Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse

PubMed Central

2013-01-01

Background Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate. Results Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species. Conclusions When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied. PMID:23281913

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

NASA Astrophysics Data System (ADS)

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

2016-03-01

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

Linking population viability, habitat suitability, and landscape simulation models for conservation planning

Treesearch

Michael A. Larson; Frank R., III Thompson; Joshua J. Millspaugh; William D. Dijak; Stephen R. Shifley

2004-01-01

Methods for habitat modeling based on landscape simulations and population viability modeling based on habitat quality are well developed, but no published study of which we are aware has effectively joined them in a single, comprehensive analysis. We demonstrate the application of a population viability model for ovenbirds (Seiurus aurocapillus)...

[Hierarchical regionalization for spatial epidemiology: a case study of thyroid cancer incidence in Yiwu, Zhejiang].

PubMed

Teng, Shizhu; Jia, Qiaojuan; Huang, Yijian; Chen, Liangcao; Fei, Xufeng; Wu, Jiaping

2015-10-01

Sporadic cases occurring in mall geographic unit could lead to extreme value of incidence due to the small population bases, which would influence the analysis of actual incidence. This study introduced a method of hierarchy clustering and partitioning regionalization, which integrates areas with small population into larger areas with enough population by using Geographic Information System (GIS) based on the principles of spatial continuity and geographical similarity (homogeneity test). This method was applied in spatial epidemiology by using a data set of thyroid cancer incidence in Yiwu, Zhejiang province, between 2010 and 2013. Thyroid cancer incidence data were more reliable and stable in the new regionalized areas. Hotspot analysis (Getis-Ord) on the incidence in new areas indicated that there was obvious case clustering in the central area of Yiwu. This method can effectively solve the problem of small population base in small geographic units in spatial epidemiological analysis of thyroid cancer incidence and can be used for other diseases and in other areas.

Conduct of a personal radiofrequency electromagnetic field measurement study: proposed study protocol.

PubMed

Röösli, Martin; Frei, Patrizia; Bolte, John; Neubauer, Georg; Cardis, Elisabeth; Feychting, Maria; Gajsek, Peter; Heinrich, Sabine; Joseph, Wout; Mann, Simon; Martens, Luc; Mohler, Evelyn; Parslow, Roger C; Poulsen, Aslak Harbo; Radon, Katja; Schüz, Joachim; Thuroczy, György; Viel, Jean-François; Vrijheid, Martine

2010-05-20

The development of new wireless communication technologies that emit radio frequency electromagnetic fields (RF-EMF) is ongoing, but little is known about the RF-EMF exposure distribution in the general population. Previous attempts to measure personal exposure to RF-EMF have used different measurement protocols and analysis methods making comparisons between exposure situations across different study populations very difficult. As a result, observed differences in exposure levels between study populations may not reflect real exposure differences but may be in part, or wholly due to methodological differences. The aim of this paper is to develop a study protocol for future personal RF-EMF exposure studies based on experience drawn from previous research. Using the current knowledge base, we propose procedures for the measurement of personal exposure to RF-EMF, data collection, data management and analysis, and methods for the selection and instruction of study participants. We have identified two basic types of personal RF-EMF measurement studies: population surveys and microenvironmental measurements. In the case of a population survey, the unit of observation is the individual and a randomly selected representative sample of the population is needed to obtain reliable results. For microenvironmental measurements, study participants are selected in order to represent typical behaviours in different microenvironments. These two study types require different methods and procedures. Applying our proposed common core procedures in future personal measurement studies will allow direct comparisons of personal RF-EMF exposures in different populations and study areas.

Nose profile morphology and accuracy study of nose profile estimation method in Scottish subadult and Indonesian adult populations.

PubMed

Sarilita, Erli; Rynn, Christopher; Mossey, Peter A; Black, Sue; Oscandar, Fahmi

2018-05-01

This study investigated nose profile morphology and its relationship to the skull in Scottish subadult and Indonesian adult populations, with the aim of improving the accuracy of forensic craniofacial reconstruction. Samples of 86 lateral head cephalograms from Dundee Dental School (mean age, 11.8 years) and 335 lateral head cephalograms from the Universitas Padjadjaran Dental Hospital, Bandung, Indonesia (mean age 24.2 years), were measured. The method of nose profile estimation based on skull morphology previously proposed by Rynn and colleagues in 2010 (FSMP 6:20-34) was tested in this study. Following this method, three nasal aperture-related craniometrics and six nose profile dimensions were measured from the cephalograms. To assess the accuracy of the method, six nose profile dimensions were estimated from the three craniometric parameters using the published method and then compared to the actual nose profile dimensions.In the Scottish subadult population, no sexual dimorphism was evident in the measured dimensions. In contrast, sexual dimorphism of the Indonesian adult population was evident in all craniometric and nose profile dimensions; notably, males exhibited statistically significant larger values than females. The published method by Rynn and colleagues (FSMP 6:20-34, 2010) performed better in the Scottish subadult population (mean difference of maximum, 2.35 mm) compared to the Indonesian adult population (mean difference of maximum, 5.42 mm in males and 4.89 mm in females).In addition, regression formulae were derived to estimate nose profile dimensions based on the craniometric measurements for the Indonesian adult population. The published method is not sufficiently accurate for use on the Indonesian population, so the derived method should be used. The accuracy of the published method by Rynn and colleagues (FSMP 6:20-34, 2010) was sufficiently reliable to be applied in Scottish subadult population.

[Epidemiological methods used in studies in the prevalence of Tourette syndrome].

PubMed

Stefanoff, Paweł; Mazurek, Jacek

2003-01-01

Tourette syndrome (TS) prevalence was studied since the early 80-ies. Its clinical course is characterised by co-occurrence of motor and vocal tics. Results of previous epidemiological studies were surprisingly divergent: the prevalence varied from 0.5 to 115 cases per 10,000 population. The disease previously recognised as extremely rare and severe is now considered as quite common, with often moderate course. Selected methods used in studies of TS prevalence and analysis of their possible impact on study results are presented. The studies were divided into 3 groups: studies of the hospitalised population, large-scale screenings and studies involving school population, basing on characteristic and size of population, methods of selection of subjects, diagnostic and screening methods used. Studies of the hospitalised population involved patients with most severe symptoms, in different age groups, different methods of final diagnosis confirmation were used. TS prevalence varied from 0.5 up to 15 cases per 10,000 population. Procedures used in large-scale screening studies made possible the elimination of potential selection bias. Large populations were studied using transparent and repetitive confirmation of diagnoses. Their validity was additionally checked in parallel validity studies. TS prevalence was in the range 4.3 to 10 cases per 10,000 population. The highest TS prevalence was obtained in studies involving schoolchildren. Data were gathered from multiple sources: from parents, teachers and children, as well as from classroom observation. Diagnoses were made by experienced clinicians. TS prevalence obtained in school population studies was between 36.2 up to 115 per 10,000 population.

Evaluating the performance of the Lee-Carter method and its variants in modelling and forecasting Malaysian mortality

NASA Astrophysics Data System (ADS)

Zakiyatussariroh, W. H. Wan; Said, Z. Mohammad; Norazan, M. R.

2014-12-01

This study investigated the performance of the Lee-Carter (LC) method and it variants in modeling and forecasting Malaysia mortality. These include the original LC, the Lee-Miller (LM) variant and the Booth-Maindonald-Smith (BMS) variant. These methods were evaluated using Malaysia's mortality data which was measured based on age specific death rates (ASDR) for 1971 to 2009 for overall population while those for 1980-2009 were used in separate models for male and female population. The performance of the variants has been examined in term of the goodness of fit of the models and forecasting accuracy. Comparison was made based on several criteria namely, mean square error (MSE), root mean square error (RMSE), mean absolute deviation (MAD) and mean absolute percentage error (MAPE). The results indicate that BMS method was outperformed in in-sample fitting for overall population and when the models were fitted separately for male and female population. However, in the case of out-sample forecast accuracy, BMS method only best when the data were fitted to overall population. When the data were fitted separately for male and female, LCnone performed better for male population and LM method is good for female population.

Field-based random sampling without a sampling frame: control selection for a case-control study in rural Africa.

PubMed

Crampin, A C; Mwinuka, V; Malema, S S; Glynn, J R; Fine, P E

2001-01-01

Selection bias, particularly of controls, is common in case-control studies and may materially affect the results. Methods of control selection should be tailored both for the risk factors and disease under investigation and for the population being studied. We present here a control selection method devised for a case-control study of tuberculosis in rural Africa (Karonga, northern Malawi) that selects an age/sex frequency-matched random sample of the population, with a geographical distribution in proportion to the population density. We also present an audit of the selection process, and discuss the potential of this method in other settings.

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.

Differential estimates of southern flying squirrel (Glaucomys volans) population structure based on capture method

Treesearch

Kevin S. Laves; Susan C. Loeb

2005-01-01

It is commonly assumed that population estimates derived from trapping small mammals are accurate and unbiased or that estimates derived from different capture methods are comparable. We captured southern flying squirrels (Glaucmrtys volam) using two methods to study their effect on red-cockaded woodpecker (Picoides bumah) reproductive success. Southern flying...

An AFM-based pit-measuring method for indirect measurements of cell-surface membrane vesicles

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

Zhang, Xiaojun; Department of Biotechnology, Nanchang University, Nanchang, Jiangxi 330031; Chen, Yuan

2014-03-28

Highlights: • Air drying induced the transformation of cell-surface membrane vesicles into pits. • An AFM-based pit-measuring method was developed to measure cell-surface vesicles. • Our method detected at least two populations of cell-surface membrane vesicles. - Abstract: Circulating membrane vesicles, which are shed from many cell types, have multiple functions and have been correlated with many diseases. Although circulating membrane vesicles have been extensively characterized, the status of cell-surface membrane vesicles prior to their release is less understood due to the lack of effective measurement methods. Recently, as a powerful, micro- or nano-scale imaging tool, atomic force microscopy (AFM)more » has been applied in measuring circulating membrane vesicles. However, it seems very difficult for AFM to directly image/identify and measure cell-bound membrane vesicles due to the similarity of surface morphology between membrane vesicles and cell surfaces. Therefore, until now no AFM studies on cell-surface membrane vesicles have been reported. In this study, we found that air drying can induce the transformation of most cell-surface membrane vesicles into pits that are more readily detectable by AFM. Based on this, we developed an AFM-based pit-measuring method and, for the first time, used AFM to indirectly measure cell-surface membrane vesicles on cultured endothelial cells. Using this approach, we observed and quantitatively measured at least two populations of cell-surface membrane vesicles, a nanoscale population (<500 nm in diameter peaking at ∼250 nm) and a microscale population (from 500 nm to ∼2 μm peaking at ∼0.8 μm), whereas confocal microscopy only detected the microscale population. The AFM-based pit-measuring method is potentially useful for studying cell-surface membrane vesicles and for investigating the mechanisms of membrane vesicle formation/release.« less

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

Count data, detection probabilities, and the demography, dynamics, distribution, and decline of amphibians.

PubMed

Schmidt, Benedikt R

2003-08-01

The evidence for amphibian population declines is based on count data that were not adjusted for detection probabilities. Such data are not reliable even when collected using standard methods. The formula C = Np (where C is a count, N the true parameter value, and p is a detection probability) relates count data to demography, population size, or distributions. With unadjusted count data, one assumes a linear relationship between C and N and that p is constant. These assumptions are unlikely to be met in studies of amphibian populations. Amphibian population data should be based on methods that account for detection probabilities.

Psychological Abuse between Parents: Associations with Child Maltreatment from a Population-Based Sample

ERIC Educational Resources Information Center

Chang, Jen Jen; Theodore, Adrea D.; Martin, Sandra L.; Runyan, Desmond K.

2008-01-01

Objective: This study examined the association between partner psychological abuse and child maltreatment perpetration. Methods: This cross-sectional study examined a population-based sample of mothers with children aged 0-17 years in North and South Carolina (n = 1,149). Mothers were asked about the occurrence of potentially neglectful or abusive…

Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study.

PubMed

Fan, Ming; Kuwahara, Hiroyuki; Wang, Xiaolei; Wang, Suojin; Gao, Xin

2015-11-01

Parameter estimation is a challenging computational problem in the reverse engineering of biological systems. Because advances in biotechnology have facilitated wide availability of time-series gene expression data, systematic parameter estimation of gene circuit models from such time-series mRNA data has become an important method for quantitatively dissecting the regulation of gene expression. By focusing on the modeling of gene circuits, we examine here the performance of three types of state-of-the-art parameter estimation methods: population-based methods, online methods and model-decomposition-based methods. Our results show that certain population-based methods are able to generate high-quality parameter solutions. The performance of these methods, however, is heavily dependent on the size of the parameter search space, and their computational requirements substantially increase as the size of the search space increases. In comparison, online methods and model decomposition-based methods are computationally faster alternatives and are less dependent on the size of the search space. Among other things, our results show that a hybrid approach that augments computationally fast methods with local search as a subsequent refinement procedure can substantially increase the quality of their parameter estimates to the level on par with the best solution obtained from the population-based methods while maintaining high computational speed. These suggest that such hybrid methods can be a promising alternative to the more commonly used population-based methods for parameter estimation of gene circuit models when limited prior knowledge about the underlying regulatory mechanisms makes the size of the parameter search space vastly large. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Robust inference of population structure for ancestry prediction and correction of stratification in the presence of relatedness.

PubMed

Conomos, Matthew P; Miller, Michael B; Thornton, Timothy A

2015-05-01

Population structure inference with genetic data has been motivated by a variety of applications in population genetics and genetic association studies. Several approaches have been proposed for the identification of genetic ancestry differences in samples where study participants are assumed to be unrelated, including principal components analysis (PCA), multidimensional scaling (MDS), and model-based methods for proportional ancestry estimation. Many genetic studies, however, include individuals with some degree of relatedness, and existing methods for inferring genetic ancestry fail in related samples. We present a method, PC-AiR, for robust population structure inference in the presence of known or cryptic relatedness. PC-AiR utilizes genome-screen data and an efficient algorithm to identify a diverse subset of unrelated individuals that is representative of all ancestries in the sample. The PC-AiR method directly performs PCA on the identified ancestry representative subset and then predicts components of variation for all remaining individuals based on genetic similarities. In simulation studies and in applications to real data from Phase III of the HapMap Project, we demonstrate that PC-AiR provides a substantial improvement over existing approaches for population structure inference in related samples. We also demonstrate significant efficiency gains, where a single axis of variation from PC-AiR provides better prediction of ancestry in a variety of structure settings than using 10 (or more) components of variation from widely used PCA and MDS approaches. Finally, we illustrate that PC-AiR can provide improved population stratification correction over existing methods in genetic association studies with population structure and relatedness. © 2015 WILEY PERIODICALS, INC.

Effect of genotyped cows in the reference population on the genomic evaluation of Holstein cattle.

PubMed

Uemoto, Y; Osawa, T; Saburi, J

2017-03-01

This study evaluated the dependence of reliability and prediction bias on the prediction method, the contribution of including animals (bulls or cows), and the genetic relatedness, when including genotyped cows in the progeny-tested bull reference population. We performed genomic evaluation using a Japanese Holstein population, and assessed the accuracy of genomic enhanced breeding value (GEBV) for three production traits and 13 linear conformation traits. A total of 4564 animals for production traits and 4172 animals for conformation traits were genotyped using Illumina BovineSNP50 array. Single- and multi-step methods were compared for predicting GEBV in genotyped bull-only and genotyped bull-cow reference populations. No large differences in realized reliability and regression coefficient were found between the two reference populations; however, a slight difference was found between the two methods for production traits. The accuracy of GEBV determined by single-step method increased slightly when genotyped cows were included in the bull reference population, but decreased slightly by multi-step method. A validation study was used to evaluate the accuracy of GEBV when 800 additional genotyped bulls (POPbull) or cows (POPcow) were included in the base reference population composed of 2000 genotyped bulls. The realized reliabilities of POPbull were higher than those of POPcow for all traits. For the gain of realized reliability over the base reference population, the average ratios of POPbull gain to POPcow gain for production traits and conformation traits were 2.6 and 7.2, respectively, and the ratios depended on heritabilities of the traits. For regression coefficient, no large differences were found between the results for POPbull and POPcow. Another validation study was performed to investigate the effect of genetic relatedness between cows and bulls in the reference and test populations. The effect of genetic relationship among bulls in the reference population was also assessed. The results showed that it is important to account for relatedness among bulls in the reference population. Our studies indicate that the prediction method, the contribution ratio of including animals, and genetic relatedness could affect the prediction accuracy in genomic evaluation of Holstein cattle, when including genotyped cows in the reference population.

A Comparison of Rule-based Analysis with Regression Methods in Understanding the Risk Factors for Study Withdrawal in a Pediatric Study.

PubMed

Haghighi, Mona; Johnson, Suzanne Bennett; Qian, Xiaoning; Lynch, Kristian F; Vehik, Kendra; Huang, Shuai

2016-08-26

Regression models are extensively used in many epidemiological studies to understand the linkage between specific outcomes of interest and their risk factors. However, regression models in general examine the average effects of the risk factors and ignore subgroups with different risk profiles. As a result, interventions are often geared towards the average member of the population, without consideration of the special health needs of different subgroups within the population. This paper demonstrates the value of using rule-based analysis methods that can identify subgroups with heterogeneous risk profiles in a population without imposing assumptions on the subgroups or method. The rules define the risk pattern of subsets of individuals by not only considering the interactions between the risk factors but also their ranges. We compared the rule-based analysis results with the results from a logistic regression model in The Environmental Determinants of Diabetes in the Young (TEDDY) study. Both methods detected a similar suite of risk factors, but the rule-based analysis was superior at detecting multiple interactions between the risk factors that characterize the subgroups. A further investigation of the particular characteristics of each subgroup may detect the special health needs of the subgroup and lead to tailored interventions.

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

[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.

The role of self-defined race/ethnicity in population structure control.

PubMed

Liu, X-Q; Paterson, A D; John, E M; Knight, J A

2006-07-01

Population-based association studies are powerful tools for the genetic mapping of complex diseases. However, this method is sensitive to potential confounding by population structure. While statistical methods that use genetic markers to detect and control for population structure have been the focus of current literature, the utility of self-defined race/ethnicity in controlling for population structure has been controversial. In this study of 1334 individuals, who self-identified as either African American, European American or Hispanic, we demonstrated that when the true underlying genetic structure and the self-defined racial/ethnic groups were roughly in agreement with each other, the self-defined race/ethnicity information was useful in the control of population structure.

Advancing Methods for U.S. Transgender Health Research

PubMed Central

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

2016-01-01

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

Confidence intervals for population allele frequencies: the general case of sampling from a finite diploid population of any size.

PubMed

Fung, Tak; Keenan, Kevin

2014-01-01

The estimation of population allele frequencies using sample data forms a central component of studies in population genetics. These estimates can be used to test hypotheses on the evolutionary processes governing changes in genetic variation among populations. However, existing studies frequently do not account for sampling uncertainty in these estimates, thus compromising their utility. Incorporation of this uncertainty has been hindered by the lack of a method for constructing confidence intervals containing the population allele frequencies, for the general case of sampling from a finite diploid population of any size. In this study, we address this important knowledge gap by presenting a rigorous mathematical method to construct such confidence intervals. For a range of scenarios, the method is used to demonstrate that for a particular allele, in order to obtain accurate estimates within 0.05 of the population allele frequency with high probability (> or = 95%), a sample size of > 30 is often required. This analysis is augmented by an application of the method to empirical sample allele frequency data for two populations of the checkerspot butterfly (Melitaea cinxia L.), occupying meadows in Finland. For each population, the method is used to derive > or = 98.3% confidence intervals for the population frequencies of three alleles. These intervals are then used to construct two joint > or = 95% confidence regions, one for the set of three frequencies for each population. These regions are then used to derive a > or = 95%% confidence interval for Jost's D, a measure of genetic differentiation between the two populations. Overall, the results demonstrate the practical utility of the method with respect to informing sampling design and accounting for sampling uncertainty in studies of population genetics, important for scientific hypothesis-testing and also for risk-based natural resource management.

Applying Research Methods to a Gerontological Population: Matching Data Collection to Characteristics of Older Persons

ERIC Educational Resources Information Center

Weil, Joyce

2015-01-01

As Baby Boomers reach 65 years of age and methods of studying older populations are becoming increasingly varied (e.g., including mixed methods designs, on-line surveys, and video-based environments), there is renewed interest in evaluating methodologies used to collect data with older persons. The goal of this article is to examine…

Genealogy-based methods for inference of historical recombination and gene flow and their application in Saccharomyces cerevisiae.

PubMed

Jenkins, Paul A; Song, Yun S; Brem, Rachel B

2012-01-01

Genetic exchange between isolated populations, or introgression between species, serves as a key source of novel genetic material on which natural selection can act. While detecting historical gene flow from DNA sequence data is of much interest, many existing methods can be limited by requirements for deep population genomic sampling. In this paper, we develop a scalable genealogy-based method to detect candidate signatures of gene flow into a given population when the source of the alleles is unknown. Our method does not require sequenced samples from the source population, provided that the alleles have not reached fixation in the sampled recipient population. The method utilizes recent advances in algorithms for the efficient reconstruction of ancestral recombination graphs, which encode genealogical histories of DNA sequence data at each site, and is capable of detecting the signatures of gene flow whose footprints are of length up to single genes. Further, we employ a theoretical framework based on coalescent theory to test for statistical significance of certain recombination patterns consistent with gene flow from divergent sources. Implementing these methods for application to whole-genome sequences of environmental yeast isolates, we illustrate the power of our approach to highlight loci with unusual recombination histories. By developing innovative theory and methods to analyze signatures of gene flow from population sequence data, our work establishes a foundation for the continued study of introgression and its evolutionary relevance.

Genealogy-Based Methods for Inference of Historical Recombination and Gene Flow and Their Application in Saccharomyces cerevisiae

PubMed Central

Jenkins, Paul A.; Song, Yun S.; Brem, Rachel B.

2012-01-01

Genetic exchange between isolated populations, or introgression between species, serves as a key source of novel genetic material on which natural selection can act. While detecting historical gene flow from DNA sequence data is of much interest, many existing methods can be limited by requirements for deep population genomic sampling. In this paper, we develop a scalable genealogy-based method to detect candidate signatures of gene flow into a given population when the source of the alleles is unknown. Our method does not require sequenced samples from the source population, provided that the alleles have not reached fixation in the sampled recipient population. The method utilizes recent advances in algorithms for the efficient reconstruction of ancestral recombination graphs, which encode genealogical histories of DNA sequence data at each site, and is capable of detecting the signatures of gene flow whose footprints are of length up to single genes. Further, we employ a theoretical framework based on coalescent theory to test for statistical significance of certain recombination patterns consistent with gene flow from divergent sources. Implementing these methods for application to whole-genome sequences of environmental yeast isolates, we illustrate the power of our approach to highlight loci with unusual recombination histories. By developing innovative theory and methods to analyze signatures of gene flow from population sequence data, our work establishes a foundation for the continued study of introgression and its evolutionary relevance. PMID:23226196

Genotyping faecal samples of Bengal tiger Panthera tigris tigris for population estimation: a pilot study.

PubMed

Bhagavatula, Jyotsna; Singh, Lalji

2006-10-17

Bengal tiger Panthera tigris tigris the National Animal of India, is an endangered species. Estimating populations for such species is the main objective for designing conservation measures and for evaluating those that are already in place. Due to the tiger's cryptic and secretive behaviour, it is not possible to enumerate and monitor its populations through direct observations; instead indirect methods have always been used for studying tigers in the wild. DNA methods based on non-invasive sampling have not been attempted so far for tiger population studies in India. We describe here a pilot study using DNA extracted from faecal samples of tigers for the purpose of population estimation. In this study, PCR primers were developed based on tiger-specific variations in the mitochondrial cytochrome b for reliably identifying tiger faecal samples from those of sympatric carnivores. Microsatellite markers were developed for the identification of individual tigers with a sibling Probability of Identity of 0.005 that can distinguish even closely related individuals with 99.9% certainty. The effectiveness of using field-collected tiger faecal samples for DNA analysis was evaluated by sampling, identification and subsequently genotyping samples from two protected areas in southern India. Our results demonstrate the feasibility of using tiger faecal matter as a potential source of DNA for population estimation of tigers in protected areas in India in addition to the methods currently in use.

Population structure of Angiostrongylus cantonensis (Nematoda: Metastrongylidae) in Thailand based on PCR-RAPD markers.

PubMed

Thaenkham, Urusa; Pakdee, Wallop; Nuamtanong, Supaporn; Maipanich, Wanna; Pubampen, Somchit; Sa-Nguankiat, Surapol; Komalamisra, Chalit

2012-05-01

Angiostrongylus cantonensis is the causative agent of angiostrongyliasis, which is widely distributed throughout the world. It can specifically infect many species of intermediate and definitive hosts. This study examined the genetic differentiation and population structure using the RAPD-PCR method of parasites obtained from 8 different geographical areas of Thailand. Based on 8 primers, high levels of genetic diversity and low levels of gene flow among populations were found. Using genetic distance and neighbor-joining dendrogram methods, A. cantonensis in Thailand could be divided into two groups with statistically significant genetic differentiation of the two populations. However, genotypic variations and haplotype relationships need to be further elucidated using other markers.

Diagnosis of Dementia by Machine learning methods in Epidemiological studies: a pilot exploratory study from south India.

PubMed

Bhagyashree, Sheshadri Iyengar Raghavan; Nagaraj, Kiran; Prince, Martin; Fall, Caroline H D; Krishna, Murali

2018-01-01

There are limited data on the use of artificial intelligence methods for the diagnosis of dementia in epidemiological studies in low- and middle-income country (LMIC) settings. A culture and education fair battery of cognitive tests was developed and validated for population based studies in low- and middle-income countries including India by the 10/66 Dementia Research Group. We explored the machine learning methods based on the 10/66 battery of cognitive tests for the diagnosis of dementia based in a birth cohort study in South India. The data sets for 466 men and women for this study were obtained from the on-going Mysore Studies of Natal effect of Health and Ageing (MYNAH), in south India. The data sets included: demographics, performance on the 10/66 cognitive function tests, the 10/66 diagnosis of mental disorders and population based normative data for the 10/66 battery of cognitive function tests. Diagnosis of dementia from the rule based approach was compared against the 10/66 diagnosis of dementia. We have applied machine learning techniques to identify minimal number of the 10/66 cognitive function tests required for diagnosing dementia and derived an algorithm to improve the accuracy of dementia diagnosis. Of 466 subjects, 27 had 10/66 diagnosis of dementia, 19 of whom were correctly identified as having dementia by Jrip classification with 100% accuracy. This pilot exploratory study indicates that machine learning methods can help identify community dwelling older adults with 10/66 criterion diagnosis of dementia with good accuracy in a LMIC setting such as India. This should reduce the duration of the diagnostic assessment and make the process easier and quicker for clinicians, patients and will be useful for 'case' ascertainment in population based epidemiological studies.

Computing travel time when the exact address is unknown: a comparison of point and polygon ZIP code approximation methods.

PubMed

Berke, Ethan M; Shi, Xun

2009-04-29

Travel time is an important metric of geographic access to health care. We compared strategies of estimating travel times when only subject ZIP code data were available. Using simulated data from New Hampshire and Arizona, we estimated travel times to nearest cancer centers by using: 1) geometric centroid of ZIP code polygons as origins, 2) population centroids as origin, 3) service area rings around each cancer center, assigning subjects to rings by assuming they are evenly distributed within their ZIP code, 4) service area rings around each center, assuming the subjects follow the population distribution within the ZIP code. We used travel times based on street addresses as true values to validate estimates. Population-based methods have smaller errors than geometry-based methods. Within categories (geometry or population), centroid and service area methods have similar errors. Errors are smaller in urban areas than in rural areas. Population-based methods are superior to the geometry-based methods, with the population centroid method appearing to be the best choice for estimating travel time. Estimates in rural areas are less reliable.

Validity of body composition methods across ethnic population groups.

PubMed

Deurenberg, P; Deurenberg-Yap, M

2003-10-01

Most in vivo body composition methods rely on assumptions that may vary among different population groups as well as within the same population group. The assumptions are based on in vitro body composition (carcass) analyses. The majority of body composition studies were performed on Caucasians and much of the information on validity methods and assumptions were available only for this ethnic group. It is assumed that these assumptions are also valid for other ethnic groups. However, if apparent differences across ethnic groups in body composition 'constants' and body composition 'rules' are not taken into account, biased information on body composition will be the result. This in turn may lead to misclassification of obesity or underweight at an individual as well as a population level. There is a need for more cross-ethnic population studies on body composition. Those studies should be carried out carefully, with adequate methodology and standardization for the obtained information to be valuable.

Population Size Estimation of Men Who Have Sex with Men in Tbilisi, Georgia; Multiple Methods and Triangulation of Findings.

PubMed

Sulaberidze, Lela; Mirzazadeh, Ali; Chikovani, Ivdity; Shengelia, Natia; Tsereteli, Nino; Gotsadze, George

2016-01-01

An accurate estimation of the population size of men who have sex with men (MSM) is critical to the success of HIV program planning and to monitoring of the response to epidemic as a whole, but is quite often missing. In this study, our aim was to estimate the population size of MSM in Tbilisi, Georgia and compare it with other estimates in the region. In the absence of a gold standard for estimating the population size of MSM, this study reports a range of methods, including network scale-up, mobile/web apps multiplier, service and unique object multiplier, network-based capture-recapture, Handcock RDS-based and Wisdom of Crowds methods. To apply all these methods, two surveys were conducted: first, a household survey among 1,015 adults from the general population, and second, a respondent driven sample of 210 MSM. We also conducted a literature review of MSM size estimation in Eastern European and Central Asian countries. The median population size of MSM generated from all previously mentioned methods was estimated to be 5,100 (95% Confidence Interval (CI): 3,243~9,088). This corresponds to 1.42% (95%CI: 0.9%~2.53%) of the adult male population in Tbilisi. Our size estimates of the MSM population (1.42% (95%CI: 0.9%~2.53%) of the adult male population in Tbilisi) fall within ranges reported in other Eastern European and Central Asian countries. These estimates can provide valuable information for country level HIV prevention program planning and evaluation. Furthermore, we believe, that our results will narrow the gap in data availability on the estimates of the population size of MSM in the region.

Systematic Review of the Use of Online Questionnaires among the Geriatric Population

PubMed Central

Remillard, Meegan L.; Mazor, Kathleen M.; Cutrona, Sarah L.; Gurwitz, Jerry H.; Tjia, Jennifer

2014-01-01

Background/Objectives The use of internet-based questionnaires to collect information from older adults is not well established. This systematic literature review of studies using online questionnaires in older adult populations aims to 1. describe methodologic approaches to population targeting and sampling and 2. summarize limitations of Internet-based questionnaires in geriatric populations. Design, Setting, Participants We identified English language articles using search terms for geriatric, age 65 and over, Internet survey, online survey, Internet questionnaire, and online questionnaire in PubMed and EBSCO host between 1984 and July 2012. Inclusion criteria were: study population mean age ≥65 years old and use of an online questionnaire for research. Review of 336 abstracts yielded 14 articles for full review by 2 investigators; 11 articles met inclusion criteria. Measurements Articles were extracted for study design and setting, patient characteristics, recruitment strategy, country, and study limitations. Results Eleven (11) articles were published after 2001. Studies had populations with a mean age of 65 to 78 years, included descriptive and analytical designs, and were conducted in the United States, Australia, and Japan. Recruiting methods varied widely from paper fliers and personal emails to use of consumer marketing panels. Investigator-reported study limitations included the use of small convenience samples and limited generalizability. Conclusion Online questionnaires are a feasible method of surveying older adults in some geographic regions and for some subsets of older adults, but limited Internet access constrains recruiting methods and often limits study generalizability. PMID:24635138

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.

Mixed-Methods for Comparing Tobacco Cessation Interventions

PubMed Central

Momin, Behnoosh; Neri, Antonio; Zhang, Lei; Kahende, Jennifer; Duke, Jennifer; Green, Sonya Goode; Malarcher, Ann; Stewart, Sherri L.

2017-01-01

Introduction The National Comprehensive Cancer Control Program (NCCCP) and National Tobacco Control Program (NTCP) are both well-positioned to promote the use of population-based tobacco cessation interventions, such as state quitlines and Web-based interventions. Aims This paper outlines the methodology used to conduct a comparative effectiveness research study of traditional and Web-based tobacco cessation and quitline promotion approaches. Methods A mixed-methods study with three components was designed to address the effect of promotional activities on service usage and the comparative effectiveness of population-based smoking cessation activities across multiple states. Results/Findings The cessation intervention component followed 7,902 smokers (4,307 quitline users and 3,595 Web intervention users) to ascertain prevalence of 30-day abstinence rates 7 months after registering for smoking cessation services. User characteristics and quit success was compared across the two modalities. In the promotions component, reach and use of traditional and innovative promotion strategies were assessed for 24 states, including online advertising, state Web sites, social media, mobile applications, and their effects on quitline call volume. The partnership intervention component studied the extent of collaboration among six selected NCCCPs and NTCPs. Conclusions This study will guide program staff and clinicians with evidence-based recommendations and best practices for implementation of tobacco cessation within their patient and community populations and establish an evidence base that can be used for decision making. PMID:28243318

A combined learning algorithm for prostate segmentation on 3D CT images.

PubMed

Ma, Ling; Guo, Rongrong; Zhang, Guoyi; Schuster, David M; Fei, Baowei

2017-11-01

Segmentation of the prostate on CT images has many applications in the diagnosis and treatment of prostate cancer. Because of the low soft-tissue contrast on CT images, prostate segmentation is a challenging task. A learning-based segmentation method is proposed for the prostate on three-dimensional (3D) CT images. We combine population-based and patient-based learning methods for segmenting the prostate on CT images. Population data can provide useful information to guide the segmentation processing. Because of inter-patient variations, patient-specific information is particularly useful to improve the segmentation accuracy for an individual patient. In this study, we combine a population learning method and a patient-specific learning method to improve the robustness of prostate segmentation on CT images. We train a population model based on the data from a group of prostate patients. We also train a patient-specific model based on the data of the individual patient and incorporate the information as marked by the user interaction into the segmentation processing. We calculate the similarity between the two models to obtain applicable population and patient-specific knowledge to compute the likelihood of a pixel belonging to the prostate tissue. A new adaptive threshold method is developed to convert the likelihood image into a binary image of the prostate, and thus complete the segmentation of the gland on CT images. The proposed learning-based segmentation algorithm was validated using 3D CT volumes of 92 patients. All of the CT image volumes were manually segmented independently three times by two, clinically experienced radiologists and the manual segmentation results served as the gold standard for evaluation. The experimental results show that the segmentation method achieved a Dice similarity coefficient of 87.18 ± 2.99%, compared to the manual segmentation. By combining the population learning and patient-specific learning methods, the proposed method is effective for segmenting the prostate on 3D CT images. The prostate CT segmentation method can be used in various applications including volume measurement and treatment planning of the prostate. © 2017 American Association of Physicists in Medicine.

Demographic and health situation of children in conditions of economic destabilization in the Ukraine.

PubMed

Pantyley, Viktoriya

2014-01-01

In new conditions of socio-economic development in the Ukraine, the health of the population of children is considered as the most reliable indicator of socio-economic development of the country. The primary goal of the study was analysis of the effect of contemporary socio-economic transformations, their scope, and strength of effect on the demographic and social situation of children in various regions of the Ukraine. The methodological objectives of the study were as follows: development of a synthetic measure of the state of health of the population of children, based on the Hellwig's method, and selection of districts in the Ukraine according to the present health-demographic situation of children. The study was based on statistical data from the State Statistics Service of Ukraine, Centre of Medical Statistics in Kiev, Ukrainian Ministry of Defence, as well as Ministry of Education and Science, Youth and Sports of Ukraine. The following research methods were used: analysis of literature and Internet sources, selection and analysis of statistical materials, cartographic and statistical methods. Basic indices of the demographic and health situation of the population of children were analyzed, as well as factors of a socio-economic nature which affect this situation. A set of variables was developed for the synthetic evaluation of the state of health of the population of children. The typology of the Ukrainian districts was performed according to the state of health of the child population, based on the Hellwig's taxonomic method. Deterioration was observed of selected quality parameters, as well as a change in the strength and directions of effect of factors of organizational-institutional, socioeconomic, historical and cultural nature on the population of children potential.

Multi-population Genomic Relationships for Estimating Current Genetic Variances Within and Genetic Correlations Between Populations.

PubMed

Wientjes, Yvonne C J; Bijma, Piter; Vandenplas, Jérémie; Calus, Mario P L

2017-10-01

Different methods are available to calculate multi-population genomic relationship matrices. Since those matrices differ in base population, it is anticipated that the method used to calculate genomic relationships affects the estimate of genetic variances, covariances, and correlations. The aim of this article is to define the multi-population genomic relationship matrix to estimate current genetic variances within and genetic correlations between populations. The genomic relationship matrix containing two populations consists of four blocks, one block for population 1, one block for population 2, and two blocks for relationships between the populations. It is known, based on literature, that by using current allele frequencies to calculate genomic relationships within a population, current genetic variances are estimated. In this article, we theoretically derived the properties of the genomic relationship matrix to estimate genetic correlations between populations and validated it using simulations. When the scaling factor of across-population genomic relationships is equal to the product of the square roots of the scaling factors for within-population genomic relationships, the genetic correlation is estimated unbiasedly even though estimated genetic variances do not necessarily refer to the current population. When this property is not met, the correlation based on estimated variances should be multiplied by a correction factor based on the scaling factors. In this study, we present a genomic relationship matrix which directly estimates current genetic variances as well as genetic correlations between populations. Copyright © 2017 by the Genetics Society of America.

Including the Group Quarters Population in the US Synthesized Population Database

PubMed Central

Chasteen, Bernadette M.; Wheaton, William D.; Cooley, Philip C.; Ganapathi, Laxminarayana; Wagener, Diane K.

2011-01-01

In 2005, RTI International researchers developed methods to generate synthesized population data on US households for the US Synthesized Population Database. These data are used in agent-based modeling, which simulates large-scale social networks to test how changes in the behaviors of individuals affect the overall network. Group quarters are residences where individuals live in close proximity and interact frequently. Although the Synthesized Population Database represents the population living in households, data for the nation’s group quarters residents are not easily quantified because of US Census Bureau reporting methods designed to protect individuals’ privacy. Including group quarters population data can be an important factor in agent-based modeling because the number of residents and the frequency of their interactions are variables that directly affect modeling results. Particularly with infectious disease modeling, the increased frequency of agent interaction may increase the probability of infectious disease transmission between individuals and the probability of disease outbreaks. This report reviews our methods to synthesize data on group quarters residents to match US Census Bureau data. Our goal in developing the Group Quarters Population Database was to enable its use with RTI’s US Synthesized Population Database in the Modeling of Infectious Diseases Agent Study. PMID:21841972

A method of studying wild bird populations by mist-netting and banding

USGS Publications Warehouse

Stamm, D.D.; Davis, D.E.; Robbins, C.S.

1960-01-01

1. Progress is reported toward development of a method of bird-population study based on mist-netting and banding. A definite pattern of arrangement and schedule of operation are presented. 2. Nets were operated for a total of 4200 net-hours during which 966 captures were made (23.0 birds per 100 net-hours). A total of 431 adult breeding birds were banded and 38 per cent of them were recaptured. 3. A breeding bird census was made simultaneously in the same area by the Williams spot-mapping technique. 4. Estimates of population by recapture agreed closely with the spot-mappmg census. 5. Some birds are demonstrated to have overlapping home-ranges much larger than their singing territories. 6. Recruitment and net-shyness distort recapture estimates of population .but the method allows detection and assessment of their influence in the population dealt with here. 7. The method produced integrated information on population density and dynamics, movement and behavior. 8. The procedure is especially well adapted to studies of disease agents in bird populations. 9. A simple scheme for description of the habitat in terms of relative abundance and frequency of occurrence of tree species was used.

[Respondent-Driven Sampling: a new sampling method to study visible and hidden populations].

PubMed

Mantecón, Alejandro; Juan, Montse; Calafat, Amador; Becoña, Elisardo; Román, Encarna

2008-01-01

The paper introduces a variant of chain-referral sampling: respondent-driven sampling (RDS). This sampling method shows that methods based on network analysis can be combined with the statistical validity of standard probability sampling methods. In this sense, RDS appears to be a mathematical improvement of snowball sampling oriented to the study of hidden populations. However, we try to prove its validity with populations that are not within a sampling frame but can nonetheless be contacted without difficulty. The basics of RDS are explained through our research on young people (aged 14 to 25) who go clubbing, consume alcohol and other drugs, and have sex. Fieldwork was carried out between May and July 2007 in three Spanish regions: Baleares, Galicia and Comunidad Valenciana. The presentation of the study shows the utility of this type of sampling when the population is accessible but there is a difficulty deriving from the lack of a sampling frame. However, the sample obtained is not a random representative one in statistical terms of the target population. It must be acknowledged that the final sample is representative of a 'pseudo-population' that approximates to the target population but is not identical to it.

Comparison of self-report influenza vaccination coverage with data from a population based computerized vaccination registry and factors associated with discordance.

PubMed

Jiménez-García, Rodrigo; Hernandez-Barrera, Valentín; Rodríguez-Rieiro, Cristina; Carrasco Garrido, Pilar; López de Andres, Ana; Jimenez-Trujillo, Isabel; Esteban-Vasallo, María D; Domínguez-Berjón, Maria Felicitas; de Miguel-Diez, Javier; Astray-Mochales, Jenaro

2014-07-31

We aim to compare influenza vaccination coverages obtained using two different methods; a population based computerized vaccination registry and self-reported influenza vaccination status as captured by a population survey. The study was conducted in the Autonomous Community of Madrid (ACM), Spain, and refers to the 2011/12 influenza vaccination campaign. Information on influenza vaccination status according to a computerized registry was extracted from the SISPAL database and crossed with the electronic clinical records in primary care (ECRPC). Self-reported vaccine uptake was obtained from subjects living in the ACM included in the 2011-12 Spanish National Health Survey (SNHS). Independent study variables included: age, sex, immigrant status and the presence of high risk chronic conditions. Vaccination coverages were calculated according to study variables. Crude and adjusted prevalence ratios were computed to assess concordance. The study population included 5,245,238 adults living in the ACM in year 2011 with an individual ECRPC and 1449 adult living the ACM and interviewed in the SNHS from October 2011 to June 2012. The weighted vaccination coverage for the study population according to self-reported data was 19.77% and 15.04% from computerized registries resulting in a crude prevalence ratio (cPR) of 1.31 (95% CI 1.20-1.44) so self-reported data significantly overestimated 31% the registry coverage. Self-reported coverages are always higher than registry based coverages when the study population is stratified by the study variables. Self-reported overestimation was higher among men than women, younger age groups, immigrants and those without chronic conditions. Both methods provide the most concordant estimations for the target population of the influenza vaccine. Self-report influenza vaccination uptake overestimates vaccination registries coverages. The validity of self-report seems to be negatively affected by socio-demographic variables and the absence of chronic conditions. Possible strategies must be considered and implemented to improve both coverage estimation methods. Copyright © 2014 Elsevier Ltd. All rights reserved.

Validity and feasibility of a satellite imagery-based method for rapid estimation of displaced populations

PubMed Central

2013-01-01

Background Estimating the size of forcibly displaced populations is key to documenting their plight and allocating sufficient resources to their assistance, but is often not done, particularly during the acute phase of displacement, due to methodological challenges and inaccessibility. In this study, we explored the potential use of very high resolution satellite imagery to remotely estimate forcibly displaced populations. Methods Our method consisted of multiplying (i) manual counts of assumed residential structures on a satellite image and (ii) estimates of the mean number of people per structure (structure occupancy) obtained from publicly available reports. We computed population estimates for 11 sites in Bangladesh, Chad, Democratic Republic of Congo, Ethiopia, Haiti, Kenya and Mozambique (six refugee camps, three internally displaced persons’ camps and two urban neighbourhoods with a mixture of residents and displaced) ranging in population from 1,969 to 90,547, and compared these to “gold standard” reference population figures from census or other robust methods. Results Structure counts by independent analysts were reasonably consistent. Between one and 11 occupancy reports were available per site and most of these reported people per household rather than per structure. The imagery-based method had a precision relative to reference population figures of <10% in four sites and 10–30% in three sites, but severely over-estimated the population in an Ethiopian camp with implausible occupancy data and two post-earthquake Haiti sites featuring dense and complex residential layout. For each site, estimates were produced in 2–5 working person-days. Conclusions In settings with clearly distinguishable individual structures, the remote, imagery-based method had reasonable accuracy for the purposes of rapid estimation, was simple and quick to implement, and would likely perform better in more current application. However, it may have insurmountable limitations in settings featuring connected buildings or shelters, a complex pattern of roofs and multi-level buildings. Based on these results, we discuss possible ways forward for the method’s development. PMID:23343099

Validity and feasibility of a satellite imagery-based method for rapid estimation of displaced populations.

PubMed

Checchi, Francesco; Stewart, Barclay T; Palmer, Jennifer J; Grundy, Chris

2013-01-23

Estimating the size of forcibly displaced populations is key to documenting their plight and allocating sufficient resources to their assistance, but is often not done, particularly during the acute phase of displacement, due to methodological challenges and inaccessibility. In this study, we explored the potential use of very high resolution satellite imagery to remotely estimate forcibly displaced populations. Our method consisted of multiplying (i) manual counts of assumed residential structures on a satellite image and (ii) estimates of the mean number of people per structure (structure occupancy) obtained from publicly available reports. We computed population estimates for 11 sites in Bangladesh, Chad, Democratic Republic of Congo, Ethiopia, Haiti, Kenya and Mozambique (six refugee camps, three internally displaced persons' camps and two urban neighbourhoods with a mixture of residents and displaced) ranging in population from 1,969 to 90,547, and compared these to "gold standard" reference population figures from census or other robust methods. Structure counts by independent analysts were reasonably consistent. Between one and 11 occupancy reports were available per site and most of these reported people per household rather than per structure. The imagery-based method had a precision relative to reference population figures of <10% in four sites and 10-30% in three sites, but severely over-estimated the population in an Ethiopian camp with implausible occupancy data and two post-earthquake Haiti sites featuring dense and complex residential layout. For each site, estimates were produced in 2-5 working person-days. In settings with clearly distinguishable individual structures, the remote, imagery-based method had reasonable accuracy for the purposes of rapid estimation, was simple and quick to implement, and would likely perform better in more current application. However, it may have insurmountable limitations in settings featuring connected buildings or shelters, a complex pattern of roofs and multi-level buildings. Based on these results, we discuss possible ways forward for the method's development.

Winter bird population studies and project prairie birds for surveying grassland birds

USGS Publications Warehouse

Twedt, D.J.; Hamel, P.B.; Woodrey, M.S.

2008-01-01

We compared 2 survey methods for assessing winter bird communities in temperate grasslands: Winter Bird Population Study surveys are area-searches that have long been used in a variety of habitats whereas Project Prairie Bird surveys employ active-flushing techniques on strip-transects and are intended for use in grasslands. We used both methods to survey birds on 14 herbaceous reforested sites and 9 coastal pine savannas during winter and compared resultant estimates of species richness and relative abundance. These techniques did not yield similar estimates of avian populations. We found Winter Bird Population Studies consistently produced higher estimates of species richness, whereas Project Prairie Birds produced higher estimates of avian abundance for some species. When it is important to identify all species within the winter bird community, Winter Bird Population Studies should be the survey method of choice. If estimates of the abundance of relatively secretive grassland bird species are desired, the use of Project Prairie Birds protocols is warranted. However, we suggest that both survey techniques, as currently employed, are deficient and recommend distance- based survey methods that provide species-specific estimates of detection probabilities be incorporated into these survey methods.

Estimation of the size of the female sex worker population in Rwanda using three different methods

PubMed Central

Kayitesi, Catherine; Gwiza, Aimé; Ruton, Hinda; Koleros, Andrew; Gupta, Neil; Balisanga, Helene; Riedel, David J; Nsanzimana, Sabin

2014-01-01

HIV prevalence is disproportionately high among female sex workers compared to the general population. Many African countries lack useful data on the size of female sex worker populations to inform national HIV programmes. A female sex worker size estimation exercise using three different venue-based methodologies was conducted among female sex workers in all provinces of Rwanda in August 2010. The female sex worker national population size was estimated using capture–recapture and enumeration methods, and the multiplier method was used to estimate the size of the female sex worker population in Kigali. A structured questionnaire was also used to supplement the data. The estimated number of female sex workers by the capture–recapture method was 3205 (95% confidence interval: 2998–3412). The female sex worker size was estimated at 3348 using the enumeration method. In Kigali, the female sex worker size was estimated at 2253 (95% confidence interval: 1916–2524) using the multiplier method. Nearly 80% of all female sex workers in Rwanda were found to be based in the capital, Kigali. This study provided a first-time estimate of the female sex worker population size in Rwanda using capture–recapture, enumeration, and multiplier methods. The capture–recapture and enumeration methods provided similar estimates of female sex worker in Rwanda. Combination of such size estimation methods is feasible and productive in low-resource settings and should be considered vital to inform national HIV programmes. PMID:25336306

Estimation of the size of the female sex worker population in Rwanda using three different methods.

PubMed

Mutagoma, Mwumvaneza; Kayitesi, Catherine; Gwiza, Aimé; Ruton, Hinda; Koleros, Andrew; Gupta, Neil; Balisanga, Helene; Riedel, David J; Nsanzimana, Sabin

2015-10-01

HIV prevalence is disproportionately high among female sex workers compared to the general population. Many African countries lack useful data on the size of female sex worker populations to inform national HIV programmes. A female sex worker size estimation exercise using three different venue-based methodologies was conducted among female sex workers in all provinces of Rwanda in August 2010. The female sex worker national population size was estimated using capture-recapture and enumeration methods, and the multiplier method was used to estimate the size of the female sex worker population in Kigali. A structured questionnaire was also used to supplement the data. The estimated number of female sex workers by the capture-recapture method was 3205 (95% confidence interval: 2998-3412). The female sex worker size was estimated at 3348 using the enumeration method. In Kigali, the female sex worker size was estimated at 2253 (95% confidence interval: 1916-2524) using the multiplier method. Nearly 80% of all female sex workers in Rwanda were found to be based in the capital, Kigali. This study provided a first-time estimate of the female sex worker population size in Rwanda using capture-recapture, enumeration, and multiplier methods. The capture-recapture and enumeration methods provided similar estimates of female sex worker in Rwanda. Combination of such size estimation methods is feasible and productive in low-resource settings and should be considered vital to inform national HIV programmes. © The Author(s) 2015.

Medicare Part D Enrollment in a Biracial Community-Based Population of Older Adults

ERIC Educational Resources Information Center

Skarupski, Kimberly A.; Mendes de Leon, Carlos F.; Barnes, Lisa L.; Evans, Denis A.

2009-01-01

Purpose: The Medicare Prescription Drug Benefit (Part D) program debuted in January 2006. We ascertained the sociodemographic and health characteristics of Blacks and Whites who enrolled in the early stages of the program. Design and Methods: Data were collected between April 2006 and October 2007 from an ongoing population-based biracial study of…

Towards Evidence-Based Practice in Language Intervention for Bilingual Children

ERIC Educational Resources Information Center

Thordardottir, Elin

2010-01-01

Evidence-based practice requires that clinical decisions be based on evidence from rigorously controlled research studies. At this time, very few studies have directly examined the efficacy of clinical intervention methods for bilingual children. Clinical decisions for this population cannot, therefore, be based on the strongest forms of research…

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

Size matters: insights from an allometric approach to evaluate control methods for invasive Australian Rhinella marina.

PubMed

Beaty, Lynne E; Salice, Christopher J

2013-10-01

Invasive species are costly and difficult to control. In order to gain a mechanistic understanding of potential control measures, individual-based models uniquely parameterized to reflect the salient life-history characteristics of invasive species are useful. Using invasive Australian Rhinella marina as a case study, we constructed a cohort- and individual-based population simulation that incorporates growth and body size of terrestrial stages. We used this allometric approach to examine the efficacy of nontraditional control methods (i.e., tadpole alarm chemicals and native meat ants) that may have indirect effects on population dynamics mediated by effects on body size. We compared population estimates resulting from these control methods with traditional hand removal. We also conducted a sensitivity analysis to investigate the effect that model parameters, specifically those associated with growth and body size, had on adult population estimates. Incremental increases in hand removal of adults and juveniles caused nonlinear decreases in adult population estimates, suggesting less return with increased investment in hand-removal efforts. Applying tadpole alarm chemicals or meat ants decreased adult population estimates on the same level as removing 15-25% of adults and juveniles by hand. The combined application of tadpole alarm chemicals and meat ants resulted in approximately 80% decrease in adult abundance, the largest of any applied control method. In further support of the nontraditional control methods, which greatly affected the metamorph stage, our model was most sensitive to changes in metamorph survival, juvenile survival, metamorph growth rate, and adult survival. Our results highlight the use and insights that can be gained from individual-based models that incorporate growth and body size and the potential success that nontraditional control methods could have in controlling established, invasive Rhinella marina populations.

Benefits of extensive recruitment effort persist during follow-ups and are consistent across age group and survey method. The TRAILS study

PubMed Central

2012-01-01

Background Extensive recruitment effort at baseline increases representativeness of study populations by decreasing non-response and associated bias. First, it is not known to what extent increased attrition occurs during subsequent measurement waves among subjects who were hard-to-recruit at baseline and what characteristics the hard-to-recruit dropouts have compared to the hard-to-recruit retainers. Second, it is unknown whether characteristics of hard-to-recruit responders in a prospective population based cohort study are similar across age group and survey method. Methods First, we compared first wave (T1) easy-to-recruit with hard-to-recruit responders of the TRacking Adolescents’ Individual Lives Survey (TRAILS), a prospective population based cohort study of Dutch (pre)adolescents (at first wave: n = 2230, mean age = 11.09 (SD 0.56), 50.8% girls), with regard to response rates at subsequent measurement waves. Second, easy-to-recruit and hard-to-recruit participants at the fourth TRAILS measurement wave (n = 1881, mean age = 19.1 (SD 0.60), 52.3% girls) were compared with fourth wave non-responders and earlier stage drop-outs on family composition, socioeconomic position (SEP), intelligence (IQ), education, sociometric status, substance use, and psychopathology. Results First, over 60% of the hard-to-recruit responders at the first wave were retained in the sample eight years later at the fourth measurement wave. Hard-to-recruit dropouts did not differ from hard-to-recruit retainers. Second, extensive recruitment efforts for the web based survey convinced a population of nineteen year olds with similar characteristics as the hard-to-recruit eleven year olds that were persuaded to participate in a school-based survey. Some characteristics associated with being hard-to-recruit (as compared to being easy-to-recruit) were more pronounced among non-responders, resembling the baseline situation (De Winter et al.2005). Conclusions First, extensive recruitment effort at the first assessment wave of a prospective population based cohort study has long lasting positive effects. Second, characteristics of hard-to-recruit responders are largely consistent across age groups and survey methods. PMID:22747967

Electrophoretic cell separation using microspheres. [purification of lymphocytes

NASA Technical Reports Server (NTRS)

Smolka, A.; Sachs, G.

1980-01-01

Methods of cell separation based on the electrokinetic properties of the cell membrane offer a degree of discrimination among cell populations which is not available with methods based on cell size or density alone. Studies aimed at extending red cell separations using microspheres to purification of lymphocytes.

Prevalence of autosomal dominant polycystic kidney disease in the European Union.

PubMed

Willey, Cynthia J; Blais, Jaime D; Hall, Anthony K; Krasa, Holly B; Makin, Andrew J; Czerwiec, Frank S

2017-08-01

Autosomal dominant polycystic kidney disease (ADPKD) is a leading cause of end-stage renal disease, but estimates of its prevalence vary by >10-fold. The objective of this study was to examine the public health impact of ADPKD in the European Union (EU) by estimating minimum prevalence (point prevalence of known cases) and screening prevalence (minimum prevalence plus cases expected after population-based screening). A review of the epidemiology literature from January 1980 to February 2015 identified population-based studies that met criteria for methodological quality. These examined large German and British populations, providing direct estimates of minimum prevalence and screening prevalence. In a second approach, patients from the 2012 European Renal Association‒European Dialysis and Transplant Association (ERA-EDTA) Registry and literature-based inflation factors that adjust for disease severity and screening yield were used to estimate prevalence across 19 EU countries (N = 407 million). Population-based studies yielded minimum prevalences of 2.41 and 3.89/10 000, respectively, and corresponding estimates of screening prevalences of 3.3 and 4.6/10 000. A close correspondence existed between estimates in countries where both direct and registry-derived methods were compared, which supports the validity of the registry-based approach. Using the registry-derived method, the minimum prevalence was 3.29/10 000 (95% confidence interval 3.27-3.30), and if ADPKD screening was implemented in all countries, the expected prevalence was 3.96/10 000 (3.94-3.98). ERA-EDTA-based prevalence estimates and application of a uniform definition of prevalence to population-based studies consistently indicate that the ADPKD point prevalence is <5/10 000, the threshold for rare disease in the EU. © The Author 2016. Published by Oxford University Press on behalf of ERA-EDTA.

Regarding on the prototype solutions for the nonlinear fractional-order biological population model

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

Baskonus, Haci Mehmet, E-mail: hmbaskonus@gmail.com; Bulut, Hasan

2016-06-08

In this study, we have submitted to literature a method newly extended which is called as Improved Bernoulli sub-equation function method based on the Bernoulli Sub-ODE method. The proposed analytical scheme has been expressed with steps. We have obtained some new analytical solutions to the nonlinear fractional-order biological population model by using this technique. Two and three dimensional surfaces of analytical solutions have been drawn by wolfram Mathematica 9. Finally, a conclusion has been submitted by mentioning important acquisitions founded in this study.

Measurements of the populations of metastable and resonance levels in the plasma of an RF capacitive discharge in argon

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

Vasilieva, A. N.; Voloshin, D. G.; Kovalev, A. S., E-mail: kovalev@dnph.phys.msu.su

2015-05-15

The behavior of the populations of two metastable and two lower resonance levels of argon atoms in the plasma of an RF capacitive discharge was studied. The populations were measured by two methods: the method of emission self-absorption and the method based on measurements of the intensity ratios of spectral lines. It is shown that the populations of resonance levels increase with increasing power deposited in the discharge, whereas the populations of metastable levels is independent of the RF power. The distribution of the populations over energy levels is not equilibrium under these conditions. The population kinetics of argon atomicmore » levels in the discharge plasma is simulated numerically. The distribution function of plasma electrons recovered from the measured populations of atomic levels and numerical simulations is found to be non-Maxwellian.« less

Joint Inference of Population Assignment and Demographic History

PubMed Central

Choi, Sang Chul; Hey, Jody

2011-01-01

A new approach to assigning individuals to populations using genetic data is described. Most existing methods work by maximizing Hardy–Weinberg and linkage equilibrium within populations, neither of which will apply for many demographic histories. By including a demographic model, within a likelihood framework based on coalescent theory, we can jointly study demographic history and population assignment. Genealogies and population assignments are sampled from a posterior distribution using a general isolation-with-migration model for multiple populations. A measure of partition distance between assignments facilitates not only the summary of a posterior sample of assignments, but also the estimation of the posterior density for the demographic history. It is shown that joint estimates of assignment and demographic history are possible, including estimation of population phylogeny for samples from three populations. The new method is compared to results of a widely used assignment method, using simulated and published empirical data sets. PMID:21775468

Comparison of 3 estimation methods of mycophenolic acid AUC based on a limited sampling strategy in renal transplant patients.

PubMed

Hulin, Anne; Blanchet, Benoît; Audard, Vincent; Barau, Caroline; Furlan, Valérie; Durrbach, Antoine; Taïeb, Fabrice; Lang, Philippe; Grimbert, Philippe; Tod, Michel

2009-04-01

A significant relationship between mycophenolic acid (MPA) area under the plasma concentration-time curve (AUC) and the risk for rejection has been reported. Based on 3 concentration measurements, 3 approaches have been proposed for the estimation of MPA AUC, involving either a multilinear regression approach model (MLRA) or a Bayesian estimation using either gamma absorption or zero-order absorption population models. The aim of the study was to compare the 3 approaches for the estimation of MPA AUC in 150 renal transplant patients treated with mycophenolate mofetil and tacrolimus. The population parameters were determined in 77 patients (learning study). The AUC estimation methods were compared in the learning population and in 73 patients from another center (validation study). In the latter study, the reference AUCs were estimated by the trapezoidal rule on 8 measurements. MPA concentrations were measured by liquid chromatography. The gamma absorption model gave the best fit. In the learning study, the AUCs estimated by both Bayesian methods were very similar, whereas the multilinear approach was highly correlated but yielded estimates about 20% lower than Bayesian methods. This resulted in dosing recommendations differing by 250 mg/12 h or more in 27% of cases. In the validation study, AUC estimates based on the Bayesian method with gamma absorption model and multilinear regression approach model were, respectively, 12% higher and 7% lower than the reference values. To conclude, the bicompartmental model with gamma absorption rate gave the best fit. The 3 AUC estimation methods are highly correlated but not concordant. For a given patient, the same estimation method should always be used.

Hepameta-- prevalence of hepatitis B/C and metabolic syndrome in population living in separated and segregated Roma settlements: a methodology for a cross-sectional population-based study using community-based approach.

