Sample records for population based analysis

  1. 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

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

    DTIC Science & Technology

    2013-03-01

    TITLE: Image Based Biomarker of Breast Cancer Risk: Analysis of Risk Disparity among Minority Populations PRINCIPAL INVESTIGATOR: Fengshan Liu...SUBTITLE 5a. CONTRACT NUMBER Image Based Biomarker of Breast Cancer Risk: Analysis of Risk Disparity among Minority Populations 5b. GRANT NUMBER...identifying the prevalence of women with incomplete visualization of the breast . We developed a code to estimate the breast cancer risks using the

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

    PubMed Central

    Tawfik, A

    2015-01-01

    Background The prostate-specific antigen (PSA) blood test has become widely used in Canada to test for prostate cancer (PC), the most common cancer among Canadian men. Data suggest that population-based PSA screening may not improve overall survival. Objectives This analysis aimed to review existing economic evaluations of population-based PSA screening, determine current spending on opportunistic PSA screening in Ontario, and estimate the cost of introducing a population-based PSA screening program in the province. Methods A systematic literature search was performed to identify economic evaluations of population-based PSA screening strategies published from 1998 to 2013. Studies were assessed for their methodological quality and applicability to the Ontario setting. An original cost analysis was also performed, using data from Ontario administrative sources and from the published literature. One-year costs were estimated for 4 strategies: no screening, current (opportunistic) screening of men aged 40 years and older, current (opportunistic) screening of men aged 50 to 74 years, and population-based screening of men aged 50 to 74 years. The analysis was conducted from the payer perspective. Results The literature review demonstrated that, overall, population-based PSA screening is costly and cost-ineffective but may be cost-effective in specific populations. Only 1 Canadian study, published 15 years ago, was identified. Approximately $119.2 million is being spent annually on PSA screening of men aged 40 years and older in Ontario, including close to $22 million to screen men younger than 50 and older than 74 years of age (i.e., outside the target age range for a population-based program). A population-based screening program in Ontario would cost approximately $149.4 million in the first year. Limitations Estimates were based on the synthesis of data from a variety of sources, requiring several assumptions and causing uncertainty in the results. For example, where

  4. [Optimum population analysis of Jilin Province, China based on comprehensive carrying capacity.

    PubMed

    Li, Xiu Xia; Meng, Mei

    2017-10-01

    The regional moderate population model was constructed using state-space method, and the weights of relevant factors were obtained using principal component analysis. The optimum population of Jilin Province during 2005-2014 was calculated and the causes for its formation were discussed. The results showed that the optimum population of Jilin Province was in deficit from 2005-2014, and the imbalance existed between the population, resources and environment. The resources carrying population was significantly higher than the economic carrying and the ecological carrying population, indicating that the economic development of Jilin Province was established at the expense of destroying the environment. Moreover, the land resources carrying population was substantially higher than the water and energy carrying population, which was at a deficit, indicating that the economic development of Jilin Province was based on the depletion of energy and water resources. In the future, water resources carrying capacity should be improved according to the local conditions, the energy efficiency should be enhanced via the development of new energy sources, the extensive and consumption-based resource utilization should be transformed to the intensive and low-carbon type, and the production mode and consumption patterns should be changed to protect the ecological environment.

  5. SSR and morphological trait based population structure analysis of 130 diverse flax (Linum usitatissimum L.) accessions.

    PubMed

    Choudhary, Shashi Bhushan; Sharma, Hariom Kumar; Kumar, Arroju Anil; Maruthi, Rangappa Thimmaiah; Mitra, Jiban; Chowdhury, Isholeena; Singh, Binay Kumar; Karmakar, Pran Gobinda

    2017-02-01

    A total of 130 flax accessions of diverse morphotypes and worldwide origin were assessed for genetic diversity and population structure using 11 morphological traits and microsatellite markers (15 gSSRs and 7 EST-SSRs). Analysis performed after classifying these accessions on the basis of plant height, branching pattern, seed size, Indian/foreign origin into six categories called sub-populations viz. fibre type exotic, fibre type indigenous, intermediate type exotic, intermediate type indigenous, linseed type exotic and linseed type indigenous. The study assessed different diversity indices, AMOVA, population structure and included a principal coordinate analysis based on different marker systems. The highest diversity was exhibited by gSSR markers (SI=0.46; He=0.31; P=85.11). AMOVA based on all markers explained significant difference among fibre type, intermediate type and linseed type populations of flax. In terms of variation explained by different markers, EST-SSR markers (12%) better differentiated flax populations compared to morphological (9%) and gSSR (6%) markers at P=0.01. The maximum Nei's unbiased genetic distance (D=0.11) was observed between fibre type and linseed type exotic sub-populations based on EST-SSR markers. The combined structure analysis by using all markers grouped Indian fibre type accessions (63.4%) in a separate cluster along with the Indian intermediate type (48.7%), whereas Indian accessions (82.16%) of linseed type constituted an independent cluster. These findings were supported by the results of the principal coordinate analysis. Morphological markers employed in the study found complementary with microsatellite based markers in deciphering genetic diversity and population structure of the flax germplasm. Copyright © 2016 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

  6. 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.

  7. 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.

  8. Real-time Position Based Population Data Analysis and Visualization Using Heatmap for Hazard Emergency Response

    NASA Astrophysics Data System (ADS)

    Ding, R.; He, T.

    2017-12-01

    With the increased popularity in mobile applications and services, there has been a growing demand for more advanced mobile technologies that utilize real-time Location Based Services (LBS) data to support natural hazard response efforts. Compared to traditional sources like the census bureau that often can only provide historical and static data, an LBS service can provide more current data to drive a real-time natural hazard response system to more accurately process and assess issues such as population density in areas impacted by a hazard. However, manually preparing or preprocessing the data to suit the needs of the particular application would be time-consuming. This research aims to implement a population heatmap visual analytics system based on real-time data for natural disaster emergency management. System comprised of a three-layered architecture, including data collection, data processing, and visual analysis layers. Real-time, location-based data meeting certain polymerization conditions are collected from multiple sources across the Internet, then processed and stored in a cloud-based data store. Parallel computing is utilized to provide fast and accurate access to the pre-processed population data based on criteria such as the disaster event and to generate a location-based population heatmap as well as other types of visual digital outputs using auxiliary analysis tools. At present, a prototype system, which geographically covers the entire region of China and combines population heat map based on data from the Earthquake Catalogs database has been developed. It Preliminary results indicate that the generation of dynamic population density heatmaps based on the prototype system has effectively supported rapid earthquake emergency rescue and evacuation efforts as well as helping responders and decision makers to evaluate and assess earthquake damage. Correlation analyses that were conducted revealed that the aggregation and movement of people

  9. Worry about breast cancer recurrence: a population-based analysis.

    PubMed

    Tewari, Apoorva; Chagpar, Anees B

    2014-07-01

    As more patients with breast cancer survive treatment, the importance of their long-term quality of life is increasing. One important concern for many survivors is fear of recurrence. To better understand worry about recurrence, we conducted a population-based statistical analysis. The National Health Interview Survey (NHIS) is the largest annual source of health information for the U.S. population. We obtained data from the 2010 survey, which asked breast cancer survivors about their fear of recurrence and quality of life. Data were analyzed using SUDAAN software. The 2010 NHIS sample represented 2,668,697 breast cancer survivors. On univariate analysis, worry about recurrence was correlated with current age (P = 0.03) and radiation therapy (P = 0.04). Worry was strongly associated with perceived risk of recurrence (P < 0.01) and decreased overall quality of life (P < 0.01) as well as lower self-reported physical (P < 0.01) and mental (P < 0.01) health and poor satisfaction with social activities and relationships (P < 0.01). On multivariate analysis, worry was not independently associated with decreased quality of life (P = 0.09). However, those who "always worried" about recurrence had a lower quality of life (odds ratio, 0.06; 95% confidence interval, 0.01 to 0.45). Worry about recurrence among breast cancer survivors is associated with age and radiation therapy and is correlated with self-reported physical health, mental health, social relationships, and overall quality of life. It is a significant predictor of decreased quality of life in those who worry the most. Screening for worry about recurrence is an important measure for the improvement of quality of life among breast cancer survivors.

  10. Age distribution and age-related outcomes of olfactory neuroblastoma: a population-based analysis.

    PubMed

    Yin, Zhenzhen; Wang, Youyou; Wu, Yuemei; Zhang, Ximei; Wang, Fengming; Wang, Peiguo; Tao, Zhen; Yuan, Zhiyong

    2018-01-01

    The objective of the study was to describe the age distribution and to evaluate the role of prognostic value of age on survival in patients diagnosed with olfactory neuroblastoma (ONB). A population-based retrospective analysis was conducted. The population-based study of patients in the Surveillance, Epidemiology, and End Results (SEER) tumor registry, who were diagnosed with ONB from 1973 to 2014, were retrospectively analyzed. The cohort included 876 patients with a median age of 54 years. There was a unimodal distribution of age and ONBs most frequently occurred in the fifth to sixth decades of life. Kaplan-Meier analysis demonstrated overall survival (OS) and cancer-specific survival (CSS) rates of 69% and 78% at 5 years. Multivariable Cox regression analysis showed that age, SEER stage, and surgery were independent prognostic factors for CSS. The risk of overall death and cancer-specific death increased 3.1% and 1.6% per year, respectively. Patients aged >60 years presented significantly poor OS and CSS compared with patients aged ≤60 years, even in patients with loco-regional disease or in those treated with surgery. This study highlights the growing evidence that there is a unimodal age distribution of ONB and that age is an important adverse prognostic factor.

  11. 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

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

    USGS Publications Warehouse

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

    2006-01-01

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

  13. Clinical evaluation of a novel population-based regression analysis for detecting glaucomatous visual field progression.

    PubMed

    Kovalska, M P; Bürki, E; Schoetzau, A; Orguel, S F; Orguel, S; Grieshaber, M C

    2011-04-01

    The distinction of real progression from test variability in visual field (VF) series may be based on clinical judgment, on trend analysis based on follow-up of test parameters over time, or on identification of a significant change related to the mean of baseline exams (event analysis). The aim of this study was to compare a new population-based method (Octopus field analysis, OFA) with classic regression analyses and clinical judgment for detecting glaucomatous VF changes. 240 VF series of 240 patients with at least 9 consecutive examinations available were included into this study. They were independently classified by two experienced investigators. The results of such a classification served as a reference for comparison for the following statistical tests: (a) t-test global, (b) r-test global, (c) regression analysis of 10 VF clusters and (d) point-wise linear regression analysis. 32.5 % of the VF series were classified as progressive by the investigators. The sensitivity and specificity were 89.7 % and 92.0 % for r-test, and 73.1 % and 93.8 % for the t-test, respectively. In the point-wise linear regression analysis, the specificity was comparable (89.5 % versus 92 %), but the sensitivity was clearly lower than in the r-test (22.4 % versus 89.7 %) at a significance level of p = 0.01. A regression analysis for the 10 VF clusters showed a markedly higher sensitivity for the r-test (37.7 %) than the t-test (14.1 %) at a similar specificity (88.3 % versus 93.8 %) for a significant trend (p = 0.005). In regard to the cluster distribution, the paracentral clusters and the superior nasal hemifield progressed most frequently. The population-based regression analysis seems to be superior to the trend analysis in detecting VF progression in glaucoma, and may eliminate the drawbacks of the event analysis. Further, it may assist the clinician in the evaluation of VF series and may allow better visualization of the correlation between function and structure owing to VF

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

    PubMed

    Thriskos, P; Zintzaras, E; Germenis, A

    2007-03-01

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

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

    PubMed

    Fujiwara, Masami

    2007-09-01

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

  16. A hospital-based birth weight analysis using computerized perinatal data base for a Chinese population.

    PubMed

    Fu, Jing; Yu, Mei

    2011-04-01

    We aimed to construct birth weight-for-gestational age nomograms based on a computerized perinatal data base in a hospital-based Chinese population. Retrospectively collected 28,052 singleton deliveries at Women and Children's Medical Center, Guangzhou, China. Standard curves of birth weight from 27 to 43 week's gestation were computed. The nomograms included the 5th, 10th, 25th, 50th, 75th, 90th, and 95th percentiles and standard deviations. 79.9% pregnant women delivered between 38, 39, and 40 gestational week, and the mean birth weights are 3160, 3282, and 3388 g, respectively. Preterm birth is 5.7%. In general, male birth weights are greater than females at each gestational week. The hospital-based Chinese population birth weight is lower than that of North American and Scandinavian population. A different standard birth weight is needed for different population. A hospital-based birth weight curve by gestational week is established, which can be a useful tool to estimate intrauterine fetal growth to define SGA or LGA fetuses.

  17. 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

  18. Time-frequency analysis of neuronal populations with instantaneous resolution based on noise-assisted multivariate empirical mode decomposition.

    PubMed

    Alegre-Cortés, J; Soto-Sánchez, C; Pizá, Á G; Albarracín, A L; Farfán, F D; Felice, C J; Fernández, E

    2016-07-15

    Linear analysis has classically provided powerful tools for understanding the behavior of neural populations, but the neuron responses to real-world stimulation are nonlinear under some conditions, and many neuronal components demonstrate strong nonlinear behavior. In spite of this, temporal and frequency dynamics of neural populations to sensory stimulation have been usually analyzed with linear approaches. In this paper, we propose the use of Noise-Assisted Multivariate Empirical Mode Decomposition (NA-MEMD), a data-driven template-free algorithm, plus the Hilbert transform as a suitable tool for analyzing population oscillatory dynamics in a multi-dimensional space with instantaneous frequency (IF) resolution. The proposed approach was able to extract oscillatory information of neurophysiological data of deep vibrissal nerve and visual cortex multiunit recordings that were not evidenced using linear approaches with fixed bases such as the Fourier analysis. Texture discrimination analysis performance was increased when Noise-Assisted Multivariate Empirical Mode plus Hilbert transform was implemented, compared to linear techniques. Cortical oscillatory population activity was analyzed with precise time-frequency resolution. Similarly, NA-MEMD provided increased time-frequency resolution of cortical oscillatory population activity. Noise-Assisted Multivariate Empirical Mode Decomposition plus Hilbert transform is an improved method to analyze neuronal population oscillatory dynamics overcoming linear and stationary assumptions of classical methods. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    USGS Publications Warehouse

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

    2013-01-01

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

  20. Variables associated with olfactory disorders in adults: A U.S. population-based analysis.

    PubMed

    Noel, Julia; Habib, Al-Rahim R; Thamboo, Andrew; Patel, Zara M

    2017-03-01

    Olfactory dysfunction is known to have significant social, psychological, and safety implications. Despite increasingly recognized prevalence, potential risk factors for olfactory loss have been arbitrarily documented and knowledge is limited in scale. The aim of this study is to identify potential demographic and exposure variables correlating with olfactory dysfunction. Cross-sectional analysis of the 2011-2012 and 2013-2014 editions of the National Health Examination and Nutrition Survey was performed. The utilized survey reports from a nationally representative sample of about 5000 persons each year located in counties across the United States. There is an interview and physical examination component which includes demographic, socioeconomic, dietary, and health-related questions as well as medical, dental, physiologic measurements, and laboratory tests. 3594 adult respondents from 2011 to 2012 and 3708 respondents from 2013 to 2014 were identified from the above population-based database. The frequency of self-reported disorders as well as performance on odor identification testing was determined in relation to demographic factors, occupational or environmental exposures, and urinary levels of environmental and industrial compounds. In both subjective and objective analysis, smell disorders were significantly more common with increasing age. While the non-Hispanic Black and non-Hispanic Asian populations were less likely to report subjective olfactory loss, they, along with Hispanics, performed more poorly on odor identification than Caucasians. Those with limited education had a decreased prevalence of hyposmia. Women outperformed men on smell testing. Those reporting exposure to vapors were more likely to experience olfactory dysfunction, and urinary levels of manganese, 2-Thioxothiazolidine-4-carboxylic acid, and 2-Aminothiazoline-4-carboxylic acid were lower among respondents with subjective smell disturbance. In odor detection, elevated serum levels of

  1. Thin-plate spline analysis of the cranial base in African, Asian and European populations and its relationship with different malocclusions.

    PubMed

    Rosas, Antonio; Bastir, Markus; Alarcón, Jose Antonio; Kuroe, Kazuto

    2008-09-01

    To test the hypothesis that midline basicranial orientation and posterior cranial base length are discriminating factors between adults of different populations and its potential maxillo/mandibular disharmonies. Twenty-nine 2D landmarks of the midline cranial base, the face and the mandible of dry skull X-rays from three major populations (45 Asians, 34 Africans, 64 Europeans) were digitized and analysed by geometric morphometrics. We used, first, MANOVA to test for mean shape differences between populations; then, principal components analysis (PCA) to assess the overall variation in the sample and finally, canonical variate analysis (CVA) with jack-knife validations (N=1000) to analyse the anatomical features that best distinguished among populations. Significant mean shapes differences were shown between populations (P<0.001). CVA revealed two significant axes of discrimination (P<0.001). Jack-knife validation correctly identified 92% of 15,000 unknowns. In Africans the whole cranial base is rotated into a forward-downward position, while in Asians it is rotated in the opposite way. The Europeans occupied an intermediate position. African and Asian samples showed a maxillo/mandibular prognathism. African prognathism was produced by an anterior positioned maxilla, Asian prognathism by retruded anterior cranial base and increase of the posterior cranial base length. Europeans showed a trend towards retracted mandibles with relatively shorter posterior cranial bases. The results supported the hypothesis that basicranial orientation and posterior cranial base length are valid factors to distinguish between geographic groups. The whole craniofacial configuration underlying a particular maxillo-facial disharmony must be considered in diagnosis, growth predictions and resulting treatment planning.

  2. An analysis of population-based prenatal screening for overt hypothyroidism.

    PubMed

    Bryant, Stefanie N; Nelson, David B; McIntire, Donald D; Casey, Brian M; Cunningham, F Gary

    2015-10-01

    The purpose of the study was to evaluate pregnancy outcomes of hypothyroidism that were identified in a population-based prenatal screening program. This is a secondary analysis of a prospective prenatal population-based study in which serum thyroid analytes were obtained from November 2000 to April 2003. Initial screening thresholds were intentionally inclusive (thyroid-stimulating hormone [TSH], >3.0 mU/L; free thyroxine, <0.9 ng/dL); those who screened positive were referred for confirmatory testing in a hospital-based laboratory. Hypothyroidism was identified and treated if TSH level was >4.5 mU/L and if fT4 level was <0.76 ng/dL. Perinatal outcomes in these women and those who screened positive but unconfirmed to have hypothyroidism were compared with women with euthyroidism. Outcomes were then analyzed according to initial TSH levels. A total of 26,518 women completed initial screening: 24,584 women (93%) were euthyroid, and 284 women (1%) had abnormal initial values that suggested hypothyroidism. Of those referred, 232 women (82%) underwent repeat testing, and 47 women (0.2% initially screened) were confirmed to have hypothyroidism. Perinatal outcomes of women with treated overt hypothyroidism were similar to women with euthyroidism. Higher rates of pregnancy-related hypertension were identified in the 182 women with unconfirmed hypothyroidism when compared with women with euthyroidism (P < .001); however, this association was seen only in women with initial TSH >4.5 mU/L (adjusted odds ratio, 2.53; 95% confidence interval, 1.4-4.5). The identification and treatment of overt hypothyroidism results in pregnancy outcomes similar to women with euthyroidism. Unconfirmed screening results suggestive of hypothyroidism portend pregnancy risks similar to women with subclinical hypothyroidism, specifically preeclampsia; however, this increased risk was seen only in women with initial TSH levels of >4.5 mU/L and suggests that this is a more clinically relevant

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

    PubMed Central

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

    2016-01-01

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

  4. Computer-aided system of evaluation for population-based all-in-one service screening (CASE-PASS): from study design to outcome analysis with bias adjustment.

    PubMed

    Chen, Li-Sheng; Yen, Amy Ming-Fang; Duffy, Stephen W; Tabar, Laszlo; Lin, Wen-Chou; Chen, Hsiu-Hsi

    2010-10-01

    Population-based routine service screening has gained popularity following an era of randomized controlled trials. The evaluation of these service screening programs is subject to study design, data availability, and the precise data analysis for adjusting bias. We developed a computer-aided system that allows the evaluation of population-based service screening to unify these aspects and facilitate and guide the program assessor to efficiently perform an evaluation. This system underpins two experimental designs: the posttest-only non-equivalent design and the one-group pretest-posttest design and demonstrates the type of data required at both the population and individual levels. Three major analyses were developed that included a cumulative mortality analysis, survival analysis with lead-time adjustment, and self-selection bias adjustment. We used SAS AF software to develop a graphic interface system with a pull-down menu style. We demonstrate the application of this system with data obtained from a Swedish population-based service screen and a population-based randomized controlled trial for the screening of breast, colorectal, and prostate cancer, and one service screening program for cervical cancer with Pap smears. The system provided automated descriptive results based on the various sources of available data and cumulative mortality curves corresponding to the study designs. The comparison of cumulative survival between clinically and screen-detected cases without a lead-time adjustment are also demonstrated. The intention-to-treat and noncompliance analysis with self-selection bias adjustments are also shown to assess the effectiveness of the population-based service screening program. Model validation was composed of a comparison between our adjusted self-selection bias estimates and the empirical results on effectiveness reported in the literature. We demonstrate a computer-aided system allowing the evaluation of population-based service screening

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

    PubMed Central

    2010-01-01

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

  6. Cost-effectiveness and budget impact analysis of a population-based screening program for colorectal cancer.

    PubMed

    Pil, L; Fobelets, M; Putman, K; Trybou, J; Annemans, L

    2016-07-01

    Colorectal cancer (CRC) is one of the leading causes of cancer mortality in Belgium. In Flanders (Belgium), a population-based screening program with a biennial immunochemical faecal occult blood test (iFOBT) in women and men aged 56-74 has been organised since 2013. This study assessed the cost-effectiveness and budget impact of the colorectal population-based screening program in Flanders (Belgium). A health economic model was conducted, consisting of a decision tree simulating the screening process and a Markov model, with a time horizon of 20years, simulating natural progression. Predicted mortality and incidence, total costs, and quality-adjusted life-years (QALYs) with and without the screening program were calculated in order to determine the incremental cost-effectiveness ratio of CRC screening. Deterministic and probabilistic sensitivity analyses were conducted, taking into account uncertainty of the model parameters. Mortality and incidence were predicted to decrease over 20years. The colorectal screening program in Flanders is found to be cost-effective with an ICER of 1681/QALY (95% CI -1317 to 6601) in males and €4,484/QALY (95% CI -3254 to 18,163). The probability of being cost-effective given a threshold of €35,000/QALY was 100% and 97.3%, respectively. The budget impact analysis showed the extra cost for the health care payer to be limited. This health economic analysis has shown that despite the possible adverse effects of screening and the extra costs for the health care payer and the patient, the population-based screening program for CRC in Flanders is cost-effective and should therefore be maintained. Copyright © 2016 European Federation of Internal Medicine. Published by Elsevier B.V. All rights reserved.

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

    PubMed Central

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

    2008-01-01

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

  8. Area-level poverty and preterm birth risk: a population-based multilevel analysis.

    PubMed

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

    2008-09-15

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

  9. Neighborhood social capital is associated with participation in health checks of a general population: a multilevel analysis of a population-based lifestyle intervention- the Inter99 study.

    PubMed

    Bender, Anne Mette; Kawachi, Ichiro; Jørgensen, Torben; Pisinger, Charlotta

    2015-07-22

    Participation in population-based preventive health check has declined over the past decades. More research is needed to determine factors enhancing participation. The objective of this study was to examine the association between two measures of neighborhood level social capital on participation in the health check phase of a population-based lifestyle intervention. The study population comprised 12,568 residents of 73 Danish neighborhoods in the intervention group of a large population-based lifestyle intervention study - the Inter99. Two measures of social capital were applied; informal socializing and voting turnout. In a multilevel analysis only adjusting for age and sex, a higher level of neighborhood social capital was associated with higher probability of participating in the health check. Inclusion of both individual socioeconomic position and neighborhood deprivation in the model attenuated the coefficients for informal socializing, while voting turnout became non-significant. Higher level of neighborhood social capital was associated with higher probability of participating in the health check phase of a population-based lifestyle intervention. Most of the association between neighborhood social capital and participation in preventive health checks can be explained by differences in individual socioeconomic position and level of neighborhood deprivation. Nonetheless, there seems to be some residual association between social capital and health check participation, suggesting that activating social relations in the community may be an avenue for boosting participation rates in population-based health checks. ClinicalTrials.gov (registration no. NCT00289237 ).

  10. Iraqi Population Displacement Analysis

    DTIC Science & Technology

    2016-11-01

    CENTER FOR ARMY ANALYSIS 6001 GOETHALS ROAD FORT BELVOIR, VA 22060-5230 CAA-2015098 IRAQI POPULATION DISPLACEMENT ANALYSIS NOVEMBER 2016...CONTRACT NUMBER Iraqi Population Displacement Analysis PDMC 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER Ms...NOTES 14. ABSTRACT The purpose of this study was to inform CJ34 Civil Military Operations decisions on placement of internally displaced person (IDP

  11. 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.

  12. Population structure and covariate analysis based on pairwise microsatellite allele matching frequencies.

    PubMed

    Givens, Geof H; Ozaksoy, Isin

    2007-01-01

    We describe a general model for pairwise microsatellite allele matching probabilities. The model can be used for analysis of population substructure, and is particularly focused on relating genetic correlation to measurable covariates. The approach is intended for cases when the existence of subpopulations is uncertain and a priori assignment of samples to hypothesized subpopulations is difficult. Such a situation arises, for example, with western Arctic bowhead whales, where genetic samples are available only from a possibly mixed migratory assemblage. We estimate genetic structure associated with spatial, temporal, or other variables that may confound the detection of population structure. In the bowhead case, the model permits detection of genetic patterns associated with a temporally pulsed multi-population assemblage in the annual migration. Hypothesis tests for population substructure and for covariate effects can be carried out using permutation methods. Simulated and real examples illustrate the effectiveness and reliability of the approach and enable comparisons with other familiar approaches. Analysis of the bowhead data finds no evidence for two temporally pulsed subpopulations using the best available data, although a significant pattern found by other researchers using preliminary data is also confirmed here. Code in the R language is available from www.stat.colostate.edu/~geof/gammmp.html.

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

    PubMed

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

    2017-10-03

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

  14. Cost effectiveness of population based BRCA1 founder mutation testing in Sephardi Jewish women.

    PubMed

    Patel, Shreeya; Legood, Rosa; Evans, D Gareth; Turnbull, Clare; Antoniou, Antonis C; Menon, Usha; Jacobs, Ian; Manchanda, Ranjit

    2018-04-01

    Population-based BRCA1/BRCA2 founder-mutation testing has been demonstrated as cost effective compared with family history based testing in Ashkenazi Jewish women. However, only 1 of the 3 Ashkenazi Jewish BRCA1/BRCA2 founder mutations (185delAG[c.68_69delAG]), 5382insC[c.5266dupC]), and 6174delT[c.5946delT]) is found in the Sephardi Jewish population (185delAG[c.68_69delAG]), and the overall prevalence of BRCA mutations in the Sephardi Jewish population is accordingly lower (0.7% compared with 2.5% in the Ashkenazi Jewish population). Cost-effectiveness analyses of BRCA testing have not previously been performed at these lower BRCA prevalence levels seen in the Sephardi Jewish population. Here we present a cost-effectiveness analysis for UK and US populations comparing population testing with clinical criteria/family history-based testing in Sephardi Jewish women. A Markov model was built comparing the lifetime costs and effects of population-based BRCA1 testing, with testing using family history-based clinical criteria in Sephardi Jewish women aged ≥30 years. BRCA1 carriers identified were offered magnetic resonance imaging/mammograms and risk-reducing surgery. Costs are reported at 2015 prices. Outcomes include breast cancer, ovarian cancer, and excess deaths from heart disease. All costs and outcomes are discounted at 3.5%. The time horizon is lifetime, and perspective is payer. The incremental cost-effectiveness ratio per quality-adjusted life-year was calculated. Parameter uncertainty was evaluated through 1-way and probabilistic sensitivity analysis. Population testing resulted in gain in life expectancy of 12 months (quality-adjusted life-year = 1.00). The baseline discounted incremental cost-effectiveness ratio for UK population-based testing was £67.04/quality-adjusted life-year and for US population was $308.42/quality-adjusted life-year. Results were robust in the 1-way sensitivity analysis. The probabilistic sensitivity analysis showed 100% of

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

    PubMed

    Helewa, Ramzi M; Turner, Donna; Wirtzfeld, Debrah; Park, Jason; Hochman, David; Czaykowski, Piotr; Singh, Harminder; Shu, Emma; Xue, Lin; McKay, Andrew

    2013-06-17

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

  16. Population viability analysis for endangered Roanoke logperch

    USGS Publications Warehouse

    Roberts, James H.; Angermeier, Paul; Anderson, Gregory B.

    2016-01-01

    A common strategy for recovering endangered species is ensuring that populations exceed the minimum viable population size (MVP), a demographic benchmark that theoretically ensures low long-term extinction risk. One method of establishing MVP is population viability analysis, a modeling technique that simulates population trajectories and forecasts extinction risk based on a series of biological, environmental, and management assumptions. Such models also help identify key uncertainties that have a large influence on extinction risk. We used stochastic count-based simulation models to explore extinction risk, MVP, and the possible benefits of alternative management strategies in populations of Roanoke logperch Percina rex, an endangered stream fish. Estimates of extinction risk were sensitive to the assumed population growth rate and model type, carrying capacity, and catastrophe regime (frequency and severity of anthropogenic fish kills), whereas demographic augmentation did little to reduce extinction risk. Under density-dependent growth, the estimated MVP for Roanoke logperch ranged from 200 to 4200 individuals, depending on the assumed severity of catastrophes. Thus, depending on the MVP threshold, anywhere from two to all five of the logperch populations we assessed were projected to be viable. Despite this uncertainty, these results help identify populations with the greatest relative extinction risk, as well as management strategies that might reduce this risk the most, such as increasing carrying capacity and reducing fish kills. Better estimates of population growth parameters and catastrophe regimes would facilitate the refinement of MVP and extinction-risk estimates, and they should be a high priority for future research on Roanoke logperch and other imperiled stream-fish species.

  17. Transgender Population Size in the United States: a Meta-Regression of Population-Based Probability Samples

    PubMed Central

    Sevelius, Jae M.

    2017-01-01

    Background. Transgender individuals have a gender identity that differs from the sex they were assigned at birth. The population size of transgender individuals in the United States is not well-known, in part because official records, including the US Census, do not include data on gender identity. Population surveys today more often collect transgender-inclusive gender-identity data, and secular trends in culture and the media have created a somewhat more favorable environment for transgender people. Objectives. To estimate the current population size of transgender individuals in the United States and evaluate any trend over time. Search methods. In June and July 2016, we searched PubMed, Cumulative Index to Nursing and Allied Health Literature, and Web of Science for national surveys, as well as “gray” literature, through an Internet search. We limited the search to 2006 through 2016. Selection criteria. We selected population-based surveys that used probability sampling and included self-reported transgender-identity data. Data collection and analysis. We used random-effects meta-analysis to pool eligible surveys and used meta-regression to address our hypothesis that the transgender population size estimate would increase over time. We used subsample and leave-one-out analysis to assess for bias. Main results. Our meta-regression model, based on 12 surveys covering 2007 to 2015, explained 62.5% of model heterogeneity, with a significant effect for each unit increase in survey year (F = 17.122; df = 1,10; b = 0.026%; P = .002). Extrapolating these results to 2016 suggested a current US population size of 390 adults per 100 000, or almost 1 million adults nationally. This estimate may be more indicative for younger adults, who represented more than 50% of the respondents in our analysis. Authors’ conclusions. Future national surveys are likely to observe higher numbers of transgender people. The large variety in questions used to ask

  18. Genetic analysis of Mexican Criollo cattle populations.

    PubMed

    Ulloa-Arvizu, R; Gayosso-Vázquez, A; Ramos-Kuri, M; Estrada, F J; Montaño, M; Alonso, R A

    2008-10-01

    The objective of this study was to evaluate the genetic structure of Mexican Criollo cattle populations using microsatellite genetic markers. DNA samples were collected from 168 animals from four Mexican Criollo cattle populations, geographically isolated in remote areas of Sierra Madre Occidental (West Highlands). Also were included samples from two breeds with Iberian origin: the fighting bull (n = 24) and the milking central American Criollo (n = 24) and one Asiatic breed: Guzerat (n = 32). Genetic analysis consisted of the estimation of the genetic diversity in each population by the allele number and the average expected heterozygosity found in nine microsatellite loci. Furthermore, genetic relationships among the populations were defined by their genetic distances. Our data shows that Mexican cattle populations have a relatively high level of genetic diversity based either on the mean number of alleles (10.2-13.6) and on the expected heterozygosity (0.71-0.85). The degree of observed homozygosity within the Criollo populations was remarkable and probably caused by inbreeding (reduced effective population size) possibly due to reproductive structure within populations. Our data shows that considerable genetic differentiation has been occurred among the Criollo cattle populations in different regions of Mexico.

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

    PubMed

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

    2007-07-01

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

  20. Assessment of diversity among populations of Rauvolfia serpentina Benth. Ex. Kurtz. from Southern Western Ghats of India, based on chemical profiling, horticultural traits and RAPD analysis.

    PubMed

    Nair, Vadakkemuriyil Divya; Raj, Rajan Pillai Dinesh; Panneerselvam, Rajaram; Gopi, Ragupathi

    2014-01-01

    Genetic, morphological and chemical variations of ten natural populations of Rauvolfia serpentina Benth. Ex. Kurtz. from Southern Western Ghats of India were assessed using RAPD markers reserpine content and morphological traits. An estimate of genetic diversity and differentiation between genotypes of breeding germplasm is of key importance for its improvement. Populations were collected from different geographical regions. Data obtained through three different methods were compared and the correlation among them was estimated. Statistical analysis showed significant differences for all horticultural characteristics among the accessions suggesting that selection for relevant characteristics could be possible. Variation in the content of Reserpine ranges from 0.192 g/100 g (population from Tusharagiri) to 1.312 g/100 g (population from Aryankavu). A high diversity within population and high genetic differentiation among them based on RAPDs were revealed caused both by habitat fragmentation of the low size of most populations and the low level of gene flow among them. The UPGMA dendrogram and PCA analysis based on reserpine content yielded higher separation among populations indicated specific adaptation of populations into clusters each of them including populations closed to their geographical origin. Genetic, chemical and morphological data were correlated based on Mantel test. Given the high differentiation among populations conservation strategies should take into account genetic diversity and chemical variation levels in relation to bioclimatic and geographic location of populations. Our results also indicate that RAPD approach along with horticultural analysis seemed to be best suited for assessing with high accuracy the genetic relationships among distinct R. serpentina accessions. © 2013.

  1. 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. Published by Elsevier Ltd.

  2. Central nervous system infections and stroke -- a population-based analysis.

    PubMed

    Chien, L-N; Chi, N-F; Hu, C-J; Chiou, H-Y

    2013-10-01

    Chronic central nervous system (CNS) infections have been found to associate with cerebrovascular complications. Acute CNS infections are more common than chronic CNS infections, but whether they could increase the risk of vascular diseases has not been studied. The study cohort comprised all adult patients with diagnoses of CNS infections from Taiwan National Health Insurance Research Database during 2000-2009 (n = 533). The comparison group were matched by age, sex, urbanization, diagnostic year, and vascular risk factors of cases (cases and controls = 1:5). Patients were tracked for at least 1 year. Kaplan-Meier analysis was used to compare the risk of stroke and acute myocardial infarction (AMI) after adjusting censoring subjects. After adjusting the patients demographic characteristics and comorbidities, the risk of patients with CNS infections developing stroke was 2.75-3.44 times greater than their comparison group. More than 70% of the stroke events were occurring within 1 year after CNS infections. The risk of AMI was not found as we compared patients with and without CNS infections. The population-based cohort study suggested that adult patients with CNS infections have higher risk to develop stroke but not AMI, and the risk is marked within a year after infections. © 2013 John Wiley & Sons A/S.

  3. Cost-effectiveness of population based BRCA testing with varying Ashkenazi Jewish ancestry.

    PubMed

    Manchanda, Ranjit; Patel, Shreeya; Antoniou, Antonis C; Levy-Lahad, Ephrat; Turnbull, Clare; Evans, D Gareth; Hopper, John L; Macinnis, Robert J; Menon, Usha; Jacobs, Ian; Legood, Rosa

    2017-11-01

    Population-based BRCA1/BRCA2 testing has been found to be cost-effective compared with family history-based testing in Ashkenazi-Jewish women were >30 years old with 4 Ashkenazi-Jewish grandparents. However, individuals may have 1, 2, or 3 Ashkenazi-Jewish grandparents, and cost-effectiveness data are lacking at these lower BRCA prevalence estimates. We present an updated cost-effectiveness analysis of population BRCA1/BRCA2 testing for women with 1, 2, and 3 Ashkenazi-Jewish grandparents. Decision analysis model. Lifetime costs and effects of population and family history-based testing were compared with the use of a decision analysis model. 56% BRCA carriers are missed by family history criteria alone. Analyses were conducted for United Kingdom and United States populations. Model parameters were obtained from the Genetic Cancer Prediction through Population Screening trial and published literature. Model parameters and BRCA population prevalence for individuals with 3, 2, or 1 Ashkenazi-Jewish grandparent were adjusted for the relative frequency of BRCA mutations in the Ashkenazi-Jewish and general populations. Incremental cost-effectiveness ratios were calculated for all Ashkenazi-Jewish grandparent scenarios. Costs, along with outcomes, were discounted at 3.5%. The time horizon of the analysis is "life-time," and perspective is "payer." Probabilistic sensitivity analysis evaluated model uncertainty. Population testing for BRCA mutations is cost-saving in Ashkenazi-Jewish women with 2, 3, or 4 grandparents (22-33 days life-gained) in the United Kingdom and 1, 2, 3, or 4 grandparents (12-26 days life-gained) in the United States populations, respectively. It is also extremely cost-effective in women in the United Kingdom with just 1 Ashkenazi-Jewish grandparent with an incremental cost-effectiveness ratio of £863 per quality-adjusted life-years and 15 days life gained. Results show that population-testing remains cost-effective at the £20,000-30000 per quality

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

    PubMed Central

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

    2014-01-01

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

  5. Associations of Urinary Cotinine-Verified Active and Passive Smoking with Thyroid Function: Analysis of Population-Based Nationally Representative Data.

    PubMed

    Kang, Jihun; Kong, Eunhee; Choi, Jongsoon

    2018-05-01

    The effects of active and passive smoking on thyroid function in the Korean population have not been determined. Furthermore, related research is based on self-reported smoking status, which may be inaccurate, especially among women. The present study aimed at evaluating the association between biochemically verified smoking status and thyroid function in a nationally representative Korean population. This population-based cross-sectional study included 3404 subjects without thyroid disease who were not taking thyroid medication. Smoking status was identified using self-reported data and urinary cotinine levels. Kruskal-Wallis and Jonckheere-Terpstra trend tests were performed to evaluate the association between smoking exposure and thyroid function. Multivariate logistic regression analysis was used to estimate the effect of smoking on subclinical hypothyroidism (SCH). Biochemically verified active and passive smoking rates were 43.4% and 23.3% among men and 10.0% and 22.9% among women, respectively. Active smokers had significantly lower iodine levels than passive smokers and nonsmokers. Active smoking was associated with decreased serum thyrotropin (TSH) levels among both sexes, although only men exhibited a dose-response relationship between increasing smoking exposure and decreasing TSH levels. Passive smoking slightly decreased TSH levels, but the decrease was not statistically significant. The risk of SCH decreased with increasing smoking exposure in the multivariate-adjusted analysis (p for trend = 0.027 among men and 0.042 among women). Active and passive smoking were associated with decreasing serum TSH levels and a lower risk of SCH in a Korean population. These associations might be related to lower urinary iodine levels in active smokers.

  6. Population-based contracting (population health): part II.

    PubMed

    Jacofsky, D J

    2017-11-01

    Modern healthcare contracting is shifting the responsibility for improving quality, enhancing community health and controlling the total cost of care for patient populations from payers to providers. Population-based contracting involves capitated risk taken across an entire population, such that any included services within the contract are paid for by the risk-bearing entity throughout the term of the agreement. Under such contracts, a risk-bearing entity, which may be a provider group, a hospital or another payer, administers the contract and assumes risk for contractually defined services. These contracts can be structured in various ways, from professional fee capitation to full global per member per month diagnosis-based risk. The entity contracting with the payer must have downstream network contracts to provide the care and facilities that it has agreed to provide. Population health is a very powerful model to reduce waste and costs. It requires a deep understanding of the nuances of such contracting and the appropriate infrastructure to manage both networks and risk. Cite this article: Bone Joint J 2017;99-B:1431-4. ©2017 The British Editorial Society of Bone & Joint Surgery.

  7. 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.

  8. Budget impact analysis of switching to digital mammography in a population-based breast cancer screening program: a discrete event simulation model.

    PubMed

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

    2014-01-01

    To assess the budgetary impact of switching from screen-film mammography to full-field digital mammography in a population-based breast cancer screening program. 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. 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. 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.

  9. 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

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

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

    Tjong, Harianto; Li, Wenyuan; Kalhor, Reza

    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. Here, 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 themore » 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.« less

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

    DOE PAGES

    Tjong, Harianto; Li, Wenyuan; Kalhor, Reza; ...

    2016-03-07

    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. Here, 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 themore » 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.« less

  12. Population-based analysis of Alzheimer's disease risk alleles implicates genetic interactions.

    PubMed

    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

    2014-05-01

    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 nonadditive interactions on LOAD status prediction performance. 2419 samples from the Cache County Memory Study were genotyped for APOE and nine LOAD risk loci from AlzGene.org. We used logistic regression and receiver operator characteristic analysis to assess the LOAD status prediction performance of these loci using additive and nonadditive models and compared odds ratios and PAFs between AlzGene.org and Cache County. Odds ratios were comparable between Cache County and AlzGene.org when identical single nucleotide polymorphisms were genotyped. PAFs from AlzGene.org ranged from 2.25% to 37%; those from Cache County ranged from .05% to 20%. Including non-APOE alleles significantly improved LOAD status prediction performance (area under the curve = .80) over APOE alone (area under the curve = .78) when not constrained to an additive relationship (p < .03). We identified potential allelic interactions (p values uncorrected): CD33-MS4A4E (synergy factor = 5.31; p < .003) and CLU-MS4A4E (synergy factor = 3.81; p < .016). Although nonadditive 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. Copyright © 2014 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  13. [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.

  14. 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

  15. Contrasting results from molecular and pedigree-based population diversity measures in captive zebra highlight challenges facing genetic management of zoo populations.

    PubMed

    Ito, Hideyuki; Ogden, Rob; Langenhorst, Tanya; Inoue-Murayama, Miho

    2017-01-01

    Zoo conservation breeding programs manage the retention of population genetic diversity through analysis of pedigree records. The range of demographic and genetic indices determined through pedigree analysis programs allows the conservation of diversity to be monitored relative to the particular founder population for a species. Such approaches are based on a number of well-documented founder assumptions, however without knowledge of actual molecular genetic diversity there is a risk that pedigree-based measures will be misinterpreted and population genetic diversity misunderstood. We examined the genetic diversity of the captive populations of Grevy's zebra, Hartmann's mountain zebra and plains zebra in Japan and the United Kingdom through analysis of mitochondrial DNA sequences. Very low nucleotide variability was observed in Grevy's zebra. The results were evaluated with respect to current and historic diversity in the wild, and indicate that low genetic diversity in the captive population is likely a result of low founder diversity, which in turn suggests relatively low wild genetic diversity prior to recent population declines. Comparison of molecular genetic diversity measures with analogous diversity indices generated from the studbook data for Grevy's zebra and Hartmann's mountain zebra show contrasting patterns, with Grevy's zebra displaying markedly less molecular diversity than mountain zebra, despite studbook analysis indicating that the Grevy's zebra population has substantially more founders, greater effective population size, lower mean kinship, and has suffered less loss of gene diversity. These findings emphasize the need to validate theoretical estimates of genetic diversity in captive breeding programs with empirical molecular genetic data. Zoo Biol. 36:87-94, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  16. Population Viability Analysis of Riverine Fishes

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

    Bates, P.; Chandler, J.; Jager, H.I.

    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 tomore » 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).« less

  17. 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

  18. 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,…

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

    PubMed

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

    2015-11-01

    Cyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time-consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping-by-sequencing and Pool-Seq. This method yielded thousands of SNPs and allowed us to study the relationships between populations of different origins or pathotypes. Validation of the method on well-characterized populations also demonstrated that it was a powerful and accurate tool for population genetics. The genomewide allele frequencies of 23 populations of golden nematode, from nine countries and representing the five known pathotypes, were compared. A clear separation of the pathotypes and fine genetic relationships between and among global populations were obtained using this method. In addition to being powerful, this tool has proven to be very time- and cost-efficient and could be applied to other cyst nematode species. © 2015 Her Majesty the Queen in Right of Canada Molecular Ecology Resources © 2015 John Wiley & Sons Ltd Reproduced with the permission of the Minister of Agriculture and Agri-food.

  20. Subphenotypes of mild-to-moderate COPD by factor and cluster analysis of pulmonary function, CT imaging and breathomics in a population-based survey.

    PubMed

    Fens, Niki; van Rossum, Annelot G J; Zanen, Pieter; van Ginneken, Bram; van Klaveren, Rob J; Zwinderman, Aeilko H; Sterk, Peter J

    2013-06-01

    Classification of COPD is currently based on the presence and severity of airways obstruction. However, this may not fully reflect the phenotypic heterogeneity of COPD in the (ex-) smoking community. We hypothesized that factor analysis followed by cluster analysis of functional, clinical, radiological and exhaled breath metabolomic features identifies subphenotypes of COPD in a community-based population of heavy (ex-) smokers. Adults between 50-75 years with a smoking history of at least 15 pack-years derived from a random population-based survey as part of the NELSON study underwent detailed assessment of pulmonary function, chest CT scanning, questionnaires and exhaled breath molecular profiling using an electronic nose. Factor and cluster analyses were performed on the subgroup of subjects fulfilling the GOLD criteria for COPD (post-BD FEV1/FVC < 0.70). Three hundred subjects were recruited, of which 157 fulfilled the criteria for COPD and were included in the factor and cluster analysis. Four clusters were identified: cluster 1 (n = 35; 22%): mild COPD, limited symptoms and good quality of life. Cluster 2 (n = 48; 31%): low lung function, combined emphysema and chronic bronchitis and a distinct breath molecular profile. Cluster 3 (n = 60; 38%): emphysema predominant COPD with preserved lung function. Cluster 4 (n = 14; 9%): highly symptomatic COPD with mildly impaired lung function. In a leave-one-out validation analysis an accuracy of 97.4% was reached. This unbiased taxonomy for mild to moderate COPD reinforces clusters found in previous studies and thereby allows better phenotyping of COPD in the general (ex-) smoking population.

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

    PubMed

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

    2016-01-01

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

  2. 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.

  3. 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

  4. Associations of all-cause mortality with census-based neighbourhood deprivation and population density in Japan: a multilevel survival analysis.

    PubMed

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

    2014-01-01

    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. 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. 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. 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 deprived neighbourhoods.

  5. 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

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

    PubMed

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

    2015-10-19

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

  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. Physiogenomic analysis of the Puerto Rican population.

    PubMed

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

    2009-04-01

    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. 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. 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. 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.

  9. 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

  10. Population-level analysis and validation of an individual-based cutthroat trout model

    Treesearch

    Steven F. Railsback; Bret C. Harvey; Roland H. Lamberson; Derek E. Lee; Claasen Nathan J.; Shuzo Yoshihara

    2002-01-01

    Abstract - An individual-based model of stream trout is analyzed by testing its ability to reproduce patterns of population-level behavior observed in real trout: (1) "self-thinning," a negative power relation between weight and abundance; (2) a "critical period" of density-dependent mortality in young-of-the-year; (3) high and age-speci...

  11. Lower urinary tract symptoms and urinary incontinence in a geriatric cohort - a population-based analysis.

    PubMed

    Wehrberger, Clemens; Madersbacher, Stephan; Jungwirth, Susanne; Fischer, Peter; Tragl, Karl-Heinz

    2012-11-01

    To assess prevalence and severity of lower urinary tract function in 85-year-old men and women. Little is known on the prevalence of lower urinary tract dysfunction in this geriatric age group, which is now the fastest growing sector of the population worldwide. The Vienna Trans-Danube Aging study (VITA) is a longitudinal, population-based study initiated in 2000 that included men/women aged 75 years living in a well-defined area in Vienna. The main purpose of the VITA study was to identify risk factors for incident Alzheimer's disease. All study participants alive in 2010 were contacted by mail to complete a detailed questionnaire on various aspects of lower urinary tract symptoms (LUTS) and urinary incontinence (UI). The response rate was 68%, resulting in a total of 262 questionnaires available for analysis (men n= 96; women n= 166). All study participants were 85 years of age. Urinary incontinence defined as any involuntary loss during the past 4 weeks was reported by 24% of men and 35% of women (P= 0.04). Stress UI was more frequent in women (39%) than in men (14%, P < 0.01), the difference for urge UI (women 35%, men 25%) was on the border of statistical significance (P= 0.05). Only four individuals (1.5%) needed permanent catheterization. Urgency (women 56%, men 54%) and daytime frequency (women 70%, men 74%) were equally distributed (P > 0.05). Nocturia more often than twice was more prevalent in men (69%) than in women (49%) (P= 0.02). Overactive bladder, according to International Continence Society criteria, was present in 55% of women and 50% of men. No difference regarding quality of life impairment as the result of LUTS and UI was noticed between sexes. A few co-morbidities were identified to correlate with UI and storage symptoms. These data provide insights into the prevalence and severity of LUTS and UI in individuals in their eighties, to our knowledge the largest population-based study in this age group. Demographic changes in upcoming decades

  12. CNV analysis in the Lithuanian population.

    PubMed

    Urnikyte, A; Domarkiene, I; Stoma, S; Ambrozaityte, L; Uktveryte, I; Meskiene, R; Kasiulevičius, V; Burokiene, N; Kučinskas, V

    2016-05-04

    Although copy number variation (CNV) has received much attention, knowledge about the characteristics of CNVs such as occurrence rate and distribution in the genome between populations and within the same population is still insufficient. In this study, Illumina 770 K HumanOmniExpress-12 v1.0 (and v1.1) arrays were used to examine the diversity and distribution of CNVs in 286 unrelated individuals from the two main ethnolinguistic groups of the Lithuanian population (Aukštaičiai and Žemaičiai) (see Additional file 3). For primary data analysis, the Illumina GenomeStudio™ Genotyping Module v1.9 and two algorithms, cnvPartition 3.2.0 and QuantiSNP 2.0, were used to identify high-confidence CNVs. A total of 478 autosomal CNVs were detected by both algorithms, and those were clustered in 87 copy number variation regions (CNVRs), spanning ~12.5 Mb of the genome (see Table 1). At least 8.6 % of the CNVRs were unique and had not been reported in the Database of Genomic Variants. Most CNVRs (57.5 %) were rare, with a frequency of <1 %, whereas common CNVRs with at least 5 % frequency made up only 1.1 % of all CNVRs identified. About 49 % of non-singleton CNVRs were shared between Aukštaičiai and Žemaičiai, and the remaining CNVRs were specific to each group. Many of the CNVs detected (66 %) overlapped with known UCSC gene regions. The ethnolinguistic groups of the Lithuanian population could not be differentiated based on CNV profiles, which may reflect their geographical proximity and suggest the homogeneity of the Lithuanian population. In addition, putative novel CNVs unique to the Lithuanian population were identified. The results of our study enhance the CNV map of the Lithuanian population.

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

    PubMed

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

    2012-06-01

    The notoriously multi-resistant Staphylococcus haemolyticus is an emerging pathogen causing serious infections in immunocompromised patients. Defining the population structure is important to detect outbreaks and spread of antimicrobial resistant clones. Currently, the standard typing technique is pulsed-field gel electrophoresis (PFGE). In this study we describe novel molecular typing schemes for S. haemolyticus using multi locus sequence typing (MLST) and multi locus variable number of tandem repeats (VNTR) analysis. Seven housekeeping genes (MLST) and five VNTR loci (MLVF) were selected for the novel typing schemes. A panel of 45 human and veterinary S. haemolyticus isolates was investigated. The collection had diverse PFGE patterns (38 PFGE types) and was sampled over a 20 year-period from eight countries. MLST resolved 17 sequence types (Simpsons index of diversity [SID]=0.877) and MLVF resolved 14 repeat types (SID=0.831). We found a low sequence diversity. Phylogenetic analysis clustered the isolates in three (MLST) and one (MLVF) clonal complexes, respectively. Taken together, neither the MLST nor the MLVF scheme was suitable to resolve the population structure of this S. haemolyticus collection. Future MLVF and MLST schemes will benefit from addition of more variable core genome sequences identified by comparing different fully sequenced S. haemolyticus genomes. Copyright © 2012 Elsevier B.V. All rights reserved.

  14. Evidence for Association of the E23K Variant of KCNJ11 Gene with Type 2 Diabetes in Tunisian Population: Population-Based Study and Meta-Analysis

    PubMed Central

    Lasram, Khaled; Ben Halim, Nizar; Hsouna, Sana; Kefi, Rym; Arfa, Imen; Ghazouani, Welid; Jamoussi, Henda; Benrahma, Houda; Kharrat, Najla; Rebai, Ahmed; Ben Ammar, Slim; Bahri, Sonia; Barakat, Abdelhamid; Abid, Abdelmajid; Abdelhak, Sonia

    2014-01-01

    Aims. Genetic association studies have reported the E23K variant of KCNJ11 gene to be associated with Type 2 diabetes. In Arab populations, only four studies have investigated the role of this variant. We aimed to replicate and validate the association between the E23K variant and Type 2 diabetes in Tunisian and Arab populations. Methods. We have performed a case-control association study including 250 Tunisian patients with Type 2 diabetes and 267 controls. Allelic association has also been evaluated by 2 meta-analyses including all population-based studies among Tunisians and Arabs (2 and 5 populations, resp.). Results. A significant association between the E23K variant and Type 2 diabetes was found (OR = 1.6, 95% CI = 1.14–2.27, and P = 0.007). Furthermore, our meta-analysis has confirmed the significant role of the E23K variant in susceptibility of Type 2 diabetes in Tunisian and Arab populations (OR = 1.29, 95% CI = 1.15–1.46, and P < 10−3 and OR = 1.33, 95% CI = 1.13–1.56, and P = 0.001, resp.). Conclusion. Both case-control and meta-analyses results revealed the significant association between the E23K variant of KCNJ11 and Type 2 diabetes among Tunisians and Arabs. PMID:25165692

  15. A GWAS meta-analysis from 5 population-based cohorts implicates ion channel genes in the pathogenesis of irritable bowel syndrome.

    PubMed

    Bonfiglio, F; Henström, M; Nag, A; Hadizadeh, F; Zheng, T; Cenit, M C; Tigchelaar, E; Williams, F; Reznichenko, A; Ek, W E; Rivera, N V; Homuth, G; Aghdassi, A A; Kacprowski, T; Männikkö, M; Karhunen, V; Bujanda, L; Rafter, J; Wijmenga, C; Ronkainen, J; Hysi, P; Zhernakova, A; D'Amato, M

    2018-04-19

    Irritable bowel syndrome (IBS) shows genetic predisposition, however, large-scale, powered gene mapping studies are lacking. We sought to exploit existing genetic (genotype) and epidemiological (questionnaire) data from a series of population-based cohorts for IBS genome-wide association studies (GWAS) and their meta-analysis. Based on questionnaire data compatible with Rome III Criteria, we identified a total of 1335 IBS cases and 9768 asymptomatic individuals from 5 independent European genotyped cohorts. Individual GWAS were carried out with sex-adjusted logistic regression under an additive model, followed by meta-analysis using the inverse variance method. Functional annotation of significant results was obtained via a computational pipeline exploiting ontology and interaction networks, and tissue-specific and gene set enrichment analyses. Suggestive GWAS signals (P ≤ 5.0 × 10 -6 ) were detected for 7 genomic regions, harboring 64 gene candidates to affect IBS risk via functional or expression changes. Functional annotation of this gene set convincingly (best FDR-corrected P = 3.1 × 10 -10 ) highlighted regulation of ion channel activity as the most plausible pathway affecting IBS risk. Our results confirm the feasibility of population-based studies for gene-discovery efforts in IBS, identify risk genes and loci to be prioritized in independent follow-ups, and pinpoint ion channels as important players and potential therapeutic targets warranting further investigation. © 2018 John Wiley & Sons Ltd.

  16. Simultaneous pharmacogenetics-based population pharmacokinetic analysis of darunavir and ritonavir in HIV-infected patients.

    PubMed

    Moltó, José; Xinarianos, George; Miranda, Cristina; Pushpakom, Sudeep; Cedeño, Samandhy; Clotet, Bonaventura; Owen, Andrew; Valle, Marta

    2013-07-01

    Darunavir is a potent protease inhibitor of HIV. To enhance its pharmacokinetic profile, darunavir must be co-administered with ritonavir. There is wide inter-patient variability in darunavir pharmacokinetics among HIV-infected individuals, however. Darunavir is a known substrate for influx transporters, such as the 1A2 and the 1B1 members of the solute carrier organic anion transporter family (SLCO1A2, SLCO1B1), as well as for efflux transporters such as the multi-drug resistance protein 1 (MRP1). The aim of this study was to develop a semi-mechanistic population pharmacokinetic model for darunavir and ritonavir administered in HIV-infected adults. The desired model would incorporate patient characteristics and pharmacogenetic data contributing to variability in drug concentrations and also take into account the interaction between the two compounds. A population pharmacokinetic analysis was performed with 705 plasma samples from 75 Caucasian individuals receiving darunavir/ritonavir (600/100 mg twice daily) for at least 4 weeks. At least one full pharmacokinetic profile was obtained for each participant, and darunavir and ritonavir concentrations in plasma were determined by high performance liquid chromatography. Genotyping for 148 polymorphisms in genes coding for transporters or metabolizing enzymes was conducted by two methods: MALDI-TOF mass spectrometry and real-time polymerase chain reaction-based allelic discrimination. A population pharmacokinetic model was developed for darunavir and for ritonavir. The effect of single nucleotide polymorphisms on the post hoc individual pharmacokinetic parameters was first explored using graphic methods and regression analysis. Those covariates related to changes in darunavir or ritonavir pharmacokinetic parameters were then further evaluated using non-linear mixed effects modeling (NONMEM version VII). Darunavir and ritonavir pharmacokinetics were best described by a two- and one-compartment model, respectively, both

  17. Suicide among nursing home residents in Australia: A national population-based retrospective analysis of medico-legal death investigation information.

    PubMed

    Murphy, Briony J; Bugeja, Lyndal C; Pilgrim, Jennifer L; Ibrahim, Joseph E

    2018-05-01

    Suicide among nursing home residents is a growing public health concern, currently lacking in empirical research. This study aims to describe the frequency and nature of suicide among nursing home residents in Australia. This research comprised a national population-based retrospective analysis of suicide deaths among nursing home residents in Australia reported to the Coroner between July 2000 and December 2013. Cases were identified using the National Coronial Information System, and data collected from paper-based coroners' records on individual, incident, and organizational factors, as well as details of the medico-legal death investigation. Data analysis comprised univariate and bivariate descriptive statistical techniques; ecological analysis of incidence rates using population denominators; and comparison of age and sex of suicide cases to deaths from other causes using logistic regression. The study identified 141 suicides among nursing home residents, occurring at a rate of 0.02 deaths per 100 000 resident bed days. The ratio of deaths from suicide to deaths from any other cause was higher in males than females (OR = 3.56, 95%CI = 2.48-5.12, P = <0.001). Over half of the residents who died from suicide had a diagnosis of depression (n = 93, 66.0%) and had resided in the nursing home for less than 12 months (n = 71, 50.3%). Common major life stressors identified in suicide cases included the following: health deterioration (n = 112, 79.4%); isolation and loneliness (n = 60, 42.6%); and maladjustment to nursing home life (n = 42, 29.8%). This research provides a foundational understanding of suicide among nursing home residents in Australia and contributes important new information to the international knowledge base. Copyright © 2018 John Wiley & Sons, Ltd.

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

    PubMed Central

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

    2016-01-01

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

  19. [Comparative study of the population structure and population assignment of sockeye salmon Oncorhynchus nerka from West Kamchatka based on RAPD-PCR and microsatellite polymorphism].

    PubMed

    Zelenina, D A; Khrustaleva, A M; Volkov, A A

    2006-05-01

    Using two types of molecular markers, a comparative analysis of the population structure of sockeye salmon from West Kamchatka as well as population assignment of each individual fish were carried out. The values of a RAPD-PCR-based population assignment test (94-100%) were somewhat higher than those based on microsatellite data (74-84%). However, these results seem quite satisfactory because of high polymorphism of the microsatellite loci examined. The UPGMA dendrograms of genetic similarity of three largest spawning populations, constructed using each of the methods, were highly reliable, which was demonstrated by high bootstrap indices (100% in the case of RAPD-PCR; 84 and 100%, in the case of microsatellite analysis), though the resultant trees differed from one another. The different topology of the trees, in our view, is explained by the fact that the employed methods explored different parts of the genome; hence, the obtained results, albeit valid, may not correlate. Thus, to enhance reliability of the results, several methods of analysis should be used concurrently.

  20. [Analysis of genetico-demographic structure of rural populations living near the Semipalatinsk nuclear test site].

    PubMed

    Sviatova, G S; Berezina, G M; Abil'dinova, G Zh

    2001-12-01

    Rural populations neighboring the Semipalatinsk nuclear test site were used as a model to develop and test an integrated population-genetic approach to analysis of the medical genetic situation and environmental conditions in the areas studied. The contributions of individual factors of population dynamics into the formation of the genetic load were also assessed. The informative values of some genetic markers were estimated. Based on these estimates, a mathematical model was constructed that makes it possible to calculate numerical scores for analysis of the genetic loads in populations differing in environmental exposure.

  1. PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

    PubMed Central

    Purcell, Shaun ; Neale, Benjamin ; Todd-Brown, Kathe ; Thomas, Lori ; Ferreira, Manuel A. R. ; Bender, David ; Maller, Julian ; Sklar, Pamela ; de Bakker, Paul I. W. ; Daly, Mark J. ; Sham, Pak C. 

    2007-01-01

    Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis. PMID:17701901

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

    PubMed

    Penno, Erin; Gauld, Robin; Audas, Rick

    2013-11-08

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

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

    PubMed

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

    2014-10-01

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

  4. 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.

