non-Steroidal anti-inflammatory drugs (SOS) project. Methods We used longitudinal patient data from seven databases (GePaRD, IPCI, OSSIFF, Pedianet, PHARMO, SISR, and THIN) to calculate prevalence rates of NSAID use among children (0–18 years of age) from Germany, Italy, Netherlands, and United Kingdom. All databases contained a representative population sample and recorded demographics, diagnoses, and drug prescriptions. Prevalence rates of NSAID use were stratified by age, sex, and calendar time. The person-time of NSAID exposure was calculated by using the duration of the prescription supply. We calculated incidence rates for serious adverse events of interest. For these adverse events of interest, sample size calculations were conducted (alpha = 0.05; 1-beta = 0.8) to determine the amount of NSAID exposure time that would be required for safety studies in children. Results The source population comprised 7.7 million children with a total of 29.6 million person-years of observation. Of those, 1.3 million children were exposed to at least one of 45 NSAIDs during observation time. Overall prevalence rates of NSAID use in children differed across countries, ranging from 4.4 (Italy) to 197 (Germany) per 1000 person-years in 2007. For Germany, United Kingdom, and Italian pediatricians, we observed high rates of NSAID use among children aged one to four years. For all four countries, NSAID use increased with older age categories for children older than 11. In this analysis, only for ibuprofen (the most frequently used NSAID), enough exposure was available to detect a weak association (relative risk of 2) between exposure and asthma exacerbation (the most common serious adverse event of interest

  9. 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.

  10. SSR-based identification of genetic groups within European populations of Tuber aestivum Vittad.

    PubMed

    Molinier, Virginie; Murat, Claude; Peter, Martina; Gollotte, Armelle; De la Varga, Herminia; Meier, Barbara; Egli, Simon; Belfiori, Beatrice; Paolocci, Francesco; Wipf, Daniel

    2016-02-01

    Tuber species are ectomycorrhizal ascomycetes establishing relationships with different host trees and forming hypogeous fruiting bodies known as truffles. Among Tuber species, Tuber aestivum Vittad. has a wide distributional range being found naturally all over Europe. Here, we performed large-scale population genetic analyses in T. aestivum to (i) investigate its genetic diversity at the European scale, (ii) characterize its genetic structure and test for the presence of ecotypes and (iii) shed light into its demographic history. To reach these goals, 230 ascocarps from different populations were genotyped using 15 polymorphic simple sequence repeat markers. We identified 181 multilocus genotypes and four genetic groups which did not show a clear geographical separation; although, one of them was present exclusively in Southeast France, Italy and Spain. Fixation index values between pairs of genetic groups were generally high and ranged from 0.29 to 0.45. A significant deficit of heterozygosity indicated a population expansion instead of a recent population bottleneck, suggesting that T. aestivum is not endangered in Europe, not even in Mediterranean regions. Our study based on a large-scale population genetic analysis suggests that genetically distinct populations and likely ecotypes within T. aestivum are present. In turn, this study paves the way to future investigations aimed at addressing the biological and/or ecological factors that have concurred in shaping the population genetic structure of this species. Present results should also have implications for the truffle market since defining genetic markers are now possible at least for some specific T. aestivum genetic groups. PMID:26070448

  11. Population-Based Provider Engagement in Delivery of Evidence-Based Parenting Interventions: Challenges and Solutions

    ERIC Educational Resources Information Center

    Shapiro, Cheri J.; Prinz, Ronald J.; Sanders, Matthew R.

    2010-01-01

    Population-wide interventions do not often address parenting, and relatively little is known about large scale dissemination of evidence-based parenting interventions. Most parenting interventions are not designed to reach the majority of parents in a geographic area or to influence prevalence rates for a problem, nor do they take full advantage…

  12. 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.

  13. Glycemic Change After Pancreaticoduodenectomy: A Population-Based Study.

    PubMed

    Wu, Jin-Ming; Ho, Te-Wei; Kuo, Ting-Chun; Yang, Ching-Yao; Lai, Hong-Shiee; Chiang, Pin-Yi; Hsieh, Su-Hua; Lai, Feipei; Tien, Yu-Wen

    2015-07-01

    The purpose of this population-based study was to determine the change of glucose metabolism in patients undergoing pancreaticoduodenectomy (PD).We conducted a nationwide cohort study using data from Taiwan's National Health Insurance Research Database collected between 2000 and 2010. Our sample included 861 subjects with type 2 diabetes mellitus (DM) and 3914 subjects without DM.Of 861 subjects with type 2 diabetes, 174 patients (20.2%) experienced resolution of their diabetes after PD, including patients with pancreatic ductal adenocarcinoma (PDAC) (20.5%), and non-PDAC (20.1%). Using a multiple logistic regression model, we found that subjects with comorbid chronic pancreatitis (odds ratio, 0.356; 95% CI, 0.167-0.759; P = 0.007) and use of insulin (odds ratio, 0.265; 95% CI, 0.171-0.412; P < 0.001) had significantly lower rates of resolution of diabetes. In the 3914 subjects without diabetes, the only statistically significant comorbidity contributing to pancreatogenic diabetes was chronic pancreatitis (odds ratio, 1.446; 95% CI, 1.146-1.823; P = 0.002).Subjects with comorbid chronic pancreatitis and use of insulin had lower rates of resolution of DM after PD. In subjects without diabetes, chronic pancreatitis contributed significantly to the development of pancreatogenic DM. PMID:26166104

  14. Provider communication on perinatal depression: a population-based study.

    PubMed

    Farr, Sherry L; Ko, Jean Y; Burley, Kim; Gupta, Seema

    2016-02-01

    Women's lack of knowledge on symptoms of perinatal depression and treatment resources is a barrier to receiving care. We sought to estimate the prevalence and predictors of discussing depression with a prenatal care provider. We used the 2011 population-based data from 24 sites participating in the Pregnancy Risk Assessment Monitoring System (n = 32,827 women with recent live births) to examine associations between maternal characteristics and report that a prenatal care provider discussed with her what to do if feeling depressed during or after pregnancy. Overall, 71.9 % of women reported discussing perinatal depression with their prenatal care provider (range 60.7 % in New York City to 85.6 % in Maine). Women were more likely to report a discussion on perinatal depression with their provider if they they were 18-29 years of age than over 35 years of age compared to older (adjusted prevalence ratio [aPR] 18 to 19 y = 1.08, 20 to 24 y = 1.10, 25 to 29 y = 1.09), unmarried (aPR = 1.07) compared to married, had <12 years of education (aPR = 1.05) compared to > 12 years, and had no previous live births (aPR = 1.03) compared to ≥ 1 live births. Research is needed on effective ways to educate women about perinatal depression and whether increased knowledge on perinatal depression results in higher rates of treatment and shorter duration of symptoms. PMID:25578631

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. Phylogeographic Analysis of Mitochondrial DNA in Northern Asian Populations

    PubMed Central

    Derenko, Miroslava ; Malyarchuk, Boris ; Grzybowski, Tomasz ; Denisova, Galina ; Dambueva, Irina ; Perkova, Maria ; Dorzhu, Choduraa ; Luzina, Faina ; Lee, Hong Kyu ; Vanecek, Tomas ; Villems, Richard ; Zakharov, Ilia 

    2007-01-01

    To elucidate the human colonization process of northern Asia and human dispersals to the Americas, a diverse subset of 71 mitochondrial DNA (mtDNA) lineages was chosen for complete genome sequencing from the collection of 1,432 control-region sequences sampled from 18 autochthonous populations of northern, central, eastern, and southwestern Asia. On the basis of complete mtDNA sequencing, we have revised the classification of haplogroups A, D2, G1, M7, and I; identified six new subhaplogroups (I4, N1e, G1c, M7d, M7e, and J1b2a); and fully characterized haplogroups N1a and G1b, which were previously described only by the first hypervariable segment (HVS1) sequencing and coding-region restriction-fragment–length polymorphism analysis. Our findings indicate that the southern Siberian mtDNA pool harbors several lineages associated with the Late Upper Paleolithic and/or early Neolithic dispersals from both eastern Asia and southwestern Asia/southern Caucasus. Moreover, the phylogeography of the D2 lineages suggests that southern Siberia is likely to be a geographical source for the last postglacial maximum spread of this subhaplogroup to northern Siberia and that the expansion of the D2b branch occurred in Beringia ∼7,000 years ago. In general, a detailed analysis of mtDNA gene pools of northern Asians provides the additional evidence to rule out the existence of a northern Asian route for the initial human colonization of Asia. PMID:17924343

  20. 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

  1. 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.