PubMed

Gecková, Andrea Madarasová; Jarcuska, Peter; Mareková, Mária; Pella, Daniel; Siegfried, Leonard; Jarcuska, Pavol; Halánová, Monika

2014-03-01

Roma represent one of the largest and oldest minorities in Europe. Health of many of them, particularly those living in settlements, is heavily compromised by poor dwelling, low educational level, unemployment, and poverty rooted in generational poverty, segregation and discrimination. The cross-sectional population-based study using community based approach aimed to map the prevalence of viral hepatitis B/C and metabolic syndrome in the population living in separated and segregated Roma settlements and to compare it with the occurrence of the same health indicators in the majority population, considering selected risk and protective factors of these health indicators. The sample consisted of 452 Roma (mean age = 34.7; 35.2% men) and 403 non-Roma (mean age = 33.5; 45.9% men) respondents. Data were collected in 2011 via questionnaire, anthropometric measures and analysed blood and urine samples. A methodology used in the study as well as in the following scientific papers is described in the Methods section (i.e. study design, procedures, samples, methods including questionnaire, anthropometric measurements, physical measurements, blood and urine measurements). There are regions of declining prosperity due to high unemployment, long-term problems with poverty and depleted resources. Populations living in these areas, i.e. in Central and Eastern Europe in Roma settlements, are at risk of poverty, social exclusion and other factors affecting health. Therefore, we should look for successful long-term strategies and tools (e.g. Roma mediators, terrain work) in order to improve the future prospects of these minorities.

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 prior conditions. The method is implemented in the software NetStruct (available at https://giligreenbaum.wordpress.com/software/). PMID:26888080

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 prior conditions. The method is implemented in the software NetStruct (available at https://giligreenbaum.wordpress.com/software/). Copyright © 2016 by the Genetics Society of America.

MRI-based hip cartilage measures in osteoarthritic and non-osteoarthritic individuals: a systematic review

PubMed Central

Aguilar, Hector N; Battié, Michele C

2017-01-01

Osteoarthritis is a common hip joint disease, involving loss of articular cartilage. The prevalence and prognosis of hip osteoarthritis have been difficult to determine, with various clinical and radiological methods used to derive epidemiological estimates exhibiting significant heterogeneity. MRI-based methods directly visualise hip joint cartilage, and offer potential to more reliably define presence and severity of osteoarthritis, but have been underused. We performed a systematic review of MRI-based estimates of hip articular cartilage in the general population and in patients with established osteoarthritis, using MEDLINE, EMBASE and SCOPUS current to June 2016, with search terms such as ‘hip’, ‘femoral head’, ‘cartilage’, ‘volume’, ‘thickness’, ‘MRI’, etc. Ultimately, 11 studies were found appropriate for inclusion, but they were heterogeneous in osteoarthritis assessment methodology and composition. Overall, the studies consistently demonstrate the reliability and potential clinical utility of MRI-based estimates. However, no longitudinal data or reference values for hip cartilage thickness or volume have been published, limiting the ability of MRI to define or risk-stratify hip osteoarthritis. MRI-based techniques are available to quantify articular cartilage signal, volume, thickness and defects, which could establish the sequence and rate of articular cartilage changes at the hip that yield symptomatic osteoarthritis. However, prevalence and rates of progression of hip osteoarthritis have not been established in any MRI studies in the general population. Future investigations could fill this important knowledge gap using robust MRI methods in population-based cross-sectional and longitudinal studies. PMID:28405471

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

Development of a novel cell sorting method that samples population diversity in flow cytometry.

PubMed

Osborne, Geoffrey W; Andersen, Stacey B; Battye, Francis L

2015-11-01

Flow cytometry based electrostatic cell sorting is an important tool in the separation of cell populations. Existing instruments can sort single cells into multi-well collection plates, and keep track of cell of origin and sorted well location. However currently single sorted cell results reflect the population distribution and fail to capture the population diversity. Software was designed that implements a novel sorting approach, "Slice and Dice Sorting," that links a graphical representation of a multi-well plate to logic that ensures that single cells are sampled and sorted from all areas defined by the sort region/s. Therefore the diversity of the total population is captured, and the more frequently occurring or rarer cell types are all sampled. The sorting approach was tested computationally, and using functional cell based assays. Computationally we demonstrate that conventional single cell sorting can sample as little as 50% of the population diversity dependant on the population distribution, and that Slice and Dice sorting samples much more of the variety present within a cell population. We then show by sorting single cells into wells using the Slice and Dice sorting method that there are cells sorted using this method that would be either rarely sorted, or not sorted at all using conventional single cell sorting approaches. The present study demonstrates a novel single cell sorting method that samples much more of the population diversity than current methods. It has implications in clonal selection, stem cell sorting, single cell sequencing and any areas where population heterogeneity is of importance. © 2015 International Society for Advancement of Cytometry.

Use and misuse of mixed methods in population oral health research: A scoping review.

PubMed

Gupta, A; Keuskamp, D

2018-05-30

Despite the known benefits of a mixed methods approach in health research, little is known of its use in the field of population oral health. To map the extent of literature using a mixed methods approach to examine population oral health outcomes. For a comprehensive search of all the available literature published in the English language, databases including PubMed, Dentistry and Oral Sciences Source (DOSS), CINAHL, Web of Science and EMBASE (including Medline) were searched using a range of keywords from inception to October 2017. Only peer-reviewed, population-based studies of oral health outcomes conducted among non-institutionalised participants and using mixed methods were considered eligible for inclusion. Only nine studies met the inclusion criteria and were included in the review. The most frequent oral health outcome investigated was caries experience. However, most studies lacked a theoretical rationale or framework for using mixed methods, or supporting the use of qualitative data. Concurrent triangulation with a convergent design was the most commonly used mixed methods typology for integrating quantitative and qualitative data. The tools used to collect quantitative and qualitative data were mostly limited to surveys and interviews. With growing complexity recognised in the determinants of oral disease, future studies addressing population oral health outcomes are likely to benefit from the use of mixed methods. Explicit consideration of theoretical framework and methodology will strengthen those investigations. Copyright© 2018 Dennis Barber Ltd.

High coffee consumption and different brewing methods in relation to postmenopausal endometrial cancer risk in the Norwegian women and cancer study: a population-based prospective study.

PubMed

Gavrilyuk, Oxana; Braaten, Tonje; Skeie, Guri; Weiderpass, Elisabete; Dumeaux, Vanessa; Lund, Eiliv

2014-03-25

Coffee and its compounds have been proposed to inhibit endometrial carcinogenesis. Studies in the Norwegian population can be especially interesting due to the high coffee consumption and increasing incidence of endometrial cancer in the country. A total of 97 926 postmenopausal Norwegian women from the population-based prospective Norwegian Women and Cancer (NOWAC) Study, were included in the present analysis. We evaluated the general association between total coffee consumption and endometrial cancer risk as well as the possible impact of brewing method. Multivariate Cox regression analysis was used to estimate risks, and heterogeneity tests were performed to compare brewing methods. During an average of 10.9 years of follow-up, 462 incident endometrial cancer cases were identified. After multivariate adjustment, significant risk reduction was found among participants who drank ≥8 cups/day of coffee with a hazard ratio of 0.52 (95% confidence interval, CI 0.34-0.79). However, we did not observe a significant dose-response relationship. No significant heterogeneity in risk was found when comparing filtered and boiled coffee brewing methods. A reduction in endometrial cancer risk was observed in subgroup analyses among participants who drank ≥8 cups/day and had a body mass index ≥25 kg/m2, and in current smokers. These data suggest that in this population with high coffee consumption, endometrial cancer risk decreases in women consuming ≥8 cups/day, independent of brewing method.

Using small-area variations to inform health care service planning: what do we 'need' to know?

PubMed

Mercuri, Mathew; Birch, Stephen; Gafni, Amiram

2013-12-01

Allocating resources on the basis of population need is a health care policy goal in many countries. Thus, resources must be allocated in accordance with need if stakeholders are to achieve policy goals. Small area methods have been presented as a means for revealing important information that can assist stakeholders in meeting policy goals. The purpose of this review is to examine the extent to which small area methods provide information relevant to meeting the goals of a needs-based health care policy. We present a conceptual framework explaining the terms 'demand', 'need', 'use' and 'supply', as commonly used in the literature. We critically review the literature on small area methods through the lens of this framework. 'Use' cannot be used as a proxy or surrogate of 'need'. Thus, if the goal of health care policy is to provide equal access for equal need, then traditional small area methods are inadequate because they measure small area variations in use of services in different populations, independent of the levels of need in those populations. Small area methods can be modified by incorporating direct measures of relative population need from population health surveys or by adjusting population size for levels of health risks in populations such as the prevalence of smoking and low birth weight. This might improve what can be learned from studies employing small area methods if they are to inform needs-based health care policies. © 2013 John Wiley & Sons Ltd.

Population Estimation Methods for Free-Ranging Dogs: A Systematic Review.

PubMed

Belo, Vinícius Silva; Werneck, Guilherme Loureiro; da Silva, Eduardo Sérgio; Barbosa, David Soeiro; Struchiner, Claudio José

2015-01-01

The understanding of the structure of free-roaming dog populations is of extreme importance for the planning and monitoring of populational control strategies and animal welfare. The methods used to estimate the abundance of this group of dogs are more complex than the ones used with domiciled owned dogs. In this systematic review, we analyze the techniques and the results obtained in studies that seek to estimate the size of free-ranging dog populations. Twenty-six studies were reviewed regarding the quality of execution and their capacity to generate valid estimates. Seven of the eight publications that take a simple count of the animal population did not consider the different probabilities of animal detection; only one study used methods based on distances; twelve relied on capture-recapture models for closed populations without considering heterogeneities in capture probabilities; six studies applied their own methods with different potential and limitations. Potential sources of bias in the studies were related to the inadequate description or implementation of animal capturing or viewing procedures and to inadequacies in the identification and registration of dogs. Thus, there was a predominance of estimates with low validity. Abundance and density estimates carried high variability, and all studies identified a greater number of male dogs. We point to enhancements necessary for the implementation of future studies and to potential updates and revisions to the recommendations of the World Health Organization with respect to the estimation of free-ranging dog populations.

Experimental design and quantitative analysis of microbial community multiomics.

PubMed

Mallick, Himel; Ma, Siyuan; Franzosa, Eric A; Vatanen, Tommi; Morgan, Xochitl C; Huttenhower, Curtis

2017-11-30

Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data. We highlight studies that have identified molecular bioactives that influence human health, and we suggest steps for scaling translational microbiome research to high-throughput target discovery across large populations.

Mixed-Methods for Comparing Tobacco Cessation Interventions.

PubMed

Momin, Behnoosh; Neri, Antonio; Zhang, Lei; Kahende, Jennifer; Duke, Jennifer; Green, Sonya Goode; Malarcher, Ann; Stewart, Sherri L

2017-03-01

The National Comprehensive Cancer Control Program (NCCCP) and National Tobacco Control Program (NTCP) are both well-positioned to promote the use of population-based tobacco cessation interventions, such as state quitlines and Web-based interventions. This paper outlines the methodology used to conduct a comparative effectiveness research study of traditional and Web-based tobacco cessation and quitline promotion approaches. A mixed-methods study with three components was designed to address the effect of promotional activities on service usage and the comparative effectiveness of population-based smoking cessation activities across multiple states. The cessation intervention component followed 7,902 smokers (4,307 quitline users and 3,595 Web intervention users) to ascertain prevalence of 30-day abstinence rates 7 months after registering for smoking cessation services. User characteristics and quit success was compared across the two modalities. In the promotions component, reach and use of traditional and innovative promotion strategies were assessed for 24 states, including online advertising, state Web sites, social media, mobile applications, and their effects on quitline call volume. The partnership intervention component studied the extent of collaboration among six selected NCCCPs and NTCPs. This study will guide program staff and clinicians with evidence-based recommendations and best practices for implementation of tobacco cessation within their patient and community populations and establish an evidence base that can be used for decision making.

Comparison of Address-based Sampling and Random-digit Dialing Methods for Recruiting Young Men as Controls in a Case-Control Study of Testicular Cancer Susceptibility

PubMed Central

Clagett, Bartholt; Nathanson, Katherine L.; Ciosek, Stephanie L.; McDermoth, Monique; Vaughn, David J.; Mitra, Nandita; Weiss, Andrew; Martonik, Rachel; Kanetsky, Peter A.

2013-01-01

Random-digit dialing (RDD) using landline telephone numbers is the historical gold standard for control recruitment in population-based epidemiologic research. However, increasing cell-phone usage and diminishing response rates suggest that the effectiveness of RDD in recruiting a random sample of the general population, particularly for younger target populations, is decreasing. In this study, we compared landline RDD with alternative methods of control recruitment, including RDD using cell-phone numbers and address-based sampling (ABS), to recruit primarily white men aged 18–55 years into a study of testicular cancer susceptibility conducted in the Philadelphia, Pennsylvania, metropolitan area between 2009 and 2012. With few exceptions, eligible and enrolled controls recruited by means of RDD and ABS were similar with regard to characteristics for which data were collected on the screening survey. While we find ABS to be a comparably effective method of recruiting young males compared with landline RDD, we acknowledge the potential impact that selection bias may have had on our results because of poor overall response rates, which ranged from 11.4% for landline RDD to 1.7% for ABS. PMID:24008901

Young People's Risk of Suicide Attempts in Relation to Parental Death: A Population-Based Register Study

ERIC Educational Resources Information Center

Jakobsen, Ida Skytte; Christiansen, Erik

2011-01-01

Background: The objective of this study was to examine the association between the death of a biological parent and subsequent suicide attempts by young people (aged 10-22 years), and to explore sociodemographic factors as modifying factors in the process. Methods: The study used a nested case-control design. The full study population was obtained…

Counting the stunted children in a population: a criticism of old and new approaches and a conciliatory proposal.

PubMed

Monteiro, C A

1991-01-01

Two methods for estimating the prevalence of growth retardation in a population are evaluated: the classical method, which is based on the proportion of children whose height is more than 2 standard deviations below the expected mean of a reference population; and a new method recently proposed by Mora, which is based on the whole height distribution of observed and reference populations. Application of the classical method to several simulated populations leads to the conclusion that in most situations in developing countries the prevalence of growth retardation is grossly underestimated, and reflects only the presence of severe growth deficits. A second constraint with this method is a marked reduction of the relative differentials between more and less exposed strata. Application of Mora's method to the same simulated populations reduced but did not eliminate these constraints. A novel method for estimating the prevalence of growth retardation, which is based also on the whole height distribution of observed and reference populations, is also described and evaluated. This method produces better estimates of the true prevalence of growth retardation with no reduction in relative differentials.

Exploring student learning profiles in algebra-based studio physics: A person-centered approach

NASA Astrophysics Data System (ADS)

Pond, Jarrad W. T.; Chini, Jacquelyn J.

2017-06-01

In this study, we explore the strategic self-regulatory and motivational characteristics of students in studio-mode physics courses at three universities with varying student populations and varying levels of success in their studio-mode courses. We survey students using questions compiled from several existing questionnaires designed to measure students' study strategies, attitudes toward and motivations for learning physics, organization of scientific knowledge, experiences outside the classroom, and demographics. Using a person-centered approach, we utilize cluster analysis methods to group students into learning profiles based on their individual responses to better understand the strategies and motives of algebra-based studio physics students. Previous studies have identified five distinct learning profiles across several student populations using similar methods. We present results from first-semester and second-semester studio-mode introductory physics courses across three universities. We identify these five distinct learning profiles found in previous studies to be present within our population of introductory physics students. In addition, we investigate interactions between these learning profiles and student demographics. We find significant interactions between a student's learning profile and their experience with high school physics, major, gender, grade expectation, and institution. Ultimately, we aim to use this method of analysis to take the characteristics of students into account in the investigation of successful strategies for using studio methods of physics instruction within and across institutions.

Childhood ADHD Is Strongly Associated with a Broad Range of Psychiatric Disorders during Adolescence: A Population-Based Birth Cohort Study

ERIC Educational Resources Information Center

Yoshimasu, Kouichi; Barbaresi, William J.; Colligan, Robert C.; Voigt, Robert G.; Killian, Jill M.; Weaver, Amy L.; Katusic, Slavica K.

2012-01-01

Background: To evaluate associations between attention-deficit/hyperactivity disorder (ADHD) and comorbid psychiatric disorders using research-identified incident cases of ADHD and population-based controls. Methods: Subjects included a birth cohort of all children born 1976-1982 remaining in Rochester, MN after age five (n = 5,718). Among them we…

Men's and Women's Health Beliefs Differentially Predict Coronary Heart Disease Incidence in a Population-Based Sample

ERIC Educational Resources Information Center

Korin, Maya Rom; Chaplin, William F.; Shaffer, Jonathan A.; Butler, Mark J.; Ojie, Mary-Jane; Davidson, Karina W.

2013-01-01

Objective: To examine gender differences in the association between beliefs in heart disease preventability and 10-year incidence of coronary heart disease (CHD) in a population-based sample. Methods: A total of 2,688 Noninstitutionalized Nova Scotians without prior CHD enrolled in the Nova Scotia Health Study (NSHS95) and were followed for 10…

Economic Impact of Dyspepsia in Rural and Urban Malaysia: A Population-Based Study

PubMed Central

Yadav, Hematram; Everett, Simon M; Goh, Khean-Lee

2012-01-01

Background/Aims The economic impact of dyspepsia in regions with a diverse healthcare system remains uncertain. This study aimed to estimate the costs of dyspepsia in a rural and urban population in Malaysia. Methods Economic evaluation was performed based on the cost-of-illness method. Resource utilization and quality of life data over a specific time frame, were collected to determine direct, indirect and intangible costs related to dyspepsia. Results The prevalences of dyspepsia in the rural (n = 2,000) and urban (n = 2,039) populations were 14.6% and 24.3% respectively. Differences in socioeconomic status and healthcare utilisation between both populations were considerable. The cost of dyspepsia per 1,000 population per year was estimated at USD14,816.10 and USD59,282.20 in the rural and urban populations respectively. The cost per quality adjusted life year for dyspepsia in rural and urban adults was USD16.30 and USD69.75, respectively. Conclusions The economic impact of dyspepsia is greater in an urban compared to a rural setting. Differences in socioeconomic status and healthcare utilisation between populations are thought to contribute to this difference. PMID:22323987

Research on the evaluation method of rural hollowing based on RS and GIS technology: a case study of the Ningxia Hui autonomous region in China

NASA Astrophysics Data System (ADS)

Yin, Kai; Wen, MeiPing; Zhang, FeiFei; Yuan, Chao; Chen, Qiang; Zhang, Xiupeng

2016-10-01

With the acceleration of urbanization in China, most rural areas formed a widespread phenomenon, i.e., destitute village, labor population loss, land abandonment and rural hollowing. And it formed a unique hollow village problem in China finally. The governance of hollow village was the objective need of the development of economic and social development in rural area for Chinese government, and the research on the evaluation method of rural hollowing was the premise and basis of the hollow village governance. In this paper, several evaluation methods were used to evaluate the rural hollowing based on the survey data, land use data, social and economic development data. And these evaluation indexes were the transition of homesteads, the development intensity of rural residential areas, the per capita housing construction area, the residential population proportion in rural area, and the average annual electricity consumption, which can reflect the rural hollowing degree from the land, population, and economy point of view, respectively. After that, spatial analysis method of GIS was used to analyze the evaluation result for each index. Based on spatial raster data generated by Kriging interpolation, we carried out re-classification of all the results. Using the fuzzy clustering method, the rural hollowing degree in Ningxia area was reclassified based on the two spatial scales of county and village. The results showed that the rural hollowing pattern in the Ningxia Hui Autonomous Region had a spatial distribution characteristics that the rural hollowing degree was obvious high in the middle of the study area but was low around the study area. On a county scale, the specific performances of the serious rural hollowing were the higher degree of extensive land use, and the lower level of rural economic development and population transfer concentration. On a village scale, the main performances of the rural hollowing were the rural population loss and idle land. The evaluation method of rural hollowing constructed in this paper can effectively carry out a comprehensive degree zoning of rural hollowing, which can make orderly decision support plans of hollow village governance for the government.

Customized versus population-based growth curves: prediction of low body fat percent at term corrected gestational age following preterm birth.

PubMed

Law, Tameeka L; Katikaneni, Lakshmi D; Taylor, Sarah N; Korte, Jeffrey E; Ebeling, Myla D; Wagner, Carol L; Newman, Roger B

2012-07-01

Compare customized versus population-based growth curves for identification of small-for-gestational-age (SGA) and body fat percent (BF%) among preterm infants. Prospective cohort study of 204 preterm infants classified as SGA or appropriate-for-gestational-age (AGA) by population-based and customized growth curves. BF% was determined by air-displacement plethysmography. Differences between groups were compared using bivariable and multivariable linear and logistic regression analyses. Customized curves reclassified 30% of the preterm infants as SGA. SGA infants identified by customized method only had significantly lower BF% (13.8 ± 6.0) than the AGA (16.2 ± 6.3, p = 0.02) infants and similar to the SGA infants classified by both methods (14.6 ± 6.7, p = 0.51). Customized growth curves were a significant predictor of BF% (p = 0.02), whereas population-based growth curves were not a significant independent predictor of BF% (p = 0.50) at term corrected gestational age. Customized growth potential improves the differentiation of SGA infants and low BF% compared with a standard population-based growth curve among a cohort of preterm infants.

Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999-2009.

PubMed

Brown, Tyler S; Narechania, Apurva; Walker, John R; Planet, Paul J; Bifani, Pablo J; Kolokotronis, Sergios-Orestis; Kreiswirth, Barry N; Mathema, Barun

2016-11-21

Whole genome sequencing (WGS) has rapidly become an important research tool in tuberculosis epidemiology and is likely to replace many existing methods in public health microbiology in the near future. WGS-based methods may be particularly useful in areas with less diverse Mycobacterium tuberculosis populations, such as New York City, where conventional genotyping is often uninformative and field epidemiology often difficult. This study applies four candidate strategies for WGS-based identification of emerging M. tuberculosis subpopulations, employing both phylogenomic and population genetics methods. M. tuberculosis subpopulations in New York City and New Jersey can be distinguished via phylogenomic reconstruction, evidence of demographic expansion and subpopulation-specific signatures of selection, and by determination of subgroup-defining nucleotide substitutions. These methods identified known historical outbreak clusters and previously unidentified subpopulations within relatively monomorphic M. tuberculosis endemic clone groups. Neutrality statistics based on the site frequency spectrum were less useful for identifying M. tuberculosis subpopulations, likely due to the low levels of informative genetic variation in recently diverged isolate groups. In addition, we observed that isolates from New York City endemic clone groups have acquired multiple non-synonymous SNPs in virulence- and growth-associated pathways, and relatively few mutations in drug resistance-associated genes, suggesting that overall pathoadaptive fitness, rather than the acquisition of drug resistance mutations, has played a central role in the evolutionary history and epidemiology of M. tuberculosis subpopulations in New York City. Our results demonstrate that some but not all WGS-based methods are useful for detection of emerging M. tuberculosis clone groups, and support the use of phylogenomic reconstruction in routine tuberculosis laboratory surveillance, particularly in areas with relatively less diverse M. tuberculosis populations. Our study also supports the use of wider-reaching phylogenomic and population genomic methods in tuberculosis public health practice, which can support tuberculosis control activities by identifying genetic polymorphisms contributing to epidemiological success in local M. tuberculosis populations and possibly explain why certain isolate groups are apparently more successful in specific host populations.

SimBA: simulation algorithm to fit extant-population distributions.

PubMed

Parida, Laxmi; Haiminen, Niina

2015-03-14

Simulation of populations with specified characteristics such as allele frequencies, linkage disequilibrium etc., is an integral component of many studies, including in-silico breeding optimization. Since the accuracy and sensitivity of population simulation is critical to the quality of the output of the applications that use them, accurate algorithms are required to provide a strong foundation to the methods in these studies. In this paper we present SimBA (Simulation using Best-fit Algorithm) a non-generative approach, based on a combination of stochastic techniques and discrete methods. We optimize a hill climbing algorithm and extend the framework to include multiple subpopulation structures. Additionally, we show that SimBA is very sensitive to the input specifications, i.e., very similar but distinct input characteristics result in distinct outputs with high fidelity to the specified distributions. This property of the simulation is not explicitly modeled or studied by previous methods. We show that SimBA outperforms the existing population simulation methods, both in terms of accuracy as well as time-efficiency. Not only does it construct populations that meet the input specifications more stringently than other published methods, SimBA is also easy to use. It does not require explicit parameter adaptations or calibrations. Also, it can work with input specified as distributions, without an exemplar matrix or population as required by some methods. SimBA is available at http://researcher.ibm.com/project/5669 .

Overcoming statistical bias to estimate genetic mating systems in open populations: a comparison of Bateman's principles between the sexes in a sex-role-reversed pipefish.

PubMed

Mobley, Kenyon B; Jones, Adam G

2013-03-01

The genetic mating system is a key component of the sexual selection process, yet methods for the quantification of mating systems remain controversial. One approach involves metrics derived from Bateman's principles, which are based on variances in mating and reproductive success and the relationship between them. However, these measures are extremely difficult to measure for both sexes in open populations, because missing data can result in biased estimates. Here, we develop a novel approach for the estimation of mating system metrics based on Bateman's principles and apply it to a microsatellite-based parentage analysis of a natural population of the dusky pipefish, Syngnathus floridae. Our results show that both male and female dusky pipefish have significantly positive Bateman gradients. However, females exhibit larger values of the opportunity for sexual selection and the opportunity for selection compared to males. These differences translate into a maximum intensity of sexual selection (S'max) for females three times larger than that for males. Overall, this study identifies a critical source of bias that affects studies of mating systems in open populations, presents a novel method for overcoming this bias, and applies this method for the first time in a sex-role-reversed pipefish. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Generation of Boundary Manikin Anthropometry

NASA Technical Reports Server (NTRS)

Young, Karen S.; Margerum, Sarah; Barr, Abbe; Ferrer, Mike A.; Rajulu, Sudhakar

2008-01-01

The purpose of this study was to develop 3D digital boundary manikins that are representative of the anthropometry of a unique population. These digital manikins can be used by designers to verify and validate that the components of the spacesuit design satisfy the requirements specified in the Human Systems Integration Requirements (HSIR) document. Currently, the HSIR requires the suit to accommodate the 1st percentile American female to the 99th percentile American male. The manikin anthropometry was derived using two methods: Principal Component Analysis (PCA) and Whole Body Posture Based Analysis (WBPBA). PCA is a statistical method for reducing a multidimensional data set by using eigenvectors and eigenvalues. The goal is to create a reduced data set that encapsulates the majority of the variation in the population. WBPBA is a multivariate analytical approach that was developed by the Anthropometry and Biomechanics Facility (ABF) to identify the extremes of the population for a given body posture. WBPBA is a simulation-based method that finds extremes in a population based on anthropometry and posture whereas PCA is based solely on anthropometry. Both methods yield a list of subjects and their anthropometry from the target population; PCA resulted in 20 female and 22 male subjects anthropometry and WBPBA resulted in 7 subjects' anthropometry representing the extreme subjects in the target population. The subjects anthropometry is then used to 'morph' a baseline digital scan of a person with the same body type to create a 3D digital model that can be used as a tool for designers, the details of which will be discussed in subsequent papers.

High coffee consumption and different brewing methods in relation to postmenopausal endometrial cancer risk in the Norwegian Women and Cancer Study: a population-based prospective study

PubMed Central

2014-01-01

Background Coffee and its compounds have been proposed to inhibit endometrial carcinogenesis. Studies in the Norwegian population can be especially interesting due to the high coffee consumption and increasing incidence of endometrial cancer in the country. Methods A total of 97 926 postmenopausal Norwegian women from the population-based prospective Norwegian Women and Cancer (NOWAC) Study, were included in the present analysis. We evaluated the general association between total coffee consumption and endometrial cancer risk as well as the possible impact of brewing method. Multivariate Cox regression analysis was used to estimate risks, and heterogeneity tests were performed to compare brewing methods. Results During an average of 10.9 years of follow-up, 462 incident endometrial cancer cases were identified. After multivariate adjustment, significant risk reduction was found among participants who drank ≥8 cups/day of coffee with a hazard ratio of 0.52 (95% confidence interval, CI 0.34-0.79). However, we did not observe a significant dose-response relationship. No significant heterogeneity in risk was found when comparing filtered and boiled coffee brewing methods. A reduction in endometrial cancer risk was observed in subgroup analyses among participants who drank ≥8 cups/day and had a body mass index ≥25 kg/m2, and in current smokers. Conclusions These data suggest that in this population with high coffee consumption, endometrial cancer risk decreases in women consuming ≥8 cups/day, independent of brewing method. PMID:24666820

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.

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

PubMed

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

2014-06-01

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

Measuring taste impairment in epidemiologic studies: the Beaver Dam Offspring Study.

PubMed

Cruickshanks, K J; Schubert, C R; Snyder, D J; Bartoshuk, L M; Huang, G H; Klein, B E K; Klein, R; Nieto, F J; Pankow, J S; Tweed, T S; Krantz, E M; Moy, G S

2009-07-01

Taste or gustatory function may play an important role in determining diet and nutritional status and therefore indirectly impact health. Yet there have been few attempts to study the spectrum of taste function and dysfunction in human populations. Epidemiologic studies are needed to understand the impact of taste function and dysfunction on public health, to identify modifiable risk factors, and to develop and test strategies to prevent clinically significant dysfunction. However, measuring taste function in epidemiologic studies is challenging and requires repeatable, efficient methods that can measure change over time. Insights gained from translating laboratory-based methods to a population-based study, the Beaver Dam Offspring Study (BOSS) will be shared. In this study, a generalized labeled magnitude scale (gLMS) method was used to measure taste intensity of filter paper disks saturated with salt, sucrose, citric acid, quinine, or 6-n-propylthiouracil, and a gLMS measure of taste preferences was administered. In addition, a portable, inexpensive camera system to capture digital images of fungiform papillae and a masked grading system to measure the density of fungiform papillae were developed. Adult children of participants in the population-based Epidemiology of Hearing Loss Study in Beaver Dam, Wisconsin, are eligible for this ongoing study. The parents were residents of Beaver Dam and 43-84 years of age in 1987-1988; offspring ranged in age from 21-84 years in 2005-2008. Methods will be described in detail and preliminary results about the distributions of taste function in the BOSS cohort will be presented.

Are PCI Service Volumes Associated with 30-Day Mortality? A Population-Based Study from Taiwan.

PubMed

Yu, Tsung-Hsien; Chou, Ying-Yi; Wei, Chung-Jen; Tung, Yu-Chi

2017-11-09

The volume-outcome relationship has been discussed for over 30 years; however, the findings are inconsistent. This might be due to the heterogeneity of service volume definitions and categorization methods. This study takes percutaneous coronary intervention (PCI) as an example to examine whether the service volume was associated with PCI 30-day mortality, given different service volume definitions and categorization methods. A population-based, cross-sectional multilevel study was conducted. Two definitions of physician and hospital volume were used: (1) the cumulative PCI volume in a previous year before each PCI; (2) the cumulative PCI volume within the study period. The volume was further treated in three ways: (1) a categorical variable based on the American Heart Association's recommendation; (2) a semi-data-driven categorical variable based on k-means clustering algorithm; and (3) a data-driven categorical variable based on the Generalized Additive Model. The results showed that, after adjusting the patient-, physician-, and hospital-level covariates, physician volume was associated inversely with PCI 30-day mortality, but hospital volume was not, no matter which definitions and categorization methods of service volume were applied. Physician volume is negatively associated with PCI 30-day mortality, but the results might vary because of definition and categorization method.

Digital radiographic evaluation of mandibular third molar for age estimation in young adults and adolescents of South Indian population using modified Demirjian's method

PubMed Central

Mohammed, Rezwana Begum; Koganti, Ravichandra; Kalyan, Siva V.; Tircouveluri, Saritha; Singh, Johar Rajvinder; Srinivasulu, Enganti

2014-01-01

In recent years, it has become increasingly important to determine the age of living people for a variety of reasons, including identifying criminal and legal responsibility and for many other social events such as birth certificate, marriage, beginning a job, joining the army and retirement Objectives: The aim of this study was to assess the developmental stages of mandibular third molar for estimation of dental age (DA) in different age groups and to evaluate the possible correlation between DA and chronological age (CA) in South Indian population. Materials and Methods: Digital orthopantomography of 330 subjects (165 males, 165 females) who fit the study and the criteria were obtained. Assessment of mandibular third molar development was performed using Demirjian et al., modified method and DA was assessed using tooth specific stages. Results and Discussion: The present study showed a significant correlation between DA and CA in both males and females. Third molar development commenced around 9 years and root completion takes place around 18.9 years in males and in females 9 years and 18.6 years respectively. Demirjian modified method underestimated the mean age of males by 0.8 years and females by 0.5 years and also showed that females mature earlier than males in selected population. Conclusion: Digital radiographic assessment of mandibular third molar development can be used to generate mean DA using Demirjian modified method and also the estimated age range for an individual of unknown CA. Since the Demirjian method is based on French-Canadian population, to enhance the accuracy of forensic age estimates based on third molar development, the use of population-specific standards is recommended. PMID:25177143

Estimating Kinship in Admixed Populations

PubMed Central

Thornton, Timothy; Tang, Hua; Hoffmann, Thomas J.; Ochs-Balcom, Heather M.; Caan, Bette J.; Risch, Neil

2012-01-01

Genome-wide association studies (GWASs) are commonly used for the mapping of genetic loci that influence complex traits. A problem that is often encountered in both population-based and family-based GWASs is that of identifying cryptic relatedness and population stratification because it is well known that failure to appropriately account for both pedigree and population structure can lead to spurious association. A number of methods have been proposed for identifying relatives in samples from homogeneous populations. A strong assumption of population homogeneity, however, is often untenable, and many GWASs include samples from structured populations. Here, we consider the problem of estimating relatedness in structured populations with admixed ancestry. We propose a method, REAP (relatedness estimation in admixed populations), for robust estimation of identity by descent (IBD)-sharing probabilities and kinship coefficients in admixed populations. REAP appropriately accounts for population structure and ancestry-related assortative mating by using individual-specific allele frequencies at SNPs that are calculated on the basis of ancestry derived from whole-genome analysis. In simulation studies with related individuals and admixture from highly divergent populations, we demonstrate that REAP gives accurate IBD-sharing probabilities and kinship coefficients. We apply REAP to the Mexican Americans in Los Angeles, California (MXL) population sample of release 3 of phase III of the International Haplotype Map Project; in this sample, we identify third- and fourth-degree relatives who have not previously been reported. We also apply REAP to the African American and Hispanic samples from the Women's Health Initiative SNP Health Association Resource (WHI-SHARe) study, in which hundreds of pairs of cryptically related individuals have been identified. PMID:22748210

A Method for Inferring an Individual’s Genetic Ancestry and Degree of Admixture Associated with Six Major Continental Populations

PubMed Central

Libiger, Ondrej; Schork, Nicholas J.

2013-01-01

The determination of the ancestry and genetic backgrounds of the subjects in genetic and general epidemiology studies is a crucial component in the analysis of relevant outcomes or associations. Although there are many methods for differentiating ancestral subgroups among individuals based on genetic markers only a few of these methods provide actual estimates of the fraction of an individual’s genome that is likely to be associated with different ancestral populations. We propose a method for assigning ancestry that works in stages to refine estimates of ancestral population contributions to individual genomes. The method leverages genotype data in the public domain obtained from individuals with known ancestries. Although we showcase the method in the assessment of ancestral genome proportions leveraging largely continental populations, the strategy can be used for assessing within-continent or more subtle ancestral origins with the appropriate data. PMID:23335941

Population size estimation of men who have sex with men through the network scale-up method in Japan.

PubMed

Ezoe, Satoshi; Morooka, Takeo; Noda, Tatsuya; Sabin, Miriam Lewis; Koike, Soichi

2012-01-01

Men who have sex with men (MSM) are one of the groups most at risk for HIV infection in Japan. However, size estimates of MSM populations have not been conducted with sufficient frequency and rigor because of the difficulty, high cost and stigma associated with reaching such populations. This study examined an innovative and simple method for estimating the size of the MSM population in Japan. We combined an internet survey with the network scale-up method, a social network method for estimating the size of hard-to-reach populations, for the first time in Japan. An internet survey was conducted among 1,500 internet users who registered with a nationwide internet-research agency. The survey participants were asked how many members of particular groups with known population sizes (firepersons, police officers, and military personnel) they knew as acquaintances. The participants were also asked to identify the number of their acquaintances whom they understood to be MSM. Using these survey results with the network scale-up method, the personal network size and MSM population size were estimated. The personal network size was estimated to be 363.5 regardless of the sex of the acquaintances and 174.0 for only male acquaintances. The estimated MSM prevalence among the total male population in Japan was 0.0402% without adjustment, and 2.87% after adjusting for the transmission error of MSM. The estimated personal network size and MSM prevalence seen in this study were comparable to those from previous survey results based on the direct-estimation method. Estimating population sizes through combining an internet survey with the network scale-up method appeared to be an effective method from the perspectives of rapidity, simplicity, and low cost as compared with more-conventional methods.

[Assessing incident cardiovascular and metabolic diseases in epidemiological cohort studies in Germany].

PubMed

Herrmann, Wolfram J; Weikert, Cornelia; Bergmann, Manuela; Boeing, Heiner; Katzke, Verena A; Kaaks, Rudolf; Tiller, Daniel; Greiser, Karin Halina; Heier, Margit; Meisinger, Christa; Schmidt, Carsten Oliver; Neuhauser, Hannelore; Heidemann, Christin; Jünger, Claus; Wild, Philipp S; Schramm, Sara Helena; Jöckel, Karl-Heinz; Dörr, Marcus; Pischon, Tobias

2018-04-01

Cardiovascular and metabolic diseases are a major cause of mortality and loss of quality of life in Germany. Research into risk factors of these diseases requires large population-based cohort studies. Complete and accurate assessment of the incidence of cardiovascular and metabolic diseases is a key element for valid interpretation of the results from such studies. Our aim was to identify population-based cohort studies with incidence of cardiovascular and metabolic diseases in Germany and to summarize their methods for assessment and classification of disease endpoints, including myocardial infarction, type 2 diabetes, stroke, heart failure, and arterial hypertension. Within the framework of a workshop, representatives of the ascertained population-based cohort studies in Germany with incidence of cardiovascular or metabolic diseases were invited to present and to systematically provide information on their methods of endpoint identification. We identified eight studies from different regions in Germany with a total of 100,571 participants, aged 18-83 years at baseline. Self-reporting by study participants is the major source for further inquiries to assess disease endpoints in these studies. Most studies use additional data sources to verify the incidence of diseases, such as documents provided by the treating physician or hospital. Our results highlight the central role of self-reporting and the efforts associated with identification and verification of disease endpoints in cohort studies. They also provide a basis for future population-based studies that aim for standardized assessment of the incidence of cardiovascular and metabolic diseases.

Dasymetric high resolution population distribution estimates for improved decision making, with a case study of sea-level rise vulnerability in Boca Raton, Florida

NASA Astrophysics Data System (ADS)

Ziegler, Hannes Moritz

Planners and managers often rely on coarse population distribution data from the census for addressing various social, economic, and environmental problems. In the analysis of physical vulnerabilities to sea-level rise, census units such as blocks or block groups are coarse relative to the required decision-making application. This study explores the benefits offered from integrating image classification and dasymetric mapping at the household level to provide detailed small area population estimates at the scale of residential buildings. In a case study of Boca Raton, FL, a sea-level rise inundation grid based on mapping methods by NOAA is overlaid on the highly detailed population distribution data to identify vulnerable residences and estimate population displacement. The enhanced spatial detail offered through this method has the potential to better guide targeted strategies for future development, mitigation, and adaptation efforts.

The problem of estimating recent genetic connectivity in a changing world.

PubMed

Samarasin, Pasan; Shuter, Brian J; Wright, Stephen I; Rodd, F Helen

2017-02-01

Accurate understanding of population connectivity is important to conservation because dispersal can play an important role in population dynamics, microevolution, and assessments of extirpation risk and population rescue. Genetic methods are increasingly used to infer population connectivity because advances in technology have made them more advantageous (e.g., cost effective) relative to ecological methods. Given the reductions in wildlife population connectivity since the Industrial Revolution and more recent drastic reductions from habitat loss, it is important to know the accuracy of and biases in genetic connectivity estimators when connectivity has declined recently. Using simulated data, we investigated the accuracy and bias of 2 common estimators of migration (movement of individuals among populations) rate. We focused on the timing of the connectivity change and the magnitude of that change on the estimates of migration by using a coalescent-based method (Migrate-n) and a disequilibrium-based method (BayesAss). Contrary to expectations, when historically high connectivity had declined recently: (i) both methods over-estimated recent migration rates; (ii) the coalescent-based method (Migrate-n) provided better estimates of recent migration rate than the disequilibrium-based method (BayesAss); (iii) the coalescent-based method did not accurately reflect long-term genetic connectivity. Overall, our results highlight the problems with comparing coalescent and disequilibrium estimates to make inferences about the effects of recent landscape change on genetic connectivity among populations. We found that contrasting these 2 estimates to make inferences about genetic-connectivity changes over time could lead to inaccurate conclusions. © 2016 Society for Conservation Biology.

Using a Marginal Structural Model to Design a Theory-Based Mass Media Campaign

PubMed Central

Taguri, Masataka; Ishikawa, Yoshiki

2016-01-01

Background The essential first step in the development of mass media health campaigns is to identify specific beliefs of the target audience. The challenge is to prioritize suitable beliefs derived from behavioral theory. The purpose of this study was to identify suitable beliefs to target in a mass media campaign to change behavior using a new method to estimate the possible effect size of a small set of beliefs. Methods Data were drawn from the 2010 Japanese Young Female Smoker Survey (n = 500), conducted by the Japanese Ministry of Health, Labor and Welfare. Survey measures included intention to quit smoking, psychological beliefs (attitude, norms, and perceived control) based on the theory of planned behavior and socioeconomic status (age, education, household income, and marital status). To identify suitable candidate beliefs for a mass media health campaign, we estimated the possible effect size required to change the intention to quit smoking among the population of young Japanese women using the population attributable fraction from a marginal structural model. Results Thirteen percent of study participants intended to quit smoking. The marginal structural model estimated a population attributable fraction of 47 psychological beliefs (21 attitudes, 6 norms, and 19 perceived controls) after controlling for socioeconomic status. The belief, “I could quit smoking if my husband or significant other recommended it” suggested a promising target for a mass media campaign (population attributable fraction = 0.12, 95% CI = 0.02–0.23). Messages targeting this belief could possibly improve intention rates by up to 12% among this population. The analysis also suggested the potential for regulatory action. Conclusions This study proposed a method by which campaign planners can develop theory-based mass communication strategies to change health behaviors at the population level. This method might contribute to improving the quality of future mass health communication strategies and further research is needed. PMID:27441626

MixFit: Methodology for Computing Ancestry-Related Genetic Scores at the Individual Level and Its Application to the Estonian and Finnish Population Studies.

PubMed

Haller, Toomas; Leitsalu, Liis; Fischer, Krista; Nuotio, Marja-Liisa; Esko, Tõnu; Boomsma, Dorothea Irene; Kyvik, Kirsten Ohm; Spector, Tim D; Perola, Markus; Metspalu, Andres

2017-01-01

Ancestry information at the individual level can be a valuable resource for personalized medicine, medical, demographical and history research, as well as for tracing back personal history. We report a new method for quantitatively determining personal genetic ancestry based on genome-wide data. Numerical ancestry component scores are assigned to individuals based on comparisons with reference populations. These comparisons are conducted with an existing analytical pipeline making use of genotype phasing, similarity matrix computation and our addition-multidimensional best fitting by MixFit. The method is demonstrated by studying Estonian and Finnish populations in geographical context. We show the main differences in the genetic composition of these otherwise close European populations and how they have influenced each other. The components of our analytical pipeline are freely available computer programs and scripts one of which was developed in house (available at: www.geenivaramu.ee/en/tools/mixfit).

Coexisting Psychiatric Problems and Stressful Life Events in Adults with Symptoms of ADHD--A Large Swedish Population-Based Study of Twins

ERIC Educational Resources Information Center

Friedrichs, Bettina; Igl, Wilmar; Larsson, Henrik; Larsson, Jan-Olov

2012-01-01

Objective: To explore the associations of subtypes of adult ADHD with other psychiatric problems, stressful life events, and sex differences. Method: Odds ratios were calculated using information from 17,899 participants from a population-based survey of adult twins born in Sweden between 1959 and 1985. Results: Symptoms of attention deficit…

Cause-Specific Mortality and Death Certificate Reporting in Adults with Moderate to Profound Intellectual Disability

ERIC Educational Resources Information Center

Tyrer, F.; McGrother, C.

2009-01-01

Background: The study of premature deaths in people with intellectual disability (ID) has become the focus of recent policy initiatives in England. This is the first UK population-based study to explore cause-specific mortality in adults with ID compared with the general population. Methods: Cause-specific standardised mortality ratios (SMRs) and…

Outline-based morphometrics, an overlooked method in arthropod studies?

PubMed

Dujardin, Jean-Pierre; Kaba, D; Solano, P; Dupraz, M; McCoy, K D; Jaramillo-O, N

2014-12-01

Modern methods allow a geometric representation of forms, separating size and shape. In entomology, as well as in many other fields involving arthropod studies, shape variation has proved useful for species identification and population characterization. In medical entomology, it has been applied to very specific questions such as population structure, reinfestation of insecticide-treated areas and cryptic species recognition. For shape comparisons, great importance is given to the quality of landmarks in terms of comparability. Two conceptually and statistically separate approaches are: (i) landmark-based morphometrics, based on the relative position of a few anatomical "true" or "traditional" landmarks, and (ii) outline-based morphometrics, which captures the contour of forms through a sequence of close "pseudo-landmarks". Most of the studies on insects of medical, veterinary or economic importance make use of the landmark approach. The present survey makes a case for the outline method, here based on elliptic Fourier analysis. The collection of pseudo-landmarks may require the manual digitization of many points and, for this reason, might appear less attractive. It, however, has the ability to compare homologous organs or structures having no landmarks at all. This strength offers the possibility to study a wider range of anatomical structures and thus, a larger range of arthropods. We present a few examples highlighting its interest for separating close or cryptic species, or characterizing conspecific geographic populations, in a series of different vector organisms. In this simple application, i.e. the recognition of close or cryptic forms, the outline approach provided similar scores as those obtained by the landmark-based approach. Copyright © 2014 Elsevier B.V. All rights reserved.

A robust and efficient statistical method for genetic association studies using case and control samples from multiple cohorts

PubMed Central

2013-01-01

Background The theoretical basis of genome-wide association studies (GWAS) is statistical inference of linkage disequilibrium (LD) between any polymorphic marker and a putative disease locus. Most methods widely implemented for such analyses are vulnerable to several key demographic factors and deliver a poor statistical power for detecting genuine associations and also a high false positive rate. Here, we present a likelihood-based statistical approach that accounts properly for non-random nature of case–control samples in regard of genotypic distribution at the loci in populations under study and confers flexibility to test for genetic association in presence of different confounding factors such as population structure, non-randomness of samples etc. Results We implemented this novel method together with several popular methods in the literature of GWAS, to re-analyze recently published Parkinson’s disease (PD) case–control samples. The real data analysis and computer simulation show that the new method confers not only significantly improved statistical power for detecting the associations but also robustness to the difficulties stemmed from non-randomly sampling and genetic structures when compared to its rivals. In particular, the new method detected 44 significant SNPs within 25 chromosomal regions of size < 1 Mb but only 6 SNPs in two of these regions were previously detected by the trend test based methods. It discovered two SNPs located 1.18 Mb and 0.18 Mb from the PD candidates, FGF20 and PARK8, without invoking false positive risk. Conclusions We developed a novel likelihood-based method which provides adequate estimation of LD and other population model parameters by using case and control samples, the ease in integration of these samples from multiple genetically divergent populations and thus confers statistically robust and powerful analyses of GWAS. On basis of simulation studies and analysis of real datasets, we demonstrated significant improvement of the new method over the non-parametric trend test, which is the most popularly implemented in the literature of GWAS. PMID:23394771

Governance for public health and health equity: The Tröndelag model for public health work.

PubMed

Lillefjell, Monica; Magnus, Eva; Knudtsen, Margunn SkJei; Wist, Guri; Horghagen, Sissel; Espnes, Geir Arild; Maass, Ruca; Anthun, Kirsti Sarheim

2018-06-01

Multi-sectoral governance of population health is linked to the realization that health is the property of many societal systems. This study aims to contribute knowledge and methods that can strengthen the capacities of municipalities regarding how to work more systematically, knowledge-based and multi-sectoral in promoting health and health equity in the population. Process evaluation was conducted, applying a mixed-methods research design, combining qualitative and quantitative data collection methods. Processes strengthening systematic and multi-sectoral development, implementation and evaluation of research-based measures to promote health, quality of life, and health equity in, for and with municipalities were revealed. A step-by-step model, that emphasizes the promotion of knowledge-based, systematic, multi-sectoral public health work, as well as joint ownership of local resources, initiatives and policies has been developed. Implementation of systematic, knowledge-based and multi-sectoral governance of public health measures in municipalities demand shared understanding of the challenges, updated overview of the population health and impact factors, anchoring in plans, new skills and methods for selection and implementation of measures, as well as development of trust, ownership, shared ethics and goals among those involved.

Population assessment of tropical tuna based on their associative behavior around floating objects.

PubMed

Capello, M; Deneubourg, J L; Robert, M; Holland, K N; Schaefer, K M; Dagorn, L

2016-11-03

Estimating the abundance of pelagic fish species is a challenging task, due to their vast and remote habitat. Despite the development of satellite, archival and acoustic tagging techniques that allow the tracking of marine animals in their natural environments, these technologies have so far been underutilized in developing abundance estimations. We developed a new method for estimating the abundance of tropical tuna that employs these technologies and exploits the aggregative behavior of tuna around floating objects (FADs). We provided estimates of abundance indices based on a simulated set of tagged fish and studied the sensitivity of our method to different association dynamics, FAD numbers, population sizes and heterogeneities of the FAD-array. Taking the case study of yellowfin tuna (Thunnus albacares) acoustically-tagged in Hawaii, we implemented our approach on field data and derived for the first time the ratio between the associated and the total population. With more extensive and long-term monitoring of FAD-associated tunas and good estimates of the numbers of fish at FADs, our method could provide fisheries-independent estimates of populations of tropical tuna. The same approach can be applied to obtain population assessments for any marine and terrestrial species that display associative behavior and from which behavioral data have been acquired using acoustic, archival or satellite tags.

Solving the problem of negative populations in approximate accelerated stochastic simulations using the representative reaction approach.

PubMed

Kadam, Shantanu; Vanka, Kumar

2013-02-15

Methods based on the stochastic formulation of chemical kinetics have the potential to accurately reproduce the dynamical behavior of various biochemical systems of interest. However, the computational expense makes them impractical for the study of real systems. Attempts to render these methods practical have led to the development of accelerated methods, where the reaction numbers are modeled by Poisson random numbers. However, for certain systems, such methods give rise to physically unrealistic negative numbers for species populations. The methods which make use of binomial variables, in place of Poisson random numbers, have since become popular, and have been partially successful in addressing this problem. In this manuscript, the development of two new computational methods, based on the representative reaction approach (RRA), has been discussed. The new methods endeavor to solve the problem of negative numbers, by making use of tools like the stochastic simulation algorithm and the binomial method, in conjunction with the RRA. It is found that these newly developed methods perform better than other binomial methods used for stochastic simulations, in resolving the problem of negative populations. Copyright © 2012 Wiley Periodicals, Inc.

Influence of Food on Paediatric Gastrointestinal Drug Absorption Following Oral Administration: A Review

PubMed Central

Batchelor, Hannah K.

2015-01-01

The objective of this paper was to review existing information regarding food effects on drug absorption within paediatric populations. Mechanisms that underpin food–drug interactions were examined to consider potential differences between adult and paediatric populations, to provide insights into how this may alter the pharmacokinetic profile in a child. Relevant literature was searched to retrieve information on food–drug interaction studies undertaken on: (i) paediatric oral drug formulations; and (ii) within paediatric populations. The applicability of existing methodology to predict food effects in adult populations was evaluated with respect to paediatric populations where clinical data was available. Several differences in physiology, anatomy and the composition of food consumed within a paediatric population are likely to lead to food–drug interactions that cannot be predicted based on adult studies. Existing methods to predict food effects cannot be directly extrapolated to allow predictions within paediatric populations. Development of systematic methods and guidelines is needed to address the general lack of information on examining food–drug interactions within paediatric populations. PMID:27417362

Tracking rural-to-urban migration in China: Lessons from the 2005 inter-census population survey.

PubMed

Ebenstein, Avraham; Zhao, Yaohui

2015-01-01

We examined migration in China using the 2005 inter-census population survey, in which migrants were registered at both their place of original (hukou) residence and at their destination. We find evidence that the estimated number of internal migrants in China is extremely sensitive to the enumeration method. We estimate that the traditional destination-based survey method fails to account for more than a third of migrants found using comparable origin-based methods. The 'missing' migrants are disproportionately young, male, and holders of rural hukou. We find that origin-based methods are more effective at capturing migrants who travel short distances for short periods, whereas destination-based methods are more effective when entire households have migrated and no remaining family members are located at the hukou location. We conclude with a set of policy recommendations for the design of population surveys in countries with large migrant populations.

Mapping Urban Risk: Flood Hazards, Race, & Environmental Justice In New York”

PubMed Central

Maantay, Juliana; Maroko, Andrew

2009-01-01

This paper demonstrates the importance of disaggregating population data aggregated by census tracts or other units, for more realistic population distribution/location. A newly-developed mapping method, the Cadastral-based Expert Dasymetric System (CEDS), calculates population in hyper-heterogeneous urban areas better than traditional mapping techniques. A case study estimating population potentially impacted by flood hazard in New York City compares the impacted population determined by CEDS with that derived by centroid-containment method and filtered areal weighting interpolation. Compared to CEDS, 37 percent and 72 percent fewer people are estimated to be at risk from floods city-wide, using conventional areal weighting of census data, and centroid-containment selection, respectively. Undercounting of impacted population could have serious implications for emergency management and disaster planning. Ethnic/racial populations are also spatially disaggregated to determine any environmental justice impacts with flood risk. Minorities are disproportionately undercounted using traditional methods. Underestimating more vulnerable sub-populations impairs preparedness and relief efforts. PMID:20047020

Functional Performance in Young Australian Children with Achondroplasia

ERIC Educational Resources Information Center

Ireland, Penelope Jane; McGill, James; Zankl, Andreas; Ware, Robert S.; Pacey, Verity; Ault, Jenny; Savarirayan, Ravi; Sillence, David; Thompson, Elizabeth M.; Townshend, Sharron; Johnston, Leanne Marie

2011-01-01

Aim: The aim of this study was to determine population-specific developmental milestones for independence in self-care, mobility, and social cognitive skills in children with achondroplasia, the most common skeletal dysplasia. Methods: Population-based recruitment from October 2008 to October 2010 identified 44 Australian children with…

Methodology Series Module 5: Sampling Strategies.

PubMed

Setia, Maninder Singh

2016-01-01

Once the research question and the research design have been finalised, it is important to select the appropriate sample for the study. The method by which the researcher selects the sample is the ' Sampling Method'. There are essentially two types of sampling methods: 1) probability sampling - based on chance events (such as random numbers, flipping a coin etc.); and 2) non-probability sampling - based on researcher's choice, population that accessible & available. Some of the non-probability sampling methods are: purposive sampling, convenience sampling, or quota sampling. Random sampling method (such as simple random sample or stratified random sample) is a form of probability sampling. It is important to understand the different sampling methods used in clinical studies and mention this method clearly in the manuscript. The researcher should not misrepresent the sampling method in the manuscript (such as using the term ' random sample' when the researcher has used convenience sample). The sampling method will depend on the research question. For instance, the researcher may want to understand an issue in greater detail for one particular population rather than worry about the ' generalizability' of these results. In such a scenario, the researcher may want to use ' purposive sampling' for the study.

Tablet-Based Education to Reduce Depression-Related Stigma

ERIC Educational Resources Information Center

Lu, Catherine; Winkelman, Megan; Wong, Shane Shucheng

2016-01-01

Objectives: This study investigated the efficacy of a tablet-based multimedia education application, the Project Not Alone Depression Module, in improving depression literacy and reducing depression stigma among a community-based mental health clinic population. Methods: A total of 93 participants completed either a tablet-based multimedia…

Culturally Grounded Prevention for Minority Youth Populations: A Systematic Review of the Literature

PubMed Central

Lauricella, Michela; Valdez, Jessica K.; Okamoto, Scott K.; Helm, Susana; Zaremba, Colleen

2016-01-01

Contemporary prevention science has focused on the application of cultural adaptations of evidence-based prevention programs for minority youth populations. Far less is known about culturally grounded methods that are intended to organically develop prevention programs within specific populations and communities. This article systematically reviews recent literature on culturally grounded interventions used to prevent health disparities in ethnic minority youth populations. In this review, we assessed 31 peer-reviewed articles published in 2003 or later that fit inclusionary criteria pertaining to the development and evaluation of culturally grounded prevention programs. The evaluated studies indicated different approaches toward cultural grounding, as well as specific populations, geographic regions, and health issues that have been targeted. Specifically, the findings indicated that most of the studies focused on the development and evaluation of culturally grounded HIV/STI and substance abuse prevention programs for Mexican American, African American, and American Indian/Alaska Native youth residing in the South or Southwestern U.S. These studies largely relied on community-based participatory or qualitative research methods to develop programs from the “ground up.” This review has implications for the development of future culturally grounded and culturally adapted prevention programs targeting underserved minority youth populations and geographic regions. Specifically, it identifies populations and regions where culturally grounded prevention efforts are underdeveloped or non-existent, providing some scientific direction for the future development of these types of programs. PMID:26733384

Culturally Grounded Prevention for Minority Youth Populations: A Systematic Review of the Literature.

PubMed

Lauricella, Michela; Valdez, Jessica K; Okamoto, Scott K; Helm, Susana; Zaremba, Colleen

2016-02-01

Contemporary prevention science has focused on the application of cultural adaptations of evidence-based prevention programs for minority youth populations. Far less is known about culturally grounded methods that are intended to organically develop prevention programs within specific populations and communities. This article systematically reviews recent literature on culturally grounded interventions used to prevent health disparities in ethnic minority youth populations. In this review, we assessed 31 peer-reviewed articles published in 2003 or later that fit inclusionary criteria pertaining to the development and evaluation of culturally grounded prevention programs. The evaluated studies indicated different approaches toward cultural grounding, as well as specific populations, geographic regions, and health issues that have been targeted. Specifically, the findings indicated that most of the studies focused on the development and evaluation of culturally grounded HIV/STI and substance abuse prevention programs for Mexican-American, African American, and American Indian/Alaska Native youth residing in the South or Southwestern US. These studies largely relied on community-based participatory or qualitative research methods to develop programs from the "ground up." This review has implications for the development of future culturally grounded and culturally adapted prevention programs targeting underserved minority youth populations and geographic regions. Specifically, it identifies populations and regions where culturally grounded prevention efforts are underdeveloped or non-existent, providing some scientific direction for the future development of these types of programs.

Digital radiographic evaluation of mandibular third molar for age estimation in young adults and adolescents of South Indian population using modified Demirjian's method.

PubMed

Mohammed, Rezwana Begum; Koganti, Ravichandra; Kalyan, Siva V; Tircouveluri, Saritha; Singh, Johar Rajvinder; Srinivasulu, Enganti

2014-09-01

In recent years, it has become increasingly important to determine the age of living people for a variety of reasons, including identifying criminal and legal responsibility and for many other social events such as birth certificate, marriage, beginning a job, joining the army and retirement. The aim of this study was to assess the developmental stages of mandibular third molar for estimation of dental age (DA) in different age groups and to evaluate the possible correlation between DA and chronological age (CA) in South Indian population. Digital orthopantomography of 330 subjects (165 males, 165 females) who fit the study and the criteria were obtained. Assessment of mandibular third molar development was performed using Demirjian et al., modified method and DA was assessed using tooth specific stages. The present study showed a significant correlation between DA and CA in both males and females. Third molar development commenced around 9 years and root completion takes place around 18.9 years in males and in females 9 years and 18.6 years respectively. Demirjian modified method underestimated the mean age of males by 0.8 years and females by 0.5 years and also showed that females mature earlier than males in selected population. Digital radiographic assessment of mandibular third molar development can be used to generate mean DA using Demirjian modified method and also the estimated age range for an individual of unknown CA. Since the Demirjian method is based on French-Canadian population, to enhance the accuracy of forensic age estimates based on third molar development, the use of population-specific standards is recommended.

On estimation of time-dependent attributable fraction from population-based case-control studies.

PubMed

Zhao, Wei; Chen, Ying Qing; Hsu, Li

2017-09-01

Population attributable fraction (PAF) is widely used to quantify the disease burden associated with a modifiable exposure in a population. It has been extended to a time-varying measure that provides additional information on when and how the exposure's impact varies over time for cohort studies. However, there is no estimation procedure for PAF using data that are collected from population-based case-control studies, which, because of time and cost efficiency, are commonly used for studying genetic and environmental risk factors of disease incidences. In this article, we show that time-varying PAF is identifiable from a case-control study and develop a novel estimator of PAF. Our estimator combines odds ratio estimates from logistic regression models and density estimates of the risk factor distribution conditional on failure times in cases from a kernel smoother. The proposed estimator is shown to be consistent and asymptotically normal with asymptotic variance that can be estimated empirically from the data. Simulation studies demonstrate that the proposed estimator performs well in finite sample sizes. Finally, the method is illustrated by a population-based case-control study of colorectal cancer. © 2017, The International Biometric Society.

The Forgotten Learning Disability – Epidemiology of Written Language Disorder in a Population-Based Birth Cohort (1976-1982), Rochester, Minnesota

PubMed Central

Katusic, Slavica K.; Colligan, Robert C.; Weaver, Amy L.; Barbaresi, William J.