  5. Genetic diversity analysis of Capparis spinosa L. populations by using ISSR markers.

    PubMed

    Liu, C; Xue, G P; Cheng, B; Wang, X; He, J; Liu, G H; Yang, W J

    2015-12-09

    Capparis spinosa L. is an important medicinal species in the Xinjiang Province of China. Ten natural populations of C. spinosa from 3 locations in North, Central, and South Xinjiang were studied using morphological trait inter simple sequence repeat (ISSR) molecular markers to assess the genetic diversity and population structure. In this study, the 10 ISSR primers produced 313 amplified DNA fragments, with 52% of fragments being polymorphic. Unweighted pair-group method with arithmetic average (UPGMA) cluster analysis indicated that 10 C. spinosa populations were clustered into 3 geographically distinct groups. The Nei gene of C. spinosa populations in different regions had Diversity and Shannon's information index ranges of 0.1312-0.2001 and 0.1004-0.1875, respectively. The 362 markers were used to construct the dendrogram based on the UPGMA cluster analysis. The dendrogram indicated that 10 populations of C. spinosa were clustered into 3 geographically distinct groups. The results showed these genotypes have high genetic diversity, and can be used for an alternative breeding program.

  6. Microsatellite data analysis for population genetics

    USDA-ARS?s Scientific Manuscript database

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

  7. Temporal trends in stroke incidence in South Asian, Chinese and white patients: A population based analysis.

    PubMed

    Khan, Nadia A; McAlister, Finlay A; Pilote, Louise; Palepu, Anita; Quan, Hude; Hill, Michael D; Fang, Jiming; Kapral, Moira K

    2017-01-01

    Little is known about potential ethnic differences in stroke incidence. We compared incidence and time trends of ischemic stroke and primary intracerebral hemorrhage in South Asian, Chinese and white persons in a population-based study. Population based census and administrative data analysis in the provinces of Ontario and British Columbia, Canada using validated ICD 9/ICD 10 coding for acute ischemic and hemorrhagic stroke (1997-2010). There were 3290 South Asians, 4444 Chinese and 160944 white patients with acute ischemic stroke and 535 South Asian, 1376 Chinese and 21842 white patients with intracerebral hemorrhage. South Asians were younger than whites at onset of stroke (70 vs. 74 years for ischemic and 67 vs. 71 years for hemorrhagic stroke). Age and sex adjusted ischemic stroke incidence in 2010 was 43% lower in Chinese and 63% lower in South Asian than in White patients. Age and sex adjusted intracerebral hemorrhage incidence was 18% higher in Chinese patients, and 66% lower in South Asian relative to white patients. Stroke incidence declined in all ethnic groups (relative reduction 69% in South Asians, 25% in Chinese, and 34% in white patients for ischemic stroke and for intracerebral hemorrhage, 79% for South Asians, 51% for Chinese and 30% in white patients). Although stroke rates declined across all ethnic groups, these rates differed significantly by ethnicity. Further study is needed to understand mechanisms underlying the higher ischemic stroke incidence in white patients and intracerebral hemorrhage in Chinese patients.

  8. Risk factors for financial hardship in patients receiving adjuvant chemotherapy for colon cancer: a population-based exploratory analysis.

    PubMed

    Shankaran, Veena; Jolly, Sanjay; Blough, David; Ramsey, Scott D

    2012-05-10

    Characteristics that predispose patients to financial hardship during cancer treatment are poorly understood. We therefore conducted a population-based exploratory analysis of potential factors associated with financial hardship and treatment nonadherence during and following adjuvant chemotherapy for colon cancer. Patients diagnosed with stage III colon cancer between 2008 and 2010 were identified from a population-based cancer registry representing 13 counties in Washington state. Patients were asked to complete a comprehensive survey on treatment-related costs. Patients were considered to have experienced financial hardship if they accrued debt, sold or refinanced their home, borrowed money from friends or family, or experienced a 20% or greater decline in their annual income as a result of treatment-related expenses. Logistic regression analysis was used to investigate factors associated with financial hardship and treatment nonadherence. A total of 284 responses were obtained from 555 eligible patients (response rate, 51.2%). Nearly all patients in the final sample were insured during treatment. In this sample, 38% of patients reported one or more financial hardships as a result of treatment. The factors most closely associated with treatment-related financial hardship were younger age and lower annual household income. Younger age, lower income, and unemployment or disability (which occurred in most instances following diagnosis) were most closely associated with treatment nonadherence. A significant proportion of patients undergoing adjuvant chemotherapy for stage III colon cancer may experience financial hardship, despite having health insurance coverage. Interventions to help at-risk patients early on during therapy may prevent long-term financial adverse effects.

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

    PubMed

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

    2008-02-01

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

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

    PubMed Central

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

    2005-01-01

    Ecosystem conservation requires the presence of native carnivores, yet in North America, the distributions of many larger carnivores have contracted. Large carnivores live at low densities and require large areas to thrive at the population level. Therefore, if human-dominated landscapes fragment remaining carnivore populations, small and demographically vulnerable populations may result. Grizzly bear range contraction in the conterminous USA has left four fragmented populations, three of which remain along the Canada–USA border. A tenet of grizzly bear conservation is that the viability of these populations requires demographic linkage (i.e. inter-population movement of both sexes) to Canadian bears. Using individual-based genetic analysis, our results suggest this demographic connection has been severed across their entire range in southern Canada by a highway and associated settlements, limiting female and reducing male movement. Two resulting populations are vulnerably small (≤100 animals) and one of these is completely isolated. Our results suggest that these trans-border bear populations may be more threatened than previously thought and that conservation efforts must expand to include international connectivity management. They also demonstrate the ability of genetic analysis to detect gender-specific demographic population fragmentation in recently disturbed systems, a traditionally intractable yet increasingly important ecological measurement worldwide. PMID:16243699

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

    PubMed

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

    2005-11-22

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

  12. Population genetics analysis of Phlebotomus papatasi sand flies from Egypt and Jordan based on mitochondrial cytochrome b haplotypes.

    PubMed

    Flanley, Catherine M; Ramalho-Ortigao, Marcelo; Coutinho-Abreu, Iliano V; Mukbel, Rami; Hanafi, Hanafi A; El-Hossary, Shabaan S; Fawaz, Emad El-Din Y; Hoel, David F; Bray, Alexander W; Stayback, Gwen; Shoue, Douglas A; Kamhawi, Shaden; Karakuş, Mehmet; Jaouadi, Kaouther; Yaghoobie-Ershadi, Mohammad Reza; Krüger, Andreas; Amro, Ahmad; Kenawy, Mohamed Amin; Dokhan, Mostafa Ramadhan; Warburg, Alon; Hamarsheh, Omar; McDowell, Mary Ann

    2018-03-27

    Phlebotomus papatasi sand flies are major vectors of Leishmania major and phlebovirus infection in North Africa and across the Middle East to the Indian subcontinent. Population genetics is a valuable tool in understanding the level of genetic variability present in vector populations, vector competence, and the development of novel control strategies. This study investigated the genetic differentiation between P. papatasi populations in Egypt and Jordan that inhabit distinct ecotopes and compared this structure to P. papatasi populations from a broader geographical range. A 461 base pair (bp) fragment from the mtDNA cytochrome b (cyt b) gene was PCR amplified and sequenced from 116 individual female sand flies from Aswan and North Sinai, Egypt, as well as Swaimeh and Malka, Jordan. Haplotypes were identified and used to generate a median-joining network, F ST values and isolation-by-distance were also evaluated. Additional sand fly individuals from Afghanistan, Iran, Israel, Jordan, Libya, Tunisia and Turkey were included as well as previously published haplotypes to provide a geographically broad genetic variation analysis. Thirteen haplotypes displaying nine variant sites were identified from P. papatasi collected in Egypt and Jordan. No private haplotypes were identified from samples in North Sinai, Egypt, two were observed in Aswan, Egypt, four from Swaimeh, Jordan and two in Malka, Jordan. The Jordan populations clustered separately from the Egypt populations and produced more private haplotypes than those from Egypt. Pairwise F ST values fall in the range 0.024-0.648. The clustering patterns and pairwise F ST values indicate a strong differentiation between Egyptian and Jordanian populations, although this population structure is not due to isolation-by-distance. Other factors, such as environmental influences and the genetic variability in the circulating Le. major parasites, could possibly contribute to this heterogeneity. The present study aligns with

  13. Risk of colorectal cancer in patients with ulcerative colitis: a meta-analysis of population-based cohort studies.

    PubMed

    Jess, Tine; Rungoe, Christine; Peyrin-Biroulet, Laurent

    2012-06-01

    Patients with ulcerative colitis (UC) have an increased risk of developing colorectal cancer (CRC). Studies examining the magnitude of this association have yielded conflicting results. We performed a meta-analysis of population-based cohort studies to determine the risk of CRC in patients with UC. We used MEDLINE, EMBASE, Cochrane, and CINAHL to perform a systematic literature search. We included 8 studies in the meta-analysis on the basis of strict inclusion and exclusion criteria. We calculated pooled standardized incidence ratios (SIRs) with 95% confidence intervals (CIs) for risk of CRC in patients with UC and performed meta-regression analyses of the effect of cohort size, calendar period, observation time, percentage with proctitis, and rates of colectomy on the risk of CRC. An average of 1.6% of patients with UC was diagnosed with CRC during 14 years of follow-up. SIRs ranged from 1.05 to 3.1, with a pooled SIR of 2.4 (95% CI, 2.1-2.7). Men with UC had a greater risk of CRC (SIR, 2.6; 95% CI, 2.2-3.0) than women (SIR, 1.9; 95% CI, 1.5-2.3). Young age was a risk factor for CRC (SIR, 8.6; 95% CI, 3.8-19.5; although this might have resulted from small numbers), as was extensive colitis (SIR, 4.8; 95% CI, 3.9-5.9). In meta-regression analyses, only cohort size was associated with risk of CRC. In population-based cohorts, UC increases the risk of CRC 2.4-fold. Male sex, young age at diagnosis with UC, and extensive colitis increase the risk. Copyright © 2012 AGA Institute. Published by Elsevier Inc. All rights reserved.

  14. Use of Mobile Device Data To Better Estimate Dynamic Population Size for Wastewater-Based Epidemiology.

    PubMed

    Thomas, Kevin V; Amador, Arturo; Baz-Lomba, Jose Antonio; Reid, Malcolm

    2017-10-03

    Wastewater-based epidemiology is an established approach for quantifying community drug use and has recently been applied to estimate population exposure to contaminants such as pesticides and phthalate plasticizers. A major source of uncertainty in the population weighted biomarker loads generated is related to estimating the number of people present in a sewer catchment at the time of sample collection. Here, the population quantified from mobile device-based population activity patterns was used to provide dynamic population normalized loads of illicit drugs and pharmaceuticals during a known period of high net fluctuation in the catchment population. Mobile device-based population activity patterns have for the first time quantified the high degree of intraday, week, and month variability within a specific sewer catchment. Dynamic population normalization showed that per capita pharmaceutical use remained unchanged during the period when static normalization would have indicated an average reduction of up to 31%. Per capita illicit drug use increased significantly during the monitoring period, an observation that was only possible to measure using dynamic population normalization. The study quantitatively confirms previous assessments that population estimates can account for uncertainties of up to 55% in static normalized data. Mobile device-based population activity patterns allow for dynamic normalization that yields much improved temporal and spatial trend analysis.

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

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

    Moerk, Anna-Karin, E-mail: anna-karin.mork@ki.s; Jonsson, Fredrik; Pharsight, a Certara company, St. Louis, MO

    2009-11-01

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

  16. Sexual minority youth and depressive symptoms or depressive disorder: A systematic review and meta-analysis of population-based studies.

    PubMed

    Lucassen, Mathijs Fg; Stasiak, Karolina; Samra, Rajvinder; Frampton, Christopher Ma; Merry, Sally N

    2017-08-01

    Research has suggested that sexual minority young people are more likely to have depressive symptoms or depressive disorder, but to date most studies in the field have relied on convenience-based samples. This study overcomes this limitation by systematically reviewing the literature from population-based studies and conducting a meta-analysis to identify whether depressive disorder and depressive symptoms are elevated in sexual minority youth. A systematic review and meta-analysis were conducted and informed by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement to determine if rates of depressive symptoms or depressive disorder differ for sexual minority youth, relative to heterosexual adolescents. MEDLINE, PsycINFO, EMBASE and ERIC databases were searched. Studies reporting depressive symptom data or the prevalence of depressive disorder in population-based samples of adolescents, which included sexual minority youth and heterosexual young people, were included in the review. A meta-analysis was conducted to examine differences between groups. Twenty-three articles met the inclusion criteria. The proportion of sexual minority youth in the studies ranged from 2.3% to 12%. Sexual minority youth reported higher rates of depressive symptoms and depressive disorder (odds ratio = 2.94, p < 0.001 and standardized mean difference, d = 0.39, p < 0.001) in comparison to heterosexual young people. Female sexual minority youth were more likely to report depressive symptoms when compared to male sexual minority youth (standardized mean difference, d = 0.34, p < 0.001). Limitations included variations in how sexuality was operationalized and how depressive symptoms or depressive disorder was measured. There is robust evidence that rates of depressive disorder and depressive symptoms are elevated in sexual minority youth in comparison to heterosexual young people. Despite the elevated risk of depressive symptoms or

  17. Higher risk for thyroid diseases in physicians than in the general population: a Taiwan nationwide population-based secondary analysis study.

    PubMed

    Chen, T-Y; Hsu, C-C; Feng, I-J; Wang, J-J; Su, S-B; Guo, H-R; Huang, C-C; Lin, H-J

    2017-03-01

    Physicians have high work stress, responsibility for night shifts and chances of exposure to medical radiation, which may increase the risk for thyroid diseases. We conducted this study to assess the risk for thyroid diseases in physicians, which remain unclear. We used a secondary analysis of the Taiwan National Health Insurance Research Database for this study. After excluding thyroid diseases occurring before 2006 and residents, physicians and general population were identified by matching with age and sex in 2009 in a 1:2 ratio. The risk for thyroid diseases was compared between the physicians and general population and among physicians by tracing their medical histories between 2006 and 2012. In total, 28,649 physicians and 57,298 general population were identified. Physicians had a higher risk for overall thyroid diseases than the general population [odds ratio (OR): 1.27; 95% confidence interval (CI): 1.10-1.47], including individual thyroid disease: thyroid cancer (OR: 1.89; 95% CI: 1.22-2.95), hypothyroidism (OR: 1.64; 95% CI: 1.23-2.18) and thyroiditis (OR: 1.48; 95% CI: 1.00-2.19). We showed that physicians had a significantly higher risk for thyroid diseases than the general population. This reminds us to pay more attention to thyroid diseases in physicians. Further studies about the underlying mechanisms are warranted. © The Author 2016. Published by Oxford University Press on behalf of the Association of Physicians. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  18. Genetic diversity and population structure analysis in Perilla frutescens from Northern areas of China based on simple sequence repeats.

    PubMed

    Ma, S J; Sa, K J; Hong, T K; Lee, J K

    2017-09-21

    In this study, 21 simple sequence repeat (SSR) markers were used to evaluate the genetic diversity and population structure among 77 Perilla accessions from high-latitude and middle-latitude areas of China. Ninety-five alleles were identified with an average of 4.52 alleles per locus. The average polymorphic information content (PIC) and genetic diversity values were 0.346 and 0.372, respectively. The level of genetic diversity and PIC value for cultivated accessions of Perilla frutescens var. frutescens from middle-latitude areas were higher than accessions from high-latitude areas. Based on the dendrogram of unweighted pair group method with arithmetic mean (UPGMA), all accessions were classified into four major groups with a genetic similarity of 46%. All accessions of the cultivated var. frutescens were discriminated from the cultivated P. frutescens var. crispa. Furthermore, most accessions of the cultivated var. frutescens collected in high-latitude and middle-latitude areas were distinguished depending on their geographical location. However, the geographical locations of several accessions of the cultivated var. frutescens have no relation with their positions in the UPGMA dendrogram and population structure. This result implies that the diffusion of accessions of the cultivated Perilla crop in the northern areas of China might be through multiple routes. On the population structure analysis, 77 Perilla accessions were divided into Group I, Group II, and an admixed group based on a membership probability threshold of 0.8. Finally, the findings in this study can provide useful theoretical knowledge for further study on the population structure and genetic diversity of Perilla and benefit for Perilla crop breeding and germplasm conservation.

  19. 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

  20. Adélie penguin population diet monitoring by analysis of food DNA in scats.

    PubMed

    Jarman, Simon N; McInnes, Julie C; Faux, Cassandra; Polanowski, Andrea M; Marthick, James; Deagle, Bruce E; Southwell, Colin; Emmerson, Louise

    2013-01-01

    The Adélie penguin is the most important animal currently used for ecosystem monitoring in the Southern Ocean. The diet of this species is generally studied by visual analysis of stomach contents; or ratios of isotopes of carbon and nitrogen incorporated into the penguin from its food. There are significant limitations to the information that can be gained from these methods. We evaluated population diet assessment by analysis of food DNA in scats as an alternative method for ecosystem monitoring with Adélie penguins as an indicator species. Scats were collected at four locations, three phases of the breeding cycle, and in four different years. A novel molecular diet assay and bioinformatics pipeline based on nuclear small subunit ribosomal RNA gene (SSU rDNA) sequencing was used to identify prey DNA in 389 scats. Analysis of the twelve population sample sets identified spatial and temporal dietary change in Adélie penguin population diet. Prey diversity was found to be greater than previously thought. Krill, fish, copepods and amphipods were the most important food groups, in general agreement with other Adélie penguin dietary studies based on hard part or stable isotope analysis. However, our DNA analysis estimated that a substantial portion of the diet was gelatinous groups such as jellyfish and comb jellies. A range of other prey not previously identified in the diet of this species were also discovered. The diverse prey identified by this DNA-based scat analysis confirms that the generalist feeding of Adélie penguins makes them a useful indicator species for prey community composition in the coastal zone of the Southern Ocean. Scat collection is a simple and non-invasive field sampling method that allows DNA-based estimation of prey community differences at many temporal and spatial scales and provides significant advantages over alternative diet analysis approaches.

  1. 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.

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

    PubMed

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

    2015-02-01

    Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69,903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.

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

    PubMed

    Pron, G

    2015-01-01

    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. 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. A systematic review of bibliographic databases was performed for systematic reviews or randomized controlled trials (RCT) of PSA-based population screening programs for PC. A broad search strategy was employed to identify studies reporting on key outcomes of PC mortality and all-cause mortality. 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. There was no evidence of a PC mortality reduction in the American PLCO trial, which

  4. Population-Based Analysis and Projections of Liver Supply Under Redistricting.

    PubMed

    Parikh, Neehar D; Marrero, Wesley J; Sonnenday, Christopher J; Lok, Anna S; Hutton, David W; Lavieri, Mariel S

    2017-09-01

    To reduce the geographic heterogeneity in liver transplant allocation, the United Network of Organ Sharing has proposed redistricting, which is impacted by both donor supply and liver transplantation demand. We aimed to determine the impact of demographic changes on the redistricting proposal and characterize causes behind geographic heterogeneity in donor supply. We analyzed adult donors from 2002 to 2014 from the United Network of Organ Sharing database and calculated regional liver donation and utilization stratified by age, race, and body mass index. We used US population data to make regional projections of available donors from 2016 to 2025, incorporating the proposed 8-region redistricting plan. We used donors/100 000 population age 18 to 84 years (D/100K) as a measure of equity. We calculated a coefficient of variation (standard deviation/mean) for each regional model. We performed an exploratory analysis where we used national rates of donation, utilization and both for each regional model. The overall projected D/100K will decrease from 2.53 to 2.49 from 2016 to 2025. The coefficient of variation in 2016 is expected to be 20.3% in the 11-region model and 13.2% in the 8-region model. We found that standardizing regional donation and utilization rates would reduce geographic heterogeneity to 4.9% in the 8-region model and 4.6% in the 11-region model. The 8-region allocation model will reduce geographic variation in donor supply to a significant extent; however, we project that geographic disparity will marginally increase over time. Though challenging, interventions to better standardize donation and utilization rates would be impactful in reducing geographic heterogeneity in organ supply.

  5. 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

  6. 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.

  7. 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.

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

    PubMed

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

    2014-05-01

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

  9. 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

  10. Time Trends in Breast Cancer Among Indian Women Population: An Analysis of Population Based Cancer Registry Data.

    PubMed

    Chaturvedi, Meesha; Vaitheeswaran, K; Satishkumar, K; Das, Priyanka; Stephen, S; Nandakumar, A

    2015-12-01

    The trends observed in cancer breast among Indian women are an indication of effect of changing lifestyle in population. To draw an appropriate inference regarding the trends of a particular type of cancer in a country, it is imperative to glance at the reliable data collected by Population Based Cancer Registries over a period of time. To give an insight of changing trends of breast cancer which have taken place over a period of time among women in Cancer Registries of India. Breast Cancer trends for invasive breast cancer in women in Indian Registries have varied during the selected period. Occurrence of breast cancers has also shown geographical variation in India. This data was collected by means of a 'Standard Core Proforma' designed by NCRP conforming to the data fields as suggested by International norms. The Proforma was filled by trained Registry workers based on interview/ hospital medical records/ supplementing data by inputs from treating surgeons/radiation oncologists/involved physicians/pathologists. The contents of the Proforma are entered into specifically created software and transmitted electronically to the coordinating center at Bangalore. The registries contributing to more number of years of data are called as older registries, while other recently established registries are called newer registries. While there has been an increase recorded in breast cancer in most of the registries, some of them have recorded an insignificant increase. Comparison of Age Adjusted Rates (AARs) among Indian Registries has been carried out after which trends observed in populations covered by Indian Registries are depicted. A variation in broad age groups of females and the proneness of females developing breast cancer over the period 1982 to 2010 has been shown. Comparisons of Indian registries with International counterparts have also been carried out. There are marked changes in incidence rates of cancer breast which have occurred in respective registries in a

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

    PubMed

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

    2010-10-01

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

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

    PubMed Central

    SCOTT, KIRSTEN M.; ABHINAV, KUMAR; WIJESEKERA, LOKESH; GANESALINGAM, JEBAN; GOLDSTEIN, LAURA H.; JANSSEN, ANNA; DOUGHERTY, ANDREW; WILLEY, EMMA; STANTON, BIBA R.; TURNER, MARTIN R.; AMPONG, MARY-ANN; SAKEL, MOHAMMED; ORRELL, RICHARD; HOWARD, ROBIN; SHAW, CHRISTOPHER E.; LEIGH, P. NIGEL; AL-CHALABI, AMMAR

    2011-01-01

    We aimed to assess whether rural residence is associated with amyotrophic lateral sclerosis in the south-east of England using a population based register. Previous studies in different populations have produced contradictory findings. Residence defined by London borough or non-metropolitan district at time of diagnosis was recorded for each incident case in the South-East England ALS Register between 1995 and 2005. Each of the 26 boroughs or districts of the catchment area of the register was classified according to population density. Age- and sex-adjusted incidence of ALS was calculated for each region and the relationship with population density tested by linear regression, thereby controlling for the underlying population structure. We found that population density in region of residence at diagnosis explained 25% of the variance in ALS rates (r = 0.5, p < 0.01). Thus, in this cohort in the south-east of England, people with ALS were more likely to be resident in areas of high population density at diagnosis. PMID:20429684

  13. Injury risk functions based on population-based finite element model responses: Application to femurs under dynamic three-point bending.

    PubMed

    Park, Gwansik; Forman, Jason; Kim, Taewung; Panzer, Matthew B; Crandall, Jeff R

    2018-02-28

    The goal of this study was to explore a framework for developing injury risk functions (IRFs) in a bottom-up approach based on responses of parametrically variable finite element (FE) models representing exemplar populations. First, a parametric femur modeling tool was developed and validated using a subject-specific (SS)-FE modeling approach. Second, principal component analysis and regression were used to identify parametric geometric descriptors of the human femur and the distribution of those factors for 3 target occupant sizes (5th, 50th, and 95th percentile males). Third, distributions of material parameters of cortical bone were obtained from the literature for 3 target occupant ages (25, 50, and 75 years) using regression analysis. A Monte Carlo method was then implemented to generate populations of FE models of the femur for target occupants, using a parametric femur modeling tool. Simulations were conducted with each of these models under 3-point dynamic bending. Finally, model-based IRFs were developed using logistic regression analysis, based on the moment at fracture observed in the FE simulation. In total, 100 femur FE models incorporating the variation in the population of interest were generated, and 500,000 moments at fracture were observed (applying 5,000 ultimate strains for each synthesized 100 femur FE models) for each target occupant characteristics. Using the proposed framework on this study, the model-based IRFs for 3 target male occupant sizes (5th, 50th, and 95th percentiles) and ages (25, 50, and 75 years) were developed. The model-based IRF was located in the 95% confidence interval of the test-based IRF for the range of 15 to 70% injury risks. The 95% confidence interval of the developed IRF was almost in line with the mean curve due to a large number of data points. The framework proposed in this study would be beneficial for developing the IRFs in a bottom-up manner, whose range of variabilities is informed by the population-based

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

    PubMed

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

    2007-11-01

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

  15. Population-based Incidence of Intraocular Lens Exchange in Olmsted County, Minnesota.

    PubMed

    Bothun, Erick D; Cavalcante, Lilian C B; Hodge, David O; Patel, Sanjay V

    2018-03-01

    To determine the population-based incidence of pseudophakic intraocular lens exchange in Olmsted County, Minnesota. Retrospective review of a population-based cohort. Patients undergoing pseudophakic intraocular lens exchange in Olmsted County, Minnesota, between January 1, 1986 and December 31, 2016 were identified from the Rochester Epidemiology Project medical record linkage system. Indications and outcomes were determined, and the incidence rate was calculated as cases per 1 000 000 person-years. Poisson regression analysis was used to assess changes in incidence over time, and the cumulative probability of needing a lens exchange was estimated by Kaplan-Meier analysis. Eighty cases of intraocular lens exchange were identified, yielding an overall age- and sex-adjusted incidence rate of 28.4 per million (confidence interval [CI], 22.1-34.7), which increased over the study period (P = .04). The 30-year cumulative probability of intraocular lens exchange among patients undergoing cataract surgery was 1.5% (CI, 0.6%-2.4%), increasing at a relatively constant rate. Dislocated lenses accounted for 72.5% of lens exchanges. Unplanned refractive outcome of primary cataract surgery and uveitis-glaucoma-hyphema syndrome from squared-edged haptics emerged as newer indications for intraocular lens exchange. The population-based incidence of pseudophakic intraocular lens exchange has increased over the last 30 years, and can be explained by the increase in incidence rate of cataract surgery over the same period. Surgeons should be aware of emerging indications of intraocular lens exchange, which reflect changes in lens design and increasing expectations of refractive outcomes. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Cost-effectiveness analysis of population-based tobacco control strategies in the prevention of cardiovascular diseases in Tanzania.

    PubMed

    Ngalesoni, Frida; Ruhago, George; Mayige, Mary; Oliveira, Tiago Cravo; Robberstad, Bjarne; Norheim, Ole Frithjof; Higashi, Hideki

    2017-01-01

    Tobacco consumption contributes significantly to the global burden of disease. The prevalence of smoking is estimated to be increasing in many low-income countries, including Tanzania, especially among women and youth. Even so, the implementation of tobacco control measures has been discouraging in the country. Efforts to foster investment in tobacco control are hindered by lack of evidence on what works and at what cost. We aim to estimate the cost and cost-effectiveness of population-based tobacco control strategies in the prevention of cardiovascular diseases (CVD) in Tanzania. A cost-effectiveness analysis was performed using an Excel-based Markov model, from a governmental perspective. We employed an ingredient approach and step-down methodologies in the costing exercise following a government perspective. Epidemiological data and efficacy inputs were derived from the literature. We used disability-adjusted life years (DALYs) averted as the outcome measure. A probabilistic sensitivity analysis was carried out with Ersatz to incorporate uncertainties in the model parameters. Our model results showed that all five tobacco control strategies were very cost-effective since they fell below the ceiling ratio of one GDP per capita suggested by the WHO. Increase in tobacco taxes was the most cost-effective strategy, while a workplace smoking ban was the least cost-effective option, with a cost-effectiveness ratio of US$5 and US$267, respectively. Even though all five interventions are deemed very cost-effective in the prevention of CVD in Tanzania, more research on budget impact analysis is required to further assess the government's ability to implement these interventions.

  17. Qualifications and Competencies for Population Health Management Positions: A Content Analysis of Job Postings.

    PubMed

    Meyer, Melanie

    2017-12-01

    The need for population health management expertise has increased as the health care industry shifts toward value-based care. However, many organizations report hiring gaps as they seek to fill positions. The purpose of this study was to analyze the types of population health management positions for which health care organizations are hiring, including qualifications and competencies required for these positions. A content analysis was conducted on 271 job postings collected during a 2-month period. A typology of qualifications and competencies was developed based on the content analysis. Profiles were generated for the top 5 job title classifications: directors, coordinators, care managers, analysts, and specialists. This study highlights the investment health care organizations are making in population health management and the prominent role these positions are playing in the health care environment today. Many organizations are building out population health management teams resulting in multiple positions at different levels being added. As the market demands competent candidates who are equipped with specialized population health expertise as well as practical experience in program development, technology applications, care management, and analytics, professional education programs will need to adapt curricula to address the required areas. Competencies for specific job title classifications may need further evaluation and refinement over time. Study results can be used by organizations for strategic planning, by educators to target needed qualifications and competencies, and by researchers and policy advisors to assess progress toward value-based care.

  18. Population based screening for chronic kidney disease: cost effectiveness study.

    PubMed

    Manns, Braden; Hemmelgarn, Brenda; Tonelli, Marcello; Au, Flora; Chiasson, T Carter; Dong, James; Klarenbach, Scott

    2010-11-08

    To determine the cost effectiveness of one-off population based screening for chronic kidney disease based on estimated glomerular filtration rate. Cost utility analysis of screening with estimated glomerular filtration rate alone compared with no screening (with allowance for incidental finding of cases of chronic kidney disease). Analyses were stratified by age, diabetes, and the presence or absence of proteinuria. Scenario and sensitivity analyses, including probabilistic sensitivity analysis, were performed. Costs were estimated in all adults and in subgroups defined by age, diabetes, and hypertension. Publicly funded Canadian healthcare system. Large population based laboratory cohort used to estimate mortality rates and incidence of end stage renal disease for patients with chronic kidney disease over a five year follow-up period. Patients had not previously undergone assessment of glomerular filtration rate. Lifetime costs, end stage renal disease, quality adjusted life years (QALYs) gained, and incremental cost per QALY gained. Compared with no screening, population based screening for chronic kidney disease was associated with an incremental cost of $C463 (Canadian dollars in 2009; equivalent to about £275, €308, US $382) and a gain of 0.0044 QALYs per patient overall, representing a cost per QALY gained of $C104 900. In a cohort of 100 000 people, screening for chronic kidney disease would be expected to reduce the number of people who develop end stage renal disease over their lifetime from 675 to 657. In subgroups of people with and without diabetes, the cost per QALY gained was $C22 600 and $C572 000, respectively. In a cohort of 100 000 people with diabetes, screening would be expected to reduce the number of people who develop end stage renal disease over their lifetime from 1796 to 1741. In people without diabetes with and without hypertension, the cost per QALY gained was $C334 000 and $C1 411 100, respectively. Population based

  19. 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.

  20. 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.

  1. PopHR: a knowledge-based platform to support integration, analysis, and visualization of population health data.

    PubMed

    Shaban-Nejad, Arash; Lavigne, Maxime; Okhmatovskaia, Anya; Buckeridge, David L

    2017-01-01

    Population health decision makers must consider complex relationships between multiple concepts measured with differential accuracy from heterogeneous data sources. Population health information systems are currently limited in their ability to integrate data and present a coherent portrait of population health. Consequentially, these systems can provide only basic support for decision makers. The Population Health Record (PopHR) is a semantic web application that automates the integration and extraction of massive amounts of heterogeneous data from multiple distributed sources (e.g., administrative data, clinical records, and survey responses) to support the measurement and monitoring of population health and health system performance for a defined population. The design of the PopHR draws on the theories of the determinants of health and evidence-based public health to harmonize and explicitly link information about a population with evidence about the epidemiology and control of chronic diseases. Organizing information in this manner and linking it explicitly to evidence is expected to improve decision making related to the planning, implementation, and evaluation of population health and health system interventions. In this paper, we describe the PopHR platform and discuss the architecture, design, key modules, and its implementation and use. © 2016 New York Academy of Sciences.

  2. Population-based trend analysis of laparoscopic Nissen and Toupet fundoplications for gastroesophageal reflux disease.

    PubMed

    Zingg, U; Rosella, L; Guller, U

    2010-12-01

    The Nissen and Toupet fundoplications are the most commonly used techniques for surgical treatment of gastroesophageal reflux disease. To date, no population-based trend analysis has been reported examining the choice of procedure and short-term outcomes. This study was designed to analyze trends in the use of Nissen versus Toupet fundoplications, and corresponding short-term outcomes during a 10-year period between 1995 and 2004. A trend analysis was performed of 873 patients (Toupet: 254 patients, Nissen: 619 patients) prospectively enrolled in the database of the Swiss Association for Laparoscopic and Thoracoscopic Surgery. The frequency of the performed techniques remained stable during the observation period (p value for trend 0.206). The average postoperative and total length of hospital stay both significantly decreased during the 10-year period from 5.6 to 4.0 days and 6.8 to 4.8 days, respectively (both p values for trend <0.001). The average duration of surgery decreased significantly from 141 minutes to 121 minutes (p value for trend <0.001). There was a trend towards less complications in later years (2000-2004) compared to early years (1995-1999, p = 0.058). Conversion rates were significantly lower in later years compared with early years (p = 0.004). This is the first trend analysis in the literature reporting clinical outcomes of 873 prospectively enrolled patients undergoing Nissen and Toupet fundoplications during a 10-year period. The proportion of laparoscopic Nissen versus Toupet fundoplications remained stable over time, indicating that literature reports of the advantages of one procedure over the other had minimal influence on surgeons' choice of technique. Length of hospital stay, duration of surgery, morbidity, and conversion rate decreased over time, reflecting the learning curve. Clearly, patient outcomes have much improved during the 10-year observation period.

  3. Asian Versus Non-Asian Outcomes in Nasopharyngeal Carcinoma: A North American Population-based Analysis.

    PubMed

    Hamilton, Sarah N; Ho, Cheryl; Laskin, Janessa; Zhai, Yongliang; Mak, Paul; Wu, Jonn

    2016-12-01

    The effect of ethnicity on nasopharyngeal cancer (NPC) outcomes is unclear. This retrospective analysis examines survival and the impact of concurrent chemoradiation (chemoRT) among Asian and non-Asian patients. Subjects included 380 consecutive patients with NPC treated at a Canadian institution from 2000 to 2009. Five-year Kaplan-Meier progression-free survival (PFS), disease-specific survival (DSS), and overall survival (OS) were compared between Asian (n=279) and non-Asian (n=101) subjects. Multivariable analysis was performed using Cox regression modeling. Two-variable interaction terms with concurrent chemoRT were used to examine whether concurrent chemoRT conferred different effects among subgroups. Asian subjects presented with earlier stage (P=0.005), were younger, had better performance status, and were less likely smokers (all P<0.001). Survival among Asian versus non-Asian subjects with stage I/II NPC were: PFS 68% versus 59% (P=0.04), DSS 87% versus 77% (P=0.08), and OS 84% versus 74% (P=0.003). Corresponding rates with stage III/IVA/IVB disease were PFS 49% versus 42% (P=0.12), DSS 72% versus 46% (P=0.001), and OS 70% versus 44% (P<0.001). On multivariable analysis, Asian ethnicity, age below 65 years, ECOG performance status 0-1, early stage, staging MRI use, and concurrent chemoRT were associated with improved DSS and OS (P<0.05). On testing interactions with concurrent chemoRT, Asian versus non-Asian ethnicity was significant (hazard ratio 3.9), suggesting that concurrent chemoRT conferred more benefit among non-Asian compared with Asian subjects. In this population-based study, Asian ethnicity was associated with improved DSS and OS. Concurrent chemoRT conferred more benefit among non-Asian compared with Asian subjects.

  4. Efficient population-scale variant analysis and prioritization with VAPr.

    PubMed

    Birmingham, Amanda; Mark, Adam M; Mazzaferro, Carlo; Xu, Guorong; Fisch, Kathleen M

    2018-04-06

    With the growing availability of population-scale whole-exome and whole-genome sequencing, demand for reproducible, scalable variant analysis has spread within genomic research communities. To address this need, we introduce the Python package VAPr (Variant Analysis and Prioritization). VAPr leverages existing annotation tools ANNOVAR and MyVariant.info with MongoDB-based flexible storage and filtering functionality. It offers biologists and bioinformatics generalists easy-to-use and scalable analysis and prioritization of genomic variants from large cohort studies. VAPr is developed in Python and is available for free use and extension under the MIT License. An install package is available on PyPi at https://pypi.python.org/pypi/VAPr, while source code and extensive documentation are on GitHub at https://github.com/ucsd-ccbb/VAPr. kfisch@ucsd.edu.

  5. Development of National Program of Cancer Registries SAS Tool for Population-Based Cancer Relative Survival Analysis.

    PubMed

    Dong, Xing; Zhang, Kevin; Ren, Yuan; Wilson, Reda; O'Neil, Mary Elizabeth

    2016-01-01

    Studying population-based cancer survival by leveraging the high-quality cancer incidence data collected by the Centers for Disease Control and Prevention's National Program of Cancer Registries (NPCR) can offer valuable insight into the cancer burden and impact in the United States. We describe the development and validation of a SASmacro tool that calculates population-based cancer site-specific relative survival estimates comparable to those obtained through SEER*Stat. The NPCR relative survival analysis SAS tool (NPCR SAS tool) was developed based on the relative survival method and SAS macros developed by Paul Dickman. NPCR cancer incidence data from 25 states submitted in November 2012 were used, specifically cases diagnosed from 2003 to 2010 with follow-up through 2010. Decennial and annual complete life tables published by the National Center for Health Statistics (NCHS) for 2000 through 2009 were used. To assess comparability between the 2 tools, 5-year relative survival rates were calculated for 25 cancer sites by sex, race, and age group using the NPCR SAS tool and the National Cancer Institute's SEER*Stat 8.1.5 software. A module to create data files for SEER*Stat was also developed for the NPCR SAS tool. Comparison of the results produced by both SAS and SEER*Stat showed comparable and reliable relative survival estimates for NPCR data. For a majority of the sites, the net differences between the NPCR SAS tool and SEER*Stat-produced relative survival estimates ranged from -0.1% to 0.1%. The estimated standard errors were highly comparable between the 2 tools as well. The NPCR SAS tool will allow researchers to accurately estimate cancer 5-year relative survival estimates that are comparable to those produced by SEER*Stat for NPCR data. Comparison of output from the NPCR SAS tool and SEER*Stat provided additional quality control capabilities for evaluating data prior to producing NPCR relative survival estimates.

  6. Early childhood measles vaccinations are not associated with paediatric IBD: a population-based analysis.

    PubMed

    Shaw, Souradet Y; Blanchard, James F; Bernstein, Charles N

    2015-04-01

    Early childhood vaccinations have been hypothesized to contribute to the emergence of paediatric inflammatory bowel disease [IBD] in developed countries. Using linked population-based administrative databases, we aimed to explore the association between vaccination with measles-containing vaccines and the risk for IBD. This was a case-control study using the University of Manitoba IBD Epidemiology Database [UMIBDED]. The UMIBDED was linked to the Manitoba Immunization Monitoring System [MIMS], a population-based database of immunizations administered in Manitoba. All paediatric IBD cases in Manitoba, born after 1989 and diagnosed before March 31, 2008, were included. Controls were matched to cases on the basis of age, sex, and region of residence at time of diagnosis. Measles-containing vaccinations received in the first 2 years of life were documented, with vaccinations categorized as 'None' or 'Complete', with completeness defined according to Manitoba's vaccination schedule. Conditional logistic regression models were fitted to the data, with models adjusted for physician visits in the first 2 years of life and area-level socioeconomic status at case date. A total of 951 individuals [117 cases and 834 controls] met eligibility criteria, with average age of diagnosis among cases at 11 years. The proportion of IBD cases with completed vaccinations was 97%, compared with 94% of controls. In models adjusted for physician visits and area-level socioeconomic status, no statistically significant association was detected between completed measles vaccinations and the risk of IBD (adjusted odds ratio [AOR]: 1.5; 95% confidence interval [CI]: 0.5-4.4; p = 0.419]. No significant association between completed measles-containing vaccination in the first 2 years of life and paediatric IBD could be demonstrated in this population-based study. Copyright © 2015 European Crohn’s and Colitis Organisation (ECCO). Published by Oxford University Press. All rights reserved. For

  7. Medical resource use and expenditure in patients with chronic heart failure: a population-based analysis of 88 195 patients.

    PubMed

    Farré, Nuria; Vela, Emili; Clèries, Montse; Bustins, Montse; Cainzos-Achirica, Miguel; Enjuanes, Cristina; Moliner, Pedro; Ruiz, Sonia; Verdú-Rotellar, Jose Maria; Comín-Colet, Josep

    2016-09-01

    Heart failure (HF) is one of the diseases with greater healthcare expenditure. However, little is known about the cost of HF at a population level. Hence, our aim was to study the population-level distribution and predictors of healthcare expenditure in patients with HF. This was a population-based longitudinal study including all prevalent HF cases in Catalonia (Spain) on 31 December 2012 (n = 88 195). We evaluated 1-year healthcare resource use and expenditure using the Health Department (CatSalut) surveillance system that collects detailed information on healthcare usage for the entire population. Mean age was 77.4 (12) years; 55% were women. One-year mortality rate was 14%. All-cause emergency department visits and unplanned hospitalizations were required at least once in 53.4% and 30.8% of patients, respectively. During 2013, a total of €536.2 million were spent in the care of HF patients (7.1% of the total healthcare budget). The main source of expenditure was hospitalization (39% of the total) whereas outpatient care represented 20% of the total expenditure. In the general population, outpatient care and hospitalization were the main expenses. In multivariate analysis, younger age, higher presence of co-morbidities, and a recent HF or all-cause hospitalization were independently associated with higher healthcare expenditure. In Catalonia, a large portion of the annual healthcare budget is devoted to HF patients. Unplanned hospitalization represents the main source of healthcare-related expenditure. The knowledge of how expenditure is distributed in a non-selected HF population might allow health providers to plan the distribution of resources in patients with HF. © 2016 The Authors. European Journal of Heart Failure © 2016 European Society of Cardiology.

  8. Effect of socioeconomic inequalities on cholecystectomy outcomes: a 10-year population-based analysis.

    PubMed

    Lu, Ping; Yang, Nan-Ping; Chang, Nien-Tzu; Lai, K Robert; Lin, Kai-Biao; Chan, Chien-Lung

    2018-02-13

    Although numerous epidemiological studies on cholecystectomy have been conducted worldwide, only a few have considered the effect of socioeconomic inequalities on cholecystectomy outcomes. Specifically, few studies have focused on the low-income population (LIP). A nationwide prospective study based on the Taiwan National Health Insurance dataset was conducted during 2003-2012. The International Classification of ICD-9-CM procedure codes 51.2 and 51.21-51.24 were identified as the inclusion criteria for cholecystectomy. Temporal trends were analyzed using a joinpoint regression, and the hierarchical linear modeling (HLM) method was used as an analytical strategy to evaluate the group-level and individual-level factors. Interactions between age, gender and SES were also tested in HLM model. Analyses were conducted on 225,558 patients. The incidence rates were 167.81 (95% CI: 159.78-175.83) per 100,000 individuals per year for the LIP and 123.24 (95% CI: 116.37-130.12) per 100,000 individuals per year for the general population (GP). After cholecystectomy, LIP patients showed higher rates of 30-day mortality, in-hospital complications, and readmission for complications, but a lower rate of routine discharge than GP patients. The hospital costs and length of stay for LIP patients were higher than those for GP patients. The multilevel analysis using HLM revealed that adverse socioeconomic status significantly negatively affects the outcomes of patients undergoing cholecystectomy. Additionally, male sex, advanced age, and high Charlson Comorbidity Index (CCI) scores were associated with higher rates of in-hospital complications and 30-day mortality. We also observed that the 30-day mortality rates for patients who underwent cholecystectomy in regional hospitals and district hospitals were significantly higher than those of patients receiving care in a medical center. Patients with a disadvantaged finance status appeared to be more vulnerable to cholecystectomy surgery

  9. Sinonasal adenoid cystic carcinoma: a population-based analysis of 694 cases.

    PubMed

    Unsal, Aykut A; Chung, Sei Y; Zhou, Albert H; Baredes, Soly; Eloy, Jean Anderson

    2017-03-01

    Currently, limited literature exists about sinonasal adenoid cystic carcinoma (SNACC). In this study, we analyze the demographics, survival, and treatment efficacy of this rare entity. Our study was a retrospective population-based analysis of SNACC in the Surveillance, Epidemiology, and End Results (SEER) database assessing the 40-year time-frame of 1973 to 2013. Six hundred ninety-four SNACC patients were identified; 53.2% were female and 46.8% were male. Caucasians were most commonly affected (77.1%). SNACC most often arose from the maxillary sinuses, followed by the nasal cavity. The majority of SNACC cases presented as stage IV disease. Nodal and distant metastases were present in 3.6% and 7.1% of all cases, respectively. Overall 5-, 10-, and 20-year disease-specific survival (DSS) rates were 66.5%, 41.1%, and 17.6%, respectively. The presence of distant metastasis dropped the 5-year DSS rate from 64.5% to 20.0%. Cases treated with combined surgery and adjuvant radiotherapy had a slightly improved 5-year DSS rate compared with surgery alone (73.5% vs 72.5%). Surgery alone resulted in higher 10- and 20-year DSS rates (54.2% and 36.8%, respectively) when compared with combined therapy (44.2% and 15.5%), radiotherapy alone (10.8% and 0%), and no surgery or radiotherapy (9.3% and 0%). This study represents the largest cohort of SNACC patients to date. Factors that confer a survival benefit in SNACC include M0 disease, and presentation primarily in the nasal cavity. Overall low rates of nodal metastasis may not warrant the use of elective neck dissections, unless there is clinical suspicion. Modalities of therapy that include surgery greatly improve survival. Adjuvant radiotherapy appears to slightly improve 5-year disease-free survival but does not impact long-term survival. © 2016 ARS-AAOA, LLC.

  10. An individual-based model of zebrafish population dynamics accounting for energy dynamics.

    PubMed

    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.

  11. 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

  12. Analysis of urban-rural population dynamics for China.

    PubMed

    Shen, J

    1991-12-01

    The population dynamics of China are presented in a multiregional demographic model using regional estimates or mortality and migration based on the 1% population sample survey in 1987. An open ended population account is generated for period cohort a, gender g of region i (urban) and j (rural) using population, birth, death, and migration. Demographic rates and equations for flows of nonsurviving migrants of period cohort a of gender g are estimated using the forward demographic rate definition. Out-migration rates for period cohort a of gender g are defined by migration flow divided by the initial population. The death rate for period cohort A1 and A are estimated using a single region method. Death and migration rates are simultaneously estimated with an iterative procedure. The population accounts estimates and demographic rates are provided for the period ending 1986-87 for male births, males in period cohorts 10 and 20, female births, and females in period cohorts 10 and 20. The urban and rural population projection model is based on the population accounts concept and assumes fixed rates of mortality, migration, and normal fertility for the base year 1987. The results of this projection are a population of 1090 million that will grow to 1304 million in 2000, 1720 million in 2050, and 1791 million in 2087. Urban population will expand from 44.2% in 1988 to 46.6% in 2000, and 54.7% in 2087. The labor population of males 18-65 years and females 18-60 years will increase from 58.8% in 1988 to 59.7% in 2000 and decline to 58.4% by 2087. The old age population of males 65 years and females 60 years will increase from 6.5% in 1988 to 7.9% in 2000, and 16.3% in 2087. The mean age increased from 28.3 years in 1988 to 37 in 2087. Urban population may be underprojected; migration problems are recognized. Fertility also is likely to decline. An alternative projection (B) is given to account for the U-shape distribution and urban fertility of 1.8 in 2000, increasing to

  13. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

    PubMed

    Pradhan, Sharat Kumar; Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai; Pandit, Elssa

    2016-01-01

    Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright's F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.

  14. 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

  15. Company observational post-marketing studies: drug risk assessment and drug research in special populations--a study-based analysis.

    PubMed

    Hasford, J; Lamprecht, T

    1998-01-01

    Company observational post-marketing studies (COPS) claim to provide essential data about drug risks and effectiveness in special populations not admitted to pre-approval clinical trials. Since COPS are often mainly regarded as a marketing activity, this study-based analysis tries to evaluate the scientific contributions of COPS. Thirty-five COPS were identified by hand-searching through medical journals, writing to pharmaceutical manufacturers and using MEDLINE. Fourteen COPS evaluated cardiovascular drugs, 9 evaluated NSAIDs and 12 evaluated various other indications. Thirty-five COPS listed effectiveness, 31 listed safety and 8 listed patient compliance as principal objectives. Not a single COPS included a control group. Seventeen of 21 evaluable COPS mentioned extensive exclusion criteria similar to those in clinical trials. Median observation time was 8 weeks, too short for chronic diseases and for adverse drug reactions with longer latency periods. One new adverse event was regarded. Global assessments of the outcomes by physicians dominated and were not based on objective clinical findings. None of the studies specified any details concerning the standardisation of observations or quality-control procedures. The current COPS scheme does not contribute significantly to our knowledge of drug safety and the effects in special populations. Despite serious criticism over the past 20 years, the poor quality of COPS compared with dramatic improvements of pre-approval trials - implies a need for detailed guidelines for non-experimental phase IV research, similar to the Good Clinical Practice-Guideline of the European Community.

  16. [Static Retinal Vessel Analysis in Population-based Study SHIP-Trend].

    PubMed

    Theophil, Constanze; Jürgens, Clemens; Großjohann, Rico; Kempin, Robert; Ittermann, Till; Nauck, Matthias; Völzke, Henry; Tost, Frank H W

    2017-08-24

    Background Interdisciplinary investigations of possible connections between general diseases and ophthalmological changes are difficult to perform in the clinical environment. But they are gaining in importance as a result of the age-related increase in chronic diseases. The collection of health-related parameters in the Study of Health in Pomerania (SHIP) project allows to derive conclusions for the general population. Methods The population-based SHIP trend study was conducted between 2008 and 2012 in Greifswald. The baseline cohort included 4420 subjects (response 50.1%) at the age of 20 to 84 years. The pre-existence of arterial hypertension, diabetes mellitus and smoking status were questioned in a standardized questionnaire, the blood pressure and the HbA 1c were determined by the laboratory. The vascular diameter of retinal arterioles and venules were determined by means of non-mydriatic fundus images and the retinal arterial (CRAE) and venous equivalent (CRVE) were calculated therefrom. The association of diabetes mellitus, HbA 1c , smoking status and blood pressure with the retinal vascular parameters was tested for age and sex with linear regression models. Results In 3218 subjects with evaluable standardized fundus photographs, significant associations of elevated HbA 1c (> 6.5%), smoking status and systolic and diastolic blood pressure were found with the retinal vessel widths CRAE and CRVE. Anamnestic diabetes mellitus, on the other hand, was not associated with any of the vascular parameters. Conclusion This research study reveals a relevant correlation between general diseases and the retinal blood flow in the eye. Therefore, general diseases can induce ophthalmological changes and eye examination can provide information for the assessment of general diseases. Georg Thieme Verlag KG Stuttgart · New York.

  17. New Insights on Taxonomy, Phylogeny and Population Genetics of Leishmania (Viannia) Parasites Based on Multilocus Sequence Analysis

    PubMed Central

    Boité, Mariana C.; Mauricio, Isabel L.; Miles, Michael A.; Cupolillo, Elisa

    2012-01-01

    species status of some entities. Furthermore, it contributes to the phylogeny of L. (Viannia) and might be helpful for epidemiological and population genetics analysis based on haplotype/diplotype determinations and inferences. PMID:23133690

  18. Cost-effectiveness analysis of population-based tobacco control strategies in the prevention of cardiovascular diseases in Tanzania

    PubMed Central

    Ngalesoni, Frida; Ruhago, George; Mayige, Mary; Oliveira, Tiago Cravo; Robberstad, Bjarne; Norheim, Ole Frithjof; Higashi, Hideki

    2017-01-01

    Background Tobacco consumption contributes significantly to the global burden of disease. The prevalence of smoking is estimated to be increasing in many low-income countries, including Tanzania, especially among women and youth. Even so, the implementation of tobacco control measures has been discouraging in the country. Efforts to foster investment in tobacco control are hindered by lack of evidence on what works and at what cost. Aims We aim to estimate the cost and cost-effectiveness of population-based tobacco control strategies in the prevention of cardiovascular diseases (CVD) in Tanzania. Materials and methods A cost-effectiveness analysis was performed using an Excel-based Markov model, from a governmental perspective. We employed an ingredient approach and step-down methodologies in the costing exercise following a government perspective. Epidemiological data and efficacy inputs were derived from the literature. We used disability-adjusted life years (DALYs) averted as the outcome measure. A probabilistic sensitivity analysis was carried out with Ersatz to incorporate uncertainties in the model parameters. Results Our model results showed that all five tobacco control strategies were very cost-effective since they fell below the ceiling ratio of one GDP per capita suggested by the WHO. Increase in tobacco taxes was the most cost-effective strategy, while a workplace smoking ban was the least cost-effective option, with a cost-effectiveness ratio of US$5 and US$267, respectively. Conclusions Even though all five interventions are deemed very cost-effective in the prevention of CVD in Tanzania, more research on budget impact analysis is required to further assess the government’s ability to implement these interventions. PMID:28767722

  19. 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.

  20. 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

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

    ERIC Educational Resources Information Center

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

    2011-01-01

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

  2. Genome-Wide Meta-Analysis of Sciatica in Finnish Population.

    PubMed

    Lemmelä, Susanna; Solovieva, Svetlana; Shiri, Rahman; Benner, Christian; Heliövaara, Markku; Kettunen, Johannes; Anttila, Verneri; Ripatti, Samuli; Perola, Markus; Seppälä, Ilkka; Juonala, Markus; Kähönen, Mika; Salomaa, Veikko; Viikari, Jorma; Raitakari, Olli T; Lehtimäki, Terho; Palotie, Aarno; Viikari-Juntura, Eira; Husgafvel-Pursiainen, Kirsti

    2016-01-01

    Sciatica or the sciatic syndrome is a common and often disabling low back disorder in the working-age population. It has a relatively high heritability but poorly understood molecular mechanisms. The Finnish population is a genetic isolate where small founder population and bottleneck events have led to enrichment of certain rare and low frequency variants. We performed here the first genome-wide association (GWAS) and meta-analysis of sciatica. The meta-analysis was conducted across two GWAS covering 291 Finnish sciatica cases and 3671 controls genotyped and imputed at 7.7 million autosomal variants. The most promising loci (p<1x10-6) were replicated in 776 Finnish sciatica patients and 18,489 controls. We identified five intragenic variants, with relatively low frequencies, at two novel loci associated with sciatica at genome-wide significance. These included chr9:14344410:I (rs71321981) at 9p22.3 (NFIB gene; p = 1.30x10-8, MAF = 0.08) and four variants at 15q21.2: rs145901849, rs80035109, rs190200374 and rs117458827 (MYO5A; p = 1.34x10-8, MAF = 0.06; p = 2.32x10-8, MAF = 0.07; p = 3.85x10-8, MAF = 0.06; p = 4.78x10-8, MAF = 0.07, respectively). The most significant association in the meta-analysis, a single base insertion rs71321981 within the regulatory region of the transcription factor NFIB, replicated in an independent Finnish population sample (p = 0.04). Despite identifying 15q21.2 as a promising locus, we were not able to replicate it. It was differentiated; the lead variants within 15q21.2 were more frequent in Finland (6-7%) than in other European populations (1-2%). Imputation accuracies of the three significantly associated variants (chr9:14344410:I, rs190200374, and rs80035109) were validated by genotyping. In summary, our results suggest a novel locus, 9p22.3 (NFIB), which may be involved in susceptibility to sciatica. In addition, another locus, 15q21.2, emerged as a promising one, but failed to replicate.

  3. Genome-Wide Meta-Analysis of Sciatica in Finnish Population

    PubMed Central

    Lemmelä, Susanna; Solovieva, Svetlana; Shiri, Rahman; Benner, Christian; Heliövaara, Markku; Kettunen, Johannes; Anttila, Verneri; Ripatti, Samuli; Perola, Markus; Seppälä, Ilkka; Juonala, Markus; Kähönen, Mika; Salomaa, Veikko; Viikari, Jorma; Raitakari, Olli T.; Lehtimäki, Terho; Palotie, Aarno; Viikari-Juntura, Eira; Husgafvel-Pursiainen, Kirsti

    2016-01-01

    Sciatica or the sciatic syndrome is a common and often disabling low back disorder in the working-age population. It has a relatively high heritability but poorly understood molecular mechanisms. The Finnish population is a genetic isolate where small founder population and bottleneck events have led to enrichment of certain rare and low frequency variants. We performed here the first genome-wide association (GWAS) and meta-analysis of sciatica. The meta-analysis was conducted across two GWAS covering 291 Finnish sciatica cases and 3671 controls genotyped and imputed at 7.7 million autosomal variants. The most promising loci (p<1x10-6) were replicated in 776 Finnish sciatica patients and 18,489 controls. We identified five intragenic variants, with relatively low frequencies, at two novel loci associated with sciatica at genome-wide significance. These included chr9:14344410:I (rs71321981) at 9p22.3 (NFIB gene; p = 1.30x10-8, MAF = 0.08) and four variants at 15q21.2: rs145901849, rs80035109, rs190200374 and rs117458827 (MYO5A; p = 1.34x10-8, MAF = 0.06; p = 2.32x10-8, MAF = 0.07; p = 3.85x10-8, MAF = 0.06; p = 4.78x10-8, MAF = 0.07, respectively). The most significant association in the meta-analysis, a single base insertion rs71321981 within the regulatory region of the transcription factor NFIB, replicated in an independent Finnish population sample (p = 0.04). Despite identifying 15q21.2 as a promising locus, we were not able to replicate it. It was differentiated; the lead variants within 15q21.2 were more frequent in Finland (6–7%) than in other European populations (1–2%). Imputation accuracies of the three significantly associated variants (chr9:14344410:I, rs190200374, and rs80035109) were validated by genotyping. In summary, our results suggest a novel locus, 9p22.3 (NFIB), which may be involved in susceptibility to sciatica. In addition, another locus, 15q21.2, emerged as a promising one, but failed to replicate. PMID:27764105

  4. Extreme Gleason Upgrading From Biopsy to Radical Prostatectomy: A Population-based Analysis.

    PubMed

    Winters, Brian R; Wright, Jonathan L; Holt, Sarah K; Lin, Daniel W; Ellis, William J; Dalkin, Bruce L; Schade, George R

    2016-10-01

    To examine the risk factors associated with the odds of extreme Gleason upgrading at radical prostatectomy (RP) (defined as a Gleason prognostic group score increase of ≥2), we utilized a large, population-based cancer registry. The Surveillance, Epidemiologic, and End Results database was queried (2010-2011) for all patients diagnosed with Gleason 3 + 3 or 3 + 4 on prostate needle biopsy. Available clinicopathologic factors and the odds of upgrading and extreme upgrading at RP were evaluated using multivariate logistic regression. A total of 12,459 patients were identified, with a median age of 61 (interquartile range: 56-65) and a diagnostic prostate-specific antigen (PSA) of 5.5 ng/mL (interquartile range: 4.3-7.5). Upgrading was observed in 34% of men, including 44% of 7402 patients with Gleason 3 + 3 and 19% of 5057 patients with Gleason 3 + 4 disease. Age, clinical stage, diagnostic PSA, and % prostate needle biopsy cores positive were independently associated with odds of any upgrading at RP. In baseline Gleason 3 + 3 disease, extreme upgrading was observed in 6%, with increasing age, diagnostic PSA, and >50% core positivity associated with increased odds. In baseline Gleason 3 + 4 disease, extreme upgrading was observed in 4%, with diagnostic PSA and palpable disease remaining predictive. Positive surgical margins were significantly higher in patients with extreme upgrading at RP (P < .001). Gleason upgrading at RP is common in this large population-based cohort, including extreme upgrading in a clinically significant portion. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Community-based cardiovascular health interventions in vulnerable populations: a systematic review.

    PubMed

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

    2014-07-01

    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. This article provides a critical review of community-based cardiovascular disease interventions to improve cardiovascular health behaviors and factors among vulnerable populations based on the American Heart Association's 7 metrics of ideal cardiovascular health. In February 2011, 4 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. This search strategy resulted in the retrieval of 7120 abstracts. Each abstract was reviewed by at least 2 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 multicomponent. Healthcare providers were the most frequent interventionists. Interventions aimed at decreasing blood pressure were the most promising, whereas 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. This analysis provides a step toward understanding the current literature on cardiovascular interventions for vulnerable population. The next step should be integrating the identified successful interventions into larger health systems and/or social policies.

  6. Predicting the number of emergency department presentations in Western Australia: a population-based time series analysis.

    PubMed

    Mai, Qun; Aboagye-Sarfo, Patrick; Sanfilippo, Frank M; Preen, David B; Fatovich, Daniel M

    2015-02-01

    To predict the number of ED presentations in Western Australia (WA) in the next 5 years, stratified by place of treatment, age, triage and disposition. We conducted a population-based time series analysis of 7 year monthly WA statewide ED presentation data from the financial years 2006/07 to 2012/13 using univariate autoregressive integrated moving average (ARIMA) and multivariate vector-ARIMA techniques. ED presentations in WA were predicted to increase from 990,342 in 2012/13 to 1,250,991 (95% CI: 982,265-1,519,718) in 2017/18, an increase of 260,649 (or 26.3%). The majority of this increase would occur in metropolitan WA (84.2%). The compound annual growth rate (CAGR) in metropolitan WA in the next 5 years was predicted to be 6.5% compared with 2.0% in the non-metropolitan area. The greatest growth in metropolitan WA would be in ages 65 and over (CAGR, 6.9%), triage categories 2 and 3 (8.3% and 7.7%, respectively) and admitted (9.8%) cohorts. The only predicted decrease was triage category 5 (-5.3%). ED demand in WA will exceed population growth. The highest growth will be in patients with complex care needs. An integrated system-wide strategy is urgently required to ensure access, quality and sustainability of the health system. © 2015 Australasian College for Emergency Medicine and Australasian Society for Emergency Medicine.