  2. 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

  3. POPULATION-BASED EXPOSURE MODELING FOR AIR POLLUTANTS AT EPA'S NATIONAL EXPOSURE RESEARCH LABORATORY

    EPA Science Inventory

    The US EPA's National Exposure Research Laboratory (NERL) has been developing, applying, and evaluating population-based exposure models to improve our understanding of the variability in personal exposure to air pollutants. Estimates of population variability are needed for E...

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

    PubMed Central

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

    2015-01-01

    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 podoplaninhigh 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. PMID:26484194

  5. 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.

  6. 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

  7. New Population Synthesis Techniques in the Analysis of Interacting Binaries

    NASA Astrophysics Data System (ADS)

    Nelson, Lorne

    2012-02-01

    Novel approaches to understanding the observed properties of interacting binaries containing compact accretors such as neutron stars and white dwarfs are examined. Explaining the evolution of these systems is a computationally challenging problem because the vector space of initial conditions that describes the progenitor binaries is wide-ranging. There are large variations in the chemical abundance (e.g., metallicity), binary mass correlations, and assumed input physics. In this paper we compare two very different strategies to synthesize a specific subset of the currently observed population of compact binaries. Both involve the pre-computing a large grid of representative models. In the first case, the grid of initial conditions is densely packed thereby allowing us to identify the spectrum of initial conditions and the most probable evolutionary channels leading to the formation of the observed binaries. In the second, the grid is accurately interpolated to provide us with the ensemble properties of the currently observed population of interacting binaries (e.g., Cataclysmic Variables). As an example of the utility of the first approach, we have taken advantage of the multicore processing power of the fast, new stellar evolution code known as MESA to compute an extensive grid of binary evolution tracks for low- and intermediate-mass X-ray binaries. The grid is about two orders of magnitude larger than any previous computation of X-ray binary evolution and includes more than 40,000 models. It comprises 60 initial donor masses over the range of 1 to 4 Modot and, for each of these, 700 initial orbital periods over the range of 10 to 250 hours were chosen. Using a 'traceback' analysis, we show how the extremely massive neutron star (1.97 Modot) in the binary pulsar PSR J1614-2230 is likely to have evolved. We find that the initial donor stars which produce the closest relatives to PSR J1614-2230 are likely to have had a mass of between approximately 3.4 to 3

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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.

  16. Detailed Analysis of Japanese Population Substructure with a Focus on the Southwest Islands of Japan

    PubMed Central

    Nishiyama, Takeshi; Kishino, Hirohisa; Suzuki, Sadao; Ando, Ryosuke; Niimura, Hideshi; Uemura, Hirokazu; Horita, Mikako; Ohnaka, Keizo; Kuriyama, Nagato; Mikami, Haruo; Takashima, Naoyuki; Mastuo, Keitaro; Guang, Yin; Wakai, Kenji; Hamajima, Nobuyuki; Tanaka, Hideo

    2012-01-01

    Uncovering population structure is important for properly conducting association studies and for examining the demographic history of a population. Here, we examined the Japanese population substructure using data from the Japan Multi-Institutional Collaborative Cohort (J-MICC), which covers all but the northern region of Japan. Using 222 autosomal loci from 4502 subjects, we investigated population substructure by estimating FST among populations, testing population differentiation, and performing principal component analysis (PCA) and correspondence analysis (CA). All analyses revealed a low but significant differentiation between the Amami Islanders and the mainland Japanese population. Furthermore, we examined the genetic differentiation between the mainland population, Amami Islanders and Okinawa Islanders using six loci included in both the Pan-Asian SNP (PASNP) consortium data and the J-MICC data. This analysis revealed that the Amami and Okinawa Islanders were differentiated from the mainland population. In conclusion, we revealed a low but significant level of genetic differentiation between the mainland population and populations in or to the south of the Amami Islands, although genetic variation between both populations might be clinal. Therefore, the possibility of population stratification must be considered when enrolling the islander population of this area, such as in the J-MICC study. PMID:22509376

  17. 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

  18. [Methodological aspects of a political-economic analysis of population].

    PubMed

    Lisina, N V; Ruzavina, E I

    1988-01-01

    The authors examine the role of political and economic factors in the study of population issues, with a focus on the relationship between demographic factors and the standard of living of a society. Attention is paid to the division of the population into the economically active and the inactive. PMID:12342147

  19. Analysis of paternal lineages in Brazilian and African populations

    PubMed Central

    2010-01-01

    The present-day Brazilian population is a consequence of the admixture of various peoples of very different origins, namely, Amerindians, Europeans and Africans. The proportion of each genetic contribution is known to be very heterogeneous throughout the country. The aim of the present study was to compare the male lineages present in two distinct Brazilian populations, as well as to evaluate the African contribution to their male genetic substrate. Thus, two Brazilian population samples from Manaus (State of Amazon) and Ribeirão Preto (State of São Paulo) and three African samples from Guinea Bissau, Angola and Mozambique were typed for a set of nine Y chromosome specific STRs. The data were compared with those from African, Amerindian and European populations. By using Y-STR haplotype information, low genetic distances were found between the Manaus and Ribeirão Preto populations, as well as between these and others from Iberia. Likewise, no significant distances were observed between any of the African samples from Angola, Mozambique and Guinea Bissau. Highly significant Rst values were found between both Brazilian samples and all the African and Amerindian populations. The absence of a significant Sub-Saharan African male component resulting from the slave trade, and the low frequency in Amerindian ancestry Y-lineages in the Manaus and Ribeirão Preto population samples are in accordance with the accentuated gender asymmetry in admixture processes that has been systematically reported in colonial South American populations. PMID:21637407

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

    USGS Publications Warehouse

    Noon, B.R.; Sauer, J.R.

    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.

  1. 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

  2. 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.

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

    PubMed Central

    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 (FROH) 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

  4. BARS REJUVENATING BULGES? EVIDENCE FROM STELLAR POPULATION ANALYSIS

    SciTech Connect

    Coelho, P.; Gadotti, D. A. E-mail: dgadotti@eso.org

    2011-12-10

    We obtained stellar ages and metallicities via spectrum fitting for a sample of 575 bulges with spectra available from the Sloan Digital Sky Survey. The structural properties of the galaxies have been studied in detail in 2009 by Gadotti and the sample contains 251 bulges in galaxies with bars. Using the whole sample, where galaxy stellar mass distributions for barred and unbarred galaxies are similar, we find that bulges in barred and unbarred galaxies occupy similar loci in the age versus metallicity plane. However, the distribution of bulge ages in barred galaxies shows an excess of populations younger than {approx}4 Gyr, when compared to bulges in unbarred galaxies. Kolmogorov-Smirnov statistics confirm that the age distributions are different with a significance of 99.94%. If we select sub-samples for which the bulge stellar mass distributions are similar for barred and unbarred galaxies, this excess vanishes for galaxies with bulge mass log M < 10.1 M{sub Sun }, while for more massive galaxies we find a bimodal bulge age distribution for barred galaxies only, corresponding to two normal distributions with mean ages of 10.4 and 4.7 Gyr. We also find twice as much active galactic nuclei among barred galaxies, as compared to unbarred galaxies, for low-mass bulges. By combining a large sample of high-quality data with sophisticated image and spectral analysis, we are able to find evidence that the presence of bars affects the mean stellar ages of bulges. This lends strong support to models in which bars trigger star formation activity in the centers of galaxies.

  5. 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. PMID:25710874

  6. An improved multi-objective evolutionary memetic algorithm based on multi-population and its application

    NASA Astrophysics Data System (ADS)

    Xiao, Zhongliang

    2012-04-01

    In this paper, we set up a mathematical model to solve the problem of airport ground services. In this model, we set objective function of cost and time, and the purpose is making it minimized. Base on the analysis of scheduling characteristic, we use the multi-population co-evolutionary Memetic algorithm (MAMC) which is with the elitist strategy to realize the model. From the result we can see that our algorithm is better than the genetic algorithm in this problem and we can see that our algorithm is convergence. So we can summarize that it can be a better optimization to airport ground services problem.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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. PMID:18216057

  12. 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.

  13. 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

  14. [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

  15. 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

  16. Population analysis of vitamin D receptor polymorphisms and the role of genetic ancestry in an admixed population

    PubMed Central

    Lins, Tulio C.; Vieira, Rodrigo G.; Grattapaglia, Dario; Pereira, Rinaldo W.