2009-01-01

OBJECTIVE The aim of this study was to report the incidence rates and other epidemiologic characterizations of Written Language Disorder (WLD). There have been no epidemiologic studies on the incidence of WLD in the United States and the use of a population-based birth cohort, longitudinally followed, is the most powerful method to reach this objective. METHODS In this population-based, retrospective birth cohort study, subjects included 5718 children born 1976-1982 in Rochester, Minnesota who remained in the community after age 5 years. Records from all public and nonpublic schools, medical facilities, and private tutorial services were reviewed and results of all individually administered IQ and achievement tests, and extensive medical, educational, and socioeconomic information were collected. The essential features of writing problems from the DSM-IV-TR were included in our operationalized definition of WLD. WLD incident cases were established using research criteria based on 3 formulas (regression-based discrepancy, non-regression-based discrepancy, low achievement). RESULTS Cumulative incidence rates of WLD varied from 6.9% to 14.7% depending on the formula. Boys were 2-3 times more likely to be affected than girls, regardless of the formula. Among all WLD cases (N=806), 25% (N=203) had WLD without Reading Disability (RD). Specifics of the writing problems were identified for 87% (N=702) of WLD cases. CONCLUSION In this population-based birth cohort of school aged children, WLD was at least as frequent as RD, and significantly more frequent among boys than girls. PMID:19403496

A method for modelling GP practice level deprivation scores using GIS

PubMed Central

Strong, Mark; Maheswaran, Ravi; Pearson, Tim; Fryers, Paul

2007-01-01

Background A measure of general practice level socioeconomic deprivation can be used to explore the association between deprivation and other practice characteristics. An area-based categorisation is commonly chosen as the basis for such a deprivation measure. Ideally a practice population-weighted area-based deprivation score would be calculated using individual level spatially referenced data. However, these data are often unavailable. One approach is to link the practice postcode to an area-based deprivation score, but this method has limitations. This study aimed to develop a Geographical Information Systems (GIS) based model that could better predict a practice population-weighted deprivation score in the absence of patient level data than simple practice postcode linkage. Results We calculated predicted practice level Index of Multiple Deprivation (IMD) 2004 deprivation scores using two methods that did not require patient level data. Firstly we linked the practice postcode to an IMD 2004 score, and secondly we used a GIS model derived using data from Rotherham, UK. We compared our two sets of predicted scores to "gold standard" practice population-weighted scores for practices in Doncaster, Havering and Warrington. Overall, the practice postcode linkage method overestimated "gold standard" IMD scores by 2.54 points (95% CI 0.94, 4.14), whereas our modelling method showed no such bias (mean difference 0.36, 95% CI -0.30, 1.02). The postcode-linked method systematically underestimated the gold standard score in less deprived areas, and overestimated it in more deprived areas. Our modelling method showed a small underestimation in scores at higher levels of deprivation in Havering, but showed no bias in Doncaster or Warrington. The postcode-linked method showed more variability when predicting scores than did the GIS modelling method. Conclusion A GIS based model can be used to predict a practice population-weighted area-based deprivation measure in the absence of patient level data. Our modelled measure generally had better agreement with the population-weighted measure than did a postcode-linked measure. Our model may also avoid an underestimation of IMD scores in less deprived areas, and overestimation of scores in more deprived areas, seen when using postcode linked scores. The proposed method may be of use to researchers who do not have access to patient level spatially referenced data. PMID:17822545

Triceps and Subscapular Skinfold Thickness Percentiles and Cut-Offs for Overweight and Obesity in a Population-Based Sample of Schoolchildren and Adolescents in Bogota, Colombia.

PubMed

Ramírez-Vélez, Robinson; López-Cifuentes, Mario Ferney; Correa-Bautista, Jorge Enrique; González-Ruíz, Katherine; González-Jiménez, Emilio; Córdoba-Rodríguez, Diana Paola; Vivas, Andrés; Triana-Reina, Hector Reynaldo; Schmidt-RioValle, Jacqueline

2016-09-24

The assessment of skinfold thickness is an objective measure of adiposity. The aims of this study were to establish Colombian smoothed centile charts and LMS L (Box-Cox transformation), M (median), and S (coefficient of variation) tables for triceps, subscapular, and triceps + subscapular skinfolds; appropriate cut-offs were selected using receiver operating characteristic (ROC) analysis based on a population-based sample of children and adolescents in Bogotá, Colombia. A cross-sectional study was conducted in 9618 children and adolescents (55.7% girls; age range of 9-17.9 years). Triceps and subscapular skinfold measurements were obtained using standardized methods. We calculated the triceps + subscapular skinfold (T + SS) sum. Smoothed percentile curves for triceps and subscapular skinfold thickness were derived using the LMS method. ROC curve analyses were used to evaluate the optimal cut-off point of skinfold thickness for overweight and obesity, based on the International Obesity Task Force definitions. Subscapular and triceps skinfolds and T + SS were significantly higher in girls than in boys (p < 0.001). The ROC analysis showed that subscapular and triceps skinfolds and T + SS have a high discriminatory power in the identification of overweight and obesity in the sample population in this study. Our results provide sex- and age-specific normative reference standards for skinfold thickness values from a population from Bogotá, Colombia.

A population-based study on health and living conditions in areas with mixed Sami and Norwegian settlements – the SAMINOR 2 questionnaire study

PubMed Central

Brustad, Magritt; Hansen, Ketil Lenert; Broderstad, Ann Ragnhild; Hansen, Solrunn; Melhus, Marita

2014-01-01

Objectives To describe the method, data collection procedure and participation in The Population-based Study on Health and Living Conditions in Areas with both Sami and Norwegian Settlements – the SAMINOR 2 questionnaire study. Study design Cross-sectional and semi-longitudinal. Methods In 2012, all inhabitants aged 18–69 and living in selected municipalities with both Sami and Norwegian settlements in Mid and Northern Norway were posted an invitation to participate in a questionnaire survey covering several topics related to health and living conditions. The geographical area was similar to the area where the SAMINOR 1 study was conducted in 2003/2004 with the exception of one additional municipality. Participants could alternatively use a web-based questionnaire with identical question and answer categories as the posted paper version. Results In total, 11,600 (27%) participated (16% used the web-based questionnaire), with a higher participation rate among those over 50 (37% for women and 32% for men). Some geographical variation in participation rates was found. In addition, for those invited who also participated in the SAMINOR 1 study, we found that the participation rates increased with the level of education and income, while there was little difference in participation rates across ethnic groups. Conclusion The knowledge generated from future theme-specific research utilizing the SAMINOR 2 database has the potential to benefit the general population in this geographical area of Norway, and the Sami people in particular, by providing knowledge-based insight into the health and living conditions of the multi-ethnic population in these parts of Norway. PMID:24971230

Water availability and vulnerability of 225 large cities in the United States

NASA Astrophysics Data System (ADS)

Padowski, Julie C.; Jawitz, James W.

2012-12-01

This study presents a quantitative national assessment of urban water availability and vulnerability for 225 U.S. cities with population greater than 100,000. Here, the urban assessments account for not only renewable water flows, but also the extracted, imported, and stored water that urban systems access through constructed infrastructure. These sources represent important hydraulic components of the urban water supply, yet are typically excluded from water scarcity assessments. Results from this hydraulic-based assessment were compared to those obtained using a more conventional method that estimates scarcity solely based on local renewable flows. The inclusion of hydraulic components increased the mean availability to cities, leading to a significantly lower portion of the total U.S. population considered "at risk" for water scarcity (17%) than that obtained from the runoff method (47%). Water vulnerability was determined based on low-flow conditions, and smaller differences were found for this metric between at-risk populations using the runoff (66%) and hydraulic-based (54%) methods. The large increase in the susceptible population between the scarcity measures evaluated using the hydraulic method may better reconcile the seeming contradiction in the United States between perceptions of natural water abundance and widespread water scarcity. Additionally, urban vulnerability measures developed here were validated using a media text analysis. Vulnerability assessments that included hydraulic components were found to correlate with the frequency of urban water scarcity reports in the popular press while runoff-based measures showed no significant correlation, suggesting that hydraulic-based assessments provide better context for understanding the nature and severity of urban water scarcity issues.

Evaluation of an urban traffic Noise-Exposed population based on points of interest and noise maps: The case of Guangzhou.

PubMed

Wang, Haibo; Chen, Hanjie; Cai, Ming

2018-08-01

The primary objective of this study was to develop an evaluation method for assessing an urban traffic noise-exposed population and apply it in the main urban area of Guangzhou. The method based on points of interest (POIs) and noise map is realized in several steps. First, after regionalizing based on road networks and executing a cluster analysis for regions according to the properties of POIs, the environmental noise functional regions (NFRs) of the urban area are presented. Then, surrounding POIs are used to infer the type of buildings, and according to the attraction of different building types and the whole population of the region, the population distribution at the building level is calculated. Finally, with the help of a noise map, an evaluation method for assessing an urban traffic noise-exposed population is proposed. The method is applied in the main urban area of Guangzhou, and the results reveal the followings. 1) At daytime and nighttime, 23.63% and 30.53% of the population, respectively, experience noise levels that exceed the noise standards. The per capita noise exposure value at daytime and nighttime is 0.9 dB and 2.0 dB, respectively. 2) The percentages of the exposed population of Yuexiu District were 28.89% at daytime and 35.65% at nighttime, which are the largest, followed by the exposed population percentages of Liwan, Haizhu, and Tianhe Districts. 3) From the view of different classes of NFRs, the percentages of the exposed population of Class 1 and Class 4 are larger than the percentages of the exposed population from the other classes, especially at nighttime (48.24% of Class 1 and 40.79% of Class 4). 4) Although there are masses of people affected by traffic noise, a large percentage of them (85%) experience not more than 5 dB of traffic noise superscale. Copyright © 2018 Elsevier Ltd. All rights reserved.

HacDivSel: Two new methods (haplotype-based and outlier-based) for the detection of divergent selection in pairs of populations

PubMed Central

2017-01-01

The detection of genomic regions involved in local adaptation is an important topic in current population genetics. There are several detection strategies available depending on the kind of genetic and demographic information at hand. A common drawback is the high risk of false positives. In this study we introduce two complementary methods for the detection of divergent selection from populations connected by migration. Both methods have been developed with the aim of being robust to false positives. The first method combines haplotype information with inter-population differentiation (FST). Evidence of divergent selection is concluded only when both the haplotype pattern and the FST value support it. The second method is developed for independently segregating markers i.e. there is no haplotype information. In this case, the power to detect selection is attained by developing a new outlier test based on detecting a bimodal distribution. The test computes the FST outliers and then assumes that those of interest would have a different mode. We demonstrate the utility of the two methods through simulations and the analysis of real data. The simulation results showed power ranging from 60–95% in several of the scenarios whilst the false positive rate was controlled below the nominal level. The analysis of real samples consisted of phased data from the HapMap project and unphased data from intertidal marine snail ecotypes. The results illustrate that the proposed methods could be useful for detecting locally adapted polymorphisms. The software HacDivSel implements the methods explained in this manuscript. PMID:28423003

Toward a Biology of Menopause.

ERIC Educational Resources Information Center

Goodman, Madeleine

1980-01-01

Discusses research dealing with the study of menopause. Underscores the problems with the case study method. Discusses two population-based studies and the problems of age adjustment and measurement in menopause research. Highlights alternate research strategies. (MK)

Rapid and Specific Method for Evaluating Streptomyces Competitive Dynamics in Complex Soil Communities

USDA-ARS?s Scientific Manuscript database

Quantifying target microbial populations in complex communities remains a barrier to studying species interactions in soil environments. Quantitative real-time PCR (qPCR) offers a rapid and specific means to assess populations of target microorganisms. SYBR Green and TaqMan-based qPCR assays were de...

[Commentary on "group and organization: a dimension of collaboration of anthropology and epidemiology" by Song LM and Wang N].

PubMed

Liao, Su-Su; Zhang, Qing-Ning; Hou, Lei

2012-10-01

Epidemiology, as the study of occurrence and distribution of diseases or health events in specified populations and the application of the study to control health problems, is not just a method to study determinants of diseases at individual level through analysis of mass data based on individuals. To achieve the aims on the control of health problems in specified populations, Epidemiology should be public health-oriented to reduce incidence, prevalence and mortality, and should include study on determinants at the population level. Interdisplinarity and systems science will facilitate the breakthrough in improving health of the populations.

Methodology Series Module 5: Sampling Strategies

PubMed Central

Setia, Maninder Singh

2016-01-01

Once the research question and the research design have been finalised, it is important to select the appropriate sample for the study. The method by which the researcher selects the sample is the ‘ Sampling Method’. There are essentially two types of sampling methods: 1) probability sampling – based on chance events (such as random numbers, flipping a coin etc.); and 2) non-probability sampling – based on researcher's choice, population that accessible & available. Some of the non-probability sampling methods are: purposive sampling, convenience sampling, or quota sampling. Random sampling method (such as simple random sample or stratified random sample) is a form of probability sampling. It is important to understand the different sampling methods used in clinical studies and mention this method clearly in the manuscript. The researcher should not misrepresent the sampling method in the manuscript (such as using the term ‘ random sample’ when the researcher has used convenience sample). The sampling method will depend on the research question. For instance, the researcher may want to understand an issue in greater detail for one particular population rather than worry about the ‘ generalizability’ of these results. In such a scenario, the researcher may want to use ‘ purposive sampling’ for the study. PMID:27688438

Reliability of Different Mark-Recapture Methods for Population Size Estimation Tested against Reference Population Sizes Constructed from Field Data

PubMed Central

Grimm, Annegret; Gruber, Bernd; Henle, Klaus

2014-01-01

Reliable estimates of population size are fundamental in many ecological studies and biodiversity conservation. Selecting appropriate methods to estimate abundance is often very difficult, especially if data are scarce. Most studies concerning the reliability of different estimators used simulation data based on assumptions about capture variability that do not necessarily reflect conditions in natural populations. Here, we used data from an intensively studied closed population of the arboreal gecko Gehyra variegata to construct reference population sizes for assessing twelve different population size estimators in terms of bias, precision, accuracy, and their 95%-confidence intervals. Two of the reference populations reflect natural biological entities, whereas the other reference populations reflect artificial subsets of the population. Since individual heterogeneity was assumed, we tested modifications of the Lincoln-Petersen estimator, a set of models in programs MARK and CARE-2, and a truncated geometric distribution. Ranking of methods was similar across criteria. Models accounting for individual heterogeneity performed best in all assessment criteria. For populations from heterogeneous habitats without obvious covariates explaining individual heterogeneity, we recommend using the moment estimator or the interpolated jackknife estimator (both implemented in CAPTURE/MARK). If data for capture frequencies are substantial, we recommend the sample coverage or the estimating equation (both models implemented in CARE-2). Depending on the distribution of catchabilities, our proposed multiple Lincoln-Petersen and a truncated geometric distribution obtained comparably good results. The former usually resulted in a minimum population size and the latter can be recommended when there is a long tail of low capture probabilities. Models with covariates and mixture models performed poorly. Our approach identified suitable methods and extended options to evaluate the performance of mark-recapture population size estimators under field conditions, which is essential for selecting an appropriate method and obtaining reliable results in ecology and conservation biology, and thus for sound management. PMID:24896260

The Impact of Hearing Loss on Quality of Life in Older Adults

ERIC Educational Resources Information Center

Dalton, Dayna S.; Cruickshanks, Karen J.; Klein, Barbara E. K.; Klein, Ronald; Wiley, Terry L.; Nondahl, David M.

2003-01-01

Purpose: The authors investigate the impact of hearing loss on quality of life in a large population of older adults. Design and Methods: Data are from the 5-year follow-up Epidemiology of Hearing Loss Study, a population-based longitudinal study of age-related hearing impairment conducted in Beaver Dam, WI. Participants (N = 2,688) were 53-97…

Anthropometric methods for obesity screening in schoolchildren: the Ouro Preto Study.

PubMed

Cándido, A P C; Alosta, J P S; Oliveira, C T; Freitas, R N; Freitas, S N; Machado-Coelho, G L L

2012-01-01

Childhood obesity is increasing dramatically in last decades. To evaluate the usefulness of body mass index (BMI), skinfold thickness (ST), waist circumference (WC), and foot-to-foot bioelectrical impedance (BIA-FF) for screening for obesity in mixed-race population, using the tetrapolar bioelectrical impedance (BIA-T) technique as reference method. A cross-sectional-based population study was performed in the city of Ouro Preto, Brazil, in 2006. Schoolchildren aged 6-15 years (n = 788) was randomly selected according to age and sex stratified by the proportion of students in each schools of the city. Nonparametric receiver operating characteristic (ROC) analysis was used to define the sensitivity and specificity for each method studied using the tetrapolar method as reference. The BMI and the BIA-FF were the most suitable for adiposity screening in pre-pubertal and pubertal stages because they present a better balance between sensitivity and specificity, and smaller misclassification. For post-pubertal boys, the BF-ST-D was the best body fat assessment method. The results suggest that BIA-FF and BMI are choice methods for obesity screening in mixed population and that the method choice for body fat screening must be done according to sexual maturity of boys and girls. The present study demonstrates the need to perform studies in wider mixed-race population to determine anthropometric parameters and to examine the predictive ability of methods and cut-offs here elucidated in the development of obesity.

Estimating neural response functions from fMRI

PubMed Central

Kumar, Sukhbinder; Penny, William

2014-01-01

This paper proposes a methodology for estimating Neural Response Functions (NRFs) from fMRI data. These NRFs describe non-linear relationships between experimental stimuli and neuronal population responses. The method is based on a two-stage model comprising an NRF and a Hemodynamic Response Function (HRF) that are simultaneously fitted to fMRI data using a Bayesian optimization algorithm. This algorithm also produces a model evidence score, providing a formal model comparison method for evaluating alternative NRFs. The HRF is characterized using previously established “Balloon” and BOLD signal models. We illustrate the method with two example applications based on fMRI studies of the auditory system. In the first, we estimate the time constants of repetition suppression and facilitation, and in the second we estimate the parameters of population receptive fields in a tonotopic mapping study. PMID:24847246

Trends in Health Information-Seeking Behaviour in the U.S. Foreign-Born Population Based on the Health Information National Trends Survey, 2005-2014

ERIC Educational Resources Information Center

Yoon, JungWon; Huang, Hong; Soojung Kim

2017-01-01

Introduction: This study investigated trends in the health information-seeking behaviour of the U.S. foreign-born population over a ten-year period and examined whether health information disparities between this population and native-born citizens have decreased. Method: Data were collected from six iterations of the Health Information National…

Continuous Adaptive Population Reduction (CAPR) for Differential Evolution Optimization.

PubMed

Wong, Ieong; Liu, Wenjia; Ho, Chih-Ming; Ding, Xianting

2017-06-01

Differential evolution (DE) has been applied extensively in drug combination optimization studies in the past decade. It allows for identification of desired drug combinations with minimal experimental effort. This article proposes an adaptive population-sizing method for the DE algorithm. Our new method presents improvements in terms of efficiency and convergence over the original DE algorithm and constant stepwise population reduction-based DE algorithm, which would lead to a reduced number of cells and animals required to identify an optimal drug combination. The method continuously adjusts the reduction of the population size in accordance with the stage of the optimization process. Our adaptive scheme limits the population reduction to occur only at the exploitation stage. We believe that continuously adjusting for a more effective population size during the evolutionary process is the major reason for the significant improvement in the convergence speed of the DE algorithm. The performance of the method is evaluated through a set of unimodal and multimodal benchmark functions. In combining with self-adaptive schemes for mutation and crossover constants, this adaptive population reduction method can help shed light on the future direction of a completely parameter tune-free self-adaptive DE algorithm.

Group-regularized individual prediction: theory and application to pain.

PubMed

Lindquist, Martin A; Krishnan, Anjali; López-Solà, Marina; Jepma, Marieke; Woo, Choong-Wan; Koban, Leonie; Roy, Mathieu; Atlas, Lauren Y; Schmidt, Liane; Chang, Luke J; Reynolds Losin, Elizabeth A; Eisenbarth, Hedwig; Ashar, Yoni K; Delk, Elizabeth; Wager, Tor D

2017-01-15

Multivariate pattern analysis (MVPA) has become an important tool for identifying brain representations of psychological processes and clinical outcomes using fMRI and related methods. Such methods can be used to predict or 'decode' psychological states in individual subjects. Single-subject MVPA approaches, however, are limited by the amount and quality of individual-subject data. In spite of higher spatial resolution, predictive accuracy from single-subject data often does not exceed what can be accomplished using coarser, group-level maps, because single-subject patterns are trained on limited amounts of often-noisy data. Here, we present a method that combines population-level priors, in the form of biomarker patterns developed on prior samples, with single-subject MVPA maps to improve single-subject prediction. Theoretical results and simulations motivate a weighting based on the relative variances of biomarker-based prediction-based on population-level predictive maps from prior groups-and individual-subject, cross-validated prediction. Empirical results predicting pain using brain activity on a trial-by-trial basis (single-trial prediction) across 6 studies (N=180 participants) confirm the theoretical predictions. Regularization based on a population-level biomarker-in this case, the Neurologic Pain Signature (NPS)-improved single-subject prediction accuracy compared with idiographic maps based on the individuals' data alone. The regularization scheme that we propose, which we term group-regularized individual prediction (GRIP), can be applied broadly to within-person MVPA-based prediction. We also show how GRIP can be used to evaluate data quality and provide benchmarks for the appropriateness of population-level maps like the NPS for a given individual or study. Copyright © 2015 Elsevier Inc. All rights reserved.

A comparison of pedigree- and DNA-based measures for identifying inbreeding depression in the critically endangered Attwater's Prairie-chicken.

PubMed

Hammerly, Susan C; Morrow, Michael E; Johnson, Jeff A

2013-11-01

The primary goal of captive breeding programmes for endangered species is to prevent extinction, a component of which includes the preservation of genetic diversity and avoidance of inbreeding. This is typically accomplished by minimizing mean kinship in the population, thereby maintaining equal representation of the genetic founders used to initiate the captive population. If errors in the pedigree do exist, such an approach becomes less effective for minimizing inbreeding depression. In this study, both pedigree- and DNA-based methods were used to assess whether inbreeding depression existed in the captive population of the critically endangered Attwater's Prairie-chicken (Tympanuchus cupido attwateri), a subspecies of prairie grouse that has experienced a significant decline in abundance and concurrent reduction in neutral genetic diversity. When examining the captive population for signs of inbreeding, variation in pedigree-based inbreeding coefficients (f(pedigree)) was less than that obtained from DNA-based methods (f(DNA)). Mortality of chicks and adults in captivity were also positively correlated with parental relatedness (r(DNA)) and f(DNA), respectively, while no correlation was observed with pedigree-based measures when controlling for additional variables such as age, breeding facility, gender and captive/release status. Further, individual homozygosity by loci (HL) and parental rDNA values were positively correlated with adult mortality in captivity and the occurrence of a lethal congenital defect in chicks, respectively, suggesting that inbreeding may be a contributing factor increasing the frequency of this condition among Attwater's Prairie-chickens. This study highlights the importance of using DNA-based methods to better inform management decisions when pedigrees are incomplete or errors may exist due to uncertainty in pairings. © 2013 John Wiley & Sons Ltd.

Population Size Estimation of Men Who Have Sex with Men through the Network Scale-Up Method in Japan

PubMed Central

Ezoe, Satoshi; Morooka, Takeo; Noda, Tatsuya; Sabin, Miriam Lewis; Koike, Soichi

2012-01-01

Background Men who have sex with men (MSM) are one of the groups most at risk for HIV infection in Japan. However, size estimates of MSM populations have not been conducted with sufficient frequency and rigor because of the difficulty, high cost and stigma associated with reaching such populations. This study examined an innovative and simple method for estimating the size of the MSM population in Japan. We combined an internet survey with the network scale-up method, a social network method for estimating the size of hard-to-reach populations, for the first time in Japan. Methods and Findings An internet survey was conducted among 1,500 internet users who registered with a nationwide internet-research agency. The survey participants were asked how many members of particular groups with known population sizes (firepersons, police officers, and military personnel) they knew as acquaintances. The participants were also asked to identify the number of their acquaintances whom they understood to be MSM. Using these survey results with the network scale-up method, the personal network size and MSM population size were estimated. The personal network size was estimated to be 363.5 regardless of the sex of the acquaintances and 174.0 for only male acquaintances. The estimated MSM prevalence among the total male population in Japan was 0.0402% without adjustment, and 2.87% after adjusting for the transmission error of MSM. Conclusions The estimated personal network size and MSM prevalence seen in this study were comparable to those from previous survey results based on the direct-estimation method. Estimating population sizes through combining an internet survey with the network scale-up method appeared to be an effective method from the perspectives of rapidity, simplicity, and low cost as compared with more-conventional methods. PMID:22563366

How are qualitative methods used in diabetes research? A 30-year systematic review.

PubMed

Hennink, Monique M; Kaiser, Bonnie N; Sekar, Swathi; Griswold, Emily P; Ali, Mohammed K

2017-02-01

We aimed to describe how qualitative methods are used in global research on diabetes and identify opportunities whereby qualitative methods could further benefit our understanding of the human experience of diabetes and interventions to address it. We conducted a systematic review of National Library of Medicine, EMBASE, and Web of Science electronic databases to identify original research articles that used qualitative methods to study diabetes between 1980 and 2011. We identified 554 eligible articles and categorised these by geographic region, year of publication, study population, study design, research question, qualitative data collection methods, and journal type. Results show low use of qualitative methods in diabetes research over the past 30 years. The majority of articles (75%) reported using substantive qualitative research, while mixed-methods research has remained underutilised. Eighty-five per cent of articles reported studies conducted in North America or Europe, with few studies in developing countries. Most articles reported recruiting clinic-based populations (58%). Over half (54%) of research questions focused on patient experience and 24% on diabetes management. Qualitative methods can provide important insights about socio-cultural aspects of disease to improve disease management. However, they remain underutilised for understanding the diabetes experience, especially in Africa and Asia and amongst non-clinic populations.

People with dementia in nursing home research: a methodological review of the definition and identification of the study population.

PubMed

Palm, Rebecca; Jünger, Saskia; Reuther, Sven; Schwab, Christian G G; Dichter, Martin N; Holle, Bernhard; Halek, Margareta

2016-04-05

There are various definitions and diagnostic criteria for dementia, leading to discrepancies in case ascertainment in both clinical practice and research. We reviewed the different definitions, approaches and measurements used to operationalize dementia in health care studies in German nursing homes with the aim of discussing the implications of different approaches. We conducted a systematic search of the MEDLINE and CINAHL databases to identify pre-2016 studies conducted in German nursing homes that focused on residents with dementia or cognitive impairment. In- or exclusion of studies were consented by all authors; data extraction was independently carried out by 2 authors (RP, SJ). The studies' sampling methods were compared with respect to their inclusion criteria, assessment tools and methods used to identify the study population. We summarized case ascertainment methods from 64 studies. Study participants were identified based on a diagnosis that was evaluated during the study, or a recorded medical dementia diagnosis, or a recorded medical diagnosis either with additional cognitive screenings or using screening tests exclusively. The descriptions of the diagnostics that were applied to assess a diagnosis of dementia were not fully transparent in most of the studies with respect to either a clear reference definition of dementia or applied diagnostic criteria. If reported, various neuropsychological tests were used, mostly without a clear rationale for their selection. Pragmatic considerations often determine the sampling strategy; they also may explain the variances we detected in the different studies. Variations in sampling methods impede the comparability of study results. There is a need to consent case ascertainment strategies in dementia studies in health service research in nursing homes. These strategies should consider resource constraints and ethical issues that are related to the vulnerable population of nursing home residents. Additionally, reporting about dementia studies in nursing homes need to be improved. If a diagnosis cannot be evaluated based on either ICD or DSM criteria, the study population may not be reported as having dementia. If a diagnosis is evaluated based on ICD or DSM criteria within the study, there is a need for more transparency of the diagnostic process.

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.

Improving data retention in EEG research with children using child-centered eye tracking

PubMed Central

Maguire, Mandy J.; Magnon, Grant; Fitzhugh, Anna E.

2014-01-01

Background Event Related Potentials (ERPs) elicited by visual stimuli have increased our understanding of developmental disorders and adult cognitive abilities for decades; however, these studies are very difficult with populations who cannot sustain visual attention such as infants and young children. Current methods for studying such populations include requiring a button response, which may be impossible for some participants, and experimenter monitoring, which is subject to error, highly variable, and spatially imprecise. New Method We developed a child-centered methodology to integrate EEG data acquisition and eye-tracking technologies that uses “attention-getters” in which stimulus display is contingent upon the child’s gaze. The goal was to increase the number of trials retained. Additionally, we used the eye-tracker to categorize and analyze the EEG data based on gaze to specific areas of the visual display, compared to analyzing based on stimulus presentation. Results Compared with Existing Methods The number of trials retained was substantially improved using the child-centered methodology compared to a button-press response in 7–8 year olds. In contrast, analyzing the EEG based on eye gaze to specific points within the visual display as opposed to stimulus presentation provided too few trials for reliable interpretation. Conclusions By using the linked EEG-eye-tracker we significantly increased data retention. With this method, studies can be completed with fewer participants and a wider range of populations. However, caution should be used when epoching based on participants’ eye gaze because, in this case, this technique provided substantially fewer trials. PMID:25251555

Methods for inferring health-related social networks among coworkers from online communication patterns.

PubMed

Matthews, Luke J; DeWan, Peter; Rula, Elizabeth Y

2013-01-01

Studies of social networks, mapped using self-reported contacts, have demonstrated the strong influence of social connections on the propensity for individuals to adopt or maintain healthy behaviors and on their likelihood to adopt health risks such as obesity. Social network analysis may prove useful for businesses and organizations that wish to improve the health of their populations by identifying key network positions. Health traits have been shown to correlate across friendship ties, but evaluating network effects in large coworker populations presents the challenge of obtaining sufficiently comprehensive network data. The purpose of this study was to evaluate methods for using online communication data to generate comprehensive network maps that reproduce the health-associated properties of an offline social network. In this study, we examined three techniques for inferring social relationships from email traffic data in an employee population using thresholds based on: (1) the absolute number of emails exchanged, (2) logistic regression probability of an offline relationship, and (3) the highest ranked email exchange partners. As a model of the offline social network in the same population, a network map was created using social ties reported in a survey instrument. The email networks were evaluated based on the proportion of survey ties captured, comparisons of common network metrics, and autocorrelation of body mass index (BMI) across social ties. Results demonstrated that logistic regression predicted the greatest proportion of offline social ties, thresholding on number of emails exchanged produced the best match to offline network metrics, and ranked email partners demonstrated the strongest autocorrelation of BMI. Since each method had unique strengths, researchers should choose a method based on the aspects of offline behavior of interest. Ranked email partners may be particularly useful for purposes related to health traits in a social network.

Methods for Inferring Health-Related Social Networks among Coworkers from Online Communication Patterns

PubMed Central

Matthews, Luke J.; DeWan, Peter; Rula, Elizabeth Y.

2013-01-01

Studies of social networks, mapped using self-reported contacts, have demonstrated the strong influence of social connections on the propensity for individuals to adopt or maintain healthy behaviors and on their likelihood to adopt health risks such as obesity. Social network analysis may prove useful for businesses and organizations that wish to improve the health of their populations by identifying key network positions. Health traits have been shown to correlate across friendship ties, but evaluating network effects in large coworker populations presents the challenge of obtaining sufficiently comprehensive network data. The purpose of this study was to evaluate methods for using online communication data to generate comprehensive network maps that reproduce the health-associated properties of an offline social network. In this study, we examined three techniques for inferring social relationships from email traffic data in an employee population using thresholds based on: (1) the absolute number of emails exchanged, (2) logistic regression probability of an offline relationship, and (3) the highest ranked email exchange partners. As a model of the offline social network in the same population, a network map was created using social ties reported in a survey instrument. The email networks were evaluated based on the proportion of survey ties captured, comparisons of common network metrics, and autocorrelation of body mass index (BMI) across social ties. Results demonstrated that logistic regression predicted the greatest proportion of offline social ties, thresholding on number of emails exchanged produced the best match to offline network metrics, and ranked email partners demonstrated the strongest autocorrelation of BMI. Since each method had unique strengths, researchers should choose a method based on the aspects of offline behavior of interest. Ranked email partners may be particularly useful for purposes related to health traits in a social network. PMID:23418436

Association between pregnancy complications and small-for-gestational-age birth weight defined by customized fetal growth standard versus a population-based standard.

PubMed

Odibo, Anthony O; Francis, Andre; Cahill, Alison G; Macones, George A; Crane, James P; Gardosi, Jason

2011-03-01

To derive coefficients for developing a customized growth chart for a Mid-Western US population, and to estimate the association between pregnancy outcomes and smallness for gestational age (SGA) defined by the customized growth chart compared with a population-based growth chart for the USA. A retrospective cohort study of an ultrasound database using 54,433 pregnancies meeting inclusion criteria was conducted. Coefficients for customized centiles were derived using 42,277 pregnancies and compared with those obtained from other populations. Two adverse outcome indicators were defined (greater than 7 day stay in the neonatal unit and stillbirth [SB]), and the risk for each outcome was calculated for the groups of pregnancies defined as SGA by the population standard and SGA by the customized standard using 12,456 pregnancies for the validation sample. The growth potential expressed as weight at 40 weeks in this population was 3524 g (standard error: 402 g). In the validation population, 4055 cases of SGA were identified using both population and customized standards. The cases additionally identified as SGA by the customized method had a significantly increased risk of each of the adverse outcome categories. The sensitivity and specificity of those identified as SGA by customized method only for detecting pregnancies at risk for SB was 32.7% (95% confidence interval [CI] 27.0-38.8%) and 95.1% (95% CI: 94.7-95.0%) versus 0.8% (95% CI 0.1-2.7%) and 98.0% (95% CI 97.8-98.2%)for those identified by only the population-based method, respectively. SGA defined by customized growth potential is able to identify substantially more pregnancies at a risk for adverse outcome than the currently used national standard for fetal growth.

Automated finite element modeling of the lumbar spine: Using a statistical shape model to generate a virtual population of models.

PubMed

Campbell, J Q; Petrella, A J

2016-09-06

Population-based modeling of the lumbar spine has the potential to be a powerful clinical tool. However, developing a fully parameterized model of the lumbar spine with accurate geometry has remained a challenge. The current study used automated methods for landmark identification to create a statistical shape model of the lumbar spine. The shape model was evaluated using compactness, generalization ability, and specificity. The primary shape modes were analyzed visually, quantitatively, and biomechanically. The biomechanical analysis was performed by using the statistical shape model with an automated method for finite element model generation to create a fully parameterized finite element model of the lumbar spine. Functional finite element models of the mean shape and the extreme shapes (±3 standard deviations) of all 17 shape modes were created demonstrating the robust nature of the methods. This study represents an advancement in finite element modeling of the lumbar spine and will allow population-based modeling in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assessing the Effectiveness of "Wise Guys": A Mixed-Methods Approach

ERIC Educational Resources Information Center

Herrman, Judith W.; Gordon, Mellissa; Rahmer, Brian; Moore, Christopher C.; Habermann, Barbara; Haigh, Katherine M.

2017-01-01

Previous research raised questions on the validity of survey studies with the teen population. As one response, our team implemented a mixed-methods study to evaluate an evidence-based, interactive curriculum, "Wise Guys," which is designed to promote healthy relationships and sexual behavior in young men ages 4-17. The current study…

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

PubMed

Torkzaban, Bahareh; Kayvanjoo, Amir Hossein; Ardalan, Arman; Mousavi, Soraya; Mariotti, Roberto; Baldoni, Luciana; Ebrahimie, Esmaeil; Ebrahimi, Mansour; Hosseini-Mazinani, Mehdi

2015-01-01

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

A general method to determine sampling windows for nonlinear mixed effects models with an application to population pharmacokinetic studies.

PubMed

Foo, Lee Kien; McGree, James; Duffull, Stephen

2012-01-01

Optimal design methods have been proposed to determine the best sampling times when sparse blood sampling is required in clinical pharmacokinetic studies. However, the optimal blood sampling time points may not be feasible in clinical practice. Sampling windows, a time interval for blood sample collection, have been proposed to provide flexibility in blood sampling times while preserving efficient parameter estimation. Because of the complexity of the population pharmacokinetic models, which are generally nonlinear mixed effects models, there is no analytical solution available to determine sampling windows. We propose a method for determination of sampling windows based on MCMC sampling techniques. The proposed method attains a stationary distribution rapidly and provides time-sensitive windows around the optimal design points. The proposed method is applicable to determine sampling windows for any nonlinear mixed effects model although our work focuses on an application to population pharmacokinetic models. Copyright © 2012 John Wiley & Sons, Ltd.

Adapt-Mix: learning local genetic correlation structure improves summary statistics-based analyses

PubMed Central

Park, Danny S.; Brown, Brielin; Eng, Celeste; Huntsman, Scott; Hu, Donglei; Torgerson, Dara G.; Burchard, Esteban G.; Zaitlen, Noah

2015-01-01

Motivation: Approaches to identifying new risk loci, training risk prediction models, imputing untyped variants and fine-mapping causal variants from summary statistics of genome-wide association studies are playing an increasingly important role in the human genetics community. Current summary statistics-based methods rely on global ‘best guess’ reference panels to model the genetic correlation structure of the dataset being studied. This approach, especially in admixed populations, has the potential to produce misleading results, ignores variation in local structure and is not feasible when appropriate reference panels are missing or small. Here, we develop a method, Adapt-Mix, that combines information across all available reference panels to produce estimates of local genetic correlation structure for summary statistics-based methods in arbitrary populations. Results: We applied Adapt-Mix to estimate the genetic correlation structure of both admixed and non-admixed individuals using simulated and real data. We evaluated our method by measuring the performance of two summary statistics-based methods: imputation and joint-testing. When using our method as opposed to the current standard of ‘best guess’ reference panels, we observed a 28% decrease in mean-squared error for imputation and a 73.7% decrease in mean-squared error for joint-testing. Availability and implementation: Our method is publicly available in a software package called ADAPT-Mix available at https://github.com/dpark27/adapt_mix. Contact: noah.zaitlen@ucsf.edu PMID:26072481

Duration of Sleep and ADHD Tendency among Adolescents in China

ERIC Educational Resources Information Center

Lam, Lawrence T.; Yang, L.

2008-01-01

Objective: This study investigates the association between duration of sleep and ADHD tendency among adolescents. Method: This population-based health survey uses a two-stage random cluster sampling design. Participants ages 13 to 17 are recruited from the total population of adolescents attending high school in one city of China. Duration of…

A Systematic Evaluation of ADHD and Comorbid Psychopathology in a Population-Based Twin Sample

ERIC Educational Resources Information Center

Volk, Heather E.; Neuman, Rosalind J.; Todd, Richard D.

2005-01-01

Objective: Clinical and population samples demonstrate that attention-deficit/hyperactivity disorder (ADHD) occurs with other disorders. Comorbid disorder clustering within ADHD subtypes is not well studied. Method: Latent class analysis (LCA) examined the co-occurrence of DSM-IV ADHD, oppositional defiant disorder (ODD), conduct disorder (CD),…

Applications of Small Area Estimation to Generalization with Subclassification by Propensity Scores

ERIC Educational Resources Information Center

Chan, Wendy

2018-01-01

Policymakers have grown increasingly interested in how experimental results may generalize to a larger population. However, recently developed propensity score-based methods are limited by small sample sizes, where the experimental study is generalized to a population that is at least 20 times larger. This is particularly problematic for methods…

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

PubMed

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

2012-08-01

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

Management and Prevalence of Long-Term Conditions in Primary Health Care for Adults with Intellectual Disabilities Compared with the General Population: A Population-Based Cohort Study

ERIC Educational Resources Information Center

Cooper, Sally-Ann; Hughes-McCormack, Laura; Greenlaw, Nicola; McConnachie, Alex; Allan, Linda; Baltzer, Marion; McArthur, Laura; Henderson, Angela; Melville, Craig; McSkimming, Paula; Morrison, Jill

2018-01-01

Background: In the UK, general practitioners/family physicians receive pay for performance on management of long-term conditions, according to best-practice indicators. Method: Management of long-term conditions was compared between 721 adults with intellectual disabilities and the general population (n = 764,672). Prevalence of long-term…

Adjusting Expected Mortality Rates Using Information From a Control Population: An Example Using Socioeconomic Status.

PubMed

Bower, Hannah; Andersson, Therese M-L; Crowther, Michael J; Dickman, Paul W; Lambe, Mats; Lambert, Paul C

2018-04-01

Expected or reference mortality rates are commonly used in the calculation of measures such as relative survival in population-based cancer survival studies and standardized mortality ratios. These expected rates are usually presented according to age, sex, and calendar year. In certain situations, stratification of expected rates by other factors is required to avoid potential bias if interest lies in quantifying measures according to such factors as, for example, socioeconomic status. If data are not available on a population level, information from a control population could be used to adjust expected rates. We have presented two approaches for adjusting expected mortality rates using information from a control population: a Poisson generalized linear model and a flexible parametric survival model. We used a control group from BCBaSe-a register-based, matched breast cancer cohort in Sweden with diagnoses between 1992 and 2012-to illustrate the two methods using socioeconomic status as a risk factor of interest. Results showed that Poisson and flexible parametric survival approaches estimate similar adjusted mortality rates according to socioeconomic status. Additional uncertainty involved in the methods to estimate stratified, expected mortality rates described in this study can be accounted for using a parametric bootstrap, but this might make little difference if using a large control population.

Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models

PubMed Central

Boskova, Veronika; Bonhoeffer, Sebastian; Stadler, Tanja

2014-01-01

Quantifying epidemiological dynamics is crucial for understanding and forecasting the spread of an epidemic. The coalescent and the birth-death model are used interchangeably to infer epidemiological parameters from the genealogical relationships of the pathogen population under study, which in turn are inferred from the pathogen genetic sequencing data. To compare the performance of these widely applied models, we performed a simulation study. We simulated phylogenetic trees under the constant rate birth-death model and the coalescent model with a deterministic exponentially growing infected population. For each tree, we re-estimated the epidemiological parameters using both a birth-death and a coalescent based method, implemented as an MCMC procedure in BEAST v2.0. In our analyses that estimate the growth rate of an epidemic based on simulated birth-death trees, the point estimates such as the maximum a posteriori/maximum likelihood estimates are not very different. However, the estimates of uncertainty are very different. The birth-death model had a higher coverage than the coalescent model, i.e. contained the true value in the highest posterior density (HPD) interval more often (2–13% vs. 31–75% error). The coverage of the coalescent decreases with decreasing basic reproductive ratio and increasing sampling probability of infecteds. We hypothesize that the biases in the coalescent are due to the assumption of deterministic rather than stochastic population size changes. Both methods performed reasonably well when analyzing trees simulated under the coalescent. The methods can also identify other key epidemiological parameters as long as one of the parameters is fixed to its true value. In summary, when using genetic data to estimate epidemic dynamics, our results suggest that the birth-death method will be less sensitive to population fluctuations of early outbreaks than the coalescent method that assumes a deterministic exponentially growing infected population. PMID:25375100

Genotype-Based Association Mapping of Complex Diseases: Gene-Environment Interactions with Multiple Genetic Markers and Measurement Error in Environmental Exposures

PubMed Central

Lobach, Irvna; Fan, Ruzone; Carroll, Raymond T.

2011-01-01

With the advent of dense single nucleotide polymorphism genotyping, population-based association studies have become the major tools for identifying human disease genes and for fine gene mapping of complex traits. We develop a genotype-based approach for association analysis of case-control studies of gene-environment interactions in the case when environmental factors are measured with error and genotype data are available on multiple genetic markers. To directly use the observed genotype data, we propose two genotype-based models: genotype effect and additive effect models. Our approach offers several advantages. First, the proposed risk functions can directly incorporate the observed genotype data while modeling the linkage disequihbrium information in the regression coefficients, thus eliminating the need to infer haplotype phase. Compared with the haplotype-based approach, an estimating procedure based on the proposed methods can be much simpler and significantly faster. In addition, there is no potential risk due to haplotype phase estimation. Further, by fitting the proposed models, it is possible to analyze the risk alleles/variants of complex diseases, including their dominant or additive effects. To model measurement error, we adopt the pseudo-likelihood method by Lobach et al. [2008]. Performance of the proposed method is examined using simulation experiments. An application of our method is illustrated using a population-based case-control study of association between calcium intake with the risk of colorectal adenoma development. PMID:21031455

Invited review: study design considerations for clinical research in veterinary radiology and radiation oncology.

PubMed

Scrivani, Peter V; Erb, Hollis N

2013-01-01

High quality clinical research is essential for advancing knowledge in the areas of veterinary radiology and radiation oncology. Types of clinical research studies may include experimental studies, method-comparison studies, and patient-based studies. Experimental studies explore issues relative to pathophysiology, patient safety, and treatment efficacy. Method-comparison studies evaluate agreement between techniques or between observers. Patient-based studies investigate naturally acquired disease and focus on questions asked in clinical practice that relate to individuals or populations (e.g., risk, accuracy, or prognosis). Careful preplanning and study design are essential in order to achieve valid results. A key point to planning studies is ensuring that the design is tailored to the study objectives. Good design includes a comprehensive literature review, asking suitable questions, selecting the proper sample population, collecting the appropriate data, performing the correct statistical analyses, and drawing conclusions supported by the available evidence. Most study designs are classified by whether they are experimental or observational, longitudinal or cross-sectional, and prospective or retrospective. Additional features (e.g., controlled, randomized, or blinded) may be described that address bias. Two related challenging aspects of study design are defining an important research question and selecting an appropriate sample population. The sample population should represent the target population as much as possible. Furthermore, when comparing groups, it is important that the groups are as alike to each other as possible except for the variables of interest. Medical images are well suited for clinical research because imaging signs are categorical or numerical variables that might be predictors or outcomes of diseases or treatments. © 2013 Veterinary Radiology & Ultrasound.

Research progress of plant population genomics based on high-throughput sequencing.

PubMed

Wang, Yun-sheng

2016-08-01

Population genomics, a new paradigm for population genetics, combine the concepts and techniques of genomics with the theoretical system of population genetics and improve our understanding of microevolution through identification of site-specific effect and genome-wide effects using genome-wide polymorphic sites genotypeing. With the appearance and improvement of the next generation high-throughput sequencing technology, the numbers of plant species with complete genome sequences increased rapidly and large scale resequencing has also been carried out in recent years. Parallel sequencing has also been done in some plant species without complete genome sequences. These studies have greatly promoted the development of population genomics and deepened our understanding of the genetic diversity, level of linking disequilibium, selection effect, demographical history and molecular mechanism of complex traits of relevant plant population at a genomic level. In this review, I briely introduced the concept and research methods of population genomics and summarized the research progress of plant population genomics based on high-throughput sequencing. I also discussed the prospect as well as existing problems of plant population genomics in order to provide references for related studies.

A Markov chain model for studying suicide dynamics: an illustration of the Rose theorem

PubMed Central

2014-01-01

Background High-risk strategies would only have a modest effect on suicide prevention within a population. It is best to incorporate both high-risk and population-based strategies to prevent suicide. This study aims to compare the effectiveness of suicide prevention between high-risk and population-based strategies. Methods A Markov chain illness and death model is proposed to determine suicide dynamic in a population and examine its effectiveness for reducing the number of suicides by modifying certain parameters of the model. Assuming a population with replacement, the suicide risk of the population was estimated by determining the final state of the Markov model. Results The model shows that targeting the whole population for suicide prevention is more effective than reducing risk in the high-risk tail of the distribution of psychological distress (i.e. the mentally ill). Conclusions The results of this model reinforce the essence of the Rose theorem that lowering the suicidal risk in the population at large may be more effective than reducing the high risk in a small population. PMID:24948330

Assessment of public health impact of work-related asthma.

PubMed

Jaakkola, Maritta S; Jaakkola, Jouni J K

2012-03-05

Asthma is among the most common chronic diseases in working-aged populations and occupational exposures are important causal agents. Our aims were to evaluate the best methods to assess occurrence, public health impact, and burden to society related to occupational or work-related asthma and to achieve comparable estimates for different populations. We addressed three central questions: 1: What is the best method to assess the occurrence of occupational asthma? We evaluated: 1) assessment of the occurrence of occupational asthma per se, and 2) assessment of adult-onset asthma and the population attributable fractions due to specific occupational exposures. 2: What are the best methods to assess public health impact and burden to society related to occupational or work-related asthma? We evaluated methods based on assessment of excess burden of disease due to specific occupational exposures. 3: How to achieve comparable estimates for different populations? We evaluated comparability of estimates of occurrence and burden attributable to occupational asthma based on different methods. Assessment of the occurrence of occupational asthma per se can be used in countries with good coverage of the identification system for occupational asthma, i.e. countries with well-functioning occupational health services. Assessment based on adult-onset asthma and population attributable fractions due to specific occupational exposures is a good approach to estimate the occurrence of occupational asthma at the population level. For assessment of public health impact from work-related asthma we recommend assessing excess burden of disease due to specific occupational exposures, including excess incidence of asthma complemented by an assessment of disability from it. International comparability of estimates can be best achieved by methods based on population attributable fractions. Public health impact assessment for occupational asthma is central in prevention and health policy planning and could be improved by purposeful development of methods for assessing health benefits from preventive actions. Registry-based methods are suitable for evaluating time-trends of occurrence at a given population but for international comparisons they face serious limitations. Assessment of excess burden of disease due to specific occupational exposure is a useful measure, when there is valid information on population exposure and attributable fractions.

Geographic origin and individual assignment of Shorea platyclados (Dipterocarpaceae) for forensic identification

PubMed Central

Diway, Bibian; Khoo, Eyen

2017-01-01

The development of timber tracking methods based on genetic markers can provide scientific evidence to verify the origin of timber products and fulfill the growing requirement for sustainable forestry practices. In this study, the origin of an important Dark Red Meranti wood, Shorea platyclados, was studied by using the combination of seven chloroplast DNA and 15 short tandem repeats (STRs) markers. A total of 27 natural populations of S. platyclados were sampled throughout Malaysia to establish population level and individual level identification databases. A haplotype map was generated from chloroplast DNA sequencing for population identification, resulting in 29 multilocus haplotypes, based on 39 informative intraspecific variable sites. Subsequently, a DNA profiling database was developed from 15 STRs allowing for individual identification in Malaysia. Cluster analysis divided the 27 populations into two genetic clusters, corresponding to the region of Eastern and Western Malaysia. The conservativeness tests showed that the Malaysia database is conservative after removal of bias from population subdivision and sampling effects. Independent self-assignment tests correctly assigned individuals to the database in an overall 60.60−94.95% of cases for identified populations, and in 98.99−99.23% of cases for identified regions. Both the chloroplast DNA database and the STRs appear to be useful for tracking timber originating in Malaysia. Hence, this DNA-based method could serve as an effective addition tool to the existing forensic timber identification system for ensuring the sustainably management of this species into the future. PMID:28430826

Improving Foster Parent Engagement: Using Qualitative Methods to Guide Tailoring of Evidence-based Engagement Strategies

PubMed Central

Conover, Kate L.; Cox, Julia Revillion

2014-01-01

Objective This qualitative study examined applicability and need for tailoring of an evidence-based engagement intervention, combined with Trauma-focused Cognitive Behavioral Therapy, for foster parents. Method Qualitative methods were used, including individual interviews with participating foster parents (N = 7), review of interview findings with an independent group of foster parents (N = 5), and review of the combined foster parent findings by child welfare caseworkers (N = 5), an important stakeholder group. Results The engagement intervention, with its primary focus on perceptual barriers (e.g., past experiences with mental health), was relevant for the foster care population. However, the study identified areas for tailoring to better recognize and address the unique needs and situation of foster parents as substitute caregivers. Conclusions Perceptually-focused engagement interventions may have broad applicability to a range of populations, including foster parents, with the potential for improving caregiver participation in children’s mental health services. PMID:24611600

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

PubMed Central

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

2016-01-01

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

Effective size of two feral domestic cat populations (Felis catus L): effect of the mating system.

PubMed

Kaeuffer, R; Pontier, D; Devillard, S; Perrin, N

2004-02-01

A variety of behavioural traits have substantial effects on the gene dynamics and genetic structure of local populations. The mating system is a plastic trait that varies with environmental conditions in the domestic cat (Felis catus) allowing an intraspecific comparison of the impact of this feature on genetic characteristics of the population. To assess the potential effect of the heterogenity of males' contribution to the next generation on variance effective size, we applied the ecological approach of Nunney & Elam (1994) based upon a demographic and behavioural study, and the genetic 'temporal methods' of Waples (1989) and Berthier et al. (2002) using microsatellite markers. The two cat populations studied were nearly closed, similar in size and survival parameters, but differed in their mating system. Immigration appeared extremely restricted in both cases due to environmental and social constraints. As expected, the ratio of effective size to census number (Ne/N) was higher in the promiscuous cat population (harmonic mean = 42%) than in the polygynous one (33%), when Ne was calculated from the ecological method. Only the genetic results based on Waples' estimator were consistent with the ecological results, but failed to evidence an effect of the mating system. Results based on the estimation of Berthier et al. (2002) were extremely variable, with Ne sometimes exceeding census size. Such low reliability in the genetic results should retain attention for conservation purposes.

Suicide Risk Assessment and Prevention: A Systematic Review Focusing on Veterans.

PubMed

Nelson, Heidi D; Denneson, Lauren M; Low, Allison R; Bauer, Brian W; O'Neil, Maya; Kansagara, Devan; Teo, Alan R

2017-10-01

Suicide rates in veteran and military populations in the United States are high. This article reviews studies of the accuracy of methods to identify individuals at increased risk of suicide and the effectiveness and adverse effects of health care interventions relevant to U.S. veteran and military populations in reducing suicide and suicide attempts. Trials, observational studies, and systematic reviews relevant to U.S. veterans and military personnel were identified in searches of MEDLINE, PsycINFO, SocINDEX, and Cochrane databases (January 1, 2008, to September 11, 2015), on Web sites, and in reference lists. Investigators extracted and confirmed data and dual-rated risk of bias for included studies. Nineteen studies evaluated accuracy of risk assessment methods, including models using retrospective electronic records data and clinician- or patient-rated instruments. Most methods demonstrated sensitivity ≥80% or area-under-the-curve values ≥.70 in single studies, including two studies based on electronic records of veterans and military personnel, but specificity varied. Suicide rates were reduced in six of eight observational studies of population-level interventions. Only two of ten trials of individual-level psychotherapy reported statistically significant differences between treatment and usual care. Risk assessment methods have been shown to be sensitive predictors of suicide and suicide attempts, but the frequency of false positives limits their clinical utility. Research to refine these methods and examine clinical applications is needed. Studies of suicide prevention interventions are inconclusive; trials of population-level interventions and promising therapies are required to support their clinical use.

Using a Marginal Structural Model to Design a Theory-Based Mass Media Campaign.

PubMed

Nishiuchi, Hiromu; Taguri, Masataka; Ishikawa, Yoshiki

2016-01-01

The essential first step in the development of mass media health campaigns is to identify specific beliefs of the target audience. The challenge is to prioritize suitable beliefs derived from behavioral theory. The purpose of this study was to identify suitable beliefs to target in a mass media campaign to change behavior using a new method to estimate the possible effect size of a small set of beliefs. Data were drawn from the 2010 Japanese Young Female Smoker Survey (n = 500), conducted by the Japanese Ministry of Health, Labor and Welfare. Survey measures included intention to quit smoking, psychological beliefs (attitude, norms, and perceived control) based on the theory of planned behavior and socioeconomic status (age, education, household income, and marital status). To identify suitable candidate beliefs for a mass media health campaign, we estimated the possible effect size required to change the intention to quit smoking among the population of young Japanese women using the population attributable fraction from a marginal structural model. Thirteen percent of study participants intended to quit smoking. The marginal structural model estimated a population attributable fraction of 47 psychological beliefs (21 attitudes, 6 norms, and 19 perceived controls) after controlling for socioeconomic status. The belief, "I could quit smoking if my husband or significant other recommended it" suggested a promising target for a mass media campaign (population attributable fraction = 0.12, 95% CI = 0.02-0.23). Messages targeting this belief could possibly improve intention rates by up to 12% among this population. The analysis also suggested the potential for regulatory action. This study proposed a method by which campaign planners can develop theory-based mass communication strategies to change health behaviors at the population level. This method might contribute to improving the quality of future mass health communication strategies and further research is needed.

Triceps and Subscapular Skinfold Thickness Percentiles and Cut-Offs for Overweight and Obesity in a Population-Based Sample of Schoolchildren and Adolescents in Bogota, Colombia

PubMed Central

Ramírez-Vélez, Robinson; López-Cifuentes, Mario Ferney; Correa-Bautista, Jorge Enrique; González-Ruíz, Katherine; González-Jiménez, Emilio; Córdoba-Rodríguez, Diana Paola; Vivas, Andrés; Triana-Reina, Hector Reynaldo; Schmidt-RioValle, Jacqueline

2016-01-01

The assessment of skinfold thickness is an objective measure of adiposity. The aims of this study were to establish Colombian smoothed centile charts and LMS L (Box–Cox transformation), M (median), and S (coefficient of variation) tables for triceps, subscapular, and triceps + subscapular skinfolds; appropriate cut-offs were selected using receiver operating characteristic (ROC) analysis based on a population-based sample of children and adolescents in Bogotá, Colombia. A cross-sectional study was conducted in 9618 children and adolescents (55.7% girls; age range of 9–17.9 years). Triceps and subscapular skinfold measurements were obtained using standardized methods. We calculated the triceps + subscapular skinfold (T + SS) sum. Smoothed percentile curves for triceps and subscapular skinfold thickness were derived using the LMS method. ROC curve analyses were used to evaluate the optimal cut-off point of skinfold thickness for overweight and obesity, based on the International Obesity Task Force definitions. Subscapular and triceps skinfolds and T + SS were significantly higher in girls than in boys (p < 0.001). The ROC analysis showed that subscapular and triceps skinfolds and T + SS have a high discriminatory power in the identification of overweight and obesity in the sample population in this study. Our results provide sex- and age-specific normative reference standards for skinfold thickness values from a population from Bogotá, Colombia. PMID:27669294

An elusive paleodemography? A comparison of two methods for estimating the adult age distribution of deaths at late Classic Copan, Honduras.

PubMed

Storey, Rebecca

2007-01-01

Comparison of different adult age estimation methods on the same skeletal sample with unknown ages could forward paleodemographic inference, while researchers sort out various controversies. The original aging method for the auricular surface (Lovejoy et al., 1985a) assigned an age estimation based on several separate characteristics. Researchers have found this original method hard to apply. It is usually forgotten that before assigning an age, there was a seriation, an ordering of all available individuals from youngest to oldest. Thus, age estimation reflected the place of an individual within its sample. A recent article (Buckberry and Chamberlain, 2002) proposed a revised method that scores theses various characteristics into age stages, which can then be used with a Bayesian method to estimate an adult age distribution for the sample. Both methods were applied to the adult auricular surfaces of a Pre-Columbian Maya skeletal population from Copan, Honduras and resulted in age distributions with significant numbers of older adults. However, contrary to the usual paleodemographic distribution, one Bayesian estimation based on uniform prior probabilities yielded a population with 57% of the ages at death over 65, while another based on a high mortality life table still had 12% of the individuals aged over 75 years. The seriation method yielded an age distribution more similar to that known from preindustrial historical situations, without excessive longevity of adults. Paleodemography must still wrestle with its elusive goal of accurate adult age estimation from skeletons, a necessary base for demographic study of past populations. (c) 2006 Wiley-Liss, Inc

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

Population delineation of polar bears using satellite collar data

USGS Publications Warehouse

Bethke, R.; Taylor, Mitchell K.; Amstrup, Steven C.; Messier, François

1996-01-01

To produce reliable estimates of the size or vital rates of a given population, it is important that the boundaries of the population under study are clearly defined. This is particularly critical for large, migratory animals where levels of sustainable harvest are based on these estimates, and where small errors may have serious long-term consequences for the population. Once populations are delineated, rates of exchange between adjacent populations can be determined and accounted/corrected for when calculating abundance (e.g., based on mark-recapture data). Using satellite radio-collar locations for polar bears in the western Canadian Arctic, we illustrate one approach to delineating wildlife populations that integrates cluster analysis methods for determining group membership with home range plotting procedures to define spatial utilization. This approach is flexible with respect to the specific procedures used and provides an objective and quantitative basis for defining population boundaries.

Prevalence of non-traumatic spinal cord injury in Victoria, Australia.

PubMed

New, P W; Farry, A; Baxter, D; Noonan, V K

2013-02-01

Forecasting using population modelling. To determine the prevalence of non-traumatic spinal cord injury (NTSCI) on 30 June 2010. Victoria, Australia. Modelling used the following data: incidence of NTSCI based on state-wide, population-based, health-administration database of hospital admissions; state and national population profiles and life tables; levels of NTSCI based on national rehabilitation outcomes data; and life expectancy for persons with SCI. The total population prevalence rate was 367.2 per million, whereas the prevalence in adults aged 16 years and older was estimated to be 2027, equivalent to a population prevalence rate of 455 per million persons. There were more males (1097) with NTSCI (prevalence rate males 197.8 per million population; females 169.1 per million population) and the prevalence was much higher among those with paraplegia (prevalence rate 269.3 per million compared to 97.8 per million with tetraplegia) and incomplete NTSCI. Ventilator dependency (prevalence rate 1.6 per million population) and paediatric NTSCI (prevalence rate 6 per million population ≤ 15 years old) were extremely rare. We have reported a method for calculating an estimate of the prevalence of NTSCI that provides information that will be vital to optimise health care planning for this group of highly disabled members of society. It is suggested that refinements to the modelling methods are required to enhance its reliability. Future projects should be directed at refining the mortality ratios and performing cohort survival studies.