  7. 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

  8. The implementation of DRG-based hospital reimbursement in Switzerland: A population-based perspective.

    PubMed

    Busato, André; von Below, Georg

    2010-10-16

    Switzerland introduces a DRG (Diagnosis Related Groups) based system for hospital financing in 2012 in order to increase efficiency and transparency of Swiss health care. DRG-based hospital reimbursement is not simultaneously realized in all Swiss cantons and several cantons already implemented DRG-based financing irrespective of the national agenda, a setting that provides an opportunity to compare the situation in different cantons. Effects of introducing DRGs anticipated for providers and insurers are relatively well known but it remains less clear what effects DRGs will have on served populations. The objective of the study is therefore to analyze differences of volume and major quality indicators of care between areas with or without DRG-based hospital reimbursement from a population based perspective. Small area analysis of all hospitalizations in acute care hospitals and of all consultations reimbursed by mandatory basic health insurance for physicians in own practice during 2003-2007. The results show fewer hospitalizations and a relocation of resources to outpatient care in areas with DRG reimbursement. Overall burden of disease expressed as per capita DRG cost weights was almost identical between the two types of hospital reimbursement and no distinct temporal differences were detected in this respect. But the results show considerably higher 90-day rehospitalization rates in DRG areas. The study provides evidence of both desired and harmful effects related to the implementation of DRGs. Systematic monitoring of outcomes and quality of care are therefore essential elements to maintain in the Swiss health system after DRG's are implemented on a nationwide basis in 2012.

  9. Intervention analysis of power plant impact on fish populations

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

    Madenjian, C.P.

    1984-10-01

    Intervention analysis was applied to 10 yr (years 1973-1982) of field fish abundance data at the D. C. Cook Nuclear Power Plant, southeastern Lake Michigan. Three log-transformed catch series, comprising monthly observations, were examined for each combination of two species (alewife, Alosa pseudoharenga, or yellow perch, Perca flavescens) and gear (trawl or gill net): catch at the plant discharged transect, catch at the reference transect, and the ratio of plant catch to reference catch. Time series separated by age groups were examined. Based on intervention analysis, no change in the abundance of fish populations could be attributed to plant operation.more » Additionally, a modification of the intervention analysis technique was applied to investigate trends in abundance at both the plant discharge and reference transects. Significant declines were detected for abundance of alewife adults at both of the transects. Results of the trend analysis support the contention that the alewives have undergone a lakewide decrease in abundance during the 1970s.« less

  10. Health-Related Lifestyle Factors and Sexual Dysfunction: A Meta-Analysis of Population-Based Research.

    PubMed

    Allen, Mark S; Walter, Emma E

    2018-04-01

    -adjusted models and tests of potential moderators using meta-regression. Limitations include low statistical power in models testing diet, caffeine, and cannabis use as risk factors. Results provide compelling evidence that cigarette smoking, alcohol, and physical activity are important for sexual dysfunction. Insufficient research was available to draw conclusions regarding risk factors for premature ejaculation or for cannabis use as a risk factor. These findings should be of interest to clinicians treating men and women with complaints relating to symptoms of sexual dysfunction. Allen MS, Walter EE. Health-Related Lifestyle Factors and Sexual Dysfunction: A Meta-Analysis of Population-Based Research. J Sex Med 2018;15:458-475. Copyright © 2018 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

  11. [An analysis of the 1987 population situation in China].

    PubMed

    Li, R

    1988-01-01

    Presented here is an analysis of some of the manually collected data from a 1% random sample of China's population taken on 7/1/87. 1)Population growth: The population grew 6.36% from 1982-87 to give a total population of 1,072,330,000. Even though the average annual growth rate of 1.24% during these years is slower than the growth rate of the 1950s and 1960s, this does not mean that China can be complacent about it. Due to China's large population base, every year its population increases by about 13,000,000, with serious implications for consumerism, education and labor. The natural rate of growth dropped during 1982-84, but by 1987, it had increased again to 1981 levels. If China is to limit its population to 1.25 billion by 2000, the average annual growth rate must remain below 1.23%, which is lower than the figures of recent years. 2) Sex differences: the population was 51.1% male and 48.9% female. 3) Age structure: 28.68% of the population were 14 years and younger; 65.86% were between 15-64 years; 5.46% were 65 years and older. The median age was 24.2 years. The percentage of the 0-14 year bracket dropped about 7.6% from 1953-87, while the 15-64 year olds increased 6.6% and the 65 years and older group increased 1%. On the surface, a 1% increase of the aged would not present a problem to China taken as a whole. However, when densely populated areas such as Shanghai are looked at, the situation demands immediate attention. 4) Ethnic groups: 92% of the population were Han. Minorities increased 5% annually between 1982-87 to comprise 8% of the population. This rapid growth among minorities is due in part to official permission for families to bear more than one child, and to better sanitary and medical attention. 6) Population distribution: 37.1% of the population lived in urban areas, as compared with 10% in 1949. By 1990 the urban population could reach 40%, creating serious social, economic and political pressure on cities.

  12. Population-Based Assessment of Exposure to Risk Behaviors in Motion Pictures

    PubMed Central

    Sargent, James D.; Worth, Keilah A.; Beach, Michael; Gerrard, Meg; Heatherton, Todd F.

    2008-01-01

    The aim of most population-based studies of media is to relate a specific exposure to an outcome of interest. A research program has been developed that evaluates exposure to different components of movies in an attempt of assess the association of such exposure with the adoption of substance use during adolescence. To assess exposure to movie substance use, one must measure both viewing time and content. In developing the exposure measure, the study team was interested in circumventing a common problem in exposure measurement, where measures often conflate exposure to media with attention to media. Our aim in this paper is to present a validated measure of exposure to entertainment media, the Beach method, which combines recognition of a movie title with content analysis of the movie for substance use, to generate population based measures of exposure to substance use in this form of entertainment. PMID:19122801

  13. Population-Based Assessment of Exposure to Risk Behaviors in Motion Pictures.

    PubMed

    Sargent, James D; Worth, Keilah A; Beach, Michael; Gerrard, Meg; Heatherton, Todd F

    2008-01-01

    The aim of most population-based studies of media is to relate a specific exposure to an outcome of interest. A research program has been developed that evaluates exposure to different components of movies in an attempt of assess the association of such exposure with the adoption of substance use during adolescence. To assess exposure to movie substance use, one must measure both viewing time and content. In developing the exposure measure, the study team was interested in circumventing a common problem in exposure measurement, where measures often conflate exposure to media with attention to media. Our aim in this paper is to present a validated measure of exposure to entertainment media, the Beach method, which combines recognition of a movie title with content analysis of the movie for substance use, to generate population based measures of exposure to substance use in this form of entertainment.

  14. 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

  15. [Breast cancer incidence related with a population-based screening program].

    PubMed

    Natal, Carmen; Caicoya, Martín; Prieto, Miguel; Tardón, Adonina

    2015-02-20

    To compare breast cancer cumulative incidence, time evolution and stage at diagnosis between participants and non-participant women in a population-based screening program. Cohort study of breast cancer incidence in relation to participation in a population screening program. The study population included women from the target population of the screening program. The source of information for diagnostics and stages was the population-based cancer registry. The analysis period was 1999-2010. The Relative Risk for invasive, in situ, and total cancers diagnosed in participant women compared with non-participants were respectively 1.16 (0.94-1.43), 2.98 (1.16-7.62) and 1.22 (0.99-1.49). The Relative Risk for participants versus non-participants was 2.47 (1.55-3.96) for diagnosis at stagei, 2.58 (1.67-3.99) for T1 and 2.11 (1.38-3.23) for negative lymph node involvement. The cumulative incidence trend had two joint points in both arms, with an Annual Percent of Change of 92.3 (81.6-103.5) between 1999-2001, 18.2 (16.1-20.3) between 2001-2005 and 5.9 (4.0-7.8) for the last period in participants arm, and 72.6 (58.5-87.9) between 1999-2001, 12.6 (7.9-17.4) between 2001-2005, and 8.6 (6.5-10.6) in the last period in the non-participant arm. Participating in the breast cancer screening program analyzed increased the in situ cumulative cancer incidence, but not the invasive and total incidence. Diagnoses were earlier in the participant arm. Copyright © 2014 Elsevier España, S.L.U. All rights reserved.

  16. Economic evaluation of a group-based exercise program for falls prevention among the older community-dwelling population.

    PubMed

    McLean, Kendra; Day, Lesley; Dalton, Andrew

    2015-03-26

    Falls among older people are of growing concern globally. Implementing cost-effective strategies for their prevention is of utmost importance given the ageing population and associated potential for increased costs of fall-related injury over the next decades. The purpose of this study was to undertake a cost-utility analysis and secondary cost-effectiveness analysis from a healthcare system perspective, of a group-based exercise program compared to routine care for falls prevention in an older community-dwelling population. A decision analysis using a decision tree model was based on the results of a previously published randomised controlled trial with a community-dwelling population aged over 70. Measures of falls, fall-related injuries and resource use were directly obtained from trial data and supplemented by literature-based utility measures. A sub-group analysis was performed of women only. Cost estimates are reported in 2010 British Pound Sterling (GBP). The ICER of GBP£51,483 per QALY for the base case analysis was well above the accepted cost-effectiveness threshold of GBP£20,000 to £30,000 per QALY, but in a sensitivity analysis with minimised program implementation the incremental cost reached GBP£25,678 per QALY. The ICER value at 95% confidence in the base case analysis was GBP£99,664 per QALY and GBP£50,549 per QALY in the lower cost analysis. Males had a 44% lower injury rate if they fell, compared to females resulting in a more favourable ICER for the women only analysis. For women only the ICER was GBP£22,986 per QALY in the base case and was below the cost-effectiveness threshold for all other variations of program implementation. The ICER value at 95% confidence was GBP£48,212 in the women only base case analysis and GBP£23,645 in the lower cost analysis. The base case incremental cost per fall averted was GBP£652 (GBP£616 for women only). A threshold analysis indicates that this exercise program cannot realistically break even. The

  17. Population-based studies of antithyroid drugs and sudden cardiac death

    PubMed Central

    van Noord, Charlotte; Sturkenboom, Miriam C J M; Straus, Sabine M J M; Hofman, Albert; Witteman, Jacqueline C M; Stricker, Bruno H Ch

    2009-01-01

    AIM Thyroid free T4 is associated with QTc-interval prolongation, which is a risk factor for sudden cardiac death (SCD). Hyperthyroidism has been associated with SCD in case reports, but there are no population-based studies confirming this. The aim was to investigate whether use of antithyroid drugs (as a direct cause or as an indicator of poorly controlled hyperthyroidism) is associated with an increased risk of SCD. METHODS We studied the occurrence of SCD in a two-step procedure in two different Dutch populations. First, the prospective population-based Rotterdam Study including 7898 participants (≥55 years old). Second, we used the Integrated Primary Care Information (IPCI) database, which is a longitudinal general practice research database to see whether we could replicate results from the first study. Drug use at the index date was assessed with prescription information from automated pharmacies (Rotterdam Study) or drug prescriptions from general practices (IPCI). We used a Cox proportional hazards model in a cohort analysis, adjusted for age, gender and use of QTc prolonging drugs (Rotterdam Study) and conditional logistic regression analysis in a case–control analysis, matched for age, gender, practice and calendar time and adjusted for arrhythmia and cerebrovascular ischaemia (IPCI). RESULTS In the Rotterdam Study, 375 participants developed SCD during follow-up. Current use of antithyroid drugs was associated with SCD [adjusted hazard ratio 3.9; 95% confidence interval (CI) 1.7, 8.7]. IPCI included 1424 cases with SCD and 14 443 controls. Also in IPCI, current use of antithyroid drugs was associated with SCD (adjusted odds ratio 2.9; 95% CI 1.1, 7.4). CONCLUSIONS Use of antithyroid drugs was associated with a threefold increased risk of SCD. Although this might be directly caused by antithyroid drug use, it might be more readily explained by underlying poorly controlled hyperthyroidism, since treated patients who developed SCD still had low thyroid

  18. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update.

    PubMed

    Peakall, Rod; Smouse, Peter E

    2012-10-01

    GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G'(ST), G''(ST), Jost's D(est) and F'(ST) through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised. GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx. rod.peakall@anu.edu.au.

  19. Breast and ovarian cancer risks to carriers of the BRCA1 5382insC and 185delAG and BRCA2 6174delT mutations: a combined analysis of 22 population based studies

    PubMed Central

    Antoniou, A; Pharoah, P; Narod, S; Risch, H; Eyfjord, J; Hopper, J; Olsson, H; Johannsson, O; Borg, A; Pasini, B; Radice, P; Manoukian, S; Eccles, D; Tang, N; Olah, E; Anton-Culver, H; Warner, E; Lubinski, J; Gronwald, J; Gorski, B; Tulinius, H; Thorlacius, S; Eerola, H; Nevanlinna, H; Syrjakoski, K; Kallioniemi, O; Thompson, D; Evans, C; Peto, J; Lalloo, F; Evans, D; Easton, D

    2005-01-01

    A recent report estimated the breast cancer risks in carriers of the three Ashkenazi founder mutations to be higher than previously published estimates derived from population based studies. In an attempt to confirm this, the breast and ovarian cancer risks associated with the three Ashkenazi founder mutations were estimated using families included in a previous meta-analysis of populatrion based studies. The estimated breast cancer risks for each of the founder BRCA1 and BRCA2 mutations were similar to the corresponding estimates based on all BRCA1 or BRCA2 mutations in the meta-analysis. These estimates appear to be consistent with the observed prevalence of the mutations in the Ashkenazi Jewish population. PMID:15994883

  20. Automated Analysis of a Nematode Population-based Chemosensory Preference Assay

    PubMed Central

    Chai, Cynthia M.; Cronin, Christopher J.; Sternberg, Paul W.

    2017-01-01

    The nematode, Caenorhabditis elegans' compact nervous system of only 302 neurons underlies a diverse repertoire of behaviors. To facilitate the dissection of the neural circuits underlying these behaviors, the development of robust and reproducible behavioral assays is necessary. Previous C. elegans behavioral studies have used variations of a "drop test", a "chemotaxis assay", and a "retention assay" to investigate the response of C. elegans to soluble compounds. The method described in this article seeks to combine the complementary strengths of the three aforementioned assays. Briefly, a small circle in the middle of each assay plate is divided into four quadrants with the control and experimental solutions alternately placed. After the addition of the worms, the assay plates are loaded into a behavior chamber where microscope cameras record the worms' encounters with the treated regions. Automated video analysis is then performed and a preference index (PI) value for each video is generated. The video acquisition and automated analysis features of this method minimizes the experimenter's involvement and any associated errors. Furthermore, minute amounts of the experimental compound are used per assay and the behavior chamber's multi-camera setup increases experimental throughput. This method is particularly useful for conducting behavioral screens of genetic mutants and novel chemical compounds. However, this method is not appropriate for studying stimulus gradient navigation due to the close proximity of the control and experimental solution regions. It should also not be used when only a small population of worms is available. While suitable for assaying responses only to soluble compounds in its current form, this method can be easily modified to accommodate multimodal sensory interaction and optogenetic studies. This method can also be adapted to assay the chemosensory responses of other nematode species. PMID:28745641

  1. 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

  2. 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

  3. Choice-Based Conjoint Analysis: Classification vs. Discrete Choice Models

    NASA Astrophysics Data System (ADS)

    Giesen, Joachim; Mueller, Klaus; Taneva, Bilyana; Zolliker, Peter

    Conjoint analysis is a family of techniques that originated in psychology and later became popular in market research. The main objective of conjoint analysis is to measure an individual's or a population's preferences on a class of options that can be described by parameters and their levels. We consider preference data obtained in choice-based conjoint analysis studies, where one observes test persons' choices on small subsets of the options. There are many ways to analyze choice-based conjoint analysis data. Here we discuss the intuition behind a classification based approach, and compare this approach to one based on statistical assumptions (discrete choice models) and to a regression approach. Our comparison on real and synthetic data indicates that the classification approach outperforms the discrete choice models.

  4. 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

  5. Are brief alcohol interventions targeting alcohol use efficacious in military and veteran populations? A meta-analysis.

    PubMed

    Doherty, A M; Mason, C; Fear, N T; Rona, R; Greenberg, N; Goodwin, L

    2017-09-01

    Rates of hazardous and harm-related drinking are higher in the military and veteran populations compared to the general population. Brief alcohol interventions (BAIs) targeting alcohol use appear to reduce harmful drinking in the general population. However, less is known about the efficacy of BAIs targeting alcohol in military and veteran populations. A systematic review and meta-analysis was conducted to assess the type and efficacy of BAIs used to reduce alcohol use in military and veteran populations conducted from 2000 onwards. The meta-analysis was conducted using a standardised outcome measure of change in average weekly drinks (AWDs) from baseline to follow-up. The search revealed 10 papers that met the search criteria, and that reported data on 11 interventions included in the systematic review. 8 papers (reporting on 9 different interventions) were included in the meta-analysis after 2 papers were excluded for which the relevant outcome data were not available. There was no overall effect of BAIs; a non-significant weekly drink reduction of 0.95 drinks was found (95% CI, -0.17 to 2.07). This lack of efficacy persisted regardless of military group (conscripts, serving or veterans) and method of delivery (i.e., face-to-face, web-based or written information). Furthermore, sensitivity analyses revealed this small drink reduction was driven mainly by a single study. Based on these findings, existing BAIs do not seem to be efficacious in reducing alcohol use in military populations, despite some encouraging results from one electronic intervention which was of extensive duration. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. The natural history of Dandy-Walker syndrome in the United States: A population-based analysis

    PubMed Central

    McClelland, Shearwood; Ukwuoma, Onyinyechi I.; Lunos, Scott; Okuyemi, Kolawole S.

    2015-01-01

    Background: Dandy-Walker syndrome (DWS) is a congenital disorder typically manifesting with hydrocephalus. The classic anatomic hallmarks of DWS are hypoplasia of the cerebellar vermis, anterior-posterior enlargement of the posterior fossa, upward displacement of the torcula and transverse sinuses, and cystic dilatation of the fourth ventricle. Aims: Although optimal treatment of DWS typically requires neurosurgical intervention to prevent intracranial pressure increases incompatible with life, the natural history of this disorder has yet to be evaluated on a nationwide level. Settings and Design/Materials and Methods: The Kids’ Inpatient Database covering 1997-2003 was used for analysis. Children younger than age 18 admitted for DWS (ICD-9-CM = 742.3) were analyzed with a matched control group. The primary procedure codes for operative CSF drainage were coded into the analysis. The incidence of DWS was 0.136%; 14,599 DWS patients were included. Statistical Analysis Used: Multiple logistic regression models were used. Odds ratios (OR) were reported with 95% confidence intervals. Results and Conclusions: Mortality (OR = 10.02; P < 0.0001) and adverse discharge disposition (OR = 4.59; P < 0.0001) were significantly greater in DWS patients compared with controls. 20.4% of DWS patients received operative cerebrospinal fluid (CSF) drainage, 81-times more than controls (P < 0.0001). CSF drainage reduced mortality by 44% among DWS patients (P < 0.0001). Although DWS is associated with a 10-fold increase in mortality, operative CSF drainage nearly halves the mortality rate. Based on these findings (Class IIB evidence), it is likely that the increased mortality associated with DWS is directly attributable to the nearly 80% of DWS patients who did not receive operative CSF drainage for hydrocephalus. Consequently, increased access to neurosurgical intervention could reduce the mortality rate of DWS towards that of the general population. PMID:25552847

  7. Advance notification letters increase adherence in colorectal cancer screening: a population-based randomized trial.

    PubMed

    van Roon, A H C; Hol, L; Wilschut, J A; Reijerink, J C I Y; van Vuuren, A J; van Ballegooijen, M; Habbema, J D F; van Leerdam, M E; Kuipers, Ernst J

    2011-06-01

    The population benefit of screening depends not only on the effectiveness of the test, but also on adherence, which, for colorectal cancer (CRC) screening remains low. An advance notification letter may increase adherence, however, no population-based randomized trials have been conducted to provide evidence of this. In 2008, a representative sample of the Dutch population (aged 50-74 years) was randomized. All 2493 invitees in group A were sent an advance notification letter, followed two weeks later by a standard invitation. The 2507 invitees in group B only received the standard invitation. Non-respondents in both groups were sent a reminder 6 weeks after the invitation. The advance notification letters resulted in a significantly higher adherence (64.4% versus 61.1%, p-value 0.019). Multivariate logistic regression analysis showed no significant interactions between group and age, sex, or socio-economic status. Cost analysis showed that the incremental cost per additional detected advanced neoplasia due to sending an advance notification letter was € 957. This population-based randomized trial demonstrates that sending an advance notification letter significantly increases adherence by 3.3%. The incremental cost per additional detected advanced neoplasia is acceptable. We therefore recommend that such letters are incorporated within the standard CRC-screening invitation process. Copyright © 2011 Elsevier Inc. All rights reserved.

  8. Factors associated with quality of life in active childhood epilepsy: a population-based study.

    PubMed

    Reilly, Colin; Atkinson, Patricia; Das, Krishna B; Chin, Richard F M; Aylett, Sarah E; Burch, Victoria; Gillberg, Christopher; Scott, Rod C; Neville, Brian G R

    2015-05-01

    Improving health-related quality of life (HRQOL), rather than just reducing seizures, should be the principal goal in comprehensive management of childhood epilepsy. There is a lack of population-based data on predictors of HRQOL in childhood epilepsy. The Children with Epilepsy in Sussex Schools (CHESS) study is a prospective, population-based study involving school-aged children (5-15 years) with active epilepsy (on one or more AED and/or had a seizure in the last year) in a defined geographical area in the UK. Eighty-five of 115 (74% of eligible population) children underwent comprehensive psychological assessment including measures of cognition, behaviour, and motor functioning. Parents of the children completed the Quality of Life in Childhood Epilepsy (QOLCE).Clinical data on eligible children was extracted using a standardised pro forma. Linear regression analysis was undertaken to identify factors significantly associated with total Quality of Life in this population. Factors independently significantly associated (p < .05) with total QOLCE scores were seizures before 24 months, cognitive impairment (IQ < 85), anxiety, and parent reported school attendance difficulty. These factors were also significantly associated with total QOLCE when children with IQ < 50 were excluded from analysis. The majority of factors associated with parent reported HRQOL in active childhood epilepsy are related to neurobehavioural and/or psychosocial aspects of the condition. Copyright © 2015 European Paediatric Neurology Society. Published by Elsevier Ltd. All rights reserved.

  9. Methylenetetrahydrofolate reductase polymorphisms and susceptibility to acute lymphoblastic leukemia in a Chinese population: a meta-analysis.

    PubMed

    Xiao, Yi; Deng, Tao-Ran; Su, Chang-Liang; Shang, Zhen

    2014-01-01

    Although many epidemiologic studies have investigated the methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms and their association with acute lymphoblastic leukemia (ALL), definitive conclusions cannot be drawn. To clarify the effects of MTHFR polymorphisms on the risk of ALL, a meta-analysis was performed in a Chinese population. A computerized literature search was carried out in PubMed, the Chinese Biomedicine (CBM) database, China National Knowledge Infrastructure (CNKI) platform, and the Wanfang database (Chinese) to collect relevant articles. A total of 11 articles including 1,738 ALL cases and 2,438 controls were included in this meta-analysis. Overall, a significantly decreased association was found between the MTHFR C677T polymorphism and ALL risk when all studies in Chinese populations were pooled into the meta-analysis. In subgroup analyses stratified by age, ethnicity, and source of controls, the same results were observed in children, in population-based studies, and in people with no stated ethnicity. However, a significantly increased association was also found for MTHFR C677T in hospital-based studies, and for MTHFR A1298C in people with no stated ethnicity. Our results suggest that the MTHFR C677T and A1298C polymorphisms may be potential biomarkers for ALL risk in Chinese populations, and studies with a larger sample size and wider population spectrum are required before definitive conclusions can be drawn. © 2014 S. Karger GmbH, Freiburg.

  10. 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

  11. 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.

  12. Molecular diversity and population structure of the forage grass Hemarthria compressa (Poaceae) in south China based on SRAP markers.

    PubMed

    Huang, L-K; Zhang, X-Q; Xie, W-G; Zhang, J; Cheng, L; Yan, H D

    2012-08-16

    Hemarthria compressa is one of the most important and widely utilized forage crops in south China, owing to its high forage yield and capability of adaptation to hot and humid conditions. We examined the population structure and genetic variation within and among 12 populations of H. compressa in south China using sequence-related amplified polymorphism (SRAP) markers. High genetic diversity was found in these samples [percentage polymorphic bands (PPB) = 82.21%, Shannon's diversity index (I) = 0.352]. However, there was relatively low level of genetic diversity at the population level (PPB = 29.17%, I = 0.155). A high degree of genetic differentiation among populations was detected based on other measures and molecular markers (Nei's genetic diversity analysis: G(ST) = 54.19%; AMOVA analysis: F(ST) = 53.35%). The SRAP markers were found to be more efficient than ISSR markers for evaluating population diversity. Based on these findings, we propose changes in sampling strategies for appraising and utilizing the genetic resources of this species.

  13. Patterns of cannabis use in patients with Inflammatory Bowel Disease: A population based analysis.

    PubMed

    Weiss, Alexandra; Friedenberg, Frank

    2015-11-01

    Tobacco use patterns and effects in patients with Inflammatory Bowel Disease have been extensively studied, however the role and patterns of cannabis use remains poorly defined. Our aim was to evaluate patterns of marijuana use in a large population based survey. Cases were identified from the NHANES database from the National Center for Health Statistics for the time period from January, 2009 through December, 2010 as having ulcerative colitis or Crohn's disease, and exact matched with controls using the Propensity Score Module of SPSS, based on age, gender, and sample weighted using the nearest neighbor method. After weighting, 2084,895 subjects with IBD and 2013,901 control subjects were identified with no significant differences in demographic characteristics. Subjects with IBD had a higher incidence of ever having used marijuana/hashish (M/H) (67.3% vs. 60.0%) and an earlier age of onset of M/H use (15.7 years vs. 19.6 years). Patients with IBD were less likely to have used M/H every month for a year, but more likely to use a heavier amount per day (64.9% subjects with IBD used three or more joints per day vs. 80.5% of subjects without IBD used two or fewer joints per day). In multivariable logistic regression, presence of IBD, male gender, and age over 40 years predicted M/H use. Our study is the first to evaluate marijuana patterns in a large-scale population based survey. Older, male IBD patients have the highest odds of marijuana use. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  14. 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

  15. Customized vs population-based growth charts to identify neonates at risk of adverse outcome: systematic review and Bayesian meta-analysis of observational studies.

    PubMed

    Chiossi, G; Pedroza, C; Costantine, M M; Truong, V T T; Gargano, G; Saade, G R

    2017-08-01

    To compare the effectiveness of customized vs population-based growth charts for the prediction of adverse pregnancy outcomes. MEDLINE, ClinicalTrials.gov and The Cochrane Library were searched up to 31 May 2016 to identify interventional and observational studies comparing adverse outcomes among large- (LGA) and small- (SGA) for-gestational-age neonates, when classified according to customized vs population-based growth charts. Perinatal mortality and admission to the neonatal intensive care unit (NICU) of both SGA and LGA neonates, intrauterine fetal demise (IUFD) and neonatal mortality of SGA neonates, and neonatal shoulder dystocia and hypoglycemia as well as maternal third- and fourth-degree perineal lacerations in LGA pregnancies were evaluated. The electronic search identified 237 records that were examined based on title and abstract, of which 27 full-text articles were examined for eligibility. After excluding seven articles, 20 observational studies were included in a Bayesian meta-analysis. Neonates classified as SGA according to customized growth charts had higher risks of IUFD (odds ratio (OR), 7.8 (95% CI, 4.2-12.3)), neonatal death (OR, 3.5 (95% CI, 1.1-8.0)), perinatal death (OR, 5.8 (95% CI, 3.8-7.8)) and NICU admission (OR, 3.6 (95% CI, 2.0-5.5)) than did non-SGA cases. Neonates classified as SGA according to population-based growth charts also had increased risk for adverse outcomes, albeit the point estimates of the pooled ORs were smaller: IUFD (OR, 3.3 (95% CI, 1.9-5.0)), neonatal death (OR, 2.9 (95% CI, 1.2-4.5)), perinatal death (OR, 4.0 (95% CI, 2.8-5.1)) and NICU admission (OR, 2.4 (95% CI, 1.7-3.2)). For LGA vs non-LGA, there were no differences in pooled ORs for perinatal death, NICU admission, hypoglycemia and maternal third- and fourth-degree perineal lacerations when classified according to either the customized or the population-based approach. In contrast, both approaches indicated that LGA neonates are at increased risk for

  16. Image-driven Population Analysis through Mixture Modeling

    PubMed Central

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

    2009-01-01

    We present iCluster, a fast and efficient algorithm that clusters a set of images while co-registering them using a parameterized, nonlinear transformation model. The output of the algorithm is a small number of template images that represent different modes in a population. This is in contrast with traditional, hypothesis-driven computational anatomy approaches that assume a single template to construct an atlas. We derive the algorithm based on a generative model of an image population as a mixture of deformable template images. We validate and explore our method in four experiments. In the first experiment, we use synthetic data to explore the behavior of the algorithm and inform a design choice on parameter settings. In the second experiment, we demonstrate the utility of having multiple atlases for the application of localizing temporal lobe brain structures in a pool of subjects that contains healthy controls and schizophrenia patients. Next, we employ iCluster to partition a data set of 415 whole brain MR volumes of subjects aged 18 through 96 years into three anatomical subgroups. Our analysis suggests that these subgroups mainly correspond to age groups. The templates reveal significant structural differences across these age groups that confirm previous findings in aging research. In the final experiment, we run iCluster on a group of 15 patients with dementia and 15 age-matched healthy controls. The algorithm produces two modes, one of which contains dementia patients only. These results suggest that the algorithm can be used to discover sub-populations that correspond to interesting structural or functional “modes.” PMID:19336293

  17. On the relationship between cell cycle analysis with ergodic principles and age-structured cell population models.

    PubMed

    Kuritz, K; Stöhr, D; Pollak, N; Allgöwer, F

    2017-02-07

    Cyclic processes, in particular the cell cycle, are of great importance in cell biology. Continued improvement in cell population analysis methods like fluorescence microscopy, flow cytometry, CyTOF or single-cell omics made mathematical methods based on ergodic principles a powerful tool in studying these processes. In this paper, we establish the relationship between cell cycle analysis with ergodic principles and age structured population models. To this end, we describe the progression of a single cell through the cell cycle by a stochastic differential equation on a one dimensional manifold in the high dimensional dataspace of cell cycle markers. Given the assumption that the cell population is in a steady state, we derive transformation rules which transform the number density on the manifold to the steady state number density of age structured population models. Our theory facilitates the study of cell cycle dependent processes including local molecular events, cell death and cell division from high dimensional "snapshot" data. Ergodic analysis can in general be applied to every process that exhibits a steady state distribution. By combining ergodic analysis with age structured population models we furthermore provide the theoretic basis for extensions of ergodic principles to distribution that deviate from their steady state. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    USDA-ARS?s Scientific Manuscript database

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

  19. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update

    PubMed Central

    Peakall, Rod; Smouse, Peter E.

    2012-01-01

    Summary: GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G′ST, G′′ST, Jost’s Dest and F′ST through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised. Availability and implementation: GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx. Contact: rod.peakall@anu.edu.au PMID:22820204

  20. [Analysis of Camellia rosthorniana populations fecundity].

    PubMed

    Cao, Guoxing; Zhong, Zhangcheng; Xie, Deti; Liu, Yun

    2004-03-01

    With the method of space substituting time, the structure of Camellia rosthorniana populations in three forest communities, i.e., Jiant bamboo forest, coniferous and broad-leaved mixed forest, and evergreen broad-leaved forest in Mt. Jinyun was investigated, and based on static life-tables, the fecundity tables and reproductive value tables of C. rosthorniana populations were constructed. Each reproductive parameter and its relation to bionomic strategies of C. rosthorniana populations were also analyzed. The results indicated that in evergreen broad-leaved forest, C. rosthorniana population had the longest life span and the greatest fitness. The stage of maximum reproductive value increased with increasing stability of the community. The sum of each population's reproductive value, residual reproductive value and total reproductive value for the whole life-history of C. rosthorniana also increased with increasing maturity of the community, showing their inherent relationships with reproductive fitness. As regards to bionomic strategy, C. rosthorniana showed mainly the characteristics of a k-strategies, but in less stable community, the reproductive parameters were greatly changed, showing some characteristics of a r-strategies.

  1. Recommended GIS Analysis Methods for Global Gridded Population Data

    NASA Astrophysics Data System (ADS)

    Frye, C. E.; Sorichetta, A.; Rose, A.

    2017-12-01

    When using geographic information systems (GIS) to analyze gridded, i.e., raster, population data, analysts need a detailed understanding of several factors that affect raster data processing, and thus, the accuracy of the results. Global raster data is most often provided in an unprojected state, usually in the WGS 1984 geographic coordinate system. Most GIS functions and tools evaluate data based on overlay relationships (area) or proximity (distance). Area and distance for global raster data can be either calculated directly using the various earth ellipsoids or after transforming the data to equal-area/equidistant projected coordinate systems to analyze all locations equally. However, unlike when projecting vector data, not all projected coordinate systems can support such analyses equally, and the process of transforming raster data from one coordinate space to another often results unmanaged loss of data through a process called resampling. Resampling determines which values to use in the result dataset given an imperfect locational match in the input dataset(s). Cell size or resolution, registration, resampling method, statistical type, and whether the raster represents continuous or discreet information potentially influence the quality of the result. Gridded population data represent estimates of population in each raster cell, and this presentation will provide guidelines for accurately transforming population rasters for analysis in GIS. Resampling impacts the display of high resolution global gridded population data, and we will discuss how to properly handle pyramid creation using the Aggregate tool with the sum option to create overviews for mosaic datasets.

  2. AN INDIVIDUAL-BASED MODEL OF COTTUS POPULATION DYNAMICS

    EPA Science Inventory

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

  3. High-Cost Users of Prescription Drugs: A Population-Based Analysis from British Columbia, Canada.

    PubMed

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

    2017-04-01

    To examine variation in pharmaceutical spending and patient characteristics across prescription drug user groups. British Columbia's population-based linked administrative health and sociodemographic databases (N = 3,460,763). We classified individuals into empirically derived prescription drug user groups based on pharmaceutical spending patterns outside hospitals from 2007 to 2011. We examined variation in patient characteristics, mortality, and health services usage and applied hierarchical clustering to determine patterns of concurrent drug use identifying high-cost patients. Approximately 1 in 20 British Columbians had persistently high prescription costs for 5 consecutive years, accounting for 42 percent of 2011 province-wide pharmaceutical spending. Less than 1 percent of the population experienced discrete episodes of high prescription costs; an additional 2.8 percent transitioned to or from high-cost episodes of unknown duration. Persistent high-cost users were more likely to concurrently use multiple chronic medications; episodic and transitory users spent more on specialized medicines, including outpatient cancer drugs. Cluster analyses revealed heterogeneity in concurrent medicine use within high-cost groups. Whether low, moderate, or high, costs of prescription drugs for most individuals are persistent over time. Policies controlling high-cost use should focus on reducing polypharmacy and encouraging price competition in drug classes used by ordinary and high-cost users alike. © 2016 The Authors. Health Services Research published by Wiley Periodicals, Inc. on behalf of Health Research and Educational Trust.

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

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

    Cleary, A J; Smith, S G; Vassilevska, T K

    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 parallelmore » computers and maturation of the technology from an academic to a lab setting.« less

  5. 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

  6. 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.

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

    PubMed

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

    2014-02-01

    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. 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. 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. 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. Copyright © 2014 The Authors. Birth Defects Research (Part A) published by Wiley Periodicals, Inc.

  8. Education as a predictor of chronic periodontitis: a systematic review with meta-analysis population-based studies.

    PubMed

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

    2011-01-01

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

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

    USGS Publications Warehouse

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

    2003-01-01

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

  10. Aligning population-based care management with chronic disease complexity.

    PubMed

    Hewner, Sharon; Seo, Jin Young; Gothard, Sandra E; Johnson, Barbara J

    2014-01-01

    Risk-stratified care management requires knowledge of the complexity of chronic disease and comorbidity, information that is often not readily available in the primary care setting. The purpose of this article was to describe a population-based approach to risk-stratified care management that could be applied in primary care. Three populations (Medicaid, Medicare, and privately insured) at a regional health plan were divided into risk-stratified cohorts based on chronic disease and complexity, and utilization was compared before and after the implementation of population-specific care management teams of nurses. Risk-stratified care management was associated with reductions in hospitalization rates in all three populations, but the opportunities to avoid admissions were different. Knowledge of population complexity is critical to the development of risk-stratified care management in primary care, and a complexity matrix can help nurses identify gaps in care and align interventions to cohort and population needs. Copyright © 2014 Elsevier Inc. All rights reserved.

  11. Computer based experimental studies of the Fry method of strain analysis on 2- and 3- dimensional grain populations

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

    Longiaru, S.; Bhattacharyya, T.

    1985-01-01

    Inherent in Fry's (1979) all-object separation method of strain analysis are the subtle conditions that 1) the grains or phenocrysts being counted are of equal diameter and 2) that the true centers of such grains lie within the plane of measurement. When such conditions are met, the technique yields accurate, easily interpreted voids within all-object separation (AOS) plots for both deformed and non-deformed populations. Natural grain or phenocryst populations generally do not conform to these limitation and practical application of the technique from either a cut rock surface or thin section often yields diffuse patterns that are not easily interpreted.more » The authors examine the effect of grain size variation and grain/matrix ratio on AOS diagrams developed from computer generated spherical grain populations constructed in both two and three dimensions. They employ a random number generator and simple fitting algorithm to develop grain populations with known statistical parameters. Such control allows for the modeling of many types of natural grain size populations such as fluvial sandstones, porphyritic ash flow tuffs, augen gneisses, etc. They show that significant grain size variation in a two dimensional population contributes substantial noise in to the AOS diagram and that an additional level of noise is encountered when dealing with slices through populations modeled in three dimensions. Some of this noise can be eliminated by rigorous sampling of only subsets of the total grain population.« less

  12. Identification of dietary patterns in urban population of Argentina: study on diet-obesity relation in population-based prevalence study.

    PubMed

    Pou, Sonia Alejandra; Del Pilar Díaz, María; De La Quintana, Ana Gabriela; Forte, Carla Antonella; Aballay, Laura Rosana

    2016-12-01

    In Argentina, obesity prevalence rose from 14.6% in 2005 to 20.8% in 2013. Although the number of studies on noncommunicable diseases and dietary patterns as a unique dietary exposure measure has increased, information on this topic remains scarce in developing countries. This is the first population-based study investigating the association between diet and obesity using a dietary pattern approach in Argentina. We aimed (a) to identify current dietary patterns of the population of Córdoba city, (b) to investigate its association with obesity prevalence, and (c) to identify and describe dietary patterns from the subgroup of people with obesity. The Córdoba Obesity and Diet Study (CODIES) was conducted in Córdoba city by using a random sample of n = 4,327 subjects between 2005 and 2012. Empirically derived dietary patterns were identified through principal component factor analysis. A multiple logistic regression analysis was used to investigate the association of dietary patterns with obesity. Four dietary patterns were identified, called " Starchy-Sugar ", " Prudent ", " Western ", and " Sugary drinks ". High scores for the " Western " pattern (with strongest factor loading on meats/eggs, processed meats, and alcohol) showed a positive association with obesity (OR: 1.33, 95% CI: 1.06-1.67, for third versus first tertile of factor score). " Meats/Cheeses " and " Snacks/Alcohol " patterns emerged in people with obesity. The findings suggest that high adherence to the " Western " pattern promoted obesity in this urban population. In addition, people with obesity showed characteristic dietary patterns that differ from those identified in the overall population.

  13. Quality of care received and patient-reported regret in prostate cancer: Analysis of a population-based prospective cohort.

    PubMed

    Holmes, Jordan A; Bensen, Jeannette T; Mohler, James L; Song, Lixin; Mishel, Merle H; Chen, Ronald C

    2017-01-01

    Meeting quality of care standards in oncology is recognized as important by physicians, professional organizations, and payers. Data from a population-based cohort of patients with prostate cancer were used to examine whether receipt of care was consistent with published consensus metrics and whether receiving high-quality care was associated with less patient-reported treatment decisional regret. Patients with incident prostate cancer were enrolled in collaboration with the North Carolina Central Cancer Registry, with an oversampling of minority patients. Medical record abstraction was used to determine whether participants received high-quality care based on 5 standards: 1) discussion of all treatment options; 2) complete workup (prostate-specific antigen, Gleason grade, and clinical stage); 3) low-risk participants did not undergo a bone scan; 4) high-risk participants treated with radiotherapy (RT) received androgen deprivation therapy; and 5) participants treated with RT received conformal or intensity-modulated RT. Treatment decisional regret was assessed using a validated instrument. A total of 804 participants were analyzed. Overall, 66% of African American and 73% of white participants received care that met all standards (P = .03); this racial difference was confirmed by multivariable analysis. Care that included "discussion of all treatment options" was found to be associated with less patient-reported regret on univariable analysis (P = .03) and multivariable analysis (odds ratio, 0.59; 95% confidence interval, 0.37-0.95). The majority of participants received high-quality care, but racial disparity existed. Participants who discussed all treatment options appeared to have less treatment decisional regret. To the authors' knowledge, this is the first study to demonstrate an association between a quality of care metric and patient-reported outcome. Cancer 2017;138-143. © 2016 American Cancer Society. © 2016 American Cancer Society.

  14. Y-Chromosome Haplogroups in the Bosnian-Herzegovinian Population Based on 23 Y-STR Loci.

    PubMed

    Doğan, Serkan; Ašić, Adna; Doğan, Gulsen; Besic, Larisa; Marjanovic, Damir

    2016-07-01

    In a study of the Bosnian-Herzegovinian (B&H) population, Y-chromosome marker frequencies for 100 individuals, generated using the PowerPlex Y23 kit, were used to perform Y-chromosome haplogroup assignment via Whit Athey's Haplogroup Predictor. This algorithm determines Y-chromosome haplogroups from Y-chromosome short tandem repeat (Y-STR) data using a Bayesian probability-based approach. The most frequent haplogroup appeared to be I2a, with a prevalence of 49%, followed by R1a and E1b1b, each accounting for 17% of all haplogroups within the population. Remaining haplogroups were J2a (5%), I1 (4%), R1b (4%), J2b (2%), G2a (1%), and N (1%). These results confirm previously published preliminary B&H population data published over 10 years ago, especially the prediction about the B&H population being a part of the Western Balkan area, which served as the Last Glacial Maximum refuge for the Paleolithic human European population. Furthermore, the results corroborate the hypothesis that this area was a significant stopping point on the "Middle East-Europe highway" during the Neolithic farmer migrations. Finally, since these results are almost completely in accordance with previously published data on B&H and neighboring populations generated by Y-chromosome single nucleotide polymorphism analysis, it can be concluded that in silico analysis of Y-STRs is a reliable method for approximation of the Y-chromosome haplogroup diversity of an examined population.

  15. Designing Home-Based Telemedicine Systems for the Geriatric Population: An Empirical Study.

    PubMed

    Narasimha, Shraddhaa; Agnisarman, Sruthy; Chalil Madathil, Kapil; Gramopadhye, Anand; McElligott, James T

    2018-02-01

    Background and Introduction: Telemedicine, the process of providing healthcare remotely using communication devices, has the potential to be useful for the geriatric population when specifically designed for this age group. This study explored the design of four video telemedicine systems currently available and outlined issues with these systems that impact usability among the geriatric population. Based on the results, design suggestions were developed to improve telemedicine systems for this population. Using a between-subjects experimental design, the study considered four telemedicine systems used in Medical University of South Carolina. The study was conducted at a local retirement home. The participant pool consisted of 40 adults, 60 years or older. The dependent measures used were the mean times for telemedicine session initiation and video session, mean number of errors, post-test satisfaction ratings, the NASA-Task Load Index (NASA-TLX) workload measures, and the IBM-Computer Systems Usability Questionnaire measures. Statistical significance was found among the telemedicine systems' initiation times. The analysis of the qualitative data revealed several issues, including lengthy e-mail content, icon placement, and chat box design, which affect the usability of these systems for the geriatric population. Human factor-based design modifications, including short, precise e-mail content, appropriately placed icons, and the inclusion of instructions, are recommended to address the issues found in the qualitative study.

  16. Antidepressant Use After Aneurysmal Subarachnoid Hemorrhage: A Population-Based Case-Control Study.

    PubMed

    Huttunen, Jukka; Lindgren, Antti; Kurki, Mitja I; Huttunen, Terhi; Frösen, Juhana; von Und Zu Fraunberg, Mikael; Koivisto, Timo; Kälviäinen, Reetta; Räikkönen, Katri; Viinamäki, Heimo; Jääskeläinen, Juha E; Immonen, Arto

    2016-09-01

    To elucidate the predictors of antidepressant use after subarachnoid hemorrhage from saccular intracranial aneurysm (sIA-SAH) in a population-based cohort with matched controls. The Kuopio sIA database includes all unruptured and ruptured sIA cases admitted to the Kuopio University Hospital from its defined catchment population in Eastern Finland, with 3 matched controls for each patient. The use of all prescribed medicines has been fused from the Finnish national registry of prescribed medicines. In the present study, 2 or more purchases of antidepressant medication indicated antidepressant use. The risk factors of the antidepressant use were analyzed in 940 patients alive 12 months after sIA-SAH, and the classification tree analysis was used to create a predicting model for antidepressant use after sIA-SAH. The 940 12-month survivors of sIA-SAH had significantly more antidepressant use (odds ratio, 2.6; 95% confidence interval, 2.2-3.1) than their 2676 matched controls (29% versus 14%). Classification tree analysis, based on independent risk factors, was used for the best prediction model of antidepressant use after sIA-SAH. Modified Rankin Scale until 12 months was the most potent predictor, followed by condition (Hunt and Hess Scale) and age on admission for sIA-SAH. The sIA-SAH survivors use significantly more often antidepressants, indicative of depression, than their matched population controls. Even with a seemingly good recovery (modified Rankin Scale score, 0) at 12 months after sIA-SAH, there is a significant risk of depression requiring antidepressant medication. © 2016 American Heart Association, Inc.

  17. 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

  18. Coherent population transfer in multilevel systems with magnetic sublevels. II. Algebraic analysis

    NASA Astrophysics Data System (ADS)

    Martin, J.; Shore, B. W.; Bergmann, K.

    1995-07-01

    We extend previous theoretical work on coherent population transfer by stimulated Raman adiabatic passage for states involving nonzero angular momentum. The pump and Stokes fields are either copropagating or counterpropagating with the corresponding linearly polarized electric-field vectors lying in a common plane with the magnetic-field direction. Zeeman splitting lifts the magnetic sublevel degeneracy. We present an algebraic analysis of dressed-state properties to explain the behavior noted in numerical studies. In particular, we discuss conditions which are likely to lead to a failure of complete population transfer. The applied strategy, based on simple methods of linear algebra, will also be successful for other types of discrete multilevel systems, provided the rotating-wave and adiabatic approximation are valid.

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  20. Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia.

    PubMed

    Tapio, Miika; Ozerov, Mikhail; Tapio, Ilma; Toro, Miguel A; Marzanov, Nurbiy; Cinkulov, Mirjana; Goncharenko, Galina; Kiselyova, Tatyana; Murawski, Maziek; Kantanen, Juha

    2010-08-10

    Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation. Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity. During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success.

  1. Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia

    PubMed Central

    2010-01-01

    Background Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation. Results Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity. Conclusions During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success. PMID:20698974

  2. Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools.

    PubMed

    Fuller, Zachary L; Niño, Elina L; Patch, Harland M; Bedoya-Reina, Oscar C; Baumgarten, Tracey; Muli, Elliud; Mumoki, Fiona; Ratan, Aakrosh; McGraw, John; Frazier, Maryann; Masiga, Daniel; Schuster, Stephen; Grozinger, Christina M; Miller, Webb

    2015-07-10

    With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including F ST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions. We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea. These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows ( http://usegalaxy.org/r/kenyanbee ) that can be applied to any model system with genomic information.

  3. Dietary patterns and colorectal cancer: results from a Canadian population-based study.

    PubMed

    Chen, Zhi; Wang, Peizhong Peter; Woodrow, Jennifer; Zhu, Yun; Roebothan, Barbara; Mclaughlin, John R; Parfrey, Patrick S

    2015-01-15

    The relationship between major dietary patterns and colorectal cancer (CRC) in other populations largely remains consistent across studies. The objective of the present study is to assess if dietary patterns are associated with the risk of CRC in the population of Newfoundland and Labrador (NL). Data from a population based case-control study in the province of NL were analyzed, including 506 CRC patients (306 men and 200 women) and 673 controls (400 men and 273 women), aged 20-74 years. Dietary habits were assessed by a 169-item food frequency questionnaire (FFQ). Logistic regression analyses were performed to investigate the association between dietary patterns and the CRC risk. Three major dietary patterns were derived using factor analysis, namely a Meat-diet pattern, a Plant-based diet pattern and a Sugary-diet pattern. In combination the three dietary patterns explained 74% of the total variance in food intake. Results suggest that the Meat-diet and the Sugary-diet increased the risk of CRC with corresponding odds ratios (ORs) of 1.84 (95% CI: 1.19-2.86) and 2.26 (95% CI: 1.39-3.66) for people in the highest intake quintile compared to those in the lowest. Whereas plant-based diet pattern decreases the risk of CRC with a corresponding OR of 0.55 (95% CI: 0.35-0.87). Even though odds ratios (ORs) were not always statistically significant, largely similar associations across three cancer sites were found: the proximal colon, the distal colon, and the rectum. The finding that Meat-diet/Sugary-diet patterns increased and Plant-based diet pattern decreased the risk of CRC would guide the promotion of healthy eating for primary prevention of CRC in this population.

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

    ERIC Educational Resources Information Center

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

    2008-01-01

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

  5. Cluster analysis in phenotyping a Portuguese population.

    PubMed

    Loureiro, C C; Sa-Couto, P; Todo-Bom, A; Bousquet, J

    2015-09-03

    Unbiased cluster analysis using clinical parameters has identified asthma phenotypes. Adding inflammatory biomarkers to this analysis provided a better insight into the disease mechanisms. This approach has not yet been applied to asthmatic Portuguese patients. To identify phenotypes of asthma using cluster analysis in a Portuguese asthmatic population treated in secondary medical care. Consecutive patients with asthma were recruited from the outpatient clinic. Patients were optimally treated according to GINA guidelines and enrolled in the study. Procedures were performed according to a standard evaluation of asthma. Phenotypes were identified by cluster analysis using Ward's clustering method. Of the 72 patients enrolled, 57 had full data and were included for cluster analysis. Distribution was set in 5 clusters described as follows: cluster (C) 1, early onset mild allergic asthma; C2, moderate allergic asthma, with long evolution, female prevalence and mixed inflammation; C3, allergic brittle asthma in young females with early disease onset and no evidence of inflammation; C4, severe asthma in obese females with late disease onset, highly symptomatic despite low Th2 inflammation; C5, severe asthma with chronic airflow obstruction, late disease onset and eosinophilic inflammation. In our study population, the identified clusters were mainly coincident with other larger-scale cluster analysis. Variables such as age at disease onset, obesity, lung function, FeNO (Th2 biomarker) and disease severity were important for cluster distinction. Copyright © 2015. Published by Elsevier España, S.L.U.

  6. [Oral cancer in Cali, Colombia: a population-based analysis of incidence and mortality trends].

    PubMed

    Ordóñez, Dora; Aragón, Natalia; García, Luz Stella; Collazos, Paola; Bravo, Luis Eduardo

    2014-01-01

    To describe the time trends of the incidence and mortality rates of oral cancer (OC) in Cali, Colombia between 1962-2007. Age-standardized (Segi's world population) incidence (ASIR) and mortality (ASMR) rates for oral cancer were estimated using data from the Population-based Cancer Registry of Cali, Colombia and from the database of the Municipal Secretary of Public Health (MSPH) respectively. Annual percentage change (APC) was used to measure the changes in rates over time. 1637 new cases of oral cancer were registered in the CPCR and the mean age upon diagnosis was 60 years. The ASIR decreased from 1962-2007 in men APC= 1.3 (IC95%:-2.0; -0.6) and women APC= -1.0 (IC95%: -1.7; -0.4).The ASMR decreased from 1984-2001 only in men, APC=2.8 (IC95%: -4.1; -1.5). There was a significant decrease in the incidence and mortality rates for OC in Cali, Colombia. The type of tumor associated to these changes was the squamous cell carcinoma.

  7. 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.

  8. Smoking, cessation, and cessation counseling in patients with cancer: A population-based analysis.

    PubMed

    Ramaswamy, Apoorva T; Toll, Benjamin A; Chagpar, Anees B; Judson, Benjamin L

    2016-04-15

    Smoking is known to be carcinogenic and an important factor in the outcome of cancer treatment. However, to the authors' knowledge, smoking habits and smoking cessation counseling in patients with cancer have been poorly studied. The authors sought to analyze smoking habits among Americans diagnosed with cancer in a nationally representative dataset. The cancer supplement of the National Health Interview Survey (NHIS) in 2010 was used to obtain information regarding self-reported smoking behavior in a representative sample of the US population. Cancer history, smoking history, quitting behavior, cessation counseling, cessation approaches, and sociodemographic variables were analyzed. A total of 27,157 individuals were interviewed for the NHIS in 2010, representing 216,052,891 individuals, 7,058,135 of whom had ever smoked and 13,188,875 of whom had been told that they had cancer. Approximately 51.7% of individuals diagnosed with cancer and who were active smokers reported being counseled to quit smoking by a health professional within the previous 12 months. Cancer survivors were no more likely to quit smoking than individuals in the general population. Those diagnosed with a tobacco-related cancer were found to be no more likely to report quitting smoking than those with other types of cancers. Rates of quitting did not appear to vary based on the type of smoking cessation method used (P = .50). Patients with cancer, including those diagnosed with a tobacco-related cancer, do not appear to be more likely to quit smoking than the general population. Only approximately one-half of patients with cancer who smoke are counseled to quit. Smoking cessation in patients with cancer is an important area for intervention and investigation. © 2016 American Cancer Society.

  9. Etiology and management of esophageal food impaction: a population based study.

    PubMed

    Gretarsdottir, Helga M; Jonasson, Jon Gunnlaugur; Björnsson, Einar S

    2015-05-01

    Esophageal food impaction (FI) is a common clinical problem with limited information on incidence. Previous population based studies are lacking. The incidence, main etiological factors, recurrence and outcome of FI was determined in the present study in a population based setting. This was a study of consecutive adult patients who presented with FI from 2008 to 2013 at the National University Hospital of Iceland. The mean crude incidence rate of FI was calculated. Retrospective analysis was undertaken on relevant clinical data such as type of bolus, management, complications, recurrence rate, risk factors for recurrence, and outcome. Overall 308 patients had endoscopically confirmed FI, males 199/308 (65%), median age 62 years. The mean crude incidence was 25 per 100,000 inhabitants per year. The types of FI was meat (68%), fish (12%), vegetable (4%) and other food/objects (16%). Causes for the FI included: esophageal strictures (45%), hiatal hernia (22%), eosinophilic esophagitis (EoE) (16%) and esophageal carcinoma (2%). Recurrence appeared in 21%, in which 24/48 (50%) had EoE vs. 40/260 (15%) in others (p = 0.0001). The removal of the foreign body was successful in 98% of the cases during the first endoscopy. Endoscopic associated complications included four (1.3%) aspirations, one (0.3%) esophageal perforation and one Boerhaave syndrome at presentation (both had EoE). The incidence of FI is the highest reported to date. EoE was strongly associated with recurrence of FI. In a population based setting endoscopy is a safe and effective procedure for removing FI.

  10. A population-based job exposure matrix for power-frequency magnetic fields.

    PubMed

    Bowman, Joseph D; Touchstone, Jennifer A; Yost, Michael G

    2007-09-01

    A population-based job exposure matrix (JEM) was developed to assess personal exposures to power-frequency magnetic fields (MF) for epidemiologic studies. The JEM compiled 2,317 MF measurements taken on or near workers by 10 studies in the United States, Sweden, New Zealand, Finland, and Italy. A database was assembled from the original data for six studies plus summary statistics grouped by occupation from four other published studies. The job descriptions were coded into the 1980 Standard Occupational Classification system (SOC) and then translated to the 1980 job categories of the U.S. Bureau of the Census (BOC). For each job category, the JEM database calculated the arithmetic mean, standard deviation, geometric mean, and geometric standard deviation of the workday-average MF magnitude from the combined data. Analysis of variance demonstrated that the combining of MF data from the different sources was justified, and that the homogeneity of MF exposures in the SOC occupations was comparable to JEMs for solvents and particulates. BOC occupation accounted for 30% of the MF variance (p < 10(-6)), and the contrast (ratio of the between-job variance to the total of within- and between-job variances) was 88%. Jobs lacking data had their exposures inferred from measurements on similar occupations. The JEM provided MF exposures for 97% of the person-months in a population-based case-control study and 95% of the jobs on death certificates in a registry study covering 22 states. Therefore, we expect this JEM to be useful in other population-based epidemiologic studies.

  11. The Case for Diabetes Population Health Improvement: Evidence-Based Programming for Population Outcomes in Diabetes.

    PubMed

    Golden, Sherita Hill; Maruthur, Nisa; Mathioudakis, Nestoras; Spanakis, Elias; Rubin, Daniel; Zilbermint, Mihail; Hill-Briggs, Felicia

    2017-07-01

    The goal of this review is to describe diabetes within a population health improvement framework and to review the evidence for a diabetes population health continuum of intervention approaches, including diabetes prevention and chronic and acute diabetes management, to improve clinical and economic outcomes. Recent studies have shown that compared to usual care, lifestyle interventions in prediabetes lower diabetes risk at the population-level and that group-based programs have low incremental medial cost effectiveness ratio for health systems. Effective outpatient interventions that improve diabetes control and process outcomes are multi-level, targeting the patient, provider, and healthcare system simultaneously and integrate community health workers as a liaison between the patient and community-based healthcare resources. A multi-faceted approach to diabetes management is also effective in the inpatient setting. Interventions shown to promote safe and effective glycemic control and use of evidence-based glucose management practices include provider reminder and clinical decision support systems, automated computer order entry, provider education, and organizational change. Future studies should examine the cost-effectiveness of multi-faceted outpatient and inpatient diabetes management programs to determine the best financial models for incorporating them into diabetes population health strategies.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  13. Individualized head-related transfer functions based on population grouping.

    PubMed

    Xu, Song; Li, Zhizhong; Salvendy, Gavriel

    2008-11-01

    A method is proposed to divide a population into different groups for partial individualization of head-related transfer functions (HRTFs). Borrowing the basic idea in sizing system design, factor analysis is used to identify the most representative measurements which are then in a case study used to group the population. The comparison between the group mean HRTFs and the population mean HRTFs shows that the group mean HRTFs could greatly reduce spectral distortion at most sampled positions.

  14. Interindividual registration and dose mapping for voxelwise population analysis of rectal toxicity in prostate cancer radiotherapy

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

    Dréan, Gaël; Acosta, Oscar, E-mail: Oscar.Acosta@univ-rennes1.fr; Simon, Antoine

    2016-06-15

    Purpose: Recent studies revealed a trend toward voxelwise population analysis in order to understand the local dose/toxicity relationships in prostate cancer radiotherapy. Such approaches require, however, an accurate interindividual mapping of the anatomies and 3D dose distributions toward a common coordinate system. This step is challenging due to the high interindividual variability. In this paper, the authors propose a method designed for interindividual nonrigid registration of the rectum and dose mapping for population analysis. Methods: The method is based on the computation of a normalized structural description of the rectum using a Laplacian-based model. This description takes advantage of themore » tubular structure of the rectum and its centerline to be embedded in a nonrigid registration-based scheme. The performances of the method were evaluated on 30 individuals treated for prostate cancer in a leave-one-out cross validation. Results: Performance was measured using classical metrics (Dice score and Hausdorff distance), along with new metrics devised to better assess dose mapping in relation with structural deformation (dose-organ overlap). Considering these scores, the proposed method outperforms intensity-based and distance maps-based registration methods. Conclusions: The proposed method allows for accurately mapping interindividual 3D dose distributions toward a single anatomical template, opening the way for further voxelwise statistical analysis.« less

  15. Solitary plasmacytoma: population-based analysis of survival trends and effect of various treatment modalities in the USA.

    PubMed

    Thumallapally, Nishitha; Meshref, Ahmed; Mousa, Mohammed; Terjanian, Terenig

    2017-01-05

    , age <60 years and treatment with either RT or surgery showed superior survival rates. Progression to multiple myeloma (MM) was noted in 551 patients. Age >60 years was associated with a lower 5-year survival in patients who progressed to MM compared to those who were diagnosed initially with MM (15.1 vs 16.6%). Finally, those who received RT and progressed to MM still had a higher chance of survival than those who were diagnosed with MM initially and treated with RT/surgery (21.8% vs 15.9%, p < 0.05). A review of the pertinent literature indicates that we provided the most comprehensive population-based analysis of SP to date. Moreover, our study contributes to the establishment of the optimal SP treatment modality, as RT is the favored option in frontline settings. Consensus is currently lacking regarding the benefits of combined treatment including surgery. Thus, the findings reported here elucidate the role of primary treatment modalities while also demonstrating the quantifiable benefits of combining RT with surgery in relation to different primary tumor sites. While our results are promising, they should be confirmed through further large-scale randomized studies.