    2011-01-01

    The vitamin D receptor (VDR) is an essential protein related to bone metabolism. Some VDR alleles are differentially distributed among ethnic populations and display variable patterns of linkage disequilibrium (LD). In this study, 200 unrelated Brazilians were genotyped using 21 VDR single nucleotide polymorphisms (SNPs) and 28 ancestry informative markers. The patterns of LD and haplotype distribution were compared among Brazilian and the HapMap populations of African (YRI), European (CEU) and Asian (JPT+CHB) origins. Conditional regression and haplotype-specific analysis were performed using estimates of individual genetic ancestry in Brazilians as a quantitative trait. Similar patterns of LD were observed in the 5′ and 3′ gene regions. However, the frequency distribution of haplotype blocks varied among populations. Conditional regression analysis identified haplotypes associated with European and Amerindian ancestry, but not with the proportion of African ancestry. Individual ancestry estimates were associated with VDR haplotypes. These findings reinforce the need to correct for population stratification when performing genetic association studies in admixed populations. PMID:21931507

  17. Cyberbullying among Finnish adolescents – a population-based study

    PubMed Central

    2012-01-01

    Background Cyberbullying, threatening or harassing another via the internet or mobile phones, does not cause physically harm and thus the consequences are less visible. Little research has been performed on the occurrence of cyberbullying among adolescents or the perception of its seriousness. Only a few population-based studies have been published, none of which included research on the witnessing of cyberbullying. Here, we examined exposure to cyberbullying during the last year, and its frequency and perceived seriousness among 12 to 18-year-old adolescents in Finland. We studied four dimensions of cyberbullying: being a victim, bully, or both victim and bully of cyberbullying, and witnessing the cyberbullying of friends. Methods Self-administered questionnaires, including four questions on cyberbullying, were mailed to a representative sample of 12-, 14-, 16-, and 18-year-old Finns in 2009 (the Adolescent Health and Lifestyle Survey). The respondents could answer via the internet or paper questionnaire. Results The number of respondents was 5516 and the response rate was 56%. Girls more often than boys reported experiencing at least one dimension of cyberbullying during the last year. The proportion was highest among 14-year-olds and lowest among 18-year-olds of both sexes. Among girls, the most commonly encountered dimension was witnessing the cyberbullying of friends (16%); and being a victim was slightly more common than being a bully (11% vs. 9%). Among boys, an equal proportion, approximately 10%, had been a victim, a bully, or had witnessed cyberbullying. The proportion of bully-victims was 4%. Serious and disruptive cyberbullying was experienced by 2% of respondents and weekly cyberbullying by 1%; only 0.5% of respondents had been bullied weekly and considered bullying serious and disruptive. Conclusions Adolescents are commonly exposed to cyberbullying, but it is rarely frequent or considered serious or disruptive. Cyberbullying exposure differed between

  18. Familial risk of cerebral palsy: population based cohort study

    PubMed Central

    Wilcox, Allen J; Lie, Rolv T; Moster, Dag

    2014-01-01

    Objective To investigate risks of recurrence of cerebral palsy in family members with various degrees of relatedness to elucidate patterns of hereditability. Design Population based cohort study. Setting Data from the Medical Birth Registry of Norway, linked to the Norwegian social insurance scheme to identify cases of cerebral palsy and to databases of Statistics Norway to identify relatives. Participants 2 036 741 Norwegians born during 1967-2002, 3649 of whom had a diagnosis of cerebral palsy; 22 558 pairs of twins, 1 851 144 pairs of first degree relatives, 1 699 856 pairs of second degree relatives, and 5 165 968 pairs of third degree relatives were identified. Main outcome measure Cerebral palsy. Results If one twin had cerebral palsy, the relative risk of recurrence of cerebral palsy was 15.6 (95% confidence interval 9.8 to 25) in the other twin. In families with an affected singleton child, risk was increased 9.2 (6.4 to 13)-fold in a subsequent full sibling and 3.0 (1.1 to 8.6)-fold in a half sibling. Affected parents were also at increased risk of having an affected child (6.5 (1.6 to 26)-fold). No evidence was found of differential transmission through mothers or fathers, although the study had limited power to detect such differences. For people with an affected first cousin, only weak evidence existed for an increased risk (1.5 (0.9 to 2.7)-fold). Risks in siblings or cousins were independent of sex of the index case. After exclusion of preterm births (an important risk factor for cerebral palsy), familial risks remained and were often stronger. Conclusions People born into families in which someone already has cerebral palsy are themselves at elevated risk, depending on their degree of relatedness. Elevated risk may extend even to third degree relatives (first cousins). The patterns of risk suggest multifactorial inheritance, in which multiple genes interact with each other and with environmental factors. These data offer additional

  19. 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

  20. 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

  1. Population Structure and Inbreeding From Pedigree Analysis of Purebred Dogs

    PubMed Central

    Calboli, Federico C. F.; Sampson, Jeff; Fretwell, Neale; Balding, David J.

    2008-01-01

    Dogs are of increasing interest as models for human diseases, and many canine population-association studies are beginning to emerge. The choice of breeds for such studies should be informed by a knowledge of factors such as inbreeding, genetic diversity, and population structure, which are likely to depend on breed-specific selective breeding patterns. To address the lack of such studies we have exploited one of the world's most extensive resources for canine population-genetics studies: the United Kingdom (UK) Kennel Club registration database. We chose 10 representative breeds and analyzed their pedigrees since electronic records were established around 1970, corresponding to about eight generations before present. We find extremely inbred dogs in each breed except the greyhound and estimate an inbreeding effective population size between 40 and 80 for all but 2 breeds. For all but 3 breeds, >90% of unique genetic variants are lost over six generations, indicating a dramatic effect of breeding patterns on genetic diversity. We introduce a novel index Ψ for measuring population structure directly from the pedigree and use it to identify subpopulations in several breeds. As well as informing the design of canine population genetics studies, our results have implications for breeding practices to enhance canine welfare. PMID:18493074

  2. Metamodels for Transdisciplinary Analysis of Wildlife Population Dynamics

    PubMed Central

    Lacy, Robert C.; Miller, Philip S.; Nyhus, Philip J.; Pollak, J. P.; Raboy, Becky E.; Zeigler, Sara L.

    2013-01-01

    Wildlife population models have been criticized for their narrow disciplinary perspective when analyzing complexity in coupled biological – physical – human systems. We describe a “metamodel” approach to species risk assessment when diverse threats act at different spatiotemporal scales, interact in non-linear ways, and are addressed by distinct disciplines. A metamodel links discrete, individual models that depict components of a complex system, governing the flow of information among models and the sequence of simulated events. Each model simulates processes specific to its disciplinary realm while being informed of changes in other metamodel components by accessing common descriptors of the system, populations, and individuals. Interactions among models are revealed as emergent properties of the system. We introduce a new metamodel platform, both to further explain key elements of the metamodel approach and as an example that we hope will facilitate the development of other platforms for implementing metamodels in population biology, species risk assessments, and conservation planning. We present two examples – one exploring the interactions of dispersal in metapopulations and the spread of infectious disease, the other examining predator-prey dynamics – to illustrate how metamodels can reveal complex processes and unexpected patterns when population dynamics are linked to additional extrinsic factors. Metamodels provide a flexible, extensible method for expanding population viability analyses beyond models of isolated population demographics into more complete representations of the external and intrinsic threats that must be understood and managed for species conservation. PMID:24349567

  3. Experimental analysis of methods for measuring small mammal populations

    USGS Publications Warehouse

    Stickel, L.F.

    1946-01-01

    SUMMARY: The Peromyscus leucopus on a 17-acre study area were live-trapped, marked, and released over a seven-day period. On the three following nights intensive snap-trapping was done on the central acre of the study plot. The animals caught by snap traps in the central acre represented the population of the central acre and several surrounding acres. By the currently accepted methods of interpreting snap-trap data, the population per acre would be considered to be 23 adults. The live-trap data show that the true population was between six and seven adults per acre. Modern methods of live-trapping are shown to be valid for population studies. Two methods are presented for the conversion of live-trap data into per acre figures. Errors involved in the current use of snap-trap data are discussed and snap-trap methods are shown to be invalid for determining actual population numbers. It should be practical to use a snap-trap quadrant technique to obtain a relative measure or index figure for small mammal populations.