Identification of Bacterial Populations in Drinking Water Using 16S rRNA-Based Sequence Analyses

EPA Science Inventory

Intracellular RNA is rapidly degraded in stressed cells and is more unstable outside of the cell than DNA. As a result, RNA-based methods have been suggested to study the active microbial fraction in environmental matrices. The aim of this study was to identify bacterial populati...

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 knowledge and analysis might support an effort to build an effective population-based medicine approach. PMID:23256543

A bootstrap based space-time surveillance model with an application to crime occurrences

NASA Astrophysics Data System (ADS)

Kim, Youngho; O'Kelly, Morton

2008-06-01

This study proposes a bootstrap-based space-time surveillance model. Designed to find emerging hotspots in near-real time, the bootstrap based model is characterized by its use of past occurrence information and bootstrap permutations. Many existing space-time surveillance methods, using population at risk data to generate expected values, have resulting hotspots bounded by administrative area units and are of limited use for near-real time applications because of the population data needed. However, this study generates expected values for local hotspots from past occurrences rather than population at risk. Also, bootstrap permutations of previous occurrences are used for significant tests. Consequently, the bootstrap-based model, without the requirement of population at risk data, (1) is free from administrative area restriction, (2) enables more frequent surveillance for continuously updated registry database, and (3) is readily applicable to criminology and epidemiology surveillance. The bootstrap-based model performs better for space-time surveillance than the space-time scan statistic. This is shown by means of simulations and an application to residential crime occurrences in Columbus, OH, year 2000.

In defence of model-based inference in phylogeography

PubMed Central

Beaumont, Mark A.; Nielsen, Rasmus; Robert, Christian; Hey, Jody; Gaggiotti, Oscar; Knowles, Lacey; Estoup, Arnaud; Panchal, Mahesh; Corander, Jukka; Hickerson, Mike; Sisson, Scott A.; Fagundes, Nelson; Chikhi, Lounès; Beerli, Peter; Vitalis, Renaud; Cornuet, Jean-Marie; Huelsenbeck, John; Foll, Matthieu; Yang, Ziheng; Rousset, Francois; Balding, David; Excoffier, Laurent

2017-01-01

Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model-based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model-based inference in population genetics. PMID:29284924

Modelling population distribution using remote sensing imagery and location-based data

NASA Astrophysics Data System (ADS)

Song, J.; Prishchepov, A. V.

2017-12-01

Detailed spatial distribution of population density is essential for city studies such as urban planning, environmental pollution and city emergency, even estimate pressure on the environment and human exposure and risks to health. However, most of the researches used census data as the detailed dynamic population distribution are difficult to acquire, especially in microscale research. This research describes a method using remote sensing imagery and location-based data to model population distribution at the function zone level. Firstly, urban functional zones within a city were mapped by high-resolution remote sensing images and POIs. The workflow of functional zones extraction includes five parts: (1) Urban land use classification. (2) Segmenting images in built-up area. (3) Identification of functional segments by POIs. (4) Identification of functional blocks by functional segmentation and weight coefficients. (5) Assessing accuracy by validation points. The result showed as Fig.1. Secondly, we applied ordinary least square and geographically weighted regression to assess spatial nonstationary relationship between light digital number (DN) and population density of sampling points. The two methods were employed to predict the population distribution over the research area. The R²of GWR model were in the order of 0.7 and typically showed significant variations over the region than traditional OLS model. The result showed as Fig.2.Validation with sampling points of population density demonstrated that the result predicted by the GWR model correlated well with light value. The result showed as Fig.3. Results showed: (1) Population density is not linear correlated with light brightness using global model. (2) VIIRS night-time light data could estimate population density integrating functional zones at city level. (3) GWR is a robust model to map population distribution, the adjusted R2 of corresponding GWR models were higher than the optimal OLS models, confirming that GWR models demonstrate better prediction accuracy. So this method provide detailed population density information for microscale citizen studies.

Population structure of humpback whales in the western and central South Pacific Ocean as determined by vocal exchange among populations.

PubMed

Garland, Ellen C; Goldizen, Anne W; Lilley, Matthew S; Rekdahl, Melinda L; Garrigue, Claire; Constantine, Rochelle; Hauser, Nan Daeschler; Poole, M Michael; Robbins, Jooke; Noad, Michael J

2015-08-01

For cetaceans, population structure is traditionally determined by molecular genetics or photographically identified individuals. Acoustic data, however, has provided information on movement and population structure with less effort and cost than traditional methods in an array of taxa. Male humpback whales (Megaptera novaeangliae) produce a continually evolving vocal sexual display, or song, that is similar among all males in a population. The rapid cultural transmission (the transfer of information or behavior between conspecifics through social learning) of different versions of this display between distinct but interconnected populations in the western and central South Pacific region presents a unique way to investigate population structure based on the movement dynamics of a song (acoustic) display. Using 11 years of data, we investigated an acoustically based population structure for the region by comparing stereotyped song sequences among populations and years. We used the Levenshtein distance technique to group previously defined populations into (vocally based) clusters based on the overall similarity of their song display in space and time. We identified the following distinct vocal clusters: western cluster, 1 population off eastern Australia; central cluster, populations around New Caledonia, Tonga, and American Samoa; and eastern region, either a single cluster or 2 clusters, one around the Cook Islands and the other off French Polynesia. These results are consistent with the hypothesis that each breeding aggregation represents a distinct population (each occupied a single, terminal node) in a metapopulation, similar to the current understanding of population structure based on genetic and photo-identification studies. However, the central vocal cluster had higher levels of song-sharing among populations than the other clusters, indicating that levels of vocal connectivity varied within the region. Our results demonstrate the utility and value of using culturally transmitted vocal patterns as a way of defining connectivity to infer population structure. We suggest vocal patterns be incorporated by the International Whaling Commission in conjunction with traditional methods in the assessment of structure. © 2015, Society for Conservation Biology.

Differences in reported sepsis incidence according to study design: a literature review.

PubMed

Mariansdatter, Saga Elise; Eiset, Andreas Halgreen; Søgaard, Kirstine Kobberøe; Christiansen, Christian Fynbo

2016-10-12

Sepsis and severe sepsis are common conditions in hospital settings, and are associated with high rates of morbidity and mortality, but reported incidences vary considerably. In this literature review, we describe the variation in reported population-based incidences of sepsis and severe sepsis. We also examine methodological and demographic differences between studies that may explain this variation. We carried out a literature review searching three major databases and reference lists of relevant articles, to identify all original studies reporting the incidence of sepsis or severe sepsis in the general population. Two authors independently assessed all articles, and the final decision to exclude an article was reached by consensus. We extracted data according to predetermined variables, including study country, sepsis definition, and data source. We then calculated descriptive statistics for the reported incidences of sepsis and severe sepsis. The studies were classified according to the method used to identify cases of sepsis or severe sepsis: chart-based (i.e. review of patient charts) or code-based (i.e. predetermined International Classification of Diseases [ICD] codes). Among 482 articles initially screened, we identified 23 primary publications reporting incidence of sepsis and/or severe sepsis in the general population. The reported incidences ranged from 74 to 1180 per 100,000 person-years and 3 to 1074 per 100,000 person-years for sepsis and severe sepsis, respectively. Most chart-based studies used the Bone criteria (or a modification hereof) and Protein C Worldwide Evaluation in Severe Sepsis (PROWESS) study criteria to identify cases of sepsis and severe sepsis. Most code-based studies used ICD-9 codes, but the number of codes used ranged from 1 to more than 1200. We found that the incidence varied according to how sepsis was identified (chart-based vs. code-based), calendar year, data source, and world region. The reported incidences of sepsis and severe sepsis in the general population varied greatly between studies. Such differences may be attributable to differences in the methods used to collect the data, the study period, or the world region where the study was undertaken. This finding highlights the importance of standardised definitions and acquisition of data regarding sepsis and severe sepsis.

Star Formation Histories of Local Group Dwarf Galaxies. (Ludwig Biermann Award Lecture 1996)

NASA Astrophysics Data System (ADS)

Grebel, E. K.

The star formation histories of dwarf galaxies in the Local Group are reviewed. First the question of Local Group membership is considered based on various criteria. The properties of 31 (36) galaxies are consistent with likely (potential) Local Group membership. To study the star formation histories of these galaxies, a multi-parameter problem needs to be solved: Ages, metallicities, population fractions, and spatial variations must be determined, which depend crucially on the knowledge of reddening and distance. The basic methods for studying resolvable stellar populations are summarized. One method is demonstrated using the Fornax dwarf spheroidal galaxy. A comprehensive compilation of the star formation histories of dwarf irregulars, dwarf ellipticals, and dwarf spheroidals in the Local Group is presented and visualized through Hodge's population boxes. All galaxies appear to have differing fractions of old and intermediate-age populations, and those sufficiently massive and undisturbed to retain and recycle their gas are still forming stars today. Star formation has occurred either in distinct episodes or continuously over long periods of time. Metallicities and enrichment vary widely. Constraints on merger and remnant scenarios are discussed, and a unified picture based on the current knowledge is presented. Primary goals for future observations are: accurate age determinations based on turnoff photometry, detection of subpopulations distinct in age, metallicity, and/or spatial distribution; improved distances; and astrometric studies to derive orbits and constrain past and future interactions.

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

A measure of association for ordered categorical data in population-based studies

PubMed Central

Nelson, Kerrie P; Edwards, Don

2016-01-01

Ordinal classification scales are commonly used to define a patient’s disease status in screening and diagnostic tests such as mammography. Challenges arise in agreement studies when evaluating the association between many raters’ classifications of patients’ disease or health status when an ordered categorical scale is used. In this paper, we describe a population-based approach and chance-corrected measure of association to evaluate the strength of relationship between multiple raters’ ordinal classifications where any number of raters can be accommodated. In contrast to Shrout and Fleiss’ intraclass correlation coefficient, the proposed measure of association is invariant with respect to changes in disease prevalence. We demonstrate how unique characteristics of individual raters can be explored using random effects. Simulation studies are conducted to demonstrate the properties of the proposed method under varying assumptions. The methods are applied to two large-scale agreement studies of breast cancer screening and prostate cancer severity. PMID:27184590

Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato.

PubMed

Ohyama, Akio; Shirasawa, Kenta; Matsunaga, Hiroshi; Negoro, Satomi; Miyatake, Koji; Yamaguchi, Hirotaka; Nunome, Tsukasa; Iwata, Hiroyoshi; Fukuoka, Hiroyuki; Hayashi, Takeshi

2017-08-01

Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato. So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F 2 population derived from a cross between two commercial F 1 cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F 1 cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F 2 plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.

Generation of Human Induced Pluripotent Stem Cells Using RNA-Based Sendai Virus System and Pluripotency Validation of the Resulting Cell Population.

PubMed

Chichagova, Valeria; Sanchez-Vera, Irene; Armstrong, Lyle; Steel, David; Lako, Majlinda

2016-01-01

Human induced pluripotent stem cells (hiPSCs) provide a platform for studying human disease in vitro, increase our understanding of human embryonic development, and provide clinically relevant cell types for transplantation, drug testing, and toxicology studies. Since their discovery, numerous advances have been made in order to eliminate issues such as vector integration into the host genome, low reprogramming efficiency, incomplete reprogramming and acquisition of genomic instabilities. One of the ways to achieve integration-free reprogramming is by using RNA-based Sendai virus. Here we describe a method to generate hiPSCs with Sendai virus in both feeder-free and feeder-dependent culture systems. Additionally, we illustrate methods by which to validate pluripotency of the resulting stem cell population.

Systematic review of proposed definitions of nocturnal polyuria and population-based evidence of their diagnostic accuracy.

PubMed

Olesen, Tine Kold; Denys, Marie-Astrid; Vande Walle, Johan; Everaert, Karel

2018-02-06

Background Evidence of diagnostic accuracy for proposed definitions of nocturnal polyuria is currently unclear. Purpose Systematic review to determine population-based evidence of the diagnostic accuracy of proposed definitions of nocturnal polyuria based on data from frequency-volume charts. Methods Seventeen pre-specified search terms identified 351 unique investigations published from 1990 to 2016 in BIOSIS, Embase, Embase Alerts, International Pharmaceutical Abstract, Medline, and Cochrane. Thirteen original communications were included in this review based on pre-specified exclusion criteria. Data were extracted from each paper regarding subject age, sex, ethnicity, health status, sample size, data collection methods, and diagnostic discrimination of proposed definitions including sensitivity, specificity, positive and negative predictive value. Results The sample size of study cohorts, participant age, sex, ethnicity, and health status varied considerably in 13 studies reporting on the diagnostic performance of seven different definitions of nocturnal polyuria using frequency-volume chart data from 4968 participants. Most study cohorts were small, mono-ethnic, including only Caucasian males aged 50 or higher with primary or secondary polyuria that were compared to a control group of healthy men without nocturia in prospective or retrospective settings. Proposed definitions had poor discriminatory accuracy in evaluations based on data from subjects independent from the original study cohorts with findings being similar regarding the most widely evaluated definition endorsed by ICS. Conclusions Diagnostic performance characteristics for proposed definitions of nocturnal polyuria show poor to modest discrimination and are not based on sufficient level of evidence from representative, multi-ethnic population-based data from both females and males of all adult ages.

Age assessment based on third molar mineralisation : An epidemiological-radiological study on a Central-European population.

PubMed

Hofmann, Elisabeth; Robold, Matthias; Proff, Peter; Kirschneck, Christian

2017-03-01

The method published in 1973 by Demirjian et al. to assess age based on the mineralisation stage of permanent teeth is standard practice in forensic and orthodontic diagnostics. From age 14 onwards, however, this method is only applicable to third molars. No current epidemiological data on third molar mineralisation are available for Caucasian Central-Europeans. Thus, a method for assessing age in this population based on third molar mineralisation is presented, taking into account possible topographic and gender-specific differences. The study included 486 Caucasian Central-European orthodontic patients (9-24 years) with unaffected dental development. In an anonymized, randomized, and blinded manner, one orthopantomogram of each patient at either start, mid or end of treatment was visually analysed regarding the mineralisation stage of the third molars according to the method by Demirjian et al. Corresponding topographic and gender-specific point scores were determined and added to form a dental maturity score. Prediction equations for age assessment were derived by linear regression analysis with chronological age and checked for reliability within the study population. Mineralisation of the lower third molars was slower than mineralisation of the upper third molars, whereas no jaw-side-specific differences were detected. Gender-specific differences were relatively small, but girls reached mineralisation stage C earlier than boys, whereas boys showed an accelerated mineralisation between the ages of 15 and 16. The global equation generated by regression analysis (age = -1.103 + 0.268 × dental maturity score 18 + 28 + 38 + 48) is sufficiently accurate and reliable for clinical use. Age assessment only based on either maxilla or mandible also shows good prognostic reliability.

An empirical comparison of isolate-based and sample-based definitions of antimicrobial resistance and their effect on estimates of prevalence.

PubMed

Humphry, R W; Evans, J; Webster, C; Tongue, S C; Innocent, G T; Gunn, G J

2018-02-01

Antimicrobial resistance is primarily a problem in human medicine but there are unquantified links of transmission in both directions between animal and human populations. Quantitative assessment of the costs and benefits of reduced antimicrobial usage in livestock requires robust quantification of transmission of resistance between animals, the environment and the human population. This in turn requires appropriate measurement of resistance. To tackle this we selected two different methods for determining whether a sample is resistant - one based on screening a sample, the other on testing individual isolates. Our overall objective was to explore the differences arising from choice of measurement. A literature search demonstrated the widespread use of testing of individual isolates. The first aim of this study was to compare, quantitatively, sample level and isolate level screening. Cattle or sheep faecal samples (n=41) submitted for routine parasitology were tested for antimicrobial resistance in two ways: (1) "streak" direct culture onto plates containing the antimicrobial of interest; (2) determination of minimum inhibitory concentration (MIC) of 8-10 isolates per sample compared to published MIC thresholds. Two antibiotics (ampicillin and nalidixic acid) were tested. With ampicillin, direct culture resulted in more than double the number of resistant samples than the MIC method based on eight individual isolates. The second aim of this study was to demonstrate the utility of the observed relationship between these two measures of antimicrobial resistance to re-estimate the prevalence of antimicrobial resistance from a previous study, in which we had used "streak" cultures. Boot-strap methods were used to estimate the proportion of samples that would have tested resistant in the historic study, had we used the isolate-based MIC method instead. Our boot-strap results indicate that our estimates of prevalence of antimicrobial resistance would have been considerably lower in the historic study had the MIC method been used. Finally we conclude that there is no single way of defining a sample as resistant to an antimicrobial agent. The method used greatly affects the estimated prevalence of antimicrobial resistance in a sampled population of animals, thus potentially resulting in misleading results. Comparing methods on the same samples allows us to re-estimate the prevalence from other studies, had other methods for determining resistance been used. The results of this study highlight the importance of establishing what the most appropriate measure of antimicrobial resistance is, for the proposed purpose of the results. Copyright © 2017 Elsevier B.V. All rights reserved.

Feasibility of Population Health Analytics and Data Visualization for Decision Support in the Infectious Diseases Domain

PubMed Central

Del Fiol, Guilherme; Butler, Jorie; Livnat, Yarden; Mayer, Jeanmarie; Samore, Matthew; Jones, Makoto; Weir, Charlene

2016-01-01

Summary Objective Big data or population-based information has the potential to reduce uncertainty in medicine by informing clinicians about individual patient care. The objectives of this study were: 1) to explore the feasibility of extracting and displaying population-based information from an actual clinical population’s database records, 2) to explore specific design features for improving population display, 3) to explore perceptions of population information displays, and 4) to explore the impact of population information display on cognitive outcomes. Methods We used the Veteran’s Affairs (VA) database to identify similar complex patients based on a similar complex patient case. Study outcomes measures were 1) preferences for population information display 2) time looking at the population display, 3) time to read the chart, and 4) appropriateness of plans with pre- and post-presentation of population data. Finally, we redesigned the population information display based on our findings from this study. Results The qualitative data analysis for preferences of population information display resulted in four themes: 1) trusting the big/population data can be an issue, 2) embedded analytics is necessary to explore patient similarities, 3) need for tools to control the view (overview, zoom and filter), and 4) different presentations of the population display can be beneficial to improve the display. We found that appropriateness of plans was at 60% for both groups (t9=-1.9; p=0.08), and overall time looking at the population information display was 2.3 minutes versus 3.6 minutes with experts processing information faster than non-experts (t8= -2.3, p=0.04). Conclusion A population database has great potential for reducing complexity and uncertainty in medicine to improve clinical care. The preferences identified for the population information display will guide future health information technology system designers for better and more intuitive display. PMID:27437065

Efficient computation of the joint sample frequency spectra for multiple populations.

PubMed

Kamm, John A; Terhorst, Jonathan; Song, Yun S

2017-01-01

A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences and provides a highly efficient dimensional reduction of large-scale population genomic variation data. Recently, there has been much interest in analyzing the joint SFS data from multiple populations to infer parameters of complex demographic histories, including variable population sizes, population split times, migration rates, admixture proportions, and so on. SFS-based inference methods require accurate computation of the expected SFS under a given demographic model. Although much methodological progress has been made, existing methods suffer from numerical instability and high computational complexity when multiple populations are involved and the sample size is large. In this paper, we present new analytic formulas and algorithms that enable accurate, efficient computation of the expected joint SFS for thousands of individuals sampled from hundreds of populations related by a complex demographic model with arbitrary population size histories (including piecewise-exponential growth). Our results are implemented in a new software package called momi (MOran Models for Inference). Through an empirical study we demonstrate our improvements to numerical stability and computational complexity.

Efficient computation of the joint sample frequency spectra for multiple populations

PubMed Central

Kamm, John A.; Terhorst, Jonathan; Song, Yun S.

2016-01-01

A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences and provides a highly efficient dimensional reduction of large-scale population genomic variation data. Recently, there has been much interest in analyzing the joint SFS data from multiple populations to infer parameters of complex demographic histories, including variable population sizes, population split times, migration rates, admixture proportions, and so on. SFS-based inference methods require accurate computation of the expected SFS under a given demographic model. Although much methodological progress has been made, existing methods suffer from numerical instability and high computational complexity when multiple populations are involved and the sample size is large. In this paper, we present new analytic formulas and algorithms that enable accurate, efficient computation of the expected joint SFS for thousands of individuals sampled from hundreds of populations related by a complex demographic model with arbitrary population size histories (including piecewise-exponential growth). Our results are implemented in a new software package called momi (MOran Models for Inference). Through an empirical study we demonstrate our improvements to numerical stability and computational complexity. PMID:28239248

Estimating abundance of an open population with an N-mixture model using auxiliary data on animal movements.

PubMed

Ketz, Alison C; Johnson, Therese L; Monello, Ryan J; Mack, John A; George, Janet L; Kraft, Benjamin R; Wild, Margaret A; Hooten, Mevin B; Hobbs, N Thompson

2018-04-01

Accurate assessment of abundance forms a central challenge in population ecology and wildlife management. Many statistical techniques have been developed to estimate population sizes because populations change over time and space and to correct for the bias resulting from animals that are present in a study area but not observed. The mobility of individuals makes it difficult to design sampling procedures that account for movement into and out of areas with fixed jurisdictional boundaries. Aerial surveys are the gold standard used to obtain data of large mobile species in geographic regions with harsh terrain, but these surveys can be prohibitively expensive and dangerous. Estimating abundance with ground-based census methods have practical advantages, but it can be difficult to simultaneously account for temporary emigration and observer error to avoid biased results. Contemporary research in population ecology increasingly relies on telemetry observations of the states and locations of individuals to gain insight on vital rates, animal movements, and population abundance. Analytical models that use observations of movements to improve estimates of abundance have not been developed. Here we build upon existing multi-state mark-recapture methods using a hierarchical N-mixture model with multiple sources of data, including telemetry data on locations of individuals, to improve estimates of population sizes. We used a state-space approach to model animal movements to approximate the number of marked animals present within the study area at any observation period, thereby accounting for a frequently changing number of marked individuals. We illustrate the approach using data on a population of elk (Cervus elaphus nelsoni) in Northern Colorado, USA. We demonstrate substantial improvement compared to existing abundance estimation methods and corroborate our results from the ground based surveys with estimates from aerial surveys during the same seasons. We develop a hierarchical Bayesian N-mixture model using multiple sources of data on abundance, movement and survival to estimate the population size of a mobile species that uses remote conservation areas. The model improves accuracy of inference relative to previous methods for estimating abundance of open populations. © 2018 by the Ecological Society of America.

Five radiographic methods for assessing skeletal maturity in a Spanish population: is there a correlation?

PubMed

Camacho-Basallo, Paula; Yáñez-Vico, Rosa-María; Solano-Reina, Enrique; Iglesias-Linares, Alejandro

2017-03-01

The need for accurate techniques of estimating age has sharply increased in line with the rise in illegal migration and the political, economic and socio-demographic problems that this poses in developed countries today. The methods routinely employed for determining chronological age are mainly based on determining skeletal maturation using radiological techniques. The objective of this study was to correlate five different methods for assessing skeletal maturation. 606 radiographs of growing patients were analyzed, and each patient was classified according to two cervical vertebral-based methods, two hand-wrist-based methods and one tooth-based method. Spearman's rank-order correlation coefficient was applied to assess the relationship between chronological age and the five methods of assessing maturation, as well as correlations between the five methods (p < 0.05). Spearman's rank correlation coefficients for chronological age and cervical vertebral maturation stage using both methods were 0.656/0.693 (p < 0.001), respectively, for males. For females, the correlation was stronger for both methods. The correlation coefficients for chronological age against the two hand-wrist assessment methods were statistically significant only for Fishman's method, 0.722 (p < 0.001) and 0.839 (p < 0.001), respectively for males and females. The cervical vertebral, hand-wrist and dental maturation methods of assessment were all found to correlate strongly with each other, irrespective of gender, except for Grave and Brown's method. The results found the strongest correlation between the second molars and females, and the second premolar and males. This study sheds light on and correlates with the five radiographic methods most commonly used for assessing skeletal maturation in a Spanish population in southern Europe.

Voxel based morphometry in optical coherence tomography: validation and core findings

NASA Astrophysics Data System (ADS)

Antony, Bhavna J.; Chen, Min; Carass, Aaron; Jedynak, Bruno M.; Al-Louzi, Omar; Solomon, Sharon D.; Saidha, Shiv; Calabresi, Peter A.; Prince, Jerry L.

2016-03-01

Optical coherence tomography (OCT) of the human retina is now becoming established as an important modality for the detection and tracking of various ocular diseases. Voxel based morphometry (VBM) is a long standing neuroimaging analysis technique that allows for the exploration of the regional differences in the brain. There has been limited work done in developing registration based methods for OCT, which has hampered the advancement of VBM analyses in OCT based population studies. Following on from our recent development of an OCT registration method, we explore the potential benefits of VBM analysis in cohorts of healthy controls (HCs) and multiple sclerosis (MS) patients. Specifically, we validate the stability of VBM analysis in two pools of HCs showing no significant difference between the two populations. Additionally, we also present a retrospective study of age and sex matched HCs and relapsing remitting MS patients, demonstrating results consistent with the reported literature while providing insight into the retinal changes associated with this MS subtype.

Facebook advertisements recruit parents of children with cancer for an online survey of web-based research preferences.

PubMed

Akard, Terrah Foster; Wray, Sarah; Gilmer, Mary Jo

2015-01-01

Studies involving samples of children with life-threatening illnesses and their families face significant challenges, including inadequate sample sizes and limited diversity. Social media recruitment and Web-based research methods may help address such challenges yet have not been explored in pediatric cancer populations. This study examined the feasibility of using Facebook advertisements to recruit parent caregivers of children and teenagers with cancer. We also explored the feasibility of Web-based video recording in pediatric palliative care populations by surveying parents of children with cancer regarding (a) their preferences for research methods and (b) technological capabilities of their computers and phones. Facebook's paid advertising program was used to recruit parent caregivers of children currently living with cancer to complete an electronic survey about research preferences and technological capabilities. The advertising campaign generated 3 897 981 impressions, which resulted in 1050 clicks at a total cost of $1129.88. Of 284 screened individuals, 106 were eligible. Forty-five caregivers of children with cancer completed the entire electronic survey. Parents preferred and had technological capabilities for Web-based and electronic research methods. Participant survey responses are reported. Facebook was a useful, cost-effective method to recruit a diverse sample of parent caregivers of children with cancer. Web-based video recording and data collection may be feasible and desirable in samples of children with cancer and their families. Web-based methods (eg, Facebook, Skype) may enhance communication and access between nurses and pediatric oncology patients and their families.

Qualitative methods to ensure acceptability of behavioral and social interventions to the target population

PubMed Central

Ayala, Guadalupe X.; Elder, John P.

2013-01-01

This paper introduces qualitative methods for assessing the acceptability of an intervention. Acceptability refers to determining how well an intervention will be received by the target population and the extent to which the new intervention or its components might meet the needs of the target population and organizational setting. In this paper, we focus on two common qualitative methods for conducting acceptability research and their advantages and disadvantages: focus groups and interviews. We provide examples from our own research and other studies to demonstrate the use of these methods for conducting acceptability research and how one might adapt this approach for oral health research. Finally, we present emerging methods for conducting acceptability research, including the use of community-based participatory research, as well as the utility of conducting acceptability research for assessing the appropriateness of measures in intervention research. PMID:21656958

High throughput single cell counting in droplet-based microfluidics.

PubMed

Lu, Heng; Caen, Ouriel; Vrignon, Jeremy; Zonta, Eleonora; El Harrak, Zakaria; Nizard, Philippe; Baret, Jean-Christophe; Taly, Valérie

2017-05-02

Droplet-based microfluidics is extensively and increasingly used for high-throughput single-cell studies. However, the accuracy of the cell counting method directly impacts the robustness of such studies. We describe here a simple and precise method to accurately count a large number of adherent and non-adherent human cells as well as bacteria. Our microfluidic hemocytometer provides statistically relevant data on large populations of cells at a high-throughput, used to characterize cell encapsulation and cell viability during incubation in droplets.

Searching for rigour in the reporting of mixed methods population health research: a methodological review.

PubMed

Brown, K M; Elliott, S J; Leatherdale, S T; Robertson-Wilson, J

2015-12-01

The environments in which population health interventions occur shape both their implementation and outcomes. Hence, when evaluating these interventions, we must explore both intervention content and context. Mixed methods (integrating quantitative and qualitative methods) provide this opportunity. However, although criteria exist for establishing rigour in quantitative and qualitative research, there is poor consensus regarding rigour in mixed methods. Using the empirical example of school-based obesity interventions, this methodological review examined how mixed methods have been used and reported, and how rigour has been addressed. Twenty-three peer-reviewed mixed methods studies were identified through a systematic search of five databases and appraised using the guidelines for Good Reporting of a Mixed Methods Study. In general, more detailed description of data collection and analysis, integration, inferences and justifying the use of mixed methods is needed. Additionally, improved reporting of methodological rigour is required. This review calls for increased discussion of practical techniques for establishing rigour in mixed methods research, beyond those for quantitative and qualitative criteria individually. A guide for reporting mixed methods research in population health should be developed to improve the reporting quality of mixed methods studies. Through improved reporting, mixed methods can provide strong evidence to inform policy and practice. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Epidemiology of diabetic retinopathy and maculopathy in Africa: a systematic review

PubMed Central

Burgess, P I; MacCormick, I J C; Harding, S P; Bastawrous, A; Beare, N A V; Garner, P

2013-01-01

Abstract Aim To summarize findings from studies reporting the prevalence and incidence of diabetic retinopathy and diabetic maculopathy in African countries in light of the rising prevalence of diabetes mellitus. Methods Using a predefined search strategy, we systematically searched MEDLINE, EMBASE, Science Citation index and Conference Proceedings Citation index, African Index Medicus and the grey literature database ‘OpenSIGLE’ for studies published between January 1990 and February 2011. Included studies reported prevalence or incidence of diabetic retinopathy or diabetic maculopathy of subjects with diabetes resident in African countries. Results Sixty-two studies from 21 countries were included: three population-based surveys; two cohort studies; five case–control studies; 32 diabetes clinic-based, nine eye clinic-based and 11 other hospital-based surveys. Included studies varied considerably in terms of patient selection, method of assessing the eye and retinopathy classification. In population-based studies, the reported prevalence range in patients with diabetes for diabetic retinopathy was 30.2 to 31.6%, proliferative diabetic retinopathy 0.9 to 1.3%, and any maculopathy 1.2 to 4.5%. In diabetes clinic-based surveys, the reported prevalence range for diabetic retinopathy was 7.0 to 62.4%, proliferative diabetic retinopathy 0 to 6.9%, and any maculopathy 1.2 to 31.1%. No obvious association between prevalence and income level of the country was detected. Conclusions Large, community-based cross-sectional and cohort studies are needed to investigate rates and determinants of prevalence of diabetic retinopathy, incidence and progression in Africa. Consensus is needed on the most appropriate methods of identification and classification of retinopathy for research and clinical practice. Estimates of prevalence of diabetic retinopathy, proliferative diabetic retinopathy and maculopathy are comparable with recent European and American studies. PMID:22817387

Venous Thromboembolism and Cerebrovascular Events in Patients with Giant Cell Arteritis: A Population-Based Retrospective Cohort Study

PubMed Central

Crowson, Cynthia S.; Makol, Ashima; Ytterberg, Steven R.; Saitta, Antonino; Salvarani, Carlo; Matteson, Eric L.; Warrington, Kenneth J.

2016-01-01

Objective To investigate the incidence of venous thromboembolism (VTE) and cerebrovascular events in a community-based incidence cohort of patients with giant cell arteritis (GCA) compared to the general population. Methods A population-based inception cohort of patients with incident GCA between January 1, 1950 and December 31, 2009 in Olmsted County, Minnesota and a cohort of non-GCA subjects from the same population were assembled and followed until December 31, 2013. Confirmed VTE and cerebrovascular events were identified through direct medical record review. Results The study population included 244 patients with GCA with a mean ± SD age at diagnosis of 76.2 ± 8.2 years (79% women) and an average length of follow-up of 10.2 ± 6.8 years. Compared to non-GCA subjects of similar age and sex, patients diagnosed with GCA had a higher incidence (%) of amaurosis fugax (cumulative incidence ± SE: 2.1 ± 0.9 versus 0, respectively; p = 0.014) but similar rates of stroke, transient ischemic attack (TIA), and VTE. Among patients with GCA, neither baseline characteristics nor laboratory parameters at diagnosis reliably predicted risk of VTE or cerebrovascular events. Conclusion In this population-based study, the incidence of VTE, stroke and TIA was similar in patients with GCA compared to non-GCA subjects. PMID:26901431

Changes in anthropometrical data of the Hungarian child and adult population during the last thirty years based on family studies conducted by the Department of Forensic Medicine at Budapest.

PubMed

Magyar, Lóránt; Bellovits, Orsolya; Bujdosó, Györgyi

2006-06-01

Studies of the Hungarian child and adult population have revealed striking changes over the past thirty years with respect to body height and body mass, an observation, which has also been confirmed by other investigations (Gyenis & Joubert 2003, Maródi et. al. 2002). Based on these deviations the authors were interested in the variability of some anthropometrical head measures, which are of particular importance for forensic anthropological questions concerning face reconstruction (Editorial 2001, Jayprakash et. al. 2001, Szilvdssy & Kritscher 1997, Szilvdssy et al. 1997). The majority of such reconstruction methods, however, do not take into consideration the process of secular trend. It is the aim of this study to improve the anthropological basis for exact reconstruction methods by elaboration of temporal changes of face, head and body measures of the Hungarian population collected during the past thirty years. For this data from 2353 adults and 861 children investigated in 1974, and 869 adults 287 children investigated between 1994 and 2004 are available.

Persistency of accuracy of genomic breeding values for different simulated pig breeding programs in developing countries.

PubMed

Akanno, E C; Schenkel, F S; Sargolzaei, M; Friendship, R M; Robinson, J A B

2014-10-01

Genetic improvement of pigs in tropical developing countries has focused on imported exotic populations which have been subjected to intensive selection with attendant high population-wide linkage disequilibrium (LD). Presently, indigenous pig population with limited selection and low LD are being considered for improvement. Given that the infrastructure for genetic improvement using the conventional BLUP selection methods are lacking, a genome-wide selection (GS) program was proposed for developing countries. A simulation study was conducted to evaluate the option of using 60 K SNP panel and observed amount of LD in the exotic and indigenous pig populations. Several scenarios were evaluated including different size and structure of training and validation populations, different selection methods and long-term accuracy of GS in different population/breeding structures and traits. The training set included previously selected exotic population, unselected indigenous population and their crossbreds. Traits studied included number born alive (NBA), average daily gain (ADG) and back fat thickness (BFT). The ridge regression method was used to train the prediction model. The results showed that accuracies of genomic breeding values (GBVs) in the range of 0.30 (NBA) to 0.86 (BFT) in the validation population are expected if high density marker panels are utilized. The GS method improved accuracy of breeding values better than pedigree-based approach for traits with low heritability and in young animals with no performance data. Crossbred training population performed better than purebreds when validation was in populations with similar or a different structure as in the training set. Genome-wide selection holds promise for genetic improvement of pigs in the tropics. © 2014 Blackwell Verlag GmbH.

Often Asked but Rarely Answered: Can Asians Meet DSM-5/ICD-10 Autism Spectrum Disorder Criteria?

PubMed Central

Kim, So Hyun; Koh, Yun-Joo; Lim, Eun-Chung; Kim, Soo-Jeong; Leventhal, Bennett L.

2016-01-01

Abstract Objectives: To evaluate whether Asian (Korean children) populations can be validly diagnosed with autism spectrum disorder (ASD) using Western-based diagnostic instruments and criteria based on Diagnostic and Statistical Manual on Mental Disorders, 5th edition (DSM-5). Methods: Participants included an epidemiologically ascertained 7–14-year-old (N = 292) South Korean cohort from a larger prevalence study (N = 55,266). Main outcomes were based on Western-based diagnostic methods for Korean children using gold standard instruments, Autism Diagnostic Interview-Revised, and Autism Diagnostic Observation Schedule. Factor analysis and ANOVAs were performed to examine factor structure of autism symptoms and identify phenotypic differences between Korean children with ASD and non-ASD diagnoses. Results: Using Western-based diagnostic methods, Korean children with ASD were successfully identified with moderate-to-high diagnostic validity (sensitivities/specificities ranging 64%–93%), strong internal consistency, and convergent/concurrent validity. The patterns of autism phenotypes in a Korean population were similar to those observed in a Western population with two symptom domains (social communication and restricted and repetitive behavior factors). Statistically significant differences in the use of socially acceptable communicative behaviors (e.g., direct gaze, range of facial expressions) emerged between ASD versus non-ASD cases (mostly p < 0.001), ensuring that these can be a similarly valid part of the ASD phenotype in both Asian and Western populations. Conclusions: Despite myths, biases, and stereotypes about Asian social behavior, Asians (at least Korean children) typically use elements of reciprocal social interactions similar to those in the West. Therefore, standardized diagnostic methods widely used for ASD in Western culture can be validly used as part of the assessment process and research with Koreans and, possibly, other Asians. PMID:27315155

Combining matched and unmatched control groups in case-control studies.

PubMed

le Cessie, Saskia; Nagelkerke, Nico; Rosendaal, Frits R; van Stralen, Karlijn J; Pomp, Elisabeth R; van Houwelingen, Hans C

2008-11-15

Multiple control groups in case-control studies are used to control for different sources of confounding. For example, cases can be contrasted with matched controls to adjust for multiple genetic or unknown lifestyle factors and simultaneously contrasted with an unmatched population-based control group. Inclusion of different control groups for a single exposure analysis yields several estimates of the odds ratio, all using only part of the data. Here the authors introduce an easy way to combine odds ratios from several case-control analyses with the same cases. The approach is based upon methods used for meta-analysis but takes into account the fact that the same cases are used and that the estimated odds ratios are therefore correlated. Two ways of estimating this correlation are discussed: sandwich methodology and the bootstrap. Confidence intervals for the pooled estimates and a test for checking whether the odds ratios in the separate case-control studies differ significantly are derived. The performance of the method is studied by simulation and by applying the methods to a large study on risk factors for thrombosis, the MEGA Study (1999-2004), wherein cases with first venous thrombosis were included with a matched control group of partners and an unmatched population-based control group.

How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota.

PubMed

Grégory, Dubourg; Chaudet, Hervé; Lagier, Jean-Christophe; Raoult, Didier

2018-03-01

Describing the human hut gut microbiota is one the most exciting challenges of the 21 st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.

Influence Based Learning Program Scientific Learning Approach to Science Students Generic Skills

ERIC Educational Resources Information Center

Wahyuni, Ida; Amdani, Khairul

2016-01-01

This study aims to determine the influence of scientific approach based learning program (P2BPS) against generic science skills of students. The method used in this research is "quasi experiment" with "two-group pretest posttest" design.The population in this study were all students who take courses in general physics II at the…

Surveillance of traumatic firefighter fatalities: an assessment of four systems.

PubMed

Estes, Chris R; Marsh, Suzanne M; Castillo, Dawn N

2011-01-01

Firefighters regularly respond to hazardous situations that put them at risk for fatal occupational injuries. Traumatic occupational fatality surveillance is a foundation for understanding the problem and developing prevention strategies. We assessed four surveillance systems for their utility in characterizing firefighter fatalities and informing prevention measures. We examined three population-based systems (the Bureau of Labor Statistics' Census of Fatal Occupational Injuries and systems maintained by the United States Fire Administration and the National Fire Protection Association) and one case-based system (data collected through the National Institute for Occupational Safety and Health Fire Fighter Fatality Investigation and Prevention Program). From each system, we selected traumatic fatalities among firefighters for 2003-2006. Then we compared case definitions, methods for case ascertainment, variables collected, and rate calculation methods. Overall magnitude of fatalities differed among systems. The population-based systems were effective in characterizing the circumstances of traumatic firefighter fatalities. The case-based surveillance system was effective in formulating detailed prevention recommendations, which could not be made based on the population-based data alone. Methods for estimating risk were disparate and limited fatality rate comparisons between firefighters and other workers. The systems included in this study contribute toward a greater understanding of firefighter fatalities. Areas of improvement for these systems should continue to be identified as they are used to direct research and prevention efforts.

Facebook Ads Recruit Parents of Children with Cancer for an Online Survey of Web-Based Research Preferences

PubMed Central

Akard, Terrah Foster; Wray, Sarah; Gilmer, Mary

2014-01-01

Background Studies involving samples of children with life-threatening illnesses and their families face significant challenges, including inadequate sample sizes and limited diversity. Social media recruitment and web-based research methods may help address such challenges yet have not been explored in pediatric cancer populations. Objective This study examined the feasibility of using Facebook ads to recruit parent caregivers of children and teens with cancer. We also explored the feasibility of web-based video recording in pediatric palliative care populations by surveying parents of children with cancer regarding (a) their preferences for research methods and (b) technological capabilities of their computers and phones. Methods Facebook's paid advertising program was used to recruit parent caregivers of children currently living with cancer to complete an electronic survey about research preferences and technological capabilities. Results The advertising campaign generated 3,897,981 impressions which resulted in 1050 clicks at a total cost of $1129.88. Of 284 screened individuals, 106 were eligible. Forty-five caregivers of children with cancer completed the entire electronic survey. Parents preferred and had technological capabilities for web-based and electronic research methods. Participant survey responses are reported. Conclusion Facebook was a useful, cost-effective method to recruit a diverse sample of parent caregivers of children with cancer. Web-based video recording and data collection may be feasible and desirable in samples of children with cancer and their families. Implications for Practice Web-based methods (e.g., Facebook, Skype) may enhance communication and access between nurses and pediatric oncology patients and their families. PMID:24945264

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 FE model responses. Specifically, this method mitigates the uncertainties in applying empirical scaling and may improve IRF fidelity when a limited number of experimental specimens are available.

A Population-Based Assessment of the Agreement Between Grading of Goniophotographic Images and Gonioscopy in the Chinese-American Eye Study (CHES)

PubMed Central

Murakami, Yohko; Wang, Dandan; Burkemper, Bruce; Lin, Shan C.; Varma, Rohit

2016-01-01

Purpose To compare grading of goniophotographic images and gonioscopy in assessing the iridocorneal angle. Methods In a population-based, cross-sectional study, participants underwent gonioscopy and goniophotographic imaging during the same visit. The iridocorneal angle was classified as closed if the posterior trabecular meshwork could not be seen. A single masked observer graded the goniophotographic images, and each eye was classified as having angle closure based on the number of closed quadrants. Agreement between the methods was analyzed by calculating kappa (κ) and first-order agreement coefficient (AC1) statistics and comparison of area under receiver operating characteristic curves (AUC). Results A total of 4149 Chinese Americans (3994 eyes) were included in this study. The agreement for angle closure diagnosis between gonioscopy and EyeCam was moderate to excellent (κ = 0.60, AC1 0.90, AUC 0.76–0.80). Conclusions Detection of iridocorneal angle closure based on goniophotographic imaging shows moderate to very good agreement with angle closure assessment using gonioscopy. PMID:27571018

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.

[New population curves in spanish extremely preterm neonates].

PubMed

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

2014-08-01

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

Impact of floating population on the epidemic of tuberculosis: a spatial analysis

NASA Astrophysics Data System (ADS)

Jia, Zhongwei; He, Xiaoxin; Zhao, Wenjuan; An, Yansheng; Cao, Wuchun; Li, Xiaowen

2007-06-01

According to the report issued by the Health Bureau of Beijing that the number of newly registered active pulmonary tuberculosis cases in floating population exceeded half of that in registered permanent residence in 2006. More attention has been paid to the tuberculosis of floating population. Materials and methods: The population data included in the studied was reported by the Beijing Police Bureau in 2004, and the case source from 2004 to 2006 was provided by Beijing Research Institute for TB Control. Two GIS-based methods have been used to detect the hot spots of tuberculosis in 18 districts of Beijing. Results: The distributions of hot spots of tuberculosis in Beijing are significantly associated with that of floating people. Most likely cluster from all population matches with those from floating population, which is stable from 2004 to 2006. Conclusion: The spatial analytical results indicated that the floating population has a drastic influence on the epidemic of tuberculosis in Beijing. The tuberculosis control measures should incorporate the effect of floating population.

Analysis of anatomic variability in children with low mathematical skills

NASA Astrophysics Data System (ADS)

Han, Zhaoying; Fuchs, Lynn; Davis, Nikki; Cannistraci, Christopher J.; Anderson, Adam W.; Gore, John C.; Dawant, Benoit M.

2008-03-01

Mathematical difficulty affects approximately 5-9% of the population. Studies on individuals with dyscalculia, a neurologically based math disorder, provide important insight into the neural correlates of mathematical ability. For example, cognitive theories, neuropsychological studies, and functional neuroimaging studies in individuals with dyscalculia suggest that the bilateral parietal lobes and intraparietal sulcus are central to mathematical performance. The purpose of the present study was to investigate morphological differences in a group of third grade children with poor math skills. We compare population averages of children with low math skill (MD) to gender and age matched controls with average math ability. Anatomical data were gathered with high resolution MRI and four different population averaging methods were used to study the effect of the normalization technique on the results. Statistical results based on the deformation fields between the two groups show anatomical differences in the bilateral parietal lobes, right frontal lobe, and left occipital/parietal lobe.

A random spatial sampling method in a rural developing nation

Treesearch

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

2014-01-01

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

Variations in suicide method and in suicide occurrence by season and day of the week in Russia and the Nenets Autonomous Okrug, Northwestern Russia: a retrospective population-based mortality study.

PubMed

Sumarokov, Yury A; Brenn, Tormod; Kudryavtsev, Alexander V; Nilssen, Odd

2015-09-23

Suicide is an important world health issue, especially in territories inhabited by indigenous people. This investigated differences in suicide rates, suicide methods, and suicide occurrence by month and day of the week among the indigenous and non-indigenous populations of the Nenets Autonomous Okrug (NAO) and to compare the findings from the NAO with national Russian statistics. In this retrospective population-based mortality study we investigated all suicides that occurred in the NAO in 2002-2012 (N = 252). Suicide method and the month and day of the week suicide occurred was taken from autopsy reports and disaggregated by ethnic group (indigenous and non-indigenous) and sex. Data from the NAO were then compared with national data from the Russian Federal Statistics Service (Rosstat). Hanging was the most common suicide method in the NAO in both indigenous and non-indigenous populations. The proportion of suicides by hanging among males was lower in the NAO than in national data (69.3 vs 86.2 %), but the inverse was true for females (86.5 vs 74.9 %). Suicide by firearm and by cutting was significantly higher among the indigenous population in the NAO when compared with national data. Peaks in suicide occurrence were observed in May and September in the NAO, whereas national data showed only one peak in May. Suicide occurrence in the indigenous population of the NAO was highest in April, while the non-indigenous population showed peaks in May and September. Suicide occurrence in the NAO was highest on Fridays; in national data this occurrence was highest on Mondays. We showed different relative frequencies of suicide by hanging, cutting, and firearm, as well as different suicide occurrence by month and day of the week in the NAO compared with Russia as a whole. These results can be used to plan suicide prevention activities in the Russian Arctic.

Global Epidemiology of Amyotrophic Lateral Sclerosis: a Systematic Review of the Published Literature

PubMed Central

Chiò, A; Logroscino, G; Traynor, BJ; Collins, J; Simeone, JC; Goldstein, LA; White, LA

2014-01-01

Background Amyotrophic lateral sclerosis (ALS) is relatively rare, yet the economic and social burden is substantial. Having accurate incidence and prevalence estimates would facilitate efficient allocation of healthcare resources. Objective To provide a comprehensive and critical review of the epidemiologic literature on ALS. Methods MEDLINE and EMBASE (1995–2011) databases of population-based studies on ALS incidence and prevalence reporting quantitative data were analyzed. Data extracted included study location and time, design and data sources, case ascertainment methods, and incidence and/or prevalence rates. Medians and inter-quartile ranges (IQRs) were calculated, and ALS case estimates derived using 2010 population estimates. Results In all, 37 articles met inclusion criteria. In Europe, the median (IQR) incidence rate (/100,000 population) was 2.08 (1.47–2.43), corresponding to an estimated 15,355 (10,852–17,938) cases. Median (IQR) prevalence (/100,000 population) was 5.40 (4.06–7.89), or 39,863 (29,971–58,244) prevalent cases. Conclusions Disparity in rates among ALS incidence and prevalence studies may be due to differences in study design or true variations in population demographics, such as age, and geography, including environmental factors and genetic predisposition. Additional large-scale studies that use standardized case ascertainment methods are needed to more accurately assess the true global burden of ALS. PMID:23860588

Self-reported indications for antidepressant use in a population-based cohort of middle-aged and elderly.

PubMed

Aarts, Nikkie; Noordam, Raymond; Hofman, Albert; Tiemeier, Henning; Stricker, Bruno H; Visser, Loes E

2016-10-01

Background Population-based studies investigating indications for antidepressant prescribing mostly rely on diagnoses from general practitioners. However, diagnostic codes might be incomplete and drugs may be prescribed 'off-label' for indications not investigated in clinical trials. Objective We aimed to study indications for antidepressant use based on self-report. Also, we studied the presence of depressive symptoms associated with the self-reported indications. Setting Our study population of antidepressant users was selected based on interview data between 1997 and 2013 from the prospective population-based Rotterdam Study cohort (age >45 years). Method Antidepressant use, self-reported indication for use, and presence of depressive symptoms (Center for Epidemiological Studies Depression Scale) were based on interview. Self-reported indications were categorized by the researchers into officially approved, clinically-accepted and commonly mentioned off-label indications. Main outcome measures A score of 16 and higher on the Center for Epidemiological Studies Depression Scale was considered as indicator for clinically-relevant depressive symptoms. Results The majority of 914 antidepressant users reported 'depression' (52.4 %) as indication for treatment. Furthermore, anxiety, stress and sleep disorders were reported in selective serotonin reuptake inhibitor and other antidepressant users (ranging from 5.9 to 13.3 %). The indication 'pain' was commonly mentioned by tricyclic antidepressant users (19.0 %). Indications were statistically significantly associated with higher depressive symptom scores when compared to non-users (n = 10,979). Conclusions Depression was the main indication for antidepressant treatment. However, our findings suggest that antidepressants are also used for off-label indications, subthreshold disorders and complex situations, which were all associated with clinically-relevant depressive symptoms in the middle-aged and elderly population.

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

USGS Publications Warehouse

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

2014-01-01

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

Prevalence of Candida bracarensis and Candida nivariensis in a Spanish collection of yeasts: comparison of results from a reference centre and from a population-based surveillance study of candidemia.

PubMed

Cuenca-Estrella, M; Gomez-Lopez, A; Isla, G; Rodriguez, D; Almirante, B; Pahissa, A; Rodriguez-Tudela, J L

2011-07-01

Two new species related to Candida glabrata, i.e., Candida nivariensis and Candida bracarensis, have been proposed. The occurrence of these species among isolates collected in a Spanish mycology reference laboratory in 2008-2009 was reviewed. In addition, strains recovered as part of an active population-based surveillance of candidemia conducted in Barcelona between 2002 and 2003 were also analyzed. Among 143 clinical isolates received in 2008-2009, three (2%) were identified as C. bracarensis and none as C. nivariensis through sequencing of their ribosomal DNA. Of the 31 strains initially identified as C. glabrata in the 2002-2003 population-based study (0.38 cases/100,000 population), none were found to belong to these related new species. Results from in vitro susceptibility studies of C. bracarensis isolates were comparable to those found with C. glabrata. Since new and cryptic species have been described, periodic surveillance including the use of molecular identification methods seems to be necessary in order to determine their frequency, geographical distribution and susceptibility profile.

Design Appropriate Models Based on Intelligent Dimension in Fars Education Organization

ERIC Educational Resources Information Center

Goodarzi, Shahbaz; Fallah, Vahid; Saffarian, Saeid

2016-01-01

The purpose of this study is to determine the dimensions of smart schools in the Fars education system and provide a suitable model. The research method is descriptive survey. The study population consisted of all school principals Fars Province in the academic 2014-2015 and number of them was 1364. The sample volume using Cochran method was 302…

Refining aging criteria for northern sea otters in Washington State

USGS Publications Warehouse

Schuler, Krysten L.; Baker, Bridget B.; Mayer, Karl A.; Perez-Heydrich, Carolina; Holahan, Paula M.; Thomas, Nancy J.; White, C. LeAnn

2018-01-01

Measurement of skull ossification patterns is a standard method for aging various mammalian species and has been used to age Russian, Californian, and Alaskan sea otter populations. Cementum annuli counts have also been verified as an accurate aging method for the Alaskan sea otter population. In this study, cementum annuli count results and skull ossification patterns were compared as methods for aging the northern sea otter (Enhydra lutris kenyoni) population in Washington State. Significant agreement was found between the two methods suggesting that either method could be used to age the Washington population of otters. This study also found that ossification of the squamosal-jugal suture at the ventral glenoid fossa can be used to differentiate male subadults from adults. To assist field biologists or others without access to cementum annuli or skull ossification analysis techniques, a suite of morphologic, physiologic, and developmental characteristics were analyzed to assess whether a set of these more easily accessible parameters could also predict age class for the Washington population of otters. Tooth condition score, evidence of reproductive activity in females, and tooth eruption pattern were identified as the most useful criteria for classifying Washington sea otters as pups, juveniles, subadults, or adults/aged adults. A simple decision tree based on characteristics accessible in the field or at necropsy was created that can be used to reliably predict age class of Washington sea otters as determined by cementum annuli.

A Distribution-based Method for Assessing The Differences between Clinical Trial Target Populations and Patient Populations in Electronic Health Records

PubMed Central

Li, Y.; Ryan, P.; Zhang, Y.; Liu, F.; Gao, J.; Bigger, J.T.; Hripcsak, G.

2014-01-01

Summary Objective To improve the transparency of clinical trial generalizability and to illustrate the method using Type 2 diabetes as an example. Methods Our data included 1,761 diabetes clinical trials and the electronic health records (EHR) of 26,120 patients with Type 2 diabetes who visited Columbia University Medical Center of New-York Presbyterian Hospital. The two populations were compared using the Generalizability Index for Study Traits (GIST) on the earliest diagnosis age and the mean hemoglobin A1c (HbA1c) values. Results Greater than 70% of Type 2 diabetes studies allow patients with HbA1c measures between 7 and 10.5, but less than 40% of studies allow HbA1c<7 and fewer than 45% of studies allow HbA1c>10.5. In the real-world population, only 38% of patients had HbA1c between 7 and 10.5, with 12% having values above the range and 52% having HbA1c<7. The GIST for HbA1c was 0.51. Most studies adopted broad age value ranges, with the most common restrictions excluding patients >80 or <18 years. Most of the real-world population fell within this range, but 2% of patients were <18 at time of first diagnosis and 8% were >80. The GIST for age was 0.75. Conclusions We contribute a scalable method to profile and compare aggregated clinical trial target populations with EHR patient populations. We demonstrate that Type 2 diabetes studies are more generalizable with regard to age than they are with regard to HbA1c. We found that the generalizability of age increased from Phase 1 to Phase 3 while the generalizability of HbA1c decreased during those same phases. This method can generalize to other medical conditions and other continuous or binary variables. We envision the potential use of EHR data for examining the generalizability of clinical trials and for defining population-representative clinical trial eligibility criteria. PMID:25024761

Heterogeneity in risk of prostate cancer: A Swedish population-based cohort study of competing risks and type 2 diabetes mellitus.

PubMed

Häggström, Christel; Van Hemelrijck, Mieke; Garmo, Hans; Robinson, David; Stattin, Pär; Rowley, Mark; Coolen, Anthony C C; Holmberg, Lars

2018-05-09

Most previous studies of prostate cancer have not taken into account that men in the studied populations are also at risk of competing event, and that these men may have different susceptibility to prostate cancer risk. The aim of this study was to investigate heterogeneity in risk of prostate cancer, using a recently developed latent class regression method for competing risks. We further aimed to elucidate the association between type 2 diabetes mellitus (T2DM) and prostate cancer risk, and to compare the results with conventional methods for survival analysis. We analysed the risk of prostate cancer in 126,482 men from the comparison cohort of the Prostate Cancer Data base Sweden (PCBaSe) 3.0. During a mean follow-up of 6 years 6,036 men were diagnosed with prostate cancer and 22,393 men died. We detected heterogeneity in risk of prostate cancer with two distinct latent classes in the study population. The smaller class included 9% of the study population in which men had a higher risk of prostate cancer and the risk was stronger associated with class membership than any of the covariates included in the study. Moreover, we found no association between T2DM and risk of prostate cancer after removal of the effect of informative censoring due to competing risks. The recently developed latent class for competing risks method could be used to provide new insights in precision medicine with the target to classify individuals regarding different susceptibility to a particular disease, reaction to a risk factor or response to treatment. This article is protected by copyright. All rights reserved. © 2018 UICC.

Respondent-driven sampling for an adolescent health study in vulnerable urban settings: a multi-country study.

PubMed

Decker, Michele R; Marshall, Beth Dail; Emerson, Mark; Kalamar, Amanda; Covarrubias, Laura; Astone, Nan; Wang, Ziliang; Gao, Ersheng; Mashimbye, Lawrence; Delany-Moretlwe, Sinead; Acharya, Rajib; Olumide, Adesola; Ojengbede, Oladosu; Blum, Robert W; Sonenstein, Freya L

2014-12-01

The global adolescent population is larger than ever before and is rapidly urbanizing. Global surveillance systems to monitor youth health typically use household- and school-based recruitment methods. These systems risk not reaching the most marginalized youth made vulnerable by conditions of migration, civil conflict, and other forms of individual and structural vulnerability. We describe the methodology of the Well-Being of Adolescents in Vulnerable Environments survey, which used respondent-driven sampling (RDS) to recruit male and female youth aged 15-19 years and living in economically distressed urban settings in Baltimore, MD; Johannesburg, South Africa; Ibadan, Nigeria; New Delhi, India; and Shanghai, China (migrant youth only) for a cross-sectional study. We describe a shared recruitment and survey administration protocol across the five sites, present recruitment parameters, and illustrate challenges and necessary adaptations for use of RDS with youth in disadvantaged urban settings. We describe the reach of RDS into populations of youth who may be missed by traditional household- and school-based sampling. Across all sites, an estimated 9.6% were unstably housed; among those enrolled in school, absenteeism was pervasive with 29% having missed over 6 days of school in the past month. Overall findings confirm the feasibility, efficiency, and utility of RDS in quickly reaching diverse samples of youth, including those both in and out of school and those unstably housed, and provide direction for optimizing RDS methods with this population. In our rapidly urbanizing global landscape with an unprecedented youth population, RDS may serve as a valuable tool in complementing existing household- and school-based methods for health-related surveillance that can guide policy. Copyright © 2014 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Respondent-driven sampling for an adolescent health study in vulnerable urban settings: a multi-country study

PubMed Central

Decker, Michele R.; Marshall, Beth; Emerson, Mark; Kalamar, Amanda; Covarrubias, Laura; Astone, Nan; Wang, Ziliang; Gao, Ersheng; Mashimbye, Lawrence; Delany-Moretlwe, Sinead; Acharya, Rajib; Olumide, Adesola; Ojengbede, Oladosu; Blum, Robert

2015-01-01

The global adolescent population is larger than ever before and is rapidly urbanizing. Global surveillance systems to monitor youth health typically use household- and school-based recruitment methods. These systems risk not reaching the most marginalized youth made vulnerable by conditions of migration, civil conflict and other forms of individual and structural vulnerability. We describe the methodology of the Well Being of Adolescents in Vulnerable Environments (WAVE) survey, which used respondent-driven sampling (RDS) to recruit male and female youth aged 15 to 19 years and living in economically distressed urban settings in Baltimore, USA, Johannesburg, South Africa, Ibadan, Nigeria, Delhi, India and Shanghai, China (migrant youth only) for a cross-sectional study. We describe a shared recruitment and survey administration protocol across the five sites, present recruitment parameters, and illustrate challenges and necessary adaptations for use of RDS with youth in disadvantaged urban settings. We describe the reach of RDS into populations of youth who may be missed by traditional householdbased and school-based sampling. Across all sites, an estimated 9.6% were unstably housed; among those enrolled in school, absenteeism was pervasive with 29% having missed over 6 days of school in the past month. Overall findings confirm the feasibility, efficiency and utility of RDS in quickly reaching diverse samples of youth, including those both in and out of school and those unstably housed, and provide direction for optimizing RDS methods with this population. In our rapidly urbanizing global landscape with an unprecedented youth population, RDS may serve as a valuable tool in complementing existing household- and school-based methods for health-related surveillance that can guide policy. PMID:25454005

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

PubMed Central

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

2018-01-01

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

[Assessment of ecosystem in giant panda distribution area based on entropy method and coefficient of variation].

PubMed

Yan, Zhi Gang; Li, Jun Qing

2017-12-01

The areas of the habitat and bamboo forest, and the size of the giant panda wild population have greatly increased, while habitat fragmentation and local population isolation have also intensified in recent years. Accurate evaluation of ecosystem status of the panda in the giant panda distribution area is important for giant panda conservation. The ecosystems of the distribution area and six mountain ranges were subdivided into habitat and population subsystems based on the hie-rarchical system theory. Using the panda distribution area as the study area and the three national surveys as the time node, the evolution laws of ecosystems were studied using the entropy method, coefficient of variation, and correlation analysis. We found that with continuous improvement, some differences existed in the evolution and present situation of the ecosystems of six mountain ranges could be divided into three groups. Ecosystems classified into the same group showed many commonalities, and difference between the groups was considerable. Problems of habitat fragmentation and local population isolation became more serious, resulting in ecosystem degradation. Individuali-zed ecological protection measures should be formulated and implemented in accordance with the conditions in each mountain system to achieve the best results.