  16. 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

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

    PubMed

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

    2014-08-01

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

  18. Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation

    PubMed Central

    Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

    2015-01-01

    Mapping expression quantitative trait loci (eQTLs) has been shown as a powerful tool to uncover the genetic underpinnings of many complex traits at molecular level. In this paper, we present an integrative analysis approach that leverages eQTL data collected from multiple population groups. In particular, our approach effectively identifies multiple independent cis-eQTL signals that are consistent across populations, accounting for population heterogeneity in allele frequencies and linkage disequilibrium patterns. Furthermore, by integrating genomic annotations, our analysis framework enables high-resolution functional analysis of eQTLs. We applied our statistical approach to analyze the GEUVADIS data consisting of samples from five population groups. From this analysis, we concluded that i) jointly analysis across population groups greatly improves the power of eQTL discovery and the resolution of fine mapping of causal eQTL ii) many genes harbor multiple independent eQTLs in their cis regions iii) genetic variants that disrupt transcription factor binding are significantly enriched in eQTLs (p-value = 4.93 × 10-22). PMID:25906321

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

    PubMed Central

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

    2008-01-01

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

  20. 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

    2015-08-01

    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. 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. 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 the other 15·6%, the two definitions

  1. Designing a Community-Based Population Health Model.

    PubMed

    Durovich, Christopher J; Roberts, Peter W

    2018-02-01

    The pace of change from volume-based to value-based payment in health care varies dramatically among markets. Regardless of the ultimate disposition of the Affordable Care Act, employers and public-private payers will continue to increase pressure on health care providers to assume financial risk for populations in the form of shared savings, bundled payments, downside risk, or even capitation. This article outlines a suggested road map and practical considerations for health systems that are building or planning to build population health capabilities to meet the needs of their local markets. The authors review the traditional core capabilities needed to address the medical determinants of health for a population. They also share an innovative approach to community service integration to address the social determinants of health and the engagement of families to improve their own health and well-being. The foundational approach is to connect insurance products, the health care delivery system, and community service agencies around the family's well-being goals using human-centered design strategy.

  2. Population stress: A spatiotemporal analysis of population change and land development at the county level in the contiguous United States, 2001-2011.

    PubMed

    Chi, Guangqing; Ho, Hung Chak

    2018-01-01

    The past century has witnessed rapidly increasing population-land conflicts due to exponential population growth and its many consequences. Although the measures of population-land conflicts are many, there lacks a model that appropriately considers both the social and physical contexts of population-land conflicts. In this study we introduce the concept of population stress , which identifies areas with populations growing faster than the lands available for sustainable development. Specifically, population stress areas are identified by comparing population growth and land development as measured by land developability in the contiguous United States from 2001 to 2011. Our approach is based on a combination of spatial multicriteria analysis, zonal statistics, and spatiotemporal modeling. We found that the population growth of a county is associated with the decrease of land developability, along with the spatial influences of surrounding counties. The Midwest and the traditional "Deep South" counties would have less population stress with future land development, whereas the Southeast Coast, Washington State, Northern Texas, and the Southwest would face more stress due to population growth that is faster than the loss of suitable lands for development. The factors contributing to population stress may differ from place to place. Our population stress concept is useful and innovative for understanding population stress due to land development and can be applied to other regions as well as global research. It can act as a basis towards developing coherent sustainable land use policies. Coordination among local governments and across different levels of governments in the twenty-first century is a must for effective land use planning.

  3. 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.

  4. A Population-Based Analysis of Application of WHO Nomenclature in Pathology Reports of Pulmonary Neuroendocrine Tumors.

    PubMed

    Derks, Jules L; van Suylen, Robert Jan; Thunnissen, Erik; den Bakker, Michael A; Smit, Egbert F; Groen, Harry J M; Speel, Ernst J M; Dingemans, Anne-Marie C

    2016-04-01

    Pulmonary neuroendocrine tumors (pNETs) are difficult to classify. We performed a population-based analysis to investigate the application of pNET nomenclature in daily pathology practice. Conclusions from pathology reports (2003-2012) describing carcinoids, (large cell) neuroendocrine carcinomas (NECs), and carcinomas with neuroendocrine features/differentiation were retrieved from the Dutch Pathology Registry by queries on location and diagnosis and screened for terminology. Cases with a nonpulmonary or unknown origin and small cell lung cancer were excluded. Diagnoses were clustered into subgroups and the retrieved terminology was compared with the 2015 World Health Organization (WHO) diagnoses. By means of an online questionnaire, interpretation of the non-WHO nomenclature retrieved from pathology reports was evaluated (by 35 physicians and 19 pathologists). A total of 3216 unique pathology report conclusions with 55 different pNET diagnoses (n = 3052) and 20 uncertain diagnoses (n = 164) were analyzed. Non-WHO nomenclature was used in 15% of diagnoses (n = 488). Diagnoses could be clustered into carcinoids (n = 1086), NEC (n = 1316), carcinomas with neuroendocrine features/differentiation (n = 624), and unspecified pNETs (n = 26). Non-WHO nomenclature within these clusters was found for 7% of carcinoids, 20% of NECs, 13% of carcinomas with neuroendocrine features/differentiation, and 100% of unspecified pNETs and was observed more often in conclusions regarding biopsy or cytological specimens (62% and 12%) compared with resection specimens (26%). Analysis of the questionnaire results revealed that 4 of 19 diagnoses based on non-WHO nomenclature were uniformly interpreted (>50% agreement) by physicians, as were 10 of 19 diagnoses by pathologists. In 15% of pNETs other than small cell lung cancer, a non-WHO nomenclature diagnosis was provided, more frequently on the basis of smaller specimens. The interpretation was different between physicians and

  5. Hypervolemia for hypertension pathophysiology: a population-based study.

    PubMed

    Hür, Ender; Özişik, Melih; Ural, Cihan; Yildiz, Gürsel; Mağden, Kemal; Köse, Sennur Budak; Köktürk, Füruzan; Büyükuysal, Çağatay; Yildirim, Ibrahim; Süleymanlar, Gültekin; Ateş, Kenan; Duman, Soner

    2014-01-01

    Hypertension and hypervolemia relationship was proven among renal disease, although it is not known in normal population. Present study determines the fluid distribution defects in relation to blood pressure. In a population-based survey in Turkey demographics, height, weight, blood pressure, urine analysis, and serum creatinine measurements were recorded. Bioimpedance measured with the Body Composition Monitor. Total 2034 population of 71.6% male, mean age 47 ± 12.6 (18-89) years, systolic blood pressure (SBP) 134.7 ± 20, diastolic blood pressure 77.9 ± 11.6 mmHg. Body mass index (BMI) was 28.5 ± 4.5 (15.8-50.6) kg/m(2); overhydration was 0.05 ± 1.05 L. There was a correlation between extracellular water (ECW)/height and SBP (r = 0.21, P < 0.001). Receiver operating characteristic (ROC) curve with the performance of 0.60 (P < 0.001) that showed cut-off value of ECW/height was 10.06 L/m, with the 69% sensitivity and 45% specificity for SBP: 140 mmHg values. Risk factors for high SBP were increase of ECW/Height, age, BMI and presence of diabetes. ECW/height, SBP, and fat tissue index (FTI) increased in BMI categories (low, normal, and obese) and in diabetics. SBP and FTI were lower in smokers. High blood pressure may be accompanied by increased extracellular volume indices. In the future volume status assessment could be of use in evaluating the effectiveness of pharmacological intervention in the treatment of hypertension.

  6. Predictive Model and Software for Inbreeding-Purging Analysis of Pedigreed Populations

    PubMed Central

    García-Dorado, Aurora; Wang, Jinliang; López-Cortegano, Eugenio

    2016-01-01

    The inbreeding depression of fitness traits can be a major threat to the survival of populations experiencing inbreeding. However, its accurate prediction requires taking into account the genetic purging induced by inbreeding, which can be achieved using a “purged inbreeding coefficient”. We have developed a method to compute purged inbreeding at the individual level in pedigreed populations with overlapping generations. Furthermore, we derive the inbreeding depression slope for individual logarithmic fitness, which is larger than that for the logarithm of the population fitness average. In addition, we provide a new software, PURGd, based on these theoretical results that allows analyzing pedigree data to detect purging, and to estimate the purging coefficient, which is the parameter necessary to predict the joint consequences of inbreeding and purging. The software also calculates the purged inbreeding coefficient for each individual, as well as standard and ancestral inbreeding. Analysis of simulation data show that this software produces reasonably accurate estimates for the inbreeding depression rate and for the purging coefficient that are useful for predictive purposes. PMID:27605515

  7. 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

  8. 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

  9. The natural history of Dandy-Walker syndrome in the United States: A population-based analysis.

    PubMed

    McClelland, Shearwood; Ukwuoma, Onyinyechi I; Lunos, Scott; Okuyemi, Kolawole S

    2015-01-01

    Dandy-Walker syndrome (DWS) is a congenital disorder typically manifesting with hydrocephalus. The classic anatomic hallmarks of DWS are hypoplasia of the cerebellar vermis, anterior-posterior enlargement of the posterior fossa, upward displacement of the torcula and transverse sinuses, and cystic dilatation of the fourth ventricle. Although optimal treatment of DWS typically requires neurosurgical intervention to prevent intracranial pressure increases incompatible with life, the natural history of this disorder has yet to be evaluated on a nationwide level. The Kids' Inpatient Database covering 1997-2003 was used for analysis. Children younger than age 18 admitted for DWS (ICD-9-CM = 742.3) were analyzed with a matched control group. The primary procedure codes for operative CSF drainage were coded into the analysis. The incidence of DWS was 0.136%; 14,599 DWS patients were included. Multiple logistic regression models were used. Odds ratios (OR) were reported with 95% confidence intervals. Mortality (OR = 10.02; P < 0.0001) and adverse discharge disposition (OR = 4.59; P < 0.0001) were significantly greater in DWS patients compared with controls. 20.4% of DWS patients received operative cerebrospinal fluid (CSF) drainage, 81-times more than controls (P < 0.0001). CSF drainage reduced mortality by 44% among DWS patients (P < 0.0001). Although DWS is associated with a 10-fold increase in mortality, operative CSF drainage nearly halves the mortality rate. Based on these findings (Class IIB evidence), it is likely that the increased mortality associated with DWS is directly attributable to the nearly 80% of DWS patients who did not receive operative CSF drainage for hydrocephalus. Consequently, increased access to neurosurgical intervention could reduce the mortality rate of DWS towards that of the general population.

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

    PubMed

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

    2010-05-01

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

  11. Participation Dynamics in Population-Based Longitudinal HIV Surveillance in Rural South Africa

    PubMed Central

    Larmarange, Joseph; Mossong, Joël; Bärnighausen, Till; Newell, Marie Louise

    2015-01-01

    Population-based HIV surveillance is crucial to inform understanding of the HIV pandemic and evaluate HIV interventions, but little is known about longitudinal participation patterns in such settings. We investigated the dynamics of longitudinal participation patterns in a high HIV prevalence surveillance setting in rural South Africa between 2003 and 2012, taking into account demographic dynamics. At any given survey round, 22,708 to 30,495 persons were eligible. Although the yearly participation rates were relatively modest (26% to 46%), cumulative rates increased substantially with multiple recruitment opportunities: 68% of eligible persons participated at least once, 48% at least twice and 31% at least three times after five survey rounds. We identified two types of study fatigue: at the individual level, contact and consent rates decreased with multiple recruitment opportunities and, at the population level, these rates also decreased over calendar time, independently of multiple recruitment opportunities. Using sequence analysis and hierarchical clustering, we identified three broad individual participation profiles: consenters (20%), switchers (43%) and refusers (37%). Men were over represented among refusers, women among consenters, and temporary non-residents among switchers. The specific subgroup of persons who were systemically not contacted or refusers constitutes a challenge for population-based surveillance and interventions. PMID:25875851

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

    PubMed

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

    2003-11-01

    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.

  13. 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

  14. Understanding the Connection Between Traumatic Brain Injury and Alzheimer’s Disease: A Population Based Medical Record Review Analysis

    DTIC Science & Technology

    2016-10-01

    AWARD NUMBER: W81XWH-15-1-0573 TITLE: Understanding the Connection Between Traumatic Brain Injury and Alzheimer’s Disease: A Population-Based...Sep 2015 - 14 Sep 2016 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Understanding the Connection Between Traumatic Brain Injury and Alzheimer’s Disease...TERMS Population; epidemiology; dementia; neurocognitive disorders; brain injuries; Parkinsonian disorders 16. SECURITY CLASSIFICATION OF: U 17

  15. Population-based biobank participants’ preferences for receiving genetic test results

    PubMed Central

    Yamamoto, Kayono; Hachiya, Tsuyoshi; Fukushima, Akimune; Nakaya, Naoki; Okayama, Akira; Tanno, Kozo; Aizawa, Fumie; Tokutomi, Tomoharu; Hozawa, Atsushi; Shimizu, Atsushi

    2017-01-01

    There are ongoing debates on issues relating to returning individual research results (IRRs) and incidental findings (IFs) generated by genetic research in population-based biobanks. To understand how to appropriately return genetic results from biobank studies, we surveyed preferences for returning IRRs and IFs among participants of the Tohoku Medical Megabank Project (TMM). We mailed a questionnaire to individuals enrolled in the TMM cohort study (Group 1; n=1031) and a group of Tohoku region residents (Group 2; n=2314). The respondents were required to be over 20 years of age. Nearly 90% of Group 1 participants and over 80% of Group 2 participants expressed a preference for receiving their genetic test results. Furthermore, over 60% of both groups preferred to receive their genetic results ‘from a genetic specialist.’ A logistic regression analysis revealed that engaging in ‘health-conscious behaviors’ (such as regular physical activity, having a healthy diet, intentionally reducing alcohol intake and/or smoking and so on) was significant, positively associated with preferring to receive their genetic test results (odds ratio=2.397 (Group 1) and 1.897 (Group 2)). Our findings provided useful information and predictors regarding the return of IRRs and IFs in a population-based biobank. PMID:28794501

  16. gQTL: A Web Application for QTL Analysis Using the Collaborative Cross Mouse Genetic Reference Population.

    PubMed

    Konganti, Kranti; Ehrlich, Andre; Rusyn, Ivan; Threadgill, David W

    2018-06-07

    Multi-parental recombinant inbred populations, such as the Collaborative Cross (CC) mouse genetic reference population, are increasingly being used for analysis of quantitative trait loci (QTL). However specialized analytic software for these complex populations is typically built in R that works only on command-line, which limits the utility of these powerful resources for many users. To overcome analytic limitations, we developed gQTL, a web accessible, simple graphical user interface application based on the DOQTL platform in R to perform QTL mapping using data from CC mice. Copyright © 2018, G3: Genes, Genomes, Genetics.

  17. 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…

  18. Atlas-Based Ventricular Shape Analysis for Understanding Congenital Heart Disease.

    PubMed

    Farrar, Genevieve; Suinesiaputra, Avan; Gilbert, Kathleen; Perry, James C; Hegde, Sanjeet; Marsden, Alison; Young, Alistair A; Omens, Jeffrey H; McCulloch, Andrew D

    2016-12-01

    Congenital heart disease is associated with abnormal ventricular shape that can affect wall mechanics and may be predictive of long-term adverse outcomes. Atlas-based parametric shape analysis was used to analyze ventricular geometries of eight adolescent or adult single-ventricle CHD patients with tricuspid atresia and Fontans. These patients were compared with an "atlas" of non-congenital asymptomatic volunteers, resulting in a set of z-scores which quantify deviations from the control population distribution on a patient-by-patient basis. We examined the potential of these scores to: (1) quantify abnormalities of ventricular geometry in single ventricle physiologies relative to the normal population; (2) comprehensively quantify wall motion in CHD patients; and (3) identify possible relationships between ventricular shape and wall motion that may reflect underlying functional defects or remodeling in CHD patients. CHD ventricular geometries at end-diastole and end-systole were individually compared with statistical shape properties of an asymptomatic population from the Cardiac Atlas Project. Shape analysis-derived model properties, and myocardial wall motions between end-diastole and end-systole, were compared with physician observations of clinical functional parameters. Relationships between altered shape and altered function were evaluated via correlations between atlas-based shape and wall motion scores. Atlas-based shape analysis identified a diverse set of specific quantifiable abnormalities in ventricular geometry or myocardial wall motion in all subjects. Moreover, this initial cohort displayed significant relationships between specific shape abnormalities such as increased ventricular sphericity and functional defects in myocardial deformation, such as decreased long-axis wall motion. These findings suggest that atlas-based ventricular shape analysis may be a useful new tool in the management of patients with CHD who are at risk of impaired ventricular

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

    PubMed

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

    2015-12-08

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

  20. 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

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

    PubMed

    Akram, Nuzhat A; Farooqi, Shakeel R

    2014-01-01

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

  2. The Case for Diabetes Population Health Improvement: Evidence-Based Programming for Population Outcomes in Diabetes

    PubMed Central

    Maruthur, Nisa; Mathioudakis, Nestoras; Spanakis, Elias; Rubin, Daniel; Zilbermint, Mihail; Hill-Briggs, Felicia

    2017-01-01

    Purpose of Review The goal of this review is to describe diabetes within a population health improvement framework and to review the evidence for a diabetes population health continuum of intervention approaches, including diabetes prevention and chronic and acute diabetes management, to improve clinical and economic outcomes. Recent Findings Recent studies have shown that compared to usual care, lifestyle interventions in prediabetes lower diabetes risk at the population-level and that group-based programs have low incremental medial cost effectiveness ratio for health systems. Effective outpatient interventions that improve diabetes control and process outcomes are multi-level, targeting the patient, provider, and healthcare system simultaneously and integrate community health workers as a liaison between the patient and community-based healthcare resources. A multi-faceted approach to diabetes management is also effective in the inpatient setting. Interventions shown to promote safe and effective glycemic control and use of evidence-based glucose management practices include provider reminder and clinical decision support systems, automated computer order entry, provider education, and organizational change. Summary Future studies should examine the cost-effectiveness of multi-faceted outpatient and inpatient diabetes management programs to determine the best financial models for incorporating them into diabetes population health strategies. PMID:28567711

  3. Hippocampal atrophy in people with memory deficits: results from the population-based IPREA study.

    PubMed

    Ferrarini, Luca; van Lew, Baldur; Reiber, Johan H C; Gandin, Claudia; Galluzzo, Lucia; Scafato, Emanuele; Frisoni, Giovanni B; Milles, Julien; Pievani, Michela

    2014-07-01

    Clinical studies have shown that hippocampal atrophy is present before dementia in people with memory deficits and can predict dementia development. The question remains whether this association holds in the general population. This is of interest for the possible use of hippocampal atrophy to screen population for preventive interventions. The aim of this study was to assess hippocampal volume and shape abnormalities in elderly adults with memory deficits in a cross-sectional population-based study. We included individuals participating in the Italian Project on the Epidemiology of Alzheimer Disease (IPREA) study: 75 cognitively normal individuals (HC), 31 individuals with memory deficits (MEM), and 31 individuals with memory deficits not otherwise specified (MEMnos). Hippocampal volumes and shape were extracted through manual tracing and the growing and adaptive meshes (GAMEs) shape-modeling algorithm. We investigated between-group differences in hippocampal volume and shape, and correlations with memory deficits. In MEM participants, hippocampal volumes were significantly smaller than in HC and were mildly associated with worse memory scores. Memory-associated shape changes mapped to the anterior hippocampus. Shape-based analysis detected no significant difference between MEM and HC, while MEMnos showed shape changes in the posterior hippocampus compared with HC and MEM groups. These findings support the discriminant validity of hippocampal volumetry as a biomarker of memory impairment in the general population. The detection of shape changes in MEMnos but not in MEM participants suggests that shape-based biomarkers might lack sensitivity to detect Alzheimer's-like pathology in the general population.

  4. Effect of interleukin-6 polymorphism on risk of preterm birth within population strata: a meta-analysis.

    PubMed

    Wu, Wilfred; Clark, Erin A S; Stoddard, Gregory J; Watkins, W Scott; Esplin, M Sean; Manuck, Tracy A; Xing, Jinchuan; Varner, Michael W; Jorde, Lynn B

    2013-04-25

    Because of the role of inflammation in preterm birth (PTB), polymorphisms in and near the interleukin-6 gene (IL6) have been association study targets. Several previous studies have assessed the association between PTB and a single nucleotide polymorphism (SNP), rs1800795, located in the IL6 gene promoter region. Their results have been inconsistent and SNP frequencies have varied strikingly among different populations. We therefore conducted a meta-analysis with subgroup analysis by population strata to: (1) reduce the confounding effect of population structure, (2) increase sample size and statistical power, and (3) elucidate the association between rs1800975 and PTB. We reviewed all published papers for PTB phenotype and SNP rs1800795 genotype. Maternal genotype and fetal genotype were analyzed separately and the analyses were stratified by population. The PTB phenotype was defined as gestational age (GA) < 37 weeks, but results from earlier GA were selected when available. All studies were compared by genotype (CC versus CG+GG), based on functional studies.For the maternal genotype analysis, 1,165 PTBs and 3,830 term controls were evaluated. Populations were stratified into women of European descent (for whom the most data were available) and women of heterogeneous origin or admixed populations. All ancestry was self-reported. Women of European descent had a summary odds ratio (OR) of 0.68, (95% confidence interval (CI) 0.51 - 0.91), indicating that the CC genotype is protective against PTB. The result for non-European women was not statistically significant (OR 1.01, 95% CI 0.59 - 1.75). For the fetal genotype analysis, four studies were included; there was no significant association with PTB (OR 0.98, 95% CI 0.72 - 1.33). Sensitivity analysis showed that preterm premature rupture of membrane (PPROM) may be a confounding factor contributing to phenotype heterogeneity. IL6 SNP rs1800795 genotype CC is protective against PTB in women of European descent. It is

  5. Role of mtDNA haplogroups in the prevalence of osteoarthritis in different geographic populations: a meta-analysis.

    PubMed

    Shen, Jin-Ming; Feng, Lei; Feng, Chun

    2014-01-01

    Osteoarthritis (OA) is the most common form of arthritis and has become an increasingly important public-health problem. However, the pathogenesis of OA is still unclear. In recent years, its correlation with mtDNA haplogroups attracts much attention. We aimed to perform a meta-analysis to investigate the association between mtDNA haplogroups and OA. Published English or Chinese literature from PubMed, Web of Science, SDOS, and CNKI was retrieved up until April 15, 2014. Case-control or cohort studies that detected the frequency of mtDNA haplogroups in OA patients and controls were included. The quality of the included studies was evaluated by the Newcastle-Ottawa Scale (NOS) assessment. A meta-analysis was conducted to calculate pooled odds ratio (OR) with 95% confidence interval (CI) through the random or fixed effect model, which was selected based on the between-study heterogeneity assessed by Q test and I2 test. Subgroup analysis was performed to explore the origin of heterogeneity. A total of 6 case-control studies (10590 cases and 7161 controls) with an average NOS score of 6.9 were involved. For the analysis between mtDNA haplogroup J and OA, random model was selected due to high heterogeneity. No significant association was found initially (OR = 0.73, 95%CI: 0.52-1.03), however, once any study from UK population was removed the association emerged. Further subgroup analysis demonstrated that there was a significant association in Spain population (OR = 0.57, 95%CI: 0.46-0.71), but not in UK population. Also, subgroup analysis revealed that there was a significant correlation between cluster TJ and OA in Spain population (OR = 0.70, 95%CI: 0.58-0.84), although not in UK population. No significant correlation was found between haplogroup T/cluster HV/cluster KU and OA. Our current meta-analysis suggests that mtDNA haplogroup J and cluster TJ correlate with the risk of OA in Spanish population, but the associations in other populations require

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

    PubMed

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

    2010-08-01

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

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

    PubMed

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

    2016-09-21

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

  8. Using natural language processing for identification of herpes zoster ophthalmicus cases to support population-based study.

    PubMed

    Zheng, Chengyi; Luo, Yi; Mercado, Cheryl; Sy, Lina; Jacobsen, Steven J; Ackerson, Brad; Lewin, Bruno; Tseng, Hung Fu

    2018-06-19

    Diagnosis codes are inadequate for accurately identifying herpes zoster ophthalmicus (HZO). There is significant lack of population-based studies on HZO due to the high expense of manual review of medical records. To assess whether HZO can be identified from the clinical notes using natural language processing (NLP). To investigate the epidemiology of HZO among HZ population based on the developed approach. A retrospective cohort analysis. A total of 49,914 southern California residents aged over 18 years, who had a new diagnosis of HZ. An NLP-based algorithm was developed and validated with the manually curated validation dataset (n=461). The algorithm was applied on over 1 million clinical notes associated with the study population. HZO versus non-HZO cases were compared by age, sex, race, and comorbidities. We measured the accuracy of NLP algorithm. NLP algorithm achieved 95.6% sensitivity and 99.3% specificity. Compared to the diagnosis codes, NLP identified significant more HZO cases among HZ population (13.9% versus 1.7%). Compared to the non-HZO group, the HZO group was older, had more males, had more Whites, and had more outpatient visits. We developed and validated an automatic method to identify HZO cases with high accuracy. As one of the largest studies on HZO, our finding emphasizes the importance of preventing HZ in the elderly population. This method can be a valuable tool to support population-based studies and clinical care of HZO in the era of big data. This article is protected by copyright. All rights reserved.

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

    PubMed

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

    2014-03-01

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

  11. Genetic diversity and population structure analysis between Indian red jungle fowl and domestic chicken using microsatellite markers.

    PubMed

    Kumar, Vinay; Shukla, Sanjeev K; Mathew, Jose; Sharma, Deepak

    2015-01-01

    The present study was conducted to assess the genetic diversity, population structure, and relatedness in Indian red jungle fowl (RJF, Gallus gallus murgi) from northern India and three domestic chicken populations (gallus gallus domesticus), maintained at the institute farms, namely White Leghorn (WL), Aseel (AS) and Red Cornish (RC) using 25 microsatellite markers. All the markers were polymorphic, the number of alleles at each locus ranged from five (MCW0111) to forty-three (LEI0212) with an average number of 19 alleles per locus. Across all loci, the mean expected heterozygosity and polymorphic information content were 0.883 and 0.872, respectively. Population-specific alleles were found in each population. A UPGMA dendrogram based on shared allele distances clearly revealed two major clusters among the four populations; cluster I had genotypes from RJF and WL whereas cluster II had AS and RC genotypes. Furthermore, the estimation of population structure was performed to understand how genetic variation is partitioned within and among populations. The maximum ▵K value was observed for K = 4 with four identified clusters. Furthermore, factorial analysis clearly showed four clustering; each cluster represented the four types of population used in the study. These results clearly, demonstrate the potential of microsatellite markers in elucidating the genetic diversity, relationships, and population structure analysis in RJF and domestic chicken populations.

  12. Genome-wide association analysis of gender differences in major depressive disorder in the Netherlands NESDA and NTR population-based samples.

    PubMed

    Aragam, Nagesh; Wang, Ke-Sheng; Pan, Yue

    2011-10-01

    Major depressive disorder (MDD) is a universally prevalent, genetic, and environment dependent mental condition that disables people of every culture, race, gender, and age. While the gender differences for MDD have been widely reported in literature, few genome-wide analyses of gender differences have been reported to date. We conducted a genome-wide association analysis of gender differences for MDD using the Netherlands NESDA and NTR population-based samples (1726 cases and 1630 controls). PLINK software was used to analyze the genome-wide association data of Perlegen 600 K SNP Chips. We identified 40 male-specific and 56 female-specific MDD associated SNPs with P-values less than 10(-4). The best male-specific SNP was rs9352774 (P=2.26 × 10(-6)) within LGSN gene while the best female-specific SNP was rs2715148 (P=5.64 × 10(-7)) within PCLO gene. We also found 38 SNPs showing gene × gender interactions in influencing MDD (P<10(-4)). The best SNP was rs12692709 (P=5.75 × 10(-6)) near FIGN gene at 2q24.3 while the next best SNP was rs11039588 (P=1.16 × 10(-5)) within OR4B1 gene. The findings from this study need be replicated in other populations. These results provide genetic basis for gender differences in MDD and will serve as a resource for replication in other populations to elucidate the potential role of these genetic variants in MDD. Copyright © 2011 Elsevier B.V. All rights reserved.

  13. Method of confidence domains in the analysis of noise-induced extinction for tritrophic population system

    NASA Astrophysics Data System (ADS)

    Bashkirtseva, Irina; Ryashko, Lev; Ryazanova, Tatyana

    2017-09-01

    A problem of the analysis of the noise-induced extinction in multidimensional population systems is considered. For the investigation of conditions of the extinction caused by random disturbances, a new approach based on the stochastic sensitivity function technique and confidence domains is suggested, and applied to tritrophic population model of interacting prey, predator and top predator. This approach allows us to analyze constructively the probabilistic mechanisms of the transition to the noise-induced extinction from both equilibrium and oscillatory regimes of coexistence. In this analysis, a method of principal directions for the reducing of the dimension of confidence domains is suggested. In the dispersion of random states, the principal subspace is defined by the ratio of eigenvalues of the stochastic sensitivity matrix. A detailed analysis of two scenarios of the noise-induced extinction in dependence on parameters of considered tritrophic system is carried out.

  14. Spectral Entropy Based Neuronal Network Synchronization Analysis Based on Microelectrode Array Measurements

    PubMed Central

    Kapucu, Fikret E.; Välkki, Inkeri; Mikkonen, Jarno E.; Leone, Chiara; Lenk, Kerstin; Tanskanen, Jarno M. A.; Hyttinen, Jari A. K.

    2016-01-01

    Synchrony and asynchrony are essential aspects of the functioning of interconnected neuronal cells and networks. New information on neuronal synchronization can be expected to aid in understanding these systems. Synchronization provides insight in the functional connectivity and the spatial distribution of the information processing in the networks. Synchronization is generally studied with time domain analysis of neuronal events, or using direct frequency spectrum analysis, e.g., in specific frequency bands. However, these methods have their pitfalls. Thus, we have previously proposed a method to analyze temporal changes in the complexity of the frequency of signals originating from different network regions. The method is based on the correlation of time varying spectral entropies (SEs). SE assesses the regularity, or complexity, of a time series by quantifying the uniformity of the frequency spectrum distribution. It has been previously employed, e.g., in electroencephalogram analysis. Here, we revisit our correlated spectral entropy method (CorSE), providing evidence of its justification, usability, and benefits. Here, CorSE is assessed with simulations and in vitro microelectrode array (MEA) data. CorSE is first demonstrated with a specifically tailored toy simulation to illustrate how it can identify synchronized populations. To provide a form of validation, the method was tested with simulated data from integrate-and-fire model based computational neuronal networks. To demonstrate the analysis of real data, CorSE was applied on in vitro MEA data measured from rat cortical cell cultures, and the results were compared with three known event based synchronization measures. Finally, we show the usability by tracking the development of networks in dissociated mouse cortical cell cultures. The results show that temporal correlations in frequency spectrum distributions reflect the network relations of neuronal populations. In the simulated data, CorSE unraveled the

  15. Population-based study on infant mortality.

    PubMed

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

    2017-03-01

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

  16. Genetic variation and forensic characteristic analysis of 25 STRs of a novel fluorescence co-amplification system in Chinese Southern Shaanxi Han population

    PubMed Central

    Liu, Yao-Shun; Chen, Jian-Gang; Mei, Ting; Guo, Yu-Xin; Meng, Hao-Tian; Li, Jian-Fei; Wei, Yuan-Yuan; Jin, Xiao-Ye; Zhu, Bo-Feng; Zhang, Li-Ping

    2017-01-01

    We analyzed the genetic polymorphisms of 15 autosomal and 10 Y-chromosomal STR loci in 214 individuals of Han population from Southern Shaanxi of China and studied the genetic relationships between Southern Shaanxi Han and other populations. We observed a total of 150 alleles at 15 autosomal STR loci with the corresponding allelic frequencies ranging from 0.0023 to 0.5210, and the combined power of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999999999998866 and 0.999998491, respectively. For the 10 Y-STR loci, totally 100 different haplotypes were obtained, of which 94 were unique. The discriminatory capacity and haplotype diversity values of the 10 Y-STR loci were 0.9259 and 0.998269, respectively. The results demonstrated high genetic diversities of the 25 STR loci in the population for forensic applications. We constructed neighbor-joining tree and conducted principal component analysis based on 15 autosomal STR loci and conducted multidimensional scaling analysis and constructed neighbor-joining tree based on 10 Y-STR loci. The results of population genetic analyses based on both autosomal and Y-chromosome STRs indicated that the studied Southern Shaanxi Han population had relatively closer genetic relationship with Eastern Han population, and distant relationships with Croatian, Serbian and Moroccan populations. PMID:28903432

  17. Genetic variation and forensic characteristic analysis of 25 STRs of a novel fluorescence co-amplification system in Chinese Southern Shaanxi Han population.

    PubMed

    Liu, Yao-Shun; Chen, Jian-Gang; Mei, Ting; Guo, Yu-Xin; Meng, Hao-Tian; Li, Jian-Fei; Wei, Yuan-Yuan; Jin, Xiao-Ye; Zhu, Bo-Feng; Zhang, Li-Ping

    2017-08-15

    We analyzed the genetic polymorphisms of 15 autosomal and 10 Y-chromosomal STR loci in 214 individuals of Han population from Southern Shaanxi of China and studied the genetic relationships between Southern Shaanxi Han and other populations. We observed a total of 150 alleles at 15 autosomal STR loci with the corresponding allelic frequencies ranging from 0.0023 to 0.5210, and the combined power of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999999999998866 and 0.999998491, respectively. For the 10 Y-STR loci, totally 100 different haplotypes were obtained, of which 94 were unique. The discriminatory capacity and haplotype diversity values of the 10 Y-STR loci were 0.9259 and 0.998269, respectively. The results demonstrated high genetic diversities of the 25 STR loci in the population for forensic applications. We constructed neighbor-joining tree and conducted principal component analysis based on 15 autosomal STR loci and conducted multidimensional scaling analysis and constructed neighbor-joining tree based on 10 Y-STR loci. The results of population genetic analyses based on both autosomal and Y-chromosome STRs indicated that the studied Southern Shaanxi Han population had relatively closer genetic relationship with Eastern Han population, and distant relationships with Croatian, Serbian and Moroccan populations.

  18. Pollen flow in the wildservice tree, Sorbus torminalis (L.) Crantz. I. Evaluating the paternity analysis procedure in continuous populations.

    PubMed

    Oddou-Muratorio, S; Houot, M-L; Demesure-Musch, B; Austerlitz, F

    2003-12-01

    The joint development of polymorphic molecular markers and paternity analysis methods provides new approaches to investigate ongoing patterns of pollen flow in natural plant populations. However, paternity studies are hindered by false paternity assignment and the nondetection of true fathers. To gauge the risk of these two types of errors, we performed a simulation study to investigate the impact on paternity analysis of: (i) the assumed values for the size of the breeding male population (NBMP), and (ii) the rate of scoring error in genotype assessment. Our simulations were based on microsatellite data obtained from a natural population of the entomophilous wild service tree, Sorbus torminalis (L.) Crantz. We show that an accurate estimate of NBMP is required to minimize both types of errors, and we assess the reliability of a technique used to estimate NBMP based on parent-offspring genetic data. We then show that scoring errors in genotype assessment only slightly affect the assessment of paternity relationships, and conclude that it is generally better to neglect the scoring error rate in paternity analyses within a nonisolated population.

  19. Serotonin transporter promoter variants: Analysis in Indian autistic and control population.

    PubMed

    Guhathakurta, Subhrangshu; Ghosh, Sagarmoy; Sinha, Swagata; Chatterjee, Anindita; Ahmed, Shabina; Chowdhury, Susanta Roy; Gangopadhyay, Prasanta Kumar; Ghosh, Saurabh; Singh, Manoranjan; Usha, Rajamma

    2006-05-30

    Serotonin transporter (5-HTT) is a transmembrane protein belonging to Na+/Cl- dependent membrane transporter family and transports 5-HT across the membranes of presynaptic neurons. 5-HTT-linked polymorphic region (5-HTTLPR) gained much interest because of the differential regulation of expression and activity of 5-HTT by its various genotypes. A population-based study has been conducted on 5-HTTLPR with 358 individuals, which included 79 autistic probands, 136 parents, and 143 controls from two subpopulations of east and northeast regions of India. The genotypic frequencies of all the groups conform to Hardy-Weinberg equilibrium. With the finding of efficacy of serotonin reuptake inhibitors in ameliorating ritualistic behavior in autistic disorder, 5-HTT emerged as a putative candidate gene for autism and association studies have been carried out in different ethnic populations. But these studies were inconclusive due to conflicting results on association. Because such a study has never been performed in the Indian population, we have tested the possible involvement of 5-HTTLPR polymorphism with autism. The present study failed to establish any association or linkage of 5-HTTLPR with autism in the Indian population by case-control studies (chi2 = 1.314, P = 0.63) and family-based approaches (TDT chi2 = 0.22, P = 0.64 and HHRR-chi2 = 0.25, P = 0.61). However, when a meta-analysis of all the available TDT data, inclusive of the present study is carried out, we observed a significant preferential transmission of S-allele from parents to the affected offspring (chi2 = 7.51, P = 0.006) indicating an association of 5-HTTLPR with autism.

  20. Population-based risk for complications after transthoracic needle lung biopsy of a pulmonary nodule: an analysis of discharge records.

    PubMed

    Wiener, Renda Soylemez; Schwartz, Lisa M; Woloshin, Steven; Welch, H Gilbert

    2011-08-02

    Because pulmonary nodules are found in up to 25% of patients undergoing computed tomography of the chest, the question of whether to perform biopsy is becoming increasingly common. Data on complications after transthoracic needle lung biopsy are limited to case series from selected institutions. To determine population-based estimates of risks for complications after transthoracic needle biopsy of a pulmonary nodule. Cross-sectional analysis. The 2006 State Ambulatory Surgery Databases and State Inpatient Databases for California, Florida, Michigan, and New York from the Healthcare Cost and Utilization Project. 15 865 adults who had transthoracic needle biopsy of a pulmonary nodule. Percentage of biopsies complicated by hemorrhage, any pneumothorax, or pneumothorax requiring a chest tube, and adjusted odds ratios for these complications associated with various biopsy characteristics, calculated by using multivariate, population-averaged generalized estimating equations. Although hemorrhage was rare, complicating 1.0% (95% CI, 0.9% to 1.2%) of biopsies, 17.8% (CI, 11.8% to 23.8%) of patients with hemorrhage required a blood transfusion. In contrast, the risk for any pneumothorax was 15.0% (CI, 14.0% to 16.0%), and 6.6% (CI, 6.0% to 7.2%) of all biopsies resulted in pneumothorax requiring a chest tube. Compared with patients without complications, those who experienced hemorrhage or pneumothorax requiring a chest tube had longer lengths of stay (P < 0.001) and were more likely to develop respiratory failure requiring mechanical ventilation (P = 0.020). Patients aged 60 to 69 years (as opposed to younger or older patients), smokers, and those with chronic obstructive pulmonary disease had higher risk for complications. Estimated risks may be inaccurate if coding of complications is incomplete. The analyzed databases contain little clinical detail (such as information on nodule characteristics or biopsy pathology) and cannot indicate whether performing the biopsy

  1. The TSH levels and risk of hypothyroidism: Results from a population based prospective cohort study in an Iranian adult's population.

    PubMed

    Aminorroaya, Ashraf; Meamar, Rokhsareh; Amini, Massoud; Feizi, Awat; Nasri, Maryam; Tabatabaei, Azamosadat; Faghihimani, Elham

    2017-06-01

    The aim of current study was to assess the relationship between serum TSH levels and hypothyroidism risk in the euthyroid population. In a population-based cohort study, a total of 615 individuals with a normal baseline TSH, from of total population (n=2254) in 2006, were followed up for 6years. TSH, total T4, thyroid peroxidase antibody (TPOAb), and thyroglobulin antibody (TgAb) were measured. The relative risk (RR) and 95% confidence interval (95%CI) were calculated based on logistic regression. The Receiver Operating Characteristic (ROC) analysis along with area under the curve (AUC) was used to prediction of future hypothyroidism. TSH level in 2006 was a significant predictor for overt hypothyroidism, in the total population (RR=3.5) and female (RR=1.37) (all, P value<0.05). A cutoff value of TSH at 2.05mIU/L [AUC: (CI95 %), 0.68 (0.44-0.92; P=0.05)] was obtained for differentiating the patients with overt hypothyroidism from euthyroid. However, this cut off was not observed when we included only negative TPO and TgAbs people in 2006. The RR of hypothyroidism increased gradually when TSH level increased from 2.06-3.6mIU/L to >3.6mIU/L in the total population and both sexes. In women, the risk of overt hypothyroidism was significantly higher in subjects with TSH above 3.6 than those subject with THS levels≤2.05 [RR: (CI95 %), 20.57(2.-207.04), P value<0.05]. A cutoff value of TSH at 2.05mIU/L could predict the development of overt hypothyroidism in future. However, it was not applicable for people with negative TPOAb and negative TgAb. Copyright © 2016 European Federation of Internal Medicine. Published by Elsevier B.V. All rights reserved.

  2. Respiratory cancer population-based survival in Mumbai, India.

    PubMed

    Yeole, Balkrishna B

    2005-01-01

    Survival experience of patients with cancer of the larynx (ICD-32) or lung (ICD-34) registered by the Mumbai (Bombay) population based cancer registry, India, during the years 1992-94 was determined. The vital statistics of the patients were established by matching with death certificates from the Mumbai Municipal death register and by active methods such as telephone enquiry, reply-paid postal enquiry, house visits and scrutiny of case records. Of the 1905 (675 larynx and 1230 lung) eligible cases for analysis, 1480 were dead (450 larynx and 1030 lung) and 425 were alive (225 larynx and 200 lung). The overall 5-year observed and relative survival rates for laryngeal cancers were 29.1% and 36.4%, and for lung cancers were 12.5% and 15.9% respectively. On multivariate analysis, age, treatment and clinical extent of disease emerged as independent predictors of survival with both cancers. People aged 55 years and above had a relative risk of four or more for laryngeal cancer and 2.3 times and more for lung cancer death as compared to those aged less than 35 years. Early detection and prompt treatment should improve overall survival from lung as well as laryngeal cancer.

  3. Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies.

    PubMed

    McGovern, Rachel A; Thielen, Alexander; Mo, Theresa; Dong, Winnie; Woods, Conan K; Chapman, Douglass; Lewis, Marilyn; James, Ian; Heera, Jayvant; Valdez, Hernan; Harrigan, P Richard

    2010-10-23

    The MOTIVATE-1 and 2 studies compared maraviroc (MVC) along with optimized background therapy (OBT) vs. placebo along with OBT in treatment-experienced patients screened as having R5-HIV (original Monogram Trofile). A subset screened with non-R5 HIV were treated with MVC or placebo along with OBT in a sister safety trial, A4001029. This analysis retrospectively examined the performance of population-based sequence analysis of HIV-1 env V3-loop to predict coreceptor tropism. Triplicate V3-loop sequences were generated using stored screening plasma samples and data was processed using custom software ('ReCall'), blinded to clinical response. Tropism was inferred using geno2pheno ('g2p'; 5% false positive rate). Primary outcomes were viral load changes after starting maraviroc; and concordance with prior screening Trofile results. Genotype and Trofile results were available for 1164 individuals with virological outcome data (N = 169 non-R5 by Trofile). Compared with Trofile, V3 genotyping had a specificity of 92.6% and a sensitivity of 67.4% for detecting non-R5 virus. However, when compared with clinical outcome, virological responses were consistently similar between Trofile and V3 genotype at weeks 8 and 24 following the initiation of therapy for patients categorized as R5. Despite differences in sensitivity for predicting non-R5 HIV, week 8 and 24 week virological responses were similar in this treatment-experienced population. These findings suggest the potential utility of V3 genotyping as an accessible assay to select patients who may benefit from maraviroc treatment. Optimization of the predictive tropism algorithm may lead to further improvement in the clinical utility of HIV genotypic tropism assays.

  4. The burden of road traffic injuries in Nigeria: results of a population-based survey.

    PubMed

    Labinjo, M; Juillard, C; Kobusingye, O C; Hyder, A A

    2009-06-01

    Mortality from road traffic injuries in sub-Saharan Africa is among the highest in the world, yet data from the region are sparse. To date, no multi-site population-based survey on road traffic injuries has been reported from Nigeria, the most populated country in Africa. To explore the epidemiology of road traffic injury in Nigeria and provide data on the populations affected and risk factors for road traffic injury. Data from a population-based survey using two-stage stratified cluster sampling. SUBJECTS/ SETTING: Road traffic injury status and demographic information were collected on 3082 respondents living in 553 households in seven of Nigeria's 37 states. Incidence rates were estimated with confidence intervals based on a Poisson distribution; Poisson regression analysis was used to calculate relative risks for associated factors. The overall road traffic injury rate was 41 per 1000 population (95% CI 34 to 49), and mortality from road traffic injuries was 1.6 per 1000 population (95% CI 0.5 to 3.8). Motorcycle crashes accounted for 54% of all road traffic injuries. The road traffic injury rates found for rural and urban respondents were not significantly different. Increased risk of injury was associated with male gender among those aged 18-44 years, with a relative risk of 2.96 when compared with women in the same age range (95% CI 1.72 to 5.09, p<0.001). The road traffic injury rates found in this survey highlight a neglected public health problem in Nigeria. Simple extrapolations from this survey suggest that over 4 million people may be injured and as many as 200 000 potentially killed as the result of road traffic crashes annually in Nigeria. Appropriate interventions in both the health and transport sectors are needed to address this significant cause of morbidity and mortality in Nigeria.

  5. 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

  6. Cultural inter-population differences do not reflect biological distances: an example of interdisciplinary analysis of populations from Eastern Adriatic coast.

    PubMed

    Bašić, Željana; Fox, Ayano R; Anterić, Ivana; Jerković, Ivan; Polašek, Ozren; Anđelinović, Šimun; Holland, Mitchell M; Primorac, Dragan

    2015-06-01

    To compare the population group from the Šopot graveyard with population groups from traditional Croatian medieval graveyards by using anthropological, craniometrics, and mitochondrial (mtDNA) analysis and to examine if the cultural differences between population groups reflect biological differences. We determined sex, age at death, pathological, and traumatic changes of skeletal remains from the Šopot graveyard and compared them with a cumulative medieval sample from the same region. We also performed principal component analysis to compare skeletal remains from Šopot with those from Ostrovica and other Central European samples according to 8 cranial measurements. Finally, we compared 46 skeletons from Šopot with medieval (Ostrovica) and contemporary populations using mDNA haplogroup profiling. The remains from Šopot were similar to the cumulative sample in lifestyle and quality of life markers. Principal component analysis showed that they were closely related to Eastern Adriatic coast sites (including Ostrovica and Šopot) in terms of cranial morphology, indicating similar biological makeup. According to mDNA testing, Šopot population showed no significant differences in the haplogroup prevalence from either medieval or contemporary populations. This study shows that the Šopot population does not significantly differ from other medieval populations from this area. Besides similar quality of life markers, these populations also had similar biological markers. Substantial archeological differences can therefore be attributed to apparent cultural influences, which in this case do not reflect biological differences.

  7. Cultural inter-population differences do not reflect biological distances: an example of interdisciplinary analysis of populations from Eastern Adriatic coast

    PubMed Central

    Bašić, Željana; Fox, Ayano R; Anterić, Ivana; Jerković, Ivan; Polašek, Ozren; Anđelinović, Šimun; Holland, Mitchell M; Primorac, Dragan

    2015-01-01

    Aim To compare the population group from the Šopot graveyard with population groups from traditional Croatian medieval graveyards by using anthropological, craniometrics, and mitochondrial (mtDNA) analysis and to examine if the cultural differences between population groups reflect biological differences. Methods We determined sex, age at death, pathological, and traumatic changes of skeletal remains from the Šopot graveyard and compared them with a cumulative medieval sample from the same region. We also performed principal component analysis to compare skeletal remains from Šopot with those from Ostrovica and other Central European samples according to 8 cranial measurements. Finally, we compared 46 skeletons from Šopot with medieval (Ostrovica) and contemporary populations using mDNA haplogroup profiling. Results The remains from Šopot were similar to the cumulative sample in lifestyle and quality of life markers. Principal component analysis showed that they were closely related to Eastern Adriatic coast sites (including Ostrovica and Šopot) in terms of cranial morphology, indicating similar biological makeup. According to mDNA testing, Šopot population showed no significant differences in the haplogroup prevalence from either medieval or contemporary populations. Conclusion This study shows that the Šopot population does not significantly differ from other medieval populations from this area. Besides similar quality of life markers, these populations also had similar biological markers. Substantial archeological differences can therefore be attributed to apparent cultural influences, which in this case do not reflect biological differences. PMID:26088847

  8. A genetic study and meta-analysis of the genetic predisposition of prostate cancer in a Chinese population.

    PubMed

    Marzec, Jacek; Mao, Xueying; Li, Meiling; Wang, Meilin; Feng, Ninghan; Gou, Xin; Wang, Guomin; Sun, Zan; Xu, Jianfeng; Xu, Hua; Zhang, Xiaoping; Zhao, Shan-Chao; Ren, Guoping; Yu, Yongwei; Wu, Yudong; Wu, Ji; Xue, Yao; Zhou, Bo; Zhang, Yanling; Xu, Xingxing; Li, Jie; He, Weiyang; Benlloch, Sara; Ross-Adams, Helen; Chen, Li; Li, Jucong; Hong, Yingqia; Kote-Jarai, Zsofia; Cui, Xingang; Hou, Jianguo; Guo, Jianming; Xu, Lei; Yin, Changjun; Zhou, Yuanping; Neal, David E; Oliver, Tim; Cao, Guangwen; Zhang, Zhengdong; Easton, Douglas F; Chelala, Claude; Al Olama, Ali Amin; Eeles, Rosalind A; Zhang, Hongwei; Lu, Yong-Jie

    2016-04-19

    Prostate cancer predisposition has been extensively investigated in European populations, but there have been few studies of other ethnic groups. To investigate prostate cancer susceptibility in the under-investigated Chinese population, we performed single-nucleotide polymorphism (SNP) array analysis on a cohort of Chinese cases and controls and then meta-analysis with data from the existing Chinese prostate cancer genome-wide association study (GWAS). Genotyping 211,155 SNPs in 495 cases and 640 controls of Chinese ancestry identified several new suggestive Chinese prostate cancer predisposition loci. However, none of them reached genome-wide significance level either by meta-analysis or replication study. The meta-analysis with the Chinese GWAS data revealed that four 8q24 loci are the main contributors to Chinese prostate cancer risk and the risk alleles from three of them exist at much higher frequencies in Chinese than European populations. We also found that several predisposition loci reported in Western populations have different effect on Chinese men. Therefore, this first extensive single-nucleotide polymorphism study of Chinese prostate cancer in comparison with European population indicates that four loci on 8q24 contribute to a great risk of prostate cancer in a considerable large proportion of Chinese men. Based on those four loci, the top 10% of the population have six- or two-fold prostate cancer risk compared with men of the bottom 10% or median risk respectively, which may facilitate the design of prostate cancer genetic risk screening and prevention in Chinese men. These findings also provide additional insights into the etiology and pathogenesis of prostate cancer.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-06-01

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

  12. 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. © 2013 Elsevier Ltd. All rights reserved.

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

    USGS Publications Warehouse

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

    2003-01-01

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

  14. Cancer Incidence in Physicians: A Taiwan National Population-based Cohort Study.

    PubMed

    Lee, Yu-Sung; Hsu, Chien-Chin; Weng, Shih-Feng; Lin, Hung-Jung; Wang, Jhi-Joung; Su, Shih-Bin; Huang, Chien-Cheng; Guo, How-Ran

    2015-11-01

    Cancer has been the leading cause of death in Taiwan since 1982. Physicians have many health-related risk factors which may contribute to cancer, such as rotating night shift, radiation, poor lifestyle, and higher exposure risk to infection and potential carcinogenic drugs. However, the cancer risk in physicians is not clear. In Taiwan's National Health Insurance Research Database, we identified 14,889 physicians as the study cohort and randomly selected 29,778 nonmedical staff patients as the comparison cohort for this national population-based cohort study. Cox proportional-hazard regression was used to compare the cancer risk between physicians and comparisons. Physician subgroups were also analyzed. Physicians had a lower all-cancer risk than did the comparisons (hazard ratio [HR] 0.86, 95% confidence interval [CI] 0.76-0.97). In the sex-based analysis, male physicians had a lower all-cancer risk than did male comparisons (HR 0.82, 95% CI 0.73-0.94); and female physicians did not (HR 1.29, 95% CI 0.88-1.91). In the cancer-type analysis, male physicians had a higher risk of prostate cancer (HR 1.72, 95% CI 1.12-2.65) and female physicians had twice the risk of breast cancer (HR 2.00, 95% CI 1.11-3.62) than did comparisons. Cancer risk was not significantly associated with physician specialties. Physicians in Taiwan had a lower all-cancer risk but higher risks for prostate and breast cancer than did the general population. These new epidemiological findings require additional study to clarify possible mechanisms.

  15. Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates

    PubMed Central

    Gill, Mandev S.; Lemey, Philippe; Bennett, Shannon N.; Biek, Roman; Suchard, Marc A.

    2016-01-01

    Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics and evolutionary biology. Kingman’s coalescent process enables inference of past population dynamics directly from molecular sequence data, and researchers have developed a number of flexible coalescent-based models for Bayesian nonparametric estimation of the effective population size as a function of time. Major goals of demographic reconstruction include identifying driving factors of effective population size, and understanding the association between the effective population size and such factors. Building upon Bayesian nonparametric coalescent-based approaches, we introduce a flexible framework that incorporates time-varying covariates that exploit Gaussian Markov random fields to achieve temporal smoothing of effective population size trajectories. To approximate the posterior distribution, we adapt efficient Markov chain Monte Carlo algorithms designed for highly structured Gaussian models. Incorporating covariates into the demographic inference framework enables the modeling of associations between the effective population size and covariates while accounting for uncertainty in population histories. Furthermore, it can lead to more precise estimates of population dynamics. We apply our model to four examples. We reconstruct the demographic history of raccoon rabies in North America and find a significant association with the spatiotemporal spread of the outbreak. Next, we examine the effective population size trajectory of the DENV-4 virus in Puerto Rico along with viral isolate count data and find similar cyclic patterns. We compare the population history of the HIV-1 CRF02_AG clade in Cameroon with HIV incidence and prevalence data and find that the effective population size is more reflective of incidence rate. Finally, we explore the hypothesis that the population dynamics of musk ox during the Late

  16. Population structure in Japanese rice population

    PubMed Central

    Yamasaki, Masanori; Ideta, Osamu

    2013-01-01

    It is essential to elucidate genetic diversity and relationships among even related individuals and populations for plant breeding and genetic analysis. Since Japanese rice breeding has improved agronomic traits such as yield and eating quality, modern Japanese rice cultivars originated from narrow genetic resource and closely related. To resolve the population structure and genetic diversity in Japanese rice population, we used a total of 706 alleles detected by 134 simple sequence repeat markers in a total of 114 cultivars composed of 94 improved varieties and 20 landraces, which are representative and important for Japanese rice breeding. The landraces exhibit greater gene diversity than improved lines, suggesting that landraces can provide additional genetic diversity for future breeding. Model-based Bayesian clustering analysis revealed six subgroups and admixture situation in the cultivars, showing good agreement with pedigree information. This method could be superior to phylogenetic method in classifying a related population. The leading Japanese rice cultivar, Koshihikari is unique due to the specific genome constitution. We defined Japanese rice diverse sets that capture the maximum number of alleles for given sample sizes. These sets are useful for a variety of genetic application in Japanese rice cultivars. PMID:23641181

  17. Asthma exacerbation and proximity of residence to major roads: a population-based matched case-control study among the pediatric Medicaid population in Detroit, Michigan

    PubMed Central

    2011-01-01

    Background The relationship between asthma and traffic-related pollutants has received considerable attention. The use of individual-level exposure measures, such as residence location or proximity to emission sources, may avoid ecological biases. Method This study focused on the pediatric Medicaid population in Detroit, MI, a high-risk population for asthma-related events. A population-based matched case-control analysis was used to investigate associations between acute asthma outcomes and proximity of residence to major roads, including freeways. Asthma cases were identified as all children who made at least one asthma claim, including inpatient and emergency department visits, during the three-year study period, 2004-06. Individually matched controls were randomly selected from the rest of the Medicaid population on the basis of non-respiratory related illness. We used conditional logistic regression with distance as both categorical and continuous variables, and examined non-linear relationships with distance using polynomial splines. The conditional logistic regression models were then extended by considering multiple asthma states (based on the frequency of acute asthma outcomes) using polychotomous conditional logistic regression. Results Asthma events were associated with proximity to primary roads with an odds ratio of 0.97 (95% CI: 0.94, 0.99) for a 1 km increase in distance using conditional logistic regression, implying that asthma events are less likely as the distance between the residence and a primary road increases. Similar relationships and effect sizes were found using polychotomous conditional logistic regression. Another plausible exposure metric, a reduced form response surface model that represents atmospheric dispersion of pollutants from roads, was not associated under that exposure model. Conclusions There is moderately strong evidence of elevated risk of asthma close to major roads based on the results obtained in this population-based

  18. Seroepidemiology of HBV infection in South-East of iran; a population based study.

    PubMed

    Salehi, M; Alavian, S M; Tabatabaei, S V; Izadi, Sh; Sanei Moghaddam, E; Amini Kafi-Abad, S; Gharehbaghian, A; Khosravi, S; Abolghasemi, H

    2012-05-01

    Hepatitis B virus (HBV) infection is a major risk factor of cirrhosis and hepatocellular carcinoma affecting billions of people globally. Since information on its prevalence in general population is mandatory for formulating effective policies, this population based serological survey was conducted in Sistan and Baluchistan, where no previous epidemiological data were available. Using random cluster sampling 3989 healthy subjects were selected from 9 districts of Sistan and Baluchistan Province in southeastern Iran. The subjects' age ranged from 6 to 65 years old. Serum samples were tested for HBcAb, HBsAg. Screening tests were carried out by the third generation of ELISA. Various risk factors were recorded and multivariate analysis was performed. The prevalence of HBsAg and HBcAb in Sistan and Baluchistan was 3.38% (95% CI 2.85; 3.98) and 23.58% (95% CI 22.29; 24.93) respectively. We found 8 cases of positive anti-HDV antibody. Predictors of HBsAg or HBcAb in multivariate analysis were age, marital status and addiction. The rate of HBV infection in Sistan and Baluchistan was higher than other parts of Iran. Approximately 25% of general population in this province had previous exposure to HBV and 3% were HBsAg carriers. Intrafamilial and addiction were major routes of HBV transmission in this province.

  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. Differences between seven measures of self-reported numbers of clients of female sex workers in southern India: implications for individual- and population-level analysis.

    PubMed

    Deering, Kathleen N; Vickerman, P; Pickles, M; Moses, S; Blanchard, J F; Ramesh, B M; Isac, S; Boily, M-C

    2013-02-01

    Quantifying sexual activity of sub-populations with high-risk sexual behaviour is important in understanding HIV epidemiology. This study examined inconsistency of seven outcomes measuring self-reported clients per month (CPM) of female sex workers (FSWs) in southern India and implications for individual/population-level analysis. Multivariate negative binomial regression was used to compare key social/environmental factors associated with each outcome. A transmission dynamics model was used to assess the impact of differences between outcomes on population-level FSW/client HIV prevalence. Outcomes based on 'clients per last working day' produced lower estimates than those based on 'clients per typical day'. Although the outcomes were strongly correlated, their averages differed by approximately two-fold (range 39.0-79.1 CPM). The CPM measure chosen did not greatly influence standard epidemiological 'risk factor' analysis. Differences across outcomes influenced HIV prevalence predictions. Due to this uncertainty, we recommend basing population-based estimates on the range of outcomes, particularly when assessing the impact of interventions.

  1. Population-based programs for increasing colorectal cancer screening in the United States.

    PubMed

    Verma, Manisha; Sarfaty, Mona; Brooks, Durado; Wender, Richard C

    2015-01-01

    Answer questions and earn CME/CNE Screening to detect polyps or cancer at an early stage has been shown to produce better outcomes in colorectal cancer (CRC). Programs with a population-based approach can reach a large majority of the eligible population and can offer cost-effective interventions with the potential benefit of maximizing early cancer detection and prevention using a complete follow-up plan. The purpose of this review was to summarize the key features of population-based programs to increase CRC screening in the United States. A search was conducted in the SCOPUS, OvidSP, and PubMed databases. The authors selected published reports of population-based programs that met at least 5 of the 6 International Agency for Research on Cancer (IARC) criteria for cancer prevention and were known to the National Colorectal Cancer Roundtable. Interventions at the level of individual practices were not included in this review. IARC cancer prevention criteria served as a framework to assess the effective processes and elements of a population-based program. Eight programs were included in this review. Half of the programs met all IARC criteria, and all programs led to improvements in screening rates. The rate of colonoscopy after a positive stool test was heterogeneous among programs. Different population-based strategies were used to promote these screening programs, including system-based, provider-based, patient-based, and media-based strategies. Treatment of identified cancer cases was not included explicitly in 4 programs but was offered through routine medical care. Evidence-based methods for promoting CRC screening at a population level can guide the development of future approaches in health care prevention. The key elements of a successful population-based approach include adherence to the 6 IARC criteria and 4 additional elements (an identified external funding source, a structured policy for positive fecal occult blood test results and confirmed cancer

  2. A Cost-Effectiveness Analysis of Stop Smoking Interventions in Substance Use Disorder Populations undergoing treatment.

    PubMed

    Healey, Andrew; Roberts, Sarah; Sevdalis, Nick; Goulding, Lucy; Wilson, Sophie; Shaw, Kate; Jolley, Caroline; Robson, Deborah

    2018-05-04

    Tobacco smoking is highly prevalent among people attending treatment for a substance use disorder (SUD). In the UK, specialist support to stop smoking is largely delivered by a national network of Stop Smoking Services, and typically comprises of behavioural support delivered by trained practitioners on an individual (one-to-one) or group basis combined with a pharmacological smoking cessation aid. We evaluate the cost-effectiveness of these interventions, and compare cost-effectiveness for interventions using group- and individual-based support, in populations under treatment for SUD. Economic modelling was used to evaluate the incremental cost-per-quality adjusted life years (QALYs) gained for smoking cessation interventions compared to alternative methods of quitting for the SUD treatment population. Allowance was made for potentially lower abstinence rates in the SUD population. The incremental cost per QALY gained from quit attempts supported through more frequently provided interventions in England ranged from around £4,700 to £12,200. These values are below the maximum cost-effectiveness threshold adopted by policy makers in England for judging whether health programmes are a cost-effective use of resources. The estimated cost-per QALY gained for Interventions using group-based behavioural support were estimated to be at least half the magnitude of those using individual support due to lower intervention costs and higher reported quit rates. Conclusions reached regarding the cost-effectiveness of group-based interventions were also found to be more robust to changes in modelling assumptions. Smoking cessation interventions were found to be cost-effective when applied to the SUD population, particularly when grouped-based behavioural support is offered alongside pharmacological treatment. This analysis has shown that smoking cessation interventions combining pharmacological treatment with behavioural support can offer a cost-effective method for increasing

  3. Query Health: standards-based, cross-platform population health surveillance

    PubMed Central

    Klann, Jeffrey G; Buck, Michael D; Brown, Jeffrey; Hadley, Marc; Elmore, Richard; Weber, Griffin M; Murphy, Shawn N

    2014-01-01

    Objective Understanding population-level health trends is essential to effectively monitor and improve public health. The Office of the National Coordinator for Health Information Technology (ONC) Query Health initiative is a collaboration to develop a national architecture for distributed, population-level health queries across diverse clinical systems with disparate data models. Here we review Query Health activities, including a standards-based methodology, an open-source reference implementation, and three pilot projects. Materials and methods Query Health defined a standards-based approach for distributed population health queries, using an ontology based on the Quality Data Model and Consolidated Clinical Document Architecture, Health Quality Measures Format (HQMF) as the query language, the Query Envelope as the secure transport layer, and the Quality Reporting Document Architecture as the result language. Results We implemented this approach using Informatics for Integrating Biology and the Bedside (i2b2) and hQuery for data analytics and PopMedNet for access control, secure query distribution, and response. We deployed the reference implementation at three pilot sites: two public health departments (New York City and Massachusetts) and one pilot designed to support Food and Drug Administration post-market safety surveillance activities. The pilots were successful, although improved cross-platform data normalization is needed. Discussions This initiative resulted in a standards-based methodology for population health queries, a reference implementation, and revision of the HQMF standard. It also informed future directions regarding interoperability and data access for ONC's Data Access Framework initiative. Conclusions Query Health was a test of the learning health system that supplied a functional methodology and reference implementation for distributed population health queries that has been validated at three sites. PMID:24699371

  4. Optimal use of colonoscopy and fecal immunochemical test for population-based colorectal cancer screening: a cost-effectiveness analysis using Japanese data.