  4. Fruit, vegetable and fat intake in a population-based sample of African Americans.

    PubMed Central

    Gary, Tiffany L.; Baptiste-Roberts, Kesha; Gregg, Edward W.; Williams, Desmond E.; Beckles, Gloria L. A.; Miller, Edgar J.; Engelgau, Michael M.

    2004-01-01

    BACKGROUND: African Americans experience high rates of obesity and other chronic diseases, which may be related, in part, to diet. However, little is known about dietary patterns in this population, particularly from population-based data sources. METHODS: A cross-sectional analysis was conducted of 2,172 African-American adults in Project DIRECT (Diabetes Interventions Reaching and Educating Communities Together). A baseline assessment was conducted using a multistaged population-based probability sample from Raleigh and Greensboro, NC. Daily fruit, vegetable and fat intake was evaluated using a modified version of the Block questionnaire, and then stratified results were analyzed by sociodemographic, health and behavior characteristics. STATA Survey commands were used to account for the complex survey design. RESULTS: Overall, a very small number of participants met national recommendations for > or = 2 servings of fruit (8%) and > or = 3 servings of vegetables (16%) per day. Many participants reported eating high-fat foods; the average daily fat intake was 86 g, and the average daily intake from saturated fat was 24 g. People with more education and higher incomes had a higher average daily fruit intake (all p < 0.05). CONCLUSIONS: The data suggest that participants' fruit, vegetable and fat intake deviated greatly from national guidelines; older people, women, participants with higher socioeconomic status and those who were physically active consumed healthier foods. These data may be useful in developing dietary and weight loss interventions for African Americans. PMID:15622690

  5. Mortality in Adults with Moderate to Profound Intellectual Disability: A Population-Based Study

    ERIC Educational Resources Information Center

    Tyrer, F.; Smith, L. K.; McGrother, C. W.

    2007-01-01

    Background: People with intellectual disability (ID) experience a variety of health inequalities compared with the general population including higher mortality rates. This is the first UK population-based study to measure the extent of excess mortality in people with ID compared with the general population. Method: Indirectly standardized…

  6. Issues Concerning Self-Report Data and Population-Based Data Sets Involving People with Intellectual Disabilities

    ERIC Educational Resources Information Center

    Emerson, Eric; Felce, David; Stancliffe, Roger J.

    2013-01-01

    This article examines two methodological issues regarding ways of obtaining and analyzing outcome data for people with intellectual disabilities: (a) self-report and proxy-report data and (b) analysis of population-based data sets. Some people with intellectual disabilities have difficulties with self-reporting due to problems of understanding and…

  7. Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the south-eastern United States and Caribbean Islands.

    PubMed

    Kao, Joyce Y; Zubair, Asif; Salomon, Matthew P; Nuzhdin, Sergey V; Campo, Daniel

    2015-04-01

    Drosophila melanogaster is postulated to have colonized North America in the past several 100 years in two waves. Flies from Europe colonized the east coast United States while flies from Africa inhabited the Caribbean, which if true, make the south-east US and Caribbean Islands a secondary contact zone for African and European D. melanogaster. This scenario has been proposed based on phenotypes and limited genetic data. In our study, we have sequenced individual whole genomes of flies from populations in the south-east US and Caribbean Islands and examined these populations in conjunction with population sequences from the west coast US, Africa, and Europe. We find that west coast US populations are closely related to the European population, likely reflecting a rapid westward expansion upon first settlements into North America. We also find genomic evidence of African and European admixture in south-east US and Caribbean populations, with a clinal pattern of decreasing proportions of African ancestry with higher latitude. Our genomic analysis of D. melanogaster populations from the south-east US and Caribbean Islands provides more evidence for the Caribbean Islands as the source of previously reported novel African alleles found in other east coast US populations. We also find the border between the south-east US and the Caribbean island to be the admixture hot zone where distinctly African-like Caribbean flies become genomically more similar to European-like south-east US flies. Our findings have important implications for previous studies examining the generation of east coast US clines via selection. PMID:25735402

  8. Population pharmacokinetic analysis of blood concentrations of robenacoxib in dogs with osteoarthritis.

    PubMed

    Fink, M; Letellier, I; Peyrou, M; Mochel, J P; Jung, M; King, J N; Gruet, P; Giraudel, J M

    2013-10-01

    The purpose of this analysis was to investigate whether the recommended daily dosage of 1-2mg/kg robenacoxib provides consistent exposure when administered to dogs with chronic osteoarthritis (OA), and the need for dose adjustment in special patient populations. Data from three prospective, multi-center field studies in 208 OA dogs were analyzed using non-linear mixed effects modeling. A model based assessment was performed with stepwise inclusion and exclusion of population characteristics to explain between-subject variability, and assess the according necessity for dose adjustment. Only the influence of bodyweight on both apparent clearance and volume were found to be significant (p<0.01). No significant influence of sex, age and breed, or kidney and liver variables was identified in this representative sample of OA dogs. The population pharmacokinetic analysis performed showed that the 1-2mg/kg dosage chosen provided consistent robenacoxib exposure in a wide range of canine patients. No other dose adjustment seems necessary. PMID:23726662

  9. Population viability analysis as a tool in wildlife conservation policy: With reference to Australia

    NASA Astrophysics Data System (ADS)

    Lindenmayer, David B.; Clark, Tim W.; Lacy, Robert C.; Thomas, Virginia C.

    1993-11-01

    Wildlife conservation policy for endangered species restoration follows a six-phase process. Population viability analysis (PVA) can play a major contributing role in four of these. PVA, as discussed here, is a technique where extinction vulnerabilities of small populations are estimated using computer simulation modeling. The benefits and limitations of using PVA in wildlife decision and policy processes are reviewed based on our direct experience. PVA permits decision makers to set time frames for management, estimate the required magnitude of restoration efforts, identify quantitative targets for species recovery, and select, implement, monitor, and evaluate management strategies. PVA is of greatest value for rare species policy and management. However, a limitation of PVA simulation models is that they are constrained by the amount of biological data available, and such data are difficult to obtain from small populations that are at immediate risk of extinction. These problems may be overcome with improved models and more data. Our experience shows benefits of PVA far outweigh its limitations, and applications of the approach are most useful when integrated with decision analysis and completed within an adaptive management philosophy. PVAs have been carried out for 14 Victorian species and less used elsewhere in Australia. Management and recovery plans are developed from these PVAs. We recommend that PVA be used to guide research programs, develop conservation strategies, and inform decision and policy making for both endangered and nonendangered species because it can significantly improve many aspects of natural resource policy and management.

  10. The Economic Base of Recent Population Growth in Nonmetropolitan Settings.

    ERIC Educational Resources Information Center

    Long, Larry; DeAre, Diana

    In the late 1970s both jobs and population were growing more rapidly outside metropolitan areas. As a group, nonmetropolitan counties not adjacent to a metropolitan area experienced a faster rate of employment growth than metropolitan areas between 1975-79. Even in rural counties (no urban place of 2,500 or more) not adjacent to a metropolitan…

  11. POPULATION-BASED EXPOSURE AND DOSE MODELING FOR AIR POLLUTANTS

    EPA Science Inventory

    This task will address EPA's need to better understand the variability in personal exposure to air pollutants for the purpose of assessing what populations are at risk for adverse health outcomes due to air pollutant exposures. To improve our understanding of exposures to air po...

  12. An Extensive Analysis of Y-Chromosomal Microsatellite Haplotypes in Globally Dispersed Human Populations

    PubMed Central

    Kayser, Manfred; Krawczak, Michael; Excoffier, Laurent; Dieltjes, Patrick; Corach, Daniel; Pascali, Vincente; Gehrig, Christian; Bernini, Luigi F.; Jespersen, Jørgen; Bakker, Egbert; Roewer, Lutz; de Knijff, Peter

    2001-01-01

    The genetic variance at seven Y-chromosomal microsatellite loci (or short tandem repeats [STRs]) was studied among 986 male individuals from 20 globally dispersed human populations. A total of 598 different haplotypes were observed, of which 437 (73.1%) were each found in a single male only. Population-specific haplotype-diversity values were .86–.99. Analyses of haplotype diversity and population-specific haplotypes revealed marked population-structure differences between more-isolated indigenous populations (e.g., Central African Pygmies or Greenland Inuit) and more-admixed populations (e.g., Europeans or Surinamese). Furthermore, male individuals from isolated indigenous populations shared haplotypes mainly with male individuals from their own population. By analysis of molecular variance, we found that 76.8% of the total genetic variance present among these male individuals could be attributed to genetic differences between male individuals who were members of the same population. Haplotype sharing between populations, ΦST statistics, and phylogenetic analysis identified close genetic affinities among European populations and among New Guinean populations. Our data illustrate that Y-chromosomal STR haplotypes are an ideal tool for the study of the genetic affinities between groups of male subjects and for detection of population structure. PMID:11254455

  13. Poppr: an R package for genetic analysis of populations with mixed (clonal/sexual) reproduction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Poppr is an R package for analysis of population genetic data. It extends the adegenet package and provides several novel tools, particularly with regard to analysis of data from admixed, clonal, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid gene...