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

PubMed

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

2006-12-01

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

Confidence intervals for the population mean tailored to small sample sizes, with applications to survey sampling.

PubMed

Rosenblum, Michael A; Laan, Mark J van der

2009-01-07

The validity of standard confidence intervals constructed in survey sampling is based on the central limit theorem. For small sample sizes, the central limit theorem may give a poor approximation, resulting in confidence intervals that are misleading. We discuss this issue and propose methods for constructing confidence intervals for the population mean tailored to small sample sizes. We present a simple approach for constructing confidence intervals for the population mean based on tail bounds for the sample mean that are correct for all sample sizes. Bernstein's inequality provides one such tail bound. The resulting confidence intervals have guaranteed coverage probability under much weaker assumptions than are required for standard methods. A drawback of this approach, as we show, is that these confidence intervals are often quite wide. In response to this, we present a method for constructing much narrower confidence intervals, which are better suited for practical applications, and that are still more robust than confidence intervals based on standard methods, when dealing with small sample sizes. We show how to extend our approaches to much more general estimation problems than estimating the sample mean. We describe how these methods can be used to obtain more reliable confidence intervals in survey sampling. As a concrete example, we construct confidence intervals using our methods for the number of violent deaths between March 2003 and July 2006 in Iraq, based on data from the study "Mortality after the 2003 invasion of Iraq: A cross sectional cluster sample survey," by Burnham et al. (2006).

New non-invasive method for early detection of metabolic syndrome in the working population.

PubMed

Romero-Saldaña, Manuel; Fuentes-Jiménez, Francisco J; Vaquero-Abellán, Manuel; Álvarez-Fernández, Carlos; Molina-Recio, Guillermo; López-Miranda, José

2016-12-01

We propose a new method for the early detection of metabolic syndrome in the working population, which was free of biomarkers (non-invasive) and based on anthropometric variables, and to validate it in a new working population. Prevalence studies and diagnostic test accuracy to determine the anthropometric variables associated with metabolic syndrome, as well as the screening validity of the new method proposed, were carried out between 2013 and 2015 on 636 and 550 workers, respectively. The anthropometric variables analysed were: blood pressure, body mass index, waist circumference, waist-height ratio, body fat percentage and waist-hip ratio. We performed a multivariate logistic regression analysis and obtained receiver operating curves to determine the predictive ability of the variables. The new method for the early detection of metabolic syndrome we present is based on a decision tree using chi-squared automatic interaction detection methodology. The overall prevalence of metabolic syndrome was 14.9%. The area under the curve for waist-height ratio and waist circumference was 0.91 and 0.90, respectively. The anthropometric variables associated with metabolic syndrome in the adjusted model were waist-height ratio, body mass index, blood pressure and body fat percentage. The decision tree was configured from the waist-height ratio (⩾0.55) and hypertension (blood pressure ⩾128/85 mmHg), with a sensitivity of 91.6% and a specificity of 95.7% obtained. The early detection of metabolic syndrome in a healthy population is possible through non-invasive methods, based on anthropometric indicators such as waist-height ratio and blood pressure. This method has a high degree of predictive validity and its use can be recommended in any healthcare context. © The European Society of Cardiology 2016.

Investigating population continuity with ancient DNA under a spatially explicit simulation framework.

PubMed

Silva, Nuno Miguel; Rio, Jeremy; Currat, Mathias

2017-12-15

Recent advances in sequencing technologies have allowed for the retrieval of ancient DNA data (aDNA) from skeletal remains, providing direct genetic snapshots from diverse periods of human prehistory. Comparing samples taken in the same region but at different times, hereafter called "serial samples", may indicate whether there is continuity in the peopling history of that area or whether an immigration of a genetically different population has occurred between the two sampling times. However, the exploration of genetic relationships between serial samples generally ignores their geographical locations and the spatiotemporal dynamics of populations. Here, we present a new coalescent-based, spatially explicit modelling approach to investigate population continuity using aDNA, which includes two fundamental elements neglected in previous methods: population structure and migration. The approach also considers the extensive temporal and geographical variance that is commonly found in aDNA population samples. We first showed that our spatially explicit approach is more conservative than the previous (panmictic) approach and should be preferred to test for population continuity, especially when small and isolated populations are considered. We then applied our method to two mitochondrial datasets from Germany and France, both including modern and ancient lineages dating from the early Neolithic. The results clearly reject population continuity for the maternal line over the last 7500 years for the German dataset but not for the French dataset, suggesting regional heterogeneity in post-Neolithic migratory processes. Here, we demonstrate the benefits of using a spatially explicit method when investigating population continuity with aDNA. It constitutes an improvement over panmictic methods by considering the spatiotemporal dynamics of genetic lineages and the precise location of ancient samples. The method can be used to investigate population continuity between any pair of serial samples (ancient-ancient or ancient-modern) and to investigate more complex evolutionary scenarios. Although we based our study on mitochondrial DNA sequences, diploid molecular markers of different types (DNA, SNP, STR) can also be simulated with our approach. It thus constitutes a promising tool for the analysis of the numerous aDNA datasets being produced, including genome wide data, in humans but also in many other species.

Sex determination using humeral dimensions in a sample from KwaZulu-Natal: an osteometric study

PubMed Central

Ogedengbe, Oluwatosin Olalekan; Ajayi, Sunday Adelaja; Komolafe, Omobola Aderibigbe; Zaw, Aung Khaing; Naidu, Edwin Coleridge Stephen

2017-01-01

The morphological characteristics of the humeral bone has been investigated in recent times with studies showing varying degrees of sexual dimorphism. Osteologists and forensic scientists have shown that sex determination methods based on skeletal measurements are population specific, and these population-specific variations are present in many body dimensions. The present study aims to establish sex identification using osteometric standards for the humerus in a contemporary KwaZulu-Natal population. A total of 11 parameters were measured in a sample of n=211 humeri (males, 113; females, 98) from the osteological collection in the Discipline of Clinical Anatomy, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa. The difference in means for nearly all variables were found to be significantly higher in males compared to females (P<0.01) with the most effective single parameter for predicting sex being the vertical head diameter having an accuracy of 82.5%. Stepwise discriminant analysis increased the overall accuracy rate to 87.7% when all measurements were jointly applied. We conclude that the humerus is an important bone which can be reliably used for sex determination based on standard metric methods despite minor tribal or ancestral differences amongst an otherwise homogenous population. PMID:29043096

Sex determination using humeral dimensions in a sample from KwaZulu-Natal: an osteometric study.

PubMed

Ogedengbe, Oluwatosin Olalekan; Ajayi, Sunday Adelaja; Komolafe, Omobola Aderibigbe; Zaw, Aung Khaing; Naidu, Edwin Coleridge Stephen; Okpara Azu, Onyemaechi

2017-09-01

The morphological characteristics of the humeral bone has been investigated in recent times with studies showing varying degrees of sexual dimorphism. Osteologists and forensic scientists have shown that sex determination methods based on skeletal measurements are population specific, and these population-specific variations are present in many body dimensions. The present study aims to establish sex identification using osteometric standards for the humerus in a contemporary KwaZulu-Natal population. A total of 11 parameters were measured in a sample of n=211 humeri (males, 113; females, 98) from the osteological collection in the Discipline of Clinical Anatomy, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa. The difference in means for nearly all variables were found to be significantly higher in males compared to females ( P <0.01) with the most effective single parameter for predicting sex being the vertical head diameter having an accuracy of 82.5%. Stepwise discriminant analysis increased the overall accuracy rate to 87.7% when all measurements were jointly applied. We conclude that the humerus is an important bone which can be reliably used for sex determination based on standard metric methods despite minor tribal or ancestral differences amongst an otherwise homogenous population.

Detection and characterization of nonspecific, sparsely-populated binding modes in the early stages of complexation

PubMed Central

Cardone, A.; Bornstein, A.; Pant, H. C.; Brady, M.; Sriram, R.; Hassan, S. A.

2015-01-01

A method is proposed to study protein-ligand binding in a system governed by specific and non-specific interactions. Strong associations lead to narrow distributions in the proteins configuration space; weak and ultra-weak associations lead instead to broader distributions, a manifestation of non-specific, sparsely-populated binding modes with multiple interfaces. The method is based on the notion that a discrete set of preferential first-encounter modes are metastable states from which stable (pre-relaxation) complexes at equilibrium evolve. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks. The method is applied to a peptide-protein complex. The peptide adopts several low-population conformers and binds in a variety of modes with a broad range of affinities. The system is thus well suited to analyze general features of binding, including conformational selection, multiplicity of binding modes, and nonspecific interactions, and to illustrate how the method can be applied to study these problems systematically. The equilibrium distributions can be used to generate biasing functions for simulations of multiprotein systems from which bulk thermodynamic quantities can be calculated. PMID:25782918

Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study - findings from Pretest 1 of the German National Cohort.

PubMed

Akmatov, Manas K; Koch, Nadine; Vital, Marius; Ahrens, Wolfgang; Flesch-Janys, Dieter; Fricke, Julia; Gatzemeier, Anja; Greiser, Halina; Günther, Kathrin; Illig, Thomas; Kaaks, Rudolf; Krone, Bastian; Kühn, Andrea; Linseisen, Jakob; Meisinger, Christine; Michels, Karin; Moebus, Susanne; Nieters, Alexandra; Obi, Nadia; Schultze, Anja; Six-Merker, Julia; Pieper, Dietmar H; Pessler, Frank

2017-05-12

We examined acceptability, preference and feasibility of collecting nasal and oropharyngeal swabs, followed by microbiome analysis, in a population-based study with 524 participants. Anterior nasal and oropharyngeal swabs were collected by certified personnel. In addition, participants self-collected nasal swabs at home four weeks later. Four swab types were compared regarding (1) participants' satisfaction and acceptance and (2) detection of microbial community structures based on deep sequencing of the 16 S rRNA gene V1-V2 variable regions. All swabbing methods were highly accepted. Microbial community structure analysis revealed 846 phylotypes, 46 of which were unique to oropharynx and 164 unique to nares. The calcium alginate tipped swab was found unsuitable for microbiome determinations. Among the remaining three swab types, there were no differences in oropharyngeal microbiomes detected and only marginal differences in nasal microbiomes. Microbial community structures did not differ between staff-collected and self-collected nasal swabs. These results suggest (1) that nasal and oropharyngeal swabbing are highly feasible methods for human population-based studies that include the characterization of microbial community structures in these important ecological niches, and (2) that self-collection of nasal swabs at home can be used to reduce cost and resources needed, particularly when serial measurements are to be taken.

Public health research: lost in translation or speaking the wrong language?

PubMed

Kansagra, Susan M; Farley, Thomas A

2011-12-01

Public health leaders, like physicians, need to make decisions that impact health based on strong evidence. To generate useful evidence for public health leaders, research must focus on interventions that have potential to impact population-level health. Often policy and environmental changes are the interventions with the greatest potential impact on population health, but studying these is difficult because of limitations in the methods typically used and emphasized in health research. To create useful evidence for policy and environmental interventions, other research methods are needed, including observational studies, the use of surveillance data for evaluation, and predictive mathematical modeling. More emphasis is needed on these types of study designs by researchers, funding agencies, and scientific journals.

An Empirical Analysis of the Impact of Recruitment Patterns on RDS Estimates among a Socially Ordered Population of Female Sex Workers in China

PubMed Central

Yamanis, Thespina J.; Merli, M. Giovanna; Neely, William Whipple; Tian, Felicia Feng; Moody, James; Tu, Xiaowen; Gao, Ersheng

2013-01-01

Respondent-driven sampling (RDS) is a method for recruiting “hidden” populations through a network-based, chain and peer referral process. RDS recruits hidden populations more effectively than other sampling methods and promises to generate unbiased estimates of their characteristics. RDS’s faithful representation of hidden populations relies on the validity of core assumptions regarding the unobserved referral process. With empirical recruitment data from an RDS study of female sex workers (FSWs) in Shanghai, we assess the RDS assumption that participants recruit nonpreferentially from among their network alters. We also present a bootstrap method for constructing the confidence intervals around RDS estimates. This approach uniquely incorporates real-world features of the population under study (e.g., the sample’s observed branching structure). We then extend this approach to approximate the distribution of RDS estimates under various peer recruitment scenarios consistent with the data as a means to quantify the impact of recruitment bias and of rejection bias on the RDS estimates. We find that the hierarchical social organization of FSWs leads to recruitment biases by constraining RDS recruitment across social classes and introducing bias in the RDS estimates. PMID:24288418

Stability-based validation of dietary patterns obtained by cluster analysis.

PubMed

Sauvageot, Nicolas; Schritz, Anna; Leite, Sonia; Alkerwi, Ala'a; Stranges, Saverio; Zannad, Faiez; Streel, Sylvie; Hoge, Axelle; Donneau, Anne-Françoise; Albert, Adelin; Guillaume, Michèle

2017-01-14

Cluster analysis is a data-driven method used to create clusters of individuals sharing similar dietary habits. However, this method requires specific choices from the user which have an influence on the results. Therefore, there is a need of an objective methodology helping researchers in their decisions during cluster analysis. The objective of this study was to use such a methodology based on stability of clustering solutions to select the most appropriate clustering method and number of clusters for describing dietary patterns in the NESCAV study (Nutrition, Environment and Cardiovascular Health), a large population-based cross-sectional study in the Greater Region (N = 2298). Clustering solutions were obtained with K-means, K-medians and Ward's method and a number of clusters varying from 2 to 6. Their stability was assessed with three indices: adjusted Rand index, Cramer's V and misclassification rate. The most stable solution was obtained with K-means method and a number of clusters equal to 3. The "Convenient" cluster characterized by the consumption of convenient foods was the most prevalent with 46% of the population having this dietary behaviour. In addition, a "Prudent" and a "Non-Prudent" patterns associated respectively with healthy and non-healthy dietary habits were adopted by 25% and 29% of the population. The "Convenient" and "Non-Prudent" clusters were associated with higher cardiovascular risk whereas the "Prudent" pattern was associated with a decreased cardiovascular risk. Associations with others factors showed that the choice of a specific dietary pattern is part of a wider lifestyle profile. This study is of interest for both researchers and public health professionals. From a methodological standpoint, we showed that using stability of clustering solutions could help researchers in their choices. From a public health perspective, this study showed the need of targeted health promotion campaigns describing the benefits of healthy dietary patterns.

A systematic review of economic evaluations of population-based sodium reduction interventions

PubMed Central

Hope, Silvia F.; Webster, Jacqui; Trieu, Kathy; Pillay, Arti; Ieremia, Merina; Bell, Colin; Snowdon, Wendy; Neal, Bruce; Moodie, Marj

2017-01-01

Objective To summarise evidence describing the cost-effectiveness of population-based interventions targeting sodium reduction. Methods A systematic search of published and grey literature databases and websites was conducted using specified key words. Characteristics of identified economic evaluations were recorded, and included studies were appraised for reporting quality using the Consolidated Health Economic Evaluation Reporting Standards (CHEERS) checklist. Results Twenty studies met the study inclusion criteria and received a full paper review. Fourteen studies were identified as full economic evaluations in that they included both costs and benefits associated with an intervention measured against a comparator. Most studies were modelling exercises based on scenarios for achieving salt reduction and assumed effects on health outcomes. All 14 studies concluded that their specified intervention(s) targeting reductions in population sodium consumption were cost-effective, and in the majority of cases, were cost saving. Just over half the studies (8/14) were assessed as being of ‘excellent’ reporting quality, five studies fell into the ‘very good’ quality category and one into the ‘good’ category. All of the identified evaluations were based on modelling, whereby inputs for all the key parameters including the effect size were either drawn from published datasets, existing literature or based on expert advice. Conclusion Despite a clear increase in evaluations of salt reduction programs in recent years, this review identified relatively few economic evaluations of population salt reduction interventions. None of the studies were based on actual implementation of intervention(s) and the associated collection of new empirical data. The studies universally showed that population-based salt reduction strategies are likely to be cost effective or cost saving. However, given the reliance on modelling, there is a need for the effectiveness of new interventions to be evaluated in the field using strong study designs and parallel economic evaluations. PMID:28355231

Visualizing diurnal population change in urban areas for emergency management.

PubMed

Kobayashi, Tetsuo; Medina, Richard M; Cova, Thomas J

2011-01-01

There is an increasing need for a quick, simple method to represent diurnal population change in metropolitan areas for effective emergency management and risk analysis. Many geographic studies rely on decennial U.S. Census data that assume that urban populations are static in space and time. This has obvious limitations in the context of dynamic geographic problems. The U.S. Department of Transportation publishes population data at the transportation analysis zone level in fifteen-minute increments. This level of spatial and temporal detail allows for improved dynamic population modeling. This article presents a methodology for visualizing and analyzing diurnal population change for metropolitan areas based on this readily available data. Areal interpolation within a geographic information system is used to create twenty-four (one per hour) population surfaces for the larger metropolitan area of Salt Lake County, Utah. The resulting surfaces represent diurnal population change for an average workday and are easily combined to produce an animation that illustrates population dynamics throughout the day. A case study of using the method to visualize population distributions in an emergency management context is provided using two scenarios: a chemical release and a dirty bomb in Salt Lake County. This methodology can be used to address a wide variety of problems in emergency management.

Resilience of aging populations after devastating earthquake event and its determinants - A case study of the Chi-Chi earthquake in Taiwan

NASA Astrophysics Data System (ADS)

Hung, Chih-Hsuan; Hung, Hung-Chih

2016-04-01

1.Background Major portions of urban areas in Asia are highly exposed and vulnerable to devastating earthquakes. Many studies identify ways to reduce earthquake risk by concentrating more on building resilience for the particularly vulnerable populations. By 2020, as the United Nations' warning, many Asian countries would become 'super-aged societies', such as Taiwan. However, local authorities rarely use resilience approach to frame earthquake disaster risk management and land use strategies. The empirically-based research about the resilience of aging populations has also received relatively little attention. Thus, a challenge arisen for decision-makers is how to enhance resilience of aging populations within the context of risk reduction. This study aims to improve the understanding of the resilience of aging populations and its changes over time in the aftermath of a destructive earthquake at the local level. A novel methodology is proposed to assess the resilience of aging populations and to characterize their changes of spatial distribution patterns, as well as to examine their determinants. 2.Methods and data An indicator-based assessment framework is constructed with the goal of identifying composite indicators (including before, during and after a disaster) that could serve as proxies for attributes of the resilience of aging populations. Using the recovery process of the Chi-Chi earthquake struck central Taiwan in 1999 as a case study, we applied a method combined a geographical information system (GIS)-based spatial statistics technique and cluster analysis to test the extent of which the resilience of aging populations is spatially autocorrelated throughout the central Taiwan, and to explain why clustering of resilient areas occurs in specific locations. Furthermore, to scrutinize the affecting factors of resilience, we develop an aging population resilience model (APRM) based on existing resilience theory. Using the APRM, we applied a multivariate regression analysis to identify and examine how various factors connect to the resilience of aging populations. To illustrate the proposed methodology, the study collected data on the resilience attributes, the disaster impacts and damages due to the Chi-Chi earthquake. The data were offered by the National Science and Technology Center for Disaster Reduction, Taiwan, as well as collected from the National Land Use Investigation, official census statistics and questionnaire surveys. 3.Results Integrating cluster analysis with GIS-based spatial statistical analysis, the resilience of aging populations were divided into five clusters of distribution patterns over the 10 years after the Chi-Chi earthquake. It shows that both population and elderly distributions were highly heterogeneous and spatial correlated across the study areas. We also demonstrated the 'hot spots' areas of the highly concentrated aging population across central Taiwan. Results of regression analysis disclosed the major factors that caused low resilience and changes of aging population distributions over time. These factors included the levels of seismic damage, infrastructure investments, as well as the land-use and socioeconomic attributes associated with the disaster areas. Finally, our findings provide stakeholders and policy-makers with better adaptive options to design and synthesize appropriate patchworks of planning measures for different types of resilience areas to reduce earthquake disaster risk.

Classification of stellar populations in globular clusters

NASA Astrophysics Data System (ADS)

Wang, Yue; Zhao, Gang; Li, Hai-Ning

2017-04-01

Possessing multiple stellar populations has been accepted as a common feature of globular clusters (GCs). Different stellar populations manifest themselves with different chemical features, e.g. the well-known O-Na anti-correlation. Generally, the first (primordial) population has O and Na abundances consistent with those of field stars with similar metallicity; while the second (polluted) population is identified by their Na overabundance and O deficiency. The fraction of the populations is an important constraint on the GC formation scenario. Several methods have been proposed for the classification of GC populations. Here we examine a criterion derived based on the distribution of Galactic field stars, which relies on Na abundance as a function of [Fe/H], to distinguish first and second stellar populations in GCs. By comparing the first population fractions of 17 GCs estimated by the field star criterion with those in the literature derived by methods related to individual GCs, we find that the field star criterion tends to overestimate the first population fractions. The population separation methods, which are related to an individual GC sample, are recommended because the diversity of GCs can be taken into consideration. Currently, more caution should be exercised if one wants to regard field stars as a reference for the identification of a GC population. However, further study on the connection between field stars and GCs populations is still needed.

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.

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

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

PubMed

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

2017-03-01

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

The allele combinations of three loci based on, liver, stomach cancers, hematencephalon, COPD and normal population: A preliminary study.

PubMed

Gai, Liping; Liu, Hui; Cui, Jing-Hui; Yu, Weijian; Ding, Xiao-Dong

2017-03-20

The purpose of this study was to examine the specific allele combinations of three loci connected with the liver cancers, stomach cancers, hematencephalon and patients with chronic obstructive pulmonary disease (COPD) and to explore the feasibility of the research methods. We explored different mathematical methods for statistical analyses to assess the association between the genotype and phenotype. At the same time we still analyses the statistical results of allele combinations of three loci by difference value method and ratio method. All the DNA blood samples were collected from patients with 50 liver cancers, 75 stomach cancers, 50 hematencephalon, 72 COPD and 200 normal populations. All the samples were from Chinese. Alleles from short tandem repeat (STR) loci were determined using the STR Profiler plus PCR amplification kit (15 STR loci). Previous research was based on combinations of single-locus alleles, and combinations of cross-loci (two loci) alleles. Allele combinations of three loci were obtained by computer counting and stronger genetic signal was obtained. The methods of allele combinations of three loci can help to identify the statistically significant differences of allele combinations between liver cancers, stomach cancers, patients with hematencephalon, COPD and the normal population. The probability of illness followed different rules and had apparent specificity. This method can be extended to other diseases and provide reference for early clinical diagnosis. Copyright © 2016. Published by Elsevier B.V.

Is a multivariate consensus representation of genetic relationships among populations always meaningful?

PubMed Central

Moazami-Goudarzi, K; Laloë, D

2002-01-01

To determine the relationships among closely related populations or species, two methods are commonly used in the literature: phylogenetic reconstruction or multivariate analysis. The aim of this article is to assess the reliability of multivariate analysis. We describe a method that is based on principal component analysis and Mantel correlations, using a two-step process: The first step consists of a single-marker analysis and the second step tests if each marker reveals the same typology concerning population differentiation. We conclude that if single markers are not congruent, the compromise structure is not meaningful. Our model is not based on any particular mutation process and it can be applied to most of the commonly used genetic markers. This method is also useful to determine the contribution of each marker to the typology of populations. We test whether our method is efficient with two real data sets based on microsatellite markers. Our analysis suggests that for closely related populations, it is not always possible to accept the hypothesis that an increase in the number of markers will increase the reliability of the typology analysis. PMID:12242255

Hybrid intelligent optimization methods for engineering problems

NASA Astrophysics Data System (ADS)

Pehlivanoglu, Yasin Volkan

The purpose of optimization is to obtain the best solution under certain conditions. There are numerous optimization methods because different problems need different solution methodologies; therefore, it is difficult to construct patterns. Also mathematical modeling of a natural phenomenon is almost based on differentials. Differential equations are constructed with relative increments among the factors related to yield. Therefore, the gradients of these increments are essential to search the yield space. However, the landscape of yield is not a simple one and mostly multi-modal. Another issue is differentiability. Engineering design problems are usually nonlinear and they sometimes exhibit discontinuous derivatives for the objective and constraint functions. Due to these difficulties, non-gradient-based algorithms have become more popular in recent decades. Genetic algorithms (GA) and particle swarm optimization (PSO) algorithms are popular, non-gradient based algorithms. Both are population-based search algorithms and have multiple points for initiation. A significant difference from a gradient-based method is the nature of the search methodologies. For example, randomness is essential for the search in GA or PSO. Hence, they are also called stochastic optimization methods. These algorithms are simple, robust, and have high fidelity. However, they suffer from similar defects, such as, premature convergence, less accuracy, or large computational time. The premature convergence is sometimes inevitable due to the lack of diversity. As the generations of particles or individuals in the population evolve, they may lose their diversity and become similar to each other. To overcome this issue, we studied the diversity concept in GA and PSO algorithms. Diversity is essential for a healthy search, and mutations are the basic operators to provide the necessary variety within a population. After having a close scrutiny of the diversity concept based on qualification and quantification studies, we improved new mutation strategies and operators to provide beneficial diversity within the population. We called this new approach as multi-frequency vibrational GA or PSO. They were applied to different aeronautical engineering problems in order to study the efficiency of these new approaches. These implementations were: applications to selected benchmark test functions, inverse design of two-dimensional (2D) airfoil in subsonic flow, optimization of 2D airfoil in transonic flow, path planning problems of autonomous unmanned aerial vehicle (UAV) over a 3D terrain environment, 3D radar cross section minimization problem for a 3D air vehicle, and active flow control over a 2D airfoil. As demonstrated by these test cases, we observed that new algorithms outperform the current popular algorithms. The principal role of this multi-frequency approach was to determine which individuals or particles should be mutated, when they should be mutated, and which ones should be merged into the population. The new mutation operators, when combined with a mutation strategy and an artificial intelligent method, such as, neural networks or fuzzy logic process, they provided local and global diversities during the reproduction phases of the generations. Additionally, the new approach also introduced random and controlled diversity. Due to still being population-based techniques, these methods were as robust as the plain GA or PSO algorithms. Based on the results obtained, it was concluded that the variants of the present multi-frequency vibrational GA and PSO were efficient algorithms, since they successfully avoided all local optima within relatively short optimization cycles.

Real-time PCR assays for monitoring anaerobic fungal biomass and population size in the rumen.

PubMed

Lwin, Khin Ohnmar; Hayakawa, Mika; Ban-Tokuda, Tomomi; Matsui, Hiroki

2011-04-01

The relationship between copy numbers of internal transcribed spacer 1 (ITS1) and biomass or zoospore count of anaerobic fungi was studied to develop a quantitative real-time PCR-based monitoring method for fungal biomass or population in the rumen. Nine fungal strains were used to determine the relationship between ITS1 copy number and fungal biomass. Rumen fluid from three sheep and a cow were used to determine the relationship between ITS1 copy number and fungal population. ITS1 copy number was determined by real-time PCR with a specific primer set for anaerobic fungi. Freeze-dried fungal cells were weighed for fungal biomass. Zoospore counts were determined by the roll-tube method. A positive correlation was observed between both ITS1 copy number and dry weight and ITS1 copy number and zoospore counts, suggesting that the use of ITS1 copy numbers is effective for estimating fungal biomass and population density. On the basis of ITS1 copy numbers, fluctuations in the fungal population in sheep rumen showed that although the values varied among individual animals, the fungal population tended to decrease after feeding. In the present study, a culture-independent method was established that will provide a powerful tool for understanding the ecology of anaerobic fungi in the rumen.

Clinical governance and research ethics as barriers to UK low-risk population-based health research?

PubMed Central

van Teijlingen, Edwin R; Douglas, Flora; Torrance, Nicola

2008-01-01

Background Since the Helsinki Declaration was introduced in 1964 as a code of practice for clinical research, it has generally been agreed that research governance is also needed in the field of public health and health promotion research. Recently, a range of factors led to the development of more stringent bureaucratic procedures, governing the conduct of low-risk population-based health research in the United Kingdom. Methods Our paper highlights a case study of the application process to medical research ethics committees in the United Kingdom for a study of the promotion of physical activity by health care providers. The case study presented here is an illustration of the challenges in conducting low-risk population-based health research. Results Our mixed-methods approach involved a questionnaire survey of and semi-structured interviews with health professionals (who were all healthy volunteers). Since our study does not involve the participation of either patients or the general population, one would expect the application to the relevant research ethics committees to be a formality. This proved not to be the case! Conclusion Research ethics committees could be counter-productive, rather than protecting the vulnerable in the research process, they can stifle low-risk population-based health research. Research ethics in health services research is first and foremost the responsibility of the researcher(s), and we need to learn to trust health service researchers again. The burden of current research governance regulation to address the perceived ethical problems is neither appropriate nor adequate. Senior researchers/academics need to educate and train students and junior researchers in the area of research ethics, whilst at the same time reducing pressures on them that lead to unethical research, such as commercial funding, inappropriate government interference and the pressure to publish. We propose that non-invasive low-risk population-based health studies such as face-to-face interviews with health and social care professionals or postal questionnaire studies with patients on non-sensitive topics are given a waiver or a light touch review. We suggest that this can be achieved through a two-staged ethics application process. The first stage starts with a one or two-page outline application which ethics committees can use as the basis to grant a waiver or request a full application. PMID:19040750

Internet-based data inclusion in a population-based European collaborative follow-up study of inflammatory bowel disease patients: Description of methods used and analysis of factors influencing response rates

PubMed Central

Wolters, Frank L; van Zeijl, Gilbert; Sijbrandij, Jildou; Wessels, Frederik; O’Morain, Colm; Limonard, Charles; Russel, Maurice G; Stockbrügger, Reinhold W

2005-01-01

AIM: To describe an Internet-based data acquisition facility for a European 10-year clinical follow-up study project of a population-based cohort of inflammatory bowel disease (IBD) patients and to investigate the influence of demographic and disease related patient characteristics on response rates. METHODS: Thirteen years ago, the European Collaborative study group of IBD (EC-IBD) initiated a population-based prospective inception cohort of 2 201 uniformly diagnosed IBD patients within 20 well-described geographical areas in 11 European countries and Israel. For the 10-year follow-up of this cohort, an electronic patient questionnaire (ePQ) and electronic physician per patient follow-up form (ePpPFU) were designed as two separate data collecting instruments and made available through an Internet-based website. Independent demographic and clinical determinants of ePQ participation were analyzed using multivariate logistic regression. RESULTS: In 958 (316 CD and 642 UC) out of a total number of 1 505 (64%) available IBD patients, originating from 13 participating centers from nine different countries, both ePQ and ePpPFU were completed. Patients older than 40 years at ePQ completion (OR: 1.53 (95%CI: 1.14-2.05)) and those with active disease during the 3 mo previous to ePQ completion (OR: 3.32 (95%CI: 1.57-7.03)) were significantly more likely to respond. CONCLUSION: An Internet-based data acquisition tool appeared successful in sustaining a unique Western-European and Israelian multi-center 10-year clinical follow-up study project in patients afflicted with IBD. PMID:16437663

The Definition of Insulin Resistance Using HOMA-IR for Americans of Mexican Descent Using Machine Learning

PubMed Central

Qu, Hui-Qi; Li, Quan; Rentfro, Anne R.; Fisher-Hoch, Susan P.; McCormick, Joseph B.

2011-01-01

Objective The lack of standardized reference range for the homeostasis model assessment-estimated insulin resistance (HOMA-IR) index has limited its clinical application. This study defines the reference range of HOMA-IR index in an adult Hispanic population based with machine learning methods. Methods This study investigated a Hispanic population of 1854 adults, randomly selected on the basis of 2000 Census tract data in the city of Brownsville, Cameron County. Machine learning methods, support vector machine (SVM) and Bayesian Logistic Regression (BLR), were used to automatically identify measureable variables using standardized values that correlate with HOMA-IR; K-means clustering was then used to classify the individuals by insulin resistance. Results Our study showed that the best cutoff of HOMA-IR for identifying those with insulin resistance is 3.80. There are 39.1% individuals in this Hispanic population with HOMA-IR>3.80. Conclusions Our results are dramatically different using the popular clinical cutoff of 2.60. The high sensitivity and specificity of HOMA-IR>3.80 for insulin resistance provide a critical fundamental for our further efforts to improve the public health of this Hispanic population. PMID:21695082

Childhood Predictors of Male Criminality: A Prospective Population-Based Follow-up Study from Age 8 to Late Adolescence

ERIC Educational Resources Information Center

Sourander, Andre; Elonheimo, Henrik; Niemela, Solja; Nuutila, Ari-Matti; Helenius, Hans; Sillanmaki, Lauri; Piha, Jorma; Tamminen, Tuula; Kumpulainen, Kirsti; Moilanen, Irma; Almqvist, Frederik

2006-01-01

Objective: To study childhood predictors for late adolescence criminality. Method: The follow-up sample included 2,713 Finnish boys born in 1981. Information about the 8-year-old boys' problem behavior was obtained from parents, teachers, and the children themselves. The follow-up information about criminal offenses was based on the national…

The Role of Perceived Control in Explaining Depressive Symptoms Associated with Driving Cessation in a Longitudinal Study

ERIC Educational Resources Information Center

Windsor, Timothy D.; Anstey, Kaarin J.; Butterworth, Peter; Luszcz, Mary A.; Andrews, Gary R.

2007-01-01

Purpose: The purpose of this article was to investigate the role of control beliefs in mediating the relationship between driving cessation and change in depressive symptoms in a population-based sample of older adults. Design and Methods: We report results from a prospective, community-based cohort study that included two waves of data collected…

Improved CT-based estimate of pulmonary gas trapping accounting for scanner and lung-volume variations in a multicenter asthmatic study.

PubMed

Choi, Sanghun; Hoffman, Eric A; Wenzel, Sally E; Castro, Mario; Lin, Ching-Long

2014-09-15

Lung air trapping is estimated via quantitative computed tomography (CT) using density threshold-based measures on an expiration scan. However, the effects of scanner differences and imaging protocol adherence on quantitative assessment are known to be problematic. This study investigates the effects of protocol differences, such as using different CT scanners and breath-hold coaches in a multicenter asthmatic study, and proposes new methods that can adjust intersite and intersubject variations. CT images of 50 healthy subjects and 42 nonsevere and 52 severe asthmatics at total lung capacity (TLC) and functional residual capacity (FRC) were acquired using three different scanners and two different coaching methods at three institutions. A fraction threshold-based approach based on the corrected Hounsfield unit of air with tracheal density was applied to quantify air trapping at FRC. The new air-trapping method was enhanced by adding a lung-shaped metric at TLC and the lobar ratio of air-volume change between TLC and FRC. The fraction-based air-trapping method is able to collapse air-trapping data of respective populations into distinct regression lines. Relative to a constant value-based clustering scheme, the slope-based clustering scheme shows the improved performance and reduced misclassification rate of healthy subjects. Furthermore, both lung shape and air-volume change are found to be discriminant variables for differentiating among three populations of healthy subjects and nonsevere and severe asthmatics. In conjunction with the lung shape and air-volume change, the fraction-based measure of air trapping enables differentiation of severe asthmatics from nonsevere asthmatics and nonsevere asthmatics from healthy subjects, critical for the development and evaluation of new therapeutic interventions. Copyright © 2014 the American Physiological Society.

Improved CT-based estimate of pulmonary gas trapping accounting for scanner and lung-volume variations in a multicenter asthmatic study

PubMed Central

Choi, Sanghun; Hoffman, Eric A.; Wenzel, Sally E.; Castro, Mario

2014-01-01

Lung air trapping is estimated via quantitative computed tomography (CT) using density threshold-based measures on an expiration scan. However, the effects of scanner differences and imaging protocol adherence on quantitative assessment are known to be problematic. This study investigates the effects of protocol differences, such as using different CT scanners and breath-hold coaches in a multicenter asthmatic study, and proposes new methods that can adjust intersite and intersubject variations. CT images of 50 healthy subjects and 42 nonsevere and 52 severe asthmatics at total lung capacity (TLC) and functional residual capacity (FRC) were acquired using three different scanners and two different coaching methods at three institutions. A fraction threshold-based approach based on the corrected Hounsfield unit of air with tracheal density was applied to quantify air trapping at FRC. The new air-trapping method was enhanced by adding a lung-shaped metric at TLC and the lobar ratio of air-volume change between TLC and FRC. The fraction-based air-trapping method is able to collapse air-trapping data of respective populations into distinct regression lines. Relative to a constant value-based clustering scheme, the slope-based clustering scheme shows the improved performance and reduced misclassification rate of healthy subjects. Furthermore, both lung shape and air-volume change are found to be discriminant variables for differentiating among three populations of healthy subjects and nonsevere and severe asthmatics. In conjunction with the lung shape and air-volume change, the fraction-based measure of air trapping enables differentiation of severe asthmatics from nonsevere asthmatics and nonsevere asthmatics from healthy subjects, critical for the development and evaluation of new therapeutic interventions. PMID:25103972

Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogies.

PubMed

Palacios, Julia A; Minin, Vladimir N

2013-03-01

Changes in population size influence genetic diversity of the population and, as a result, leave a signature of these changes in individual genomes in the population. We are interested in the inverse problem of reconstructing past population dynamics from genomic data. We start with a standard framework based on the coalescent, a stochastic process that generates genealogies connecting randomly sampled individuals from the population of interest. These genealogies serve as a glue between the population demographic history and genomic sequences. It turns out that only the times of genealogical lineage coalescences contain information about population size dynamics. Viewing these coalescent times as a point process, estimating population size trajectories is equivalent to estimating a conditional intensity of this point process. Therefore, our inverse problem is similar to estimating an inhomogeneous Poisson process intensity function. We demonstrate how recent advances in Gaussian process-based nonparametric inference for Poisson processes can be extended to Bayesian nonparametric estimation of population size dynamics under the coalescent. We compare our Gaussian process (GP) approach to one of the state-of-the-art Gaussian Markov random field (GMRF) methods for estimating population trajectories. Using simulated data, we demonstrate that our method has better accuracy and precision. Next, we analyze two genealogies reconstructed from real sequences of hepatitis C and human Influenza A viruses. In both cases, we recover more believed aspects of the viral demographic histories than the GMRF approach. We also find that our GP method produces more reasonable uncertainty estimates than the GMRF method. Copyright © 2013, The International Biometric Society.

3-dimensional examination of the adult mouse subventricular zone reveals lineage-specific microdomains.

PubMed

Azim, Kasum; Fiorelli, Roberto; Zweifel, Stefan; Hurtado-Chong, Anahi; Yoshikawa, Kazuaki; Slomianka, Lutz; Raineteau, Olivier

2012-01-01

Recent studies suggest that the subventricular zone (SVZ) of the lateral ventricle is populated by heterogeneous populations of stem and progenitor cells that, depending on their exact location, are biased to acquire specific neuronal fates. This newly described heterogeneity of SVZ stem and progenitor cells underlines the necessity to develop methods for the accurate quantification of SVZ stem and progenitor subpopulations. In this study, we provide 3-dimensional topographical maps of slow cycling "stem" cells and progenitors based on their unique cell cycle properties. These maps revealed that both cell populations are present throughout the lateral ventricle wall as well as in discrete regions of the dorsal wall. Immunodetection of transcription factors expressed in defined progenitor populations further reveals that divergent lineages have clear regional enrichments in the rostro-caudal as well as in the dorso-ventral span of the lateral ventricle. Thus, progenitors expressing Tbr2 and Dlx2 were confined to dorsal and dorso-lateral regions of the lateral ventricle, respectively, while Mash1+ progenitors were more homogeneously distributed. All cell populations were enriched in the rostral-most region of the lateral ventricle. This diversity and uneven distribution greatly impede the accurate quantification of SVZ progenitor populations. This is illustrated by measuring the coefficient of error of estimates obtained by using increasing section sampling interval. Based on our empirical data, we provide such estimates for all progenitor populations investigated in this study. These can be used in future studies as guidelines to judge if the precision obtained with a sampling scheme is sufficient to detect statistically significant differences between experimental groups if a biological effect is present. Altogether, our study underlines the need to consider the SVZ of the lateral ventricle as a complex 3D structure and define methods to accurately assess neural stem cells or progenitor diversity and population sizes in physiological or experimental paradigms.

The use of rapid review methods in health technology assessments: 3 case studies.

PubMed

Kaltenthaler, Eva; Cooper, Katy; Pandor, Abdullah; Martyn-St James, Marrissa; Chatters, Robin; Wong, Ruth

2016-08-26

Rapid reviews are of increasing importance within health technology assessment due to time and resource constraints. There are many rapid review methods available although there is little guidance as to the most suitable methods. We present three case studies employing differing methods to suit the evidence base for each review and outline some issues to consider when selecting an appropriate method. Three recently completed systematic review short reports produced for the UK National Institute for Health Research were examined. Different approaches to rapid review methods were used in the three reports which were undertaken to inform the commissioning of services within the NHS and to inform future trial design. We describe the methods used, the reasoning behind the choice of methods and explore the strengths and weaknesses of each method. Rapid review methods were chosen to meet the needs of the review and each review had distinctly different challenges such as heterogeneity in terms of populations, interventions, comparators and outcome measures (PICO) and/or large numbers of relevant trials. All reviews included at least 10 randomised controlled trials (RCTs), each with numerous included outcomes. For the first case study (sexual health interventions), very diverse studies in terms of PICO were included. P-values and summary information only were presented due to substantial heterogeneity between studies and outcomes measured. For the second case study (premature ejaculation treatments), there were over 100 RCTs but also several existing systematic reviews. Data for meta-analyses were extracted directly from existing systematic reviews with new RCT data added where available. For the final case study (cannabis cessation therapies), studies included a wide range of interventions and considerable variation in study populations and outcomes. A brief summary of the key findings for each study was presented and narrative synthesis used to summarise results for each pair of interventions compared. Rapid review methods need to be chosen to meet both the nature of the evidence base of a review and the challenges presented by the included studies. Appropriate methods should be chosen after an assessment of the evidence base.

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.

Child mental health differences amongst ethnic groups in Britain: a systematic review

PubMed Central

Goodman, Anna; Patel, Vikram; Leon, David A

2008-01-01

Background Inter-ethnic differences have been reported for many mental health outcomes in the UK, but no systematic review on child mental health has been published. The aim of this review is to compare the population-based prevalence of child mental disorders between ethnic groups in Britain, and relate these findings to ethnic differences in mental health service use. Methods A systematic search of bibliographic databases for population-based and clinic-based studies of children aged 0–19, including all ethnic groups and the main child mental disorders. We synthesised findings by comparing each minority group to the White British study sample. Results 31 population-based and 18 clinic-based studies met the inclusion criteria. Children in the main minority groups have similar or better mental health than White British children for common disorders, but may have higher rates for some less common conditions. The causes of these differences are unclear. There may be unmet need for services among Pakistani and Bangladeshi children. Conclusion Inter-ethnic differences exist but are largely unexplained. Future studies should address the challenges of cross-cultural psychiatry and investigate reasons for inter-ethnic differences. PMID:18655701

A novel accelerometer-based method to describe day-to-day exposure to potentially osteogenic vertical impacts in older adults: findings from a multi-cohort study.

PubMed

Hannam, K; Deere, K C; Hartley, A; Clark, E M; Coulson, J; Ireland, A; Moss, C; Edwards, M H; Dennison, E; Gaysin, T; Cooper, R; Wong, A; McPhee, J S; Cooper, C; Kuh, D; Tobias, J H

2017-03-01

This observational study assessed vertical impacts experienced in older adults as part of their day-to-day physical activity using accelerometry and questionnaire data. Population-based older adults experienced very limited high-impact activity. The accelerometry method utilised appeared to be valid based on comparisons between different cohorts and with self-reported activity. We aimed to validate a novel method for evaluating day-to-day higher impact weight-bearing physical activity (PA) in older adults, thought to be important in protecting against osteoporosis, by comparing results between four cohorts varying in age and activity levels, and with self-reported PA levels. Participants were from three population-based cohorts, MRC National Survey of Health and Development (NSHD), Hertfordshire Cohort Study (HCS) and Cohort for Skeletal Health in Bristol and Avon (COSHIBA), and the Master Athlete Cohort (MAC). Y-axis peaks (reflecting the vertical when an individual is upright) from a triaxial accelerometer (sampling frequency 50 Hz, range 0-16 g) worn at the waist for 7 days were classified as low (0.5-1.0 g), medium (1.0-1.5 g) or higher (≥1.5 g) impacts. There were a median of 90, 41 and 39 higher impacts/week in NSHD (age 69.5), COSHIBA (age 76.8) and HCS (age 78.5) participants, respectively (total n = 1512). In contrast, MAC participants (age 68.5) had a median of 14,322 higher impacts/week. In the three population cohorts combined, based on comparison of beta coefficients, moderate-high-impact activities as assessed by PA questionnaire were suggestive of stronger association with higher impacts from accelerometers (0.25 [0.17, 0.34]), compared with medium (0.18 [0.09, 0.27]) and low impacts (0.13 [0.07,0.19]) (beta coefficient, with 95 % CI). Likewise in MAC, reported moderate-high-impact activities showed a stronger association with higher impacts (0.26 [0.14, 0.37]), compared with medium (0.14 [0.05, 0.22]) and low impacts (0.03 [-0.02, 0.08]). Our new accelerometer method appears to provide valid measures of higher vertical impacts in older adults. Results obtained from the three population-based cohorts indicate that older adults generally experience very limited higher impact weight-bearing PA.

"The solution needs to be complex." Obese adults' attitudes about the effectiveness of individual and population based interventions for obesity

PubMed Central

2010-01-01

Background Previous studies of public perceptions of obesity interventions have been quantitative and based on general population surveys. This study aims to explore the opinions and attitudes of obese individuals towards population and individual interventions for obesity in Australia. Methods Qualitative methods using in-depth semi-structured telephone interviews with a community sample of obese adults (Body Mass Index ≥30). Theoretical, purposive and strategic recruitment techniques were used to ensure a broad sample of obese individuals with different types of experiences with their obesity. Participants were asked about their attitudes towards three population based interventions (regulation, media campaigns, and public health initiatives) and three individual interventions (tailored fitness programs, commercial dieting, and gastric banding surgery), and the effectiveness of these interventions. Results One hundred and forty two individuals (19-75 years) were interviewed. Participants strongly supported non-commercial interventions that were focused on encouraging individuals to make healthy lifestyle changes (regulation, physical activity programs, and public health initiatives). There was less support for interventions perceived to be invasive or high risk (gastric band surgery), stigmatising (media campaigns), or commercially motivated and promoting weight loss techniques (commercial diets and gastric banding surgery). Conclusion Obese adults support non-commercial, non-stigmatising interventions which are designed to improve lifestyles, rather than promote weight loss. PMID:20633250

Dengue fever spreading based on probabilistic cellular automata with two lattices

NASA Astrophysics Data System (ADS)

Pereira, F. M. M.; Schimit, P. H. T.

2018-06-01

Modeling and simulation of mosquito-borne diseases have gained attention due to a growing incidence in tropical countries in the past few years. Here, we study the dengue spreading in a population modeled by cellular automata, where there are two lattices to model the human-mosquitointeraction: one lattice for human individuals, and one lattice for mosquitoes in order to enable different dynamics in populations. The disease considered is the dengue fever with one, two or three different serotypes coexisting in population. Although many regions exhibit the incidence of only one serotype, here we set a complete framework to also study the occurrence of two and three serotypes at the same time in a population. Furthermore, the flexibility of the model allows its use to other mosquito-borne diseases, like chikungunya, yellow fever and malaria. An approximation of the cellular automata is proposed in terms of ordinary differential equations; the spreading of mosquitoes is studied and the influence of some model parameters are analyzed with numerical simulations. Finally, a method to combat dengue spreading is simulated based on a reduction of mosquito birth and mosquito bites in population.

Rare variant association analysis in case-parents studies by allowing for missing parental genotypes.

PubMed

Li, Yumei; Xiang, Yang; Xu, Chao; Shen, Hui; Deng, Hongwen

2018-01-15

The development of next-generation sequencing technologies has facilitated the identification of rare variants. Family-based design is commonly used to effectively control for population admixture and substructure, which is more prominent for rare variants. Case-parents studies, as typical strategies in family-based design, are widely used in rare variant-disease association analysis. Current methods in case-parents studies are based on complete case-parents data; however, parental genotypes may be missing in case-parents trios, and removing these data may lead to a loss in statistical power. The present study focuses on testing for rare variant-disease association in case-parents study by allowing for missing parental genotypes. In this report, we extended the collapsing method for rare variant association analysis in case-parents studies to allow for missing parental genotypes, and investigated the performance of two methods by using the difference of genotypes between affected offspring and their corresponding "complements" in case-parent trios and TDT framework. Using simulations, we showed that, compared with the methods just only using complete case-parents data, the proposed strategy allowing for missing parental genotypes, or even adding unrelated affected individuals, can greatly improve the statistical power and meanwhile is not affected by population stratification. We conclude that adding case-parents data with missing parental genotypes to complete case-parents data set can greatly improve the power of our strategy for rare variant-disease association.

The priority group index: a proposed new method incorporating high risk and population burden to identify target populations for public health interventions.

PubMed

Zhang, Bo; Cohen, Joanna E; OʼConnor, Shawn

2014-01-01

Selection of priority groups is important for health interventions. However, no quantitative method has been developed. To develop a quantitative method to support the process of selecting priority groups for public health interventions based on both high risk and population health burden. Secondary data analysis of the 2010 Canadian Community Health Survey. Canadian population. Survey respondents. We identified priority groups for 3 diseases: heart disease, stroke, and chronic lower respiratory diseases. Three measures--prevalence, population counts, and adjusted odds ratios (OR)--were calculated for subpopulations (sociodemographic characteristics and other risk factors). A Priority Group Index (PGI) was calculated by summing the rank scores of these 3 measures. Of the 30 priority groups identified by the PGI (10 for each of the 3 disease outcomes), 7 were identified on the basis of high prevalence only, 5 based on population count only, 3 based on high OR only, and the remainder based on combinations of these. The identified priority groups were all in line with the literature as risk factors for the 3 diseases, such as elderly people for heart disease and stroke and those with low income for chronic lower respiratory diseases. The PGI was thus able to balance both high risk and population burden approaches in selecting priority groups, and thus it would address health inequities as well as disease burden in the overall population. The PGI is a quantitative method to select priority groups for public health interventions; it has the potential to enhance the effective use of limited public resources.

Increasing incidence of pyogenic spondylodiscitis: a 14-year population-based study.

PubMed

Kehrer, Michala; Pedersen, Court; Jensen, Thøger G; Lassen, Annmarie T

2014-04-01

Smaller studies indicate that the incidence of pyogenic spondylodiscitis is increasing, possible related to a growing elderly population. Data supporting this is sparse, and we therefore studied patient characteristics and changes in spondylodiscitis incidence 1995-2008. In a population-based study we identified all patients aged ≥18 years treated for pyogenic spondylodiscitis in Funen County, Denmark (population 483 123). Annual incidences were determined. Demographics, symptoms and diagnostic methods were recorded. We found 192 cases: median age 66.6 years; 57.3% men; 76.6% culture positive cases. Staphylococcus aureus was the most common pathogen (55.1%). During 1995-2008 the overall incidence, incidence of culture negative cases, and incidence of cases due to S. aureus increased 2.2-5.8, 0.3-1.8, and 1.6-2.5 cases per 100 000 person years, respectively. The elderly had the highest incidence compared to those aged ≤70 years (rate ratio for men 5.9 (95% CI: 4.2-8.5) and for women 3.5 (95% CI: 2.3-5.3)). During 1995-2008 the overall incidence of S. aureus and culture negative cases of spondylodiscitis increased and remained highest among the elderly. Whether the increase is real or is a result of improved diagnostic methods and workup remains unknown. Copyright © 2013 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Using CBPR Methods in College Health Research: Exploring Excessive Alcohol Consumption

ERIC Educational Resources Information Center

Bulmer, Sandra M.; Barton, Barbara A.; Liefeld, Julie; Montauti, Sara; Santos, Stephanie; Richard, Melissa; Hnath, Laura; Pelletier, Kara; Lalanne, Jude

2016-01-01

Community-based participatory research (CBPR) is a collaborative methodology that uniquely involves stakeholders in all stages of the research process. CBPR has been widely utilized in the field of public health, but not widely employed with college populations. This study utilized CBPR methods within a college community to gain insight into…

Accuracy of Predicted Genomic Breeding Values in Purebred and Crossbred Pigs.

PubMed

Hidalgo, André M; Bastiaansen, John W M; Lopes, Marcos S; Harlizius, Barbara; Groenen, Martien A M; de Koning, Dirk-Jan

2015-05-26

Genomic selection has been widely implemented in dairy cattle breeding when the aim is to improve performance of purebred animals. In pigs, however, the final product is a crossbred animal. This may affect the efficiency of methods that are currently implemented for dairy cattle. Therefore, the objective of this study was to determine the accuracy of predicted breeding values in crossbred pigs using purebred genomic and phenotypic data. A second objective was to compare the predictive ability of SNPs when training is done in either single or multiple populations for four traits: age at first insemination (AFI); total number of piglets born (TNB); litter birth weight (LBW); and litter variation (LVR). We performed marker-based and pedigree-based predictions. Within-population predictions for the four traits ranged from 0.21 to 0.72. Multi-population prediction yielded accuracies ranging from 0.18 to 0.67. Predictions across purebred populations as well as predicting genetic merit of crossbreds from their purebred parental lines for AFI performed poorly (not significantly different from zero). In contrast, accuracies of across-population predictions and accuracies of purebred to crossbred predictions for LBW and LVR ranged from 0.08 to 0.31 and 0.11 to 0.31, respectively. Accuracy for TNB was zero for across-population prediction, whereas for purebred to crossbred prediction it ranged from 0.08 to 0.22. In general, marker-based outperformed pedigree-based prediction across populations and traits. However, in some cases pedigree-based prediction performed similarly or outperformed marker-based prediction. There was predictive ability when purebred populations were used to predict crossbred genetic merit using an additive model in the populations studied. AFI was the only exception, indicating that predictive ability depends largely on the genetic correlation between PB and CB performance, which was 0.31 for AFI. Multi-population prediction was no better than within-population prediction for the purebred validation set. Accuracy of prediction was very trait-dependent. Copyright © 2015 Hidalgo et al.

NPP-VIIRS DNB-based reallocating subpopulations to mercury in Urumqi city cluster, central Asia

NASA Astrophysics Data System (ADS)

Zhou, X.; Feng, X. B.; Dai, W.; Li, P.; Ju, C. Y.; Bao, Z. D.; Han, Y. L.

2017-02-01

Accurate and update assignment of population-related environmental matters onto fine grid cells in oasis cities of arid areas remains challenging. We present the approach based on Suomi National Polar-orbiting Partnership (S-NPP) -Visible Infrared Imaging Radiometer Suite (VIIRS) Day/Night Band (DNB) to reallocate population onto a regular finer surface. The number of potential population to the mercury were reallocated onto 0.1x0.1 km reference grid in Urumqi city cluster of China’s Xinjiang, central Asia. The result of Monte Carlo modelling indicated that the range of 0.5 to 2.4 million people was reliable. The study highlights that the NPP-VIIRS DNB-based multi-layered, dasymetric, spatial method enhances our abilities to remotely estimate the distribution and size of target population at the street-level scale and has the potential to transform control strategies for epidemiology, public policy and other socioeconomic fields.

PCR-based methods for the detection of L1014 kdr mutation in Anopheles culicifacies sensu lato

PubMed Central

Singh, Om P; Bali, Prerna; Hemingway, Janet; Subbarao, Sarala K; Dash, Aditya P; Adak, Tridibes

2009-01-01

Background Anopheles culicifacies s.l., a major malaria vector in India, has developed widespread resistance to DDT and is becoming resistant to pyrethroids–the only insecticide class recommended for the impregnation of bed nets. Knock-down resistance due to a point mutation in the voltage gated sodium channel at L1014 residue (kdr) is a common mechanism of resistance to DDT and pyrethroids. The selection of this resistance may pose a serious threat to the success of the pyrethroid-impregnated bed net programme. This study reports the presence of kdr mutation (L1014F) in a field population of An. culicifacies s.l. and three new PCR-based methods for kdr genotyping. Methods The IIS4-IIS5 linker to IIS6 segments of the para type voltage gated sodium channel gene of DDT and pyrethroid resistant An. culicifacies s.l. population from the Surat district of India was sequenced. This revealed the presence of an A-to-T substitution at position 1014 leading to a leucine-phenylalanine mutation (L1014F) in a few individuals. Three molecular methods viz. Allele Specific PCR (AS-PCR), an Amplification Refractory Mutation System (ARMS) and Primer Introduced Restriction Analysis-PCR (PIRA-PCR) were developed and tested for kdr genotyping. The specificity of the three assays was validated following DNA sequencing of the samples genotyped. Results The genotyping of this An. culicifacies s.l. population by the three PCR based assays provided consistent result and were in agreement with DNA sequencing result. A low frequency of the kdr allele mostly in heterozygous condition was observed in the resistant population. Frequencies of the different genotypes were in Hardy-Weinberg equilibrium. Conclusion The Leu-Phe mutation, which generates the kdr phenotype in many insects, was detected in a pyrethroid and DDT resistant An. culicifacies s.l. population. Three PCR-based methods were developed for kdr genotyping. All the three assays were specific. The ARMS method was refractory to non-specific amplification in non-stringent amplification conditions. The PIRA-PCR assay is able to detect both the codons for the phenylalanine mutation at kdr locus, i.e., TTT and TTC, in a single assay, although the latter codon was not found in the population genotyped. PMID:19594947

Performance comparison of first-order conditional estimation with interaction and Bayesian estimation methods for estimating the population parameters and its distribution from data sets with a low number of subjects.

PubMed

Pradhan, Sudeep; Song, Byungjeong; Lee, Jaeyeon; Chae, Jung-Woo; Kim, Kyung Im; Back, Hyun-Moon; Han, Nayoung; Kwon, Kwang-Il; Yun, Hwi-Yeol

2017-12-01

Exploratory preclinical, as well as clinical trials, may involve a small number of patients, making it difficult to calculate and analyze the pharmacokinetic (PK) parameters, especially if the PK parameters show very high inter-individual variability (IIV). In this study, the performance of a classical first-order conditional estimation with interaction (FOCE-I) and expectation maximization (EM)-based Markov chain Monte Carlo Bayesian (BAYES) estimation methods were compared for estimating the population parameters and its distribution from data sets having a low number of subjects. In this study, 100 data sets were simulated with eight sampling points for each subject and with six different levels of IIV (5%, 10%, 20%, 30%, 50%, and 80%) in their PK parameter distribution. A stochastic simulation and estimation (SSE) study was performed to simultaneously simulate data sets and estimate the parameters using four different methods: FOCE-I only, BAYES(C) (FOCE-I and BAYES composite method), BAYES(F) (BAYES with all true initial parameters and fixed ω 2 ), and BAYES only. Relative root mean squared error (rRMSE) and relative estimation error (REE) were used to analyze the differences between true and estimated values. A case study was performed with a clinical data of theophylline available in NONMEM distribution media. NONMEM software assisted by Pirana, PsN, and Xpose was used to estimate population PK parameters, and R program was used to analyze and plot the results. The rRMSE and REE values of all parameter (fixed effect and random effect) estimates showed that all four methods performed equally at the lower IIV levels, while the FOCE-I method performed better than other EM-based methods at higher IIV levels (greater than 30%). In general, estimates of random-effect parameters showed significant bias and imprecision, irrespective of the estimation method used and the level of IIV. Similar performance of the estimation methods was observed with theophylline dataset. The classical FOCE-I method appeared to estimate the PK parameters more reliably than the BAYES method when using a simple model and data containing only a few subjects. EM-based estimation methods can be considered for adapting to the specific needs of a modeling project at later steps of modeling.

Demirjian's method in the estimation of age: A study on human third molars

PubMed Central

Lewis, Amitha J.; Boaz, Karen; Nagesh, K. R; Srikant, N; Gupta, Neha; Nandita, K. P; Manaktala, Nidhi

2015-01-01

Aim: The primary aim of the following study is to estimate the chronological age based on the stages of third molar development following the eight stages (A to H) method of Demirjian et al. (along with two modifications-Orhan) and secondary aim is to compare third molar development with sex and age. Materials and Methods: The sample consisted of 115 orthopantomograms from South Indian subjects with known chronological age and gender. Multiple regression analysis was performed with chronological age as the dependable variable and third molar root development as independent variable. All the statistical analysis was performed using the SPSS 11.0 package (IBM ® Corporation). Results: Statistically no significant differences were found in third molar development between males and females. Depending on the available number of wisdom teeth in an individual, R2 varied for males from 0.21 to 0.48 and for females from 0.16 to 0.38. New equations were derived for estimating the chronological age. Conclusion: The chronological age of a South Indian individual between 14 and 22 years may be estimated based on the regression formulae. However, additional studies with a larger study population must be conducted to meet the need for population-based information on third molar development. PMID:26005306

Genetic and phenotypic variability of iris color in Buenos Aires population

PubMed Central

Hohl, Diana María; Bezus, Brenda; Ratowiecki, Julia; Catanesi, Cecilia Inés

2018-01-01

Abstract The aim of this work was to describe the phenotypic and genotypic variability related to iris color for the population of Buenos Aires province (Argentina), and to assess the usefulness of current methods of analysis for this country. We studied five Single Nucleotide Polymorphisms (SNPs) included in the IrisPlex kit, in 118 individuals, and we quantified eye color with Digital Iris Analysis Tool. The markers fit Hardy-Weinberg equilibrium for the whole sample, but not for rs12913832 within the group of brown eyes (LR=8.429; p=0.004). We found a remarkable association of HERC2 rs12913832 GG with blue color (p < 0.01) but the other markers did not show any association with iris color. The results for the Buenos Aires population differ from those of other populations of the world for these polymorphisms (p < 0,01). The differences we found might respond to the admixed ethnic composition of Argentina; therefore, methods of analysis used in European populations should be carefully applied when studying the population of Argentina. These findings reaffirm the importance of this investigation in the Argentinian population for people identification based on iris color. PMID:29658972

Novel Linkage of Individual and Geographic Data to Study Firearm Violence

PubMed Central

Branas, Charles C.; Culhane, Dennis; Richmond, Therese S.; Wiebe, Douglas J.