    PubMed

    Sekiguchi, Masau; Igarashi, Ataru; Matsuda, Takahisa; Matsumoto, Minori; Sakamoto, Taku; Nakajima, Takeshi; Kakugawa, Yasuo; Yamamoto, Seiichiro; Saito, Hiroshi; Saito, Yutaka

    2016-02-01

    There have been few cost-effectiveness analyses of population-based colorectal cancer screening in Japan, and there is no consensus on the optimal use of total colonoscopy and the fecal immunochemical test for colorectal cancer screening with regard to cost-effectiveness and total colonoscopy workload. The present study aimed to examine the cost-effectiveness of colorectal cancer screening using Japanese data to identify the optimal use of total colonoscopy and fecal immunochemical test. We developed a Markov model to assess the cost-effectiveness of colorectal cancer screening offered to an average-risk population aged 40 years or over. The cost, quality-adjusted life-years and number of total colonoscopy procedures required were evaluated for three screening strategies: (i) a fecal immunochemical test-based strategy; (ii) a total colonoscopy-based strategy; (iii) a strategy of adding population-wide total colonoscopy at 50 years to a fecal immunochemical test-based strategy. All three strategies dominated no screening. Among the three, Strategy 1 was dominated by Strategy 3, and the incremental cost per quality-adjusted life-years gained for Strategy 2 against Strategies 1 and 3 were JPY 293 616 and JPY 781 342, respectively. Within the Japanese threshold (JPY 5-6 million per QALY gained), Strategy 2 was the most cost-effective, followed by Strategy 3; however, Strategy 2 required more than double the number of total colonoscopy procedures than the other strategies. The total colonoscopy-based strategy could be the most cost-effective for population-based colorectal cancer screening in Japan. However, it requires more total colonoscopy procedures than the other strategies. Depending on total colonoscopy capacity, the strategy of adding total colonoscopy for individuals at a specified age to a fecal immunochemical test-based screening may be an optimal solution. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please

  5. 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. © 2015 John Wiley & Sons Ltd.

  6. Estimation of the genetic diversity in tetraploid alfalfa populations based on RAPD markers for breeding purposes.

    PubMed

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

    2011-01-01

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

  7. Modest overall survival improvements from 1998 to 2009 in metastatic gastric cancer patients: a population-based SEER analysis.

    PubMed

    Ebinger, Sabrina M; Warschkow, René; Tarantino, Ignazio; Schmied, Bruno M; Güller, Ulrich; Schiesser, Marc

    2016-07-01

    An increasing fraction of gastric cancer patients present with distant metastases at diagnosis. The objective of the present 11-year population-based trend analysis was to assess the survival rates in patients who underwent and in patients who did not undergo palliative gastrectomy. Patients with metastatic gastric cancer were identified from the Surveillance, Epidemiology, and End Results (SEER) database between 1998 and 2009. Time trend and impact of palliative gastrectomy on survival were assessed by both a multivariate Cox proportional hazards model and propensity score matching. We identified 8249 patients with stage IV gastric cancer. The rate of metastatic disease increased from 31.0 % in 1998 to 37.5 % in 2009 (P < 0.001). The palliative gastrectomy rate dropped from 18.8 to 10.2 % (P = 0.004). The median survival for patients who underwent palliative gastrectomy (N = 1445, 17.4 %) and for patients who did not undergo palliative gastrectomy (N = 6804, 82.4 %) was 7 and 3 months, respectively. There was an increase in median overall survival from 2 months (1998) to 3 months (2009) in the no-gastrectomy group, and from 6.5 to 8 months in the gastrectomy group. The 3-year cancer-specific survival rates were 2.1 % (95 % confidence interval 1.7-2.5 %) for patients who did not undergo palliative gastrectomy and 9.4 % (95 % confidence interval 7.8-11.2 %) for patients who underwent palliative gastrectomy (P < 0.001). Palliative gastrectomy was associated with an increased cancer-specific survival in propensity-score-adjusted Cox regression analyses (hazard ratio 0.50, 95 % confidence interval 0.46-0.55, P < 0.001). On a population-based level, only modest improvements in prognosis for metastatic gastric cancer were observed in patients who underwent and in patients who did not undergo palliative gastrectomy. Considering the low rate of midterm survivors in both groups, only a small subgroup of patients benefits from palliative

  8. Exposure to Coxiella burnetii and risk of non-Hodgkin lymphoma: a retrospective population-based analysis in the Netherlands.

    PubMed

    van Roeden, Sonja E; van Houwelingen, Fedor; Donkers, Chiel M J; Hogewoning, Sander J; de Lange, Marit M A; van der Hoek, Wim; Kampschreur, Linda M; Bonten, Marc J M; Hoepelman, Andy I M; Bleeker-Rovers, Chantal P; Wever, Peter C; Oosterheert, Jan Jelrik

    2018-05-01

    An association between Coxiella burnetii and non-Hodgkin lymphoma has been suggested. After a large Q fever epidemic in the Netherlands (2007-10), we postulated that the incidence of non-Hodgkin lymphoma would be increased during and after the epidemic in areas with a high endemicity of Q fever compared with those with low endemicity. We did a retrospective population-based analysis and calculated relative risks (RRs) of non-Hodgkin lymphoma during 1-year periods before, during, and after the Q fever epidemic, for areas with intermediate and high endemicity of Q fever compared with low endemic areas. We also calculated the RR of non-Hodgkin lymphoma in people with chronic Q fever compared with the general population. Between Jan 1, 2002, and Dec 31, 2013, 48 760 cases of non-Hodgkin lymphoma were diagnosed. The incidence of non-Hodgkin lymphoma ranged from 21·4 per 100 000 per year in 2002 to 26·7 per 100 000 per year in 2010. A significant association with non-Hodgkin lymphoma was noted in 2009 for areas with a high endemicity of Q fever compared with low endemic areas (RR 1·16, 95% CI 1·02-1·33; p=0·029); no further associations were noted in any other year or for areas with intermediate Q fever endemicity. Among 439 individuals with chronic Q fever, five developed non-Hodgkin lymphoma, yielding a crude absolute risk of 301·0 cases per 100 000 per year (RR 4·99, 95% CI 2·07-11·98; p=0·0003) compared with the general population in the Netherlands. These findings do not support the hypothesis that Q fever has a relevant causal role in the development of non-Hodgkin lymphoma. Several limitations, inherent to the design of this study, might lead to both underestimation and overestimation of the studied association. Foundation Q-support and Institut Mérieux. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Bad sleep? Don't blame the moon! A population-based study.

    PubMed

    Haba-Rubio, José; Marques-Vidal, Pedro; Tobback, Nadia; Andries, Daniela; Preisig, Martin; Kuehner, Christine; Vollenweider, Peter; Waeber, Gérard; Luca, Gianina; Tafti, Mehdi; Heinzer, Raphaël

    2015-11-01

    The aim of this study was to evaluate if there is a significant effect of lunar phases on subjective and objective sleep variables in the general population. A total of 2125 individuals (51.2% women, age 58.8 ± 11.2 years) participating in a population-based cohort study underwent a complete polysomnography (PSG) at home. Subjective sleep quality was evaluated by a self-rating scale. Sleep electroencephalography (EEG) spectral analysis was performed in 759 participants without significant sleep disorders. Salivary cortisol levels were assessed at awakening, 30 min after awakening, at 11 am, and at 8 pm. Lunar phases were grouped into full moon (FM), waxing/waning moon (WM), and new moon (NM). Overall, there was no significant difference between lunar phases with regard to subjective sleep quality. We found only a nonsignificant (p = 0.08) trend toward a better sleep quality during the NM phase. Objective sleep duration was not different between phases (FM: 398 ± 3 min, WM: 402 ± 3 min, NM: 403 ± 3 min; p = 0.31). No difference was found with regard to other PSG-derived parameters, EEG spectral analysis, or in diurnal cortisol levels. When considering only subjects with apnea/hypopnea index of <15/h and periodic leg movements index of <15/h, we found a trend toward shorter total sleep time during FM (FM: 402 ± 4, WM: 407 ± 4, NM: 415 ± 4 min; p = 0.06) and shorter-stage N2 duration (FM: 178 ± 3, WM: 182 ± 3, NM: 188 ± 3 min; p = 0.05). Our large population-based study provides no evidence of a significant effect of lunar phases on human sleep. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Plasmodium falciparum population structure in Sudan post artemisinin-based combination therapy.

    PubMed

    Bakhiet, Amani M A; Abdel-Muhsin, Abdel-Muhsin A; Elzaki, Salah-Eldin G; Al-Hashami, Zainab; Albarwani, Hamida S; AlQamashoui, Badar A; Al-Hamidhi, Salama; Idris, Mohamed A; Elagib, Atif A; Beja-Pereira, Albano; Babiker, Hamza A

    2015-08-01

    Over the past decade, Sudan has stepped up malaria control backed by WHO, and this has resulted in significant reduction in parasite rate, malaria morbidity and mortality. The present study analyzed Plasmodium falciparum parasites in four geographical separated areas, to examine whether the success in malaria control following the use of artemisinin-based combination therapy (ACT) has disrupted the population structure and evolution of the parasite. We examined 319 P. falciparum isolates collected between October 2009 and October 2012 in four different areas in Sudan (Jazira [central Sudan], Southern Darfur [western Sudan], Upper Nile [southern Sudan] and Kasala [eastern Sudan]). Twelve microsatellites were analyzed for allelic diversity, multi-locus haplotype and inter-population differentiation. Level of diversity was compared to that detected for three of the above microsatellites among P. falciparum parasites in central and eastern Sudan in 1999, prior to introduction of ACT. Diversity at each locus (unbiased heterozygosity [H]) was high in all areas (Jazira, H=0.67), (Southern Darfur, H=0.71), (Upper Nile, H=0.71), and (Kasala, H=0.63). Microsatellites were distributed widely and private alleles, detected in a single population, were rare. The extent of diversity in the above sites was similar to that seen, in 1999, in central (Khartoum, H=0.73) and eastern Sudan (Gedaref, H=0.75). Significant Linkage disequilibrium (LD) was observed between the microsatellites in all populations. Pairwise FST analysis revealed that parasites in the four areas could be considered as one population. However, the parasites in Sudan clustered away from parasites in West Africa and the Arabian Peninsula. Despite marked reduction in malaria risk in Sudan, the extent of diversity and parasite genetic structure are indicative of a large population size. Further considerable reduction in transmission would be needed before fragmented sub-population can be seen. In addition, the large

  11. Genetic differentiation and origin of the Jordanian population: an analysis of Alu insertion polymorphisms.

    PubMed

    Bahri, Raoudha; El Moncer, Wifak; Al-Batayneh, Khalid; Sadiq, May; Esteban, Esther; Moral, Pedro; Chaabani, Hassen

    2012-05-01

    Although much of Jordan is covered by desert, its north-western region forms part of the Fertile Crescent region that had given a rich past to Jordanians. This past, scarcely described by historians, is not yet clarified by sufficient genetic data. Thus in this paper we aim to determine the genetic differentiation of the Jordanian population and to discuss its origin. A total of 150 unrelated healthy Jordanians were investigated for ten Alu insertion polymorphisms. Genetic relationships among populations were estimated by a principal component (PC) plot based on the analyses of the R-matrix software. Statistical analysis showed that the Jordanian population is not significantly different from the United Arab Emirates population or the North Africans. This observation, well represented in PC plot, suggests a common origin of these populations belonging respectively to ancient Mesopotamia, Arabia, and North Africa. Our results are compatible with ancient peoples' movements from Arabia to ancient Mesopotamia and North Africa as proposed by historians and supported by previous genetic results. The original genetic profile of the Jordanian population, very likely Arabian Semitic, has not been subject to significant change despite the succession of several civilizations.

  12. Visual loss after spine surgery: a population-based study.

    PubMed

    Patil, Chirag G; Lad, Eleonora M; Lad, Shivanand P; Ho, Chris; Boakye, Maxwell

    2008-06-01

    Retrospective cohort study using National inpatient sample administrative data. To determine national estimates of visual impairment and ischemic optic neuropathy after spine surgery. Loss of vision after spine surgery is rare but has devastating complications that has gained increasing recognition in the recent literature. National population-based studies of visual complications after spine surgery are lacking. All patients from 1993 to 2002 who underwent spine surgery (Clinical Classifications software procedure code: 3, 158) and who had ischemic optic neuropathy (ION) (ICD9-CM code 377.41), central retinal artery occlusion (CRAO) (ICD9-CM code 362.31) or non-ION, non-CRAO perioperative visual impairment (ICD9-CM codes: 369, 368.4, 368.8-9368.11-13) were included. Univariate and multivariate analysis were performed to identify potential risk factors. The overall incidence of visual disturbance after spine surgery was 0.094%. Spine surgery for scoliosis correction and posterior lumbar fusion had the highest rates of postoperative visual loss of 0.28% and 0.14% respectively. Pediatric patients (<18 years) were 5.8 times and elderly patients (>84 years) were 3.2 times more likely than, patients 18 to 44 years of age to develop non-ION, non-CRAO visual loss after spine surgery. Patients with peripheral vascular disease (OR = 2.0), hypertension (OR = 1.3), and those who received blood transfusion (OR = 2.2) were more likely to develop non-ION, non-CRAO vision loss after spine surgery. Ischemic optic neuropathy was present in 0.006% of patients. Hypotension (OR = 10.1), peripheral vascular disease (OR = 6.3) and anemia (OR = 5.9) were the strongest risk factors identified for the development of ION. We used multivariate analysis to identify significant risk factors for visual loss after spine surgery. National population-based estimate of visual impairment after spine surgery confirms that ophthalmic complications after spine surgery are rare. Since visual loss may be

  13. Postoperative Mortality Among Patients With Inflammatory Bowel Diseases: A Systematic Review and Meta-analysis of Population-Based Studies.

    PubMed

    Singh, Sunny; Al-Darmaki, Ahmed; Frolkis, Alexandra D; Seow, Cynthia H; Leung, Yvette; Novak, Kerri L; Ghosh, Subrata; Eksteen, Bertus; Panaccione, Remo; Kaplan, Gilaad G

    2015-10-01

    There have been varying reports of mortality after intestinal resection for the inflammatory bowel diseases (IBDs). We performed a systematic review and meta-analysis of population-based studies to determine postoperative mortality after intestinal resection in patients with IBD. We searched Medline, EMBASE, and PubMed, from 1990 through 2015, to identify 18 articles and 3 abstracts reporting postoperative mortality among patients with IBD. The studies included 67,057 patients with ulcerative colitis (UC) and 75,971 patients with Crohn's disease (CD), from 15 countries. Mortality estimates stratified by emergent and elective surgeries were pooled separately for CD and UC using a random-effects model. To assess changes over time, the start year of the study was included as a continuous variable in a meta-regression model. In patients with UC, postoperative mortality was significantly lower among patients who underwent elective (0.7%; 95% confidence interval [CI], 0.6%-0.9%) vs emergent surgery (5.3%; 95% CI, 3.8%-7.4%). In patients with CD, postoperative mortality was significantly lower among patients who underwent elective (0.6%; 95% CI, 0.2%-1.7%) vs emergent surgery (3.6%; 95% CI, 1.8%-6.9%). Postoperative mortality did not differ for elective (P = .78) or emergent (P = .31) surgeries when patients with UC were compared with patients with CD. Postoperative mortality decreased significantly over time for patients with CD (P < .05) but not UC (P = .21). Based on a systematic review and meta-analysis, postoperative mortality was high after emergent, but not elective, intestinal resection in patients with UC or CD. Optimization of management strategies and more effective therapies are necessary to avoid emergent surgeries. Copyright © 2015 AGA Institute. Published by Elsevier Inc. All rights reserved.

  14. Calcium antagonists and deep gingival pockets in the population-based SHIP study

    PubMed Central

    Meisel, Peter; Schwahn, Christian; John, Ulrich; Kroemer, Heyo K; Kocher, Thomas

    2005-01-01

    Aim Gingival overgrowth is a common undesired side-effect in patients taking calcium channel blockers. Different reports have suggested that the drug-induced gingival hyperplasia may aggravate inflammatory periodontal disease. However, representative epidemiological data are lacking. We investigated the association between the intake of calcium antagonists and periodontitis in a population-based analysis including the most important risk factors of periodontitis. Methods In a cross-sectional epidemiological investigation involving 4290 subjects aged 20–80 years, we recorded periodontal risk factors and identified participants using calcium antagonists. Periodontal parameters, attachment loss, probing depth and number of teeth were assessed. In a subgroup analysis with matched pairs, 456 subjects using calcium antagonists and 456 without were compared for periodontal status. Results Subjects treated with calcium antagonistic drugs had significantly deeper gingival pockets than their drug-free counterparts. This was observed in the total population of 4290 and confirmed by logistic regression analyses (P < 0.001) controlled for the known risk factors of periodontitis (age, sex, smoking, education). In the matched-pair analysis only the probing depth was increased: extent probing depth ≥4 mm median 23.5 vs. 17.0% (P < 0.001); mean probing depth 3.0 ± 0.8 vs. 2.7 ± 0.9 mm (P < 0.001). No differences were found in extent and severity of clinical attachment loss and in the number of teeth. The risk of gingival overgrowth was aggravated in smokers. Conclusion In the general population, treatment with calcium antagonists leads to gingival overgrowth without an aggravation of periodontal disease. Interaction with smoking indicates the multifactorial background of the undesired effect of calcium antagonists. PMID:16236046

  15. Posttraumatic stress disorder in the nursing population: a concept analysis.

    PubMed

    Mealer, Meredith; Jones, Jacqueline

    2013-01-01

    This article is a report of an analysis of the concept of posttraumatic stress disorder (PTSD) and its application to the nursing population. Nurses are at an increased risk for work-related stress resulting in retention issues and impaired functioning in work and home environment. The nursing discipline has been inconsistent with the concepts used to describe the distress and resultant discussions related to the comprehensive nature of the distress experienced, heavily focusing on existing medical language that emphasizes disorders and psychopathology. Walker and Avant's strategy for concept analysis was used in this analysis. A literature review for 1994-2011 was conducted for the following keywords: secondary traumatic stress, compassion fatigue, vicarious traumatization, posttraumatic stress disorder, and nurse. The concept of posttraumatic stress disorder in the nursing population is best described within the context of the Nurse as Wounded Healer theory. Essential attributes include intrusions, avoidance, and hyperarousal. The consequences include worldview changes, retention issues, sleep disruption, and social network disturbances. This concept analysis viewed through The Nurse as Wounded Healer lens, offers clarity to the concept of PTSD within the nursing population and identifies limitations to prior conceptualizations. © 2013 Wiley Periodicals, Inc.

  16. A nationwide population-based study of low vision and blindness in South Korea.

    PubMed

    Park, Shin Hae; Lee, Ji Sung; Heo, Hwan; Suh, Young-Woo; Kim, Seung-Hyun; Lim, Key Hwan; Moon, Nam Ju; Lee, Sung Jin; Park, Song Hee; Baek, Seung-Hee

    2014-12-18

    To investigate the prevalence and associated risk factors of low vision and blindness in the Korean population. This cross-sectional, population-based study examined the ophthalmologic data of 22,135 Koreans aged ≥5 years from the fifth Korea National Health and Nutrition Examination Survey (KNHANES V, 2010-2012). According to the World Health Organization criteria, blindness was defined as visual acuity (VA) less than 20/400 in the better-seeing eye, and low vision as VA of 20/60 or worse but 20/400 or better in the better-seeing eye. The prevalence rates were calculated from either presenting VA (PVA) or best-corrected VA (BCVA). Multivariate regression analysis was conducted for adults aged ≥20 years. The overall prevalence rates of PVA-defined low vision and blindness were 4.98% and 0.26%, respectively, and those of BCVA-defined low vision and blindness were 0.46% and 0.05%, respectively. Prevalence increased rapidly above the age of 70 years. For subjects aged ≥70 years, the population-weighted prevalence rates of low vision, based on PVA and BCVA, were 12.85% and 3.87%, respectively, and the corresponding rates of blindness were 0.49% and 0.42%, respectively. The presenting vision problems were significantly associated with age (younger adults or elderly subjects), female sex, low educational level, and lowest household income, whereas the best-corrected vision problems were associated with age ≥ 70 years, a low educational level, and rural residence. This population-based study provides useful information for planning optimal public eye health care services in South Korea. Copyright 2015 The Association for Research in Vision and Ophthalmology, Inc.

  17. Coupling Financial Incentives With Direct Mail in Population-Based Practice.

    PubMed

    Slater, Jonathan S; Parks, Michael J; Malone, Michael E; Henly, George A; Nelson, Christina L

    2017-02-01

    Financial incentives are being used increasingly to encourage a wide array of health behaviors because of their well-established efficacy. However, little is known about how to translate incentive-based strategies to public health practice geared toward improving population-level health, and a dearth of research exists on how individuals respond to incentives through public health communication strategies such as direct mail. This study reports results of a population-based randomized controlled trial testing a direct mail, incentive-based intervention for promoting mammography uptake. The study population was composed of a random sample of Minnesota women enrolled in Medicare fee-for-service and overdue for breast cancer screening. Participants ( N = 18,939) were randomized into three groups: (1) Direct Mail only, (2) Direct Mail plus Incentive, and (3) Control. Both direct mail groups received two mailers with a message about the importance of mammography; however, Mail plus Incentive mailers also offered a $25 incentive for getting a mammogram. Logistic regression analyses measured intervention effects. Results showed the odds for receiving mammography were significantly higher for the Direct Mail plus Incentive group compared with both Direct Mail only and Control groups. The use of incentives also proved to be cost-effective. Additionally, the Direct Mail only group was more likely to receive mammography than the Control group. Findings offer experimental evidence on how the population-based strategy of direct mail coupled with a financial incentive can encourage healthy behavior, as well as how incentive-based programs can be translated into health promotion practice aimed at achieving population-level impact.

  18. Automation of GIS-based population data-collection for transportation risk analysis

    DOT National Transportation Integrated Search

    1999-11-01

    Estimation of the potential radiological risks associated with highway transport of radioactive : materials (RAM) requires input data describing population densities adjacent to all portions of : the route to be traveled. Previously, aggregated risks...

  19. Quantitative genetic analysis of the body composition and blood pressure association in two ethnically diverse populations.

    PubMed

    Ghosh, Sudipta; Dosaev, Tasbulat; Prakash, Jai; Livshits, Gregory

    2017-04-01

    The major aim of this study was to conduct comparative quantitative-genetic analysis of the body composition (BCP) and somatotype (STP) variation, as well as their correlations with blood pressure (BP) in two ethnically, culturally and geographically different populations: Santhal, indigenous ethnic group from India and Chuvash, indigenous population from Russia. Correspondently two pedigree-based samples were collected from 1,262 Santhal and1,558 Chuvash individuals, respectively. At the first stage of the study, descriptive statistics and a series of univariate regression analyses were calculated. Finally, multiple and multivariate regression (MMR) analyses, with BP measurements as dependent variables and age, sex, BCP and STP as independent variables were carried out in each sample separately. The significant and independent covariates of BP were identified and used for re-examination in pedigree-based variance decomposition analysis. Despite clear and significant differences between the populations in BCP/STP, both Santhal and Chuvash were found to be predominantly mesomorphic irrespective of their sex. According to MMR analyses variation of BP significantly depended on age and mesomorphic component in both samples, and in addition on sex, ectomorphy and fat mass index in Santhal and on fat free mass index in Chuvash samples, respectively. Additive genetic component contributes to a substantial proportion of blood pressure and body composition variance. Variance component analysis in addition to above mentioned results suggests that additive genetic factors influence BP and BCP/STP associations significantly. © 2017 Wiley Periodicals, Inc.

  20. Countries population determination to test rice crisis indicator at national level using k-means cluster analysis

    NASA Astrophysics Data System (ADS)

    Hidayat, Y.; Purwandari, T.; Sukono; Ariska, Y. D.

    2017-01-01

    This study aimed to obtain information on the population of the countries which is have similarities with Indonesia based on three characteristics, that is the democratic atmosphere, rice consumption and purchasing power of rice. It is useful as a reference material for research which tested the strength and predictability of the rice crisis indicators Unprecedented Restlessness (UR). The similarities countries with Indonesia were conducted using multivariate analysis that is non-hierarchical cluster analysis k-Means with 38 countries as the data population. This analysis is done repeatedly until the obtainment number of clusters which is capable to show the differentiator power of the three characteristics and describe the high similarity within clusters. Based on the results, it turns out with 6 clusters can describe the differentiator power of characteristics of formed clusters. However, to answer the purpose of the study, only one cluster which will be taken accordance with the criteria of success for the population of countries that have similarities with Indonesia that cluster contain Indonesia therein, there are countries which is sustain crisis and non-crisis of rice in 2008, and cluster which is have the largest member among them. This criterion is met by cluster 2, which consists of 22 countries, namely Indonesia, Brazil, Costa Rica, Djibouti, Dominican Republic, Ecuador, Fiji, Guinea-Bissau, Haiti, India, Jamaica, Japan, Korea South, Madagascar, Malaysia, Mali, Nicaragua, Panama, Peru, Senegal, Sierra Leone and Suriname.

  1. Joint genotype- and ancestry-based genome-wide association studies in admixed populations.

    PubMed

    Szulc, Piotr; Bogdan, Malgorzata; Frommlet, Florian; Tang, Hua

    2017-09-01

    In genome-wide association studies (GWAS) genetic loci that influence complex traits are localized by inspecting associations between genotypes of genetic markers and the values of the trait of interest. On the other hand, admixture mapping, which is performed in case of populations consisting of a recent mix of two ancestral groups, relies on the ancestry information at each locus (locus-specific ancestry). Recently it has been proposed to jointly model genotype and locus-specific ancestry within the framework of single marker tests. Here, we extend this approach for population-based GWAS in the direction of multimarker models. A modified version of the Bayesian information criterion is developed for building a multilocus model that accounts for the differential correlation structure due to linkage disequilibrium (LD) and admixture LD. Simulation studies and a real data example illustrate the advantages of this new approach compared to single-marker analysis or modern model selection strategies based on separately analyzing genotype and ancestry data, as well as to single-marker analysis combining genotypic and ancestry information. Depending on the signal strength, our procedure automatically chooses whether genotypic or locus-specific ancestry markers are added to the model. This results in a good compromise between the power to detect causal mutations and the precision of their localization. The proposed method has been implemented in R and is available at http://www.math.uni.wroc.pl/~mbogdan/admixtures/. © 2017 WILEY PERIODICALS, INC.

  2. Use of driving-impairing medicines by a Spanish population: a population-based registry study

    PubMed Central

    Gutierrez-Abejón, Eduardo; Herrera-Gómez, Francisco; Criado-Espegel, Paloma

    2017-01-01

    Objective To assess the use of driving-impairing medicines (DIM) in the general population with special reference to length of use and concomitant use. Design Population-based registry study. Setting The year 2015 granted medicines consumption data recorded in the Castile and León (Spain) medicine dispensation registry was consulted. Participants Medicines and DIM consumers from a Spanish population (Castile and León: 2.4 million inhabitants). Exposure Medicines and DIM consumption. Patterns of use by age and gender based on the length of use (acute: 1–7 days, subacute: 8–29 days and chronic use: ≥30 days) were of interest. Estimations regarding the distribution of licensed drivers by age and gender were employed to determine the patterns of use of DIM. Results DIM were consumed by 34.4% (95% CI 34.3% to 34.5%) of the general population in 2015, more commonly with regularity (chronic use: 22.5% vs acute use: 5.3%) and more frequently by the elderly. On average, 2.3 DIM per person were dispensed, particularly to chronic users (2.8 DIM per person). Age and gender distribution differences were observed between the Castile and León medicine dispensation registry data and the drivers’ license census data. Of all DIM dispensed, 83.8% were in the Anatomical Therapeutic Chemical code group nervous system medicines (N), which were prescribed to 29.2% of the population. Conclusions The use of DIM was frequent in the general population. Chronic use was common, but acute and subacute use should also be considered. This finding highlights the need to make patients, health professionals, health providers, medicine regulatory agencies and policy-makers at large aware of the role DIM play in traffic safety. PMID:29170289

  3. Population-based screening for anemia using first-time blood donors

    PubMed Central

    Mast, Alan E.; Steele, Whitney R.; Johnson, Bryce; Wright, David J.; Cable, Ritchard G.; Carey, Patricia; Gottschall, Jerome L.; Kiss, Joseph E.; Simon, Toby L.; Murphy, Edward L.

    2012-01-01

    Background Anemia is an important public health concern. Data from population-based surveys such as the National Health and Nutrition Examination Survey (NHANES) are the gold standard, but are obtained infrequently and include only small samples from certain minority groups. Objectives We assessed whether readily available databases of blood donor hemoglobin values could be used as a surrogate for population hemoglobin values from NHANES. Design Blood donor venous and fingerstick hemoglobin values were compared to 10,254 NHANES 2005-2008 venous hemoglobin values using demographically stratified analyses and ANOVA. Fingerstick hemoglobins or hematocrits were converted to venous hemoglobin estimates using regression analysis. Results Venous hemoglobin values from 1,609 first time donors correlated extremely well with NHANES data across different age, gender and demographic groups. Cigarette smoking increased hemoglobin by 0.26 to 0.59 g/dL depending on intensity. Converted fingerstick hemoglobin from 36,793 first time donors agreed well with NHANES hemoglobin (weighted mean hemoglobin of 15.53 g/dL for donors and 15.73 g/dL for NHANES) with similar variation in mean hemoglobin by age. However, compared to NHANES, the larger donor dataset showed reduced differences in mean hemoglobin between Blacks and other races/ethnicities. Conclusions Overall, first-time donor fingerstick hemoglobins approximate U.S. population data and represent a readily available public health resource for ongoing anemia surveillance. PMID:22460662

  4. Population-based strategies to control manufacturing epidemics.

    PubMed

    Gorini, Giuseppe

    2017-01-01

    "The multinational corporations producing tobacco, alcohol, soft drinks, and processed foods have a role of vectors in the increase of chronic diseases, so that one can speak of manufacturing epidemics. The main aim of this paper is to conduct a literature review on different approaches in population-based interventions to stem the rise in consumption of unhealthy products. Different approaches were found: • command-and-control regulations: the route is definitely more advanced for tobacco with the implementation of an international treaty, which requires 180 ratifying states to implement a series of tobacco control policies. Similar regulations have been partially adopted to reduce alcohol use and to increase taxes of sugar-sweetened beverages; • multinational corporations in few Countries can voluntarily adopt recommendations on media campaigns and on labelling of soft drinks and processed foods; • in order to reduce salt in foods, many Countries developed voluntary agreements with industries with monitoring systems to assess compliance. Population-based interventions to try to align the interests of multinational corporations with those of public health are described in literature: • the "Health Footprint" programme; • the performance-based regulation which could oblige industry to take responsibility to reduce the harmful consequences of the use of their unhealthy commodities; • the price-cap regulation, usually applied to the utilities sector, would set a cap on the price of the tobacco industry, raising the tobacco taxes by 500 million euros per year. In order to reduce the burden of chronic disease, one of the objectives of the Italian National Prevention Plan, a working group including non-governmental organizations and experts in communication, social marketing, and lifestyles should be organized by the Ministry of Health in order to identify which population-based interventions could be implemented in Italy in next years to stem the rise of

  5. 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.

  6. Association between salt and hypertension in rural and urban populations of low to middle income countries: a systematic review and meta-analysis of population based studies.

    PubMed

    Subasinghe, Asvini K; Arabshahi, Simin; Busingye, Doreen; Evans, Roger G; Walker, Karen Z; Riddell, Michaela A; Thrift, Amanda G

    2016-01-01

    The prevalence of hypertension, the greatest contributor to mortality globally, is increasing in low-and-middle income countries (LMICs). In urban regions of LMICs, excessive salt intake is associated with increased risk of hypertension. We aimed to determine whether this is the case in rural regions as well. We performed a meta-analysis of studies in rural and urban areas of LMICs in which the association of salt and hypertension were assessed using multivariable models. We identified 18 studies with a total of 134,916 participants. The prevalence of high salt intake ranged from 21.3% to 89.5% in rural and urban populations. When salt was analysed as a continuous variable, a greater impact of salt on hypertension was found in urban (n=4) (pooled effect size (ES) 1.42, 95% CI 1.19, 1.69) than in rural populations (n=4) (pooled ES 1.07, 95% CI 1.04, 1.10, p for difference <0.001). In studies where salt was analysed continuously, a greater impact of salt on hypertension was observed in lean rural populations (BMI <23 kg/m2) than in non-lean rural populations (BMI >=23 kg/m2, p for difference <0.001). The prevalence of high salt intake is similar in rural and urban regions. Excessive salt intake has a greater impact on the prevalence of hypertension in urban than rural regions. BMI appears to modify the relationship between salt and hypertension in rural populations.

  7. Productivity losses in chronic obstructive pulmonary disease: a population-based survey.

    PubMed

    Erdal, Marta; Johannessen, Ane; Askildsen, Jan Erik; Eagan, Tomas; Gulsvik, Amund; Grønseth, Rune

    2014-01-01

    We aimed to estimate incremental productivity losses (sick leave and disability) of spirometry-defined chronic obstructive pulmonary disease (COPD) in a population-based sample and in hospital-recruited patients with COPD. Furthermore, we examined predictors of productivity losses by multivariate analyses. We performed four quarterly telephone interviews of 53 and 107 population-based patients with COPD and controls, as well as 102 hospital-recruited patients with COPD below retirement age. Information was gathered regarding annual productivity loss, exacerbations of respiratory symptoms and comorbidities. Incremental productivity losses were estimated by multivariate quantile median regression according to the human capital approach, adjusting for sex, age, smoking habits, education and lung function. Main effect variables were COPD/control status, number of comorbidities and exacerbations of respiratory symptoms. Altogether 55%, 87% and 31% of population-based COPD cases, controls and hospital patients, respectively, had a paid job at baseline. The annual incremental productivity losses were 5.8 (95% CI 1.4 to 10.1) and 330.6 (95% CI 327.8 to 333.3) days, comparing population-recruited and hospital-recruited patients with COPD to controls, respectively. There were significantly higher productivity losses associated with female sex and less education. Additional adjustments for comorbidities, exacerbations and FEV1% predicted explained all productivity losses in the population-based sample, as well as nearly 40% of the productivity losses in hospital-recruited patients. Annual incremental productivity losses were more than 50 times higher in hospital-recruited patients with COPD than that of population-recruited patients with COPD. To ensure a precise estimation of societal burden, studies on patients with COPD should be population-based.

  8. Mapping population-based structural connectomes.

    PubMed

    Zhang, Zhengwu; Descoteaux, Maxime; Zhang, Jingwen; Girard, Gabriel; Chamberland, Maxime; Dunson, David; Srivastava, Anuj; Zhu, Hongtu

    2018-05-15

    Advances in understanding the structural connectomes of human brain require improved approaches for the construction, comparison and integration of high-dimensional whole-brain tractography data from a large number of individuals. This article develops a population-based structural connectome (PSC) mapping framework to address these challenges. PSC simultaneously characterizes a large number of white matter bundles within and across different subjects by registering different subjects' brains based on coarse cortical parcellations, compressing the bundles of each connection, and extracting novel connection weights. A robust tractography algorithm and streamline post-processing techniques, including dilation of gray matter regions, streamline cutting, and outlier streamline removal are applied to improve the robustness of the extracted structural connectomes. The developed PSC framework can be used to reproducibly extract binary networks, weighted networks and streamline-based brain connectomes. We apply the PSC to Human Connectome Project data to illustrate its application in characterizing normal variations and heritability of structural connectomes in healthy subjects. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. Query Health: standards-based, cross-platform population health surveillance.

    PubMed

    Klann, Jeffrey G; Buck, Michael D; Brown, Jeffrey; Hadley, Marc; Elmore, Richard; Weber, Griffin M; Murphy, Shawn N

    2014-01-01

    Understanding population-level health trends is essential to effectively monitor and improve public health. The Office of the National Coordinator for Health Information Technology (ONC) Query Health initiative is a collaboration to develop a national architecture for distributed, population-level health queries across diverse clinical systems with disparate data models. Here we review Query Health activities, including a standards-based methodology, an open-source reference implementation, and three pilot projects. Query Health defined a standards-based approach for distributed population health queries, using an ontology based on the Quality Data Model and Consolidated Clinical Document Architecture, Health Quality Measures Format (HQMF) as the query language, the Query Envelope as the secure transport layer, and the Quality Reporting Document Architecture as the result language. We implemented this approach using Informatics for Integrating Biology and the Bedside (i2b2) and hQuery for data analytics and PopMedNet for access control, secure query distribution, and response. We deployed the reference implementation at three pilot sites: two public health departments (New York City and Massachusetts) and one pilot designed to support Food and Drug Administration post-market safety surveillance activities. The pilots were successful, although improved cross-platform data normalization is needed. This initiative resulted in a standards-based methodology for population health queries, a reference implementation, and revision of the HQMF standard. It also informed future directions regarding interoperability and data access for ONC's Data Access Framework initiative. Query Health was a test of the learning health system that supplied a functional methodology and reference implementation for distributed population health queries that has been validated at three sites. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under

  10. GaitaBase: Web-based repository system for gait analysis.

    PubMed

    Tirosh, Oren; Baker, Richard; McGinley, Jenny

    2010-02-01

    The need to share gait analysis data to improve clinical decision support has been recognised since the early 1990s. GaitaBase has been established to provide a web-accessible repository system of gait analysis data to improve the sharing of data across local and international clinical and research community. It is used by several clinical and research groups across the world providing cross-group access permissions to retrieve and analyse the data. The system is useful for bench-marking and quality assurance, clinical consultation, and collaborative research. It has the capacity to increase the population sample size and improve the quality of 'normative' gait data. In addition the accumulated stored data may facilitate clinicians in comparing their own gait data with others, and give a valuable insight into how effective specific interventions have been for others. 2009 Elsevier Ltd. All rights reserved.

  11. Reappraisal of fetal abdominal circumference in an Asian population: analysis of 50,131 records.

    PubMed

    Lu, Szu-Ching; Chang, Chiung-Hsin; Yu, Chen-Hsiang; Kang, Lin; Tsai, Pei-Ying; Chang, Fong-Ming

    2008-03-01

    Fetuses from different populations may show different growth patterns. In obstetrics, fetal abdominal circumference (AC) is a very useful index for assessing fetal growth. In this study, we attempted to establish the normal fetal growth curves of AC in an Asian population in South Taiwan. We reviewed our computer ultrasound database of fetal AC records from January 1991 to December 2006. During the study period of 16 years, only the fetuses examined by ultrasonography with gestational age between 14 and 41 weeks were included. We excluded extreme bilateral records after initial analysis. Eventually, 50,131 records of AC were included for final analysis. The observed gestation-specific AC values and the predicted AC values were calculated. The best-fit regression equation of AC versus gestational age is a second-order polynomial equation. In general, fetal AC values in our population showed similar patterns to those in Western populations. Besides, we established a table of the predicted AC values based on specific gestational age, including the 5 th , 10 th , 50 th , 90 th and 95 th centiles, for clinical reference. To the best of our knowledge, our series is the largest sample of AC reported in the medical literature. We believe that the gestational age-specific nomogram of fetal AC is important for further clinical assessment of fetal growth.

  12. Commonality of Risk Factors for Mothers' Poor Oral Health and General Health: Baseline Analysis of a Population-Based Birth Cohort Study.

    PubMed

    Ha, Diep H; Spencer, A John; Thomson, W Murray; Scott, Jane A; Do, Loc G

    2018-04-01

    Objective The association between and commonality of risk factors for poor self-rated oral health (SROH) and general health (SRGH) among new mothers has not been reported. The purpose of this paper is to assess the commonality of risk factors for poor SROH and SRGH, and self-reported obesity and dental pain, among a population-based sample of new mothers in Australia. It also investigated health conditions affecting new mothers' general health. Methods Data collected at baseline of a population-based birth cohort was used. Mothers of newborns in Adelaide were approached to participate. Mothers completed a questionnaire collecting data on socioeconomic status (SES), health behaviours, dental pain, SROH, self-reported height and weight and SRGH. Analysis was conducted sequentially from bivariate to multivariable regression to estimate prevalence rate (PR) of reporting poor/fair SROH and SRGH. Results of the 1895 new mothers, some 21 and 6% rated their SROH and SRGH as poor/fair respectively. Dental pain was associated with low income and smoking status, while being obese was associated with low SES, low education and infrequent tooth brushing. SROH and SRGH was associated with low SES, smoking, and dental pain. SROH was also associated with SRGH [PR: 3.06 (2.42-3.88)]. Conclusion for practice There was a commonality of factors associated with self-rated oral health and general health. Strong associations between OH and GH were also observed. Given the importance of maternal health for future generations, there would be long-term societal benefit from addressing common risk factors for OH and GH in integrated programs.

  13. New approaches to the analysis of population trends in land birds: Comment

    USGS Publications Warehouse

    Link, W.A.; Sauer, J.R.

    1997-01-01

    James et al. (1996, Ecology 77:13-27) used data from the North American Breeding Bird Survey (BBS) to examine geographic variability in patterns of population change for 26 species of wood warblers. They emphasized the importance of evaluating nonlinear patterns of change in bird populations, proposed LOESS-based non-parametric and semi-parametric analyses of BBS data, and contrasted their results with other analyses, including those of Robbins et al. (1989, Proceedings of the National Academy of Sciences 86: 7658-7662) and Peterjohn et al. (1995, Pages 3-39 in T. E. Martin and D. M. Finch, eds. Ecology and management of Neotropical migratory birds: a synthesis and review of critical issues. Oxford University Press, New York.). In this note, we briefly comment on some of the issues that arose from their analysis of BBS data, suggest a few aspects of the survey that should inspire caution in analysts, and review the differences between the LOESS-based procedures and other procedures (e.g., Link and Sauer 1994). We strongly discourage the use of James et al.'s completely non-parametric procedure, which fails to account for observer effects. Our comparisons of estimators adds to the evidence already present in the literature of the bias associated with omitting observer information in analyses of BBS data. Bias resulting from change in observer abilities should be a consideration in any analysis of BBS data.

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

    PubMed

    Ten Haaf, Kevin; Tammemägi, Martin C; Bondy, Susan J; van der Aalst, Carlijn M; Gu, Sumei; McGregor, S Elizabeth; Nicholas, Garth; de Koning, Harry J; Paszat, Lawrence F

    2017-02-01

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

  15. Hepatitis C prevalence among the immigrant population in Spain: A systematic review and meta-analysis.

    PubMed

    Lazarus, Jeffrey V; Bromberg, Daniel J; Del Amo, Julia; Norgaard, Ole; García-Samaniego, Javier; Casellas, Aina; Calleja, José Luis; Requena-Méndez, Ana

    2018-05-11

    Spain, which has one of the largest immigrant populations in Europe, has committed to eliminating the hepatitis C virus (HCV). The aim of this study was to estimate the prevalence of HCV among migrant groups in Spain, a country of 46 million people, with an estimated HCV-antibody prevalence of 1.7%. Studies on HCV and migration in Spain were identified by systematically searching three databases from the first records to 30 November 2017, and consulting experts at the Ministry of Health and in the 17 Spanish autonomous communities. A meta-analysis was conducted to determine pooled HCV prevalence for the general migrant population. Prevalences were also calculated for high-risk migrant populations and populations who had undergone hospital screening, stratified by region of origin. Out of 243 studies identified, 26 met the eligibility criteria. The meta-analysis of the general migrant population found HCV antibody prevalence to be 1.6%. Migrants originating from European countries, including those at high or moderate risk for HCV, had the highest pooled prevalence (7.1%). In the general migrant population, prevalence was highest among sub-Saharan African migrants (3.1%) and lowest among Latin American migrants (0.2%). Based on the limited available data, the prevalence among the general migrant population was found to be the same as the general Spanish population. Further research is needed to more accurately determine HCV prevalence for the overall migrant population and specific migrant subpopulations with a higher risk in the country as a whole and in each of Spain's 17 autonomous communities. Copyright © 2018 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  16. Comparing population and incident data for optimal air ambulance base locations in Norway.

    PubMed

    Røislien, Jo; van den Berg, Pieter L; Lindner, Thomas; Zakariassen, Erik; Uleberg, Oddvar; Aardal, Karen; van Essen, J Theresia

    2018-05-24

    Helicopter emergency medical services are important in many health care systems. Norway has a nationwide physician manned air ambulance service servicing a country with large geographical variations in population density and incident frequencies. The aim of the study was to compare optimal air ambulance base locations using both population and incident data. We used municipality population and incident data for Norway from 2015. The 428 municipalities had a median (5-95 percentile) of 4675 (940-36,264) inhabitants and 10 (2-38) incidents. Optimal helicopter base locations were estimated using the Maximal Covering Location Problem (MCLP) optimization model, exploring the number and location of bases needed to cover various fractions of the population for time thresholds 30 and 45 min, in green field scenarios and conditioned on the existing base structure. The existing bases covered 96.90% of the population and 91.86% of the incidents for time threshold 45 min. Correlation between municipality population and incident frequencies was -0.0027, and optimal base locations varied markedly between the two data types, particularly when lowering the target time. The optimal solution using population density data put focus on the greater Oslo area, where one third of Norwegians live, while using incident data put focus on low population high incident areas, such as northern Norway and winter sport resorts. Using population density data as a proxy for incident frequency is not recommended, as the two data types lead to different optimal base locations. Lowering the target time increases the sensitivity to choice of data.

  17. 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…

  18. 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

  19. 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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Inference and Analysis of Population Structure Using Genetic Data and Network Theory

    PubMed Central

    Greenbaum, Gili; Templeton, Alan R.; Bar-David, Shirli

    2016-01-01

    Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition’s modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of

  1. Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

    PubMed

    Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

    2016-04-01

    Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of

  2. Analysis of Fat Intake Based on the US Department of ...

    EPA Pesticide Factsheets

    EPA released the final report, Analysis of Fat Intake Based on USDA’s 1994-1996, 1998 Continuing Survey of Food Intakes by Individuals (CSFII, Final Report). For this report, the EPA conducted an analysis of fat consumption across the U.S. population based on data derived from the U.S. Department of Agriculture's 1994-96, 1998 Continuing Survey of Food Intakes by Individuals (CSFII) and EPA's Food Commodity Intake Database (FCID). Percentiles of fat consumption were calculated on the basis of total mass and on a per-unit body-weight basis for 12 food categories and 98 demographic cohorts. In addition, dietary breakdown and fat intake percentiles were calculated for a subset of the sample population whose consumption of animal fats exceeded the 90th percentile within its age group. Many chemicals found in the environment tend to accumulate in fatty tissue. Assessing risks from these chemicals requires knowledge of dietary habits and the amount of fat present in various types of foods.

  3. Illicit drug consumption in school populations measured by wastewater analysis.

    PubMed

    Zuccato, Ettore; Gracia-Lor, Emma; Rousis, Nikolaos I; Parabiaghi, Alberto; Senta, Ivan; Riva, Francesco; Castiglioni, Sara

    2017-09-01

    Analysis of student consumption of illicit drugs (ID) by school population surveys (SPS) provides information useful for prevention, but the results may be influenced by subjective factors. We explored wastewater (WW) analysis to improve the information. We used WW analysis to measure ID consumption in eight secondary schools in Italy in 2010-13 (students aged 15-19). Samples were collected from the sewage pipes of the schools during lessons for one week each year. Samples were analysed by mass spectrometry to measure ID and consumption by students was compared to that of the general population. We found THCCOOH (human metabolite of THC) concentrations in 2010 indicating significant consumption of cannabis in all the schools and benzoylecgonine (human metabolite of cocaine) suggesting a limited consumption of cocaine in all but one school. Morphine was only found in traces, and amphetamine, methamphetamine, ecstasy, ketamine and mephedrone were not detectable. Repeated analysis showed cannabis stable until 2012 with increases in 2013, low cocaine and morphine levels, and none of the other ID. WW analysis suggested that students used amounts of cannabis comparable to the general population, with low, sporadic use of cocaine and opioids, but excluded the use of significant amounts of amphetamine, methamphetamine, ecstasy, ketamine and mephedrone. WW analysis was useful to confirm SPS figures and provides complementary findings for effective prevention strategies. This is the first time WW analysis has been used to investigate consumption of a large number of ID and new psychoactive substances (NPS) in schools. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Estimation and Partitioning of Heritability in Human Populations using Whole Genome Analysis Methods

    PubMed Central

    Vinkhuyzen, Anna AE; Wray, Naomi R; Yang, Jian; Goddard, Michael E; Visscher, Peter M

    2014-01-01

    Understanding genetic variation of complex traits in human populations has moved from the quantification of the resemblance between close relatives to the dissection of genetic variation into the contributions of individual genomic loci. But major questions remain unanswered: how much phenotypic variation is genetic, how much of the genetic variation is additive and what is the joint distribution of effect size and allele frequency at causal variants? We review and compare three whole-genome analysis methods that use mixed linear models (MLM) to estimate genetic variation, using the relationship between close or distant relatives based on pedigree or SNPs. We discuss theory, estimation procedures, bias and precision of each method and review recent advances in the dissection of additive genetic variation of complex traits in human populations that are based upon the application of MLM. Using genome wide data, SNPs account for far more of the genetic variation than the highly significant SNPs associated with a trait, but they do not account for all of the genetic variance estimated by pedigree based methods. We explain possible reasons for this ‘missing’ heritability. PMID:23988118

  5. Mitochondrial D-loop analysis for uncovering the population structure and genetic diversity among the indigenous duck (Anas platyrhynchos) populations of India.

    PubMed

    Gaur, Uma; Tantia, Madhu Sudan; Mishra, Bina; Bharani Kumar, Settypalli Tirumala; Vijh, Ramesh Kumar; Chaudhury, Ashok

    2018-03-01

    The indigenous domestic duck (Anas platyrhynchos domestica) which is domesticated from Mallard (Anas platyrhynchos) contributes significantly to poor farming community in coastal and North Eastern regions of India. For conservation and maintenance of indigenous duck populations it is very important to know the existing genetic diversity and population structure. To unravel the population structure and genetic diversity among the five indigenous duck populations of India, the mitochondrial D-loop sequences of 120 ducks were analyzed. The sequence analysis by comparison of mtDNA D-loop region (470 bp) of five Indian duck populations revealed 25 mitochondrial haplotypes. Pairwise F ST value among populations was 0.4243 (p < .01) and the range of nucleotide substitution per site (Dxy) between the five Indian duck populations was 0.00034-0.00555, and the net divergence (Da) was 0-0.00355. The phylogenetic analysis in the present study unveiled three clades. The analysis revealed genetic continuity among ducks of coastal region of the country which formed a separate group from the ducks of the inland area. Both coastal as well as the land birds revealed introgression of the out group breed Khaki Campbell, which is used for breed improvement programs in India. The observations revealed very less selection and a single matrilineal lineage of indigenous domestic ducks.

  6. Spatial accessibility of the population to urban health centres in Kermanshah, Islamic Republic of Iran: a geographic information systems analysis.

    PubMed

    Reshadat, S; Saedi, S; Zangeneh, A; Ghasemi, S R; Gilan, N R; Karbasi, A; Bavandpoor, E

    2015-09-08

    Geographic information systems (GIS) analysis has not been widely used in underdeveloped countries to ensure that vulnerable populations have accessibility to primary health-care services. This study applied GIS methods to analyse the spatial accessibility to urban primary-care centres of the population in Kermanshah city, Islamic Republic of Iran, by age and sex groups. In a descriptive-analytical study over 3 time periods, network analysis, mean centre and standard distance methods were applied using ArcGIS 9.3. The analysis was based on a standard radius of 750 m distance from health centres, walking speed of 1 m/s and desired access time to health centres of 12.5 mins. The proportion of the population with inadequate geographical access to health centres rose from 47.3% in 1997 to 58.4% in 2012. The mean centre and standard distance mapping showed that the spatial distribution of health centres in Kermanshah needed to be adjusted to changes in population distribution.

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

    PubMed Central

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

    2014-01-01

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

  8. Understanding Crystal Populations: The Role of Textural Analysis in Determining Magmatic Timescales

    NASA Astrophysics Data System (ADS)

    Jerram, D. A.

    2006-12-01

    Crystal populations in igneous rocks that erupt at the Earths surface act as records of magma chamber processes at depth, predominantly recording episodes of growth/nucleation and geochemical changes within the host body. Detailed inspection of such crystal populations, however, reveals a complex crystal cargo that comprises crystals which have grown directly from the host, crystals that have spent one or more protracted periods being isolated from the host magma and crystals that originated from a completely different magma body and/or country rock. To further interrogate this crystal cargo we can use textural analysis techniques to fully quantify the crystal population and gather important information about the population, such as crystal morphology, spatial distribution and size relationships. When quantified, such data can be used to better constrain the different components of the resultant crystal population and how they relate to each other. Additionally, by combining textural analysis information with geochemical analysis, a powerful measure of magma timescales and magma chamber processes results. In this contribution the different types of textural analysis techniques in 2D and 3D are introduced with examples from both plutonic and volcanic systems presented to highlight the roll of this approach to quantifying magma timescales.

  9. Economic burden of cancer across the European Union: a population-based cost analysis.

    PubMed

    Luengo-Fernandez, Ramon; Leal, Jose; Gray, Alastair; Sullivan, Richard

    2013-11-01

    In 2008, 2·45 million people were diagnosed with cancer and 1·23 million died because of cancer in the 27 countries of the European Union (EU). We aimed to estimate the economic burden of cancer in the EU. In a population-based cost analysis, we evaluated the cost of all cancers and also those associated with breast, colorectal, lung, and prostate cancers. We obtained country-specific aggregate data for morbidity, mortality, and health-care resource use from international and national sources. We estimated health-care costs from expenditure on care in the primary, outpatient, emergency, and inpatient settings, and also drugs. Additionally, we estimated the costs of unpaid care provided by relatives or friends of patients (ie, informal care), lost earnings after premature death, and costs associated with individuals who temporarily or permanently left employment because of illness. Cancer cost the EU €126 billion in 2009, with health care accounting for €51·0 billion (40%). Across the EU, the health-care costs of cancer were equivalent to €102 per citizen, but varied substantially from €16 per person in Bulgaria to €184 per person in Luxembourg. Productivity losses because of early death cost €42·6 billion and lost working days €9·43 billion. Informal care cost €23·2 billion. Lung cancer had the highest economic cost (€18·8 billion, 15% of overall cancer costs), followed by breast cancer (€15·0 billion, 12%), colorectal cancer (€13·1 billion, 10%), and prostate cancer (€8·43 billion, 7%). Our results show wide differences between countries, the reasons for which need further investigation. These data contribute to public health and policy intelligence, which is required to deliver affordable cancer care systems and inform effective public research funds allocation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China.

    PubMed

    Xiao, Yang; Cheng, Xuanjin; Liu, Jun; Li, Chuang; Nong, Wenyan; Bian, Yinbing; Cheung, Man Kit; Kwan, Hoi Shan

    2016-11-10

    The elucidation of genome-wide variations could help reveal aspects of divergence, domestication, and adaptation of edible mushrooms. Here, we resequenced the whole genomes of 39 wild and 21 cultivated strains of Chinese Lentinula edodes, the shiitake mushroom. We identified three distinct genetic groups in the Chinese L. edodes population with robust differentiation. Results of phylogenetic and population structure analyses suggest that the cultivated strains and most of the wild trains of L. edodes in China possess different gene pools and two outlier strains show signatures of hybridization between groups. Eighty-four candidate genes contributing to population divergence were detected in outlier analysis, 18 of which are involved in response to environmental stresses. Gene enrichment analysis of group-specific single nucleotide polymorphisms showed that the cultivated strains were genetically diversified in biological processes related to stress response. As the formation of fruiting bodies is a stress-response process, we postulate that environment factors, such as temperature, drove the population divergence of L. edodes in China by natural or artificial selection. We also found phenotypic variations between groups and identified some wild strains that have potential to diversify the genetic pool for improving agricultural traits of L. edodes cultivars in China.

  11. Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China

    PubMed Central

    Xiao, Yang; Cheng, Xuanjin; Liu, Jun; Li, Chuang; Nong, Wenyan; Bian, Yinbing; Cheung, Man Kit; Kwan, Hoi Shan

    2016-01-01

    The elucidation of genome-wide variations could help reveal aspects of divergence, domestication, and adaptation of edible mushrooms. Here, we resequenced the whole genomes of 39 wild and 21 cultivated strains of Chinese Lentinula edodes, the shiitake mushroom. We identified three distinct genetic groups in the Chinese L. edodes population with robust differentiation. Results of phylogenetic and population structure analyses suggest that the cultivated strains and most of the wild trains of L. edodes in China possess different gene pools and two outlier strains show signatures of hybridization between groups. Eighty-four candidate genes contributing to population divergence were detected in outlier analysis, 18 of which are involved in response to environmental stresses. Gene enrichment analysis of group-specific single nucleotide polymorphisms showed that the cultivated strains were genetically diversified in biological processes related to stress response. As the formation of fruiting bodies is a stress-response process, we postulate that environment factors, such as temperature, drove the population divergence of L. edodes in China by natural or artificial selection. We also found phenotypic variations between groups and identified some wild strains that have potential to diversify the genetic pool for improving agricultural traits of L. edodes cultivars in China. PMID:27830835

  12. 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.

  13. Study of risk factors for gastric cancer by populational databases analysis

    PubMed Central

    Ferrari, Fangio; Reis, Marco Antonio Moura

    2013-01-01

    AIM: To study the association between the incidence of gastric cancer and populational exposure to risk/protective factors through an analysis of international databases. METHODS: Open-access global databases concerning the incidence of gastric cancer and its risk/protective factors were identified through an extensive search on the Web. As its distribution was neither normal nor symmetric, the cancer incidence of each country was categorized according to ranges of percentile distribution. The association of each risk/protective factor with exposure was measured between the extreme ranges of the incidence of gastric cancer (under the 25th percentile and above the 75th percentile) by the use of the Mann-Whitney test, considering a significance level of 0.05. RESULTS: A variable amount of data omission was observed among all of the factors under study. A weak or nonexistent correlation between the incidence of gastric cancer and the study variables was shown by a visual analysis of scatterplot dispersion. In contrast, an analysis of categorized incidence revealed that the countries with the highest human development index (HDI) values had the highest rates of obesity in males and the highest consumption of alcohol, tobacco, fruits, vegetables and meat, which were associated with higher incidences of gastric cancer. There was no significant difference for the risk factors of obesity in females and fish consumption. CONCLUSION: Higher HDI values, coupled with a higher prevalence of male obesity and a higher per capita consumption of alcohol, tobacco, fruits, vegetables and meat, are associated with a higher incidence of gastric cancer based on an analysis of populational global data. PMID:24409066

  14. Socioeconomic Status and Childhood Cancer Incidence: A Population-Based Multilevel Analysis.

    PubMed

    Kehm, Rebecca D; Spector, Logan G; Poynter, Jenny N; Vock, David M; Osypuk, Theresa L

    2018-05-01

    The etiology of childhood cancers remains largely unknown, especially regarding environmental and behavioral risk factors. Unpacking the association between socioeconomic status (SES) and incidence may offer insight into such etiology. We tested associations between SES and childhood cancer incidence in a population-based case-cohort study (source cohort: Minnesota birth registry, 1989-2014). Cases, ages 0-14 years, were linked from the Minnesota Cancer Surveillance System to birth records through probabilistic record linkage. Controls were 4:1 frequency matched on birth year (2,947 cases and 11,907 controls). We tested associations of individual-level (maternal education) and neighborhood-level (census tract composite index) SES using logistic mixed models. In crude models, maternal education was positively associated with incidence of acute lymphoblastic leukemia (odds ratio (OR) = 1.10, 95% confidence interval (CI): 1.02, 1.19), central nervous system tumors (OR = 1.12, 95% CI: 1.04, 1.21), and neuroblastoma (OR = 1.15, 95% CI: 1.02, 1.30). Adjustment for established risk factors-including race/ethnicity, maternal age, and birth weight-substantially attenuated these positive associations. Similar patterns were observed for neighborhood-level SES. Conversely, higher maternal education was inversely associated with hepatoblastoma incidence (adjusted OR = 0.70, 95% CI: 0.51, 0.98). Overall, beyond the social patterning of established demographic and pregnancy-related exposures, SES is not strongly associated with childhood cancer incidence.

  15. Higher migraine risk in healthcare professionals than in general population: a nationwide population-based cohort study in Taiwan.

    PubMed

    Kuo, Wan-Yin; Huang, Chien-Cheng; Weng, Shih-Feng; Lin, Hung-Jung; Su, Shih-Bin; Wang, Jhi-Joung; Guo, How-Ran; Hsu, Chien-Chin

    2015-01-01

    High stress levels and shift work probably trigger migraine in healthcare professionals (HCPs). However, the migraine risk differences between HCPs and the general population is unknown. This nationwide population-based cohort study used Taiwan's National Health Insurance Research Database. Physicians (50,226), nurses (122,357), and other HCPs (pharmacists, technicians, dietitians, rehabilitation therapists, social workers, etc.) (45,736) were enrolled for the study cohort, and randomly selected non-HCPs (218,319) were enrolled for the comparison cohort. Conditional logistical regression analysis was used to compare the migraine risks. Comparisons between HCPs and between physician specialties were also done. Physicians, nurses, and other HCPs had higher migraine risks than did the general population (adjusted odds ratio [AOR]: 1.672; 95 % confidence interval [CI]: 1.468-1.905, AOR: 1.621; 95 % CI: 1.532-1.714, and AOR: 1.254; 95 % CI: 1.124-1.399, respectively) after stroke, hypertension, epilepsy, anxiety, depression, and insomnia had been adjusted for. Nurses and physicians had higher migraine risks than did other HCPs (AOR: 1.303; 95 % CI: 1.206-1.408, and AOR: 1.193; 95 % CI: 1.069-1.332, respectively). Obstetricians and gynecologists had a lower migraine risk than did other physician specialists (AOR: 0.550; 95 % CI: 0.323-0.937). HCPs in Taiwan had a higher migraine risk than did the general population. Heavy workloads, emotional stress, and rotating night shift sleep disturbances appear to be the most important risk factors. These findings should provide an important reference for promoting occupational health in HCPs in Taiwan.