  14. An Analysis of Communication as a Key Component in Leadership with Diverse School Populations

    ERIC Educational Resources Information Center

    Cagle, Jo E.; Wiley, Sandy T.

    2012-01-01

    "Effective Communication as an Essential Element of Leaders with Diverse School Populations" describes a problem based learning project focused on issues related to practices used by principals to address diverse school populations. The team found that communication between principals and diverse populations in schools was a challenge.…

  15. Genetic structure of wild boar (Sus scrofa) populations from East Asia based on microsatellite loci analyses

    PubMed Central

    2014-01-01

    Background Wild boar, Sus scrofa, is an extant wild ancestor of the domestic pig as an agro-economically important mammal. Wild boar has a worldwide distribution with its geographic origin in Southeast Asia, but genetic diversity and genetic structure of wild boar in East Asia are poorly understood. To characterize the pattern and amount of genetic variation and population structure of wild boar in East Asia, we genotyped and analyzed microsatellite loci for a total of 238 wild boar specimens from ten locations across six countries in East and Southeast Asia. Results Our data indicated that wild boar populations in East Asia are genetically diverse and structured, showing a significant correlation of genetic distance with geographic distance and implying a low level of gene flow at a regional scale. Bayesian-based clustering analysis was indicative of seven inferred genetic clusters in which wild boars in East Asia are geographically structured. The level of genetic diversity was relatively high in wild boars from Southeast Asia, compared with those from Northeast Asia. This gradient pattern of genetic diversity is consistent with an assumed ancestral population of wild boar in Southeast Asia. Genetic evidences from a relationship tree and structure analysis suggest that wild boar in Jeju Island, South Korea have a distinct genetic background from those in mainland Korea. Conclusions Our results reveal a diverse pattern of genetic diversity and the existence of genetic differentiation among wild boar populations inhabiting East Asia. This study highlights the potential contribution of genetic variation of wild boar to the high genetic diversity of local domestic pigs during domestication in East Asia. PMID:25034725

  16. Wavelet-based polarimetry analysis

    NASA Astrophysics Data System (ADS)

    Ezekiel, Soundararajan; Harrity, Kyle; Farag, Waleed; Alford, Mark; Ferris, David; Blasch, Erik

    2014-06-01

    Wavelet transformation has become a cutting edge and promising approach in the field of image and signal processing. A wavelet is a waveform of effectively limited duration that has an average value of zero. Wavelet analysis is done by breaking up the signal into shifted and scaled versions of the original signal. The key advantage of a wavelet is that it is capable of revealing smaller changes, trends, and breakdown points that are not revealed by other techniques such as Fourier analysis. The phenomenon of polarization has been studied for quite some time and is a very useful tool for target detection and tracking. Long Wave Infrared (LWIR) polarization is beneficial for detecting camouflaged objects and is a useful approach when identifying and distinguishing manmade objects from natural clutter. In addition, the Stokes Polarization Parameters, which are calculated from 0°, 45°, 90°, 135° right circular, and left circular intensity measurements, provide spatial orientations of target features and suppress natural features. In this paper, we propose a wavelet-based polarimetry analysis (WPA) method to analyze Long Wave Infrared Polarimetry Imagery to discriminate targets such as dismounts and vehicles from background clutter. These parameters can be used for image thresholding and segmentation. Experimental results show the wavelet-based polarimetry analysis is efficient and can be used in a wide range of applications such as change detection, shape extraction, target recognition, and feature-aided tracking.

  17. Cost-effectiveness of Population Screening for BRCA Mutations in Ashkenazi Jewish Women Compared With Family History–Based Testing

    PubMed Central

    Manchanda, Ranjit; Legood, Rosa; Burnell, Matthew; McGuire, Alistair; Raikou, Maria; Loggenberg, Kelly; Wardle, Jane; Sanderson, Saskia; Gessler, Sue; Side, Lucy; Balogun, Nyala; Desai, Rakshit; Kumar, Ajith; Dorkins, Huw; Wallis, Yvonne; Chapman, Cyril; Taylor, Rohan; Jacobs, Chris; Tomlinson, Ian; Beller, Uziel; Menon, Usha

    2015-01-01

    Background: Population-based testing for BRCA1/2 mutations detects the high proportion of carriers not identified by cancer family history (FH)–based testing. We compared the cost-effectiveness of population-based BRCA testing with the standard FH-based approach in Ashkenazi Jewish (AJ) women. Methods: A decision-analytic model was developed to compare lifetime costs and effects amongst AJ women in the UK of BRCA founder-mutation testing amongst: 1) all women in the population age 30 years or older and 2) just those with a strong FH (≥10% mutation risk). The model assumes that BRCA carriers are offered risk-reducing salpingo-oophorectomy and annual MRI/mammography screening or risk-reducing mastectomy. Model probabilities utilize the Genetic Cancer Prediction through Population Screening trial/published literature to estimate total costs, effects in terms of quality-adjusted life-years (QALYs), cancer incidence, incremental cost-effectiveness ratio (ICER), and population impact. Costs are reported at 2010 prices. Costs/outcomes were discounted at 3.5%. We used deterministic/probabilistic sensitivity analysis (PSA) to evaluate model uncertainty. Results: Compared with FH-based testing, population-screening saved 0.090 more life-years and 0.101 more QALYs resulting in 33 days’ gain in life expectancy. Population screening was found to be cost saving with a baseline-discounted ICER of -£2079/QALY. Population-based screening lowered ovarian and breast cancer incidence by 0.34% and 0.62%. Assuming 71% testing uptake, this leads to 276 fewer ovarian and 508 fewer breast cancer cases. Overall, reduction in treatment costs led to a discounted cost savings of £3.7 million. Deterministic sensitivity analysis and 94% of simulations on PSA (threshold £20000) indicated that population screening is cost-effective, compared with current NHS policy. Conclusion: Population-based screening for BRCA mutations is highly cost-effective compared with an FH-based approach in AJ

  18. Analysis of Complex Allozyme Polymorphisms in a Barley Population

    PubMed Central

    Weir, B. S.; Allard, R. W.; Kahler, A. L.

    1972-01-01

    Genotypes of 68,230 individuals taken from 10 generations (F4–F6, F14–F17, F24–F26) of an experimental population of barley were determined for four esterase loci. The results show that frequencies of gametic ditypes changed significantly over generations and that striking gametic phase disequilibrium developed within a few generations for each of the six pairwise combinations of loci which were monitored. The complex behavior of these four enzyme loci in the population is attributed to interactions between selection and restriction of recombination resulting from the effects of linkage and/or inbreeding. PMID:17248585

  19. Population Uncertainty in Model Ecosystem: Analysis by Stochastic Differential Equation

    NASA Astrophysics Data System (ADS)

    Morita, Satoru; Tainaka, Kei-ichi; Nagata, Hiroyasu; Yoshimura, Jin

    2008-09-01

    Perturbation experiments are carried out by the numerical simulations of a contact process and its mean-field version. Here, the mortality rate increases or decreases suddenly. It is known that fluctuation enhancement (FE) occurs after perturbation, where FE indicates population uncertainty. In the present paper, we develop a new theory of stochastic differential equation. The agreement between the theory and the mean-field simulation is almost perfect. This theory enables us to find a much stronger FE than that reported previously. We discuss the population uncertainty in the recovering process of endangered species.

  20. Anticoagulation and population risk of stroke and death in incident atrial fibrillation: a population-based cohort study

    PubMed Central

    Yu, Amy Y.X.; Malo, Shaun; Wilton, Stephen; Parkash, Ratika; Svenson, Lawrence W.; Hill, Michael D.