2010-01-01

Firearm violence is the end result of a causative web of individual-level and geographic risk factors. Few, if any, studies of firearm violence have been able to simultaneously determine the population-based relative risks that individuals experience as a result of what they were doing at a specific point in time and where they were, geographically, at a specific point in time. This paper describes the linkage of individual and geographic data that was undertaken as part of a population-based case-control study of firearm violence in Philadelphia. New methods and applications of these linked data relevant to researchers and policymakers interested in firearm violence are also discussed. PMID:20617158

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 Ontario-specific data were unavailable, data from the United States were used. Conclusions PSA screening is associated with significant costs to the health care system when the cost of the PSA test itself is considered in addition to the costs of diagnosis, staging, and treatment of screen-detected PCs. PMID:26366237

Prevalence of self-medication in the adult population of Brazil: a systematic review

PubMed Central

Domingues, Paulo Henrique Faria; Galvão, Taís Freire; de Andrade, Keitty Regina Cordeiro; de Sá, Pedro Terra Teles; Silva, Marcus Tolentino; Pereira, Mauricio Gomes

2015-01-01

OBJECTIVE To evaluate the prevalence of self-medication in Brazil’s adult population. METHODS Systematic review of cross-sectional population-based studies. The following databases were used: Medline, Embase, Scopus, ISI, CINAHL, Cochrane Library, CRD, Lilacs, SciELO, the Banco de teses brasileiras (Brazilian theses database) (Capes) and files from the Portal Domínio Público (Brazilian Public Domain). In addition, the reference lists from relevant studies were examined to identify potentially eligible articles. There were no applied restrictions in terms of the publication date, language or publication status. Data related to publication, population, methods and prevalence of self-medication were extracted by three independent researchers. Methodological quality was assessed following eight criteria related to sampling, measurement and presentation of results. The prevalences were measured from participants who used at least one medication during the recall period of the studies. RESULTS The literature screening identified 2,778 records, from which 12 were included for analysis. Most studies were conducted in the Southeastern region of Brazil, after 2000 and with a 15-day recall period. Only five studies achieved high methodological quality, of which one study had a 7-day recall period, in which the prevalence of self-medication was 22.9% (95%CI 14.6;33.9). The prevalence of self-medication in three studies of high methodological quality with a 15-day recall period was 35.0% (95%CI 29.0;40.0, I2 = 83.9%) in the adult Brazilian population. CONCLUSIONS Despite differences in the methodologies of the included studies, the results of this systematic review indicate that a significant proportion of the adult Brazilian population self-medicates. It is suggested that future research projects that assess self-medication in Brazil standardize their methods. PMID:26083944

The efficacy of respondent-driven sampling for the health assessment of minority populations.

PubMed

Badowski, Grazyna; Somera, Lilnabeth P; Simsiman, Brayan; Lee, Hye-Ryeon; Cassel, Kevin; Yamanaka, Alisha; Ren, JunHao

2017-10-01

Respondent driven sampling (RDS) is a relatively new network sampling technique typically employed for hard-to-reach populations. Like snowball sampling, initial respondents or "seeds" recruit additional respondents from their network of friends. Under certain assumptions, the method promises to produce a sample independent from the biases that may have been introduced by the non-random choice of "seeds." We conducted a survey on health communication in Guam's general population using the RDS method, the first survey that has utilized this methodology in Guam. It was conducted in hopes of identifying a cost-efficient non-probability sampling strategy that could generate reasonable population estimates for both minority and general populations. RDS data was collected in Guam in 2013 (n=511) and population estimates were compared with 2012 BRFSS data (n=2031) and the 2010 census data. The estimates were calculated using the unweighted RDS sample and the weighted sample using RDS inference methods and compared with known population characteristics. The sample size was reached in 23days, providing evidence that the RDS method is a viable, cost-effective data collection method, which can provide reasonable population estimates. However, the results also suggest that the RDS inference methods used to reduce bias, based on self-reported estimates of network sizes, may not always work. Caution is needed when interpreting RDS study findings. For a more diverse sample, data collection should not be conducted in just one location. Fewer questions about network estimates should be asked, and more careful consideration should be given to the kind of incentives offered to participants. Copyright © 2017. Published by Elsevier Ltd.

From blackbirds to black holes: Investigating capture-recapture methods for time domain astronomy

NASA Astrophysics Data System (ADS)

Laycock, Silas G. T.

2017-07-01

In time domain astronomy, recurrent transients present a special problem: how to infer total populations from limited observations. Monitoring observations may give a biassed view of the underlying population due to limitations on observing time, visibility and instrumental sensitivity. A similar problem exists in the life sciences, where animal populations (such as migratory birds) or disease prevalence, must be estimated from sparse and incomplete data. The class of methods termed Capture-Recapture is used to reconstruct population estimates from time-series records of encounters with the study population. This paper investigates the performance of Capture-Recapture methods in astronomy via a series of numerical simulations. The Blackbirds code simulates monitoring of populations of transients, in this case accreting binary stars (neutron star or black hole accreting from a stellar companion) under a range of observing strategies. We first generate realistic light-curves for populations of binaries with contrasting orbital period distributions. These models are then randomly sampled at observing cadences typical of existing and planned monitoring surveys. The classical capture-recapture methods, Lincoln-Peterson, Schnabel estimators, related techniques, and newer methods implemented in the Rcapture package are compared. A general exponential model based on the radioactive decay law is introduced which is demonstrated to recover (at 95% confidence) the underlying population abundance and duty cycle, in a fraction of the observing visits (10-50%) required to discover all the sources in the simulation. Capture-Recapture is a promising addition to the toolbox of time domain astronomy, and methods implemented in R by the biostats community can be readily called from within python.

The Evolution of Vicia ramuliflora (Fabaceae) at Tetraploid and Diploid Levels Revealed with FISH and RAPD

PubMed Central

Han, Ying; Liu, Yuan; Wang, Haoyou; Liu, Xiangjun

2017-01-01

Vicia ramuliflora L. is a widely distributed species in Eurasia with high economic value. For past 200 years, it has evolved a tetraploid cytotype and new subspecies at the diploid level. Based on taxonomy, cytogeography and other lines of evidence, previous studies have provided valuable information about the evolution of V. ramuliflora ploidy level, but due to the limited resolution of traditional methods, important questions remain. In this study, fluorescence in situ hybridization (FISH) and random amplified polymorphic DNA (RAPD) were used to analyze the evolution of V. ramuliflora at the diploid and tetraploid levels. Our aim was to reveal the genomic constitution and parents of the tetraploid V. ramuliflora and the relationships among diploid V. ramuliflora populations. Our study showed that the tetraploid cytotype of V. ramuliflora at Changbai Mountains (M) has identical 18S and 5S rDNA distribution patterns with the diploid Hengdaohezi population (B) and the diploid Dailing population (H). However, UPGMA clustering, Neighbor-Joining clustering and principal coordinates analysis based on RAPD showed that the tetraploid cytotype (M) has more close relationships with Qianshan diploid population T. Based on our results and the fact that interspecific hybridization among Vicia species is very difficult, we think that the tetraploid V. ramuliflora is an autotetraploid and its genomic origin still needs further study. In addition, our study also found that Qianshan diploid population (T) had evolved distinct new traits compared with other diploid populations, which hints that V. ramuliflora evolved further at diploid level. We suggest that diploid population T be re-classified as a new subspecies. PMID:28135314

The Evolution of Vicia ramuliflora (Fabaceae) at Tetraploid and Diploid Levels Revealed with FISH and RAPD.

PubMed

Han, Ying; Liu, Yuan; Wang, Haoyou; Liu, Xiangjun

2017-01-01

Vicia ramuliflora L. is a widely distributed species in Eurasia with high economic value. For past 200 years, it has evolved a tetraploid cytotype and new subspecies at the diploid level. Based on taxonomy, cytogeography and other lines of evidence, previous studies have provided valuable information about the evolution of V. ramuliflora ploidy level, but due to the limited resolution of traditional methods, important questions remain. In this study, fluorescence in situ hybridization (FISH) and random amplified polymorphic DNA (RAPD) were used to analyze the evolution of V. ramuliflora at the diploid and tetraploid levels. Our aim was to reveal the genomic constitution and parents of the tetraploid V. ramuliflora and the relationships among diploid V. ramuliflora populations. Our study showed that the tetraploid cytotype of V. ramuliflora at Changbai Mountains (M) has identical 18S and 5S rDNA distribution patterns with the diploid Hengdaohezi population (B) and the diploid Dailing population (H). However, UPGMA clustering, Neighbor-Joining clustering and principal coordinates analysis based on RAPD showed that the tetraploid cytotype (M) has more close relationships with Qianshan diploid population T. Based on our results and the fact that interspecific hybridization among Vicia species is very difficult, we think that the tetraploid V. ramuliflora is an autotetraploid and its genomic origin still needs further study. In addition, our study also found that Qianshan diploid population (T) had evolved distinct new traits compared with other diploid populations, which hints that V. ramuliflora evolved further at diploid level. We suggest that diploid population T be re-classified as a new subspecies.

Identity-by-Descent-Based Phasing and Imputation in Founder Populations Using Graphical Models

PubMed Central

Palin, Kimmo; Campbell, Harry; Wright, Alan F; Wilson, James F; Durbin, Richard

2011-01-01

Accurate knowledge of haplotypes, the combination of alleles co-residing on a single copy of a chromosome, enables powerful gene mapping and sequence imputation methods. Since humans are diploid, haplotypes must be derived from genotypes by a phasing process. In this study, we present a new computational model for haplotype phasing based on pairwise sharing of haplotypes inferred to be Identical-By-Descent (IBD). We apply the Bayesian network based model in a new phasing algorithm, called systematic long-range phasing (SLRP), that can capitalize on the close genetic relationships in isolated founder populations, and show with simulated and real genome-wide genotype data that SLRP substantially reduces the rate of phasing errors compared to previous phasing algorithms. Furthermore, the method accurately identifies regions of IBD, enabling linkage-like studies without pedigrees, and can be used to impute most genotypes with very low error rate. Genet. Epidemiol. 2011. © 2011 Wiley Periodicals, Inc.35:853-860, 2011 PMID:22006673

Systematic review of the use of online questionnaires of older adults.

PubMed

Remillard, Meegan L; Mazor, Kathleen M; Cutrona, Sarah L; Gurwitz, Jerry H; Tjia, Jennifer

2014-04-01

To describe methodological approaches to population targeting and sampling and to summarize limitations of Internet-based questionnaires in older adults. Systematic literature review. Studies using online questionnaires in older adult populations. English-language articles using search terms for geriatric, age 65 and over, Internet survey, online survey, Internet questionnaire, and online questionnaire in PubMed and EBSCO host between 1984 and July 2012. Inclusion criteria were study population mean age 65 and older and use of an online questionnaire for research. Review of 336 abstracts yielded 14 articles for full review by two investigators; 11 articles met inclusion criteria. Articles were extracted for study design and setting, participant characteristics, recruitment strategy, country, and study limitations. Eleven articles were published after 2001. Studies had populations with a mean age of 65 to 78, included descriptive and analytical designs, and were conducted in the United States, Australia, and Japan. Recruiting methods varied widely from paper fliers and personal e-mails to use of consumer marketing panels. Investigator-reported study limitations included the use of small convenience samples and limited generalizability. Online questionnaires are a feasible method of surveying older adults in some geographic regions and for some subsets of older adults, but limited Internet access constrains recruiting methods and often limits study generalizability. © 2014, Copyright the Authors Journal compilation © 2014, The American Geriatrics Society.

The use of customised versus population-based birthweight standards in predicting perinatal mortality.

PubMed

Zhang, X; Platt, R W; Cnattingius, S; Joseph, K S; Kramer, M S

2007-04-01

The objective of this study was to critically examine potential artifacts and biases underlying the use of 'customised' standards of birthweight for gestational age (GA). Population-based cohort study. Sweden. A total of 782,303 singletons > or =28 weeks of gestation born in 1992-2001 to Nordic mothers with complete data on birthweight; GA; and maternal age, parity, height, and pre-pregnancy weight. We compared perinatal mortality in four groups of infants based on the following classification of small for gestational age (SGA): non-SGA based on either population-based or customised standards (the reference group), SGA based on the population-based standard only, SGA based on the customised standard only, and SGA according to both standards. We used graphical methods to compare GA-specific birthweight cutoffs for SGA using the two standards and also used logistic regression to control for differences in GA and maternal pre-pregnancy body mass index (BMI) in the four groups. Perinatal mortality, including stillbirth and neonatal death. Customisation led to a large artifactual increase in the proportion of SGA infants born preterm. Adjustment for differences in GA and maternal BMI markedly reduced the excess risk among infants classified as SGA by customised standards only. The large increase in perinatal mortality risk among infants classified as SGA based on customised standards is largely an artifact due to inclusion of more preterm births.

Parsing Social Network Survey Data from Hidden Populations Using Stochastic Context-Free Grammars

PubMed Central

Poon, Art F. Y.; Brouwer, Kimberly C.; Strathdee, Steffanie A.; Firestone-Cruz, Michelle; Lozada, Remedios M.; Kosakovsky Pond, Sergei L.; Heckathorn, Douglas D.; Frost, Simon D. W.

2009-01-01

Background Human populations are structured by social networks, in which individuals tend to form relationships based on shared attributes. Certain attributes that are ambiguous, stigmatized or illegal can create a ÔhiddenÕ population, so-called because its members are difficult to identify. Many hidden populations are also at an elevated risk of exposure to infectious diseases. Consequently, public health agencies are presently adopting modern survey techniques that traverse social networks in hidden populations by soliciting individuals to recruit their peers, e.g., respondent-driven sampling (RDS). The concomitant accumulation of network-based epidemiological data, however, is rapidly outpacing the development of computational methods for analysis. Moreover, current analytical models rely on unrealistic assumptions, e.g., that the traversal of social networks can be modeled by a Markov chain rather than a branching process. Methodology/Principal Findings Here, we develop a new methodology based on stochastic context-free grammars (SCFGs), which are well-suited to modeling tree-like structure of the RDS recruitment process. We apply this methodology to an RDS case study of injection drug users (IDUs) in Tijuana, México, a hidden population at high risk of blood-borne and sexually-transmitted infections (i.e., HIV, hepatitis C virus, syphilis). Survey data were encoded as text strings that were parsed using our custom implementation of the inside-outside algorithm in a publicly-available software package (HyPhy), which uses either expectation maximization or direct optimization methods and permits constraints on model parameters for hypothesis testing. We identified significant latent variability in the recruitment process that violates assumptions of Markov chain-based methods for RDS analysis: firstly, IDUs tended to emulate the recruitment behavior of their own recruiter; and secondly, the recruitment of like peers (homophily) was dependent on the number of recruits. Conclusions SCFGs provide a rich probabilistic language that can articulate complex latent structure in survey data derived from the traversal of social networks. Such structure that has no representation in Markov chain-based models can interfere with the estimation of the composition of hidden populations if left unaccounted for, raising critical implications for the prevention and control of infectious disease epidemics. PMID:19738904

Wearable accelerometry-based technology capable of assessing functional activities in neurological populations in community settings: a systematic review

PubMed Central

2014-01-01

Background Integrating rehabilitation services through wearable systems has the potential to accurately assess the type, intensity, duration, and quality of movement necessary for procuring key outcome measures. Objectives This review aims to explore wearable accelerometry-based technology (ABT) capable of assessing mobility-related functional activities intended for rehabilitation purposes in community settings for neurological populations. In this review, we focus on the accuracy of ABT-based methods, types of outcome measures, and the implementation of ABT in non-clinical settings for rehabilitation purposes. Data sources Cochrane, PubMed, Web of Knowledge, EMBASE, and IEEE Xplore. The search strategy covered three main areas, namely wearable technology, rehabilitation, and setting. Study selection Potentially relevant studies were categorized as systems either evaluating methods or outcome parameters. Methods Methodological qualities of studies were assessed by two customized checklists, depending on their categorization and rated independently by three blinded reviewers. Results Twelve studies involving ABT met the eligibility criteria, of which three studies were identified as having implemented ABT for rehabilitation purposes in non-clinical settings. From the twelve studies, seven studies achieved high methodological quality scores. These studies were not only capable of assessing the type, quantity, and quality measures of functional activities, but could also distinguish healthy from non-healthy subjects and/or address disease severity levels. Conclusion While many studies support ABT’s potential for telerehabilitation, few actually utilized it to assess mobility-related functional activities outside laboratory settings. To generate more appropriate outcome measures, there is a clear need to translate research findings and novel methods into practice. PMID:24625308

On sample size of the kruskal-wallis test with application to a mouse peritoneal cavity study.

PubMed

Fan, Chunpeng; Zhang, Donghui; Zhang, Cun-Hui

2011-03-01

As the nonparametric generalization of the one-way analysis of variance model, the Kruskal-Wallis test applies when the goal is to test the difference between multiple samples and the underlying population distributions are nonnormal or unknown. Although the Kruskal-Wallis test has been widely used for data analysis, power and sample size methods for this test have been investigated to a much lesser extent. This article proposes new power and sample size calculation methods for the Kruskal-Wallis test based on the pilot study in either a completely nonparametric model or a semiparametric location model. No assumption is made on the shape of the underlying population distributions. Simulation results show that, in terms of sample size calculation for the Kruskal-Wallis test, the proposed methods are more reliable and preferable to some more traditional methods. A mouse peritoneal cavity study is used to demonstrate the application of the methods. © 2010, The International Biometric Society.

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

New parsimonious simulation methods and tools to assess future food and environmental security of farm populations

PubMed Central

Antle, John M.; Stoorvogel, Jetse J.; Valdivia, Roberto O.

2014-01-01

This article presents conceptual and empirical foundations for new parsimonious simulation models that are being used to assess future food and environmental security of farm populations. The conceptual framework integrates key features of the biophysical and economic processes on which the farming systems are based. The approach represents a methodological advance by coupling important behavioural processes, for example, self-selection in adaptive responses to technological and environmental change, with aggregate processes, such as changes in market supply and demand conditions or environmental conditions as climate. Suitable biophysical and economic data are a critical limiting factor in modelling these complex systems, particularly for the characterization of out-of-sample counterfactuals in ex ante analyses. Parsimonious, population-based simulation methods are described that exploit available observational, experimental, modelled and expert data. The analysis makes use of a new scenario design concept called representative agricultural pathways. A case study illustrates how these methods can be used to assess food and environmental security. The concluding section addresses generalizations of parametric forms and linkages of regional models to global models. PMID:24535388

New parsimonious simulation methods and tools to assess future food and environmental security of farm populations.

PubMed

Antle, John M; Stoorvogel, Jetse J; Valdivia, Roberto O

2014-04-05

This article presents conceptual and empirical foundations for new parsimonious simulation models that are being used to assess future food and environmental security of farm populations. The conceptual framework integrates key features of the biophysical and economic processes on which the farming systems are based. The approach represents a methodological advance by coupling important behavioural processes, for example, self-selection in adaptive responses to technological and environmental change, with aggregate processes, such as changes in market supply and demand conditions or environmental conditions as climate. Suitable biophysical and economic data are a critical limiting factor in modelling these complex systems, particularly for the characterization of out-of-sample counterfactuals in ex ante analyses. Parsimonious, population-based simulation methods are described that exploit available observational, experimental, modelled and expert data. The analysis makes use of a new scenario design concept called representative agricultural pathways. A case study illustrates how these methods can be used to assess food and environmental security. The concluding section addresses generalizations of parametric forms and linkages of regional models to global models.

A Population-based survey of risk for cancer in individuals diagnosed with myotonic dystrophy

PubMed Central

Abbott, Diana; Johnson, Nicholas E; Cannon-Albright, Lisa A.

2018-01-01

Introduction The risk of cancer in patients diagnosed with myotonic dystrophy (DM) is reported for the homogeneous Utah population. Methods Clinical data accessed from the largest Utah healthcare providers have been record-linked to the Utah Population Database (UPDB), a population-based resource also linked to the Utah Cancer Registry. Relative risks were estimated for 36 cancers of different types in 281 DM patients. Results Testicular cancer (RR=10.74; 95% CI: 1.91, 38.79), endometrial cancer (6.98; 1.24, 25.22), and Non-Hodgkins lymphoma (4.25; 1.16, 12.43) were all observed at significant excess in DM patients. Discussion This study confirms an overall increased risk of cancer in DM. Individuals diagnosed with DM might benefit from risk counseling. PMID:27064430

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

PubMed Central

2012-01-01

Background With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net. PMID:22568821

Genetic demographic networks: Mathematical model and applications.

PubMed

Kimmel, Marek; Wojdyła, Tomasz

2016-10-01

Recent improvement in the quality of genetic data obtained from extinct human populations and their ancestors encourages searching for answers to basic questions regarding human population history. The most common and successful are model-based approaches, in which genetic data are compared to the data obtained from the assumed demography model. Using such approach, it is possible to either validate or adjust assumed demography. Model fit to data can be obtained based on reverse-time coalescent simulations or forward-time simulations. In this paper we introduce a computational method based on mathematical equation that allows obtaining joint distributions of pairs of individuals under a specified demography model, each of them characterized by a genetic variant at a chosen locus. The two individuals are randomly sampled from either the same or two different populations. The model assumes three types of demographic events (split, merge and migration). Populations evolve according to the time-continuous Moran model with drift and Markov-process mutation. This latter process is described by the Lyapunov-type equation introduced by O'Brien and generalized in our previous works. Application of this equation constitutes an original contribution. In the result section of the paper we present sample applications of our model to both simulated and literature-based demographies. Among other we include a study of the Slavs-Balts-Finns genetic relationship, in which we model split and migrations between the Balts and Slavs. We also include another example that involves the migration rates between farmers and hunters-gatherers, based on modern and ancient DNA samples. This latter process was previously studied using coalescent simulations. Our results are in general agreement with the previous method, which provides validation of our approach. Although our model is not an alternative to simulation methods in the practical sense, it provides an algorithm to compute pairwise distributions of alleles, in the case of haploid non-recombining loci such as mitochondrial and Y-chromosome loci in humans. Copyright © 2016 Elsevier Inc. All rights reserved.

The HealthNuts population-based study of paediatric food allergy: validity, safety and acceptability.

PubMed

Osborne, N J; Koplin, J J; Martin, P E; Gurrin, L C; Thiele, L; Tang, M L; Ponsonby, A-L; Dharmage, S C; Allen, K J

2010-10-01

The incidence of hospital admissions for food allergy-related anaphylaxis in Australia has increased, in line with world-wide trends. However, a valid measure of food allergy prevalence and risk factor data from a population-based study is still lacking. To describe the study design and methods used to recruit infants from a population for skin prick testing and oral food challenges, and the use of preliminary data to investigate the extent to which the study sample is representative of the target population. The study sampling frame design comprises 12-month-old infants presenting for routine scheduled vaccination at immunization clinics in Melbourne, Australia. We compared demographic features of participating families to population summary statistics from the Victorian Perinatal census database, and administered a survey to those non-responders who chose not to participate in the study. Study design proved acceptable to the community with good uptake (response rate 73.4%), with 2171 participants recruited. Demographic information on the study population mirrored the Victorian population with most the population parameters measured falling within our confidence intervals (CI). Use of a non-responder questionnaire revealed that a higher proportion of infants who declined to participate (non-responders) were already eating and tolerating peanuts, than those agreeing to participate (54.4%; 95% CI 50.8, 58.0 vs. 27.4%; 95% CI 25.5, 29.3 among participants). A high proportion of individuals approached in a community setting participated in a food allergy study. The study population differed from the eligible sample in relation to family history of allergy and prior consumption and peanut tolerance, providing some insights into the internal validity of the sample. The study exhibited external validity on general demographics to all births in Victoria. © 2010 Blackwell Publishing Ltd.

Population Fisher information matrix and optimal design of discrete data responses in population pharmacodynamic experiments.

PubMed

Ogungbenro, Kayode; Aarons, Leon

2011-08-01

In the recent years, interest in the application of experimental design theory to population pharmacokinetic (PK) and pharmacodynamic (PD) experiments has increased. The aim is to improve the efficiency and the precision with which parameters are estimated during data analysis and sometimes to increase the power and reduce the sample size required for hypothesis testing. The population Fisher information matrix (PFIM) has been described for uniresponse and multiresponse population PK experiments for design evaluation and optimisation. Despite these developments and availability of tools for optimal design of population PK and PD experiments much of the effort has been focused on repeated continuous variable measurements with less work being done on repeated discrete type measurements. Discrete data arise mainly in PDs e.g. ordinal, nominal, dichotomous or count measurements. This paper implements expressions for the PFIM for repeated ordinal, dichotomous and count measurements based on analysis by a mixed-effects modelling technique. Three simulation studies were used to investigate the performance of the expressions. Example 1 is based on repeated dichotomous measurements, Example 2 is based on repeated count measurements and Example 3 is based on repeated ordinal measurements. Data simulated in MATLAB were analysed using NONMEM (Laplace method) and the glmmML package in R (Laplace and adaptive Gauss-Hermite quadrature methods). The results obtained for Examples 1 and 2 showed good agreement between the relative standard errors obtained using the PFIM and simulations. The results obtained for Example 3 showed the importance of sampling at the most informative time points. Implementation of these expressions will provide the opportunity for efficient design of population PD experiments that involve discrete type data through design evaluation and optimisation.

Quality of life in children with epilepsy and cognitive impairment: a review and a pilot study.

PubMed

Soria, Carmen; El Sabbagh, Sandra; Escolano, Sylvie; Bobet, René; Bulteau, Christine; Dellatolas, Georges

2007-01-01

Various methods have recently been proposed to assess the physical, psychological or social dimensions of quality of life (QoL) in children with epilepsy (CwE) and their families. Some methods are based exclusively on parental report and others emphasize the importance of an interview with the patient himself. In children with epilepsy and severe cognitive deficit only parental report is possible in practice; however, some parental based methods to evaluate QoL in CwE have excluded children with cognitive deficit. The present pilot study explores which items are suitable for a parental-based QoL evaluation in CwE and special educational needs, and the most frequently reported parental concerns in this special population of children.

The Complex Admixture History and Recent Southern Origins of Siberian Populations

PubMed Central

Pugach, Irina; Matveev, Rostislav; Spitsyn, Viktor; Makarov, Sergey; Novgorodov, Innokentiy; Osakovsky, Vladimir; Stoneking, Mark; Pakendorf, Brigitte

2016-01-01

Although Siberia was inhabited by modern humans at an early stage, there is still debate over whether it remained habitable during the extreme cold of the Last Glacial Maximum or whether it was subsequently repopulated by peoples with recent shared ancestry. Previous studies of the genetic history of Siberian populations were hampered by the extensive admixture that appears to have taken place among these populations, because commonly used methods assume a tree-like population history and at most single admixture events. Here we analyze geogenetic maps and use other approaches to distinguish the effects of shared ancestry from prehistoric migrations and contact, and develop a new method based on the covariance of ancestry components, to investigate the potentially complex admixture history. We furthermore adapt a previously devised method of admixture dating for use with multiple events of gene flow, and apply these methods to whole-genome genotype data from over 500 individuals belonging to 20 different Siberian ethnolinguistic groups. The results of these analyses indicate that there have been multiple layers of admixture detectable in most of the Siberian populations, with considerable differences in the admixture histories of individual populations. Furthermore, most of the populations of Siberia included here, even those settled far to the north, appear to have a southern origin, with the northward expansions of different populations possibly being driven partly by the advent of pastoralism, especially reindeer domestication. These newly developed methods to analyze multiple admixture events should aid in the investigation of similarly complex population histories elsewhere. PMID:26993256

District nursing workforce planning: a review of the methods.

PubMed

Reid, Bernie; Kane, Kay; Curran, Carol

2008-11-01

District nursing services in Northern Ireland face increasing demands and challenges which may be responded to by effective and efficient workforce planning and development. The aim of this paper is to critically analyse district nursing workforce planning and development methods, in an attempt to find a suitable method for Northern Ireland. A systematic analysis of the literature reveals four methods: professional judgement; population-based health needs; caseload analysis and dependency-acuity. Each method has strengths and weaknesses. Professional judgement offers a 'belt and braces' approach but lacks sensitivity to fluctuating patient numbers. Population-based health needs methods develop staffing algorithms that reflect deprivation and geographical spread, but are poorly understood by district nurses. Caseload analysis promotes equitable workloads but poorly performing district nursing localities may continue if benchmarking processes only consider local data. Dependency-acuity methods provide a means of equalizing and prioritizing workload but are prone to district nurses overstating factors in patient dependency or understating carers' capability. In summary a mixed method approach is advocated to evaluate and adjust the size and mix of district nursing teams using empirically determined patient dependency and activity-based variables based on the population's health needs.

Analysis of four recruitment methods for obtaining normative data through a Web-based questionnaire: a pilot study.

PubMed

Nolte, Michael T; Shauver, Melissa J; Chung, Kevin C

2015-09-01

Quality normative data requires a diverse sample of participants and plays an important role in the appropriate use of health outcomes. Using social media and other online resources for survey recruitment is a tempting prospect, but the effectiveness of these methods in collecting a diverse sample is unknown. The purpose of this study is to pilot test four methods of recruitment to determine their ability to produce a sample representative of the general US population. This project is part of a larger study to gather normative data for the Michigan Hand Outcomes Questionnaire (MHQ). We used flyers, e-mail, Facebook, and an institution-specific clinical research recruitment Web site to direct participants to complete an online version of the MHQ. Participants also provided comorbidity and demographic information. The institution-specific recruitment Web site yielded the greatest number of respondents in an age distribution that mirrored the US population. Facebook was effective for recruiting young adults, and e-mail was successful for recruiting the older adults. None of the methods was successful in reaching an ethnically diverse sample. Obtaining normative data that is truly representative of the US population is a difficult task. The use of any one recruitment method is unlikely to result in a representative sample, but a greater understanding of these methods will empower researchers to use them to target specific populations. This pilot analysis provides support for the use of Facebook and clinical research sites in addition to traditional methods of e-mail and paper flyers.

Population-production-pollution nexus based air pollution management model for alleviating the atmospheric crisis in Beijing, China.

PubMed

Zeng, X T; Tong, Y F; Cui, L; Kong, X M; Sheng, Y N; Chen, L; Li, Y P

2017-07-15

In recent years, increscent emissions in the city of Beijing due to expanded population, accelerated industrialization and inter-regional pollutant transportation have led to hazardous atmospheric pollution issues. Although a number of anthropogenic control measures have been put into use, frequent/severe haze events have still challenged regional governments. In this study, a hybrid population-production-pollution nexus model (PPP) is proposed for air pollution management and air quality planning (AMP) with the aim to coordinate human activities and environmental protection. A fuzzy-stochastic mixed quadratic programming method (FSQ) is developed and introduced into a PPP for tackling atmospheric pollution issues with uncertainties. Based on the contribution of an index of population-production-pollution, a hybrid PPP-based AMP model that considers employment structure, industrial layout pattern, production mode, pollutant purification efficiency and a pollution mitigation scheme have been applied in Beijing. Results of the adjustment of employment structure, pollution mitigation scheme, and green gross domestic product under various environmental regulation scenarios are obtained and analyzed. This study can facilitate the identification of optimized policies for alleviating population-production-emission conflict in the study region, as well as ameliorating the hazardous air pollution crisis at an urban level. Copyright © 2017 Elsevier Ltd. All rights reserved.

Population entropies estimates of proteins

NASA Astrophysics Data System (ADS)

Low, Wai Yee

2017-05-01

The Shannon entropy equation provides a way to estimate variability of amino acids sequences in a multiple sequence alignment of proteins. Knowledge of protein variability is useful in many areas such as vaccine design, identification of antibody binding sites, and exploration of protein 3D structural properties. In cases where the population entropies of a protein are of interest but only a small sample size can be obtained, a method based on linear regression and random subsampling can be used to estimate the population entropy. This method is useful for comparisons of entropies where the actual sequence counts differ and thus, correction for alignment size bias is needed. In the current work, an R based package named EntropyCorrect that enables estimation of population entropy is presented and an empirical study on how well this new algorithm performs on simulated dataset of various combinations of population and sample sizes is discussed. The package is available at https://github.com/lloydlow/EntropyCorrect. This article, which was originally published online on 12 May 2017, contained an error in Eq. (1), where the summation sign was missing. The corrected equation appears in the Corrigendum attached to the pdf.

Official statistics and claims data records indicate non-response and recall bias within survey-based estimates of health care utilization in the older population

PubMed Central

2013-01-01

Background The validity of survey-based health care utilization estimates in the older population has been poorly researched. Owing to data protection legislation and a great number of different health care insurance providers, the assessment of recall and non-response bias is challenging to impossible in many countries. The objective of our study was to compare estimates from a population-based study in older German adults with external secondary data. Methods We used data from the German KORA-Age study, which included 4,127 people aged 65–94 years. Self-report questions covered the utilization of long-term care services, inpatient services, outpatient services, and pharmaceuticals. We calculated age- and sex-standardized mean utilization rates in each domain and compared them with the corresponding estimates derived from official statistics and independent statutory health insurance data. Results The KORA-Age study underestimated the use of long-term care services (−52%), in-hospital days (−21%) and physician visits (−70%). In contrast, the assessment of drug consumption by postal self-report questionnaires yielded similar estimates to the analysis of insurance claims data (−9%). Conclusion Survey estimates based on self-report tend to underestimate true health care utilization in the older population. Direct validation studies are needed to disentangle the impact of recall and non-response bias. PMID:23286781

Monitoring Butterfly Abundance: Beyond Pollard Walks

PubMed Central

Pellet, Jérôme; Bried, Jason T.; Parietti, David; Gander, Antoine; Heer, Patrick O.; Cherix, Daniel; Arlettaz, Raphaël

2012-01-01

Most butterfly monitoring protocols rely on counts along transects (Pollard walks) to generate species abundance indices and track population trends. It is still too often ignored that a population count results from two processes: the biological process (true abundance) and the statistical process (our ability to properly quantify abundance). Because individual detectability tends to vary in space (e.g., among sites) and time (e.g., among years), it remains unclear whether index counts truly reflect population sizes and trends. This study compares capture-mark-recapture (absolute abundance) and count-index (relative abundance) monitoring methods in three species (Maculinea nausithous and Iolana iolas: Lycaenidae; Minois dryas: Satyridae) in contrasted habitat types. We demonstrate that intraspecific variability in individual detectability under standard monitoring conditions is probably the rule rather than the exception, which questions the reliability of count-based indices to estimate and compare specific population abundance. Our results suggest that the accuracy of count-based methods depends heavily on the ecology and behavior of the target species, as well as on the type of habitat in which surveys take place. Monitoring programs designed to assess the abundance and trends in butterfly populations should incorporate a measure of detectability. We discuss the relative advantages and inconveniences of current monitoring methods and analytical approaches with respect to the characteristics of the species under scrutiny and resources availability. PMID:22859980

Mitochondrial Genetic Differentiation of Spirlin (Actinopterigii: Cyprinidae) in the South Caspian Sea basin of Iran

PubMed Central

Seifali, Mahvash; Arshad, Aziz; Moghaddam, Faezeh Yazdani; Esmaeili, Hamid Reza; Kiabi, Bahram H.; Daud, Siti Khalijah; Aliabadian, Mansour

2012-01-01

Background Knowledge about Alburnoides remains lacking relative to many other species, resulting in a lack of a systematic position and taxonomic diagnosis. Basic biological information for Alburnoides has been constructed, and it is necessary to understand further and obtain more information about this species. Its phylogenetic relationships are still debated and no molecular data have been used to study this taxon in Iran. A holistic approach for genetic methods was adopted to analyze possible spirlin population differences at selected centers in the south Caspian Sea basin of Iran. Methods The phylogenetic relationships were determined based on 774 base pairs of the mitochondrial cytochrome b gene of 32 specimens of spirlin from nine locations in the south Caspian Sea drainage basin of Iran. The nucleotide sequences were subjected to phylogenetic analysis using the neighbor-joining, maximum parsimony, maximum likelihood, and Bayesian methods. Results The mitochondrial gene tree largely supports the existence of three major clades. The western populations (clade I) may be considered as Alburnoides eichwaldii, whereas the Talar river populations (clade II) are represented as Alburnoides sp.1 and the eastern populations (clade III) may be distinct taxa of Alburnoides sp.2. Conclusion This molecular evidence supports the hypothesis that A. bipunctatus does not exist in the south Caspian Sea basin of Iran, and that the western and eastern populations are distinct taxa. PMID:22654487

Spatial capture-recapture models for jointly estimating population density and landscape connectivity

USGS Publications Warehouse

Royle, J. Andrew; Chandler, Richard B.; Gazenski, Kimberly D.; Graves, Tabitha A.

2013-01-01

Population size and landscape connectivity are key determinants of population viability, yet no methods exist for simultaneously estimating density and connectivity parameters. Recently developed spatial capture–recapture (SCR) models provide a framework for estimating density of animal populations but thus far have not been used to study connectivity. Rather, all applications of SCR models have used encounter probability models based on the Euclidean distance between traps and animal activity centers, which implies that home ranges are stationary, symmetric, and unaffected by landscape structure. In this paper we devise encounter probability models based on “ecological distance,” i.e., the least-cost path between traps and activity centers, which is a function of both Euclidean distance and animal movement behavior in resistant landscapes. We integrate least-cost path models into a likelihood-based estimation scheme for spatial capture–recapture models in order to estimate population density and parameters of the least-cost encounter probability model. Therefore, it is possible to make explicit inferences about animal density, distribution, and landscape connectivity as it relates to animal movement from standard capture–recapture data. Furthermore, a simulation study demonstrated that ignoring landscape connectivity can result in negatively biased density estimators under the naive SCR model.

Spatial capture--recapture models for jointly estimating population density and landscape connectivity.

PubMed

Royle, J Andrew; Chandler, Richard B; Gazenski, Kimberly D; Graves, Tabitha A

2013-02-01

Population size and landscape connectivity are key determinants of population viability, yet no methods exist for simultaneously estimating density and connectivity parameters. Recently developed spatial capture--recapture (SCR) models provide a framework for estimating density of animal populations but thus far have not been used to study connectivity. Rather, all applications of SCR models have used encounter probability models based on the Euclidean distance between traps and animal activity centers, which implies that home ranges are stationary, symmetric, and unaffected by landscape structure. In this paper we devise encounter probability models based on "ecological distance," i.e., the least-cost path between traps and activity centers, which is a function of both Euclidean distance and animal movement behavior in resistant landscapes. We integrate least-cost path models into a likelihood-based estimation scheme for spatial capture-recapture models in order to estimate population density and parameters of the least-cost encounter probability model. Therefore, it is possible to make explicit inferences about animal density, distribution, and landscape connectivity as it relates to animal movement from standard capture-recapture data. Furthermore, a simulation study demonstrated that ignoring landscape connectivity can result in negatively biased density estimators under the naive SCR model.

Evidence-Based Practice for Children with Speech Sound Disorders: Part 1 Narrative Review

ERIC Educational Resources Information Center

Baker, Elise; McLeod, Sharynne

2011-01-01

Purpose: This article provides a comprehensive narrative review of intervention studies for children with speech sound disorders (SSD). Its companion paper (Baker & McLeod, 2011) provides a tutorial and clinical example of how speech-language pathologists (SLPs) can engage in evidence-based practice (EBP) for this clinical population. Method:…

The Incidence of Infant Physical Abuse in Alaska

ERIC Educational Resources Information Center

Gessner, Bradford D.; Moore, Martha; Hamilton, Bernita; Muth, Pam T.

2004-01-01

Objectives: To determine the incidence of and risk factors associated with infant (less than 1 year of age) physical abuse in Alaska. Methods: A population-based retrospective cohort study for the 1994-2000 resident birth cohort was conducted by linking data from birth certificates, Child Protective Services, a statewide hospital-based trauma…

Exploration of Urban Spatial Planning Evaluation Based on Humanland Harmony

NASA Astrophysics Data System (ADS)

Hu, X. S.; Ma, Q. R.; Liang, W. Q.; Wang, C. X.; Xiong, X. Q.; Han, X. H.

2017-09-01

This study puts forward a new concept, "population urbanization level forecast - driving factor analysis - urban spatial planning analysis" for achieving efficient and intensive development of urbanization considering human-land harmony. We analyzed big data for national economic and social development, studied the development trends of population urbanization and its influencing factors using the grey system model in Chengmai county of Hainan province, China. In turn, we calculated the population of Chengmai coming years based on the forecasting urbanization rate and the corresponding amount of urban construction land, and evaluated the urban spatial planning with GIS spatial analysis method in the study area. The result shows that the proposed concept is feasible for evaluation of urban spatial planning, and is meaningful for guiding the rational distribution of urban space, controlling the scale of development, improving the quality of urbanization and thus promoting highly-efficient and intensive use of limited land resource.

Knowledge-Guided Robust MRI Brain Extraction for Diverse Large-Scale Neuroimaging Studies on Humans and Non-Human Primates

PubMed Central

Wang, Yaping; Nie, Jingxin; Yap, Pew-Thian; Li, Gang; Shi, Feng; Geng, Xiujuan; Guo, Lei; Shen, Dinggang

2014-01-01

Accurate and robust brain extraction is a critical step in most neuroimaging analysis pipelines. In particular, for the large-scale multi-site neuroimaging studies involving a significant number of subjects with diverse age and diagnostic groups, accurate and robust extraction of the brain automatically and consistently is highly desirable. In this paper, we introduce population-specific probability maps to guide the brain extraction of diverse subject groups, including both healthy and diseased adult human populations, both developing and aging human populations, as well as non-human primates. Specifically, the proposed method combines an atlas-based approach, for coarse skull-stripping, with a deformable-surface-based approach that is guided by local intensity information and population-specific prior information learned from a set of real brain images for more localized refinement. Comprehensive quantitative evaluations were performed on the diverse large-scale populations of ADNI dataset with over 800 subjects (55∼90 years of age, multi-site, various diagnosis groups), OASIS dataset with over 400 subjects (18∼96 years of age, wide age range, various diagnosis groups), and NIH pediatrics dataset with 150 subjects (5∼18 years of age, multi-site, wide age range as a complementary age group to the adult dataset). The results demonstrate that our method consistently yields the best overall results across almost the entire human life span, with only a single set of parameters. To demonstrate its capability to work on non-human primates, the proposed method is further evaluated using a rhesus macaque dataset with 20 subjects. Quantitative comparisons with popularly used state-of-the-art methods, including BET, Two-pass BET, BET-B, BSE, HWA, ROBEX and AFNI, demonstrate that the proposed method performs favorably with superior performance on all testing datasets, indicating its robustness and effectiveness. PMID:24489639

Statistical power calculations for mixed pharmacokinetic study designs using a population approach.

PubMed

Kloprogge, Frank; Simpson, Julie A; Day, Nicholas P J; White, Nicholas J; Tarning, Joel

2014-09-01

Simultaneous modelling of dense and sparse pharmacokinetic data is possible with a population approach. To determine the number of individuals required to detect the effect of a covariate, simulation-based power calculation methodologies can be employed. The Monte Carlo Mapped Power method (a simulation-based power calculation methodology using the likelihood ratio test) was extended in the current study to perform sample size calculations for mixed pharmacokinetic studies (i.e. both sparse and dense data collection). A workflow guiding an easy and straightforward pharmacokinetic study design, considering also the cost-effectiveness of alternative study designs, was used in this analysis. Initially, data were simulated for a hypothetical drug and then for the anti-malarial drug, dihydroartemisinin. Two datasets (sampling design A: dense; sampling design B: sparse) were simulated using a pharmacokinetic model that included a binary covariate effect and subsequently re-estimated using (1) the same model and (2) a model not including the covariate effect in NONMEM 7.2. Power calculations were performed for varying numbers of patients with sampling designs A and B. Study designs with statistical power >80% were selected and further evaluated for cost-effectiveness. The simulation studies of the hypothetical drug and the anti-malarial drug dihydroartemisinin demonstrated that the simulation-based power calculation methodology, based on the Monte Carlo Mapped Power method, can be utilised to evaluate and determine the sample size of mixed (part sparsely and part densely sampled) study designs. The developed method can contribute to the design of robust and efficient pharmacokinetic studies.

A white-box model of S-shaped and double S-shaped single-species population growth

PubMed Central

Kalmykov, Lev V.

2015-01-01

Complex systems may be mechanistically modelled by white-box modeling with using logical deterministic individual-based cellular automata. Mathematical models of complex systems are of three types: black-box (phenomenological), white-box (mechanistic, based on the first principles) and grey-box (mixtures of phenomenological and mechanistic models). Most basic ecological models are of black-box type, including Malthusian, Verhulst, Lotka–Volterra models. In black-box models, the individual-based (mechanistic) mechanisms of population dynamics remain hidden. Here we mechanistically model the S-shaped and double S-shaped population growth of vegetatively propagated rhizomatous lawn grasses. Using purely logical deterministic individual-based cellular automata we create a white-box model. From a general physical standpoint, the vegetative propagation of plants is an analogue of excitation propagation in excitable media. Using the Monte Carlo method, we investigate a role of different initial positioning of an individual in the habitat. We have investigated mechanisms of the single-species population growth limited by habitat size, intraspecific competition, regeneration time and fecundity of individuals in two types of boundary conditions and at two types of fecundity. Besides that, we have compared the S-shaped and J-shaped population growth. We consider this white-box modeling approach as a method of artificial intelligence which works as automatic hyper-logical inference from the first principles of the studied subject. This approach is perspective for direct mechanistic insights into nature of any complex systems. PMID:26038717

The HIV care cascade: a systematic review of data sources, methodology and comparability.

PubMed

Medland, Nicholas A; McMahon, James H; Chow, Eric P F; Elliott, Julian H; Hoy, Jennifer F; Fairley, Christopher K

2015-01-01

The cascade of HIV diagnosis, care and treatment (HIV care cascade) is increasingly used to direct and evaluate interventions to increase population antiretroviral therapy (ART) coverage, a key component of treatment as prevention. The ability to compare cascades over time, sub-population, jurisdiction or country is important. However, differences in data sources and methodology used to construct the HIV care cascade might limit its comparability and ultimately its utility. Our aim was to review systematically the different methods used to estimate and report the HIV care cascade and their comparability. A search of published and unpublished literature through March 2015 was conducted. Cascades that reported the continuum of care from diagnosis to virological suppression in a demographically definable population were included. Data sources and methods of measurement or estimation were extracted. We defined the most comparable cascade elements as those that directly measured diagnosis or care from a population-based data set. Thirteen reports were included after screening 1631 records. The undiagnosed HIV-infected population was reported in seven cascades, each of which used different data sets and methods and could not be considered to be comparable. All 13 used mandatory HIV diagnosis notification systems to measure the diagnosed population. Population-based data sets, derived from clinical data or mandatory reporting of CD4 cell counts and viral load tests from all individuals, were used in 6 of 12 cascades reporting linkage, 6 of 13 reporting retention, 3 of 11 reporting ART and 6 of 13 cascades reporting virological suppression. Cascades with access to population-based data sets were able to directly measure cascade elements and are therefore comparable over time, place and sub-population. Other data sources and methods are less comparable. To ensure comparability, countries wishing to accurately measure the cascade should utilize complete population-based data sets from clinical data from elements of a centralized healthcare setting, where available, or mandatory CD4 cell count and viral load test result reporting. Additionally, virological suppression should be presented both as percentage of diagnosed and percentage of estimated total HIV-infected population, until methods to calculate the latter have been standardized.

Modeling Test and Treatment Strategies for Presymptomatic Alzheimer Disease

PubMed Central

Burke, James F.; Langa, Kenneth M.; Hayward, Rodney A.; Albin, Roger L.

2014-01-01

Objectives In this study, we developed a model of presymptomatic treatment of Alzheimer disease (AD) after a screening diagnostic evaluation and explored the circumstances required for an AD prevention treatment to produce aggregate net population benefit. Methods Monte Carlo simulation methods were used to estimate outcomes in a simulated population derived from data on AD incidence and mortality. A wide variety of treatment parameters were explored. Net population benefit was estimated in aggregated QALYs. Sensitivity analyses were performed by individually varying the primary parameters. Findings In the base-case scenario, treatment effects were uniformly positive, and net benefits increased with increasing age at screening. A highly efficacious treatment (i.e. relative risk 0.6) modeled in the base-case is estimated to save 20 QALYs per 1000 patients screened and 221 QALYs per 1000 patients treated. Conclusions Highly efficacious presymptomatic screen and treat strategies for AD are likely to produce substantial aggregate population benefits that are likely greater than the benefits of aspirin in primary prevention of moderate risk cardiovascular disease (28 QALYS per 1000 patients treated), even in the context of an imperfect treatment delivery environment. PMID:25474698

Generalizing Observational Study Results: Applying Propensity Score Methods to Complex Surveys

PubMed Central

DuGoff, Eva H; Schuler, Megan; Stuart, Elizabeth A

2014-01-01

ObjectiveTo provide a tutorial for using propensity score methods with complex survey data. Data SourcesSimulated data and the 2008 Medical Expenditure Panel Survey. Study DesignUsing simulation, we compared the following methods for estimating the treatment effect: a naïve estimate (ignoring both survey weights and propensity scores), survey weighting, propensity score methods (nearest neighbor matching, weighting, and subclassification), and propensity score methods in combination with survey weighting. Methods are compared in terms of bias and 95 percent confidence interval coverage. In Example 2, we used these methods to estimate the effect on health care spending of having a generalist versus a specialist as a usual source of care. Principal FindingsIn general, combining a propensity score method and survey weighting is necessary to achieve unbiased treatment effect estimates that are generalizable to the original survey target population. ConclusionsPropensity score methods are an essential tool for addressing confounding in observational studies. Ignoring survey weights may lead to results that are not generalizable to the survey target population. This paper clarifies the appropriate inferences for different propensity score methods and suggests guidelines for selecting an appropriate propensity score method based on a researcher’s goal. PMID:23855598

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

Reader strategies: variability and error- methodology, findings, and health policy implications from a study of the U.S. population of mammographers

NASA Astrophysics Data System (ADS)

Beam, Craig A.

2002-04-01

Each year, approximately 60% of all US women over the age of 40 utilize mammography. Through the matrix of an imaging technology, this Population of Patients (POP) interacts with a population of approximately 20,000 physicians who interpret mammograms in the US. This latter Population of Diagnosticians (POD) operationally serves as the interface between an image-centric healthcare technology system and patient. Methods: using data collected from a large POD and POP based study, I evaluate the distribution of several ROC curve-related parameters in the POD and explore the health policy implications of a population ROC curve for mammography. Results and Conclusions: Principal Components Analysis suggests that two Binormal parameters are sufficient to explain variation in the POD and implies that the Binormal model is foundational to Health Policy Research in Mammography. A population ROC curve based on percentiles of the POD can be used to set targets to achieve national health policy goals. Medical Image Perception science provides the framework. Alternatively, a restrictive policy can be envisioned using performance criteria based on area. However, the data suggests this sort of policy would be too costly in terms of reduced healthcare service capacity in the US in the face of burgeoning demands.

Influence of population versus convenience sampling on sample characteristics in studies of cognitive aging.

PubMed

Brodaty, Henry; Mothakunnel, Annu; de Vel-Palumbo, Melissa; Ames, David; Ellis, Kathryn A; Reppermund, Simone; Kochan, Nicole A; Savage, Greg; Trollor, Julian N; Crawford, John; Sachdev, Perminder S

2014-01-01

We examined whether differences in findings of studies examining mild cognitive impairment (MCI) were associated with recruitment methods by comparing sample characteristics in two contemporaneous Australian studies, using population-based and convenience sampling. The Sydney Memory and Aging Study invited participants randomly from the electoral roll in defined geographic areas in Sydney. The Australian Imaging, Biomarkers and Lifestyle Study of Ageing recruited cognitively normal (CN) individuals via media appeals and MCI participants via referrals from clinicians in Melbourne and Perth. Demographic and cognitive variables were harmonized, and similar diagnostic criteria were applied to both samples retrospectively. CN participants recruited via convenience sampling were younger, better educated, more likely to be married and have a family history of dementia, and performed better cognitively than those recruited via population-based sampling. MCI participants recruited via population-based sampling had better memory performance and were less likely to carry the apolipoprotein E ε4 allele than clinically referred participants but did not differ on other demographic variables. A convenience sample of normal controls is likely to be younger and better functioning and that of an MCI group likely to perform worse than a purportedly random sample. Sampling bias should be considered when interpreting findings. Copyright © 2014 Elsevier Inc. All rights reserved.

Setting population targets for mammals using body mass as a predictor of population persistence.

PubMed

Hilbers, Jelle P; Santini, Luca; Visconti, Piero; Schipper, Aafke M; Pinto, Cecilia; Rondinini, Carlo; Huijbregts, Mark A J

2017-04-01

Conservation planning and biodiversity assessments need quantitative targets to optimize planning options and assess the adequacy of current species protection. However, targets aiming at persistence require population-specific data, which limit their use in favor of fixed and nonspecific targets, likely leading to unequal distribution of conservation efforts among species. We devised a method to derive equitable population targets; that is, quantitative targets of population size that ensure equal probabilities of persistence across a set of species and that can be easily inferred from species-specific traits. In our method, we used models of population dynamics across a range of life-history traits related to species' body mass to estimate minimum viable population targets. We applied our method to a range of body masses of mammals, from 2 g to 3825 kg. The minimum viable population targets decreased asymptotically with increasing body mass and were on the same order of magnitude as minimum viable population estimates from species- and context-specific studies. Our approach provides a compromise between pragmatic, nonspecific population targets and detailed context-specific estimates of population viability for which only limited data are available. It enables a first estimation of species-specific population targets based on a readily available trait and thus allows setting equitable targets for population persistence in large-scale and multispecies conservation assessments and planning. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study

PubMed Central

2013-01-01

Background Demographic bottlenecks can severely reduce the genetic variation of a population or a species. Establishing whether low genetic variation is caused by a bottleneck or a constantly low effective number of individuals is important to understand a species’ ecology and evolution, and it has implications for conservation management. Recent studies have evaluated the power of several statistical methods developed to identify bottlenecks. However, the false positive rate, i.e. the rate with which a bottleneck signal is misidentified in demographically stable populations, has received little attention. We analyse this type of error (type I) in forward computer simulations of stable populations having greater than Poisson variance in reproductive success (i.e., variance in family sizes). The assumption of Poisson variance underlies bottleneck tests, yet it is commonly violated in species with high fecundity. Results With large variance in reproductive success (Vk ≥ 40, corresponding to a ratio between effective and census size smaller than 0.1), tests based on allele frequencies, allelic sizes, and DNA sequence polymorphisms (heterozygosity excess, M-ratio, and Tajima’s D test) tend to show erroneous signals of a bottleneck. Similarly, strong evidence of population decline is erroneously detected when ancestral and current population sizes are estimated with the model based method MSVAR. Conclusions Our results suggest caution when interpreting the results of bottleneck tests in species showing high variance in reproductive success. Particularly in species with high fecundity, computer simulations are recommended to confirm the occurrence of a population bottleneck. PMID:24131797

Reducing microwave absorption with fast frequency modulation.

PubMed

Qin, Juehang; Hubler, A

2017-05-01

We study the response of a two-level quantum system to a chirp signal, using both numerical and analytical methods. The numerical method is based on numerical solutions of the Schrödinger solution of the two-level system, while the analytical method is based on an approximate solution of the same equations. We find that when two-level systems are perturbed by a chirp signal, the peak population of the initially unpopulated state exhibits a high sensitivity to frequency modulation rate. We also find that the aforementioned sensitivity depends on the strength of the forcing, and weaker forcings result in a higher sensitivity, where the frequency modulation rate required to produce the same reduction in peak population would be lower. We discuss potential applications of this result in the field of microwave power transmission, as it shows applying fast frequency modulation to transmitted microwaves used for power transmission could decrease unintended absorption of microwaves by organic tissue.

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

Treesearch

H. T. Schreuder; M. S. Williams

2000-01-01

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

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

PubMed

Anderson, Eric C

2012-11-08

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

Patterns of genetic diversity at the nine forensically approved STR loci in the Indian populations.

PubMed

Dutta, Ranjan; Reddy, B Mohan; Chattopadhyay, P; Kashyap, V K; Sun, Guangyun; Deka, Ranjan

2002-02-01

Genetic diversity at the nine short tandem repeat (STR) loci, which are universally approved and widely used for forensic investigations, has been studied among nine Indian populations with diverse ethnic, linguistic, and geographic backgrounds. The nine STR loci were profiled on 902 individuals using fluorescent detection methods on an ABI377 System, with the aid of an Amp-F1 Profiler Plus Kit. The studied populations include two upper castes, Brahmin and Kayastha; a tribe, Garo, from West Bengal; a Hindu caste, Meitei, with historical links to Bengal Brahmins; a migrant group of Muslims; three tribal groups, Naga, Kuki and Hmar, from Manipur in northeast India; and a middle-ranking caste, Golla, who are seminomadic herders from Andhra Pradesh. Gene diversity analysis suggests that the average heterozygosity is uniformly high (>0.8) in the studied populations, with the coefficient of gene differentiation at 0.050 +/- 0.0054. Both neighbor-joining (NJ) and unweighted pair group method with arithmetic mean (UPGMA) trees based on DA distances bring out distinct clusters that are consistent with ethnic, linguistic, and/or geographic backgrounds of the populations. The fit of the Harpending and Ward model of regression of average heterozygosity on the gene frequency centroid is found to be good, and the observed outliers are consistent with the population structure and history of the studied populations. Our study suggests that the nine STR loci, used so far mostly for forensic investigations, can be used fruitfully for microevolutionary studies as well, and for reconstructing the phylogenetic history of human populations, at least at the local level.

SHIPS: Spectral Hierarchical Clustering for the Inference of Population Structure in Genetic Studies

PubMed Central

Bouaziz, Matthieu; Paccard, Caroline; Guedj, Mickael; Ambroise, Christophe

2012-01-01

Inferring the structure of populations has many applications for genetic research. In addition to providing information for evolutionary studies, it can be used to account for the bias induced by population stratification in association studies. To this end, many algorithms have been proposed to cluster individuals into genetically homogeneous sub-populations. The parametric algorithms, such as Structure, are very popular but their underlying complexity and their high computational cost led to the development of faster parametric alternatives such as Admixture. Alternatives to these methods are the non-parametric approaches. Among this category, AWclust has proven efficient but fails to properly identify population structure for complex datasets. We present in this article a new clustering algorithm called Spectral Hierarchical clustering for the Inference of Population Structure (SHIPS), based on a divisive hierarchical clustering strategy, allowing a progressive investigation of population structure. This method takes genetic data as input to cluster individuals into homogeneous sub-populations and with the use of the gap statistic estimates the optimal number of such sub-populations. SHIPS was applied to a set of simulated discrete and admixed datasets and to real SNP datasets, that are data from the HapMap and Pan-Asian SNP consortium. The programs Structure, Admixture, AWclust and PCAclust were also investigated in a comparison study. SHIPS and the parametric approach Structure were the most accurate when applied to simulated datasets both in terms of individual assignments and estimation of the correct number of clusters. The analysis of the results on the real datasets highlighted that the clusterings of SHIPS were the more consistent with the population labels or those produced by the Admixture program. The performances of SHIPS when applied to SNP data, along with its relatively low computational cost and its ease of use make this method a promising solution to infer fine-scale genetic patterns. PMID:23077494

Genetic diversity of Iranian honey bee (Apis mellifera meda Skorikow, 1829) populations based on ISSR markers.

PubMed

Rahimi, A; Mirmoayedi, A; Kahrizi, D; Zarei, L; Jamali, S

2016-04-30

Honey bee is one of the most important insects considering its role in agriculture,ecology and economy as a whole. In this study, the genetic diversity of different Iranian honey bee populations was evaluated using inter simple sequence repeat (ISSR) markers. During May to September 2014, 108 young worker honey bees were collected from six different populations in 30 different geoclimatic locations from Golestan, Mazendaran, Guilan, West Azerbaijan, East Azerbaijan, Ardebil provinces of Iran. DNA was extracted from the worker honey bees. The quality and quantity of extracted DNA were measured. A set of ten primers were screened with the laboratory populations of honey bees. The number of fragments produced in the different honey bee populations varied from 3 to 10, varying within 150 to 1500 bp. The used ten ISSR primers generated 40 polymorphic fragments, and the average heterozygosity for each primer was 0.266. Maximum numbers of bands were recorded for primer A1. A dendrogram based on the Unweighted Pair Group Method with Arithmetic mean (UPGMA) method generated two sub-clusters. Honey bee populations of Golestan, Mazendaran, Guilan provinces were located in the first group. The second group included honey bee populations of Ardebil, West Azerbaijan, East Azerbaijan provinces, but this group showed a close relationship with other populations. The results showed obviously the ability of the ISSR marker technique to detect the genetic diversity among the honey bee populations.