  16. Association between MTHFR C677T polymorphism and depression: a meta-analysis in the Chinese population.

    PubMed

    Jiang, Wei; Xu, Jun; Lu, Xiao-Jie; Sun, Yang

    2016-09-01

    Depression is a worldwide public health issue, and its prevalence increases each year. Although a number of studies have been conducted on the association between MTHFR C677T polymorphism and depression in China, this association remains elusive and controversial. To clarify the impact of MTHFR C677T polymorphism on the risk of depression, a meta-analysis was performed in the Chinese population. Relevant studies were identified using PubMed, Springer Link, Ovid, Chinese Wanfang Data Knowledge Service Platform, Chinese National Knowledge Infrastructure and Chinese Biology Medicine through May 5, 2015. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strength of the associations. A total of 13 case-control studies including 1895 patients and 1913 controls were involved in this meta-analysis. Overall, T variant of MTHFR C677T gene polymorphism was significantly associated with an increased risk of depression in the Chinese population (T vs. C: OR = 1.52, 95% CI = 1.24-1.85; TT + CT vs. CC: OR = 1.64, 95% CI = 1.16-2.30; TT vs. CC: OR = 2.19, 95% CI = 1.49-3.24; TT vs. CC + CT: OR = 1.80, 95% CI = 1.31-2.46). In subgroup analyses stratified by geographic area and source of controls, the significant results were found in population-based studies, in hospital-based studies, in North and South China. The risk conferred by MTHFR C677T polymorphism is higher in North China than in South China. In conclusion, this meta-analysis suggests that MTHFR C677T polymorphism is associated with depression in the Chinese population, but these associations vary in different geographic locations.

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2017-01-01

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

  19. Locating helicopter emergency medical service bases to optimise population coverage versus average response time.

    PubMed

    Garner, Alan A; van den Berg, Pieter L

    2017-10-16

    New South Wales (NSW), Australia has a network of multirole retrieval physician staffed helicopter emergency medical services (HEMS) with seven bases servicing a jurisdiction with population concentrated along the eastern seaboard. The aim of this study was to estimate optimal HEMS base locations within NSW using advanced mathematical modelling techniques. We used high resolution census population data for NSW from 2011 which divides the state into areas containing 200-800 people. Optimal HEMS base locations were estimated using the maximal covering location problem facility location optimization model and the average response time model, exploring the number of bases needed to cover various fractions of the population for a 45 min response time threshold or minimizing the overall average response time to all persons, both in green field scenarios and conditioning on the current base structure. We also developed a hybrid mathematical model where average response time was optimised based on minimum population coverage thresholds. Seven bases could cover 98% of the population within 45mins when optimised for coverage or reach the entire population of the state within an average of 21mins if optimised for response time. Given the existing bases, adding two bases could either increase the 45 min coverage from 91% to 97% or decrease the average response time from 21mins to 19mins. Adding a single specialist prehospital rapid response HEMS to the area of greatest population concentration decreased the average state wide response time by 4mins. The optimum seven base hybrid model that was able to cover 97.75% of the population within 45mins, and all of the population in an average response time of 18 mins included the rapid response HEMS model. HEMS base locations can be optimised based on either percentage of the population covered, or average response time to the entire population. We have also demonstrated a hybrid technique that optimizes response time for a given

  20. 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. © 2014 American Association of Anatomists.

  1. Chapter 11. Community analysis-based methods

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

    Cao, Y.; Wu, C.H.; Andersen, G.L.

    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. Inmore » 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.« less

  2. Occupation and malignant lymphoma: a population based case control study in Germany

    PubMed Central

    Mester, B; Nieters, A; Deeg, E; Elsner, G; Becker, N; Seidler, A

    2006-01-01

    Aims To identify occupations suspected to be associated with malignant lymphoma and to generate new hypotheses about occupational risks in a multicentre, population based case control study. Methods Male and female patients with malignant lymphoma (n = 710) aged 18–80 years of age were prospectively recruited in six study regions in Germany. For each newly recruited lymphoma case, a sex, region, and age matched control was drawn from the population registers. Odds ratios and 95% confidence intervals for major occupations and industries were calculated using conditional logistic regression analysis, adjusted for smoking (in pack‐years) and alcohol consumption. Patients with specific lymphoma subentities were additionally compared with the entire control group using unconditional logistic regression analysis. Results The following economic/industrial sectors were positively associated with lymphoma: food products, beverages, tobacco; paper products, publishing and printing; and metals. Chemicals; real estate, renting, and business activities were negatively associated with lymphoma diagnosis. The authors observed an increased overall lymphoma risk among architects; maids; farmers; glass formers; and construction workers. Shoemaking and leather goods making was negatively associated with the lymphoma diagnosis (although based on small numbers). In the occupational group analysis of lymphoma subentities, Hodgkin's lymphoma was significantly associated only with rubber and plastic products making; diffuse large B cell lymphoma risk was considerably increased among metal processors; follicular lymphoma showed highly significant risk increases for several occupational groups (medical, dental, and veterinary workers; sales workers; machinery fitters; and electrical fitters); and multiple myeloma showed a particularly pronounced risk increase for farmers as well as for agriculture and animal husbandry workers. Conclusions The results partly confirm previously

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

    PubMed

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

    2015-01-01

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

  5. Association between childhood eczema and headaches: An analysis of 19 US population-based studies.

    PubMed

    Silverberg, Jonathan I

    2016-02-01

    Atopic dermatitis (or eczema) is a chronic inflammatory disorder associated with sleep disturbances and quality-of-life impairment. Sleep disturbances have been shown to cause headaches in childhood. However, an association between eczema and headaches is not well established. We sought to determine whether childhood eczema is associated with increased headaches and whether such association is related to fatigue or sleep disturbance. We analyzed data from 401,002 children and adolescents in 19 US population-based cross-sectional studies from the National Survey of Children's Health 2003/2004 and 2007/2008 and the National Health Interview Survey 1997-2013. In multivariate models controlling for age, sex, race/ethnicity, household income, highest level of education in the family, insurance coverage, number of persons in the household, birthplace in the United States, ever history of asthma, hay fever, and food allergy, eczema was found to be associated with headaches in 14 of 19 studies. In a pooled analysis of all 19 studies, children with eczema compared with those without eczema had a significantly higher prevalence (10.7% [95% CI, 10.3% to 11.0%] vs 5.4% [95% CI, 5.3% to 5.5%]) and odds (1.52 [95% CI, 1.45-1.59]) of headaches. Mild (1.79 [95% CI, 1.07-2.98]) and severe (2.72 [95% CI, 1.33-5.57]) eczema were associated with significantly higher odds of headaches. In particular, eczema associated with atopy, fatigue, excessive daytime sleepiness, insomnia, and only 0 to 3 nights of sufficient sleep had even higher odds of headache than eczema alone. Eczema is associated with increased headaches in childhood, particularly in patients with severe disease accompanied by atopy, fatigue, and sleep disturbances. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  6. Association between childhood eczema and headaches: An analysis of 19 US population-based studies

    PubMed Central

    Silverberg, Jonathan I.

    2016-01-01

    Background Atopic dermatitis (or eczema) is a chronic inflammatory disorder associated with sleep disturbances and quality-of-life impairment. Sleep disturbances have been shown to cause headaches in childhood. However, an association between eczema and headaches is not well established. Objectives We sought to determine whether childhood eczema is associated with increased headaches and whether such association is related to fatigue or sleep disturbance. Methods We analyzed data from 401,002 children and adolescents in 19 US population-based cross-sectional studies from the National Survey of Children’s Health 2003/2004 and 2007/2008 and the National Health Interview Survey 1997–2013. Results In multivariate models controlling for age, sex, race/ethnicity, household income, highest level of education in the family, insurance coverage, number of persons in the household, birthplace in the United States, ever history of asthma, hay fever, and food allergy, eczema was found to be associated with headaches in 14 of 19 studies. In a pooled analysis of all 19 studies, children with eczema compared with those without eczema had a significantly higher prevalence (10.7% [95% CI, 10.3% to 11.0%] vs 5.4% [95% CI, 5.3% to 5.5%]) and odds (1.52 [95% CI, 1.45–1.59]) of headaches. Mild (1.79 [95% CI, 1.07–2.98]) and severe (2.72 [95% CI, 1.33–5.57]) eczema were associated with significantly higher odds of headaches. In particular, eczema associated with atopy, fatigue, excessive daytime sleepiness, insomnia, and only 0 to 3 nights of sufficient sleep had even higher odds of headache than eczema alone. Conclusions Eczema is associated with increased headaches in childhood, particularly in patients with severe disease accompanied by atopy, fatigue, and sleep disturbances. PMID:26329510

  7. Lipid Vesicle Shape Analysis from Populations Using Light Video Microscopy and Computer Vision

    PubMed Central

    Zupanc, Jernej; Drašler, Barbara; Boljte, Sabina; Kralj-Iglič, Veronika; Iglič, Aleš; Erdogmus, Deniz; Drobne, Damjana

    2014-01-01

    We present a method for giant lipid vesicle shape analysis that combines manually guided large-scale video microscopy and computer vision algorithms to enable analyzing vesicle populations. The method retains the benefits of light microscopy and enables non-destructive analysis of vesicles from suspensions containing up to several thousands of lipid vesicles (1–50 µm in diameter). For each sample, image analysis was employed to extract data on vesicle quantity and size distributions of their projected diameters and isoperimetric quotients (measure of contour roundness). This process enables a comparison of samples from the same population over time, or the comparison of a treated population to a control. Although vesicles in suspensions are heterogeneous in sizes and shapes and have distinctively non-homogeneous distribution throughout the suspension, this method allows for the capture and analysis of repeatable vesicle samples that are representative of the population inspected. PMID:25426933

  8. Estimating connectivity in marine populations: an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios.

    PubMed

    Saenz-Agudelo, P; Jones, G P; Thorrold, S R; Planes, S

    2009-04-01

    The application of spatially explicit models of population dynamics to fisheries management and the design marine reserve network systems has been limited due to a lack of empirical estimates of larval dispersal. Here we compared assignment tests and parentage analysis for examining larval retention and connectivity under two different gene flow scenarios using panda clownfish (Amphiprion polymnus) in Papua New Guinea. A metapopulation of panda clownfish in Bootless Bay with little or no genetic differentiation among five spatially discrete locations separated by 2-6 km provided the high gene flow scenario. The low gene flow scenario compared the Bootless Bay metapopulation with a genetically distinct population (F(ST )= 0.1) located at Schumann Island, New Britain, 1500 km to the northeast. We used assignment tests and parentage analysis based on microsatellite DNA data to identify natal origins of 177 juveniles in Bootless Bay and 73 juveniles at Schumann Island. At low rates of gene flow, assignment tests correctly classified juveniles to their source population. On the other hand, parentage analysis led to an overestimate of self-recruitment within the two populations due to the significant deviation from panmixia when both populations were pooled. At high gene flow (within Bootless Bay), assignment tests underestimated self-recruitment and connectivity among subpopulations, and grossly overestimated self-recruitment within the overall metapopulation. However, the assignment tests did identify immigrants from distant (genetically distinct) populations. Parentage analysis clearly provided the most accurate estimates of connectivity in situations of high gene flow.

  9. Histopathological analysis of the cutaneous changes due to kangri use in kashmiri population: a hospital based study.

    PubMed

    Hassan, Iffat; Sajad, Peerzada; Reshi, Ruby

    2013-05-01

    Kangri cancer is peculiar to the valley of Kashmir as people of all age groups are accustomed to warm their bodies by the use of Kangri baskets. The clinical spectrum of skin cancer in the Kashmir valley is entirely different from the rest of the country, which could be attributed to the use of Kangri in this geographical region.[12]. Histopathological analysis of the cutaneous changes due to kangri use in Kashmiri population. This is a prospective hospital based study. All the patients attending the outpatient department of Dermatology, STD and Leprosy at SMHS Hospital, an associated hospital of govt. medical college in Srinagar and presented with suspicious lesions (i.e., erythema ab igne, papular or nodular skin growths) due to Kangri use were taken up for the study. A detailed history including the use of Kangri and a physical examination was done in each patient followed by a histopathological examination in case of suspicious lesions. The cutaneous changes which were observed during the study period of 8 months were erythema ab igne, bowen's disease and squamous cell carcinoma. Although this is a preliminary study we will be studying more of such changes caused due to Kangri use in the future.

  10. Histopathological Analysis of the Cutaneous Changes Due to Kangri Use in Kashmiri Population: A Hospital Based Study

    PubMed Central

    Hassan, Iffat; Sajad, Peerzada; Reshi, Ruby

    2013-01-01

    Background: Kangri cancer is peculiar to the valley of Kashmir as people of all age groups are accustomed to warm their bodies by the use of Kangri baskets. The clinical spectrum of skin cancer in the Kashmir valley is entirely different from the rest of the country, which could be attributed to the use of Kangri in this geographical region.[12] Aims: Histopathological analysis of the cutaneous changes due to kangri use in Kashmiri population. Materials and Methods: This is a prospective hospital based study. All the patients attending the outpatient department of Dermatology, STD and Leprosy at SMHS Hospital, an associated hospital of govt. medical college in Srinagar and presented with suspicious lesions (i.e., erythema ab igne, papular or nodular skin growths) due to Kangri use were taken up for the study. A detailed history including the use of Kangri and a physical examination was done in each patient followed by a histopathological examination in case of suspicious lesions. Results: The cutaneous changes which were observed during the study period of 8 months were erythema ab igne, bowen's disease and squamous cell carcinoma. Conclusion: Although this is a preliminary study we will be studying more of such changes caused due to Kangri use in the future. PMID:23723467

  11. Processing and population genetic analysis of multigenic datasets with ProSeq3 software.

    PubMed

    Filatov, Dmitry A

    2009-12-01

    The current tendency in molecular population genetics is to use increasing numbers of genes in the analysis. Here I describe a program for handling and population genetic analysis of DNA polymorphism data collected from multiple genes. The program includes a sequence/alignment editor and an internal relational database that simplify the preparation and manipulation of multigenic DNA polymorphism datasets. The most commonly used DNA polymorphism analyses are implemented in ProSeq3, facilitating population genetic analysis of large multigenic datasets. Extensive input/output options make ProSeq3 a convenient hub for sequence data processing and analysis. The program is available free of charge from http://dps.plants.ox.ac.uk/sequencing/proseq.htm.

  12. Emergency medical transport of the elderly: a population-based study.

    PubMed

    Wofford, J L; Moran, W P; Heuser, M D; Schwartz, E; Velez, R; Mittelmark, M B

    1995-05-01

    Patterns of utilization of emergency medical services transport (EMS) by the elderly are poorly understood. We determined population-based rates of EMS utilization by the elderly and characterized utilization patterns by age, gender, race, and reason for transport. This observational, population-based study was conducted in Forsyth County, NC, a semi-urban county served by one convalescent ambulance service and one EMS service. Using data on all 1990 EMS transports and the 1990 U.S. census data, age-, gender-, and race-specific transport rates for persons aged 60 or older were calculated. Reasons for transport and frequency of repeat users were established. After exclusion of transports because of an address outside the county, a nonhospital destination, a scheduled transport, or missing data, 4,688 transports (78% of total) remained for analysis. The overall rate of transport was 104/1,000 county residents. Transport rates increased for successively older five-year age groups, demonstrating a 5.7-fold stepwise increase from ages 60-65 to 85+ (51/1,000 to 291/1,000). There was no difference in mean age between patients who were frequent EMS users (more than three transports during the year) (n = 66) and other elderly transportees. Reasons for transport differed little between those 60 to 84 years of age and those 85 years of age and older with the exception of chest pain, cardiac arrest, and seizures, all of which were significantly more prevalent in the younger age group.(ABSTRACT TRUNCATED AT 250 WORDS)

  13. Population-based cancer survival in the United States: Data, quality control, and statistical methods.

    PubMed

    Allemani, Claudia; Harewood, Rhea; Johnson, Christopher J; Carreira, Helena; Spika, Devon; Bonaventure, Audrey; Ward, Kevin; Weir, Hannah K; Coleman, Michel P

    2017-12-15

    Robust comparisons of population-based cancer survival estimates require tight adherence to the study protocol, standardized quality control, appropriate life tables of background mortality, and centralized analysis. The CONCORD program established worldwide surveillance of population-based cancer survival in 2015, analyzing individual data on 26 million patients (including 10 million US patients) diagnosed between 1995 and 2009 with 1 of 10 common malignancies. In this Cancer supplement, we analyzed data from 37 state cancer registries that participated in the second cycle of the CONCORD program (CONCORD-2), covering approximately 80% of the US population. Data quality checks were performed in 3 consecutive phases: protocol adherence, exclusions, and editorial checks. One-, 3-, and 5-year age-standardized net survival was estimated using the Pohar Perme estimator and state- and race-specific life tables of all-cause mortality for each year. The cohort approach was adopted for patients diagnosed between 2001 and 2003, and the complete approach for patients diagnosed between 2004 and 2009. Articles in this supplement report population coverage, data quality indicators, and age-standardized 5-year net survival by state, race, and stage at diagnosis. Examples of tables, bar charts, and funnel plots are provided in this article. Population-based cancer survival is a key measure of the overall effectiveness of services in providing equitable health care. The high quality of US cancer registry data, 80% population coverage, and use of an unbiased net survival estimator ensure that the survival trends reported in this supplement are robustly comparable by race and state. The results can be used by policymakers to identify and address inequities in cancer survival in each state and for the United States nationally. Cancer 2017;123:4982-93. Published 2017. This article is a U.S. Government work and is in the public domain in the USA. Published 2017. This article is a U

  14. 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. © 2012 Wiley Publishing Asia Pty Ltd, ISZS and IOZ/CAS.

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

    PubMed

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

    2011-02-22

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

  16. [Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants].

    PubMed

    Boronnikova, S V; Kalendar', R N

    2010-01-01

    Species-specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm' region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversity was studied in six populations of rare relic species of plants Adonis vernalis L. by means of the IRAP method; 125 polymorphic IRAP-markers were analyzed. Parameters for DNA polymorphism and genetic diversity of A. vernalis populations were determined.

  17. SULT1A1 copy number variation: ethnic distribution analysis in an Indian population.

    PubMed

    Almal, Suhani; Padh, Harish

    2017-11-01

    Cytosolic sulfotransferases (SULTs) are phase II detoxification enzymes involved in metabolism of numerous xenobiotics, drugs and endogenous compounds. Interindividual variation in sulfonation capacity is important for determining an individual's response to xenobiotics. SNPs in SULTs, mainly SULT1A1 have been associated with cancer risk and also with response to therapeutic agents. Copy number variation (CNVs) in SULT1A1 is found to be correlated with altered enzyme activity. This short report primarily focuses on CNV in SULT1A1 and its distribution among different ethnic populations around the globe. Frequency distribution of SULT1A1 copy number (CN) in 157 healthy Indian individuals was assessed using florescent-based quantitative PCR assay. A range of 1 to >4 copies, with a frequency of SULT1A1 CN =2 (64.9%) the highest, was observed in our (Indian) population. Upon comparative analysis of frequency distribution of SULT1A1 CN among diverse population groups, a statistically significant difference was observed between Indians (our data) and African-American (AA) (p = 0.0001) and South African (Tswana) (p < 0.0001) populations. Distribution of CNV in the Indian population was found to be similar to that in European-derived populations of American and Japanese. CNV of SULT1A1 varies significantly among world populations and may be one of the determinants of health and diseases.

  18. Sinonasal extramedullary plasmacytoma: a population-based incidence and survival analysis.

    PubMed

    Patel, Tapan D; Vázquez, Alejandro; Choudhary, Moaz M; Kam, David; Baredes, Soly; Eloy, Jean Anderson

    2015-09-01

    Sinonasal extramedullary plasmacytoma (SN-EMP) is a rare plasma cell neoplasm. Published literature on this tumor largely consists of case reports and case-series with small sample sizes. This study analyzed population-based data on SN-EMP patients to understand demographic and clinical features as well as incidence and survival trends. The Surveillance, Epidemiology, and End Results (SEER) database was queried for SN-EMP and other head and neck EMP (HN-EMP) cases from 1973 to 2011. Cases were analyzed to determine patient demographics, initial treatment modality, and survival outcomes. Of 778 patients identified with EMP in the head and neck region, 367 patients had SN-EMP and 411 had other HN-EMP. There was a strong male predilection found, with a male-to-female ratio of 3.65:1 in the SN-EMP group and 1.87:1 in the other HN-EMP group. The majority of the patients presented with localized disease in both SN-EMP (84.4%) and other HN-EMP (81.0%) groups. The most common treatment modality reported in this database was surgery with adjuvant radiotherapy in both SN-EMP (46.3%) and other HN-EMP (38.9%) groups, followed by radiotherapy alone (SN-EMP: 40.7%; other HN-EMP: 34.2%). Five-year and 10-year disease-specific survival rates were comparable between SN-EMP (88.2% and 83.3%, respectively) and other HN-EMP (90.0% and 87.4%, respectively) (p = 0.6016 and p = 0.4015, respectively). This study analyzed the largest cohort of SN-EMP patients to date. There was no statistically significant survival advantage found for any 1 particular treatment modality over other treatment modalities in both SN-EMP and other HN-EMP. © 2015 ARS-AAOA, LLC.

  19. Large Scale Flood Risk Analysis using a New Hyper-resolution Population Dataset

    NASA Astrophysics Data System (ADS)

    Smith, A.; Neal, J. C.; Bates, P. D.; Quinn, N.; Wing, O.

    2017-12-01

    Here we present the first national scale flood risk analyses, using high resolution Facebook Connectivity Lab population data and data from a hyper resolution flood hazard model. In recent years the field of large scale hydraulic modelling has been transformed by new remotely sensed datasets, improved process representation, highly efficient flow algorithms and increases in computational power. These developments have allowed flood risk analysis to be undertaken in previously unmodeled territories and from continental to global scales. Flood risk analyses are typically conducted via the integration of modelled water depths with an exposure dataset. Over large scales and in data poor areas, these exposure data typically take the form of a gridded population dataset, estimating population density using remotely sensed data and/or locally available census data. The local nature of flooding dictates that for robust flood risk analysis to be undertaken both hazard and exposure data should sufficiently resolve local scale features. Global flood frameworks are enabling flood hazard data to produced at 90m resolution, resulting in a mis-match with available population datasets which are typically more coarsely resolved. Moreover, these exposure data are typically focused on urban areas and struggle to represent rural populations. In this study we integrate a new population dataset with a global flood hazard model. The population dataset was produced by the Connectivity Lab at Facebook, providing gridded population data at 5m resolution, representing a resolution increase over previous countrywide data sets of multiple orders of magnitude. Flood risk analysis undertaken over a number of developing countries are presented, along with a comparison of flood risk analyses undertaken using pre-existing population datasets.

  20. 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

  1. 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…

  2. Inner and inter population structure construction of Chinese Jiangsu Han population based on Y23 STR system

    PubMed Central

    Yang, Chun; Zhang, Jianqiu

    2017-01-01

    In this study, we analyzed the genetic polymorphisms of 23 Y-STR loci from PowerPlex® Y23 system in 916 unrelated healthy male individuals from Chinese Jiangsu Han, and observed 912 different haplotypes including 908 unique haplotypes and 4 duplicate haplotypes. The haplotype diversity reached 0.99999 and the discrimination capacity and match probability were 0.9956 and 0.0011, respectively. The gene diversity values ranged from 0.3942 at DYS438 to 0.9607 at DYS385a/b. Population differentiation within 10 Jiangsu Han subpopulations were evaluated by RST values and visualized in Neighbor-Joining trees and Multi-Dimensional Scaling plots as well as population relationships between the Jiangsu Han population and other 18 Eastern Asian populations. Such results indicated that the 23 Y-STR loci were highly polymorphic in Jiangsu Han population and played crucial roles in forensic application as well as population genetics. For the first time, we reported the genetic diversity of male lineages in Jiangsu Han population at a high-resolution level of 23 Y-STR set and consequently contributed to familial searching, offender tracking, and anthropology analysis of Jiangsu Han population. PMID:28704439

  3. Single cell versus large population analysis: cell variability in elemental intracellular concentration and distribution.

    PubMed

    Malucelli, Emil; Procopio, Alessandra; Fratini, Michela; Gianoncelli, Alessandra; Notargiacomo, Andrea; Merolle, Lucia; Sargenti, Azzurra; Castiglioni, Sara; Cappadone, Concettina; Farruggia, Giovanna; Lombardo, Marco; Lagomarsino, Stefano; Maier, Jeanette A; Iotti, Stefano

    2018-01-01

    The quantification of elemental concentration in cells is usually performed by analytical assays on large populations missing peculiar but important rare cells. The present article aims at comparing the elemental quantification in single cells and cell population in three different cell types using a new approach for single cells elemental analysis performed at sub-micrometer scale combining X-ray fluorescence microscopy and atomic force microscopy. The attention is focused on the light element Mg, exploiting the opportunity to compare the single cell quantification to the cell population analysis carried out by a highly Mg-selective fluorescent chemosensor. The results show that the single cell analysis reveals the same Mg differences found in large population of the different cell strains studied. However, in one of the cell strains, single cell analysis reveals two cells with an exceptionally high intracellular Mg content compared with the other cells of the same strain. The single cell analysis allows mapping Mg and other light elements in whole cells at sub-micrometer scale. A detailed intensity correlation analysis on the two cells with the highest Mg content reveals that Mg subcellular localization correlates with oxygen in a different fashion with respect the other sister cells of the same strain. Graphical abstract Single cells or large population analysis this is the question!

  4. Design and implementation of population-based specialty care programs.

    PubMed

    Botts, Sheila R; Gee, Michael T; Chang, Christopher C; Young, Iris; Saito, Logan; Lyman, Alfred E

    2017-09-15

    The development, implementation, and scaling of 3 population-based specialty care programs in a large integrated healthcare system are reviewed, and the role of clinical pharmacy services in ensuring safe, effective, and affordable care is highlighted. The Kaiser Permanente (KP) integrated healthcare delivery model allows for rapid development and expansion of innovative population management programs involving pharmacy services. Clinical pharmacists have assumed integral roles in improving the safety and effectiveness of high-complexity, high-cost care for specialty populations. These roles require an appropriate practice scope and are supported by an advanced electronic health record with disease registries and electronic surveillance tools for care-gap identification. The 3 specialty population programs described were implemented to address variation or unrecognized gaps in care for at-risk specialty populations. The Home Phototherapy Program has leveraged internal partnerships with clinical pharmacists to improve access to cost-effective nonpharmacologic interventions for psoriasis and other skin disorders. The Multiple Sclerosis Care Program has incorporated clinical pharmacists into neurology care in order to apply clinical guidelines in a systematic manner. The KP SureNet program has used clinical pharmacists and data analytics to identify opportunities to prevent drug-related adverse outcomes and ensure timely follow-up. Specialty care programs improve quality, cost outcomes, and the patient experience by appropriating resources to provide systematic and targeted care to high-risk patients. KP leverages an integration of people, processes, and technology to develop and scale population-based specialty care. Copyright © 2017 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

  5. Secondary Data Analysis of National Surveys in Japan Toward Improving Population Health

    PubMed Central

    Ikeda, Nayu

    2016-01-01

    Secondary data analysis of national health surveys of the general population is a standard methodology for health metrics and evaluation; it is used to monitor trends in population health over time and benchmark the performance of health systems. In Japan, the government has established electronic databases of individual records from national surveys of the population’s health. However, the number of publications based on these datasets is small considering the scale and coverage of the surveys. There appear to be two major obstacles to the secondary use of Japanese national health survey data: strict data access control under the Statistics Act and an inadequate interdisciplinary research environment for resolving methodological difficulties encountered when dealing with secondary data. The usefulness of secondary analysis of survey data is evident with examples from the author’s previous studies based on vital records and the National Health and Nutrition Surveys, which showed that (i) tobacco smoking and high blood pressure are the major risk factors for adult mortality from non-communicable diseases in Japan; (ii) the decrease in mean blood pressure in Japan from the late 1980s to the early 2000s was partly attributable to the increased use of antihypertensive medication and reduced dietary salt intake; and (iii) progress in treatment coverage and control of high blood pressure is slower in Japan than in the United States and Britain. National health surveys in Japan are an invaluable asset, and findings from secondary analyses of these surveys would provide important suggestions for improving health in people around the world. PMID:26902170

  6. Model-based prediction of nephropathia epidemica outbreaks based on climatological and vegetation data and bank vole population dynamics.

    PubMed

    Haredasht, S Amirpour; Taylor, C J; Maes, P; Verstraeten, W W; Clement, J; Barrios, M; Lagrou, K; Van Ranst, M; Coppin, P; Berckmans, D; Aerts, J-M

    2013-11-01

    could be predicted 3 months ahead with a 34% mean relative prediction error (MRPE). This took into account solely the population dynamics of the carrier species (bank voles). The time series analysis also revealed that climate change, as represented by the vegetation index, changes in forest phenology derived from satellite images and directly measured air temperature, may affect the mechanics of NE transmission. NE outbreaks in Belgium were predicted 3 months ahead with a 40% MRPE, based only on the climatological and vegetation data, in this case, without any knowledge of the bank vole's population dynamics. In this research, we demonstrated that NE outbreaks can be predicted using climate and vegetation data or the bank vole's population dynamics, by using dynamic data-based models with time-varying parameters. Such a predictive modelling approach might be used as a step towards the development of new tools for the prevention of future NE outbreaks. © 2012 Blackwell Verlag GmbH.

  7. Genetic diversity in populations of Isatis glauca Aucher ex Boiss. ssp. from Central Anatolia in Turkey, as revealed by AFLP analysis.

    PubMed

    Özbek, Özlem; Görgülü, Elçin; Yıldırımlı, Şinasi

    2013-12-01

    Isatidae L. is a complex and systematically difficult genus in Brassicaceae. The genus displays great morphological polymorphism, which makes the classification of species and subspecies difficult as it is observed in Isatis glauca Aucher ex Boiss. The aim of this study is characterization of the genetic diversity in subspecies of Isatis glauca Aucher ex Boiss. distributed widely in Central Anatolia, in Turkey by using Amplified Fragment Length Polymorphism (AFLP) technique. Eight different Eco RI-Mse I primer combinations produced 805 AFLP loci, 793 (98.5%) of which were polymorphic in 67 accessions representing nine different populations. The data obtained by AFLP was computed with using GDA (Genetic Data Analysis) and STRUCTURE (version 2.3.3) software programs for population genetics. The mean proportion of the polymorphic locus (P), the mean number of alleles (A), the number of unique alleles (U) and the mean value of gene diversity (He) were 0.59, 1.59, 20, and 0.23 respectively. The coancestry coefficient (ϴ) was 0.24. The optimal number of K was identified as seven. The principal component analysis (PCA) explained 85.61% of the total genetic variation. Isatis glauca ssp. populations showed a high level of genetic diversity, and the AFLP analysis revealed that high polymorphism and differentiated subspecies could be used conveniently for population genetic studies. The principal coordinate analysis (PCoA) based on the dissimilarity matrix, the dendrogram drawn with UPGMA method and STRUCTURE cluster analysis distinguished the accessions successfully. The accessions formed distinctive population structures for populations AA, AB, E, K, and S. Populations AG1 and AG2 seemed to have similar genetic content, in addition, in both populations several hybrid individuals were observed. The accessions did not formed distinctive population structures for both populations AI and ANP. Consequently, Ankara province might be the area, where species Isatis glauca Aucher

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

    PubMed Central

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

    2012-01-01

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

  9. Including trait-based early warning signals helps predict population collapse

    PubMed Central

    Clements, Christopher F.; Ozgul, Arpat

    2016-01-01

    Foreseeing population collapse is an on-going target in ecology, and this has led to the development of early warning signals based on expected changes in leading indicators before a bifurcation. Such signals have been sought for in abundance time-series data on a population of interest, with varying degrees of success. Here we move beyond these established methods by including parallel time-series data of abundance and fitness-related trait dynamics. Using data from a microcosm experiment, we show that including information on the dynamics of phenotypic traits such as body size into composite early warning indices can produce more accurate inferences of whether a population is approaching a critical transition than using abundance time-series alone. By including fitness-related trait information alongside traditional abundance-based early warning signals in a single metric of risk, our generalizable approach provides a powerful new way to assess what populations may be on the verge of collapse. PMID:27009968

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

    PubMed

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

    2014-01-01

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

  11. Ethics, effectiveness and population health information interventions: a Canadian analysis.

    PubMed

    Greyson, Devon; Knight, Rod; Shoveller, Jean A

    2018-02-19

    Population health information interventions (PHIIs) use information in efforts to promote health. PHIIs may push information to a target audience (communication), pull information from the public (surveillance), or combine both in a bidirectional intervention. Although PHIIs have often been framed as non-invasive and ethically innocuous, in reality they may be intrusive into people's lives, affecting not only their health but their senses of security, respect, and self-determination. Ethical acceptability of PHIIs may have impacts on intervention effectiveness, potentially giving rise to unintended consequences. This article examines push, pull, and bidirectional PHIIs using empirical data from an ethnographic study of young mothers in Greater Vancouver, Canada. Data were collected from October 2013 to December 2014 via naturalistic observation and individual interviews with 37 young mothers ages 16-22. Transcribed interviews and field notes were analyzed using inductive qualitative thematic analysis. Both push and pull interventions were experienced as non-neutral by the target population, and implementation factors on a structural and individual scale affected intervention ethics and effectiveness. Based on our findings, we suggest that careful ethical consideration be applied to use of PHIIs as health promotion tools. Advancing the 'ethics of PHIIs' will benefit from empirical data that is informed by information and computer science theory and methods. Information technologies, digital health promotion services, and integrated surveillance programs reflect important areas for investigation in terms of their effects and ethics. Health promotion researchers, practitioners, and ethicists should explore these across contexts and populations.

  12. Ancestry estimation and control of population stratification for sequence-based association studies.

    PubMed

    Wang, Chaolong; Zhan, Xiaowei; Bragg-Gresham, Jennifer; Kang, Hyun Min; Stambolian, Dwight; Chew, Emily Y; Branham, Kari E; Heckenlively, John; Fulton, Robert; Wilson, Richard K; Mardis, Elaine R; Lin, Xihong; Swaroop, Anand; Zöllner, Sebastian; Abecasis, Gonçalo R

    2014-04-01

    Estimating individual ancestry is important in genetic association studies where population structure leads to false positive signals, although assigning ancestry remains challenging with targeted sequence data. We propose a new method for the accurate estimation of individual genetic ancestry, based on direct analysis of off-target sequence reads, and implement our method in the publicly available LASER software. We validate the method using simulated and empirical data and show that the method can accurately infer worldwide continental ancestry when used with sequencing data sets with whole-genome shotgun coverage as low as 0.001×. For estimates of fine-scale ancestry within Europe, the method performs well with coverage of 0.1×. On an even finer scale, the method improves discrimination between exome-sequenced study participants originating from different provinces within Finland. Finally, we show that our method can be used to improve case-control matching in genetic association studies and to reduce the risk of spurious findings due to population structure.

  13. The interplay between human population dynamics and flooding in Bangladesh: a spatial analysis

    NASA Astrophysics Data System (ADS)

    di Baldassarre, G.; Yan, K.; Ferdous, MD. R.; Brandimarte, L.

    2014-09-01

    In Bangladesh, socio-economic and hydrological processes are both extremely dynamic and inter-related. Human population patterns are often explained as a response, or adaptation strategy, to physical events, e.g. flooding, salt-water intrusion, and erosion. Meanwhile, these physical processes are exacerbated, or mitigated, by diverse human interventions, e.g. river diversion, levees and polders. In this context, this paper describes an attempt to explore the complex interplay between floods and societies in Bangladeshi floodplains. In particular, we performed a spatially-distributed analysis of the interactions between the dynamics of human settlements and flood inundation patterns. To this end, we used flooding simulation results from inundation modelling, LISFLOOD-FP, as well as global datasets of population distribution data, such as the Gridded Population of the World (20 years, from 1990 to 2010) and HYDE datasets (310 years, from 1700 to 2010). The outcomes of this work highlight the behaviour of Bangladeshi floodplains as complex human-water systems and indicate the need to go beyond the traditional narratives based on one-way cause-effects, e.g. climate change leading to migrations.

  14. Modeling wildlife populations with HexSim

    EPA Science Inventory

    HexSim is a framework for constructing spatially-explicit, individual-based computer models designed for simulating terrestrial wildlife population dynamics and interactions. HexSim is useful for a broad set of modeling applications including population viability analysis for on...

  15. An agent-based computational model for tuberculosis spreading on age-structured populations

    NASA Astrophysics Data System (ADS)

    Graciani Rodrigues, C. C.; Espíndola, Aquino L.; Penna, T. J. P.

    2015-06-01

    In this work we present an agent-based computational model to study the spreading of the tuberculosis (TB) disease on age-structured populations. The model proposed is a merge of two previous models: an agent-based computational model for the spreading of tuberculosis and a bit-string model for biological aging. The combination of TB with the population aging, reproduces the coexistence of health states, as seen in real populations. In addition, the universal exponential behavior of mortalities curves is still preserved. Finally, the population distribution as function of age shows the prevalence of TB mostly in elders, for high efficacy treatments.

  16. Propagation of population pharmacokinetic information using a Bayesian approach: comparison with meta-analysis.

    PubMed

    Dokoumetzidis, Aristides; Aarons, Leon

    2005-08-01

    We investigated the propagation of population pharmacokinetic information across clinical studies by applying Bayesian techniques. The aim was to summarize the population pharmacokinetic estimates of a study in appropriate statistical distributions in order to use them as Bayesian priors in consequent population pharmacokinetic analyses. Various data sets of simulated and real clinical data were fitted with WinBUGS, with and without informative priors. The posterior estimates of fittings with non-informative priors were used to build parametric informative priors and the whole procedure was carried on in a consecutive manner. The posterior distributions of the fittings with informative priors where compared to those of the meta-analysis fittings of the respective combinations of data sets. Good agreement was found, for the simulated and experimental datasets when the populations were exchangeable, with the posterior distribution from the fittings with the prior to be nearly identical to the ones estimated with meta-analysis. However, when populations were not exchangeble an alternative parametric form for the prior, the natural conjugate prior, had to be used in order to have consistent results. In conclusion, the results of a population pharmacokinetic analysis may be summarized in Bayesian prior distributions that can be used consecutively with other analyses. The procedure is an alternative to meta-analysis and gives comparable results. It has the advantage that it is faster than the meta-analysis, due to the large datasets used with the latter and can be performed when the data included in the prior are not actually available.

  17. Using population viability analysis, genomics, and habitat suitability to forecast future population patterns of Little Owl Athene noctua across Europe.

    PubMed

    Andersen, Line Holm; Sunde, Peter; Pellegrino, Irene; Loeschcke, Volker; Pertoldi, Cino

    2017-12-01

    The agricultural scene has changed over the past decades, resulting in a declining population trend in many species. It is therefore important to determine the factors that the individual species depend on in order to understand their decline. The landscape changes have also resulted in habitat fragmentation, turning once continuous populations into metapopulations. It is thus increasingly important to estimate both the number of individuals it takes to create a genetically viable population and the population trend. Here, population viability analysis and habitat suitability modeling were used to estimate population viability and future prospects across Europe of the Little Owl Athene noctua , a widespread species associated with agricultural landscapes. The results show a high risk of population declines over the coming 100 years, especially toward the north of Europe, whereas populations toward the southeastern part of Europe have a greater probability of persistence. In order to be considered genetically viable, individual populations must count 1,000-30,000 individuals. As Little Owl populations of several countries count <30,000, and many isolated populations in northern Europe count <1,000 individuals, management actions resulting in exchange of individuals between populations or even countries are probably necessary to prevent losing <1% genetic diversity over a 100-year period. At a continental scale, a habitat suitability analysis suggested Little Owl to be affected positively by increasing temperatures and urban areas, whereas an increased tree cover, an increasing annual rainfall, grassland, and sparsely vegetated areas affect the presence of the owl negatively. However, the low predictive power of the habitat suitability model suggests that habitat suitability might be better explained at a smaller scale.

  18. Maternal and perinatal mortality by place of delivery in sub-Saharan Africa: a meta-analysis of population-based cohort studies.

    PubMed

    Chinkhumba, Jobiba; De Allegri, Manuela; Muula, Adamson S; Robberstad, Bjarne

    2014-09-28

    Facility-based delivery has gained traction as a key strategy for reducing maternal and perinatal mortality in developing countries. However, robust evidence of impact of place of delivery on maternal and perinatal mortality is lacking. We aimed to estimate the risk of maternal and perinatal mortality by place of delivery in sub-Saharan Africa. We conducted a systematic review of population-based cohort studies reporting on risk of maternal or perinatal mortality at the individual level by place of delivery in sub-Saharan Africa. Newcastle-Ottawa Scale was used to assess study quality. Outcomes were summarized in pooled analyses using fixed and random effects models. We calculated attributable risk percentage reduction in mortality to estimate exposure effect. We report mortality ratios, crude odds ratios and associated 95% confidence intervals. We found 9 population-based cohort studies: 6 reporting on perinatal and 3 on maternal mortality. The mean study quality score was 10 out of 15 points. Control for confounders varied between the studies. A total of 36,772 pregnancy episodes were included in the analyses. Overall, perinatal mortality is 21% higher for home compared to facility-based deliveries, but the difference is only significant when produced with a fixed effects model (OR 1.21, 95% CI: 1.02-1.46) and not when produced by a random effects model (OR 1.21, 95% CI: 0.79-1.84). Under best settings, up to 14 perinatal deaths might be averted per 1000 births if the women delivered at facilities instead of homes. We found significantly increased risk of maternal mortality for facility-based compared to home deliveries (OR 2.29, 95% CI: 1.58-3.31), precluding estimates of attributable risk fraction. Evaluating the impact of facility-based delivery strategy on maternal and perinatal mortality using population-based studies is complicated by selection bias and poor control of confounders. Studies that pool data at an individual level may overcome some of these

  19. Generalizability of clinical trials of advanced melanoma in the real-world, population-based setting.

    PubMed

    Sam, Davis; Gresham, Gillian; Abdel-Rahman, Omar; Cheung, Winson Y

    2018-06-18

    Results from novel therapeutics trials are not always generalizable to real-world patients. We aimed to determine the pattern in which trial findings are applied in a population-based setting of melanoma patients and consequent treatment outcomes. Patients with unresectable disease during 2011-2014 and referred to cancer centers in a large Canadian province were retrospectively reviewed. Based on eligibility criteria as described in registration trials of vemurafenib (Vem) and ipilimumab (Ipi), we classified patients into trial-eligible and ineligible and those treated and untreated with these agents. We identified 290 patients with known BRAF status for the Vem analysis and 212 patients previously treated with first-line agents for the Ipi analysis. For the Vem cohort, a total of 49 patients were considered trial-eligible, of whom 36 (73%) received treatment. For the Ipi cohort, there were 119 trial-eligible cases of whom 43 (36%) received therapy. Factors other than eligibility criteria most frequently associated with non-treatment in these cohorts included concerns regarding treatment harm and patient preferences. In multivariable analysis, overall survival was improved in Vem cohort patients considered trial-eligible and treated compared to those who were ineligible. Within the Ipi cohort, survival was improved in trial-eligible patients regardless of whether they received Ipi compared to ineligible patients. Real-world uptake of new melanoma treatments was suboptimal, and non-use in trial-eligible patients was frequent. Future clinical trials that are more pragmatically designed to include participants who better reflect the real-world population may facilitate increased uptake of novel therapeutics into routine clinical practice.

  20. The Analysis of Cell Population Dynamics in Mammary Gland Development and Tumorigenesis

    DTIC Science & Technology

    2005-08-01

    AD Award Number: DAMD17-03-1-0498 TITLE: The Analysis of Cell Population Dynamics in Mammary Gland Development and Tumorigenesis PRINCIPAL...Summary 1 Aug 2004 - 31 Jul 2005 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER The Analysis of Cell Population Dynamics in Mammary Gland Development and...STATEMENT Approved for Public Release; Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT The mammary gland is made up of several epithelial cell

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

    PubMed

    Yu, Hwa-Lung; Chien, Lung-Chang

    2016-01-01

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

  2. Genetic Diversity and Geographic Population Structure of Bovine Neospora caninum Determined by Microsatellite Genotyping Analysis

    PubMed Central

    Regidor-Cerrillo, Javier; Díez-Fuertes, Francisco; García-Culebras, Alicia; Moore, Dadín P.; González-Warleta, Marta; Cuevas, Carmen; Schares, Gereon; Katzer, Frank; Pedraza-Díaz, Susana; Mezo, Mercedes; Ortega-Mora, Luis M.

    2013-01-01

    The cyst-forming protozoan parasite Neospora caninum is one of the main causes of bovine abortion worldwide and is of great economic importance in the cattle industry. Recent studies have revealed extensive genetic variation among N . caninum isolates based on microsatellite sequences (MSs). MSs may be suitable molecular markers for inferring the diversity of parasite populations, molecular epidemiology and the basis for phenotypic variations in N . caninum , which have been poorly defined. In this study, we evaluated nine MS markers using a panel of 11 N . caninum -derived reference isolates from around the world and 96 N . caninum bovine clinical samples and one ovine clinical sample collected from four countries on two continents, including Spain, Argentina, Germany and Scotland, over a 10-year period. These markers were used as molecular tools to investigate the genetic diversity, geographic distribution and population structure of N . caninum . Multilocus microsatellite genotyping based on 7 loci demonstrated high levels of genetic diversity in the samples from all of the different countries, with 96 microsatellite multilocus genotypes (MLGs) identified from 108 N . caninum samples. Geographic sub-structuring was present in the country populations according to pairwise F ST. Principal component analysis (PCA) and Neighbor Joining tree topologies also suggested MLG segregation partially associated with geographical origin. An analysis of the MLG relationships, using eBURST, confirmed that the close genetic relationship observed between the Spanish and Argentinean populations may be the result of parasite migration (i.e., the introduction of novel MLGs from Spain to South America) due to cattle movement. The eBURST relationships also revealed genetically different clusters associated with the abortion. The presence of linkage disequilibrium, the co-existence of specific MLGs to individual farms and eBURST MLG relationships suggest a predominant clonal

  3. Falls among the elderly: risk factors in a population-based study.

    PubMed

    Rodrigues, Iara Guimarães; Fraga, Gustavo Pereira; Barros, Marilisa Berti de Azevedo

    2014-01-01

    The aim of the present study was to identify factors associated with the occurrence of falls among elderly adults in a population-based study (ISACamp 2008). A population-based cross-sectional study was carried out with two-stage cluster sampling. The sample was composed of 1,520 elderly adults living in the urban area of the city of Campinas, São Paulo, Brazil. The occurrence of falls was analyzed based on reports of the main accident occurred in the previous 12 months. Data on socioeconomic/demographic factors and adverse health conditions were tested for possible associations with the outcome. Prevalence ratios (PR) were estimated and adjusted for gender and age using the Poisson multiple regression analysis. Falls were more frequent, after adjustment for gender and age, among female elderly participants (PR = 2.39; 95% confidence interval (95% CI) 1.47 - 3.87), elderly adults (80 years old and older) (PR = 2.50; 95% CI 1.61 - 3.88), widowed (PR = 1.74; 95% CI 1.04 - 2.89) and among elderly adults who had rheumatism/arthritis/arthrosis (PR = 1.58; 95% CI 1.00 - 2.48), osteoporosis (PR = 1.71; 95% CI 1.18 - 2.49), asthma/bronchitis/emphysema (PR = 1,73; 95% CI 1.09 - 2.74), headache (PR = 1.59; 95% CI 1.07 - 2.38), mental common disorder (PR = 1.72; 95% CI 1.12 - 2.64), dizziness (PR = 2.82; 95% CI 1.98 - 4.02), insomnia (PR = 1.75; 95% CI 1.16 - 2.65), use of multiple medications (five or more) (PR = 2.50; 95% CI 1.12 - 5.56) and use of cane/walker (PR = 2.16; 95% CI 1.19 - 3,93). The present study shows segments of the elderly population who are more prone to falls through the identification of factors associated with this outcome. The findings can contribute to the planning of public health policies and programs addressed to the prevention of falls.

  4. An isochrone data base and a rapid model for stellar population synthesis

    NASA Astrophysics Data System (ADS)

    Li, Zhongmu; Han, Zhanwen

    2008-06-01

    We first presented an isochrone data base that can be widely used for stellar population synthesis studies and colour-magnitude diagram (CMD) fitting. The data base consists of the isochrones of both single-star and binary-star simple stellar populations (ss-SSPs and bs-SSPs). The ranges for the age and metallicity of populations are 0-15 Gyr and 0.0001-0.03, respectively. All data are available for populations with two widely used initial mass functions (IMFs), that is, Salpeter IMF and Chabrier IMF. The uncertainty caused by the data base (about 0.81 per cent) is designed to be smaller than those caused by the Hurley code and widely used stellar spectra libraries (e.g. BaSeL 3.1) when it is used for stellar population synthesis. Based on the isochrone data base, we then built a rapid stellar population synthesis (RPS) model and calculated the high-resolution (0.3-Å) integrated spectral energy distributions, Lick indices and colour indices for bs-SSPs and ss-SSPs. In particular, we calculated the UBVRIJHKLM colours, ugriz colours and some composite colours that consist of magnitudes on different systems. These colours are useful for disentangling the well-known stellar age-metallicity degeneracy according to our previous work. As an example for applying the isochrone data base for CMD fitting, we fitted the CMDs of two star clusters (M67 and NGC1868) and obtained their distance moduli, colour excesses, stellar metallicities and ages. The results showed that the isochrones of bs-SSPs are closer to those of real star clusters. It suggests that we should take the effects of binary interactions into account in stellar population synthesis. We also discussed on the limitations of the application of the isochrone data base and the results of the RPS model. All the data are available at the CDS or on request to the authors. E-mail: zhongmu.li@gmail.com

  5. Velocity-based movement modeling for individual and population level inference

    USGS Publications Warehouse

    Hanks, Ephraim M.; Hooten, Mevin B.; Johnson, Devin S.; Sterling, Jeremy T.

    2011-01-01

    Understanding animal movement and resource selection provides important information about the ecology of the animal, but an animal's movement and behavior are not typically constant in time. We present a velocity-based approach for modeling animal movement in space and time that allows for temporal heterogeneity in an animal's response to the environment, allows for temporal irregularity in telemetry data, and accounts for the uncertainty in the location information. Population-level inference on movement patterns and resource selection can then be made through cluster analysis of the parameters related to movement and behavior. We illustrate this approach through a study of northern fur seal (Callorhinus ursinus) movement in the Bering Sea, Alaska, USA. Results show sex differentiation, with female northern fur seals exhibiting stronger response to environmental variables.

  6. Velocity-Based Movement Modeling for Individual and Population Level Inference

    PubMed Central

    Hanks, Ephraim M.; Hooten, Mevin B.; Johnson, Devin S.; Sterling, Jeremy T.

    2011-01-01

    Understanding animal movement and resource selection provides important information about the ecology of the animal, but an animal's movement and behavior are not typically constant in time. We present a velocity-based approach for modeling animal movement in space and time that allows for temporal heterogeneity in an animal's response to the environment, allows for temporal irregularity in telemetry data, and accounts for the uncertainty in the location information. Population-level inference on movement patterns and resource selection can then be made through cluster analysis of the parameters related to movement and behavior. We illustrate this approach through a study of northern fur seal (Callorhinus ursinus) movement in the Bering Sea, Alaska, USA. Results show sex differentiation, with female northern fur seals exhibiting stronger response to environmental variables. PMID:21931584

  7. Further Evaluation of Covariate Analysis using Empirical Bayes Estimates in Population Pharmacokinetics: the Perception of Shrinkage and Likelihood Ratio Test.

    PubMed

    Xu, Xu Steven; Yuan, Min; Yang, Haitao; Feng, Yan; Xu, Jinfeng; Pinheiro, Jose

    2017-01-01

    Covariate analysis based on population pharmacokinetics (PPK) is used to identify clinically relevant factors. The likelihood ratio test (LRT) based on nonlinear mixed effect model fits is currently recommended for covariate identification, whereas individual empirical Bayesian estimates (EBEs) are considered unreliable due to the presence of shrinkage. The objectives of this research were to investigate the type I error for LRT and EBE approaches, to confirm the similarity of power between the LRT and EBE approaches from a previous report and to explore the influence of shrinkage on LRT and EBE inferences. Using an oral one-compartment PK model with a single covariate impacting on clearance, we conducted a wide range of simulations according to a two-way factorial design. The results revealed that the EBE-based regression not only provided almost identical power for detecting a covariate effect, but also controlled the false positive rate better than the LRT approach. Shrinkage of EBEs is likely not the root cause for decrease in power or inflated false positive rate although the size of the covariate effect tends to be underestimated at high shrinkage. In summary, contrary to the current recommendations, EBEs may be a better choice for statistical tests in PPK covariate analysis compared to LRT. We proposed a three-step covariate modeling approach for population PK analysis to utilize the advantages of EBEs while overcoming their shortcomings, which allows not only markedly reducing the run time for population PK analysis, but also providing more accurate covariate tests.

  8. The role of area-level deprivation and gender in participation in population-based faecal immunochemical test (FIT) colorectal cancer screening.

    PubMed

    Clarke, Nicholas; McNamara, Deirdre; Kearney, Patricia M; O'Morain, Colm A; Shearer, Nikki; Sharp, Linda

    2016-12-01

    This study aimed to investigate the effects of sex and deprivation on participation in a population-based faecal immunochemical test (FIT) colorectal cancer screening programme. The study population included 9785 individuals invited to participate in two rounds of a population-based biennial FIT-based screening programme, in a relatively deprived area of Dublin, Ireland. Explanatory variables included in the analysis were sex, deprivation category of area of residence and age (at end of screening). The primary outcome variable modelled was participation status in both rounds combined (with "participation" defined as having taken part in either or both rounds of screening). Poisson regression with a log link and robust error variance was used to estimate relative risks (RR) for participation. As a sensitivity analysis, data were stratified by screening round. In both the univariable and multivariable models deprivation was strongly associated with participation. Increasing affluence was associated with higher participation; participation was 26% higher in people resident in the most affluent compared to the most deprived areas (multivariable RR=1.26: 95% CI 1.21-1.30). Participation was significantly lower in males (multivariable RR=0.96: 95%CI 0.95-0.97) and generally increased with increasing age (trend per age group, multivariable RR=1.02: 95%CI, 1.01-1.02). No significant interactions between the explanatory variables were found. The effects of deprivation and sex were similar by screening round. Deprivation and male gender are independently associated with lower uptake of population-based FIT colorectal cancer screening, even in a relatively deprived setting. Development of evidence-based interventions to increase uptake in these disadvantaged groups is urgently required. Copyright © 2016. Published by Elsevier Inc.

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

    PubMed

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

    2016-02-01

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

  10. Primary Squamous Cell Carcinoma of the Thyroid: A Population-Based Analysis.

    PubMed

    Au, Joshua K; Alonso, Jose; Kuan, Edward C; Arshi, Armin; St John, Maie A

    2017-07-01

    Objectives To analyze the epidemiology and describe the prognostic indicators of patients with primary squamous cell carcinoma of the thyroid. Study Design and Setting Retrospective cohort study based on a national database. Methods The US National Cancer Institute's SEER registry (Surveillance, Epidemiology, and End Results) was reviewed for patients with primary squamous cell carcinoma of the thyroid from 1973 to 2012. Study variables included age, sex, race, tumor size, tumor grade, regional and distant metastases, and treatment modality. Survival measures included overall survival (OS) and disease-specific survival (DSS). Results A total of 199 cases of primary squamous cell carcinoma of the thyroid were identified. Mean age at diagnosis was 68.1 years; 58.3% were female; and 79.4% were white. Following diagnosis, 46.3% of patients underwent surgery; 55.7%, radiation therapy; and 45.8%, surgery with radiation therapy. Kaplan-Meier analysis demonstrated OS and DSS of 16% and 21% at 5 years, respectively. Median survival after diagnosis was 9.1 months. Multivariate Cox regression analysis showed that predictors of OS and DSS included age ( P < .001, P < .001, respectively), tumor grade ( P < .001, P = .001), and tumor size ( P < .001, P = .001). Surgical management was a predictor of OS but not DSS. Conclusion Squamous cell carcinoma of the thyroid is a rare malignancy with a very poor prognosis. Surgical resection confers an overall survival benefit. Age, tumor grade, and tumor size are predictors of OS and DSS.

  11. Body-Mass Index and Pancreatic Cancer Incidence: A Pooled Analysis of Nine Population-Based Cohort Studies With More Than 340,000 Japanese Subjects.

    PubMed

    Koyanagi, Yuriko N; Matsuo, Keitaro; Ito, Hidemi; Tamakoshi, Akiko; Sugawara, Yumi; Hidaka, Akihisa; Wada, Keiko; Oze, Isao; Kitamura, Yuri; Liu, Rong; Mizoue, Tetsuya; Sawada, Norie; Nagata, Chisato; Wakai, Kenji; Nakayama, Tomio; Sadakane, Atsuko; Tanaka, Keitaro; Inoue, Manami; Tsugane, Shoichiro; Sasazuki, Shizuka

    2018-05-05

    A high body mass index (BMI) has been proposed as an important risk factor for pancreatic cancer. However, this association of BMI with pancreatic cancer risk has not been confirmed in Asian populations. We evaluated the association between BMI (either at baseline or during early adulthood) and pancreatic cancer risk by conducting a pooled analysis of nine population-based prospective cohort studies in Japan with more than 340,000 subjects. Summary hazard ratios (HRs) were estimated by pooling study-specific HRs for unified BMI categories with a random-effects model. Among Japanese men, being obese at baseline was associated with a higher risk of pancreatic cancer incidence (≥30 kg/m 2 compared with 23 to <25 kg/m 2 , adjusted HR 1.71; 95% confidence interval [CI], 1.03-2.86). A J-shaped association between BMI during early adulthood and pancreatic cancer incidence was seen in men. In contrast, we observed no clear association among women, although there may be a positive linear association between BMI at baseline and the risk of pancreatic cancer (per 1 kg/m 2 , adjusted HR 1.02; 95% CI, 1.00-1.05). Pooling of data from cohort studies with a considerable number of Japanese subjects revealed a significant positive association between obesity and pancreatic cancer risk among men. This information indicates that strategies that effectively prevent obesity among men might lead to a reduced burden of pancreatic cancer, especially in Asian populations.

  12. Measuring limitations in activities of daily living: a population-based validation of a short questionnaire.

    PubMed

    Elfering, Achim; Cronenberg, Sonja; Grebner, Simone; Tamcan, Oezguer; Müller, Urs

    2017-12-01

    A newly developed questionnaire assessing limitations in activity of daily living (LADL-Q) that should improve assessment of LADL is tested in a large population-based validation study. This survey was paper-based. Overall, 16,634 individuals who were representative of the working population in the German-speaking part of Switzerland participated in the study. Item analysis was used the final version of the LADL-Q to four items per subscale that correspond to potential problems in three body regions (back and neck, upper extremities, lower extremities). Analysis included tests for reliability, internal consistency, dimensionality and convergent validity. Test-retest reliability coefficients after 2 weeks ranged from 0.82 to 0.99 (Mdn = 0.87), with no item having a coefficient below 0.60. The median item-total coefficients ranged between moderate and good. Correlation coefficients between LADL-Q subscales and three validated clinical instruments (Western Ontario and McMaster Universities osteoarthritis index, shoulder pain disability index, Oswestry) ranged from 0.63 to 0.81. In structural equation modeling the three subscales were significantly related with two important outcomes in occupational rehabilitation: self-reported general health and daily task performance. The new LADL-Q is a brief, reliable and valid tool for assessment of LADL in studies on musculoskeletal health.

  13. 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.

  14. Minor Self-Harm and Psychiatric Disorder: A Population-Based Study

    ERIC Educational Resources Information Center

    Skegg, Keren; Nada-Raja, Shyamala; Moffit, Terrie E.

    2004-01-01

    Little is known about the extent to which minor self-harm in the general population is associated with psychiatric disorder. A population-based sample of 980 young adults was interviewed independently about past-year suicidal and self-harm behavior and thoughts, and psychiatric disorders. Self-harm included self-harmful behaviors such as…

  15. Demixed principal component analysis of neural population data.

    PubMed

    Kobak, Dmitry; Brendel, Wieland; Constantinidis, Christos; Feierstein, Claudia E; Kepecs, Adam; Mainen, Zachary F; Qi, Xue-Lian; Romo, Ranulfo; Uchida, Naoshige; Machens, Christian K

    2016-04-12

    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.

  16. Demixed principal component analysis of neural population data

    PubMed Central

    Kobak, Dmitry; Brendel, Wieland; Constantinidis, Christos; Feierstein, Claudia E; Kepecs, Adam; Mainen, Zachary F; Qi, Xue-Lian; Romo, Ranulfo; Uchida, Naoshige; Machens, Christian K

    2016-01-01

    Neurons in higher cortical areas, such as the prefrontal cortex, are often tuned to a variety of sensory and motor variables, and are therefore said to display mixed selectivity. This complexity of single neuron responses can obscure what information these areas represent and how it is represented. Here we demonstrate the advantages of a new dimensionality reduction technique, demixed principal component analysis (dPCA), that decomposes population activity into a few components. In addition to systematically capturing the majority of the variance of the data, dPCA also exposes the dependence of the neural representation on task parameters such as stimuli, decisions, or rewards. To illustrate our method we reanalyze population data from four datasets comprising different species, different cortical areas and different experimental tasks. In each case, dPCA provides a concise way of visualizing the data that summarizes the task-dependent features of the population response in a single figure. DOI: http://dx.doi.org/10.7554/eLife.10989.001 PMID:27067378

  17. Effect of registration on corpus callosum population differences found with DBM analysis

    NASA Astrophysics Data System (ADS)

    Han, Zhaoying; Thornton-Wells, Tricia A.; Gore, John C.; Dawant, Benoit M.