    2016-01-01

    Background: Atrial fibrillation increases the risk of stroke and death. Anticoagulation therapy is an effective treatment for stroke prevention, but remains underused in the community. We sought to determine the effectiveness and safety of anticoagulation therapy in an inception cohort with new-onset atrial fibrillation in the province of Alberta, Canada. Methods: We conducted a population-based cohort study of atrial fibrillation using an administrative database from Alberta's publicly funded and universally available health care system. All new-onset atrial fibrillation patients from Jan. 1, 2009, to Dec. 31, 2010, were included in the cohort and followed through Dec. 31, 2013. We assessed anticoagulation status as a predictor of stroke and death using time-to-event analysis and adjusted for sex and CHADS2 (congestive heart failure, hypertension, age ≥ 75 yr, diabetes mellitus and prior stroke or transient ischemic attack) score using Cox proportional hazards modelling. Results: We identified 10 745 patients, 7358 (68.5%) of whom received anticoagulation therapy, principally with warfarin (n = 6997, 95.1%). Anticoagulation therapy was associated with significantly decreased risk of ischemic stroke (hazard ratio [HR] 0.69, 95% confidence interval [CI] 0.58-0.82), all stroke (HR 0.77, 95% CI 0.65-0.91), all stroke and death (HR 0.70, 95% CI 0.62-0.72) and all-cause mortality (HR 0.67, 95% CI 0.62-0.72), despite an association with increased risk of hemorrhagic stroke (HR 1.92, 95% CI 1.17-3.16). There was a neutral association with subdural (HR 1.01, 95% CI 0.53-1.93) and gastrointestinal (HR 0.96, 95% CI 0.70-1.31) hemorrhage. Interpretation: Anticoagulation therapy is effective and safe for stroke prevention and decreases mortality in patients with incident atrial fibrillation. These population data support an aggressive approach to screening for atrial fibrillation and treatment with anticoagulant medicines to prevent stroke and death. PMID:27280108

  1. Population based models of cortical drug response: insights from anaesthesia

    PubMed Central

    Bojak, Ingo; Liley, David T. J.

    2008-01-01

    A great explanatory gap lies between the molecular pharmacology of psychoactive agents and the neurophysiological changes they induce, as recorded by neuroimaging modalities. Causally relating the cellular actions of psychoactive compounds to their influence on population activity is experimentally challenging. Recent developments in the dynamical modelling of neural tissue have attempted to span this explanatory gap between microscopic targets and their macroscopic neurophysiological effects via a range of biologically plausible dynamical models of cortical tissue. Such theoretical models allow exploration of neural dynamics, in particular their modification by drug action. The ability to theoretically bridge scales is due to a biologically plausible averaging of cortical tissue properties. In the resulting macroscopic neural field, individual neurons need not be explicitly represented (as in neural networks). The following paper aims to provide a non-technical introduction to the mean field population modelling of drug action and its recent successes in modelling anaesthesia. PMID:19003456

  2. 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

  3. Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems

    PubMed Central

    Stover, Lori J.; Nair, Niketh S.; Faeder, James R.

    2014-01-01

    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

  4. Friendship-based partner switching promotes cooperation in heterogeneous populations

    NASA Astrophysics Data System (ADS)

    Chen, Wei; Wu, Te; Li, Zhiwu; Wang, Long

    2016-02-01

    The forming of human social ties tends to be with similar individuals. This study concentrates on the emergence of cooperation among heterogeneous populations. A simple model is proposed by considering the impact of interplay between the evolution of strategies and that of social partnerships on cooperation dynamics. Whenever two individuals acquire the rewards by playing prisoner's dilemma game with each other, the friendship (friendship is quantified as the weight of a link) between the two individuals deepens. Individuals can switch off the social ties with the partners who are unfriendly and rewire to similar new ones. Under this partner switching mechanism, population structure is divided into several groups and cooperation can prevail. It is observed that the frequent tendency of partner switching can lead to the enhancement of cooperative behavior under the enormous temptation to defect. Moreover, the influence of discounting the relationship between different individuals is also investigated. Meanwhile, the cooperation prevails when the adjustment of friendships mainly depends on the incomes of selected individuals rather than that of their partners. Finally, it is found that too similar population fail to maximize the cooperation and there exists a moderate similarity that can optimize cooperation.

  5. A population-based approach to study the impact of PROP perception on food liking in populations along the Silk Road.

    PubMed

    Robino, Antonietta; Mezzavilla, Massimo; Pirastu, Nicola; Dognini, Maddalena; Tepper, Beverly J; Gasparini, Paolo

    2014-01-01

    Taste is one of the main factors determining food choices. Differences in PROP bitter taste perception have been implicated in individual differences in food preferences and selection. The present study examined associations between, PROP phenotypes, self-reported food liking and TAS2R38 polymorphisms, the major gene implicated in PROP bitterness, in six different populations of the Caucasus and Central Asia, located along the ancient Silk Road. Differences in the distribution of PROP phenotypes across populations were detected, with a higher frequency of super tasters in Tajikistan (31.3%) and Armenia (39.0%) and a higher frequency of non tasters in Georgia (50.9%). While no relationships were observed between PROP phenotypes and food liking using standard statistical tests, we used an approach based on comparison of distance matrices derived from these data. The first matrix compared the food liking ratings of each population to all others pairwise using the Kruskal-Wallis test (at p<0.00063), and the second one compared the distribution of PROP phenotypes across all populations in a similar manner calculating the chi-square statistic as a distance measure. A strong correlation between the two matrices was found (Mantel test: r = 0.67, p-value = 0.03), suggesting that the pattern of food liking across populations was closely related to the distribution of PROP phenotypes. This same relationship was not observed when TAS2R38 genotypes were substituted for PROP phenotypes in this analysis. Our data suggest that a population-based approach utilizing distance matrices is a useful technique for detecting PROP-related differences in food liking and can be applied to other taste phenotypes. PMID:24626196

  6. A Population-Based Approach to Study the Impact of PROP Perception on Food Liking in Populations along the Silk Road

    PubMed Central

    Robino, Antonietta; Mezzavilla, Massimo; Pirastu, Nicola; Dognini, Maddalena; Tepper, Beverly J.; Gasparini, Paolo

    2014-01-01

    Taste is one of the main factors determining food choices. Differences in PROP bitter taste perception have been implicated in individual differences in food preferences and selection. The present study examined associations between, PROP phenotypes, self-reported food liking and TAS2R38 polymorphisms, the major gene implicated in PROP bitterness, in six different populations of the Caucasus and Central Asia, located along the ancient Silk Road. Differences in the distribution of PROP phenotypes across populations were detected, with a higher frequency of super tasters in Tajikistan (31.3%) and Armenia (39.0%) and a higher frequency of non tasters in Georgia (50.9%). While no relationships were observed between PROP phenotypes and food liking using standard statistical tests, we used an approach based on comparison of distance matrices derived from these data. The first matrix compared the food liking ratings of each population to all others pairwise using the Kruskal-Wallis test (at p<0.00063), and the second one compared the distribution of PROP phenotypes across all populations in a similar manner calculating the chi-square statistic as a distance measure. A strong correlation between the two matrices was found (Mantel test: r = 0.67, p-value = 0.03), suggesting that the pattern of food liking across populations was closely related to the distribution of PROP phenotypes. This same relationship was not observed when TAS2R38 genotypes were substituted for PROP phenotypes in this analysis. Our data suggest that a population-based approach utilizing distance matrices is a useful technique for detecting PROP-related differences in food liking and can be applied to other taste phenotypes. PMID:24626196

  7. Analysis of iris surface features in populations of diverse ancestry

    PubMed Central

    Edwards, Melissa; Cha, David; Krithika, S.; Johnson, Monique; Parra, Esteban J.

    2016-01-01

    There are many textural elements that can be found in the human eye, including Fuchs’ crypts, Wolfflin nodules, pigment spots, contraction furrows and conjunctival melanosis. Although iris surface features have been well-studied in populations of European ancestry, the worldwide distribution of these traits is poorly understood. In this paper, we develop a new method of characterizing iris features from photographs of the iris. We then apply this method to a diverse sample of East Asian, European and South Asian ancestry. All five iris features showed significant differences in frequency between the three populations, indicating that iris features are largely population dependent. Although none of the features were correlated with each other in the East and South Asian groups, Fuchs’ crypts were significantly correlated with contraction furrows and pigment spots and contraction furrows were significantly associated with pigment spots in the European group. The genetic marker SEMA3A rs10235789 was significantly associated with Fuchs’ crypt grade in the European, East Asian and South Asian samples and a borderline association between TRAF3IP1 rs3739070 and contraction furrow grade was found in the European sample. The study of iris surface features in diverse populations may provide valuable information of forensic, biomedical and ophthalmological interest. PMID:26909168

  8. MICROBIAL POPULATION ANALYSIS AS A MEASURE OF ECOSYSTEM RESTORATION

    EPA Science Inventory

    During a controlled oil spill study in a freshwater wetland, four methods were used to track changes in microbial populations in response to in situ remediation treatments, including nutrient amendments and the removal of surface vegetation. Most probable number (MPN) esimates o...