Ninety-Day Postoperative Mortality after Robot-assisted Laparoscopic Prostatectomy and Retropubic Radical Prostatectomy. Nation-wide population-based study

PubMed Central

Björklund, Johan; Folkvaljon, Yasin; Cole, Alexander; Carlsson, Stefan; Robinson, David; Loeb, Stacy; Stattin, Pär; Akre, Olof

2016-01-01

Objective To assess 90-day postoperative mortality after Robot assisted laparoscopic Radical prostatectomy (RARP) and retropubic radical prostatectomy (RRP) by use of nationwide population-based registry data. Patients and methods Cohort study in the National Prostate Cancer Register (NPCR) of Sweden of 22 344 men with prostate cancer in clinical local stage T1-T3, PSA <50 μg/ml who had undergone primary RP in 1998 - 2012. Vital status was ascertained through the Total Population Register. 90-day postoperative mortality was analysed by use of logistic regression analysis and comparison of 90-day mortality with the background population were made using standardised mortality ratios (SMR). Results 29 out of 14820 men (0.20%) died after RRP and 10 out of 7524 men (0.13%) died after RARP. Mortality during the 90-day postoperative period in the cohort was lower than in an age-matched background population, SMR 0.57 (CI 95% 0.39-0.75). There was no statistically significant difference in 90-day mortality according to surgical method, RARP vs. RRP (odds ratio, OR 1.14; 95% CI, 0.46-2.81). Postoperative 90-day mortality decreased over time, 2008-2012 vs. 1998-2007 (OR 0.44; 95% CI, 0.21-0.95), mainly due to decreased mortality after RARP. Limitations of our study include the non-randomised design and that more RARP were performed in recent years compared to RRP. Conclusion 90-day postoperative mortality was low after RARP and RRP and there was nostatistically significant difference between the methods. Given the long life expectancy among men with low and intermediate risk prostate cancer, very low postoperative mortality is a prerequisite for RP which was fulfilled by both RRP and RARP. The selection of healthy men for RP is highlighted by the lower 90-day mortality after RP compared to the background population. PMID:26762928

A novel sulfate-reducing bacteria detection method based on inhibition of cysteine protease activity.

PubMed

Qi, Peng; Zhang, Dun; Wan, Yi

2014-11-01

Sulfate-reducing bacteria (SRB) have been extensively studied in corrosion and environmental science. However, fast enumeration of SRB population is still a difficult task. This work presents a novel specific SRB detection method based on inhibition of cysteine protease activity. The hydrolytic activity of cysteine protease was inhibited by taking advantage of sulfide, the characteristic metabolic product of SRB, to attack active cysteine thiol group in cysteine protease catalytic sites. The active thiol S-sulfhydration process could be used for SRB detection, since the amount of sulfide accumulated in culture medium was highly related with initial bacterial concentration. The working conditions of cysteine protease have been optimized to obtain better detection capability, and the SRB detection performances have been evaluated in this work. The proposed SRB detection method based on inhibition of cysteine protease activity avoided the use of biological recognition elements. In addition, compared with the widely used most probable number (MPN) method which would take up to at least 15days to accomplish whole detection process, the method based on inhibition of papain activity could detect SRB in 2 days, with a detection limit of 5.21×10(2) cfu mL(-1). The detection time for SRB population quantitative analysis was greatly shortened. Copyright © 2014 Elsevier B.V. All rights reserved.

The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography.

PubMed

Lapierre, Marguerite; Blin, Camille; Lambert, Amaury; Achaz, Guillaume; Rocha, Eduardo P C

2016-07-01

Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Defining Primary Care Shortage Areas: Do GIS-based Measures Yield Different Results?

PubMed

Daly, Michael R; Mellor, Jennifer M; Millones, Marco

2018-02-12

To examine whether geographic information systems (GIS)-based physician-to-population ratios (PPRs) yield determinations of geographic primary care shortage areas that differ from those based on bounded-area PPRs like those used in the Health Professional Shortage Area (HPSA) designation process. We used geocoded data on primary care physician (PCP) locations and census block population counts from 1 US state to construct 2 shortage area indicators. The first is a bounded-area shortage indicator defined without GIS methods; the second is a GIS-based measure that measures the populations' spatial proximity to PCP locations. We examined agreement and disagreement between bounded shortage areas and GIS-based shortage areas. Bounded shortage area indicators and GIS-based shortage area indicators agree for the census blocks where the vast majority of our study populations reside. Specifically, 95% and 98% of the populations in our full and urban samples, respectively, reside in census blocks where the 2 indicators agree. Although agreement is generally high in rural areas (ie, 87% of the rural population reside in census blocks where the 2 indicators agree), agreement is significantly lower compared to urban areas. One source of disagreement suggests that bounded-area measures may "overlook" some shortages in rural areas; however, other aspects of the HPSA designation process likely mitigate this concern. Another source of disagreement arises from the border-crossing problem, and it is more prevalent. The GIS-based PPRs we employed would yield shortage area determinations that are similar to those based on bounded-area PPRs defined for Primary Care Service Areas. Disagreement rates were lower than previous studies have found. © 2018 National Rural Health Association.

Probing messenger RNA conformational heterogeneity using single-molecule fluorescence anisotropy

NASA Astrophysics Data System (ADS)

Sinha, Deepak; Sastry, Srikanth; Shivashankar, G. V.

2006-03-01

In this letter we describe a method to probe biomolecular conformations and their dynamics at the single molecule level. We show, using fluorescence anisotropy based methods, that the hydrodynamic volume of biomolecules captures the intrinsic heterogeneity within a population. Population distributions of conformations and their dynamics are studied by making anisotropy measurements on one molecule at a time within a confocal volume. The mean anisotropy of mRNA is lowered on addition of salt while the spread remains the same. The intrinsic heterogeneity is revealed when conformational transitions are frozen, resulting in a drastic increase in the spread of the anisotropy. These studies reveal that mRNA samples a broad range of conformations.

Population Size Estimation of Men Who Have Sex with Men in Ho Chi Minh City and Nghe An Using Social App Multiplier Method.

PubMed

Safarnejad, Ali; Nga, Nguyen Thien; Son, Vo Hai

2017-06-01

This study aims to estimate the number of men who have sex with men (MSM) in Ho Chi Minh City (HCMC) and Nghe An province, Viet Nam, using a novel method of population size estimation, and to assess the feasibility of the method in implementation. An innovative approach to population size estimation grounded on the principles of the multiplier method, and using social app technology and internet-based surveys was undertaken among MSM in two regions of Viet Nam in 2015. Enumeration of active users of popular social apps for MSM in Viet Nam was conducted over 4 weeks. Subsequently, an independent online survey was done using respondent driven sampling. We also conducted interviews with key informants in Nghe An and HCMC on their experience and perceptions of this method and other methods of size estimation. The population of MSM in Nghe An province was estimated to be 1765 [90% CI 1251-3150]. The population of MSM in HCMC was estimated to be 37,238 [90% CI 24,146-81,422]. These estimates correspond to 0.17% of the adult male population in Nghe An province [90% CI 0.12-0.30], and 1.35% of the adult male population in HCMC [90% CI 0.87-2.95]. Our size estimates of the MSM population (1.35% [90% CI 0.87%-2.95%] of the adult male population in HCMC) fall within current standard practice of estimating 1-3% of adult male population in big cities. Our size estimates of the MSM population (0.17% [90% CI 0.12-0.30] of the adult male population in Nghe An province) are lower than the current standard practice of estimating 0.5-1.5% of adult male population in rural provinces. These estimates can provide valuable information for sub-national level HIV prevention program planning and evaluation. Furthermore, we believe that our results help to improve application of this population size estimation method in other regions of Viet Nam.

TEACH: An Ethogram-Based Method to Observe and Record Teaching Behavior

ERIC Educational Resources Information Center

Kline, Michelle Ann

2017-01-01

Teaching has attracted growing research attention in studies of human and animal behavior as a crucial behavior that coevolved with human cultural capacities. However, the synthesis of data on teaching across species and across human populations has proven elusive because researchers use a variety of definitions and methods to approach the topic.…

Training Needs Assessment of Technical Skills in Managers of Tehran Electricity Distribution Company

ERIC Educational Resources Information Center

Koohi, Amir Hasan; Ghandali, Fatemeh; Dehghan, Hasan; Ghandali, Najme

2016-01-01

Current dissertation has been conducted in order to investigate and detect training needs of the mangers (top and middle) in Tehran Electricity Distribution Company. Research method is applied kind based on its purpose. Due to data collection method, this query is descriptive-survey type. Statistical population in this study is all of managers in…

Impact of Rainfall, Land-Cover and Population Growth on Groundwater - A Case Study From Karnataka State, India

NASA Astrophysics Data System (ADS)

Srivastav, R. K.; Chinnapa Reddy, A. R.

2015-12-01

Recent trends in climate, land-use pattern and population has affected almost every portable water resources in the world. Due to depleting surface water and untimely distribution of precipitation, the demand to use groundwater has increased considerably. Further recent studies have shown that the groundwater stress is more in developing countries like India. This study focuses on understanding the impacts of three major factors (i.e., rainfall, land-cover and population growth) effecting the groundwater levels. For this purpose, the correlation between the trends in groundwater time series is compared with trends in rainfall, land-cover and population growth. To detect the trends in time series, two statistical methods namely, least square method and Mann-Kendall method, are adopted. The results were analyzed based on the measurements from 1800 observation wells in the Karnataka state, India. The data is obtained for a total of 9 year time period ranging from 2005 to 2013. A gridded precipitation data of 0.5o× 0.5o over the entire region is used. The change in land-cover and population data was approximately obtained from the local governing bodies. The early results show significant correlation between rainfall and groundwater time series trends. The outcomes will assess the vulnerability of groundwater levels under changing physical and hydroclimatic conditions, especially under climate change.

On Facilitating the use of HARDI in population studies by creating Rotation-Invariant Markers

PubMed Central

Caruyer, Emmanuel; Verma, Ragini

2014-01-01

We design and evaluate a novel method to compute rotationally invariant features using High Angular Resolution Diffusion Imaging (HARDI) data. These measures quantify the complexity of the angular diffusion profile modeled using a higher order model, thereby giving more information than classical diffusion tensor-derived parameters. The method is based on the spherical harmonic (SH) representation of the angular diffusion information, and is generalizable to a range of HARDI reconstruction models. These scalars are obtained as homogeneous polynomials of the SH representation of a HARDI reconstruction model. We show that finding such polynomials is equivalent to solving a large linear system of equations, and present a numerical method based on sparse matrices to efficiently solve this system. Among the solutions, we only keep a subset of algebraically independent polynomials, using an algorithm based on a numerical implementation of the Jacobian criterion. We compute a set of 12 or 25 rotationally invariant measures representative of the underlying white matter for the rank-4 or rank-6 spherical harmonics (SH) representation of the apparent diffusion coefficient (ADC) profile, respectively. Synthetic data was used to investigate and quantify the difference in contrast. Real data acquired with multiple repetitions showed that within subject variation in the invariants was less than the difference across subjects - facilitating their use to study population differences. These results demonstrate that our measures are able to characterize white matter, especially complex white matter found in regions of fiber crossings and hence can be used to derive new biomarkers for HARDI and can be used for HARDI-based population analysis. PMID:25465846

Social network analysis of the genetic structure of Pacific islanders.

PubMed

Terrell, John Edward

2010-05-01

Social network analysis (SNA) is a body of theory and a set of relatively new computer-aided techniques used in the analysis and study of relational data. Recent studies of autosomal markers from over 40 human populations in the south-western Pacific have further documented the remarkable degree of genetic diversity in this part of the world. I report additional analysis using SNA methods contributing new controlled observations on the structuring of genetic diversity among these islanders. These SNA mappings are then compared with model-based network expectations derived from the geographic distances among the same populations. Previous studies found that genetic divergence among island Melanesian populations is organised by island, island size/topography, and position (coastal vs. inland), and that similarities observed correlate only weakly with an isolation-by-distance model. Using SNA methods, however, improves the resolution of among population comparison, and suggests that isolation by distance constrained by social networks together with position (coastal/inland) accounts for much of the population structuring observed. The multilocus data now available is also in accord with current thinking on the impact of major biogeographical transformations on prehistoric colonisation and post-settlement human interaction in Oceania.

Assessing the Generalizability of Randomized Trial Results to Target Populations

PubMed Central

Stuart, Elizabeth A.; Bradshaw, Catherine P.; Leaf, Philip J.

2014-01-01

Recent years have seen increasing interest in and attention to evidence-based practices, where the “evidence” generally comes from well-conducted randomized trials. However, while those trials yield accurate estimates of the effect of the intervention for the participants in the trial (known as “internal validity”), they do not always yield relevant information about the effects in a particular target population (known as “external validity”). This may be due to a lack of specification of a target population when designing the trial, difficulties recruiting a sample that is representative of a pre-specified target population, or to interest in considering a target population somewhat different from the population directly targeted by the trial. This paper first provides an overview of existing design and analysis methods for assessing and enhancing the ability of a randomized trial to estimate treatment effects in a target population. It then provides a case study using one particular method, which weights the subjects in a randomized trial to match the population on a set of observed characteristics. The case study uses data from a randomized trial of School-wide Positive Behavioral Interventions and Supports (PBIS); our interest is in generalizing the results to the state of Maryland. In the case of PBIS, after weighting, estimated effects in the target population were similar to those observed in the randomized trial. The paper illustrates that statistical methods can be used to assess and enhance the external validity of randomized trials, making the results more applicable to policy and clinical questions. However, there are also many open research questions; future research should focus on questions of treatment effect heterogeneity and further developing these methods for enhancing external validity. Researchers should think carefully about the external validity of randomized trials and be cautious about extrapolating results to specific populations unless they are confident of the similarity between the trial sample and that target population. PMID:25307417

Assessing the generalizability of randomized trial results to target populations.

PubMed

Stuart, Elizabeth A; Bradshaw, Catherine P; Leaf, Philip J

2015-04-01

Recent years have seen increasing interest in and attention to evidence-based practices, where the "evidence" generally comes from well-conducted randomized trials. However, while those trials yield accurate estimates of the effect of the intervention for the participants in the trial (known as "internal validity"), they do not always yield relevant information about the effects in a particular target population (known as "external validity"). This may be due to a lack of specification of a target population when designing the trial, difficulties recruiting a sample that is representative of a prespecified target population, or to interest in considering a target population somewhat different from the population directly targeted by the trial. This paper first provides an overview of existing design and analysis methods for assessing and enhancing the ability of a randomized trial to estimate treatment effects in a target population. It then provides a case study using one particular method, which weights the subjects in a randomized trial to match the population on a set of observed characteristics. The case study uses data from a randomized trial of school-wide positive behavioral interventions and supports (PBIS); our interest is in generalizing the results to the state of Maryland. In the case of PBIS, after weighting, estimated effects in the target population were similar to those observed in the randomized trial. The paper illustrates that statistical methods can be used to assess and enhance the external validity of randomized trials, making the results more applicable to policy and clinical questions. However, there are also many open research questions; future research should focus on questions of treatment effect heterogeneity and further developing these methods for enhancing external validity. Researchers should think carefully about the external validity of randomized trials and be cautious about extrapolating results to specific populations unless they are confident of the similarity between the trial sample and that target population.

Towards a global water scarcity risk assessment framework: using scenarios and risk distributions

NASA Astrophysics Data System (ADS)

Veldkamp, Ted; Wada, Yoshihide; Aerts, Jeroen; Ward, Philip

2016-04-01

Over the past decades, changing hydro-climatic and socioeconomic conditions have led to increased water scarcity problems. A large number of studies have shown that these water scarcity conditions will worsen in the near future. Despite numerous calls for risk-based assessments of water scarcity, a framework that includes UNISDR's definition of risk does not yet exist at the global scale. This study provides a first step towards such a risk-based assessment, applying a Gamma distribution to estimate water scarcity conditions at the global scale under historic and future conditions, using multiple climate change projections and socioeconomic scenarios. Our study highlights that water scarcity risk increases given all future scenarios, up to >56.2% of the global population in 2080. Looking at the drivers of risk, we find that population growth outweigh the impacts of climate change at global and regional scales. Using a risk-based method to assess water scarcity in terms of Expected Annual Exposed Population, we show the results to be less sensitive than traditional water scarcity assessments to the use of fixed threshold to represent different levels of water scarcity. This becomes especially important when moving from global to local scales, whereby deviations increase up to 50% of estimated risk levels. Covering hazard, exposure, and vulnerability, risk-based methods are well-suited to assess water scarcity adaptation. Completing the presented risk framework therefore offers water managers a promising perspective to increase water security in a well-informed and adaptive manner.

GIS and Remote Sensing Use in the Exploration of Lyme Disease Epidemiology

PubMed Central

Ozdenerol, Esra

2015-01-01

Given the relatively recent recognition of Lyme disease (LD) by CDC in 1990 as a nationally notifiable infectious condition, the rise of reported human cases every year argues for a better understanding of its geographic scope. The aim of this inquiry was to explore research conducted on spatiotemporal patterns of Lyme disease in order to identify strategies for implementing vector and reservoir-targeted interventions. The focus of this review is on the use of GIS-based methods to study populations of the reservoir hosts, vectors and humans in addition to the spatiotemporal interactions between these populations. New GIS-based studies are monitoring occurrence at the macro-level, and helping pinpoint areas of occurrence at the micro-level, where spread within populations of reservoir hosts, clusters of infected ticks and tick to human transmission may be better understood. PMID:26633445

A simple real-time polymerase chain reaction (PCR)-based assay for authentication of the Chinese Panax ginseng cultivar Damaya from a local ginseng population.

PubMed

Wang, H; Wang, J; Li, G

2016-06-27

Panax ginseng is one of the most important medicinal plants in the Orient. Owing to its increasing demand in the world market, cultivated ginseng has become the main source of medicinal material. Among the Chinese ginseng cultivars, Damaya commands higher prices and is grown in significant proportions among the local ginseng population. Due to the lack of rapid and accurate authentication methods, Damaya is distributed among different cultivars in the local ginseng population in China. Here, we identified a unique, Damaya-specific single nucleotide polymorphism (SNP) site present in the second intron of mitochondrial cytochrome c oxidase subunit 2 (cox2). Based on this SNP, a Damaya cultivar-specific primer was designed and an allele-specific polymerase chain reaction (PCR) was optimized for the effective molecular authentication of Damaya. We designed a method by combining a simple DNA isolation method with real-time allele-specific PCR using SYBR Green I fluorescent dye, and proved its efficacy in clearly discriminated Damaya cultivar from other Chinese ginseng cultivars according to the allelic discrimination analysis. Hence, this study provides a simple and rapid assay for the differentiation and conservation of Damaya from the local Chinese ginseng population.

The prevalence of age-related maculopathy by geographic region and ethnicity.

PubMed

Klein, R; Klein, B E; Cruickshanks, K J

1999-05-01

The prevalence of age-related maculopathy (ARM) varies considerably in different locations and racial/ethnic groups around the world. At present there are insufficient data to determine whether it is likely that these differences in prevalence, especially for the early forms of ARM are due to variations in genetic and environmental factors or due to variations in age of the cohorts and methods used to ascertain and define ARM. In three population-based studies of whites living in Beaver Dam, Wisconsin, Blue Mountains, Australia, and Rotterdam, The Netherlands, in which similar methods of ascertainment and classification were used to detect and define ARM, late ARM was present in 1.2%, 1.4%, and 1.2% of the population less than 86 years of age, respectively. While data from clinical studies suggest that late ARM associated with choroidal neovascularization is rare in blacks compared with whites, some epidemiological studies suggest that late ARM may be similar in blacks and whites. There are still too few data from various ethnic/racial groups around the world and too few population-based data in older Hispanic and Asian populations to make meaningful comparisons. There is a need for further research into the distribution of ARM and its possible causes using similar methodologies to ascertain and define the disease. Further insights will be gained when genotypes associated with ARM are discovered.

Hybridization of decomposition and local search for multiobjective optimization.

PubMed

Ke, Liangjun; Zhang, Qingfu; Battiti, Roberto

2014-10-01

Combining ideas from evolutionary algorithms, decomposition approaches, and Pareto local search, this paper suggests a simple yet efficient memetic algorithm for combinatorial multiobjective optimization problems: memetic algorithm based on decomposition (MOMAD). It decomposes a combinatorial multiobjective problem into a number of single objective optimization problems using an aggregation method. MOMAD evolves three populations: 1) population P(L) for recording the current solution to each subproblem; 2) population P(P) for storing starting solutions for Pareto local search; and 3) an external population P(E) for maintaining all the nondominated solutions found so far during the search. A problem-specific single objective heuristic can be applied to these subproblems to initialize the three populations. At each generation, a Pareto local search method is first applied to search a neighborhood of each solution in P(P) to update P(L) and P(E). Then a single objective local search is applied to each perturbed solution in P(L) for improving P(L) and P(E), and reinitializing P(P). The procedure is repeated until a stopping condition is met. MOMAD provides a generic hybrid multiobjective algorithmic framework in which problem specific knowledge, well developed single objective local search and heuristics and Pareto local search methods can be hybridized. It is a population based iterative method and thus an anytime algorithm. Extensive experiments have been conducted in this paper to study MOMAD and compare it with some other state-of-the-art algorithms on the multiobjective traveling salesman problem and the multiobjective knapsack problem. The experimental results show that our proposed algorithm outperforms or performs similarly to the best so far heuristics on these two problems.

Failure to Thrive in the Term and Preterm Infants of Mothers Depressed in the Postnatal Period: A Population-Based Birth Cohort Study

ERIC Educational Resources Information Center

Drewett, Robert; Blair, Peter; Emmett, Pauline; Emond, Alan

2004-01-01

Aims: To examine the relationship between failure to thrive in preterm and term infants and postnatal depression in their mothers. Method: In a whole population birth cohort of 12,391 infants (excluding those born after term or with major congenital abnormalities) failure to thrive over the first nine months was identified using a conditional…

Detection of selective sweeps in structured populations: a comparison of recent methods.

PubMed

Vatsiou, Alexandra I; Bazin, Eric; Gaggiotti, Oscar E

2016-01-01

Identifying genomic regions targeted by positive selection has been a long-standing interest of evolutionary biologists. This objective was difficult to achieve until the recent emergence of next-generation sequencing, which is fostering the development of large-scale catalogues of genetic variation for increasing number of species. Several statistical methods have been recently developed to analyse these rich data sets, but there is still a poor understanding of the conditions under which these methods produce reliable results. This study aims at filling this gap by assessing the performance of genome-scan methods that consider explicitly the physical linkage among SNPs surrounding a selected variant. Our study compares the performance of seven recent methods for the detection of selective sweeps (iHS, nSL, EHHST, xp-EHH, XP-EHHST, XPCLR and hapFLK). We use an individual-based simulation approach to investigate the power and accuracy of these methods under a wide range of population models under both hard and soft sweeps. Our results indicate that XPCLR and hapFLK perform best and can detect soft sweeps under simple population structure scenarios if migration rate is low. All methods perform poorly with moderate-to-high migration rates, or with weak selection and very poorly under a hierarchical population structure. Finally, no single method is able to detect both starting and nearly completed selective sweeps. However, combining several methods (XPCLR or hapFLK with iHS or nSL) can greatly increase the power to pinpoint the selected region. © 2015 John Wiley & Sons Ltd.

A hierarchical model for spatial capture-recapture data

USGS Publications Warehouse

Royle, J. Andrew; Young, K.V.

2008-01-01

Estimating density is a fundamental objective of many animal population studies. Application of methods for estimating population size from ostensibly closed populations is widespread, but ineffective for estimating absolute density because most populations are subject to short-term movements or so-called temporary emigration. This phenomenon invalidates the resulting estimates because the effective sample area is unknown. A number of methods involving the adjustment of estimates based on heuristic considerations are in widespread use. In this paper, a hierarchical model of spatially indexed capture recapture data is proposed for sampling based on area searches of spatial sample units subject to uniform sampling intensity. The hierarchical model contains explicit models for the distribution of individuals and their movements, in addition to an observation model that is conditional on the location of individuals during sampling. Bayesian analysis of the hierarchical model is achieved by the use of data augmentation, which allows for a straightforward implementation in the freely available software WinBUGS. We present results of a simulation study that was carried out to evaluate the operating characteristics of the Bayesian estimator under variable densities and movement patterns of individuals. An application of the model is presented for survey data on the flat-tailed horned lizard (Phrynosoma mcallii) in Arizona, USA.

[Critical revision of the available methods for evaluate the body composition in population-based and clinical studies].

PubMed

Rezende, Fabiane; Rosado, Lina; Franceschinni, Sylvia; Rosado, Gilberto; Ribeiro, Rita; Marins, João Carlos Bouzas

2007-12-01

The corporal composition evaluation is extremely important for the individual and population nutritional state diagnosis and for the establishment of appropriate clinical-nutritional conducts. An excess of body fat is frequently associated with important metabolic alterations and chronic diseases, such as diabetes, hypertension and dyslipidemia The availability of methods to assess body composition is essential to evaluate health status of individuals. There are several methods for the corporal composition analysis, and it is important to know the limitation of each one and his/her validity so that the obtained estimates are reliable and correctly interpreted. The purpose of this study was to revise the applicability of some nutritional state indicators and corporal composition evaluation methods, such as corporal mass index, waist circumference and waist-hip relation, skinfold measurements, bioelectrical impedance analysis and near-infrared interactance.

'Aussie normals': an a priori study to develop clinical chemistry reference intervals in a healthy Australian population.

PubMed

Koerbin, G; Cavanaugh, J A; Potter, J M; Abhayaratna, W P; West, N P; Glasgow, N; Hawkins, C; Armbruster, D; Oakman, C; Hickman, P E

2015-02-01

Development of reference intervals is difficult, time consuming, expensive and beyond the scope of most laboratories. The Aussie Normals study is a direct a priori study to determine reference intervals in healthy Australian adults. All volunteers completed a health and lifestyle questionnaire and exclusion was based on conditions such as pregnancy, diabetes, renal or cardiovascular disease. Up to 91 biochemical analyses were undertaken on a variety of analytical platforms using serum samples collected from 1856 volunteers. We report on our findings for 40 of these analytes and two calculated parameters performed on the Abbott ARCHITECTci8200/ci16200 analysers. Not all samples were analysed for all assays due to volume requirements or assay/instrument availability. Results with elevated interference indices and those deemed unsuitable after clinical evaluation were removed from the database. Reference intervals were partitioned based on the method of Harris and Boyd into three scenarios, combined gender, males and females and age and gender. We have performed a detailed reference interval study on a healthy Australian population considering the effects of sex, age and body mass. These reference intervals may be adapted to other manufacturer's analytical methods using method transference.

A prevalence-based association test for case-control studies.

PubMed

Ryckman, Kelli K; Jiang, Lan; Li, Chun; Bartlett, Jacquelaine; Haines, Jonathan L; Williams, Scott M

2008-11-01

Genetic association is often determined in case-control studies by the differential distribution of alleles or genotypes. Recent work has demonstrated that association can also be assessed by deviations from the expected distributions of alleles or genotypes. Specifically, multiple methods motivated by the principles of Hardy-Weinberg equilibrium (HWE) have been developed. However, these methods do not take into account many of the assumptions of HWE. Therefore, we have developed a prevalence-based association test (PRAT) as an alternative method for detecting association in case-control studies. This method, also motivated by the principles of HWE, uses an estimated population allele frequency to generate expected genotype frequencies instead of using the case and control frequencies separately. Our method often has greater power, under a wide variety of genetic models, to detect association than genotypic, allelic or Cochran-Armitage trend association tests. Therefore, we propose PRAT as a powerful alternative method of testing for association.

Advanced Method for Isolation of Mouse Hepatocytes, Liver Sinusoidal Endothelial Cells, and Kupffer Cells.

PubMed

Liu, Jia; Huang, Xuan; Werner, Melanie; Broering, Ruth; Yang, Dongliang; Lu, Mengji

2017-01-01

Separation of pure cell populations from the liver is a prerequisite to study the role of hepatic parenchymal and non-parenchymal cells in liver physiology, pathophysiology, and immunology. Traditional methods for hepatic cell separation usually purify only single cell types from liver specimens. Here, we describe an efficient method that can simultaneously purify populations of hepatocytes (HCs), liver sinusoidal endothelial cells (LSECs), and Kupffer cells (KCs) from a single mouse liver specimen. A liberase-based perfusion technique in combination with a low-speed centrifugation and magnetic-activated cell sorting (MACS) led to the isolation and purification of HCs, KCs, and LSECs with high yields and purity.

Insurance problems among inflammatory bowel disease patients: results of a Dutch population based study

PubMed Central

Russel, M G V M; Ryan, B M; Dagnelie, P C; de Rooij, M; Sijbrandij, J; Feleus, A; Hesselink, M; Muris, J W; Stockbrugger, R

2003-01-01

Background and aims: The majority of patients with inflammatory bowel disease (IBD) have a normal life expectancy and therefore should not be weighted when applying for life assurance. There is scant literature on this topic. In this study our aim was to document and compare the incidence of difficulties in application for life and medical insurance in a population based cohort of IBD patients and matched population controls. Methods: A population based case control study of 1126 IBD patients and 1723 controls. Based on a detailed questionnaire, the frequency and type of difficulties encountered when applying for life and medical insurance in matched IBD and control populations were appraised. Results: In comparison with controls, IBD patients had an 87-fold increased risk of encountering difficulties when applying for life assurance (odds ratio (OR) 87 (95% confidence interval (CI) 31–246)), with a heavily weighted premium being the most common problem. Patients of high educational status, with continuous disease activity, and who smoked had the highest odds of encountering such problems. Medical insurance difficulties were fivefold more common in IBD patients compared with controls (OR 5.4 (95% CI 2.3–13)) although no specific disease or patient characteristics were identified as associated with such difficulties. Conclusions: This is the first detailed case control study that has investigated insurance difficulties among IBD patients. Acquiring life and medical insurance constituted a major problem for IBD patients in this study. These results are likely to be more widely representative given that most insurance companies use international guidelines for risk assessment. In view of the recent advances in therapy and promising survival data on IBD patients, evidence based guidelines for risk assessment of IBD patients by insurance companies should be drawn up to prevent possible discriminatory practices. PMID:12584216

Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis.

PubMed

Herrera, Carlos M; Bazaga, Pilar

2010-08-01

*In plants, epigenetic variations based on DNA methylation are often heritable and could influence the course of evolution. Before this hypothesis can be assessed, fundamental questions about epigenetic variation remain to be addressed in a real-world context, including its magnitude, structuring within and among natural populations, and autonomy in relation to the genetic context. *Extent and patterns of cytosine methylation, and the relationship to adaptive genetic divergence between populations, were investigated for wild populations of the southern Spanish violet Viola cazorlensis (Violaceae) using the methylation-sensitive amplified polymorphism (MSAP) technique, a modification of the amplified fragment length polymorphism method (AFLP) based on the differential sensitivity of isoschizomeric restriction enzymes to site-specific cytosine methylation. *The genome of V. cazorlensis plants exhibited extensive levels of methylation, and methylation-based epigenetic variation was structured into distinct between- and within- population components. Epigenetic differentiation of populations was correlated with adaptive genetic divergence revealed by a Bayesian population-genomic analysis of AFLP data. Significant associations existed at the individual genome level between adaptive AFLP loci and the methylation state of methylation-susceptible MSAP loci. *Population-specific, divergent patterns of correlated selection on epigenetic and genetic individual variation could account for the coordinated epigenetic-genetic adaptive population differentiation revealed by this study.

Accuracy of predicting genomic breeding values for residual feed intake in Angus and Charolais beef cattle.

PubMed

Chen, L; Schenkel, F; Vinsky, M; Crews, D H; Li, C

2013-10-01

In beef cattle, phenotypic data that are difficult and/or costly to measure, such as feed efficiency, and DNA marker genotypes are usually available on a small number of animals of different breeds or populations. To achieve a maximal accuracy of genomic prediction using the phenotype and genotype data, strategies for forming a training population to predict genomic breeding values (GEBV) of the selection candidates need to be evaluated. In this study, we examined the accuracy of predicting GEBV for residual feed intake (RFI) based on 522 Angus and 395 Charolais steers genotyped on SNP with the Illumina Bovine SNP50 Beadchip for 3 training population forming strategies: within breed, across breed, and by pooling data from the 2 breeds (i.e., combined). Two other scenarios with the training and validation data split by birth year and by sire family within a breed were also investigated to assess the impact of genetic relationships on the accuracy of genomic prediction. Three statistical methods including the best linear unbiased prediction with the relationship matrix defined based on the pedigree (PBLUP), based on the SNP genotypes (GBLUP), and a Bayesian method (BayesB) were used to predict the GEBV. The results showed that the accuracy of the GEBV prediction was the highest when the prediction was within breed and when the validation population had greater genetic relationships with the training population, with a maximum of 0.58 for Angus and 0.64 for Charolais. The within-breed prediction accuracies dropped to 0.29 and 0.38, respectively, when the validation populations had a minimal pedigree link with the training population. When the training population of a different breed was used to predict the GEBV of the validation population, that is, across-breed genomic prediction, the accuracies were further reduced to 0.10 to 0.22, depending on the prediction method used. Pooling data from the 2 breeds to form the training population resulted in accuracies increased to 0.31 and 0.43, respectively, for the Angus and Charolais validation populations. The results suggested that the genetic relationship of selection candidates with the training population has a greater impact on the accuracy of GEBV using the Illumina Bovine SNP50 Beadchip. Pooling data from different breeds to form the training population will improve the accuracy of across breed genomic prediction for RFI in beef cattle.

Spatiotemporal Interpolation Methods for the Application of Estimating Population Exposure to Fine Particulate Matter in the Contiguous U.S. and a Real-Time Web Application.

PubMed

Li, Lixin; Zhou, Xiaolu; Kalo, Marc; Piltner, Reinhard

2016-07-25

Appropriate spatiotemporal interpolation is critical to the assessment of relationships between environmental exposures and health outcomes. A powerful assessment of human exposure to environmental agents would incorporate spatial and temporal dimensions simultaneously. This paper compares shape function (SF)-based and inverse distance weighting (IDW)-based spatiotemporal interpolation methods on a data set of PM2.5 data in the contiguous U.S. Particle pollution, also known as particulate matter (PM), is composed of microscopic solids or liquid droplets that are so small that they can get deep into the lungs and cause serious health problems. PM2.5 refers to particles with a mean aerodynamic diameter less than or equal to 2.5 micrometers. Based on the error statistics results of k-fold cross validation, the SF-based method performed better overall than the IDW-based method. The interpolation results generated by the SF-based method are combined with population data to estimate the population exposure to PM2.5 in the contiguous U.S. We investigated the seasonal variations, identified areas where annual and daily PM2.5 were above the standards, and calculated the population size in these areas. Finally, a web application is developed to interpolate and visualize in real time the spatiotemporal variation of ambient air pollution across the contiguous U.S. using air pollution data from the U.S. Environmental Protection Agency (EPA)'s AirNow program.

Spatiotemporal Interpolation Methods for the Application of Estimating Population Exposure to Fine Particulate Matter in the Contiguous U.S. and a Real-Time Web Application

PubMed Central

Li, Lixin; Zhou, Xiaolu; Kalo, Marc; Piltner, Reinhard

2016-01-01

Appropriate spatiotemporal interpolation is critical to the assessment of relationships between environmental exposures and health outcomes. A powerful assessment of human exposure to environmental agents would incorporate spatial and temporal dimensions simultaneously. This paper compares shape function (SF)-based and inverse distance weighting (IDW)-based spatiotemporal interpolation methods on a data set of PM2.5 data in the contiguous U.S. Particle pollution, also known as particulate matter (PM), is composed of microscopic solids or liquid droplets that are so small that they can get deep into the lungs and cause serious health problems. PM2.5 refers to particles with a mean aerodynamic diameter less than or equal to 2.5 micrometers. Based on the error statistics results of k-fold cross validation, the SF-based method performed better overall than the IDW-based method. The interpolation results generated by the SF-based method are combined with population data to estimate the population exposure to PM2.5 in the contiguous U.S. We investigated the seasonal variations, identified areas where annual and daily PM2.5 were above the standards, and calculated the population size in these areas. Finally, a web application is developed to interpolate and visualize in real time the spatiotemporal variation of ambient air pollution across the contiguous U.S. using air pollution data from the U.S. Environmental Protection Agency (EPA)’s AirNow program. PMID:27463722

Connecting micro dynamics and population distributions in system dynamics models

PubMed Central

Rahmandad, Hazhir; Chen, Hsin-Jen; Xue, Hong; Wang, Youfa

2014-01-01

Researchers use system dynamics models to capture the mean behavior of groups of indistinguishable population elements (e.g., people) aggregated in stock variables. Yet, many modeling problems require capturing the heterogeneity across elements with respect to some attribute(s) (e.g., body weight). This paper presents a new method to connect the micro-level dynamics associated with elements in a population with the macro-level population distribution along an attribute of interest without the need to explicitly model every element. We apply the proposed method to model the distribution of Body Mass Index and its changes over time in a sample population of American women obtained from the U.S. National Health and Nutrition Examination Survey. Comparing the results with those obtained from an individual-based model that captures the same phenomena shows that our proposed method delivers accurate results with less computation than the individual-based model. PMID:25620842

The value of customised centiles in assessing perinatal mortality risk associated with parity and maternal size.

PubMed

Gardosi, J; Clausson, B; Francis, A

2009-09-01

We wanted to compare customised and population standards for defining smallness for gestational age (SGA) in the assessment of perinatal mortality risk associated with parity and maternal size. Population-based cohort study. Sweden. Swedish Birth Registry database 1992-1995 with 354 205 complete records. Coefficients were derived and applied to determine SGA by the fully customised method, or by adjustment for fetal sex only, and using the same fetal weight standard. Perinatal deaths and rates of small for gestational age (SGA) babies within subgroups stratified by parity, body mass index (BMI) and maternal size within the BMI range of 20.0-24.9. Perinatal mortality rates (PMR) had a U-shaped distribution in parity groups, increased proportionately with maternal BMI, and had no association with maternal size within the normal BMI range. For each of these subgroups, SGA rates determined by the customised method showed strong association with the PMR. In contrast, SGA based on uncustomised, population-based centiles had poor correlation with perinatal mortality. The increased perinatal mortality risk in pregnancies of obese mothers was associated with an increased risk of SGA using customised centiles, and a decreased risk of SGA using population-based centiles. The use of customised centiles to determine SGA improves the identification of pregnancies which are at increased risk of perinatal death.

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.

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 matched case-control study. PMID:21513554

Estimating numbers of greater prairie-chickens using mark-resight techniques

USGS Publications Warehouse

Clifton, A.M.; Krementz, D.G.

2006-01-01

Current monitoring efforts for greater prairie-chicken (Tympanuchus cupido pinnatus) populations indicate that populations are declining across their range. Monitoring the population status of greater prairie-chickens is based on traditional lek surveys (TLS) that provide an index without considering detectability. Estimators, such as immigration-emigration joint maximum-likelihood estimator from a hypergeometric distribution (IEJHE), can account for detectability and provide reliable population estimates based on resightings. We evaluated the use of mark-resight methods using radiotelemetry to estimate population size and density of greater prairie-chickens on 2 sites at a tallgrass prairie in the Flint Hills of Kansas, USA. We used average distances traveled from lek of capture to estimate density. Population estimates and confidence intervals at the 2 sites were 54 (CI 50-59) on 52.9 km 2 and 87 (CI 82-94) on 73.6 km2. The TLS performed at the same sites resulted in population ranges of 7-34 and 36-63 and always produced a lower population index than the mark-resight population estimate with a larger range. Mark-resight simulations with varying male:female ratios of marks indicated that this ratio was important in designing a population study on prairie-chickens. Confidence intervals for estimates when no marks were placed on females at the 2 sites (CI 46-50, 76-84) did not overlap confidence intervals when 40% of marks were placed on females (CI 54-64, 91-109). Population estimates derived using this mark-resight technique were apparently more accurate than traditional methods and would be more effective in detecting changes in prairie-chicken populations. Our technique could improve prairie-chicken management by providing wildlife biologists and land managers with a tool to estimate the population size and trends of lekking bird species, such as greater prairie-chickens.

Autism Spectrum Disorders in Hispanics and Non-Hispanics

ERIC Educational Resources Information Center

Chaidez, Virginia; Hansen, Robin L.; Hertz-Picciotto, Irva

2012-01-01

Objectives: To compare differences in autism between Hispanic and non-Hispanics. We also examined the relationship between multiple language exposure and language function and scores of children. Methods: The Childhood Autism Risks from Genetics and the Environment (CHARGE) study is an ongoing population-based case-control study with children…

Early Vocabulary Delay and Behavioral/Emotional Problems in Early Childhood: The Generation R Study

ERIC Educational Resources Information Center

Henrichs, Jens; Rescorla, Leslie; Donkersloot, Cootje; Schenk, Jacqueline J.; Raat, Hein; Jaddoe, Vincent W. V.; Hofman, Albert; Verhulst, Frank C.; Tiemeier, Henning

2013-01-01

Purpose: The authors tested associations between (a) parent-reported temporary vs. persistent vocabulary delay and (b) parent-reported behavioral/emotional problems in a sample of 5,497 young Dutch children participating in a prospective population-based study. Method: Mothers completed the MacArthur Communicative Development…

Examining biological continuity across the late holocene occupation of the Aleutian Islands using cranial morphometrics and quantitative genetic permutation.

PubMed

Maley, Blaine

2016-05-01

The number of distinct human migrations into the Aleutian Islands during the Holocene has been a recurrent debate in the anthropological literature. Stemming from Hrdlička's sorting of the prehistoric remains into two distinct populations based on archaeological context and cranial measurements, the human occupation of the Aleutian Islands has long been thought to be the consequence of two distinct human migrations, a Paleo-Aleut migration that provided the initial settlement of the islands, and a Neo-Aleut migration that replaced the original settlers around 1000 BP. This study examines the relationship of the Aleut cranial assemblages in the context of greater Alaskan population variability to assess the evidence for a substantial migration into the Aleutian Islands during the late Holocene. A battery of 29 cranial measurements that quantify global cranial shape were analyzed using Euclidean morphometric methods and quantitative genetic permutation methods to examine the plausibility for two distinct Aleut occupations ("Paleo-Aleut" and "Neo-Aleut"), the latter of which is held to share closer phenetic affinities to mainland Alaskan populations than the former. The Aleut skeletal assemblages were arranged according to temporal association, geographic location, and cranial typology, and analyzed within a comparative framework of mainland Alaskan samples using principal coordinates, biological distance and random skewers permutation methods. Regardless of how the Aleut assemblages are divided, they show greater similarity to each other than to any of the mainland Alaskan assemblages. These findings are consistent across the methodological approaches. The results obtained in this study provide no support for a cranial morphology-based subdivision of the Aleuts into two distinct samples, Hence, there is no evidence for a substantial population migration of so-called Neo-Aleuts, nor for a population replacement event of an extant Paleo-Aleut population by a mainland-affiliated Neo-Aleuts population at or after 1000 BP. © 2016 Wiley Periodicals, Inc.

[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.

Feasibility and Acceptability of a Gardening-Based Nutrition Education Program in Preschoolers from Low-Income, Minority Populations

ERIC Educational Resources Information Center

Sharma, Shreela V.; Hedberg, Ann Marie; Skala, Katherine A.; Chuang, Ru-Jye; Lewis, Tamara

2015-01-01

Garden-based lessons are gaining popularity as a means of increasing fruit and vegetable intake among children. The study objective was to pilot test a garden-based preschool curriculum for feasibility and acceptability in Harris County Department of Education Head Start using qualitative and quantitative methods. A total of 103, 3- to 5-year-old…

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

USGS Publications Warehouse

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

2005-01-01

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

Canal Configuration of Mesiobuccal Roots in Permanent Maxillary First Molars in Iranian Population: A Systematic Review

PubMed Central

Naseri, Mandana; Kharazifard, Mohammad Javad

2016-01-01

Objectives: It is essential for clinicians to have adequate knowledge about root canal configurations; although its morphology varies largely in different ethnicities and even in different individuals with the same ethnic background. The current study aims to review the root canal configurations of mesiobuccal roots of maxillary first molars in an Iranian population based on different epidemiological studies. Materials and Methods: A comprehensive search was conducted to retrieve articles related to root canal configuration and prevalence of each type of root canal based on Vertucci’s classification for the mesiobuccal root of maxillary first molars. An electronic search was conducted in Medline, Scopus and Google Scholar from January 1984 to September 2015. The articles were evaluated and methods, population, number of teeth and percentage of each root canal type evaluated in each study were summarized in the data table. Websites such as http://www.magiran.com/ , http://health.barakatkns.com/journal-internal-list and www.sid.ir were used to search all related studies published in Persian. Results: Totally, out of nine studies conducted on the Iranian populations in nine provinces of Iran and 798 teeth, the Vertucci’s type I was the most common type (35.70%), followed by type II (30.37%), type IV (16.66%), type III (7.93%) and type V (2.61%). Conclusions: From this review article, it is concluded that the root canal morphology of mesiobuccal roots of maxillary first molars in the Iranian population predominantly has more than one canal. Therefore, careful evaluation of radiographs and anatomy of the pulp chamber is essential in order to achieve a successful root canal therapy. PMID:28243306

Genome-wide association study of telomere length among South Asians identifies a second RTEL1 association signal

PubMed Central

Zhang, Chenan; Chen, Lin S; Gao, Jianjun; Roy, Shantanu; Shinkle, Justin; Sabarinathan, Mekala; Tong, Lin; Ahmed, Alauddin; Islam, Tariqul; Rakibuz-Zaman, Muhammad; Sarwar, Golam; Shahriar, Hasan; Rahman, Mahfuzar; Yunus, Mohammad; Jasmine, Farzana; Kibriya, Muhammad G; Ahsan, Habibul; Pierce, Brandon L

2018-01-01

Background Leucocyte telomere length (TL) is a potential biomarker of ageing and risk for age-related disease. Leucocyte TL is heritable and shows substantial differences by race/ethnicity. Recent genome-wide association studies (GWAS) report ~10 loci harbouring SNPs associated with leucocyte TL, but these studies focus primarily on populations of European ancestry. Objective This study aims to enhance our understanding of genetic determinants of TL across populations. Methods We performed a GWAS of TL using data on 5075 Bangladeshi adults. We measured TL using one of two technologies (qPCR or a Luminex-based method) and used standardised variables as TL phenotypes. Results Our results replicate previously reported associations in the TERC and TERT regions (P=2.2×10−8 and P=6.4×10−6, respectively). We observed a novel association signal in the RTEL1 gene (intronic SNP rs2297439; P=2.82×10−7) that is independent of previously reported TL-associated SNPs in this region. The minor allele for rs2297439 is common in South Asian populations (≥0.25) but at lower frequencies in other populations (eg, 0.07 in Northern Europeans). Among the eight other previously reported association signals, all were directionally consistent with our study, but only rs8105767 (ZNF208) was nominally significant (P=0.003). SNP-based heritability estimates were as high as 44% when analysing close relatives but much lower when analysing distant relatives only. Conclusions In this first GWAS of TL in a South Asian population, we replicate some, but not all, of the loci reported in prior GWAS of individuals of European ancestry, and we identify a novel second association signal at the RTEL1 locus. PMID:29151059

Sun Exposure and Melanoma Survival: A GEM Study

PubMed Central

Berwick, Marianne; Reiner, Anne S.; Paine, Susan; Armstrong, Bruce K.; Kricker, Anne; Goumas, Chris; Cust, Anne E.; Thomas, Nancy E.; Groben, Pamela A.; From, Lynn; Busam, Klaus; Orlow, Irene; Marrett, Loraine D.; Gallagher, Richard P.; Gruber, Stephen B.; Anton-Culver, Hoda; Rosso, Stefano; Zanetti, Roberto; Kanetsky, Peter A.; Dwyer, Terry; Venn, Alison; Lee-Taylor, Julia; Begg, Colin B.

2014-01-01

Background We previously reported a significant association between higher ultraviolet radiation exposure before diagnosis and greater survival with melanoma in a population-based study in Connecticut. We sought to evaluate the hypothesis that sun exposure prior to diagnosis was associated with greater survival in a larger, international population-based study with more detailed exposure information. Methods We conducted a multi-center, international population-based study in four countries – Australia, Italy, Canada and the United States – with 3,578 cases of melanoma with an average of 7.4 years of follow-up. Measures of sun exposure included sunburn, intermittent exposure, hours of holiday sun exposure, hours of water-related outdoor activities, ambient UVB dose, histological solar elastosis and season of diagnosis. Results Results were not strongly supportive of the earlier hypothesis. Having had any sunburn in one year within 10 years of diagnosis was inversely associated with survival; solar elastosis – a measure of lifetime cumulative exposure – was not. Additionally, none of the intermittent exposure measures – water related activities and sunny holidays - were associated with melanoma-specific survival. Estimated ambient UVB dose was not associated with survival. Conclusion Although there was an apparent protective effect of sunburns within 10 years of diagnosis, there was only weak evidence in this large, international, population-based study of melanoma that sun exposure prior to diagnosis is associated with greater melanoma-specific survival. Impact This study adds to the evidence that sun exposure prior to melanoma diagnosis has little effect on survival with melanoma. PMID:25069694

Performance of Willem's dental age estimation method in children: A systematic review and meta-analysis.

PubMed

Mohd Yusof, Mohd Yusmiaidil Putera; Wan Mokhtar, Ilham; Rajasekharan, Sivaprakash; Overholser, Rosanna; Martens, Luc

2017-11-01

Through numerous validation and method comparison studies on different populations, the Willems method exhibited a superior accuracy. This article aims to systematically examine how accurate the application of Willems dental age method on children of different age groups and its performance based on various populations and regions. A strategic literature search of PubMed, MEDLINE, Web of Science, EMBASE and hand searching were used to identify the studies published up to September 2014 that estimated the dental age using the Willems method (modified Demirjian), with a populations, intervention, comparisons and outcomes (PICO) search strategy using MeSH keywords, focusing on the question: How much Willems method deviates from the chronological age in estimating age in children? Standardized mean differences were calculated for difference of dental age to chronological age by using random effects model. Subgroup analyses were performed to evaluate potential heterogeneity. Of 116 titles retrieved based on the standardized search strategy, only 19 articles fulfilled the inclusion criteria for quantitative analysis. The pooled estimates were separately kept as underestimation (n=7) and overestimation (n=12) of chronological age groups for both genders according to primary studies. On absolute values, females (underestimated by 0.13; 95% CI: 0.09-0.18 and overestimated by 0.27; 95% CI: 0.17-0.36) exhibited better accuracy than males (underestimated by 0.28; 95% CI: 0.14-0.42 and overestimated by 0.33; 95% CI: 0.22-0.44). For comparison purposes, the overall pooled estimate overestimated the age by 0.10 (95% CI: -0.06 to 0.26) and 0.09 (95% CI: -0.09 to 0.19) for males and females, respectively. There was no significant difference between the young and older child in subgroup analysis using omnibus test. The mean age between different regions exhibited no statistically significant. The use of Willems method is appropriate to estimate age in children considering its accuracy among different populations, investigators and age groups. Copyright © 2017 Elsevier B.V. All rights reserved.

Sexual Abuse among Female High School Students in Istanbul, Turkey

ERIC Educational Resources Information Center

Alikasifoglu, Mujgan; Erginoz, Ethem; Ercan, Oya; Albayrak-Kaymak, Deniz; Uysal, Omer; Ilter, Ozdemir

2006-01-01

Objective: The objective of the study was to determine the prevalence of sexual abuse in female adolescents in Istanbul, Turkey from data collected as part of a school-based population study on health and health behaviors. Method: A stratified cluster sampling procedure was used for this cross-sectional study. The study sample included 1,955…

Seasonality of Violent Suicides in the Athens Greater Area

ERIC Educational Resources Information Center

Christodoulou, C.; Papadopoulos, I. N.; Douzenis, A.; Kanakaris, N.; Leukidis, C.; Gournellis, R.; Vlachos, K.; Papadopoulos, F. C.; Lykouras, L.

2009-01-01

The aim of the study was to ascertain suicide seasonality in the Greek population and to associate this seasonal variation with age, sex, and suicide method. Studying seasonality can be of help in establishing a public health policy, related with suicide prevention. This is an epidemiologic study based on forensic evidence. We studied the deaths…

Cultural interventions to treat addictions in Indigenous populations: findings from a scoping study

PubMed Central

2014-01-01

Background Cultural interventions offer the hope and promise of healing from addictions for Indigenous people.a However, there are few published studies specifically examining the type and impact of these interventions. Positioned within the Honouring Our Strengths: Culture as Intervention project, a scoping study was conducted to describe what is known about the characteristics of culture-based programs and to examine the outcomes collected and effects of these interventions on wellness. Methods This review followed established methods for scoping studies, including a final stage of consultation with stakeholders. The data search and extraction were also guided by the “PICO” (Patient/population, Intervention, Comparison, and Outcome) method, for which we defined each element, but did not require direct comparisons between treatment and control groups. Twelve databases from the scientific literature and 13 databases from the grey literature were searched up to October 26, 2012. Results The search strategy yielded 4,518 articles. Nineteen studies were included from the United States (58%) and Canada (42%), that involved residential programs (58%), and all (100%) integrated Western and culture-based treatment services. Seventeen types of cultural interventions were found, with sweat lodge ceremonies the most commonly (68%) enacted. Study samples ranged from 11 to 2,685 clients. Just over half of studies involved quasi-experimental designs (53%). Most articles (90%) measured physical wellness, with fewer (37%) examining spiritual health. Results show benefits in all areas of wellness, particularly by reducing or eliminating substance use problems in 74% of studies. Conclusions Evidence from this scoping study suggests that the culture-based interventions used in addictions treatment for Indigenous people are beneficial to help improve client functioning in all areas of wellness. There is a need for well-designed studies to address the question of best relational or contextual fit of cultural practices given a particular place, time, and population group. Addiction researchers and treatment providers are encouraged to work together to make further inroads into expanding the study of culture-based interventions from multiple perspectives and locations. PMID:25179797

Assessment of mycotoxin exposure in the Belgian population using biomarkers: aim, design and methods of the BIOMYCO study.

PubMed

Heyndrickx, Ellen; Sioen, Isabelle; Bellemans, Mia; De Maeyer, Mieke; Callebaut, Alfons; De Henauw, Stefaan; De Saeger, Sarah

2014-01-01

Mycotoxins are harmful food contaminants. Currently, human exposure assessment to these toxins is often based on calculations combining mycotoxin occurrence data in food with population data on food consumption. Because of limitations inherent to that approach, biomarkers have been proposed as a suitable alternative whereby a more accurate assessment of exposure at the individual level can be performed. The BIOMYCO study is designed to assess human mycotoxin exposure using urinary biomarkers of exposure. Over the different seasons of 2013 and 2014, morning urine is gathered in a representative part of the Belgian population according to a designed study protocol, whereby 140 children (3-12 years old) and 278 adults (19-65 years old) are selected based on random cluster sampling stratified for sex, age and geographical areas. Every participant completes a food frequency questionnaire to assess the consumption of relevant foodstuffs (n = 43) of both the day before the urine collection and the previous month. Validated multi-toxin LC-MS/MS methods are used to analyse aflatoxins, fumonisins, ochratoxin A, trichothecenes, zearalenone and their metabolites in morning urine. The study protocol is approved by the ethical committee of the Ghent University Hospital. Within this paper, study design and methods are described. The BIOMYCO study is the first study whereby a multi-toxin approach is applied for mycotoxin exposure assessment in adults and children on a large scale. Moreover, it is the first study that will describe the exposure to an elaborated set of mycotoxins in the Belgian population. In first instance, descriptive analysis will be performed, describing the exposure to mycotoxins for the child and adult group. Exposure of different subgroups will be compared. Furthermore, correlations between the mycotoxin concentrations measured and the food consumption reported will be estimated to explore whether the mycotoxin exposure could be explained by the consumption of certain foods.

Software Review: A program for testing capture-recapture data for closure

USGS Publications Warehouse

Stanley, Thomas R.; Richards, Jon D.

2005-01-01

Capture-recapture methods are widely used to estimate population parameters of free-ranging animals. Closed-population capture-recapture models, which assume there are no additions to or losses from the population over the period of study (i.e., the closure assumption), are preferred for population estimation over the open-population models, which do not assume closure, because heterogeneity in detection probabilities can be accounted for and this improves estimates. In this paper we introduce CloseTest, a new Microsoft® Windows-based program that computes the Otis et al. (1978) and Stanley and Burnham (1999) closure tests for capture-recapture data sets. Information on CloseTest features and where to obtain the program are provided.

ITO-based evolutionary algorithm to solve traveling salesman problem

NASA Astrophysics Data System (ADS)

Dong, Wenyong; Sheng, Kang; Yang, Chuanhua; Yi, Yunfei

2014-03-01

In this paper, a ITO algorithm inspired by ITO stochastic process is proposed for Traveling Salesmen Problems (TSP), so far, many meta-heuristic methods have been successfully applied to TSP, however, as a member of them, ITO needs further demonstration for TSP. So starting from designing the key operators, which include the move operator, wave operator, etc, the method based on ITO for TSP is presented, and moreover, the ITO algorithm performance under different parameter sets and the maintenance of population diversity information are also studied.

Demirjian's method in the estimation of age: A study on human third molars.

PubMed

Lewis, Amitha J; Boaz, Karen; Nagesh, K R; Srikant, N; Gupta, Neha; Nandita, K P; Manaktala, Nidhi

2015-01-01

The primary aim of the following study is to estimate the chronological age based on the stages of third molar development following the eight stages (A to H) method of Demirjian et al. (along with two modifications-Orhan) and secondary aim is to compare third molar development with sex and age. The sample consisted of 115 orthopantomograms from South Indian subjects with known chronological age and gender. Multiple regression analysis was performed with chronological age as the dependable variable and third molar root development as independent variable. All the statistical analysis was performed using the SPSS 11.0 package (IBM ® Corporation). Statistically no significant differences were found in third molar development between males and females. Depending on the available number of wisdom teeth in an individual, R (2) varied for males from 0.21 to 0.48 and for females from 0.16 to 0.38. New equations were derived for estimating the chronological age. The chronological age of a South Indian individual between 14 and 22 years may be estimated based on the regression formulae. However, additional studies with a larger study population must be conducted to meet the need for population-based information on third molar development.

A cautionary note on Bayesian estimation of population size by removal sampling with diffuse priors.

PubMed

Bord, Séverine; Bioche, Christèle; Druilhet, Pierre

2018-05-01

We consider the problem of estimating a population size by removal sampling when the sampling rate is unknown. Bayesian methods are now widespread and allow to include prior knowledge in the analysis. However, we show that Bayes estimates based on default improper priors lead to improper posteriors or infinite estimates. Similarly, weakly informative priors give unstable estimators that are sensitive to the choice of hyperparameters. By examining the likelihood, we show that population size estimates can be stabilized by penalizing small values of the sampling rate or large value of the population size. Based on theoretical results and simulation studies, we propose some recommendations on the choice of the prior. Then, we applied our results to real datasets. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A population-based study on health and living conditions in areas with mixed Sami and Norwegian settlements - the SAMINOR 2 questionnaire study.

PubMed

Brustad, Magritt; Hansen, Ketil Lenert; Broderstad, Ann Ragnhild; Hansen, Solrunn; Melhus, Marita

2014-01-01

To describe the method, data collection procedure and participation in The Population-based Study on Health and Living Conditions in Areas with both Sami and Norwegian Settlements - the SAMINOR 2 questionnaire study. Cross-sectional and semi-longitudinal. In 2012, all inhabitants aged 18-69 and living in selected municipalities with both Sami and Norwegian settlements in Mid and Northern Norway were posted an invitation to participate in a questionnaire survey covering several topics related to health and living conditions. The geographical area was similar to the area where the SAMINOR 1 study was conducted in 2003/2004 with the exception of one additional municipality. Participants could alternatively use a web-based questionnaire with identical question and answer categories as the posted paper version. In total, 11,600 (27%) participated (16% used the web-based questionnaire), with a higher participation rate among those over 50 (37% for women and 32% for men). Some geographical variation in participation rates was found. In addition, for those invited who also participated in the SAMINOR 1 study, we found that the participation rates increased with the level of education and income, while there was little difference in participation rates across ethnic groups. The knowledge generated from future theme-specific research utilizing the SAMINOR 2 database has the potential to benefit the general population in this geographical area of Norway, and the Sami people in particular, by providing knowledge-based insight into the health and living conditions of the multi-ethnic population in these parts of Norway.

A Systematic Evaluation of Field-Based Screening Methods for the Assessment of Anterior Cruciate Ligament (ACL) Injury Risk.

PubMed

Fox, Aaron S; Bonacci, Jason; McLean, Scott G; Spittle, Michael; Saunders, Natalie

2016-05-01

Laboratory-based measures provide an accurate method to identify risk factors for anterior cruciate ligament (ACL) injury; however, these methods are generally prohibitive to the wider community. Screening methods that can be completed in a field or clinical setting may be more applicable for wider community use. Examination of field-based screening methods for ACL injury risk can aid in identifying the most applicable method(s) for use in these settings. The objective of this systematic review was to evaluate and compare field-based screening methods for ACL injury risk to determine their efficacy of use in wider community settings. An electronic database search was conducted on the SPORTDiscus™, MEDLINE, AMED and CINAHL databases (January 1990-July 2015) using a combination of relevant keywords. A secondary search of the same databases, using relevant keywords from identified screening methods, was also undertaken. Studies identified as potentially relevant were independently examined by two reviewers for inclusion. Where consensus could not be reached, a third reviewer was consulted. Original research articles that examined screening methods for ACL injury risk that could be undertaken outside of a laboratory setting were included for review. Two reviewers independently assessed the quality of included studies. Included studies were categorized according to the screening method they examined. A description of each screening method, and data pertaining to the ability to prospectively identify ACL injuries, validity and reliability, recommendations for identifying 'at-risk' athletes, equipment and training required to complete screening, time taken to screen athletes, and applicability of the screening method across sports and athletes were extracted from relevant studies. Of 1077 citations from the initial search, a total of 25 articles were identified as potentially relevant, with 12 meeting all inclusion/exclusion criteria. From the secondary search, eight further studies met all criteria, resulting in 20 studies being included for review. Five ACL-screening methods-the Landing Error Scoring System (LESS), Clinic-Based Algorithm, Observational Screening of Dynamic Knee Valgus (OSDKV), 2D-Cam Method, and Tuck Jump Assessment-were identified. There was limited evidence supporting the use of field-based screening methods in predicting ACL injuries across a range of populations. Differences relating to the equipment and time required to complete screening methods were identified. Only screening methods for ACL injury risk were included for review. Field-based screening methods developed for lower-limb injury risk in general may also incorporate, and be useful in, screening for ACL injury risk. Limited studies were available relating to the OSDKV and 2D-Cam Method. The LESS showed predictive validity in identifying ACL injuries, however only in a youth athlete population. The LESS also appears practical for community-wide use due to the minimal equipment and set-up/analysis time required. The Clinic-Based Algorithm may have predictive value for ACL injury risk as it identifies athletes who exhibit high frontal plane knee loads during a landing task, but requires extensive additional equipment and time, which may limit its application to wider community settings.