    2011-03-01

    Deformation Based Morphometry (DBM) is a relatively new method used for characterizing anatomical differences among populations. DBM is based on the analysis of the deformation fields generated by non-rigid registration algorithms, which warp the individual volumes to one standard coordinate system. Although several studies have compared non-rigid registration algorithms for segmentation tasks, few studies have compared the effect of the registration algorithm on population differences that may be uncovered through DBM. In this study, we compared DBM results obtained with five well established non-rigid registration algorithms on the corpus callosum (CC) in thirteen subjects with Williams Syndrome (WS) and thirteen Normal Control (NC) subjects. The five non-rigid registration algorithms include: (1) The Adaptive Basis Algorithm (ABA); (2) Image Registration Toolkit (IRTK); (3) FSL Nonlinear Image Registration Tool (FSL); (4) Automatic Registration Tools (ART); and (5) the normalization algorithm available in SPM8. For each algorithm, the 3D deformation fields from all subjects to the atlas were obtained and used to calculate the Jacobian determinant (JAC) at each voxel in the mid-sagittal slice of the CC. The mean JAC maps for each group were compared quantitatively across different nonrigid registration algorithms. An ANOVA test performed on the means of the JAC over the Genu and the Splenium ROIs shows the JAC differences between nonrigid registration algorithms are statistically significant over the Genu for both groups and over the Splenium for the NC group. These results suggest that it is important to consider the effect of registration when using DBM to compute morphological differences in populations.

  18. Epidemiology of uveitis among the Chinese population in Taiwan: a population-based study.

    PubMed

    Hwang, De-Kuang; Chou, Yiing-Jeng; Pu, Cheng-Yun; Chou, Pesus

    2012-11-01

    This study aimed to investigate the incidence and prevalence of uveitis in Taiwan, and then analyzed the risk factors related to uveitis using multivariate regression. Population-based cohort study using medical claims data. We randomly selected 1 000 000 residents from the Taiwan National Health Insurance Research Database. All participants with correct registry data (96%) were included in the study. The study period was from 2000 to 2008. All types of uveitis were identified using the International Classification of Diseases, 9th revision, Clinical Modification diagnostic codes. The annual incidence and cumulative prevalence of uveitis were calculated. A univariate and a multivariate Poisson regression were used to determine the risk factors associated with uveitis. The first diagnosis of uveitis noted during the study period. The annual cumulative incidence rate of uveitis ranged from 102.2 to 122.0 cases per 100 000 persons over the study period, and the average incidence density was 111.3 cases per 100 000 person-years (95% confidence interval, 108.4-114.1). The cumulative prevalence was found to have increased from 318.8 cases per 100 000 persons in 2003 to 622.7 cases per 100 000 persons in 2008. Anterior uveitis was the most common location and accounted for 77.7% of all incident cases, which was followed by panuveitis, posterior uveitis, and intermediate uveitis. Multivariate regression analysis showed that males, the elderly, and individuals who lived in an urban area had higher incidence rates for uveitis. The epidemiology of uveitis in Taiwan differs from most previous studies in other countries. The incidence of uveitis in Taiwan has increased significantly recently. The elderly and individuals living in urban areas are the populations that are most commonly affected by uveitis. These findings are consistent with suggestions found in several recent studies. Copyright © 2012 American Academy of Ophthalmology. Published by Elsevier Inc. All rights

  19. 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.

  20. Development of a paediatric population-based model of the pharmacokinetics of rivaroxaban.

    PubMed

    Willmann, Stefan; Becker, Corina; Burghaus, Rolf; Coboeken, Katrin; Edginton, Andrea; Lippert, Jörg; Siegmund, Hans-Ulrich; Thelen, Kirstin; Mück, Wolfgang

    2014-01-01

    , pharmacokinetic values in infants and preschool children (body weight <40 kg) were lower than the 90 % confidence interval threshold of the adult reference model and, therefore, indicated that doses in these groups may need to be increased to achieve the same plasma levels as in adults. For children with body weight between 40 and 70 kg, simulated plasma pharmacokinetic parameters (C max, C 24h and AUC) overlapped with the values obtained in the corresponding adult reference simulation, indicating that body weight-related exposure was similar between these children and adults. In adolescents of >70 kg body weight, the simulated 90 % prediction interval values of AUC and C 24h were much higher than the 90 % confidence interval of the adult reference population, owing to the weight-based simulation approach, but for these patients rivaroxaban would be administered at adult fixed doses of 10 and 20 mg. The paediatric PBPK model developed here allowed an exploratory analysis of the pharmacokinetics of rivaroxaban in children to inform the dosing regimen for a clinical study in paediatric patients.

  1. Health IT-assisted population-based preventive cancer screening: a cost analysis.

    PubMed

    Levy, Douglas E; Munshi, Vidit N; Ashburner, Jeffrey M; Zai, Adrian H; Grant, Richard W; Atlas, Steven J

    2015-12-01

    Novel health information technology (IT)-based strategies harnessing patient registry data seek to improve care at a population level. We analyzed costs from a randomized trial of 2 health IT strategies to improve cancer screening compared with usual care from the perspective of a primary care network. Monte Carlo simulations were used to compare costs across management strategies. We assessed the cost of the software, materials, and personnel for baseline usual care (BUC) compared with augmented usual care (AUC [ie, automated patient outreach]) and augmented usual care with physician input (AUCPI [ie, outreach mediated by physicians' knowledge of their patient panels]) over 1 year. AUC and AUCPI each reduced the time physicians spent on cancer screening by 6.5 minutes per half-day clinical session compared with BUC without changing cancer screening rates. Assuming the value of this time accrues to the network, total costs of cancer screening efforts over the study year were $3.83 million for AUC, $3.88 million for AUCPI, and $4.10 million for BUC. AUC was cost-saving relative to BUC in 87.1% of simulations. AUCPI was cost-saving relative to BUC in 82.5% of simulations. Ongoing per patient costs were lower for both AUC ($35.63) and AUCPI ($35.58) relative to BUC ($39.51). Over the course of the study year, the value of reduced physician time devoted to preventive cancer screening outweighed the costs of the interventions. Primary care networks considering similar interventions will need to capture adequate physician time savings to offset the costs of expanding IT infrastructure.

  2. Whether the Autism Spectrum Quotient Consists of Two Different Subgroups? Cluster Analysis of the Autism Spectrum Quotient in General Population

    ERIC Educational Resources Information Center

    Kitazoe, Noriko; Fujita, Naofumi; Izumoto, Yuji; Terada, Shin-ichi; Hatakenaka, Yuhei

    2017-01-01

    The purpose of this study was to investigate whether the individuals in the general population with high scores on the Autism Spectrum Quotient constituted a single homogeneous group or not. A cohort of university students (n = 4901) was investigated by cluster analysis based on the original five subscales of the Autism Spectrum Quotient. Based on…

  3. 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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2016-08-01

    We compared the clinical efficacy of fluconazole and echinocandins in the treatment of candidemia in real practice. The CANDIPOP study is a prospective, population-based cohort study on candidemia carried out between May 2010 and April 2011 in 29 Spanish hospitals. Using strict inclusion criteria, we separately compared the impact of empirical and targeted therapy with fluconazole or echinocandins on 30-day mortality. Cox regression, including a propensity score (PS) for receiving echinocandins, stratified analysis on the PS quartiles and PS-based matched analyses, were performed. The empirical and targeted therapy cohorts comprised 316 and 421 cases, respectively; 30-day mortality was 18.7% with fluconazole and 33.9% with echinocandins (p 0.02) in the empirical therapy group and 19.8% with fluconazole and 27.7% with echinocandins (p 0.06) in the targeted therapy group. Multivariate Cox regression analysis including PS showed that empirical therapy with fluconazole was associated with better prognosis (adjusted hazard ratio 0.38; 95% confidence interval 0.17-0.81; p 0.01); no differences were found within each PS quartile or in cases matched according to PS. Targeted therapy with fluconazole did not show a significant association with mortality in the Cox regression analysis (adjusted hazard ratio 0.77; 95% confidence interval 0.41-1.46; p 0.63), in the PS quartiles or in PS-matched cases. The results were similar among patients with severe sepsis and septic shock. Empirical or targeted treatment with fluconazole was not associated with increased 30-day mortality compared to echinocandins among adults with candidemia. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  6. Population Viability Analysis of the Endangered Roan Antelope in Ruma National Park, Kenya, and Implications for Management

    PubMed Central

    2018-01-01

    Population viability analysis (PVA) was used to (1) establish causes of roan population decline for the past 30 years in Ruma National Park (RNP), the only park where wild roans remain in Kenya, and (2) predict the probability of roan persistence under existing and alternative management options. PVA was done using long-term data based on population dynamics, life history, climatic conditions, and expert knowledge. Poaching was identified as the main cause of roan decline in RNP. Several antipoaching and prioritized habitat management interventions to promote population recovery and sustainable conservation of roans are described. PVA predictions indicated that, without these interventions, the roan population cannot persist more than 3 decades. Furthermore, ensuring sustainable conservation of roans in RNP will boost tourism in Western Kenyan and thus alleviate poverty in this part of the country. Improved income from tourism will reduce the possible pressures from hunting and give greater incentives for local people to be actively engaged in roan conservation. PMID:29643756

  7. Population Viability Analysis of the Endangered Roan Antelope in Ruma National Park, Kenya, and Implications for Management.

    PubMed

    Kimanzi, Johnstone K

    2018-01-01

    Population viability analysis (PVA) was used to (1) establish causes of roan population decline for the past 30 years in Ruma National Park (RNP), the only park where wild roans remain in Kenya, and (2) predict the probability of roan persistence under existing and alternative management options. PVA was done using long-term data based on population dynamics, life history, climatic conditions, and expert knowledge. Poaching was identified as the main cause of roan decline in RNP. Several antipoaching and prioritized habitat management interventions to promote population recovery and sustainable conservation of roans are described. PVA predictions indicated that, without these interventions, the roan population cannot persist more than 3 decades. Furthermore, ensuring sustainable conservation of roans in RNP will boost tourism in Western Kenyan and thus alleviate poverty in this part of the country. Improved income from tourism will reduce the possible pressures from hunting and give greater incentives for local people to be actively engaged in roan conservation.

  8. Advancing Community–Based Research with Urban American Indian Populations: Multidisciplinary Perspectives

    PubMed Central

    Hartmann, William E.; Wendt, Dennis C.; Saftner, Melissa A.; Marcus, John; Momper, Sandra L.

    2014-01-01

    The U.S. has witnessed significant growth among urban AI populations in recent decades, and concerns have been raised that these populations face equal or greater degrees of disadvantage than their reservation counterparts. Surprisingly little urban AI research or community work has been documented in the literature, and even less has been written about the influences of urban settings on community-based work with these populations. Given the deep commitments of community psychology to empowering disadvantaged groups and understanding the impact of contextual factors on the lives of individuals and groups, community psychologists are well suited to fill these gaps in the literature. Toward informing such efforts, this work offers multidisciplinary insights from distinct idiographic accounts of community-based behavioral health research with urban AI populations. Accounts are offered by three researchers and one urban AI community organization staff member, and particular attention is given to issues of community heterogeneity, geography, membership, and collaboration. Each first-person account provides “lessons learned” from the urban context in which the research occurred. Together, these accounts suggest several important areas of consideration in research with urban AIs, some of which also seem relevant to reservation-based work. Finally, the potential role of research as a tool of empowerment for urban AI populations is emphasized, suggesting future research attend to the intersections of identity, sense of community, and empowerment in urban AI populations. PMID:24659391

  9. A population-based analysis of healthcare utilization of persons with back disorders: results from the Canadian Community Health Survey 2000-2001.

    PubMed

    Lim, Kim-Lian; Jacobs, Philip; Klarenbach, Scott

    2006-01-15

    A retrospective, population-based analysis. To analyze the utilization of a variety of healthcare services for persons with and without a chronic back disorder, and to identify factors associated with specific patterns of healthcare resource use. Although there have been studies of how chronic back disorders influence the use of specific healthcare services, we do not currently have a broad, population-based overview of how this condition influences healthcare service utilization. Person-level data were taken from the 2000-2001 Canadian Community Health Survey (CCHS), a nationwide cross-sectional survey of health determinants, health status, and health system utilization of Canadians. A series of binary logistic regressions examining healthcare resource utilization were performed on a full study sample (n = 113,229), as well as a restricted sample (n = 36,713) with attention focused on subjects with a single diagnosis of a chronic back disorder. Persons with chronic back disorders were more likely to use physician resources (multivariate odds ratio [OR] = 1.2; 95% confidence interval, 1.1-1.2), and nonphysician resources (OR range, 2.1-3.6) compared with persons without the condition, with chiropractic care having an odds ratio of 3.6 (95% confidence interval, 3.5-3.8). Higher socioeconomic status, the presence of activity-limiting pain, and depressive symptoms were associated with a significant increase in utilization of almost all healthcare services. With increasing disability as indicated by the presence of pain and functional limitations, and the presence of depressive symptoms, the higher the utilization of physician and nonphysician resources, with the exception of chiropractic care, which appears to be used by those with less severe symptoms. Lower socioeconomic status was associated with significantly lower receipt of services for almost all healthcare providers.

  10. Attitudes toward schizophrenia in the general population, psychiatric staff, physicians, and psychiatrists: a web-based survey in Japan.

    PubMed

    Hori, Hiroaki; Richards, Misty; Kawamoto, Yumiko; Kunugi, Hiroshi

    2011-04-30

    Little is known about possible differences in the attitudes toward schizophrenia between the general public and various healthcare professionals. After screening for the study enrollment, 197 subjects in the general population, 100 psychiatric staff (other than psychiatrists), 112 physicians (other than psychiatrists) and 36 psychiatrists were enrolled in a web-based survey using an Internet-based questionnaire format. To assess subjects' attitudes toward schizophrenia, we used a 13-item questionnaire created by Uçok et al. (2006), to which five items were added. These 18 items were subjected to exploratory factor analysis, which yielded three factors classified as "stigma," "underestimation of patients' abilities," and "skepticism regarding treatment." These factors were compared between the four groups using analysis of covariance (ANCOVA), controlling for potential confounders. The ANCOVA for the "stigma" factor showed that psychiatrists scored significantly lower than the other three groups. The ANCOVA for the "underestimation of patients' abilities" factor revealed that psychiatric staff scored significantly lower than the general population. The present results indicated that attitudes toward schizophrenia consist of at least three separable factors. Psychiatrists had the least negative attitudes toward schizophrenia, which was followed by the psychiatric staff, and attitudes of the general population and of physicians were equally stigmatizing. Copyright © 2010 Elsevier Ltd. All rights reserved.

  11. Chromosome 9p21 In Ischemic Stroke: Population Structure and Meta-Analysis

    PubMed Central

    Anderson, CD; Biffi, A; Rost, NS; Cortellini, L; Furie, KL; Rosand, J

    2011-01-01

    Background and Purpose Sequence variants on chromosome 9p21.3 are implicated in coronary artery disease (CAD) and myocardial infarction (MI), but studies in ischemic stroke have produced inconsistent results. We investigated whether these conflicting findings were due to false positive studies confounded by population stratification, or false negative studies that failed to account for effects specific to certain stroke subtypes. Methods After assessing for population stratification at 9p21.3 using genome-wide data, we meta-analyzed 8 ischemic stroke studies. This analysis focused on two single nucleotide polymorphisms (SNPs), rs1537378 and rs10757278, as these variants are in strong linkage disequilibrium with most SNPs analyzed in prior studies of the region. Results Principal component analysis of the genome-wide data showed no evidence of population stratification at that locus. Meta-analysis confirmed that both rs1537378 and rs10757278 are risk factors for ischemic stroke (odds ratios 1.09, [p = 0.0014], and 1.11, [p = 0.001] respectively). Subtype analysis revealed a substantial increase in the effect of each SNP for risk of large artery (LA) stroke, achieving an effect size similar to that seen in CAD/MI. Conclusions Variants on 9p21.3 are associated with ischemic stroke, and restriction of analysis to LA stroke increases effect size towards that observed in prior association studies of CAD/MI. Previous inconsistent findings are best explained by this subtype-specificity rather than any unmeasured confounding by population stratification. PMID:20395606

  12. Development and validation of a new population-based simulation model of osteoarthritis in New Zealand.

    PubMed

    Wilson, R; Abbott, J H

    2018-04-01

    To describe the construction and preliminary validation of a new population-based microsimulation model developed to analyse the health and economic burden and cost-effectiveness of treatments for knee osteoarthritis (OA) in New Zealand (NZ). We developed the New Zealand Management of Osteoarthritis (NZ-MOA) model, a discrete-time state-transition microsimulation model of the natural history of radiographic knee OA. In this article, we report on the model structure, derivation of input data, validation of baseline model parameters against external data sources, and validation of model outputs by comparison of the predicted population health loss with previous estimates. The NZ-MOA model simulates both the structural progression of radiographic knee OA and the stochastic development of multiple disease symptoms. Input parameters were sourced from NZ population-based data where possible, and from international sources where NZ-specific data were not available. The predicted distributions of structural OA severity and health utility detriments associated with OA were externally validated against other sources of evidence, and uncertainty resulting from key input parameters was quantified. The resulting lifetime and current population health-loss burden was consistent with estimates of previous studies. The new NZ-MOA model provides reliable estimates of the health loss associated with knee OA in the NZ population. The model structure is suitable for analysis of the effects of a range of potential treatments, and will be used in future work to evaluate the cost-effectiveness of recommended interventions within the NZ healthcare system. Copyright © 2018 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

  13. The association of hyperglycaemia with prevalent tuberculosis: a population-based cross-sectional study.

    PubMed

    Bailey, Sarah Lou; Ayles, Helen; Beyers, Nulda; Godfrey-Faussett, Peter; Muyoyeta, Monde; du Toit, Elizabeth; Yudkin, John S; Floyd, Sian

    2016-12-05

    Systematic reviews suggest that the incidence of diagnosed tuberculosis is two- to- three times higher in those with diabetes mellitus than in those without. Few studies have previously reported the association between diabetes or hyperglycaemia and the prevalence of active tuberculosis and none in a population-based study with microbiologically-defined tuberculosis. Most have instead concentrated on cases of diagnosed tuberculosis that present to health facilities. We had the opportunity to measure glycaemia alongside prevalent tuberculosis. A focus on prevalent tuberculosis enables estimation of the contribution of hyperglycaemia to the population prevalence of tuberculosis. A population-based cross-sectional study was conducted among adults in 24 communities from Zambia and the Western Cape (WC) province of South Africa. Prevalent tuberculosis was defined by the presence of a respiratory sample that was culture positive for M. tuberculosis. Glycaemia was measured by random blood glucose (RBG) concentration. Association with prevalent tuberculosis was explored across the whole spectrum of glycaemia. Among 27,800 Zambian and 11,367 Western Cape participants, 4,431 (15.9%) and 1,835 (16.1%) respectively had a RBG concentration ≥7.0 mmol/L, and 405 (1.5%) and 322 (2.8%) respectively had a RBG concentration ≥11.1 mmol/L. In Zambia, the prevalence of tuberculosis was 0 · 5% (142/27,395) among individuals with RBG concentration <11.1 mmol/L and also ≥11.1 mmol/L (2/405); corresponding figures for WC were 2 · 5% (272/11,045) and 4 · 0% (13/322). There was evidence for a positive linear association between hyperglycaemia and pulmonary prevalent tuberculosis. Taking a RBG cut-off 11.1 mmol/L, a combined analysis of data from Zambian and WC communities found evidence of association between hyperglycaemia and TB (adjusted odds ratio = 2 · 15, 95% CI [1 · 17-3 · 94]). The population attributable fraction of prevalent tuberculosis

  14. Epidemiology of upper urinary tract stone disease in a Taiwanese population: a nationwide, population based study.

    PubMed

    Huang, Wei-Yi; Chen, Yu-Fen; Carter, Stacey; Chang, Hong-Chiang; Lan, Chung-Fu; Huang, Kuo-How

    2013-06-01

    We investigated the epidemiology of upper urinary tract stone disease in Taiwan using a nationwide, population based database. This study was based on the National Health Insurance Research Database of Taiwan, which contains data on all medical beneficiary claims from 22.72 million enrollees, accounting for almost 99% of the Taiwanese population. The Longitudinal Health Insurance Database 2005, a subset of the National Health Insurance Research Database, contains data on all medical benefit claims from 1997 through 2010 for a subset of 1 million beneficiaries randomly sampled from the 2005 enrollment file. For epidemiological analysis we selected subjects whose claims records included the diagnosis of upper urinary tract urolithiasis. The age adjusted rate of medical care visits for upper urinary tract urolithiasis decreased by 6.5% from 1,367/100,000 subjects in 1998 to 1,278/100,000 in 2010. There was a significantly decreasing trend during the 13-year period in visits from female and all subjects (r(2) = 0.86, p = 0.001 and r(2) = 0.52, p = 0.005, respectively). In contrast, an increasing trend was noted for male subjects (r(2) = 0.45, p = 0.012). The age adjusted prevalence in 2010 was 9.01%, 5.79% and 7.38% in male, female and all subjects, respectively. The overall recurrence rate at 1 and 5 years was 6.12% and 34.71%, respectively. Male subjects had a higher recurrence rate than female subjects. Our study provides important information on the epidemiology of upper urinary tract stone disease in Taiwan, helping to quantify the burden of urolithiasis and establish strategies to decrease the risk of urolithiasis. Copyright © 2013 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  15. Population Genomic Analysis Reveals a Rich Speciation and Demographic History of Orang-utans (Pongo pygmaeus and Pongo abelii)

    PubMed Central

    Ma, Xin; Kelley, Joanna L.; Eilertson, Kirsten; Musharoff, Shaila; Degenhardt, Jeremiah D.; Martins, André L.; Vinar, Tomas; Kosiol, Carolin; Siepel, Adam; Gutenkunst, Ryan N.; Bustamante, Carlos D.

    2013-01-01

    To gain insights into evolutionary forces that have shaped the history of Bornean and Sumatran populations of orang-utans, we compare patterns of variation across more than 11 million single nucleotide polymorphisms found by previous mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our analysis of the mitochondrial data yields a far more ancient split time between the two populations (∼3.4 million years ago) than estimates based on autosomal data (0.4 million years ago), suggesting a complex speciation process with moderate levels of primarily male migration. We find that the distribution of selection coefficients consistent with the observed frequency spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to the distribution in humans. Our analysis indicates that 35% of genes have evolved under detectable negative selection. Overall, our findings suggest that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations. PMID:24194868

  16. Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii).

    PubMed

    Ma, Xin; Kelley, Joanna L; Eilertson, Kirsten; Musharoff, Shaila; Degenhardt, Jeremiah D; Martins, André L; Vinar, Tomas; Kosiol, Carolin; Siepel, Adam; Gutenkunst, Ryan N; Bustamante, Carlos D

    2013-01-01

    To gain insights into evolutionary forces that have shaped the history of Bornean and Sumatran populations of orang-utans, we compare patterns of variation across more than 11 million single nucleotide polymorphisms found by previous mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our analysis of the mitochondrial data yields a far more ancient split time between the two populations (~3.4 million years ago) than estimates based on autosomal data (0.4 million years ago), suggesting a complex speciation process with moderate levels of primarily male migration. We find that the distribution of selection coefficients consistent with the observed frequency spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to the distribution in humans. Our analysis indicates that 35% of genes have evolved under detectable negative selection. Overall, our findings suggest that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations.

  17. Consequences of population topology for studying gene flow using link-based landscape genetic methods.

    PubMed

    van Strien, Maarten J

    2017-07-01

    Many landscape genetic studies aim to determine the effect of landscape on gene flow between populations. These studies frequently employ link-based methods that relate pairwise measures of historical gene flow to measures of the landscape and the geographical distance between populations. However, apart from landscape and distance, there is a third important factor that can influence historical gene flow, that is, population topology (i.e., the arrangement of populations throughout a landscape). As the population topology is determined in part by the landscape configuration, I argue that it should play a more prominent role in landscape genetics. Making use of existing literature and theoretical examples, I discuss how population topology can influence results in landscape genetic studies and how it can be taken into account to improve the accuracy of these results. In support of my arguments, I have performed a literature review of landscape genetic studies published during the first half of 2015 as well as several computer simulations of gene flow between populations. First, I argue why one should carefully consider which population pairs should be included in link-based analyses. Second, I discuss several ways in which the population topology can be incorporated in response and explanatory variables. Third, I outline why it is important to sample populations in such a way that a good representation of the population topology is obtained. Fourth, I discuss how statistical testing for link-based approaches could be influenced by the population topology. I conclude the article with six recommendations geared toward better incorporating population topology in link-based landscape genetic studies.

  18. Anal sex practices in heterosexual and male homosexual populations: a review of population-based data.

    PubMed

    Heywood, Wendy; Smith, Anthony M A

    2012-12-01

    Anal sex is known to be an important risk factor for anal cancer. Yet compared with vaginal intercourse, little is known about anal sex practices in either heterosexual or male homosexual populations. Of the data that are available, it appears a significant and increasing minority of heterosexuals have ever practised anal intercourse. Among homosexual men, most, but not all, report anal sex, with large proportions of men engaging in both insertive and receptive anal intercourse. The most significant finding of the review was the dearth of population-based data, particularly relating to homosexual men.

  19. Combined analysis of roadside and off-road breeding bird survey data to assess population change in Alaska

    USGS Publications Warehouse

    Handel, Colleen M.; Sauer, John

    2017-01-01

    Management interest in North American birds has increasingly focused on species that breed in Alaska, USA, and Canada, where habitats are changing rapidly in response to climatic and anthropogenic factors. We used a series of hierarchical models to estimate rates of population change in 2 forested Bird Conservation Regions (BCRs) in Alaska based on data from the roadside North American Breeding Bird Survey (BBS) and the Alaska Landbird Monitoring Survey, which samples off-road areas on public resource lands. We estimated long-term (1993–2015) population trends for 84 bird species from the BBS and short-term (2003–2015) trends for 31 species from both surveys. Among the 84 species with long-term estimates, 11 had positive trends and 17 had negative trends in 1 or both BCRs; negative trends were primarily found among aerial insectivores and wetland-associated species, confirming range-wide negative continental trends for many of these birds. Three species with negative trends in the contiguous United States and southern Canada had positive trends in Alaska, suggesting different population dynamics at the northern edges of their ranges. Regional population trends within Alaska differed for several species, particularly those represented by different subspecies in the 2 BCRs, which are separated by rugged, glaciated mountain ranges. Analysis of the roadside and off-road data in a joint hierarchical model with shared parameters resulted in improved precision of trend estimates and suggested a roadside-related difference in underlying population trends for several species, particularly within the Northwestern Interior Forest BCR. The combined analysis highlights the importance of considering population structure, physiographic barriers, and spatial heterogeneity in habitat change when assessing patterns of population change across a landscape as broad as Alaska. Combined analysis of roadside and off-road survey data in a hierarchical framework may be particularly

  20. Population-based medical and disease management: an evaluation of cost and quality.

    PubMed

    Wise, Christopher G; Bahl, Vinita; Mitchell, Rita; West, Brady T; Carli, Thomas

    2006-02-01

    Reports by the Institute of Medicine and the Health Care Financing Administration have emphasized that the integration of medical care delivery, evidence-based medicine, and chronic care disease management may play a significant role in improving the quality of care and reducing medical care costs. The specific aim of this project is to assess the impact of an integrated set of care coordination tools and chronic disease management interventions on utilization, cost, and quality of care for a population of beneficiaries who have complementary health coverage through a plan designed to apply proactive medical and disease management processes. The utilization of health care services by the study population was compared to another population from the same geographic service area and covered by a traditional fee-for-service indemnity insurance plan that provided few medical or disease management services. Evaluation of the difference in utilization was based on the difference in the cost per-member-per-month (PMPM) in a 1-year measurement period, after adjusting for differences in fee schedules, case-mix and healthcare benefit design. After adjustments for both case-mix and benefit differences, the study group is $63 PMPM less costly than the comparison population for all members. Cost differences are largest in the 55-64 and 65 and above age groups. The study group is $115 PMPM lower than the comparison population for the age category of 65 years and older, after adjustments for case-mix and benefits. Health Plan Employer and Data Information Set (HEDIS)-based quality outcomes are near the 90th percentile for most indications. The cost outcomes of a population served by proactive, population-based disease management and complex care management, compared to an unmanaged population, demonstrates the potential of coordinated medical and disease management programs. Further studies utilizing appropriate methodologies would be beneficial.

  1. [Sunburn in young people: population-based study in Southern Brazil].

    PubMed

    Haack, Ricardo Lanzetta; Horta, Bernardo Lessa; Cesar, Juraci Almeida

    2008-02-01

    To assess the prevalence and risk factors for sunburn in young people. Population-based cross-sectional study using a multiple-stage sampling carried out with people living in the urban area of Pelotas, Southern Brazil, between October and December 2005. Data was collected from interviews with 1.604 subjects using a standardized pre-coded questionnaire about their family and another questionnaire applied to those aged between ten and 29 years for assessing the occurrence of sunburn episodes. Sunburn was defined as skin burning after sun exposure. Chi-square test with Yates' correction was used to compare proportions and Poisson regression with design effect control and robust adjustment of variance was applied in the multivariate analysis. Of those aged between 10 and 29 years, 1,412 reported sun exposure in the last summer. Losses and refusals were 5.5%. A total of 48.7% of the interviewees reported sunburn in the last year. The following variables were associated with sunburn in the multivariate analysis: white skin (PR=1.41; 95% CI: 1.12;1.79); higher skin sensitivity to sun exposure (PR=1.84; 95% CI: 1.64;2.06); age between 15 and 19 years (PR=1.30; 95% CI: 1.12;1.50); belonging to the higher quartile of income (PR=1.20; 95% CI: 1.01;1.42); and irregular use of sunscreens (PR=1.23; 95% CI: 1.08;1.42). The prevalence of sunburn in the population studied was high mainly among white young people with higher skin sensitivity, higher income and who used sunscreens irregularly. Sun exposure during safe times and with adequate protection should be promoted.

  2. Design of PREVENCION: a population-based study of cardiovascular disease in Peru.

    PubMed

    Medina-Lezama, Josefina; Chirinos, Julio A; Zea Díaz, Humberto; Morey, Oscar; Bolanos, Juan F; Munoz-Atahualpa, Edgar; Chirinos-Pacheco, Julio

    2005-11-02

    Latin America is undergoing the epidemiologic transition that occurred earlier in developed countries, and is likely to face a gigantic epidemic of heart disease in the next few years unless urgent action is taken. The first essential component of any effective cardiovascular disease (CVD) control program is to establish reliable estimates of cardiovascular disease-related morbidity and mortality. However, such data from population-based studies in Latin America are still lacking. In this paper, we present the design and operation of PREVENCION (Estudio Peruano de Prevalencia de Enfermedades Cardiovasculares, for Peruvian Study of the Prevalence of Cardiovascular diseases). PREVENCION is an ongoing population-based study on a representative sample of the civilian non-institutionalized population of the second largest city in Peru. Its population is comparable to the rest of the Peruvian urban population and closely resembles other Latin American populations in countries such as Bolivia and Ecuador. Our study will contribute to the enormous task of understanding and preventing CVD in Latin America.

  3. Directions for new developments on statistical design and analysis of small population group trials.

    PubMed

    Hilgers, Ralf-Dieter; Roes, Kit; Stallard, Nigel

    2016-06-14

    Most statistical design and analysis methods for clinical trials have been developed and evaluated where at least several hundreds of patients could be recruited. These methods may not be suitable to evaluate therapies if the sample size is unavoidably small, which is usually termed by small populations. The specific sample size cut off, where the standard methods fail, needs to be investigated. In this paper, the authors present their view on new developments for design and analysis of clinical trials in small population groups, where conventional statistical methods may be inappropriate, e.g., because of lack of power or poor adherence to asymptotic approximations due to sample size restrictions. Following the EMA/CHMP guideline on clinical trials in small populations, we consider directions for new developments in the area of statistical methodology for design and analysis of small population clinical trials. We relate the findings to the research activities of three projects, Asterix, IDeAl, and InSPiRe, which have received funding since 2013 within the FP7-HEALTH-2013-INNOVATION-1 framework of the EU. As not all aspects of the wide research area of small population clinical trials can be addressed, we focus on areas where we feel advances are needed and feasible. The general framework of the EMA/CHMP guideline on small population clinical trials stimulates a number of research areas. These serve as the basis for the three projects, Asterix, IDeAl, and InSPiRe, which use various approaches to develop new statistical methodology for design and analysis of small population clinical trials. Small population clinical trials refer to trials with a limited number of patients. Small populations may result form rare diseases or specific subtypes of more common diseases. New statistical methodology needs to be tailored to these specific situations. The main results from the three projects will constitute a useful toolbox for improved design and analysis of small

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

    USDA-ARS?s Scientific Manuscript database

    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...

  5. Genetic polymorphisms, forensic efficiency and phylogenetic analysis of 15 autosomal STR loci in the Kazak population of Ili Kazak Autonomous Prefecture, northwestern China.

    PubMed

    Feng, Chunmei; Wang, Xin; Wang, Xiaolong; Yu, Hao; Zhang, Guohua

    2018-03-01

    We investigated the frequencies of 15 autosomal STR loci in the Kazak population of the Ili Kazak Autonomous Prefecture with the aim of expanding the available population information in human genetic databases and for forensic DNA analysis. Genetic polymorphisms of 15 autosomal short tandem repeat (STR) loci were analysed in 456 individuals of the Kazak population from Ili Kazakh Autonomous Prefecture, northwestern China. A total of 173 alleles at 15 autosomal STR loci were found; the allele frequencies ranged from 0.5022-0.0011. The combined power of discrimination and exclusion statistics for the 15 STR loci were 0.999 999 999 85 and 0.999 998 800 65, respectively. In addition, phylogenetic analysis involving the Ili Uygur population and other relevant populations was carried out. A neighbour-joining tree and multidimensional scaling plot were generated based on Nei's standard genetic distance. Results of the population comparison indicated that the Ili Uygur population was most closely related genetically to the Uygur populations from other regions in China. These findings are consistent with the historical and geographic backgrounds of these populations.

  6. Population genetic analysis and trichothecene profiling of Fusarium graminearum from wheat in Uruguay.

    PubMed

    Pan, D; Mionetto, A; Calero, N; Reynoso, M M; Torres, A; Bettucci, L

    2016-03-11

    Fusarium graminearum sensu stricto (F. graminearum s.s.) is the major causal agent of Fusarium head blight of wheat worldwide, and contaminates grains with trichothecene mycotoxins that cause serious threats to food safety and animal health. An important aspect of managing this pathogen and reducing mycotoxin contamination of wheat is knowledge regarding its population genetics. Therefore, isolates of F. graminearum s.s. from the major wheat-growing region of Uruguay were analyzed by amplified fragment length polymorphism assays, PCR genotyping, and chemical analysis of trichothecene production. Of the 102 isolates identified as having the 15-ADON genotype via PCR genotyping, all were DON producers, but only 41 strains were also 15-ADON producers, as determined by chemical analysis. The populations were genotypically diverse but genetically similar, with significant genetic exchange occurring between them. Analysis of molecular variance indicated that most of the genetic variability resulted from differences between isolates within populations. Multilocus linkage disequilibrium analysis suggested that the isolates had a panmictic population genetic structure and that there is significant recombination occurs in F. graminearum s.s. In conclusion, tour findings provide the first detailed description of the genetic structure and trichothecene production of populations of F. graminearum s.s. from Uruguay, and expands our understanding of the agroecology of F. graminearum and of the correlation between genotypes and trichothecene chemotypes.

  7. What is the most cost-effective population-based cancer screening program for Chinese women?

    PubMed

    Woo, Pauline P S; Kim, Jane J; Leung, Gabriel M

    2007-02-20

    To develop a policy-relevant generalized cost-effectiveness (CE) model of population-based cancer screening for Chinese women. Disability-adjusted life-years (DALYs) averted and associated screening and treatment costs under population-based screening using cervical cytology (cervical cancer), mammography (breast cancer), and fecal occult blood testing (FOBT), sigmoidoscopy, FOBT plus sigmoidoscopy, or colonoscopy (colorectal cancer) were estimated, from which average and incremental CE ratios were generated. Probabilistic sensitivity analysis was undertaken to assess stochasticity, parameter uncertainty, and model assumptions. Cervical, breast, and colorectal cancers were together responsible for 13,556 DALYs (in a 1:4:3 ratio, respectively) in Hong Kong's 3.4 million female population annually. All status quo strategies were dominated, thus confirming the suboptimal efficiency of opportunistic screening. Current patterns of screening averted 471 DALYs every year, which could potentially be more than doubled to 1,161 DALYs under the same screening and treatment budgetary threshold of US $50 million with 100% Pap coverage every 4 years and 30% coverage of colonoscopy every 10 years. With higher budgetary caps, biennial mammographic screening starting at age 50 years can be introduced. Our findings have informed how best to achieve allocative efficiency in deploying scarce cancer care dollars but must be coupled with better integrated care planning, improved intersectoral coordination, increased resources, and stronger political will to realize the potential health and economic gains as demonstrated.

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

    PubMed

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

    2016-08-01

    In June 2011 the BBC Lab UK carried out a web-based survey on the causes of mental distress. The 'Stress Test' was launched on 'All in the Mind' a BBC Radio 4 programme and the test's URL was publicised on radio and TV broadcasts, and made available via BBC web pages and social media. Given the large amount of data created, over 32,800 participants, with corresponding diagnosis, demographic and socioeconomic characteristics; the dataset are potentially an important source of data for population based research on depression and anxiety. However, as respondents self-selected to participate in the online survey, the survey may comprise a non-random sample. It may be only individuals that listen to BBC Radio 4 and/or use their website that participated in the survey. In this instance using the Stress Test data for wider population based research may create sample selection bias. Focusing on the depression component of the Stress Test, this paper presents an easy-to-use method, the Two Step Probit Selection Model, to detect and statistically correct selection bias in the Stress Test. Using a Two Step Probit Selection Model; this paper did not find a statistically significant selection on unobserved factors for participants of the Stress Test. That is, survey participants who accessed and completed an online survey are not systematically different from non-participants on the variables of substantive interest. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. The Contemporary Incidence and Sequelae of Rhabdomyolysis Following Extirpative Renal Surgery: A Population Based Analysis.

    PubMed

    Gelpi-Hammerschmidt, Francisco; Tinay, Ilker; Allard, Christopher B; Su, Li-Ming; Preston, Mark A; Trinh, Quoc-Dien; Kibel, Adam S; Wang, Ye; Chung, Benjamin I; Chang, Steven L

    2016-02-01

    We evaluate the contemporary incidence and consequences of postoperative rhabdomyolysis after extirpative renal surgery. We conducted a population based, retrospective cohort study of patients who underwent extirpative renal surgery with a diagnosis of a renal mass or renal cell carcinoma in the United States between 2004 and 2013. Regression analysis was performed to evaluate 90-day mortality (Clavien grade V), nonfatal major complications (Clavien grade III-IV), hospital readmission rates, direct costs and length of stay. The final weighted cohort included 310,880 open, 174,283 laparoscopic and 69,880 robotic extirpative renal surgery cases during the 10-year study period, with 745 (0.001%) experiencing postoperative rhabdomyolysis. The presence of postoperative rhabdomyolysis led to a significantly higher incidence of 90-day nonfatal major complications (34.7% vs 7.3%, p <0.05) and higher 90-day mortality (4.4% vs 1.02%, p <0.05). Length of stay was twice as long for patients with postoperative rhabdomyolysis (incidence risk ratio 1.83, 95% CI 1.56-2.15, p <0.001). The robotic approach was associated with a higher likelihood of postoperative rhabdomyolysis (vs laparoscopic approach, OR 2.43, p <0.05). Adjusted 90-day median direct hospital costs were USD 7,515 higher for patients with postoperative rhabdomyolysis (p <0.001). Our model revealed that the combination of obesity and prolonged surgery (more than 5 hours) was associated with a higher likelihood of postoperative rhabdomyolysis developing. Our study confirms that postoperative rhabdomyolysis is an uncommon complication among patients undergoing extirpative renal surgery, but has a potentially detrimental impact on surgical morbidity, mortality and costs. Male gender, comorbidities, obesity, prolonged surgery (more than 5 hours) and a robotic approach appear to place patients at higher risk for postoperative rhabdomyolysis. Copyright © 2016 American Urological Association Education and Research

  10. Risk of placenta previa in second birth after first birth cesarean section: a population-based study and meta-analysis

    PubMed Central

    2011-01-01

    Background Objective: To compare the risk of placenta previa at second birth among women who had a cesarean section (CS) at first birth with women who delivered vaginally. Methods Retrospective cohort study of 399,674 women who gave birth to a singleton first and second baby between April 2000 and February 2009 in England. Multiple logistic regression was used to adjust the estimates for maternal age, ethnicity, deprivation, placenta previa at first birth, inter-birth interval and pregnancy complications. In addition, we conducted a meta-analysis of the reported results in peer-reviewed articles since 1980. Results The rate of placenta previa at second birth for women with vaginal first births was 4.4 per 1000 births, compared to 8.7 per 1000 births for women with CS at first birth. After adjustment, CS at first birth remained associated with an increased risk of placenta previa (odds ratio = 1.60; 95% CI 1.44 to 1.76). In the meta-analysis of 37 previously published studies from 21 countries, the overall pooled random effects odds ratio was 2.20 (95% CI 1.96-2.46). Our results from the current study is consistent with those of the meta-analysis as the pooled odds ratio for the six population-based cohort studies that analyzed second births only was 1.51 (95% CI 1.39-1.65). Conclusions There is an increased risk of placenta previa in the subsequent pregnancy after CS delivery at first birth, but the risk is lower than previously estimated. Given the placenta previa rate in England and the adjusted effect of previous CS, 359 deliveries by CS at first birth would result in one additional case of placenta previa in the next pregnancy. PMID:22103697

  11. Postoperative radioactive iodine-131 ablation is not necessary among patients with intermediate-risk differentiated thyroid carcinoma: a population-based study.

    PubMed

    Zhang, Hong; Cai, Yuechang; Zheng, Li; Zhang, Zhanlei; Jiang, Ningyi

    2017-01-01

    To assess the effectiveness of radioactive iodine (RAI) ablation among patients with intermediate-risk differentiated thyroid cancer (DTC) following surgery. This population based study obtained information from the Surveillance, Epidemiology, and End Results (SEER) Program Research Data (1973-2013). National Cancer Institute, DCCPS, Surveillance Research Programme, Surveillance Systems Branch, released April 2016, based on the November 2015 submission. A total of 93,530 patients with primary thyroid cancer were identified in the SEER database during the period of 2004-2013 and focused on patients with DTC post-operatively treated or not treated with radioactive iodine (RAI). From these 9,127 patients were selected who had intermediate-risk DTC. A total of 8,601 patients were included in this study. For the overall population, the mean age of the population was 47.3 years and the majority were female (70.5%). Kaplan-Meier analysis found the mean overall survival time (os) for subjects with no radiation therapy which was 112.9 months and 114.9 months for those who received RAI ablation treatment (P<0.001). However, thyroid cancer-specific survival was not significantly different between treatment groups (117.7 vs. 118.0 months, log-rank test P=0.164). Overall survival and thyroid cancer-specific 1 year, 5 years, and 10-years survival rates were ≥89.8% and were similar between both treated groups. Multivariate analysis found age, gender, histologic type, and degree of lymph node metastases to be associated with OS, and age, gender, degree of lymph node metastasis and extra-thyroid tumor spread were independent factors for cancer-specific survival. In DTC patients with intermediate cancer risk multivariate analysis found that RAI was associated with a reduced risk of mortality compared with no radiation therapy (HR=0.710, 95% CI: 0.562-0.897, P=0.004) but no significant difference was seen in cancer-specific survival, either based on whole study population or on

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

    USDA-ARS?s Scientific Manuscript database

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

  13. Upper gastrointestinal cancer burden in Hebei Province, China: A population-based study.

    PubMed

    Li, Dao-Juan; Liang, Di; Song, Guo-Hui; Li, Yong-Wei; Wen, Deng-Gui; Jin, Jing; He, Yu-Tong

    2017-04-14

    To investigate the incidence and mortality rates of upper gastrointestinal cancer (UGIC) in Hebei Province, China, and to identify high-risk populations to improve UGIC prevention and control. Data for UGIC patients were collected from 21 population-based cancer registries covering 15.25% of the population in Hebei Province. Mortality data were extracted from three national retrospective death surveys (1973-1975, 1990-1992 and 2004-2005). The data were stratified by 5-year age groups, gender and area (high-risk/non-high-risk areas) for analysis. The age-period-cohort and grey system model were used. The crude incidence rate of UGIC was 55.47/100000, and the adjusted rate (Segi's population) was 44.90/100000. Males in rural areas had the highest incidence rate (world age-standardized rate = 87.89/100000). The crude mortality rate of UGIC displayed a decreasing trend in Hebei Province from the 1970s to 2013, and the adjusted rate decreased by 43.81% from the 1970s (58.07/100000) to 2013 (32.63/100000). The mortality rate declined more significantly in the high-risk areas (57.26%) than in the non-high-risk areas (55.02%) from the 1970s to 2013. The median age at diagnosis of UGIC was 65.06 years in 2013. There was a notable delay in the median age at death from the 1970s (66.15 years) to 2013 (70.39 years), especially in the high-risk areas. In Cixian, the total trend of the cohort effect declined, and people aged 65-69 years were a population at relatively high risk for UGIC. We predicted that the crude mortality rates of UGIC in Cixian and Shexian would decrease to 98.80 and 133.99 per 100000 in 2018, respectively. UGIC was the major cause of cancer death in Hebei Province, and males in rural areas were a high-risk population. We should strengthen early detection and treatment of UGIC in this population.

  14. Strategic conservation of orchard germplasm based on indigenous knowledge and genetic diversity: a case study of sour orange populations in China.

    PubMed

    Ming, Feng; Liu, Qi-Kun; Shi, Jin-Lei; Wang, Wei; Lu, Bao-Rong

    2009-01-01

    To effectively conserve sour orange (Citrus aurantium L.) germplasm on two islands at the estuary of the Yangtze River in China, we estimated genetic variation and relationships of the known parental trees and their proposed descendents (young trees) using the fingerprints of random amplified polymorphic DNA (RAPD). Results based on RAPD analyses showed considerable genetic diversity in the parental populations (H(e)=0.202). The overall populations including the parental and young trees showed slightly higher genetic diversity (H(e)=0.298) than the parents, with about 10% variation between populations. An unweighted pair group method with arithmetic mean analysis dendrogram based on cluster analysis of the Jaccard similarity among individuals demonstrated a more complicated relationship of the parental and young trees from the two islands, although the young trees showed a clear association with parental trees. This indicates a significant contribution of parental trees in establishing the sour orange populations on the two islands. According to farmers' knowledge, conservation of only one or two parental trees would be sufficient because they believed that the whole populations were generated from a single mother tree. However, this study suggests that preserving most parental trees and some selected young trees with distant genetic relationships should be an effective conservation strategy for sour orange germplasm on the two islands.

  15. Estimating HIV Prevalence in Zimbabwe Using Population-Based Survey Data

    PubMed Central

    Chinomona, Amos; Mwambi, Henry Godwell

    2015-01-01

    Estimates of HIV prevalence computed using data obtained from sampling a subgroup of the national population may lack the representativeness of all the relevant domains of the population. These estimates are often computed on the assumption that HIV prevalence is uniform across all domains of the population. Use of appropriate statistical methods together with population-based survey data can enhance better estimation of national and subgroup level HIV prevalence and can provide improved explanations of the variation in HIV prevalence across different domains of the population. In this study we computed design-consistent estimates of HIV prevalence, and their respective 95% confidence intervals at both the national and subgroup levels. In addition, we provided a multivariable survey logistic regression model from a generalized linear modelling perspective for explaining the variation in HIV prevalence using demographic, socio-economic, socio-cultural and behavioural factors. Essentially, this study borrows from the proximate determinants conceptual framework which provides guiding principles upon which socio-economic and socio-cultural variables affect HIV prevalence through biological behavioural factors. We utilize the 2010–11 Zimbabwe Demographic and Health Survey (2010–11 ZDHS) data (which are population based) to estimate HIV prevalence in different categories of the population and for constructing the logistic regression model. It was established that HIV prevalence varies greatly with age, gender, marital status, place of residence, literacy level, belief on whether condom use can reduce the risk of contracting HIV and level of recent sexual activity whereas there was no marked variation in HIV prevalence with social status (measured using a wealth index), method of contraceptive and an individual’s level of education. PMID:26624280

  16. Population genetic analysis of Mountain Plover using mitochondrial DNA sequence data

    USGS Publications Warehouse

    Oyler-McCance, S.J.; St. John, J.; Knopf, F.L.; Quinn, T.W.

    2005-01-01

    Mountain Plover (Charadrius montanus) distribution and abundance have been reduced drastically in the past 30 years and the conversion of shortgrass prairie to agriculture has caused breeding populations to become geographically isolated. This, coupled with the fact that Mountain Plovers are thought to show fidelity to breeding grounds, leads to the prediction that the isolated breeding populations would be genetically distinct. This pattern, if observed, would have important management implications for a species at risk of extinction. Our study examined genetic variation at two mitochondrial regions for 20–30 individuals from each of four breeding sites. We found no evidence of significant population differentiation in the data from the control region or the ATPase 6/8 region. Nested-clade analysis revealed no relationship between haplotype phylogeny, and geography among the 47 control region haplotypes. In the ATPase 6/8 region, however, one of the two clades provided information suggesting that, historically, there has been continuous range expansion. Analysis of mismatch distributions and Tajima's D suggest that the Mountain Plover underwent a population expansion, following the Pleistocene glacial period. To explain the lack of detectable genetic differentiation among populations, despite their geographic isolation and fidelity to breeding locations, we speculate that there is sufficient female-mediated gene flow to homogenize gene pools among populations. Such gene flow might ensue if pair bonds are formed in mixed flocks on wintering grounds rather than on the summer breeding grounds.

  17. Population viability analysis of the Endangered shortnose sturgeon

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

    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 anymore » 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

  18. Breast cancer screening among shift workers: a nationwide population-based survey in Korea.

    PubMed

    Son, Heesook; Kang, Youngmi

    2017-04-01

    We aimed to examine the association between shift work types and participation in breast cancer screening (BCS) programs by comparing rates of participation for BCS among regular daytime workers and alternative shift workers using data from a nationally representative, population-based survey conducted in Korea. In addition, the results were analyzed according to sociodemographic factors, including occupation, education, income, private health insurance, age, and number of working hours a week. This secondary cross-sectional analysis used data from the 2012 Korean National Health and Nutritional Examination Survey. The target population included women aged ≥ 40 years who responded as to whether they had undergone BCS in the previous year. Accordingly, we analyzed survey data for a total of 1,193 women and used a multivariate logistic regression analysis to evaluate the differences in factors affecting BCS between regular daytime and alternative shift workers. A logistic regression analysis was performed considering private health insurance as a significant sociodemographic factor for BCS among regular daytime shift workers. In contrast, none of the tested variables could significantly predict adherence to BCS among alternative shift workers. The results of this study suggest the need for the development of comprehensive workplace breast cancer prevention programs by considering shift work types. More attention should be given to female workers with low education levels, those who are uninsured, and young workers to improve the participation rate for BCS at the workplace.

  19. Migraine and risk of cardiovascular diseases: Danish population based matched cohort study

    PubMed Central

    Szépligeti, Szimonetta Komjáthiné; Holland-Bill, Louise; Ehrenstein, Vera; Horváth-Puhó, Erzsébet; Henderson, Victor W; Sørensen, Henrik Toft

    2018-01-01

    Abstract Objective To examine the risks of myocardial infarction, stroke (ischaemic and haemorrhagic), peripheral artery disease, venous thromboembolism, atrial fibrillation or atrial flutter, and heart failure in patients with migraine and in a general population comparison cohort. Design Nationwide, population based cohort study. Setting All Danish hospitals and hospital outpatient clinics from 1995 to 2013. Participants 51 032 patients with migraine and 510 320 people from the general population matched on age, sex, and calendar year. Main outcome measures Comorbidity adjusted hazard ratios of cardiovascular outcomes based on Cox regression analysis. Results Higher absolute risks were observed among patients with incident migraine than in the general population across most outcomes and follow-up periods. After 19 years of follow-up, the cumulative incidences per 1000 people for the migraine cohort compared with the general population were 25 v 17 for myocardial infarction, 45 v 25 for ischaemic stroke, 11 v 6 for haemorrhagic stroke, 13 v 11 for peripheral artery disease, 27 v 18 for venous thromboembolism, 47 v 34 for atrial fibrillation or atrial flutter, and 19 v 18 for heart failure. Correspondingly, migraine was positively associated with myocardial infarction (adjusted hazard ratio 1.49, 95% confidence interval 1.36 to 1.64), ischaemic stroke (2.26, 2.11 to 2.41), and haemorrhagic stroke (1.94, 1.68 to 2.23), as well as venous thromboembolism (1.59, 1.45 to 1.74) and atrial fibrillation or atrial flutter (1.25, 1.16 to 1.36). No meaningful association was found with peripheral artery disease (adjusted hazard ratio 1.12, 0.96 to 1.30) or heart failure (1.04, 0.93 to 1.16). The associations, particularly for stroke outcomes, were stronger during the short term (0-1 years) after diagnosis than the long term (up to 19 years), in patients with aura than in those without aura, and in women than in men. In a subcohort of patients, the associations persisted

  20. Strong evidence for a genetic contribution to late-onset Alzheimer's disease mortality: a population-based study.

    PubMed

    Kauwe, John S K; Ridge, Perry G; Foster, Norman L; Cannon-Albright, Lisa A

    2013-01-01

    Alzheimer's disease (AD) is an international health concern that has a devastating effect on patients and families. While several genetic risk factors for AD have been identified much of the genetic variance in AD remains unexplained. There are limited published assessments of the familiality of Alzheimer's disease. Here we present the largest genealogy-based analysis of AD to date. We assessed the familiality of AD in The Utah Population Database (UPDB), a population-based resource linking electronic health data repositories for the state with the computerized genealogy of the Utah settlers and their descendants. We searched UPDB for significant familial clustering of AD to evaluate the genetic contribution to disease. We compared the Genealogical Index of Familiality (GIF) between AD individuals and randomly selected controls and estimated the Relative Risk (RR) for a range of family relationships. Finally, we identified pedigrees with a significant excess of AD deaths. The GIF analysis showed that pairs of individuals dying from AD were significantly more related than expected. This excess of relatedness was observed for both close and distant relationships. RRs for death from AD among relatives of individuals dying from AD were significantly increased for both close and more distant relatives. Multiple pedigrees had a significant excess of AD deaths. These data strongly support a genetic contribution to the observed clustering of individuals dying from AD. This report is the first large population-based assessment of the familiality of AD mortality and provides the only reported estimates of relative risk of AD mortality in extended relatives to date. The high-risk pedigrees identified show a true excess of AD mortality (not just multiple cases) and are greater in depth and width than published AD pedigrees. The presence of these high-risk pedigrees strongly supports the possibility of rare predisposition variants not yet identified.

  1. Low Divergence of Clonorchis sinensis in China Based on Multilocus Analysis

    PubMed Central

    Sun, Jiufeng; Huang, Yan; Huang, Huaiqiu; Liang, Pei; Wang, Xiaoyun; Mao, Qiang; Men, Jingtao; Chen, Wenjun; Deng, Chuanhuan; Zhou, Chenhui; Lv, Xiaoli; Zhou, Juanjuan; Zhang, Fan; Li, Ran; Tian, Yanli; Lei, Huali; Liang, Chi; Hu, Xuchu; Xu, Jin; Li, Xuerong; XinbingYu

    2013-01-01

    Clonorchis sinensis, an ancient parasite that infects a number of piscivorous mammals, attracts significant public health interest due to zoonotic exposure risks in Asia. The available studies are insufficient to reflect the prevalence, geographic distribution, and intraspecific genetic diversity of C. sinensis in endemic areas. Here, a multilocus analysis based on eight genes (ITS1, act, tub, ef-1a, cox1, cox3, nad4 and nad5 [4.986 kb]) was employed to explore the intra-species genetic construction of C. sinensis in China. Two hundred and fifty-six C. sinensis isolates were obtained from environmental reservoirs from 17 provinces of China. A total of 254 recognized Multilocus Types (MSTs) showed high diversity among these isolates using multilocus analysis. The comparison analysis of nuclear and mitochondrial phylogeny supports separate clusters in a nuclear dendrogram. Genetic differentiation analysis of three clusters (A, B, and C) showed low divergence within populations. Most isolates from clusters B and C are geographically limited to central China, while cluster A is extraordinarily genetically diverse. Further genetic analyses between different geographic distributions, water bodies and hosts support the low population divergence. The latter haplotype analyses were consistent with the phylogenetic and genetic differentiation results. A recombination network based on concatenated sequences showed a concentrated linkage recombination population in cox1, cox3, nad4 and nad5, with spatial structuring in ITS1. Coupled with the history record and archaeological evidence of C. sinensis infection in mummified desiccated feces, these data point to an ancient origin of C. sinensis in China. In conclusion, we present a likely phylogenetic structure of the C. sinensis population in mainland China, highlighting its possible tendency for biogeographic expansion. Meanwhile, ITS1 was found to be an effective marker for tracking C. sinensis infection worldwide. Thus, the

  2. Probability bounds analysis for nonlinear population ecology models.

    PubMed

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

    2015-09-01

    Mathematical models in population ecology often involve parameters that are empirically determined and inherently uncertain, with probability distributions for the uncertainties not known precisely. Propagating such imprecise uncertainties rigorously through a model to determine their effect on model outputs can be a challenging problem. We illustrate here a method for the direct propagation of uncertainties represented by probability bounds though nonlinear, continuous-time, dynamic models in population ecology. This makes it possible to determine rigorous bounds on the probability that some specified outcome for a population is achieved, which can be a core problem in ecosystem modeling for risk assessment and management. Results can be obtained at a computational cost that is considerably less than that required by statistical sampling methods such as Monte Carlo analysis. The method is demonstrated using three example systems, with focus on a model of an experimental aquatic food web subject to the effects of contamination by ionic liquids, a new class of potentially important industrial chemicals. Copyright © 2015. Published by Elsevier Inc.

  3. Workplace injuries in Fiji: a population-based study (TRIP 7)

    PubMed Central

    2013-01-01

    Background Workplace injury rates in low and middle-income countries are known to be high. Contemporary data on this topic from Pacific Island countries and territories are scant. Aims To describe the epidemiology of fatal and hospitalized workplace injuries in Fiji using a population-based trauma registry. Methods An analysis of data from a prospective population-based surveillance registry investigated the characteristics associated with workplace injuries resulting in death or hospital admission among people aged 15 years and older in Viti Levu, the largest island in the Republic of Fiji, from October 2005 to September 2006. Incidence rates were calculated using denominator data from the 2004–05 Fiji Employment Survey. Results One hundred and eighty-nine individuals met the study eligibility criteria (including nine deaths). This corresponded to annual injury-related hospitalization and death rates of 73.4 and 3.7 per 100 000 workers, respectively. Males accounted for 95% of injuries, and hospitalization rates were highest among those aged 15–29 years (33 per 100 000 workers). Fijian and Indian workers had similar rates of admission to hospital (38.3 and 31.8 per 100 000 workers, respectively). Fractures (40%) and ‘cuts/bites/open wounds’ (32%) were the commonest types of injury while ‘being hit by a person or object’ (34%), falls (27%) and ‘cutting or piercing’ injuries (27%) were the commonest mechanisms. Overall, 7% of injuries were deemed intentional. Conclusions Acknowledging the likely underestimation of the overall burden of workplace injuries, these findings support the need to identify context-specific risk factors and effective approaches to preventing workplace injuries in Fiji. PMID:23535710

  4. Workplace injuries in Fiji: a population-based study (TRIP 7).

    PubMed

    Reddy, R; Kafoa, B; Wainiqolo, I; Kool, B; Gentles, D; McCaig, E; Ameratunga, S

    2013-06-01

    Workplace injury rates in low and middle-income countries are known to be high. Contemporary data on this topic from Pacific Island countries and territories are scant. To describe the epidemiology of fatal and hospitalized workplace injuries in Fiji using a population-based trauma registry. An analysis of data from a prospective population-based surveillance registry investigated the characteristics associated with workplace injuries resulting in death or hospital admission among people aged 15 years and older in Viti Levu, the largest island in the Republic of Fiji, from October 2005 to September 2006. Incidence rates were calculated using denominator data from the 2004-05 Fiji Employment Survey. One hundred and eighty-nine individuals met the study eligibility criteria (including nine deaths). This corresponded to annual injury-related hospitalization and death rates of 73.4 and 3.7 per 100 000 workers, respectively. Males accounted for 95% of injuries, and hospitalization rates were highest among those aged 15-29 years (33 per 100 000 workers). Fijian and Indian workers had similar rates of admission to hospital (38.3 and 31.8 per 100 000 workers, respectively). Fractures (40%) and 'cuts/bites/open wounds' (32%) were the commonest types of injury while 'being hit by a person or object' (34%), falls (27%) and 'cutting or piercing' injuries (27%) were the commonest mechanisms. Overall, 7% of injuries were deemed intentional. Acknowledging the likely underestimation of the overall burden of workplace injuries, these findings support the need to identify context-specific risk factors and effective approaches to preventing workplace injuries in Fiji.

  5. Infective Endocarditis and Cancer Risk: A Population-Based Cohort Study.

    PubMed

    Sun, Li-Min; Wu, Jung-Nan; Lin, Cheng-Li; Day, Jen-Der; Liang, Ji-An; Liou, Li-Ren; Kao, Chia-Hung

    2016-03-01

    This study investigated the possible relationship between endocarditis and overall and individual cancer risk among study participants in Taiwan.We used data from the National Health Insurance program of Taiwan to conduct a population-based, observational, and retrospective cohort study. The case group consisted of 14,534 patients who were diagnosed with endocarditis between January 1, 2000 and December 31, 2010. For the control group, 4 patients without endocarditis were frequency matched to each endocarditis patient according to age, sex, and index year. Competing risks regression analysis was conducted to determine the effect of endocarditis on cancer risk.A large difference was noted in Charlson comorbidity index between endocarditis and nonendocarditis patients. In patients with endocarditis, the risk for developing overall cancer was significant and 119% higher than in patients without endocarditis (adjusted subhazard ratio = 2.19, 95% confidence interval = 1.98-2.42). Regarding individual cancers, in addition to head and neck, uterus, female breast and hematological malignancies, the risks of developing colorectal cancer, and some digestive tract cancers were significantly higher. Additional analyses determined that the association of cancer with endocarditis is stronger within the 1st 5 years after endocarditis diagnosis.This population-based cohort study found that patients with endocarditis are at a higher risk for colorectal cancer and other cancers in Taiwan. The risk was even higher within the 1st 5 years after endocarditis diagnosis. It suggested that endocarditis is an early marker of colorectal cancer and other cancers. The underlying mechanisms must still be explored and may account for a shared risk factor of infection in both endocarditis and malignancy.