  9. Analysis of iris surface features in populations of diverse ancestry.

    PubMed

    Edwards, Melissa; Cha, David; Krithika, S; Johnson, Monique; Parra, Esteban J

    2016-01-01

    There are many textural elements that can be found in the human eye, including Fuchs' crypts, Wolfflin nodules, pigment spots, contraction furrows and conjunctival melanosis. Although iris surface features have been well-studied in populations of European ancestry, the worldwide distribution of these traits is poorly understood. In this paper, we develop a new method of characterizing iris features from photographs of the iris. We then apply this method to a diverse sample of East Asian, European and South Asian ancestry. All five iris features showed significant differences in frequency between the three populations, indicating that iris features are largely population dependent. Although none of the features were correlated with each other in the East and South Asian groups, Fuchs' crypts were significantly correlated with contraction furrows and pigment spots and contraction furrows were significantly associated with pigment spots in the European group. The genetic marker SEMA3A rs10235789 was significantly associated with Fuchs' crypt grade in the European, East Asian and South Asian samples and a borderline association between TRAF3IP1 rs3739070 and contraction furrow grade was found in the European sample. The study of iris surface features in diverse populations may provide valuable information of forensic, biomedical and ophthalmological interest. PMID:26909168

  10. QTLs analysis of tillers number in F6 sorghum population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The number of tillers in sorghum is an important agronomic trait. In this study, the F6 recombinant inbred lines (RIL) population derived from the cross of sorghum lines T70 with P607 was used to construct a genetic linkage map by simple sequence repeat (SSR) markers. Seven quantitative trait locu...

  11. Models for the analysis of radon-exposed populations.

    PubMed

    Lubin, J H

    1988-01-01

    Radon-222 is a radioactive decay product of radium-226 and uranium-238, which are found throughout the crust of the earth. Studies of underground miners clearly show that exposure to radon and its decay products increases the risk of developing lung cancer. Data on standardized mortality ratios from eight cohort studies indicate that the radon-lung cancer relationship is statistically homogeneous, even though cohorts are from different types of mines and from different countries. Regression methods for cohort data based on a Poisson probability model permit a thorough consideration of risk patterns. In this report, we review these methods, wherein the disease rate in each cell of a multi-way table is modeled as a function of the cross-classifying variables. The National Academy of Sciences' Committee on the Biological Effects of Ionizing Radiation uses the Poisson regression approach to develop a model for age-specific lung cancer risk which depends on cumulative exposure, age at risk, and time since exposure. This model is reviewed and its implications discussed. The most important determinant of lung cancer is cigarette smoking. This paper discusses relative risk models for analysis of joint exposure to radon and tobacco products. The review of available studies suggests that the joint relationship of radon and smoking with lung cancer is consistent with a multiplicative model, but a submultiplicative relationship is most likely. An additive model is rejected. PMID:3051700

  12. Models for the analysis of radon-exposed populations

    SciTech Connect

    Lubin, J.H.

    1988-05-01

    Radon-222 is a radioactive decay product of radium-226 and uranium-238, which are found throughout the crust of the earth. Studies of underground miners clearly show that exposure to radon and its decay products increases the risk of developing lung cancer. Data on standardized mortality ratios from eight cohort studies indicate that the radon-lung cancer relationship is statistically homogeneous, even though cohorts are from different types of mines and from different countries. Regression methods for cohort data based on a Poisson probability model permit a thorough consideration of risk patterns. In this report, we review these methods, wherein the disease rate in each cell of a multi-way table is modeled as a function of the cross-classifying variables. The National Academy of Sciences' Committee on the Biological Effects of Ionizing Radiation uses the Poisson regression approach to develop a model for age-specific lung cancer risk which depends on cumulative exposure, age at risk, and time since exposure. This model is reviewed and its implications discussed. The most important determinant of lung cancer is cigarette smoking. This paper discusses relative risk models for analysis of joint exposure to radon and tobacco products. The review of available studies suggests that the joint relationship of radon and smoking with lung cancer is consistent with a multiplicative model, but a submultiplicative relationship is most likely. An additive model is rejected. 58 references.

  13. Chapter 11. Community analysis-based methods

    SciTech Connect

    Cao, Y.; Wu, C.H.; Andersen, G.L.; Holden, P.A.

    2010-05-01

    Microbial communities are each a composite of populations whose presence and relative abundance in water or other environmental samples are a direct manifestation of environmental conditions, including the introduction of microbe-rich fecal material and factors promoting persistence of the microbes therein. As shown by culture-independent methods, different animal-host fecal microbial communities appear distinctive, suggesting that their community profiles can be used to differentiate fecal samples and to potentially reveal the presence of host fecal material in environmental waters. Cross-comparisons of microbial communities from different hosts also reveal relative abundances of genetic groups that can be used to distinguish sources. In increasing order of their information richness, several community analysis methods hold promise for MST applications: phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), cloning/sequencing, and PhyloChip. Specific case studies involving TRFLP and PhyloChip approaches demonstrate the ability of community-based analyses of contaminated waters to confirm a diagnosis of water quality based on host-specific marker(s). The success of community-based MST for comprehensively confirming fecal sources relies extensively upon using appropriate multivariate statistical approaches. While community-based MST is still under evaluation and development as a primary diagnostic tool, results presented herein demonstrate its promise. Coupled with its inherently comprehensive ability to capture an unprecedented amount of microbiological data that is relevant to water quality, the tools for microbial community analysis are increasingly accessible, and community-based approaches have unparalleled potential for translation into rapid, perhaps real-time, monitoring platforms.

  14. Population viability analysis to identify management priorities for reintroduced elk in the Cumberland Mountains, Tennessee

    USGS Publications Warehouse

    Kindall, J.L.; Muller, L.I.; Clark, J.D.; Lupardus, J.L.; Murrow, J.L.

    2011-01-01

    We used an individual-based population model to perform a viability analysis to simulate population growth (λ) of 167 elk (Cervus elaphus manitobensis; 71 male and 96 female) released in the Cumberland Mountains, Tennessee, to estimate sustainability (i.e., λ > 1.0) and identify the most appropriate options for managing elk restoration. We transported elk from Elk Island National Park, Alberta, Canada, and from Land Between the Lakes, Kentucky, and reintroduced them beginning in December 2000 and ending in February 2003. We estimated annual survival rates for 156 radio-collared elk from December 2000 until November 2004. We used data from a nearby elk herd in Great Smoky Mountains National Park to simulate pessimistic and optimistic recruitment and performed population viability analyses to evaluate sustainability over a 25-year period. Annual survival averaged 0.799 (Total SE = 0.023). The primary identifiable sources of mortality were poaching, disease from meningeal worm (Parelaphostrongylus tenuis), and accidents (environmental causes and unintentional harvest). Population growth given pessimistic recruitment rates averaged 0.895 over 25 years (0.955 in year 1 to 0.880 in year 25); population growth was not sustainable in 100% of the runs. With the most optimistic estimates of recruitment, mean λ increased to 0.967 (1.038 in year 1 to 0.956 in year 25) with 99.6% of the runs failing to be sustainable. We suggest that further translocation efforts to increase herd size will be ineffective unless survival rates are increased in the Cumberland Mountains.

  15. Heterogeneity in ALSFRS-R decline and survival: a population-based study in Italy.

    PubMed

    Mandrioli, Jessica; Biguzzi, Sara; Guidi, Carlo; Sette, Elisabetta; Terlizzi, Emilio; Ravasio, Alessandro; Casmiro, Mario; Salvi, Fabrizio; Liguori, Rocco; Rizzi, Romana; Pietrini, Vladimiro; Borghi, Annamaria; Rinaldi, Rita; Fini, Nicola; Chierici, Elisabetta; Santangelo, Mario; Granieri, Enrico; Mussuto, Vittoria; De Pasqua, Silvia; Georgoulopoulou, Eleni; Fasano, Antonio; Ferro, Salvatore; D'Alessandro, Roberto

    2015-12-01

    Very few studies examined trend over time of the revised Amyotrophic Lateral Sclerosis Functional Rating Scale (ALSFRS-R) and factors influencing it; previous studies, then, included only patients attending tertiary ALS Centres. We studied ALSFRS-R decline, factors influencing this trend and survival in a population-based setting. From 2009 onwards, a prospective registry records all incident ALS cases among residents in Emilia Romagna (population: 4.4 million). For each patient, demographic and clinical details (including ALSFRS-R) are collected by caring physicians at each follow-up. Analysis was performed on 402 incident cases (1279 ALSFRS-R assessments). The average decline of the ALSFRS-R was 0.60 points/month during the first year after diagnosis and 0.34 points/month in the second year. ALSFRS-R decline was heterogeneous among subgroups. Repeated measures mixed model showed that ALSFRS-R score decline was influenced by age at onset (p < 0.01), phenotype (p = 0.01), body mass index (BMI) (p < 0.01), progression rate at diagnosis (ΔFS) (p < 0.01), El Escorial Criteria-Revised (p < 0.01), and FVC% at diagnosis (p < 0.01). Among these factors, at multivariate analysis, only age, site of onset and ΔFS independently influenced survival. In this first population-based study on ALSFRS-R trend, we confirm that ALSFRS-R decline is not homogeneous among ALS patients and during the disease. Factors influencing ALSFRS-R decline may not match with those affecting survival. These disease modifiers should be taken into consideration for trials design and in clinical practice during discussions with patients on prognosis. PMID:26205535

  16. Stochastic multi-scale models of competition within heterogeneous cellular populations: Simulation methods and mean-field analysis.

    PubMed

    Cruz, Roberto de la; Guerrero, Pilar; Spill, Fabian; Alarcón, Tomás

    2016-10-21

    We propose a modelling framework to analyse the stochastic behaviour of heterogeneous, multi-scale cellular populations. We illustrate our methodology with a particular example in which we study a population with an oxygen-regulated proliferation rate. Our formulation is based on an age-dependent stochastic process. Cells within the population are characterised by their age (i.e. time elapsed since they were born). The age-dependent (oxygen-regulated) birth rate is given by a stochastic model of oxygen-dependent cell cycle progression. Once the birth rate is determined, we formulate an age-dependent birth-and-death process, which dictates the time evolution of the cell population. The population is under a feedback loop which controls its steady state size (carrying capacity): cells consume oxygen which in turn fuels cell proliferation. We show that our stochastic model of cell cycle progression allows for heterogeneity within the cell population induced by stochastic effects. Such heterogeneous behaviour is reflected in variations in the proliferation rate. Within this set-up, we have established three main results. First, we have shown that the age to the G1/S transition, which essentially determines the birth rate, exhibits a remarkably simple scaling behaviour. Besides the fact that this simple behaviour emerges from a rather complex model, this allows for a huge simplification of our numerical methodology. A further result is the observation that heterogeneous populations undergo an internal process of quasi-neutral competition. Finally, we investigated the effects of cell-cycle-phase dependent therapies (such as radiation therapy) on heterogeneous populations. In particular, we have studied the case in which the population contains a quiescent sub-population. Our mean-field analysis and numerical simulations confirm that, if the survival fraction of the therapy is too high, rescue of the quiescent population occurs. This gives rise to emergence of resistance

  17. Predictors of Cerebral Palsy in Very Preterm Infants: The EPIPAGE Prospective Population-Based Cohort Study

    ERIC Educational Resources Information Center

    Beaino, Ghada; Khoshnood, Babak; Kaminski, Monique; Pierrat, Veronique; Marret, Stephane; Matis, Jacqueline; Ledesert, Bernard; Thiriez, Gerard; Fresson, Jeanne; Roze, Jean-Christophe; Zupan-Simunek, Veronique; Arnaud, Catherine; Burguet, Antoine; Larroque, Beatrice; Breart, Gerard; Ancel, Pierre-Yves

    2010-01-01

    Aim: The aim of this study was to assess the independent role of cerebral lesions on ultrasound scan, and several other neonatal and obstetric factors, as potential predictors of cerebral palsy (CP) in a large population-based cohort of very preterm infants. Method: As part of EPIPAGE, a population-based prospective cohort study, perinatal data…

  18. Universal Screening for Emotional and Behavioral Problems: Fitting a Population-Based Model

    ERIC Educational Resources Information Center

    Schanding, G. Thomas, Jr.; Nowell, Kerri P.

    2013-01-01

    Schools have begun to adopt a population-based method to conceptualizing assessment and intervention of students; however, little empirical evidence has been gathered to support this shift in service delivery. The present study examined the fit of a population-based model in identifying students' behavioral and emotional functioning using a…

  19. POPULATION AT RISK TO VARIOUS AIR POLLUTION EXPOSURES: DATA BASE 'POPATRISK'

    EPA Science Inventory

    The work reported was undertaken to provide the EPA with a user-oriented data base containing recent county-based information, for all counties in the contiguous United States, on population demographics, population mobility, climatology, emissions, air quality, and age-adjusted ...

  20. Population subdivision and molecular sequence variation: theory and analysis of Drosophila ananassae data.

    PubMed Central

    Vogl, Claus; Das, Aparup; Beaumont, Mark; Mohanty, Sujata; Stephan, Wolfgang

    2003-01-01

    Population subdivision complicates analysis of molecular variation. Even if neutrality is assumed, three evolutionary forces need to be considered: migration, mutation, and drift. Simplification can be achieved by assuming that the process of migration among and drift within subpopulations is occurring fast compared to mutation and drift in the entire population. This allows a two-step approach in the analysis: (i) analysis of population subdivision and (ii) analysis of molecular variation in the migrant pool. We model population subdivision using an infinite island model, where we allow the migration/drift parameter Theta to vary among populations. Thus, central and peripheral populations can be differentiated. For inference of Theta, we use a coalescence approach, implemented via a Markov chain Monte Carlo (MCMC) integration method that allows estimation of allele frequencies in the migrant pool. The second step of this approach (analysis of molecular variation in the migrant pool) uses the estimated allele frequencies in the migrant pool for the study of molecular variation. We apply this method to a Drosophila ananassae sequence data set. We find little indication of isolation by distance, but large differences in the migration parameter among populations. The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center. PMID:14668389

  1. Coarse-grained analysis of stochastically simulated cell populations with a positive feedback genetic network architecture.

    PubMed

    Aviziotis, I G; Kavousanakis, M E; Bitsanis, I A; Boudouvis, A G

    2015-06-01

    Among the different computational approaches modelling the dynamics of isogenic cell populations, discrete stochastic models can describe with sufficient accuracy the evolution of small size populations. However, for a systematic and efficient study of their long-time behaviour over a wide range of parameter values, the performance of solely direct temporal simulations requires significantly high computational time. In addition, when the dynamics of the cell populations exhibit non-trivial bistable behaviour, such an analysis becomes a prohibitive task, since a large ensemble of initial states need to be tested for the quest of possibly co-existing steady state solutions. In this work, we study cell populations which carry the lac operon network exhibiting solution multiplicity over a wide range of extracellular conditions (inducer concentration). By adopting ideas from the so-called "equation-free" methodology, we perform systems-level analysis, which includes numerical tasks such as the computation of coarse steady state solutions, coarse bifurcation analysis, as well as coarse stability analysis. Dynamically stable and unstable macroscopic (population level) steady state solutions are computed by means of bifurcation analysis utilising short bursts of fine-scale simulations, and the range of bistability is determined for different sizes of cell populations. The results are compared with the deterministic cell population balance model, which is valid for large populations, and we demonstrate the increased effect of stochasticity in small size populations with asymmetric partitioning mechanisms. PMID:24929336

  2. Genetic polymorphism of Hucul horse population based on 17 microsatellite loci.

    PubMed

    Fornal, Agnieszka; Radko, Anna; Piestrzyńska-Kajtoch, Agata

    2013-01-01

    Short tandem repeat (STR) loci, i.e. microsatellites are a class of genetic markers commonly used for population studies and parentage control. This study determined the usefulness of microsatellite markers recommended by International Society for Animal Genetics (ISAG) for identification and pedigree analysis in horses based on the example of Polish Hucul horse population (Equus caballus). The set of seventeen microsatellites loci was tested (AHT4, AHT5, ASB2, HMS2, HMS3, HMS6, HMS7, HTG10, HTG4, HTG6, HTG7, VHL20, ASB17, ASB23, CA425, HMS1, LEX3) for 216 individuals. All samples were genotyped and mean number of alleles per locus was estimated (7.00). Means of observed (Ho) and expected (He) heterozygosity were calculated 0.7288 and 0