  6. Geometry-based populated chessboard recognition

    NASA Astrophysics Data System (ADS)

    Xie, Youye; Tang, Gongguo; Hoff, William

    2018-04-01

    Chessboards are commonly used to calibrate cameras, and many robust methods have been developed to recognize the unoccupied boards. However, when the chessboard is populated with chess pieces, such as during an actual game, the problem of recognizing the board is much harder. Challenges include occlusion caused by the chess pieces, the presence of outlier lines and low viewing angles of the chessboard. In this paper, we present a novel approach to address the above challenges and recognize the chessboard. The Canny edge detector and Hough transform are used to capture all possible lines in the scene. The k-means clustering and a k-nearest-neighbors inspired algorithm are applied to cluster and reject the outlier lines based on their Euclidean distances to the nearest neighbors in a scaled Hough transform space. Finally, based on prior knowledge of the chessboard structure, a geometric constraint is used to find the correspondences between image lines and the lines on the chessboard through the homography transformation. The proposed algorithm works for a wide range of the operating angles and achieves high accuracy in experiments.

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

    PubMed Central

    Todokoro, Yasuhiro; Higaki, Tomomi

    2010-01-01

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

  8. The Analysis of Organizational Diagnosis on Based Six Box Model in Universities

    ERIC Educational Resources Information Center

    Hamid, Rahimi; Siadat, Sayyed Ali; Reza, Hoveida; Arash, Shahin; Ali, Nasrabadi Hasan; Azizollah, Arbabisarjou

    2011-01-01

    Purpose: The analysis of organizational diagnosis on based six box model at universities. Research method: Research method was descriptive-survey. Statistical population consisted of 1544 faculty members of universities which through random strafed sampling method 218 persons were chosen as the sample. Research Instrument were organizational…

  9. Strengthening population health interventions: developing the CollaboraKTion Framework for Community-Based Knowledge Translation.

    PubMed

    Jenkins, Emily K; Kothari, Anita; Bungay, Vicky; Johnson, Joy L; Oliffe, John L

    2016-08-30

    Much of the research and theorising in the knowledge translation (KT) field has focused on clinical settings, providing little guidance to those working in community settings. In this study, we build on previous research in community-based KT by detailing the theory driven and empirically-informed CollaboraKTion framework. A case study design and ethnographic methods were utilised to gain an in-depth understanding of the processes for conducting a community-based KT study as a means to distilling the CollaboraKTion framework. Drawing on extensive field notes describing fieldwork observations and interactions as well as evidence from the participatory research and KT literature, we detail the processes and steps undertaken in this community-based KT study as well as their rationale and the challenges encountered. In an effort to build upon existing knowledge, Kitson and colleagues' co-KT framework, which provides guidance for conducting KT aimed at addressing population-level health, was applied as a coding structure to inform the current analysis. This approach was selected because it (1) supported the application of an existing community-based KT framework to empirical data and (2) provided an opportunity to contribute to the theory and practice gaps in the community-based KT literature through an inductively derived empirical example. Analysis revealed that community-based KT is an iterative process that can be viewed as comprising five overarching processes: (1) contacting and connecting; (2) deepening understandings; (3) adapting and applying the knowledge base; (4) supporting and evaluating continued action; and (5) transitioning and embedding as well as several key elements within each of these processes (e.g. building on existing knowledge, establishing partnerships). These empirically informed theory advancements in KT and participatory research traditions are summarised in the CollaboraKTion framework. We suggest that community-based KT researchers place

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  11. Prevalence of Primary Sjögren's Syndrome in a US Population-Based Cohort.

    PubMed

    Maciel, Gabriel; Crowson, Cynthia S; Matteson, Eric L; Cornec, Divi

    2017-10-01

    To report the point prevalence of primary Sjögren's syndrome (SS) in the first US population-based study. Cases of all potential primary SS patients living in Olmsted County, Minnesota, on January 1, 2015, were retrieved using Rochester Epidemiology Project resources, and ascertained by manual medical records review. Primary SS cases were defined according to physician diagnosis. The use of diagnostic tests was assessed and the performance of classification criteria was evaluated. The number of prevalent cases in 2015 was also projected based on 1976-2005 incidence data from the same source population. A total of 106 patients with primary SS were included in the study: 86% were female, with a mean ± SD age of 64.6 ± 15.2 years, and a mean ± SD disease duration of 10.5 ± 8.4 years. A majority were anti-SSA positive (75%) and/or anti-SSB positive (58%), but only 22% met American-European Consensus Group or American College of Rheumatology criteria, because the other tests required for disease classification (ocular dryness objective assessment, salivary gland functional or morphologic tests, or salivary gland biopsy) were rarely performed in clinical practice. According to the physician diagnosis, the age- and sex-adjusted prevalence of primary SS was 10.3 per 10,000 inhabitants, but according to classification criteria, this prevalence was only 2.2 per 10,000. The analysis based on previous incidence data projected a similar 2015 prevalence rate of 11.0 per 10,000. The prevalence of primary SS in this geographically well-defined population was estimated to be between 2 and 10 per 10,000 inhabitants. Physicians rarely used tests included in the classification criteria to diagnose the disease in this community setting. © 2016, American College of Rheumatology.

  12. 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

  13. Prevalence of Mycoplasma genitalium in different population groups: systematic review andmeta-analysis.

    PubMed

    Baumann, Lukas; Cina, Manuel; Egli-Gany, Dianne; Goutaki, Myrofora; Halbeisen, Florian S; Lohrer, Gian-Reto; Ali, Hammad; Scott, Pippa; Low, Nicola

    2018-06-01

    Mycoplasma genitalium is a common cause of non-gonococcal non-chlamydial urethritis and cervicitis. Testing of asymptomatic populations has been proposed, but prevalence in asymptomatic populations is not well established. We aimed to estimate the prevalence of M. genitalium in the general population, pregnant women, men who have sex with men (MSM), commercial sex workers (CSWs) and clinic-based samples, METHODS: We searched Embase, Medline, IndMED, African Index Medicus and LILACS from 1 January 1991 to 12 July 2016 without language restrictions. We included studies with 500 participants or more. Two reviewers independently screened and selected studies and extracted data. We examined forest plots and conducted random-effects meta-analysis to estimate prevalence, if appropriate. Between-study heterogeneity was examined using the I 2 statistic and meta-regression. Of 3316 screened records, 63 were included. In randomly selected samples from the general population, the summary prevalence was 1.3% (95% CI 1.0% to 1.8%, I 2 41.5%, three studies, 9091 people) in countries with higher levels of development and 3.9% (95% CI 2.2 to 6.7, I 2 89.2%, three studies, 3809 people) in countries with lower levels. Prevalence was similar in women and men (P=0.47). In clinic based samples, prevalence estimates were higher, except in asymptomatic patients (0.8%, 95% CI 0.4 to 1.4, I 2 0.0%, three studies, 2889 people). Summary prevalence estimates were, in the following groups: pregnant women 0.9% (95% CI 0.6% to 1.4%, I 2 0%, four studies, 3472 people), MSM in the community 3.2% (95% CI 2.1 to 5.1, I 2 78.3%, five studies, 3012 people) and female CSWs in the community 15.9% (95% CI 13.5 to 18.9, I 2 79.9%, four studies, 4006 people). This systematic review can inform testing guidelines for M. genitalium . The low estimated prevalence of M. genitalium in the general population, pregnant women and asymptomatic attenders at clinics does not support expansion of testing to these

  14. Viability of in-house datamarting approaches for population genetics analysis of SNP genotypes

    PubMed Central

    Amigo, Jorge; Phillips, Christopher; Salas, Antonio; Carracedo, Ángel

    2009-01-01

    Background Databases containing very large amounts of SNP (Single Nucleotide Polymorphism) data are now freely available for researchers interested in medical and/or population genetics applications. While many of these SNP repositories have implemented data retrieval tools for general-purpose mining, these alone cannot cover the broad spectrum of needs of most medical and population genetics studies. Results To address this limitation, we have built in-house customized data marts from the raw data provided by the largest public databases. In particular, for population genetics analysis based on genotypes we have built a set of data processing scripts that deal with raw data coming from the major SNP variation databases (e.g. HapMap, Perlegen), stripping them into single genotypes and then grouping them into populations, then merged with additional complementary descriptive information extracted from dbSNP. This allows not only in-house standardization and normalization of the genotyping data retrieved from different repositories, but also the calculation of statistical indices from simple allele frequency estimates to more elaborate genetic differentiation tests within populations, together with the ability to combine population samples from different databases. Conclusion The present study demonstrates the viability of implementing scripts for handling extensive datasets of SNP genotypes with low computational costs, dealing with certain complex issues that arise from the divergent nature and configuration of the most popular SNP repositories. The information contained in these databases can also be enriched with additional information obtained from other complementary databases, in order to build a dedicated data mart. Updating the data structure is straightforward, as well as permitting easy implementation of new external data and the computation of supplementary statistical indices of interest. PMID:19344481

  15. Viability of in-house datamarting approaches for population genetics analysis of SNP genotypes.

    PubMed

    Amigo, Jorge; Phillips, Christopher; Salas, Antonio; Carracedo, Angel

    2009-03-19

    Databases containing very large amounts of SNP (Single Nucleotide Polymorphism) data are now freely available for researchers interested in medical and/or population genetics applications. While many of these SNP repositories have implemented data retrieval tools for general-purpose mining, these alone cannot cover the broad spectrum of needs of most medical and population genetics studies. To address this limitation, we have built in-house customized data marts from the raw data provided by the largest public databases. In particular, for population genetics analysis based on genotypes we have built a set of data processing scripts that deal with raw data coming from the major SNP variation databases (e.g. HapMap, Perlegen), stripping them into single genotypes and then grouping them into populations, then merged with additional complementary descriptive information extracted from dbSNP. This allows not only in-house standardization and normalization of the genotyping data retrieved from different repositories, but also the calculation of statistical indices from simple allele frequency estimates to more elaborate genetic differentiation tests within populations, together with the ability to combine population samples from different databases. The present study demonstrates the viability of implementing scripts for handling extensive datasets of SNP genotypes with low computational costs, dealing with certain complex issues that arise from the divergent nature and configuration of the most popular SNP repositories. The information contained in these databases can also be enriched with additional information obtained from other complementary databases, in order to build a dedicated data mart. Updating the data structure is straightforward, as well as permitting easy implementation of new external data and the computation of supplementary statistical indices of interest.

  16. Racial Differences in the Overall Survival of Hairy Cell Leukemia in the United States: A Population-Based Analysis of the Surveillance, Epidemiology, and End Results Database.

    PubMed

    Giri, Smith; Shrestha, Rajesh; Pathak, Ranjan; Bhatt, Vijaya Raj

    2015-08-01

    Several studies have reported excellent long-term overall survival (OS) of patients with hairy cell leukemia (HCL) without racial disparity. Studies in other cancers have demonstrated worse mortality among African American (AA) individuals. We used the Surveillance, Epidemiology, and End Results 18 database to identify HCL patients diagnosed between 1978 and 2011. Kaplan-Meier curves were plotted to estimate OS. Univariate analysis using the life table method and multivariate Cox regression model were used to determine the independent effect of race on OS. The study population included 78% men and had a median age of 56 years. Race included 93% white, 3.5% Asian/Pacific Islander, and 3.5% AA. The 10-year OS was significantly less for AA as compared with white and Asian/Pacific Islander individuals (54% vs. 72% vs. 75%; P < .001). A Kaplan-Meier survival curve showed a significantly worse OS for AA versus other races (P < .001). In a multivariate analysis, AA race remained an independent predictor for a worse OS (hazard ratio 1.77; 95% confidence interval, 1.30-2.40; P < .001) after adjusting for age, sex, year of diagnosis, and marital status. In this population-based study, only half of AA patients but more than two-thirds of HCL patients from other racial groups were alive at 10 years. Such drastic racial differences in OS of HCL patients at the population level mandates further evaluation of the contributory biological, socioeconomic, health system, and other factors. Understanding and overcoming such racial disparities might close the racial differences in OS of this potentially curable disease. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Population trends of North American shorebirds based on the International Shorebird Survey

    USGS Publications Warehouse

    Howe, M.A.; Geissler, P.H.; Harrington, B.A.

    1989-01-01

    Shorebirds (Charadiiformes) are prime candidates for population decline because of their dependence on wetlands that are being lost at a rapid pace. Thirty-six of the 49 species of shorebirds that breed in North America spend most of the year in Latin America. Because populations of most species breed and winter at remote sites , it may be feasible to monitor their numbers at migration stopovers. In this study, we used statistical trend analysis methods, developed for the North American Breeding Bird Survey, to analyze data on shorebird populations during south-bound migration in the United States. Survey data were collected by volunteers in the International Shorebird Survey (ISS). Methodological concerns over both the ISS and the trend analysis procedures are discussed in detail and biological interpretations of the results are suggested.

  18. 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.

  19. Building the Evidence Base for Population-Level Interventions: Barriers and Opportunities

    ERIC Educational Resources Information Center

    Lifsey, Sarah; Cash, Amanda; Anthony, Jodi; Mathis, Sheryl; Silva, Sandra

    2015-01-01

    Population-level interventions focused on policy, systems, and environmental change strategies are increasingly being used to affect and improve the health of populations. At the same time, emphasis on implementing evidence-based public health practices and programming is increasing, particularly at the federal level. Valuing strategies in the…

  20. [A total of 362 HLA different haplotypes and HLA recombination haplotypes based on analysis of their family pedigree in Chinese partial Han populations].

    PubMed

    Gao, Su-Qing; Cheng, Xi; Li, Qian; Li, Yu-Zhu; Deng, Zhi-Hui

    2009-06-01

    This study was aimed to discover the novel HLA recombination haplotypes and investigate the distribution of haplotypes in Chinese Han population. Based on the HLA-A, B, DRB1 typing results of 179 family members, 791 haplotypes were assigned by the mode of inheritance. The results showed that a total of 4 novel recombinant haplotypes in HLA-DRB1 locus region were observed in 4 families, which ratio of paternal to maternal chromosomes was 3:1. The recombination ratio between HLA-DRB1 and HLA-A or B loci was 0.92% (4/433). There were a total of 362 kinds of HLA-A, -B, -DRB1 haplotypes to be confirmed in Chinese Han partial population. A33-B58-DR17, A2-B46-DR9, A30-B13-DR7, A11-B13-DR15, A11-B75-DR12 and A2-B46-DR14 were the most common haplotypes that was consistent with the distribution of HLA alleles in unrelated donors. There were A1-B63-DR12, A29-B46-DR15, A1-B61-DR10, A34-B35-DR9, A29-B54-DR4, A23-B13-DR16 and A34-B62-DR15 haplotypes and so on, which were rare haplotypes not yet reported in Chinese. It is concluded that the HLA-A-B-DRB1 haplotypes would be confirmed by analysis of their family pedigree. The results obtained in this study are basic data for study of Chinese anthropology, organ transplantation and disease correlation analysis.

  1. Copy-number analysis and inference of subclonal populations in cancer genomes using Sclust.

    PubMed

    Cun, Yupeng; Yang, Tsun-Po; Achter, Viktor; Lang, Ulrich; Peifer, Martin

    2018-06-01

    The genomes of cancer cells constantly change during pathogenesis. This evolutionary process can lead to the emergence of drug-resistant mutations in subclonal populations, which can hinder therapeutic intervention in patients. Data derived from massively parallel sequencing can be used to infer these subclonal populations using tumor-specific point mutations. The accurate determination of copy-number changes and tumor impurity is necessary to reliably infer subclonal populations by mutational clustering. This protocol describes how to use Sclust, a copy-number analysis method with a recently developed mutational clustering approach. In a series of simulations and comparisons with alternative methods, we have previously shown that Sclust accurately determines copy-number states and subclonal populations. Performance tests show that the method is computationally efficient, with copy-number analysis and mutational clustering taking <10 min. Sclust is designed such that even non-experts in computational biology or bioinformatics with basic knowledge of the Linux/Unix command-line syntax should be able to carry out analyses of subclonal populations.

  2. Digital Image Analysis of Yeast Single Cells Growing in Two Different Oxygen Concentrations to Analyze the Population Growth and to Assist Individual-Based Modeling.

    PubMed

    Ginovart, Marta; Carbó, Rosa; Blanco, Mónica; Portell, Xavier

    2017-01-01

    Nowadays control of the growth of Saccharomyces to obtain biomass or cellular wall components is crucial for specific industrial applications. The general aim of this contribution is to deal with experimental data obtained from yeast cells and from yeast cultures to attempt the integration of the two levels of information, individual and population, to progress in the control of yeast biotechnological processes by means of the overall analysis of this set of experimental data, and to assist in the improvement of an individual-based model, namely, INDISIM- Saccha . Populations of S. cerevisiae growing in liquid batch culture, in aerobic and microaerophilic conditions, were studied. A set of digital images was taken during the population growth, and a protocol for the treatment and analyses of the images obtained was established. The piecewise linear model of Buchanan was adjusted to the temporal evolutions of the yeast populations to determine the kinetic parameters and changes of growth phases. In parallel, for all the yeast cells analyzed, values of direct morphological parameters, such as area, perimeter, major diameter, minor diameter, and derived ones, such as circularity and elongation, were obtained. Graphical and numerical methods from descriptive statistics were applied to these data to characterize the growth phases and the budding state of the yeast cells in both experimental conditions, and inferential statistical methods were used to compare the diverse groups of data achieved. Oxidative metabolism of yeast in a medium with oxygen available and low initial sugar concentration can be taken into account in order to obtain a greater number of cells or larger cells. Morphological parameters were analyzed statistically to identify which were the most useful for the discrimination of the different states, according to budding and/or growth phase, in aerobic and microaerophilic conditions. The use of the experimental data for subsequent modeling work was then

  3. Digital Image Analysis of Yeast Single Cells Growing in Two Different Oxygen Concentrations to Analyze the Population Growth and to Assist Individual-Based Modeling

    PubMed Central

    Ginovart, Marta; Carbó, Rosa; Blanco, Mónica; Portell, Xavier

    2018-01-01

    Nowadays control of the growth of Saccharomyces to obtain biomass or cellular wall components is crucial for specific industrial applications. The general aim of this contribution is to deal with experimental data obtained from yeast cells and from yeast cultures to attempt the integration of the two levels of information, individual and population, to progress in the control of yeast biotechnological processes by means of the overall analysis of this set of experimental data, and to assist in the improvement of an individual-based model, namely, INDISIM-Saccha. Populations of S. cerevisiae growing in liquid batch culture, in aerobic and microaerophilic conditions, were studied. A set of digital images was taken during the population growth, and a protocol for the treatment and analyses of the images obtained was established. The piecewise linear model of Buchanan was adjusted to the temporal evolutions of the yeast populations to determine the kinetic parameters and changes of growth phases. In parallel, for all the yeast cells analyzed, values of direct morphological parameters, such as area, perimeter, major diameter, minor diameter, and derived ones, such as circularity and elongation, were obtained. Graphical and numerical methods from descriptive statistics were applied to these data to characterize the growth phases and the budding state of the yeast cells in both experimental conditions, and inferential statistical methods were used to compare the diverse groups of data achieved. Oxidative metabolism of yeast in a medium with oxygen available and low initial sugar concentration can be taken into account in order to obtain a greater number of cells or larger cells. Morphological parameters were analyzed statistically to identify which were the most useful for the discrimination of the different states, according to budding and/or growth phase, in aerobic and microaerophilic conditions. The use of the experimental data for subsequent modeling work was then

  4. Population-Level Cost-Effectiveness of Implementing Evidence-Based Practices into Routine Care

    PubMed Central

    Fortney, John C; Pyne, Jeffrey M; Burgess, James F

    2014-01-01

    Objective The objective of this research was to apply a new methodology (population-level cost-effectiveness analysis) to determine the value of implementing an evidence-based practice in routine care. Data Sources/Study Setting Data are from sequentially conducted studies: a randomized controlled trial and an implementation trial of collaborative care for depression. Both trials were conducted in the same practice setting and population (primary care patients prescribed antidepressants). Study Design The study combined results from a randomized controlled trial and a pre-post-quasi-experimental implementation trial. Data Collection/Extraction Methods The randomized controlled trial collected quality-adjusted life years (QALYs) from survey and medication possession ratios (MPRs) from administrative data. The implementation trial collected MPRs and intervention costs from administrative data and implementation costs from survey. Principal Findings In the randomized controlled trial, MPRs were significantly correlated with QALYs (p = .03). In the implementation trial, patients at implementation sites had significantly higher MPRs (p = .01) than patients at control sites, and by extrapolation higher QALYs (0.00188). Total costs (implementation, intervention) were nonsignificantly higher ($63.76) at implementation sites. The incremental population-level cost-effectiveness ratio was $33,905.92/QALY (bootstrap interquartile range −$45,343.10/QALY to $99,260.90/QALY). Conclusions The methodology was feasible to operationalize and gave reasonable estimates of implementation value. PMID:25328029

  5. Child Maltreatment Among Singletons and Multiple Births in Japan: A Population-Based Study.

    PubMed

    Yokoyama, Yoshie; Oda, Terumi; Nagai, Noriyo; Sugimoto, Masako; Mizukami, Kenji

    2015-12-01

    The occurrence of multiple births has been recognized as a risk factor for child maltreatment. However, few population-based studies have examined the relationship between multiple births and child maltreatment. This study aimed to evaluate the degree of risk of child maltreatment among singletons and multiple births in Japan and to identify factors associated with increased risk. Using population-based data, we analyzed the database of records on child maltreatment and medical checkups for infants aged 1.5 years filed at Nishinomiya City Public Health Center between April 2007 and March 2011. To protect personal information, the data were transferred to anonymized electronic files for analysis. After adjusting by logistic regression for each associated factor and gestation number, multiples themselves were not associated with the risk of child maltreatment. However, compared with singletons, multiples had a significantly higher rate of risk factors for child maltreatment, including low birth weight and neural abnormality. Moreover, compared with mothers of singleton, mothers of twins had a significantly higher rate of poor health, which is a risk factor of child maltreatment. Multiples were not associated with the risk of child maltreatment. However, compared with singletons, multiples and their mothers had a significantly higher rate of risk factors of child maltreatment.

  6. Evolution of disease phenotype in adult and pediatric onset Crohn’s disease in a population-based cohort

    PubMed Central

    Lovasz, Barbara Dorottya; Lakatos, Laszlo; Horvath, Agnes; Szita, Istvan; Pandur, Tunde; Mandel, Michael; Vegh, Zsuzsanna; Golovics, Petra Anna; Mester, Gabor; Balogh, Mihaly; Molnar, Csaba; Komaromi, Erzsebet; Kiss, Lajos Sandor; Lakatos, Peter Laszlo

    2013-01-01

    AIM: To investigate the evolution of disease phenotype in adult and pediatric onset Crohn’s disease (CD) populations, diagnosed between 1977 and 2008. METHODS: Data of 506 incident CD patients were analyzed (age at diagnosis: 28.5 years, interquartile range: 22-38 years). Both in- and outpatient records were collected prospectively with a complete clinical follow-up and comprehensively reviewed in the population-based Veszprem province database, which included incident patients diagnosed between January 1, 1977 and December 31, 2008 in adult and pediatric onset CD populations. Disease phenotype according to the Montreal classification and long-term disease course was analysed according to the age at onset in time-dependent univariate and multivariate analysis. RESULTS: Among this population-based cohort, seventy-four (12.8%) pediatric-onset CD patients were identified (diagnosed ≤ 17 years of age). There was no significant difference in the distribution of disease behavior between pediatric (B1: 62%, B2: 15%, B3: 23%) and adult-onset CD patients (B1: 56%, B2: 21%, B3: 23%) at diagnosis, or during follow-up. Overall, the probability of developing complicated disease behaviour was 49.7% and 61.3% in the pediatric and 55.1% and 62.4% in the adult onset patients after 5- and 10-years of follow-up. Similarly, time to change in disease behaviour from non stricturing, non penetrating (B1) to complicated, stricturing or penetrating (B2/B3) disease was not significantly different between pediatric and adult onset CD in a Kaplan-Meier analysis. Calendar year of diagnosis (P = 0.04), ileal location (P < 0.001), perianal disease (P < 0.001), smoking (P = 0.038) and need for steroids (P < 0.001) were associated with presence of, or progression to, complicated disease behavior at diagnosis and during follow-up. A change in disease location was observed in 8.9% of patients and it was associated with smoking status (P = 0.01), but not with age at diagnosis. CONCLUSION: Long

  7. Geospatial analysis based on GIS integrated with LADAR.

    PubMed

    Fetterman, Matt R; Freking, Robert; Fernandez-Cull, Christy; Hinkle, Christopher W; Myne, Anu; Relyea, Steven; Winslow, Jim

    2013-10-07

    In this work, we describe multi-layered analyses of a high-resolution broad-area LADAR data set in support of expeditionary activities. High-level features are extracted from the LADAR data, such as the presence and location of buildings and cars, and then these features are used to populate a GIS (geographic information system) tool. We also apply line-of-sight (LOS) analysis to develop a path-planning module. Finally, visualization is addressed and enhanced with a gesture-based control system that allows the user to navigate through the enhanced data set in a virtual immersive experience. This work has operational applications including military, security, disaster relief, and task-based robotic path planning.

  8. 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.

  9. Current practices of laparoscopic inguinal hernia repair: a population-based analysis.

    PubMed

    Trevisonno, M; Kaneva, P; Watanabe, Y; Fried, G M; Feldman, L S; Andalib, A; Vassiliou, M C

    2015-10-01

    The selection of a laparoscopic approach for inguinal hernias varies among surgeons. It is unclear what is being done in actual practice. The purpose of this study was to report practice patterns for treatment of inguinal hernias among Quebec surgeons, and to identify factors that may be associated with the choice of operative approach. We studied a population-based cohort of patients who underwent an inguinal hernia repair between 2007 and 2011 in Quebec, Canada. A generalized linear model was used to identify predictors associated with the selection of a laparoscopic approach. 49,657 inguinal hernias were repaired by 478 surgeons. Laparoscopic inguinal hernia repair (LIHR) was used in 8 % of all cases. LIHR was used to repair 28 % of bilateral hernias, 10 % of recurrent hernias, 6 % of unilateral hernias, and 4 % of incarcerated hernias. 268 (56 %) surgeons did not perform any laparoscopic repairs, and 11 (2 %) surgeons performed more than 100 repairs. These 11 surgeons performed 61 % of all laparoscopic cases. Patient factors significantly associated with having LIHR included younger age, fewer comorbidities, bilateral hernias, and recurrent hernias. An open approach is favored for all clinical scenarios, even for situations where published guidelines recommend a laparoscopic approach. Surgeons remain divided on the best technique for inguinal hernia repair: while more than half never perform LIHR, the small proportion who perform many use the technique for a large proportion of their cases. There appears to be a gap between the best practices put forth in guidelines and what surgeons are doing in actual practice. Identification of barriers to the broader uptake of LIHR may help inform the design of educational programs to train those who have the desire to offer this technique for certain cases, and have the volume to overcome the learning curve.

  10. Analysis of the population genetic structure of Hb D-Los Angeles [β121 (GH4) Glu→Gln GAA→CAA] in Denizli, Turkey; genetic diversity, historical demography and estimation of the mutation rates based on haplotype variation.

    PubMed

    Ozturk, Onur; Arikan, Sanem; Atalay, Ayfer; Atalay, Erol O

    2016-07-01

    Understanding the genetic origin of the Hb D-Los Angeles hemoglobin may elucidate population interactions such as movements, migrations, and environmental effects on mutation mechanisms in human biology throughout history. Our study aimed to understand the genetic origin of Hb D-Los Angeles based on haplotype data, observed in the Denizli province of Turkey. We studied DNA samples from 40 unrelated patients with abnormal hemoglobin Hb D-Los Angeles and 59 unrelated healthy subjects from our DNA bank. Possible associated haplotypes, HWE, genetic diversity and population differentiation, population genetic structure analysis and historical-demographic analysis for the two populations were determined by Arlequin ver. 3.5. Molecular diversity results from the two populations show that both populations are genetically similar as far as development and expansion during the historical period. Historical gene flow results show high gene flow between the two populations. SSD and rg tests failed to reject the null hypothesis of population expansion which is consistent with unimodal distribution. Our estimated τ values show that the average time since the demographic expansion for normal and Hb D-Los Angeles populations ranged from approximately 42,000-38,000 ybp, respectively. Our data suggest that the Hb D-Los Angeles population originated within the normal population in Denizli, Turkey. Our results support the hypothesis that the Hb D-Los Angeles mutation may have originated in the Mediterranean area, independent from other populations such as India and China. The evaluation of such data may contribute valuable information to anthropological, paleoclimatic, archaeological, and phylogeographical approaches to human biology throughout the historical period. Am. J. Hum. Biol. 28:476-483, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  11. Communication: Charge-population based dispersion interactions for molecules and materials

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

    Stöhr, Martin; Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching; Michelitsch, Georg S.

    2016-04-21

    We introduce a system-independent method to derive effective atomic C{sub 6} coefficients and polarizabilities in molecules and materials purely from charge population analysis. This enables the use of dispersion-correction schemes in electronic structure calculations without recourse to electron-density partitioning schemes and expands their applicability to semi-empirical methods and tight-binding Hamiltonians. We show that the accuracy of our method is en par with established electron-density partitioning based approaches in describing intermolecular C{sub 6} coefficients as well as dispersion energies of weakly bound molecular dimers, organic crystals, and supramolecular complexes. We showcase the utility of our approach by incorporation of the recentlymore » developed many-body dispersion method [Tkatchenko et al., Phys. Rev. Lett. 108, 236402 (2012)] into the semi-empirical density functional tight-binding method and propose the latter as a viable technique to study hybrid organic-inorganic interfaces.« less

  12. Plastid DNA analysis reveals cryptic hybridization in invasive dalmatian toadflax populations

    Treesearch

    Andrew Boswell; Sharlene E. Sing; Sarah M. Ward

    2016-01-01

    Gene flow between Dalmatian toadflax (DT) and yellow toadflax (YT), both aggressive invaders throughout the Intermountain West, is creating hybrid populations potentially more invasive than either parent species. To determine the direction of gene flow in these hybrid populations, species-diagnostic cytoplasmic markers were developed. Markers were based on...

  13. Recent trends in morbidity and in-hospital outcomes of in-patients with peripheral arterial disease: a nationwide population-based analysis.

    PubMed

    Malyar, Nasser; Fürstenberg, Torsten; Wellmann, Jürgen; Meyborg, Matthias; Lüders, Florian; Gebauer, Katrin; Bunzemeier, Holger; Roeder, Norbert; Reinecke, Holger

    2013-09-01

    The prevalence of peripheral arterial disease (PAD) and especially of critical limb ischaemia (CLI) is announced to rise dramatically worldwide, with a considerable impact on the health care and socio-economic systems. We aimed to characterize the recent trends in morbidity and in-hospital outcome of PAD among all hospitalized patients in the entire German population between 2005 and 2009. Nationwide data of all hospitalizations in Germany in 2005, 2007, and 2009 were analysed regarding the prevalence of PAD, comorbidities, endovascular (EVR) and surgical revascularizations (SR), major and minor amputations, in-hospital mortality, and associated costs. From 2005 to 2009, total PAD cases increased by 20.7% (from 400 928 to 483 961), with an increase of CLI subset from 40.6 to 43.5%. Total EVR increased by 46%, while thromb-embolectomy, endarterectomy, and patch plastic increased by 67, 42, and 21%, respectively. Peripheral bypasses decreased by 2%. Major amputation decreased from 4.6 to 3.5%, while minor amputation slightly increased from 4.98 to 5.11%. The crude overall in-hospital mortality remained unchanged in claudicants (2.2%), while it decreased from 9.8 to 8.4% in CLI patients. However, mortality rate according to the Poisson model (n/1000 hospital residence days) increased significantly in claudicants (P < 0.001). Total reimbursement costs for PAD in-patient care increased by 21% with an average per case costs in 2009 of €4506 in a claudicant and €6791 in a CLI patient. This population-based analysis documents the significant rise of PAD, particularly of the CLI subset, and highlights the malign prognosis associated with PAD as indicated by high amputation and in-hospital mortality rates.

  14. Population norms for the EQ-5D-3L: a cross-country analysis of population surveys for 20 countries.

    PubMed

    Janssen, M F; Szende, A; Cabases, J; Ramos-Goñi, J M; Vilagut, G; König, H H

    2018-02-14

    This study provides EQ-5D population norms for 20 countries (N = 163,838), which can be used to compare profiles for patients with specific conditions with data for the average person in the general population in a similar age and/or gender group. Descriptive EQ-5D data are provided for the total population, by gender and by seven age groups. Provided index values are based on European VAS for all countries, based on TTO for 11 countries and based on VAS for 10 countries. Important differences exist in EQ-5D reported health status across countries after standardizing for population structure. Self-reported health according to all five dimensions and EQ VAS generally decreased with increasing age and was lower for females. Mean self-rated EQ VAS scores varied from 70.4 to 83.3 in the total population by country. The prior living standards (GDP per capita) in the countries studied are correlated most with the EQ VAS scores (0.58), while unemployment appeared to be significantly correlated in people over the age of 45 only. A country's expenditure on health care correlated moderately with higher ratings on the EQ VAS (0.55). EQ-5D norms can be used as reference data to assess the burden of disease of patients with specific conditions. Such information, in turn, can inform policy-making and assist in setting priorities in health care.

  15. Analysis of genetic diversity in Bolivian llama populations using microsatellites.

    PubMed

    Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

    2013-08-01

    South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations. © 2012 Blackwell Verlag GmbH.

  16. HormoneBase, a population-level database of steroid hormone levels across vertebrates

    PubMed Central

    Vitousek, Maren N.; Johnson, Michele A.; Donald, Jeremy W.; Francis, Clinton D.; Fuxjager, Matthew J.; Goymann, Wolfgang; Hau, Michaela; Husak, Jerry F.; Kircher, Bonnie K.; Knapp, Rosemary; Martin, Lynn B.; Miller, Eliot T.; Schoenle, Laura A.; Uehling, Jennifer J.; Williams, Tony D.

    2018-01-01

    Hormones are central regulators of organismal function and flexibility that mediate a diversity of phenotypic traits from early development through senescence. Yet despite these important roles, basic questions about how and why hormone systems vary within and across species remain unanswered. Here we describe HormoneBase, a database of circulating steroid hormone levels and their variation across vertebrates. This database aims to provide all available data on the mean, variation, and range of plasma glucocorticoids (both baseline and stress-induced) and androgens in free-living and un-manipulated adult vertebrates. HormoneBase (www.HormoneBase.org) currently includes >6,580 entries from 476 species, reported in 648 publications from 1967 to 2015, and unpublished datasets. Entries are associated with data on the species and population, sex, year and month of study, geographic coordinates, life history stage, method and latency of hormone sampling, and analysis technique. This novel resource could be used for analyses of the function and evolution of hormone systems, and the relationships between hormonal variation and a variety of processes including phenotypic variation, fitness, and species distributions. PMID:29786693

  17. Morpho-colorimetric analysis and seed germination of Brassica insularis Moris (Brassicaceae) populations.

    PubMed

    Santo, A; Mattana, E; Grillo, O; Bacchetta, G

    2015-03-01

    Brassica insularis is a perennial plant growing on both coastal and inland cliffs. Three seed lots from Sardinia were analysed using an image analysis system to detect differences in seed morphology, both within and among populations. Germination requirements at constant (5-25 °C) and alternating temperatures (25/10 °C), both in light and in darkness, were evaluated for all populations. In addition, the effect of a dry after-ripening period (90 days at 25 °C) was also investigated. Morpho-colorimetric analysis clearly identified seeds from different populations and discriminated three chromatic categories for seeds belonging to the Isola dei Cavoli coastal population, but not for the inland Masùa and the coastal Planu Sartu. Inter-population variability was also observed in germination behaviour. B. insularis seeds germinated, with percentages up to 60%, in a wide range of temperatures (5-25 °C), and neither light nor dry after-ripening affected final germination percentages. Moisture content measurements were made for seeds of each colour, but there were no particular differences among colours. Inter-populational variability in germination behaviour may be a survival strategy for species growing under unpredictable environmental conditions, such as under Mediterranean climate, while heteromorphy may be due to independent evolutionary divergence processes of the Isola dei Cavoli population. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

  18. Extension of landscape-based population viability models to ecoregional scales for conservation planning

    Treesearch

    Thomas W. Bonnot; Frank R. III Thompson; Joshua Millspaugh

    2011-01-01

    Landscape-based population models are potentially valuable tools in facilitating conservation planning and actions at large scales. However, such models have rarely been applied at ecoregional scales. We extended landscape-based population models to ecoregional scales for three species of concern in the Central Hardwoods Bird Conservation Region and compared model...

  19. Population-based absolute risk estimation with survey data

    PubMed Central

    Kovalchik, Stephanie A.; Pfeiffer, Ruth M.

    2013-01-01

    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

  20. Poisson-event-based analysis of cell proliferation.

    PubMed

    Summers, Huw D; Wills, John W; Brown, M Rowan; Rees, Paul

    2015-05-01

    A protocol for the assessment of cell proliferation dynamics is presented. This is based on the measurement of cell division events and their subsequent analysis using Poisson probability statistics. Detailed analysis of proliferation dynamics in heterogeneous populations requires single cell resolution within a time series analysis and so is technically demanding to implement. Here, we show that by focusing on the events during which cells undergo division rather than directly on the cells themselves a simplified image acquisition and analysis protocol can be followed, which maintains single cell resolution and reports on the key metrics of cell proliferation. The technique is demonstrated using a microscope with 1.3 μm spatial resolution to track mitotic events within A549 and BEAS-2B cell lines, over a period of up to 48 h. Automated image processing of the bright field images using standard algorithms within the ImageJ software toolkit yielded 87% accurate recording of the manually identified, temporal, and spatial positions of the mitotic event series. Analysis of the statistics of the interevent times (i.e., times between observed mitoses in a field of view) showed that cell division conformed to a nonhomogeneous Poisson process in which the rate of occurrence of mitotic events, λ exponentially increased over time and provided values of the mean inter mitotic time of 21.1 ± 1.2 hours for the A549 cells and 25.0 ± 1.1 h for the BEAS-2B cells. Comparison of the mitotic event series for the BEAS-2B cell line to that predicted by random Poisson statistics indicated that temporal synchronisation of the cell division process was occurring within 70% of the population and that this could be increased to 85% through serum starvation of the cell culture. © 2015 International Society for Advancement of Cytometry.

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

    PubMed Central

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

    2016-01-01

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

  2. Population Estimation in Singapore Based on Remote Sensing and Open Data

    NASA Astrophysics Data System (ADS)

    Guo, H.; Cao, K.; Wang, P.

    2017-09-01

    Population estimation statistics are widely used in government, commercial and educational sectors for a variety of purposes. With growing emphases on real-time and detailed population information, data users nowadays have switched from traditional census data to more technology-based data source such as LiDAR point cloud and High-Resolution Satellite Imagery. Nevertheless, such data are costly and periodically unavailable. In this paper, the authors use West Coast District, Singapore as a case study to investigate the applicability and effectiveness of using satellite image from Google Earth for extraction of building footprint and population estimation. At the same time, volunteered geographic information (VGI) is also utilized as ancillary data for building footprint extraction. Open data such as Open Street Map OSM could be employed to enhance the extraction process. In view of challenges in building shadow extraction, this paper discusses several methods including buffer, mask and shape index to improve accuracy. It also illustrates population estimation methods based on building height and number of floor estimates. The results show that the accuracy level of housing unit method on population estimation can reach 92.5 %, which is remarkably accurate. This paper thus provides insights into techniques for building extraction and fine-scale population estimation, which will benefit users such as urban planners in terms of policymaking and urban planning of Singapore.

  3. An obesity/cardiometabolic risk reduction disease management program: a population-based approach.

    PubMed

    Villagra, Victor G

    2009-04-01

    Obesity is a critical health concern that has captured the attention of public and private healthcare payers who are interested in controlling costs and mitigating the long-term economic consequences of the obesity epidemic. Population-based approaches to obesity management have been proposed that take advantage of a chronic care model (CCM), including patient self-care, the use of community-based resources, and the realization of care continuity through ongoing communications with patients, information technology, and public policy changes. Payer-sponsored disease management programs represent an important conduit to delivering population-based care founded on similar CCM concepts. Disease management is founded on population-based disease identification, evidence-based care protocols, and collaborative practices between clinicians. While substantial clinician training, technology infrastructure commitments, and financial support at the payer level will be needed for the success of disease management programs in obesity and cardiometabolic risk reduction, these barriers can be overcome with the proper commitment. Disease management programs represent an important tool to combat the growing societal risks of overweight and obesity.

  4. Effective population size and genetic structure of a Piute ground squirrel (Spermophilus mollis) population

    USGS Publications Warehouse

    Antolin, Michael F.; Van Horne, Beatrice; Berger, Michael D.

    2001-01-01

    Piute ground squirrels (Spermophilus mollis) are distributed continuously in habitat dominated by native shrubs and perennial grasses in the Snake River Birds of Prey National Conservation Area in Idaho, U.S.A. This habitat is being fragmented and replaced by exotic annual plants, changing it to a wildfire-dominated system that provides poor habitat for ground squirrels. To assess potential effects of this fragmentation on ground squirrel populations, we combined an estimate of effective population size (Ne) based upon a demographic study with a population genetic analysis. The study area included three subpopulations separated from each other by 8–13 km. The ratio of effective population size to census number (Ne/N) was 0.57. Combining Ne/N with dispersal distances from a radio-tracking study, we calculated that neighborhood size was 62.2 ha, which included between 204 and 480 individuals. Our population genetic analysis (based on randomly amplified polymorphic DNA (RAPD) and microsatellite markers) showed relatively low levels of genetic differentiation (Qpopulations 0.07–0.10) between subpopulations and no inbreeding within subpopulations (f = 0.0003). These estimates of population subdivision translate into an effective migration rate (Nem) of 2.3–3.3 per year, which represents a high level of gene flow. Invasion by exotics will reduce the overall productivity of the habitat, and will lead to isolation among subpopulations if favorable habitat patches become isolated.

  5. Predicting Health Care Utilization in Marginalized Populations: Black, Female, Street-based Sex Workers

    PubMed Central

    Varga, Leah M.; Surratt, Hilary L.

    2014-01-01

    Background Patterns of social and structural factors experienced by vulnerable populations may negatively affect willingness and ability to seek out health care services, and ultimately, their health. Methods The outcome variable was utilization of health care services in the previous 12 months. Using Andersen’s Behavioral Model for Vulnerable Populations, we examined self-reported data on utilization of health care services among a sample of 546 Black, street-based female sex workers in Miami, Florida. To evaluate the impact of each domain of the model on predicting health care utilization, domains were included in the logistic regression analysis by blocks using the traditional variables first and then adding the vulnerable domain variables. Findings The most consistent variables predicting health care utilization were having a regular source of care and self-rated health. The model that included only enabling variables was the most efficient model in predicting health care utilization. Conclusions Any type of resource, link, or connection to or with an institution, or any consistent point of care contributes significantly to health care utilization behaviors. A consistent and reliable source for health care may increase health care utilization and subsequently decrease health disparities among vulnerable and marginalized populations, as well as contribute to public health efforts that encourage preventive health. PMID:24657047

  6. Detecting population recovery using gametic disequilibrium-based effective population size estimates

    Treesearch

    David A. Tallmon; Robin S. Waples; Dave Gregovich; Michael K. Schwartz

    2012-01-01

    Recovering populations often must meet specific growth rate or abundance targets before their legal status can be changed from endangered or threatened. While the efficacy, power, and performance of population metrics to infer trends in declining populations has received considerable attention, how these same metrics perform when populations are increasing is less...

  7. Long-term survival and conditional survival of cancer patients in Japan using population-based cancer registry data

    PubMed Central

    Ito, Yuri; Miyashiro, Isao; Ito, Hidemi; Hosono, Satoyo; Chihara, Dai; Nakata-Yamada, Kayo; Nakayama, Masashi; Matsuzaka, Masashi; Hattori, Masakazu; Sugiyama, Hiromi; Oze, Isao; Tanaka, Rina; Nomura, Etsuko; Nishino, Yoshikazu; Matsuda, Tomohiro; Ioka, Akiko; Tsukuma, Hideaki; Nakayama, Tomio

    2014-01-01

    Although we usually report 5-year cancer survival using population-based cancer registry data, nowadays many cancer patients survive longer and need to be followed-up for more than 5 years. Long-term cancer survival figures are scarce in Japan. Here we report 10-year cancer survival and conditional survival using an established statistical approach. We received data on 1 387 489 cancer cases from six prefectural population-based cancer registries in Japan, diagnosed between 1993 and 2009 and followed-up for at least 5 years. We estimated the 10-year relative survival of patients who were followed-up between 2002 and 2006 using period analysis. Using this 10-year survival, we also calculated the conditional 5-year survival for cancer survivors who lived for some years after diagnosis. We reported 10-year survival and conditional survival of 23 types of cancer for 15–99-year-old patients and four types of cancer for children (0–14 years old) and adolescent and young adults (15–29 years old) patients by sex. Variation in 10-year cancer survival by site was wide, from 5% for pancreatic cancer to 95% for female thyroid cancer. Approximately 70–80% of children and adolescent and young adult cancer patients survived for more than 10 years. Conditional 5-year survival for most cancer sites increased according to years, whereas those for liver cancer and multiple myeloma did not increase. We reported 10-year cancer survival and conditional survival using population-based cancer registries in Japan. It is important for patients and clinicians to report these relevant figures using population-based data. PMID:25183551

  8. Predicting tuberculosis risk in the foreign-born population of British Columbia, Canada: study protocol for a retrospective population-based cohort study

    PubMed Central

    Ronald, Lisa A; Campbell, Jonathon R; Balshaw, Robert F; Roth, David Z; Romanowski, Kamila; Marra, Fawziah; Cook, Victoria J; Johnston, James C

    2016-01-01

    Introduction Improved understanding of risk factors for developing active tuberculosis (TB) will better inform decisions about diagnostic testing and treatment for latent TB infection (LTBI) in migrant populations in low-incidence regions. We aim to examine TB risk factors among the foreign-born population in British Columbia (BC), Canada, and to create and validate a clinically relevant multivariate risk score to predict active TB. Methods and analysis This retrospective population-based cohort study will include all foreign-born individuals who acquired permanent resident status in Canada between 1 January 1985 and 31 December 2013 and acquired healthcare coverage in BC at any point during this period. Multiple administrative databases and disease registries will be linked, including a National Immigration Database, BC Provincial Health Insurance Registration, physician billings, hospitalisations, drugs dispensed from community pharmacies, vital statistics, HIV testing and notifications, cancer, chronic kidney disease and dialysis treatment, and all TB and LTBI testing and treatment data in BC. Extended proportional hazards regression will be used to estimate risk factors for TB and to create a prognostic TB risk score. Ethics and dissemination Ethical approval for this study has been obtained from the University of British Columbia Clinical Ethics Review Board. Once completed, study findings will be presented at conferences and published in peer-reviewed journals. An online TB risk score calculator will also be created. PMID:27888179

  9. Population-based dietary approaches for the prevention of noncommunicable diseases.

    PubMed

    Somasundaram, Noel P; Kalupahana, Nishan Sudheera

    2016-04-01

    As the incidence of noncommunicable diseases such as diabetes continues to rise at an alarming rate in South-East Asia, it is imperative that urgent and population-wide strategies are adopted. The most important contributors to the rise in noncommunicable disease are a rise in mean caloric intake and a decrease in physical activity. The evidence for population-based dietary approaches to counter these factors is reviewed. Several structural and cohesive interdepartmental coordination efforts are required for effective implementation of prevention strategies. Since low- and middle-income countries may lack the frameworks for effective and integrated multi-stakeholder intervention, implementation of population-based dietary and physical-activity approaches may be delayed and may be too late for effective prevention in current at-risk cohorts. Evidence-based strategies to decrease energy intake and increase physical activity are now well established and their urgent adoption by Member States of the World Health Organization South-East Asia Region is essential. In the context of Sri Lanka, for example, it is recommended that the most effective and easy-to-implement interventions would be media campaigns, restrictions on advertisement of unhealthy foods, taxation of unhealthy foods, subsidies for production of healthy foods, and laws on nutrition labelling that introduce colour coding of packaged foods.

  10. Febrile seizures: a population-based study.

    PubMed

    Dalbem, Juliane S; Siqueira, Heloise H; Espinosa, Mariano M; Alvarenga, Regina P

    2015-01-01

    To determine the prevalence of benign febrile seizures of childhood and describe the clinical and epidemiological profile of this population. This was a population-based, cross-sectional study, carried out in the city of Barra do Bugres, MT, Brazil, from August 2012 to August 2013. Data were collected in two phases. In the first phase, a questionnaire that was previously validated in another Brazilian study was used to identify suspected cases of seizures. In the second phase, a neurological evaluation was performed to confirm diagnosis. The prevalence was 6.4/1000 inhabitants (95% CI: 3.8-10.1). There was no difference between genders. Simple febrile seizures were found in 88.8% of cases. A family history of febrile seizures in first-degree relatives and history of epilepsy was present in 33.3% and 11.1% of patients, respectively. The prevalence of febrile seizures in Midwestern Brazil was lower than that found in other Brazilian regions, probably due to the inclusion only of febrile seizures with motor manifestations and differences in socioeconomic factors among the evaluated areas. Copyright © 2015 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

  11. Use and impact of early endoscopy in elderly patients with peptic ulcer hemorrhage: a population-based analysis.

    PubMed

    Cooper, Gregory S; Kou, Tzyung Doug; Wong, Richard C K

    2009-08-01

    Upper endoscopy performed within 1 day of presentation, or early endoscopy, has been proposed as an intervention to improve the efficiency and outcomes of care for patients with peptic ulcer hemorrhage. However, the use and outcomes have not been studied in a national, U.S.-based sample. To determine the prevalence and associated outcomes of early versus delayed endoscopy in bleeding peptic ulcers. Using a 5% random sample of inpatient and outpatient Medicare claims from 2004 in patients aged 66 years and older (mean [standard deviation] age 78.4 +/- 7.7 years), we identified 2592 patients, all of whom underwent endoscopy. Univariate and multivariate models were used to determine factors associated with 30-day mortality, upper GI surgery, and length of hospital stay. Early endoscopy was performed in 1854 patients (71.5%) and was somewhat more common with outpatient management. Early endoscopy was independently associated with a significant decrease in the length of hospital stay (-1.95 days, 95% CI, -2.60 to -1.29 days) as well as a lower likelihood of surgery (odds ratio, 0.37; 95% CI, 0.21-0.66). Early endoscopy was not associated with 30-day mortality in either univariate or multivariate analyses. Use of claims data lacking clinical detail and restriction to the Medicare-age population. In this population-based study of older patients with peptic ulcer hemorrhage, early endoscopy was associated with increased efficiency of care, lower rates of surgery, and potentially improved control of hemorrhage. Thus, unless specific contraindications exist, the data support the routine use of early endoscopy.

  12. Regional analysis of population trajectories from the North American Breeding Bird Survey

    USGS Publications Warehouse

    Sauer, J.R.; Link, W.A.; Helbig, Andreas J.; Flade, Martin

    1999-01-01

    The North American Breeding Bird Survey (BBS) was started in 1966, and provides information on population change and distribution for most of the birds in North America. The geographic extent of the survey, and the logistical compromises needed to survey such a large area, present many challenges for estimation from BBS data. In this paper, we describe the survey and discuss some of the limitations of the survey design and implementation. Analysis of the survey has evolved over time as new statistical methods and insights into the analysis of count data are developed. Survey results and analysis tools for the BBS are now available over intemet; we present new methods that use generalized linear models for estimation of population change and empirical Bayes procedures for regional summaries.

  13. Cost-effectiveness analysis of HPV vaccination: comparing the general population with socially vulnerable individuals.

    PubMed

    Han, Kyu-Tae; Kim, Sun Jung; Lee, Seo Yoon; Park, Eun-Cheol

    2014-01-01

    After the WHO recommended HPV vaccination of the general population in 2009, government support of HPV vaccination programs was increased in many countries. However, this policy was not implemented in Korea due to perceived low cost-effectiveness. Thus, the aim of this study was to analyze the cost-utility of HPV vaccination programs targeted to high risk populations as compared to vaccination programs for the general population. Each study population was set to 100,000 people in a simulation study to determine the incremental cost-utility ratio (ICUR), then standard prevalence rates, cost, vaccination rates, vaccine efficacy, and the Quality-Adjusted Life-Years (QALYs) were applied to the analysis. In addition, sensitivity analysis was performed by assuming discounted vaccination cost. In the socially vulnerable population, QALYs gained through HPV vaccination were higher than that of the general population (General population: 1,019, Socially vulnerable population: 5,582). The results of ICUR showed that the cost of HPV vaccination was higher for the general population than the socially vulnerable population. (General population: 52,279,255 KRW, Socially vulnerable population: 9,547,347 KRW). Compared with 24 million KRW/QALYs as the social threshold, vaccination of the general population was not cost-effective. In contrast, vaccination of the socially vulnerable population was strongly cost-effective. The results suggest the importance and necessity of government support of HPV vaccination programs targeted to socially vulnerable populations because a targeted approach is much more cost-effective. The implementation of government support for such vaccination programs is a critical strategy for decreasing the burden of HPV infection in Korea.

  14. Prevalence of Inflammatory Bowel Disease in the Canton of Vaud (Switzerland): A population-based cohort study.

    PubMed

    Juillerat, Pascal; Pittet, Valérie; Bulliard, Jean-Luc; Guessous, Idris; Antonino, Anca Teodora; Mottet, Christian; Felley, Christian; Vader, John-Paul; Michetti, Pierre

    2008-06-01

    Because of the changing epidemiology of Inflammatory Bowel Diseases (IBD), we set out to characterize the population-based prevalence of Crohn's Disease (CD) and Ulcerative Colitis (UC) in a defined population of Switzerland. Adult IBD patients were identified by a cross-matched review of histological, hospital and gastroenterologist files throughout a geographical defined population (Canton of Vaud). Demographic factors statistically significantly associated with prevalence were evaluated using a stepwise Poisson regression analysis. Results were compared to IBD prevalence rates in other population-based studies and time trends were performed, based on a systematic literature review. Age and sex-adjusted prevalence rates were 205.7 IBD (100.7 CD and 105.0 UC) cases per 10(5) inhabitants. Among 1016 IBD patients (519 CD and 497 UC), females outnumbered males in CD (p<0.001), but males were more represented in elderly UC patients (p=0.008). Thus, being a male was statistically associated with UC (Relative Risk (RR) 1.25; p=0.013), whereas being a female was associated with CD (RR 1.27; p=0.007). Living in an urban zone was associated with both CD and UC (RR 1.49; p<0.001, 1.63; p<0.001, respectively). From 1960 to 2005, increases in UC and CD prevalences of 2.4% (95%CI, 2.1%-2.8%; p<0.001) and 3.6% (95%CI, 3.1%-4.1%; p<0.001) per annum were found in industrialised countries. Extrapolating our data to all of Switzerland yields an estimate of 12,000 IBD cases for the country, or 1 in 500 inhabitants. Our study gives support to an increase in IBD prevalence in Europe.

  15. A Danish population-based analysis of 105 mantle cell lymphoma patients: incidences, clinical features, response, survival and prognostic factors.

    PubMed

    Andersen, N S; Jensen, M K; de Nully Brown, P; Geisler, C H

    2002-02-01

    This study presents the first large clinical analysis of 105 unselected mantle cell lymphoma (MCL) patients diagnosed from 1992 to 2000 in a well-defined Danish population. The annual incidences were 0.7/100000 for men and 0.2/100000 for women, with no significant change during the study period. Of 97 evaluable cases, 43% achieved a complete response (CR) after initial therapy. The median disease-free (DFS) and overall survival (OS) rates were 15 and 30 months, respectively. In multivariate analysis, splenomegaly (P=0.002), anaemia (P=0.0001) and age (P=0.002), but not the international prognostic index (IPI) and the Ann Arbor staging system, had an independent impact on survival. Moreover, in a sub-analysis of 45 younger MCL patients (<65 years), a trend towards an OS plateau of 58% was observed in cases without splenomegaly and anaemia (n=29). Thus, in contrast to previously suggested prognostic factors, these variables may prove useful for clinical decisions in a significant subset of MCL patients.

  16. Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise

    PubMed Central

    Lah, Ljerka; Trense, Daronja; Benke, Harald; Berggren, Per; Gunnlaugsson, Þorvaldur; Lockyer, Christina; Öztürk, Ayaka; Öztürk, Bayram; Pawliczka, Iwona; Roos, Anna; Siebert, Ursula; Víkingsson, Gísli; Tiedemann, Ralph

    2016-01-01

    The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymorphisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis. PMID:27783621

  17. Population-based birth weight reference percentiles for Chinese twins.

    PubMed

    Dai, Li; Deng, Changfei; Li, Yanhua; Yi, Ling; Li, Xiaohong; Mu, Yi; Li, Qi; Yao, Qiang; Wang, Yanping

    2017-09-01

    Birth weight percentiles by gestational age are important for assessing prenatal growth and predicting postnatal outcomes of newborns. Several countries have developed nation-specific birth weight references for twins, but China still lacks such references. Birth weight data for twins born between October 2006 and September 2015 were abstracted from the China National Population-based Birth Defects Surveillance System. A total of 54,786 live twin births aged ≥28 weeks of gestation without birth defects were included in the analysis. The LMS method was adopted to generate gestational age-specific birth weight percentiles and curves for male and female twins separately. Significant differences were observed between the current reference and other references developed for Chinese or non-Chinese twins. The neonatal mortality rate in this cohort was 12.3‰, and much higher rates at very early gestation weeks were identified in small-for-gestational-age twins grouped by the newly developed reference cutoffs. The established birth weight centiles represent the first birth weight norm for contemporary Chinese twins and can be a useful tool to assess growth of twins in clinical and research settings. Key Messages There have been no population-based birth weight percentiles for Chinese twins prior to this study. The established birth weight centiles for female and male twins are markedly lower than those for Chinese singletons. Twin-specific curves should be used for determining inappropriate for gestational age in twins rather than using existing singleton reference. The birth weight percentiles for twins differed significantly from those for non-Chinese twins. In addition to ethnic influences, the observed differences could be ascribed to variations in prenatal care, fetal or maternal nutrition status or other environmental factors. Neonatal mortality rates varied considerably among twins grouped by the newly developed reference percentiles. Small

  18. Screening for Prostate Cancer Starting at Age 50-54. A Population-based Cohort Study

    PubMed Central

    Carlsson, Sigrid; Assel, Melissa; Ulmert, David; Gerdtsson, Axel; Hugosson, Jonas; Vickers, Andrew; Lilja, Hans

    2016-01-01

    Background Current prostate cancer screening guidelines conflict with respect to the age at which to initiate screening. Objective To evaluate the effect of prostate-specific antigen (PSA) screening, versus zero screening, starting at age 50-54, on prostate cancer mortality. Design, Setting, and Participants This is a population-based cohort study comparing 3,479 men aged 50 through 54 randomized to PSA-screening in the Göteborg population-based prostate cancer screening trial, initiated in 1995, versus 4,060 unscreened men aged 51 to 55 providing cryopreserved blood in the population-based Malmö Preventive Project in the pre-PSA era, during 1982-1985. Outcome measures and Statistical Analysis Cumulative incidence and incidence rate ratios of prostate cancer diagnosis, metastasis, and prostate cancer death. Results and Limitation At 17 years, regular PSA-screening in Göteborg of men in their early 50s carried a more than 2-fold higher risk of prostate cancer diagnosis compared to the unscreened men in Malmö (IRR 2.56, 95% CI 2.18, 3.02), but resulted in a substantial decrease in risk of metastases (IRR 0.43, 95% CI 0.22, 0.79) and prostate cancer death (IRR 0.29, 95% CI 0.11, 0.67). There were 57 fewer prostate cancer deaths per 10,000 men (95% CI 22, 92) in the screened group. At 17 years, the number needed to invite to PSA-screening and the number needed to diagnose to prevent one prostate cancer death was 176 and 16, respectively. The study is limited by lack of treatment information and the comparison of two different birth cohorts. Conclusions PSA screening for prostate cancer can decrease prostate cancer mortality among men aged 50–54, with NNI and NND comparable to those previously reported from the European Randomized Study of Screening for Prostate Cancer for men aged 55-69 years, at similar follow-up. Guideline groups could consider whether guidelines for PSA screening should recommend starting no later than at ages 50-54. Trial registration The G

  19. Interim 2001-based national population projections for the United Kingdom and constituent countries.

    PubMed

    Shaw, Chris

    2003-01-01

    This article describes new 2001-based national population projections which were carried out following the publication in September 2002 of the first results of the 2001 Census. These "interim" projections, carried out by the Government Actuary in consultation with the Registrars General, take preliminary account of the results of the Census which showed that the base population used in previous projections was overestimated. The interim projections also incorporate a reduced assumption of net international migration to the United Kingdom, informed by the first results of the 2001 Census and taking account of more recent migration information. The population of the United Kingdom is now projected to increase from an estimated 58.8 million in 2001 to reach 63.2 million by 2026. The projected population at 2026 is about 1.8 million (2.8 per cent) lower than in the previous (2000-based) projections.

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

    PubMed

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

    2017-06-01

    Oxytocin in the brain is related to empathy, which refers to the ability to understand and share others' internal states or responses. Previous studies have investigated the impact of OXTR rs53576, the most intensively examined polymorphism in the oxytocin receptor (OXTR) gene, on individual differences in empathy. However, these studies produced inconsistent results. In the current study, we reexamined the association of OXTR rs53576 with empathy in a relatively large population (N=1830) and also evaluated the association by a comprehensive meta-analysis (N=6631, 13 independent samples). The replication study indicated that OXTR rs53576 was indeed associated with individual differences in empathy. Individuals with a greater number of G alleles showed better empathic ability, particularly in fantasizing other's feelings and actions. The meta-analysis not only confirmed this association, but also indicated that the impact of this polymorphism was significant in both Europeans and Asians. These findings provide convincing evidence for the impact of OXTR rs53576 on empathy, highlighting the importance of OXTR gene in individuals' social cognition. Copyright © 2017. Published by Elsevier Ltd.