Effectiveness of Family, Child, and Family-Child Based Intervention on ADHD Symptoms of Students with Disabilities

ERIC Educational Resources Information Center

Malekpour, Mokhtar; Aghababaei, Sara; Hadi, Samira

2014-01-01

The aim of the present study was to investigate and compare the effectiveness of family, child, and family-child based intervention on the rate of ADHD symptoms in third grade students. The population for this study was all of students with ADHD diagnoses in the city of Isfahan, Iran. The multistage random sampling method was used to select the 60…

Techniques and results of nongame bird monitoring in North America

USGS Publications Warehouse

Robbins, C.S.; Bystrak, D.; Geissler, P.H.; Oelke, H.

1980-01-01

Long-term bird population trends based on accumulated ratios (proportional change) sometimes give a very misleading view of population change. Alternate methods of representing population change, based on the weighted means for the individual years, avoid the dangers of using ratios. Some advantages and disadvantages of various weighting techniques are discussed.

Birth Outcomes among Older Mothers in Rural versus Urban Areas: A Residence-Based Approach

ERIC Educational Resources Information Center

Lisonkova, Sarka; Sheps, Samuel B.; Janssen, Patricia A.; Lee, Shoo K.; Dahlgren, Leanne; MacNab, Ying C.

2011-01-01

Purpose: We examined the association between rural residence and birth outcomes in older mothers, the effect of parity on this association, and the trend in adverse birth outcomes in relation to the distance to the nearest hospital with cesarean-section capacity. Methods: A population-based retrospective cohort study, including all singleton…

Aboriginal Suicidal Behaviour Research: From Risk Factors to Culturally-Sensitive Interventions

PubMed Central

Katz, Laurence Y.; Elias, Brenda; O’Neil, John; Enns, Murray; Cox, Brian J.; Belik, Shay-Lee; Sareen, Jitender

2006-01-01

Introduction There is a significant amount of research demonstrating that the rate of completed suicide among Aboriginal populations is much higher than in the general population. Unfortunately, there is a paucity of research evaluating the risk factors for completed suicide and suicidal behavior in this population. There is an even greater shortage of research on evidence-based interventions for suicidal behaviour. Method A literature review was conducted to facilitate the development of an approach to the study of this complex problem. Results An approach to developing a research program that informs each step of the process with evidence from the previous steps was developed. The study of risk factors and interventions is described. Conclusions Research into the risk factors and evidence-based interventions for Aboriginal suicidal behavior are required. A programmatic approach is described in detail in this paper. It is hoped this informed approach would systematically address this important public health issue that afflicts a significant proportion of the Canadian population. PMID:18392204

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.

Evaluating manta ray mucus as an alternative DNA source for population genetics study: underwater-sampling, dry-storage and PCR success.

PubMed

Kashiwagi, Tom; Maxwell, Elisabeth A; Marshall, Andrea D; Christensen, Ana B

2015-01-01

Sharks and rays are increasingly being identified as high-risk species for extinction, prompting urgent assessments of their local or regional populations. Advanced genetic analyses can contribute relevant information on effective population size and connectivity among populations although acquiring sufficient regional sample sizes can be challenging. DNA is typically amplified from tissue samples which are collected by hand spears with modified biopsy punch tips. This technique is not always popular due mainly to a perception that invasive sampling might harm the rays, change their behaviour, or have a negative impact on tourism. To explore alternative methods, we evaluated the yields and PCR success of DNA template prepared from the manta ray mucus collected underwater and captured and stored on a Whatman FTA™ Elute card. The pilot study demonstrated that mucus can be effectively collected underwater using toothbrush. DNA stored on cards was found to be reliable for PCR-based population genetics studies. We successfully amplified mtDNA ND5, nuclear DNA RAG1, and microsatellite loci for all samples and confirmed sequences and genotypes being those of target species. As the yields of DNA with the tested method were low, further improvements are desirable for assays that may require larger amounts of DNA, such as population genomic studies using emerging next-gen sequencing.

Evaluating manta ray mucus as an alternative DNA source for population genetics study: underwater-sampling, dry-storage and PCR success

PubMed Central

Maxwell, Elisabeth A.; Marshall, Andrea D.; Christensen, Ana B.

2015-01-01

Sharks and rays are increasingly being identified as high-risk species for extinction, prompting urgent assessments of their local or regional populations. Advanced genetic analyses can contribute relevant information on effective population size and connectivity among populations although acquiring sufficient regional sample sizes can be challenging. DNA is typically amplified from tissue samples which are collected by hand spears with modified biopsy punch tips. This technique is not always popular due mainly to a perception that invasive sampling might harm the rays, change their behaviour, or have a negative impact on tourism. To explore alternative methods, we evaluated the yields and PCR success of DNA template prepared from the manta ray mucus collected underwater and captured and stored on a Whatman FTA™ Elute card. The pilot study demonstrated that mucus can be effectively collected underwater using toothbrush. DNA stored on cards was found to be reliable for PCR-based population genetics studies. We successfully amplified mtDNA ND5, nuclear DNA RAG1, and microsatellite loci for all samples and confirmed sequences and genotypes being those of target species. As the yields of DNA with the tested method were low, further improvements are desirable for assays that may require larger amounts of DNA, such as population genomic studies using emerging next-gen sequencing. PMID:26413431

Developing population models with data from marked individuals

USGS Publications Warehouse

Hae Yeong Ryu,; Kevin T. Shoemaker,; Eva Kneip,; Anna Pidgeon,; Patricia Heglund,; Brooke Bateman,; Thogmartin, Wayne E.; Reşit Akçakaya,

2016-01-01

Population viability analysis (PVA) is a powerful tool for biodiversity assessments, but its use has been limited because of the requirements for fully specified population models such as demographic structure, density-dependence, environmental stochasticity, and specification of uncertainties. Developing a fully specified population model from commonly available data sources – notably, mark–recapture studies – remains complicated due to lack of practical methods for estimating fecundity, true survival (as opposed to apparent survival), natural temporal variability in both survival and fecundity, density-dependence in the demographic parameters, and uncertainty in model parameters. We present a general method that estimates all the key parameters required to specify a stochastic, matrix-based population model, constructed using a long-term mark–recapture dataset. Unlike standard mark–recapture analyses, our approach provides estimates of true survival rates and fecundities, their respective natural temporal variabilities, and density-dependence functions, making it possible to construct a population model for long-term projection of population dynamics. Furthermore, our method includes a formal quantification of parameter uncertainty for global (multivariate) sensitivity analysis. We apply this approach to 9 bird species and demonstrate the feasibility of using data from the Monitoring Avian Productivity and Survivorship (MAPS) program. Bias-correction factors for raw estimates of survival and fecundity derived from mark–recapture data (apparent survival and juvenile:adult ratio, respectively) were non-negligible, and corrected parameters were generally more biologically reasonable than their uncorrected counterparts. Our method allows the development of fully specified stochastic population models using a single, widely available data source, substantially reducing the barriers that have until now limited the widespread application of PVA. This method is expected to greatly enhance our understanding of the processes underlying population dynamics and our ability to analyze viability and project trends for species of conservation concern.

A Venue-Based Approach to Reaching MSM, IDUs and the General Population with VCT: A Three Study Site in Kenya

PubMed Central

Singh, Kavita; Brodish, Paul; Mbai, Fiona; Kingola, Nzioki; Rinyuri, Agnes; Njeru, Carol; Mureithi, Patrick; Sambisa, William; Weir, Sharon

2014-01-01

A venue-based HIV prevention study which included Voluntary Counseling and Testing (VCT) was conducted in three diverse areas of Kenya— Malindi, Nanyuki and Rachounyo. Aims of the study were to: 1) assess the acceptability of VCT for the general population, men who have sex with men (MSM), and injecting drug users (IDUs) within the context of a venue-based approach; 2) determine if there were differences between those agreeing and not agreeing to testing; and 3) study factors associated with being HIV positive. Approximately 98% of IDUs and 97% of MSM agreed to VCT, providing evidence that populations with little access to services and whose behaviors are stigmatized and often considered illegal in their countries can be reached with needed HIV prevention services. Acceptability of VCT in the general population ranged from 60% in Malindi to 48% in Nanyuki. There were a few significant differences between those accepting and declining testing. Notably in Rachuonyo and Malindi those reporting multiple partners were more likely to accept testing. There was also evidence that riskier sexual behavior was associated with being HIV positive for both men in Rachounyo and women in Malindi. Overall HIV prevalence was higher among the individuals in this study compared to individuals sampled in the 2008–2009 Kenya Demographic and Health Survey, indicating the method is an appropriate means to reach the highest risk individuals including stigmatized populations. PMID:22198312

Assessment of sex in a modern Turkish population using cranial anthropometric parameters.

PubMed

Ekizoglu, Oguzhan; Hocaoglu, Elif; Inci, Ercan; Can, Ismail Ozgur; Solmaz, Dilek; Aksoy, Sema; Buran, Cudi Ferat; Sayin, Ibrahim

2016-07-01

The utilization of radiological imaging methods in anthropometric studies is being expanded by the application of modern imaging methods, leading to a decrease in costs, a decrease in the time required for analysis and the ability to create three-dimensional images. This retrospective study investigated 400 patients within the 18-45-years age group (mean age: 30.7±11.2years) using cranial computed tomography images. We measured 14 anthropometric parameters (basion-bregma height, basion-prosthion length, maximum cranial length and cranial base lengths, maximum cranial breadth, bizygomatic diameter, upper facial breadth, bimastoid diameter, orbital breadth, orbital length, biorbital breadth, interorbital breadth, foramen magnum breadth and foramen magnum length) of cranial measurements. The intra- and inter-observer repeatability and consistency were good. From the results of logistic regression analysis using morphometric measurements, the most conspicuous measurements in terms of dimorphism were maximum cranial length, bizygomatic diameter, basion-bregma height, and cranial base length. The most dimorphic structure was the bizygomatic diameter with an accuracy rate of 83% in females and 77% in males. In this study, 87.5% of females and 87.0% of males were classified accurately by this model including four parameters with a sensitivity of 91.5% and specificity of 85.0%. In conclusion, CT cranial morphometric analysis may be reliable for the assessment of sex in the Turkish population and is recommended for comparison of data of modern populations with those of former populations. Additionally, cranial morphometric data that we obtained from modern Turkish population may reveal population specific data, which may help current criminal investigations and identification of disaster victims. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Chlamydia prevalence in the general population: is there a sex difference? a systematic review

PubMed Central

2013-01-01

Background The focus of Chlamydia trachomatis screening and testing lies more on women than on men. The study aim was to establish by systematic review the prevalence of urogenital Chlamydia trachomatis infection in men and women in the general population. Methods Electronic databases and reference lists were searched from 2000 to 2013 using the key words “Chlamydia trachomatis”, “population-based study” and “disease prevalence”. Reference lists were checked. Studies were included in the analysis if Chlamydia trachomatis prevalence was reported for both men and women in a population-based study. Prevalence rates for men and women were described as well as highest prevalence rate by age and sex. The difference in prevalence between the sexes in each study was calculated. Results Twenty-five studies met the inclusion criteria and quality assessment for the review. In nine of the twenty-five studies there was a statistically significant sex difference in the chlamydia prevalence. In all nine studies the prevalence of chlamydia was higher in women than in men. The prevalence for women varied from 1.1% to 10.6% and for men from 0.1% to 12.1%. The average chlamydia prevalence is highly variable between countries. The highest prevalence of chlamydia occurred predominantly in younger age groups (< 25 years). The absence of symptoms in population-based urogenital chlamydia infection is common in men and women (mean 88.5% versus 68.3%). Conclusions The urogenital chlamydia trachomatis prevalence in the general population is more similar than dissimilar for men and women. A modest sex difference is apparent. The prevalence rates can be used to inform chlamydia screening strategies in general practice. PMID:24215287

Whole-Body Biodistribution, Dosimetry, and Metabolite Correction of [11C]Palmitate: A PET Tracer for Imaging of Fatty Acid Metabolism

PubMed Central

Christensen, Nana L.; Jakobsen, Steen; Schacht, Anna C.; Munk, Ole L.; Alstrup, Aage K. O.; Tolbod, Lars P.; Harms, Hendrik J.; Nielsen, Søren

2017-01-01

Introduction: Despite the decades long use of [11C]palmitate positron emission tomography (PET)/computed tomography in basic metabolism studies, only personal communications regarding dosimetry and biodistribution data have been published. Methods: Dosimetry and biodistribution studies were performed in 2 pigs and 2 healthy volunteers by whole-body [11C]palmitate PET scans. Metabolite studies were performed in 40 participants (healthy and with type 2 diabetes) under basal and hyperinsulinemic conditions. Metabolites were estimated using 2 approaches and subsequently compared: Indirect [11C]CO2 release and parent [11C]palmitate measured by a solid-phase extraction (SPE) method. Finally, myocardial fatty acid uptake was calculated in a patient cohort using input functions derived from individual metabolite correction compared with population-based metabolite correction. Results: In humans, mean effective dose was 3.23 (0.02) µSv/MBq, with the liver and myocardium receiving the highest absorbed doses. Metabolite correction using only [11C]CO2 estimates underestimated the fraction of metabolites in studies lasting more than 20 minutes. Population-based metabolite correction showed excellent correlation with individual metabolite correction in the cardiac PET validation cohort. Conclusion: First, mean effective dose of [11C]palmitate is 3.23 (0.02) µSv/MBq in humans allowing multiple scans using ∼300 MBq [11C]palmitate, and secondly, population-based metabolite correction compares well with individual correction. PMID:29073808

Evidence for association between Disrupted-in-schizophrenia 1 (DISC1) gene polymorphisms and autism in Chinese Han population: a family-based association study

PubMed Central

2011-01-01

Background Disrupted-in-Schizophrenia 1 (DISC1) gene is one of the most promising candidate genes for major mental disorders. In a previous study, a Finnish group demonstrated that DISC1 polymorphisms were associated with autism and Asperger syndrome. However, the results were not replicated in Korean population. To determine whether DISC1 is associated with autism in Chinese Han population, we performed a family-based association study between DISC1 polymorphisms and autism. Methods We genotyped seven tag single nucleotide polymorphisms (SNPs) in DISC1, spanning 338 kb, in 367 autism trios (singleton and their biological parents) including 1,101 individuals. Single SNP association and haplotype association analysis were performed using the family-based association test (FBAT) and Haploview software. Results We found three SNPs showed significant associations with autism (rs4366301: G > C, Z = 2.872, p = 0.004; rs11585959: T > C, Z = 2.199, p = 0.028; rs6668845: A > G, Z = 2.326, p = 0.02). After the Bonferroni correction, SNP rs4366301, which located in the first intron of DISC1, remained significant. When haplotype were constructed with two-markers, three haplotypes displayed significant association with autism. These results were still significant after using the permutation method to obtain empirical p values. Conclusions Our study provided evidence that the DISC1 may be the susceptibility gene of autism. It suggested DISC1 might play a role in the pathogenesis of autism. PMID:21569632

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

PubMed

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

2015-02-01

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

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

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.

Application of a PCR-based approach to identify sex in Hawaiian honeycreepers (Drepanidinae)

USGS Publications Warehouse

Jarvi, S.I.; Banko, P.C.

2000-01-01

The application of molecular techniques to conservation genetics issues can provide important guidance criteria for management of endangered species. The results from this study establish that PCR-based approaches for sex determination developed in other bird species (Griffiths and Tiwari 1995; Griffiths et al. 1996, 1998; Ellegren 1996) can be applied with a high degree of confidence to at least four species of Hawaiian honeycreepers. This provides a rapid, reliable method with which population managers can optimize sex ratios within populations of endangered species that are subject to artificial manipulation through captive breeding programmes or geographic translocation.

Line Transect Surveys Underdetect Terrestrial Mammals: Implications for the Sustainability of Subsistence Hunting

PubMed Central

Levi, Taal; Oliveira, Luiz F. B.; Luzar, Jeffrey B.; Overman, Han; Read, Jane M.

2016-01-01

Conservation of Neotropical game species must take into account the livelihood and food security needs of local human populations. Hunting management decisions should therefore rely on abundance and distribution data that are as representative as possible of true population sizes and dynamics. We simultaneously applied a commonly used encounter-based method and an infrequently used sign-based method to estimate hunted vertebrate abundance in a 48,000-km2 indigenous landscape in southern Guyana. Diurnal direct encounter data collected during three years along 216, four-kilometer -long transects consistently under-detected many diurnal and nocturnal mammal species readily detected through sign. Of 32 species analyzed, 31 were detected by both methods; however, encounters did not detect one and under-detected another 12 of the most heavily hunted species relative to sign, while sign under-detected 12 never or rarely collected species relative to encounters. The six most important game animals in the region, all ungulates, were not encountered at 11–40% of village and control sites or on 29–72% of transects where they were detected by sign. Using the sign methodology, we find that tapirs, one of the terrestrial vertebrates considered most sensitive to overexploitation, are present at many sites where they were never visually detected during distance sampling. We find that this is true for many other species as well. These high rates of under-detection suggest that behavioral changes in hunted populations may affect apparent occurrence and abundance of these populations. Accumulation curves (detection of species on transects) were much steeper for sign for 12 of 16 hunted species than for encounters, but that pattern was reversed for 12 of 16 species unhunted in our area. We conclude that collection of sign data is an efficient and effective method of monitoring hunted vertebrate populations that complements encounter and camera-trapping methods in areas impacted by hunting. Sign surveys may be the most viable method for large-scale, management-oriented studies in remote areas, particularly those focused on community-based wildlife management. PMID:27074025

Visual Aggregate Analysis of Eligibility Features of Clinical Trials

PubMed Central

He, Zhe; Carini, Simona; Sim, Ida; Weng, Chunhua

2015-01-01

Objective To develop a method for profiling the collective populations targeted for recruitment by multiple clinical studies addressing the same medical condition using one eligibility feature each time. Methods Using a previously published database COMPACT as the backend, we designed a scalable method for visual aggregate analysis of clinical trial eligibility features. This method consists of four modules for eligibility feature frequency analysis, query builder, distribution analysis, and visualization, respectively. This method is capable of analyzing (1) frequently used qualitative and quantitative features for recruiting subjects for a selected medical condition, (2) distribution of study enrollment on consecutive value points or value intervals of each quantitative feature, and (3) distribution of studies on the boundary values, permissible value ranges, and value range widths of each feature. All analysis results were visualized using Google Charts API. Five recruited potential users assessed the usefulness of this method for identifying common patterns in any selected eligibility feature for clinical trial participant selection. Results We implemented this method as a Web-based analytical system called VITTA (Visual Analysis Tool of Clinical Study Target Populations). We illustrated the functionality of VITTA using two sample queries involving quantitative features BMI and HbA1c for conditions “hypertension” and “Type 2 diabetes”, respectively. The recruited potential users rated the user-perceived usefulness of VITTA with an average score of 86.4/100. Conclusions We contributed a novel aggregate analysis method to enable the interrogation of common patterns in quantitative eligibility criteria and the collective target populations of multiple related clinical studies. A larger-scale study is warranted to formally assess the usefulness of VITTA among clinical investigators and sponsors in various therapeutic areas. PMID:25615940

Methods and background characteristics of the TOHNN study: a population-based study of oral health conditions in northern Norway

PubMed Central

Holde, Gro Eirin; Oscarson, Nils; Tillberg, Anders; Marstrander, Peter; Jönsson, Birgitta

2016-01-01

Objectives The aim of the Tromstannen – Oral Health in Northern Norway (TOHNN) study was to investigate oral health and dental-related diseases in an adult population. This article provides an overview of the background of the study and a description of the sample characteristics and methods employed in data collection. Study design Cross-sectional population-based study including a questionnaire and clinical dental examination. Methods A randomly selected sample of 2,909 individuals (20–79 years old) drawn from the population register was invited to participate in the study. The data were collected between October 2013 and November 2014 in Troms County in northern Norway. The questionnaire focused on oral health-related behaviours and attitudes, oral health-related quality of life, sense of coherence, dental anxiety and symptoms from the temporomandibular joint. The dental examinations, including radiographs, were conducted by 11 dental teams in 5 dental offices. The examination comprised of registration of dental caries, full mouth periodontal status, temporomandibular disorders, mucosal lesions and height and weight. The participants were grouped by age (20–34, 35–49, 50–64 and 65–79) and ethnicity (Norwegian, Sámi, other European and other world). Results From the original sample of 2,909 individuals, 1,986 (68.3%) people participated, of whom 1,019 (51.3%) were women. The highest attendance rate was among women 20–34 years old (80.3%) and the lowest in the oldest age group of women (55.4%). There was no difference in response rate between rural and urban areas. There was a positive correlation between population size and household gross income (p < 0.001) and education level (p < 0.001). The majority of Sámi resided in smaller municipalities. In larger cities, most participants used private dental health care services, whereas, in rural areas, most participants used the public dental health care service. Conclusion The TOHNN study has the potential to generate new knowledge on a wide range of oral health conditions beneficial to the population in Troms County. Due to the high participation rate, generalization both nationally and to the circumpolar area ought to be possible. PMID:26900910

Culturally Adaptive Walking Intervention for Korean-Chinese Female Migrant Workers.

PubMed

Cho, Sunghye; Lee, Hyeonkyeong; Kim, Jung Hee; Lee, Meenhye; Lee, Young-Me

2017-05-01

Although the literature has commonly cited that development of culturally adaptive interventions is key to improving the health outcomes of culturally and linguistically diverse populations, there have been limited culturally adaptive walking interventions specific to Korean-Chinese (KC) migrants. The objective of this study is to describe the process in development of culturally adaptive walking interventions for KC female migrant workers, using the intervention mapping (IM) method. The culturally adaptive walking intervention was developed using the IM method, which is a stepwise theory and evidence-based approach for planning interventions. The IM method process has six steps, including needs assessment, formulation of change objectives, selection of theory-based methods and practical strategies, development of an intervention program, development of an adoption and implementation plan, and development of an evaluation design. The determinants of walking behavior, including knowledge, self-efficacy, social support, and acculturation, were identified through an extensive literature review, community leader interviews, and a survey of female KC migrant workers. Appropriate intervention methods and strategies were identified based on relevant theories. Acculturation was a determinant of exercise behavior, and various methods to improve cultural adaptation were identified in the context of the lifestyles and working environments of the target population. The IM method provided a foundation for creating a health intervention for KC female migrant workers. This method could easily be useful for health care providers working with other groups.

PCR-based karyotyping of Anopheles gambiae inversion 2Rj identifies the BAMAKO chromosomal form.

PubMed

Coulibaly, Mamadou B; Pombi, Marco; Caputo, Beniamino; Nwakanma, Davis; Jawara, Musa; Konate, Lassana; Dia, Ibrahima; Fofana, Abdrahamane; Kern, Marcia; Simard, Frédéric; Conway, David J; Petrarca, Vincenzo; della Torre, Alessandra; Traoré, Sékou; Besansky, Nora J

2007-10-01

The malaria vector Anopheles gambiae is polymorphic for chromosomal inversions on the right arm of chromosome 2 that segregate nonrandomly between assortatively mating populations in West Africa. One such inversion, 2Rj, is associated with the BAMAKO chromosomal form endemic to southern Mali and northern Guinea Conakry near the Niger River. Although it exploits a unique ecology and both molecular and chromosomal data suggest reduced gene flow between BAMAKO and other A. gambiae populations, no molecular markers exist to identify this form. To facilitate study of the BAMAKO form, a PCR assay for molecular karyotyping of 2Rj was developed based on sequences at the breakpoint junctions. The assay was extensively validated using more than 700 field specimens whose karyotypes were determined in parallel by cytogenetic and molecular methods. As inversion 2Rj also occurs in SAVANNA populations outside the geographic range of BAMAKO, samples were tested from Senegal, Cameroon and western Guinea Conakry as well as from Mali. In southern Mali, where 2Rj polymorphism in SAVANNA populations was very low and most of the 2Rj homozygotes were found in BAMAKO karyotypes, the molecular and cytogenetic methods were almost perfectly congruent. Elsewhere agreement between the methods was much poorer, as the molecular assay frequently misclassified 2Rj heterozygotes as 2R+j standard homozygotes. Molecular karyotyping of 2Rj is robust and accurate on 2R+j standard and 2Rj inverted homozygotes. Therefore, the proposed approach overcomes the lack of a rapid tool for identifying the BAMAKO form across developmental stages and sexes, and opens new perspectives for the study of BAMAKO ecology and behaviour. On the other hand, the method should not be applied for molecular karyotyping of j-carriers within the SAVANNA chromosomal form.

The use and correlates of illicit silicone or “fillers” in a population-based sample of transwomen, San Francisco, 2013

PubMed Central

Wilson, Erin; Rapues, Jenna; Jin, Harry; Raymond, H. Fisher

2014-01-01

Introduction There is a dearth of studies to quantify the use of illicit fillers by transwomen. Case studies of illicit filler injections have pointed to an array of serious health complications, including death. Aim The aim of this study was to determine the population prevalence of filler use among transwomen, and to identify correlations with filler use. Methods An analysis of data collected in 2013 with a population-based sample of 234 transwomen recruited using respondent driven sampling (RDS). We used RDS weights to conduct bivariate and multivariate analyses of correlates of filler use. Main Outcome measures Main outcome measures were an RDS-weighted population prevalence of filler use among transwomen and differences in demographic characteristics, transition-related care factors and self-esteem related to appearance. Results Weighted filler prevalence among transwomen was 16.7%. Being a transwomen between 30–49 years of age, owning/renting or living with a partner/family/friend, having had and planning to have surgery in the future and having used non-prescribed hormones were all associated with filler use. HIV was not associated with filler use. Conclusions This study provides the first known estimate to date of the prevalence of filler use in a population-based sample of transwomen in San Francisco. Accessing illicit fillers may be the only choice available for many transwomen due to the cost of legal surgeries and other procedures to change one’s appearance. An important next step in this research is to determine the overall prevalence and long-term consequences of filler use among transwomen, to explore how the use of fillers is protective to the safety and wellbeing of transwomen, and to find safe and affordable alternatives to this method that meets important gender-related appearance needs. PMID:24810672

Recalibration of the Klales et al. (2012) method of sexing the human innominate for Mexican populations.

PubMed

Gómez-Valdés, Jorge A; Menéndez Garmendia, Antinea; García-Barzola, Lizbeth; Sánchez-Mejorada, Gabriela; Karam, Carlos; Baraybar, José Pablo; Klales, Alexandra

2017-03-01

The aim of this study was to test the accuracy of the Klales et al. (2012) equation for sex estimation in contemporary Mexican population. Our investigation was carried out on a sample of 203 left innominates of identified adult skeletons from the UNAM-Collection and the Santa María Xigui Cemetery, in Central Mexico. The Klales' original equation produces a sex bias in sex estimation against males (86-92% accuracy versus 100% accuracy in females). Based on these results, the Klales et al. (2012) method was recalibrated for a new cutt-of-point for sex estimation in contemporary Mexican populations. The results show cross-validated classification accuracy rates as high as 100% after recalibrating the original logistic regression equation. Recalibration improved classification accuracy and eliminated sex bias. This new formula will improve sex estimation for Mexican contemporary populations. © 2017 Wiley Periodicals, Inc.

Collective intelligence in medical diagnosis systems: A case study.

PubMed

Hernández-Chan, Gandhi S; Ceh-Varela, Edgar Eduardo; Sanchez-Cervantes, Jose L; Villanueva-Escalante, Marisol; Rodríguez-González, Alejandro; Pérez-Gallardo, Yuliana

2016-07-01

Diagnosing a patient's condition is one of the most important and challenging tasks in medicine. We present a study of the application of collective intelligence in medical diagnosis by applying consensus methods. We compared the accuracy obtained with this method against the diagnostics accuracy reached through the knowledge of a single expert. We used the ontological structures of ten diseases. Two knowledge bases were created by placing five diseases into each knowledge base. We conducted two experiments, one with an empty knowledge base and the other with a populated knowledge base. For both experiments, five experts added and/or eliminated signs/symptoms and diagnostic tests for each disease. After this process, the individual knowledge bases were built based on the output of the consensus methods. In order to perform the evaluation, we compared the number of items for each disease in the agreed knowledge bases against the number of items in the GS (Gold Standard). We identified that, while the number of items in each knowledge base is higher, the consensus level is lower. In all cases, the lowest level of agreement (20%) exceeded the number of signs that are in the GS. In addition, when all experts agreed, the number of items decreased. The use of collective intelligence can be used to increase the consensus of physicians. This is because, by using consensus, physicians can gather more information and knowledge than when obtaining information and knowledge from knowledge bases fed or populated from the knowledge found in the literature, and, at the same time, they can keep updated and collaborate dynamically. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assessing population genetic structure via the maximisation of genetic distance

PubMed Central

2009-01-01

Background The inference of the hidden structure of a population is an essential issue in population genetics. Recently, several methods have been proposed to infer population structure in population genetics. Methods In this study, a new method to infer the number of clusters and to assign individuals to the inferred populations is proposed. This approach does not make any assumption on Hardy-Weinberg and linkage equilibrium. The implemented criterion is the maximisation (via a simulated annealing algorithm) of the averaged genetic distance between a predefined number of clusters. The performance of this method is compared with two Bayesian approaches: STRUCTURE and BAPS, using simulated data and also a real human data set. Results The simulations show that with a reduced number of markers, BAPS overestimates the number of clusters and presents a reduced proportion of correct groupings. The accuracy of the new method is approximately the same as for STRUCTURE. Also, in Hardy-Weinberg and linkage disequilibrium cases, BAPS performs incorrectly. In these situations, STRUCTURE and the new method show an equivalent behaviour with respect to the number of inferred clusters, although the proportion of correct groupings is slightly better with the new method. Re-establishing equilibrium with the randomisation procedures improves the precision of the Bayesian approaches. All methods have a good precision for FST ≥ 0.03, but only STRUCTURE estimates the correct number of clusters for FST as low as 0.01. In situations with a high number of clusters or a more complex population structure, MGD performs better than STRUCTURE and BAPS. The results for a human data set analysed with the new method are congruent with the geographical regions previously found. Conclusion This new method used to infer the hidden structure in a population, based on the maximisation of the genetic distance and not taking into consideration any assumption about Hardy-Weinberg and linkage equilibrium, performs well under different simulated scenarios and with real data. Therefore, it could be a useful tool to determine genetically homogeneous groups, especially in those situations where the number of clusters is high, with complex population structure and where Hardy-Weinberg and/or linkage equilibrium are present. PMID:19900278

An opinion formation based binary optimization approach for feature selection

NASA Astrophysics Data System (ADS)

Hamedmoghadam, Homayoun; Jalili, Mahdi; Yu, Xinghuo

2018-02-01

This paper proposed a novel optimization method based on opinion formation in complex network systems. The proposed optimization technique mimics human-human interaction mechanism based on a mathematical model derived from social sciences. Our method encodes a subset of selected features to the opinion of an artificial agent and simulates the opinion formation process among a population of agents to solve the feature selection problem. The agents interact using an underlying interaction network structure and get into consensus in their opinions, while finding better solutions to the problem. A number of mechanisms are employed to avoid getting trapped in local minima. We compare the performance of the proposed method with a number of classical population-based optimization methods and a state-of-the-art opinion formation based method. Our experiments on a number of high dimensional datasets reveal outperformance of the proposed algorithm over others.

Measurement of admixture proportions and description of admixture structure in different US populations

PubMed Central

Halder, Indrani; Yang, Bao-Zhu; Kranzler, Henry R.; Stein, Murray B.; Shriver, Mark D.; Gelernter, Joel

2010-01-01

Variation in individual admixture proportions leads to heterogeneity within populations. Though novel methods and marker panels have been developed to quantify individual admixture, empirical data describing individual admixture distributions are limited. We investigated variation in individual admixture in four US populations [European American (EA), African American (AA) and Hispanics from Connecticut (EC) and California (WC)] assuming three-way intermixture among Europeans, Africans and Indigenous Americans. Admixture estimates were inferred using a panel of 36 microsatellites and 1 SNP, which have significant allele frequency differences between ancestral populations, and by using both a maximum likelihood (ML) based method and a Bayesian method implemented in the program STRUCTURE. Simulation studies showed that estimates obtained with this marker panel are within 96% of expected values. EAs had the lowest non-European admixture with both methods, but showed greater homogeneity with STRUCTURE than with ML. All other samples showed a high degree of variation in admixture estimates with both methods, were highly concordant and showed evidence of admixture stratification. With both methods, AA subjects had 16% European and <10% Indigenous American admixture on average. EC Hispanics had higher mean African admixture and the WC Hispanics higher mean Indigenous American admixture, possibly reflecting their different continental origins. PMID:19572378

[Dental manpower prediction in Israel for 2017].

PubMed

Vered, Y; Zini, A; Mann, J

2010-07-01

A recent study published by the authors indicated that according to the Israeli Central Bureau of Statistics in 2008, Israel had 5800 active dentists, a figure well below the publication by the Ministry of Health. Based on this figure, using the manpower to population ratio method, the following results were obtained: The predicted number of dentist in 2017 would be 6090, based on, the estimated number of Israel: graduates, the estimated number of dentists who would arrive in Israel as immigrants or Israelis who studied abroad, based on an attrition rate of 3% and on the assumption that the number of dentists leaving the country is negligible. Table 2, based on manpower to population ratio, indicates that by 2017, Israel would have 1 dentist per 1400 population, a ratio which is still far above what many countries present, but high for Israel. This might reflect a dramatic change, from employment in public clinics, back to private practices. The results clearly indicate that a shortage of dentists is predicted in the near future and a major brainstorming is urgently required to evaluate these results.

Psychometric Validation of the Parental Bonding Instrument in a U.K. Population-Based Sample: Role of Gender and Association With Mental Health in Mid-Late Life.

PubMed

Xu, Man K; Morin, Alexandre J S; Marsh, Herbert W; Richards, Marcus; Jones, Peter B

2016-08-01

The factorial structure of the Parental Bonding Instrument (PBI) has been frequently studied in diverse samples but no study has examined its psychometric properties from large, population-based samples. In particular, important questions have not been addressed such as the measurement invariance properties across parental and offspring gender. We evaluated the PBI based on responses from a large, representative population-based sample, using an exploratory structural equation modeling method appropriate for categorical data. Analysis revealed a three-factor structure representing "care," "overprotection," and "autonomy" parenting styles. In terms of psychometric measurement validity, our results supported the complete invariance of the PBI ratings across sons and daughters for their mothers and fathers. The PBI ratings were also robust in relation to personality and mental health status. In terms of predictive value, paternal care showed a protective effect on mental health at age 43 in sons. The PBI is a sound instrument for capturing perceived parenting styles, and is predictive of mental health in middle adulthood. © The Author(s) 2016.

Mapping the Risk of Snakebite in Sri Lanka - A National Survey with Geospatial Analysis.

PubMed

Ediriweera, Dileepa Senajith; Kasturiratne, Anuradhani; Pathmeswaran, Arunasalam; Gunawardena, Nipul Kithsiri; Wijayawickrama, Buddhika Asiri; Jayamanne, Shaluka Francis; Isbister, Geoffrey Kennedy; Dawson, Andrew; Giorgi, Emanuele; Diggle, Peter John; Lalloo, David Griffith; de Silva, Hithanadura Janaka

2016-07-01

There is a paucity of robust epidemiological data on snakebite, and data available from hospitals and localized or time-limited surveys have major limitations. No study has investigated the incidence of snakebite across a whole country. We undertook a community-based national survey and model based geostatistics to determine incidence, envenoming, mortality and geographical pattern of snakebite in Sri Lanka. The survey was designed to sample a population distributed equally among the nine provinces of the country. The number of data collection clusters was divided among districts in proportion to their population. Within districts clusters were randomly selected. Population based incidence of snakebite and significant envenoming were estimated. Model-based geostatistics was used to develop snakebite risk maps for Sri Lanka. 1118 of the total of 14022 GN divisions with a population of 165665 (0.8%of the country's population) were surveyed. The crude overall community incidence of snakebite, envenoming and mortality were 398 (95% CI: 356-441), 151 (130-173) and 2.3 (0.2-4.4) per 100000 population, respectively. Risk maps showed wide variation in incidence within the country, and snakebite hotspots and cold spots were determined by considering the probability of exceeding the national incidence. This study provides community based incidence rates of snakebite and envenoming for Sri Lanka. The within-country spatial variation of bites can inform healthcare decision making and highlights the limitations associated with estimates of incidence from hospital data or localized surveys. Our methods are replicable, and these models can be adapted to other geographic regions after re-estimating spatial covariance parameters for the particular region.

Validity of the methods to assess body fat in children and adolescents using multi-compartment models as the reference method: a systematic review.

PubMed

Silva, Danilo R P; Ribeiro, Alex S; Pavão, Fernando H; Ronque, Enio R V; Avelar, Ademar; Silva, Analiza M; Cyrino, Edilson S

2013-01-01

To analyze the validity of methods to assess body fat in children and adolescents using a systematic review. The search was conducted by two independent researchers using the MEDLINE, BioMed Central, SciELO and LILACS electronic databases. For inclusion, the articles should be written in English or Portuguese, and must have used multi-compartment models as the criterion measure of the model, with body fat measurement of whole body in non-athlete children and adolescents. A preliminary search resulted in 832 studies. After all selection steps were performed, 12 articles were included. The selected studies were published between 1997 and 2010, whose samples consisted of children and adolescents with levels of relative body fat ranging from 20.7% to 41.4%. The methods used were: dual energy X-ray absorptiometry (58.3%), isotope dilution (41.6%), skinfold thickness (33.3%), hydrostatic weighing (25%), bioelectrical impedance analysis (25%), air displacement plethysmography (16.6%), and total body electrical conductivity (8.3%). Based on the analysis of the studies, isotope dilution and air displacement plethysmography methods were the most reliable, despite the limited number of studies. As for clinical use or for population-based studies, the equation of Slaughter et al. (1998), which uses the triceps and subscapular skinfolds thickness, showed the best results for assessment of body fat in this population. Copyright © 2013 Elsevier Editora Ltda. All rights reserved.

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.

PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.

PubMed

Pereira, Luísa; Alshamali, Farida; Andreassen, Rune; Ballard, Ruth; Chantratita, Wasun; Cho, Nam Soo; Coudray, Clotilde; Dugoujon, Jean-Michel; Espinoza, Marta; González-Andrade, Fabricio; Hadi, Sibte; Immel, Uta-Dorothee; Marian, Catalin; Gonzalez-Martin, Antonio; Mertens, Gerhard; Parson, Walther; Perone, Carlos; Prieto, Lourdes; Takeshita, Haruo; Rangel Villalobos, Héctor; Zeng, Zhaoshu; Zhivotovsky, Lev; Camacho, Rui; Fonseca, Nuno A

2011-09-01

Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15-17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator ( http://cracs.fc.up.pt/popaffiliator ) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.

Genetic and morphological characterisation of the Ankole Longhorn cattle in the African Great Lakes region.

PubMed

Ndumu, Deo B; Baumung, Roswitha; Hanotte, Olivier; Wurzinger, Maria; Okeyo, Mwai A; Jianlin, Han; Kibogo, Harrison; Sölkner, Johann

2008-01-01

The study investigated the population structure, diversity and differentiation of almost all of the ecotypes representing the African Ankole Longhorn cattle breed on the basis of morphometric (shape and size), genotypic and spatial distance data. Twentyone morphometric measurements were used to describe the morphology of 439 individuals from 11 sub-populations located in five countries around the Great Lakes region of central and eastern Africa. Additionally, 472 individuals were genotyped using 15 DNA microsatellites. Femoral length, horn length, horn circumference, rump height, body length and fore-limb circumference showed the largest differences between regions. An overall FST index indicated that 2.7% of the total genetic variation was present among sub-populations. The least differentiation was observed between the two sub-populations of Mbarara south and Luwero in Uganda, while the highest level of differentiation was observed between the Mugamba in Burundi and Malagarasi in Tanzania. An estimated membership of four for the inferred clusters from a model-based Bayesian approach was obtained. Both analyses on distance-based and model-based methods consistently isolated the Mugamba sub-population in Burundi from the others.

Study of Genetic Diversity among Simmental Cross Cattle in West Sumatra Based on Microsatellite Markers

PubMed Central

Agung, Paskah Partogi; Saputra, Ferdy; Septian, Wike Andre; Lusiana; Zein, Moch. Syamsul Arifin; Sulandari, Sri; Anwar, Saiful; Wulandari, Ari Sulistyo; Said, Syahruddin; Tappa, Baharuddin

2016-01-01

A study was conducted to assess the genetic diversity among Simmental Cross cattle in West Sumatra using microsatellite DNA markers. A total of 176 individual cattle blood samples was used for obtaining DNA samples. Twelve primers of microsatellite loci as recommended by FAO were used to identify the genetic diversity of the Simmental Cross cattle population. Multiplex DNA fragment analysis method was used for allele identification. All the microsatellite loci in this study were highly polymorphic and all of the identified alleles were able to classify the cattle population into several groups based on their genetic distance. The heterozygosity values of microsatellite loci in this study ranged from 0.556 to 0.782. The polymorphism information content (PIC) value of the 12 observed loci is high (PIC>0.5). The highest PIC value in the Simmental cattle population was 0.893 (locus TGLA53), while the lowest value was 0.529 (locus BM1818). Based on the genetic distance value, the subpopulation of the Simmental Cross-Agam and the Simmental Cross-Limapuluh Kota was exceptionally close to the Simmental Purebred thus indicating that a grading-up process has taken place with the Simmental Purebred. In view of the advantages possessed by the Simmental Cross cattle and the evaluation of the genetic diversity results, a number of subpopulations in this study can be considered as the initial (base) population for the Simmental Cross cattle breeding programs in West Sumatra, Indonesia. PMID:26732442

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

PubMed

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

2014-09-25

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

Non-parametric estimation of population size changes from the site frequency spectrum.

PubMed

Waltoft, Berit Lindum; Hobolth, Asger

2018-06-11

Changes in population size is a useful quantity for understanding the evolutionary history of a species. Genetic variation within a species can be summarized by the site frequency spectrum (SFS). For a sample of size n, the SFS is a vector of length n - 1 where entry i is the number of sites where the mutant base appears i times and the ancestral base appears n - i times. We present a new method, CubSFS, for estimating the changes in population size of a panmictic population from an observed SFS. First, we provide a straightforward proof for the expression of the expected site frequency spectrum depending only on the population size. Our derivation is based on an eigenvalue decomposition of the instantaneous coalescent rate matrix. Second, we solve the inverse problem of determining the changes in population size from an observed SFS. Our solution is based on a cubic spline for the population size. The cubic spline is determined by minimizing the weighted average of two terms, namely (i) the goodness of fit to the observed SFS, and (ii) a penalty term based on the smoothness of the changes. The weight is determined by cross-validation. The new method is validated on simulated demographic histories and applied on unfolded and folded SFS from 26 different human populations from the 1000 Genomes Project.

Kinetic quantitation of cerebral PET-FDG studies without concurrent blood sampling: statistical recovery of the arterial input function.

PubMed

O'Sullivan, F; Kirrane, J; Muzi, M; O'Sullivan, J N; Spence, A M; Mankoff, D A; Krohn, K A

2010-03-01

Kinetic quantitation of dynamic positron emission tomography (PET) studies via compartmental modeling usually requires the time-course of the radio-tracer concentration in the arterial blood as an arterial input function (AIF). For human and animal imaging applications, significant practical difficulties are associated with direct arterial sampling and as a result there is substantial interest in alternative methods that require no blood sampling at the time of the study. A fixed population template input function derived from prior experience with directly sampled arterial curves is one possibility. Image-based extraction, including requisite adjustment for spillover and recovery, is another approach. The present work considers a hybrid statistical approach based on a penalty formulation in which the information derived from a priori studies is combined in a Bayesian manner with information contained in the sampled image data in order to obtain an input function estimate. The absolute scaling of the input is achieved by an empirical calibration equation involving the injected dose together with the subject's weight, height and gender. The technique is illustrated in the context of (18)F -Fluorodeoxyglucose (FDG) PET studies in humans. A collection of 79 arterially sampled FDG blood curves are used as a basis for a priori characterization of input function variability, including scaling characteristics. Data from a series of 12 dynamic cerebral FDG PET studies in normal subjects are used to evaluate the performance of the penalty-based AIF estimation technique. The focus of evaluations is on quantitation of FDG kinetics over a set of 10 regional brain structures. As well as the new method, a fixed population template AIF and a direct AIF estimate based on segmentation are also considered. Kinetics analyses resulting from these three AIFs are compared with those resulting from radially sampled AIFs. The proposed penalty-based AIF extraction method is found to achieve significant improvements over the fixed template and the segmentation methods. As well as achieving acceptable kinetic parameter accuracy, the quality of fit of the region of interest (ROI) time-course data based on the extracted AIF, matches results based on arterially sampled AIFs. In comparison, significant deviation in the estimation of FDG flux and degradation in ROI data fit are found with the template and segmentation methods. The proposed AIF extraction method is recommended for practical use.

Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring

PubMed Central

Vierheilig, J.; Savio, D.; Ley, R. E.; Mach, R. L.; Farnleitner, A. H.

2016-01-01

The applicability of next generation DNA sequencing (NGS) methods for water quality assessment has so far not been broadly investigated. This study set out to evaluate the potential of an NGS-based approach in a complex catchment with importance for drinking water abstraction. In this multicompartment investigation, total bacterial communities in water, faeces, soil, and sediment samples were investigated by 454 pyrosequencing of bacterial 16S rRNA gene amplicons to assess the capabilities of this NGS method for (i) the development and evaluation of environmental molecular diagnostics, (ii) direct screening of the bulk bacterial communities, and (iii) the detection of faecal pollution in water. Results indicate that NGS methods can highlight potential target populations for diagnostics and will prove useful for the evaluation of existing and the development of novel DNA-based detection methods in the field of water microbiology. The used approach allowed unveiling of dominant bacterial populations but failed to detect populations with low abundances such as faecal indicators in surface waters. In combination with metadata, NGS data will also allow the identification of drivers of bacterial community composition during water treatment and distribution, highlighting the power of this approach for monitoring of bacterial regrowth and contamination in technical systems. PMID:26606090

Reference set for performance testing of pediatric vaccine safety signal detection methods and systems.

PubMed

Brauchli Pernus, Yolanda; Nan, Cassandra; Verstraeten, Thomas; Pedenko, Mariia; Osokogu, Osemeke U; Weibel, Daniel; Sturkenboom, Miriam; Bonhoeffer, Jan

2016-12-12

Safety signal detection in spontaneous reporting system databases and electronic healthcare records is key to detection of previously unknown adverse events following immunization. Various statistical methods for signal detection in these different datasources have been developed, however none are geared to the pediatric population and none specifically to vaccines. A reference set comprising pediatric vaccine-adverse event pairs is required for reliable performance testing of statistical methods within and across data sources. The study was conducted within the context of the Global Research in Paediatrics (GRiP) project, as part of the seventh framework programme (FP7) of the European Commission. Criteria for the selection of vaccines considered in the reference set were routine and global use in the pediatric population. Adverse events were primarily selected based on importance. Outcome based systematic literature searches were performed for all identified vaccine-adverse event pairs and complemented by expert committee reports, evidence based decision support systems (e.g. Micromedex), and summaries of product characteristics. Classification into positive (PC) and negative control (NC) pairs was performed by two independent reviewers according to a pre-defined algorithm and discussed for consensus in case of disagreement. We selected 13 vaccines and 14 adverse events to be included in the reference set. From a total of 182 vaccine-adverse event pairs, we classified 18 as PC, 113 as NC and 51 as unclassifiable. Most classifications (91) were based on literature review, 45 were based on expert committee reports, and for 46 vaccine-adverse event pairs, an underlying pathomechanism was not plausible classifying the association as NC. A reference set of vaccine-adverse event pairs was developed. We propose its use for comparing signal detection methods and systems in the pediatric population. Published by Elsevier Ltd.

A systematic review of validated methods to capture acute bronchospasm using administrative or claims data.

PubMed

Sharifi, Mona; Krishanswami, Shanthi; McPheeters, Melissa L

2013-12-30

To identify and assess billing, procedural, or diagnosis code, or pharmacy claim-based algorithms used to identify acute bronchospasm in administrative and claims databases. We searched the MEDLINE database from 1991 to September 2012 using controlled vocabulary and key terms related to bronchospasm, wheeze and acute asthma. We also searched the reference lists of included studies. Two investigators independently assessed the full text of studies against pre-determined inclusion criteria. Two reviewers independently extracted data regarding participant and algorithm characteristics. Our searches identified 677 citations of which 38 met our inclusion criteria. In these 38 studies, the most commonly used ICD-9 code was 493.x. Only 3 studies reported any validation methods for the identification of bronchospasm, wheeze or acute asthma in administrative and claims databases; all were among pediatric populations and only 2 offered any validation statistics. Some of the outcome definitions utilized were heterogeneous and included other disease based diagnoses, such as bronchiolitis and pneumonia, which are typically of an infectious etiology. One study offered the validation of algorithms utilizing Emergency Department triage chief complaint codes to diagnose acute asthma exacerbations with ICD-9 786.07 (wheezing) revealing the highest sensitivity (56%), specificity (97%), PPV (93.5%) and NPV (76%). There is a paucity of studies reporting rigorous methods to validate algorithms for the identification of bronchospasm in administrative data. The scant validated data available are limited in their generalizability to broad-based populations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Caught Ya! A School-Based Practical Activity to Evaluate the Capture-Mark-Release-Recapture Method

ERIC Educational Resources Information Center

Kingsnorth, Crawford; Cruickshank, Chae; Paterson, David; Diston, Stephen

2017-01-01

The capture-mark-release-recapture method provides a simple way to estimate population size. However, when used as part of ecological sampling, this method does not easily allow an opportunity to evaluate the accuracy of the calculation because the actual population size is unknown. Here, we describe a method that can be used to measure the…

An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels

PubMed Central

Nassir, Rami; Kosoy, Roman; Tian, Chao; White, Phoebe A; Butler, Lesley M; Silva, Gabriel; Kittles, Rick; Alarcon-Riquelme, Marta E; Gregersen, Peter K; Belmont, John W; De La Vega, Francisco M; Seldin, Michael F

2009-01-01

Background Case-control genetic studies of complex human diseases can be confounded by population stratification. This issue can be addressed using panels of ancestry informative markers (AIMs) that can provide substantial population substructure information. Previously, we described a panel of 128 SNP AIMs that were designed as a tool for ascertaining the origins of subjects from Europe, Sub-Saharan Africa, Americas, and East Asia. Results In this study, genotypes from Human Genome Diversity Panel populations were used to further evaluate a 93 SNP AIM panel, a subset of the 128 AIMS set, for distinguishing continental origins. Using both model-based and relatively model-independent methods, we here confirm the ability of this AIM set to distinguish diverse population groups that were not previously evaluated. This study included multiple population groups from Oceana, South Asia, East Asia, Sub-Saharan Africa, North and South America, and Europe. In addition, the 93 AIM set provides population substructure information that can, for example, distinguish Arab and Ashkenazi from Northern European population groups and Pygmy from other Sub-Saharan African population groups. Conclusion These data provide additional support for using the 93 AIM set to efficiently identify continental subject groups for genetic studies, to identify study population outliers, and to control for admixture in association studies. PMID:19630973

Accounting for Population Structure in Gene-by-Environment Interactions in Genome-Wide Association Studies Using Mixed Models.

PubMed

Sul, Jae Hoon; Bilow, Michael; Yang, Wen-Yun; Kostem, Emrah; Furlotte, Nick; He, Dan; Eskin, Eleazar

2016-03-01

Although genome-wide association studies (GWASs) have discovered numerous novel genetic variants associated with many complex traits and diseases, those genetic variants typically explain only a small fraction of phenotypic variance. Factors that account for phenotypic variance include environmental factors and gene-by-environment interactions (GEIs). Recently, several studies have conducted genome-wide gene-by-environment association analyses and demonstrated important roles of GEIs in complex traits. One of the main challenges in these association studies is to control effects of population structure that may cause spurious associations. Many studies have analyzed how population structure influences statistics of genetic variants and developed several statistical approaches to correct for population structure. However, the impact of population structure on GEI statistics in GWASs has not been extensively studied and nor have there been methods designed to correct for population structure on GEI statistics. In this paper, we show both analytically and empirically that population structure may cause spurious GEIs and use both simulation and two GWAS datasets to support our finding. We propose a statistical approach based on mixed models to account for population structure on GEI statistics. We find that our approach effectively controls population structure on statistics for GEIs as well as for genetic variants.

Motor Competence Levels and Prevalence of Developmental Coordination Disorder in Spanish Children: The MOVI-KIDS Study

ERIC Educational Resources Information Center

Amador-Ruiz, Santiago; Gutierrez, David; Martínez-Vizcaíno, Vicente; Gulías-González, Roberto; Pardo-Guijarro, María J.; Sánchez-López, Mairena

2018-01-01

Background: Motor competence (MC) affects numerous aspects of children's daily life. The aims of this study were to: evaluate MC, provide population-based percentile values for MC; and determine the prevalence of developmental coordination disorder (DCD) in Spanish schoolchildren. Methods: This cross-sectional study included 1562 children aged 4…

[Dental practitioners in Israel: past, present and future].

PubMed

Mann, J; Vered, Y; Zini, A

2010-04-01

Since 1980 various studies have been published in Israel dealing with dental manpower issues, utilizing several methods such as manpower to population ratio. The dental literature pointed out that dentistry in Israel has an over supply of dentists and that manpower to population ratio is one of the highest in the world 1:770. All studies were based on the information provided by the Ministry of Health which showed that Israel has over 9500 dentists. The Israel Central Bureau of Statistics figures showed a much smaller number which was 5700 active dentists. This enormous gap in between two sources of information, following strict examination of the data revealed that the Bureau of Statistics information is reliable and hence, the real manpower to population ratio in Israel in 2008 was 1:1271. Prediction of manpower is extremely important and the base line information is crucial for future evaluations.

Gunnison sage-grouse lek site suitability modeling

USGS Publications Warehouse

Ouren, Douglas S.; Ignizio, Drew A.; Siders, Melissa; Childers, Theresa; Tucker, Karen; Seward, Nathan

2014-01-01

In order to better understand and protect species with minimal or decreasing populations, it is imperative to determine their actual existing population size. The focal species for this project is the Gunnison sage-grouse (GUSG), which became a proposed endangered species under the Endangered Species Act, thus confirming the need for better population estimates. Lek site counting during mating season has historically been the primary method for estimating population size since the grouse are very difficult to count at other times of the year. The objective of this project was to use historical data and available technology to identify additional potential lekking sites. This was done by determining areas throughout the study area that have the same landscape characteristics as those where known lekking activities occur. More accurate population counts could be the outcome of locating more lek sites. One of the remaining seven GUSG populations, the Crawford population (estimated at 128 individuals) exists in an area that includes the Gunnison Gorge National Conservation Area and the northern portion of the Black Canyon of the Gunnison National Park (our study area). While the Crawford population is small, it is still considered a self-sustaining population; the persistence and growth of this population directly contribute to genetic diversity conservation of this declining species. To date, only observational and anecdotal information about the Crawford population’s range, movements, and seasonal habitat use exist. From 1978 to the present, GUSG population monitoring has been accomplished through annual lek counts conducted each spring during GUSG mating season. Although this method has provided information on GUSG population trends, it is somewhat limited because counts are based only on known lekking sites and historically minimal efforts have been made to identify additional lek sites. To meet the objective of locating more potential lekking sites, we used a suite of spatial data, geographic information system tools, and maximum entropy species distribution tools. Based on expert knowledge and landscape variables, the modeling process evolved into a hybrid approach for delineating areas that would have a significant probability for supporting GUSG lekking activities. Based on model results, a sampling protocol was developed for model verification. The results of this project provide wildlife managers with a more sophisticated methodology to evaluate GUSG habitat for potential lekking sites.

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

PubMed

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

2015-01-01

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

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

PubMed Central

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

2014-01-01

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

Treatment intensification without improved HbA1c levels in children and adolescents with Type 1 diabetes mellitus.

PubMed

Sildorf, S M; Hertel, N T; Thomsen, J; Fredheim, S; Hastrup, H; Pipper, C; Hertz, B; Svensson, J

2016-04-01

To examine trends in diabetes treatment in Danish children and adolescents with Type 1 diabetes mellitus, comparing treatment intensity with metabolic outcomes in the population, and to describe the challenges of population-based registries in a clinical setting with rapidly changing treatment methods. This observational study is based on the Danish national population registry of childhood diabetes, which includes 99% of children diagnosed with Type 1 diabetes before the age of 15 years. We included 4527 people diagnosed between 2000 and 2012. Self-monitored blood glucose measurements, insulin injections/boluses, treatment method and metabolic control quantifications were analysed and adjusted for the effects of gender and ethnicity, the combined effect of age, visit year and duration, and for the random effects of individual and hospital settings. Treatment was intensified via an increasing number of self-monitored blood glucose measurements and injections/boluses. More than six injections/boluses and an increased number of self-monitored blood glucose measurements were significantly associated with lower metabolic control. No reduction, however, in the overall mean HbA1c concentration was observed between 2005 [66 mmol/mol (8.2%)] and 2012 [65 mmol/mol (8.1%)]. Changed registration practices in 2009 introduced artificial jumps in data. Intensifying treatment alone does not lead to improved metabolic control in the overall population despite the appearance of lower HbA1c in individuals with a greater number of self-monitored blood glucose measurements and injections/boluses. The contradictory results reflect difficulties in using observational studies to predict results of intervention in the individual. Data collected from population-based registries need to be adjusted continuously to reflect changes in care. © 2015 Diabetes UK.

Design of a digital phantom population for myocardial perfusion SPECT imaging research.

PubMed

Ghaly, Michael; Du, Yong; Fung, George S K; Tsui, Benjamin M W; Links, Jonathan M; Frey, Eric

2014-06-21

Digital phantoms and Monte Carlo (MC) simulations have become important tools for optimizing and evaluating instrumentation, acquisition and processing methods for myocardial perfusion SPECT (MPS). In this work, we designed a new adult digital phantom population and generated corresponding Tc-99m and Tl-201 projections for use in MPS research. The population is based on the three-dimensional XCAT phantom with organ parameters sampled from the Emory PET Torso Model Database. Phantoms included three variations each in body size, heart size, and subcutaneous adipose tissue level, for a total of 27 phantoms of each gender. The SimSET MC code and angular response functions were used to model interactions in the body and the collimator-detector system, respectively. We divided each phantom into seven organs, each simulated separately, allowing use of post-simulation summing to efficiently model uptake variations. Also, we adapted and used a criterion based on the relative Poisson effective count level to determine the required number of simulated photons for each simulated organ. This technique provided a quantitative estimate of the true noise in the simulated projection data, including residual MC simulation noise. Projections were generated in 1 keV wide energy windows from 48-184 keV assuming perfect energy resolution to permit study of the effects of window width, energy resolution, and crosstalk in the context of dual isotope MPS. We have developed a comprehensive method for efficiently simulating realistic projections for a realistic population of phantoms in the context of MPS imaging. The new phantom population and realistic database of simulated projections will be useful in performing mathematical and human observer studies to evaluate various acquisition and processing methods such as optimizing the energy window width, investigating the effect of energy resolution on image quality and evaluating compensation methods for degrading factors such as crosstalk in the context of single and dual isotope MPS.

Design of a digital phantom population for myocardial perfusion SPECT imaging research

NASA Astrophysics Data System (ADS)

Ghaly, Michael; Du, Yong; Fung, George S. K.; Tsui, Benjamin M. W.; Links, Jonathan M.; Frey, Eric

2014-06-01

Digital phantoms and Monte Carlo (MC) simulations have become important tools for optimizing and evaluating instrumentation, acquisition and processing methods for myocardial perfusion SPECT (MPS). In this work, we designed a new adult digital phantom population and generated corresponding Tc-99m and Tl-201 projections for use in MPS research. The population is based on the three-dimensional XCAT phantom with organ parameters sampled from the Emory PET Torso Model Database. Phantoms included three variations each in body size, heart size, and subcutaneous adipose tissue level, for a total of 27 phantoms of each gender. The SimSET MC code and angular response functions were used to model interactions in the body and the collimator-detector system, respectively. We divided each phantom into seven organs, each simulated separately, allowing use of post-simulation summing to efficiently model uptake variations. Also, we adapted and used a criterion based on the relative Poisson effective count level to determine the required number of simulated photons for each simulated organ. This technique provided a quantitative estimate of the true noise in the simulated projection data, including residual MC simulation noise. Projections were generated in 1 keV wide energy windows from 48-184 keV assuming perfect energy resolution to permit study of the effects of window width, energy resolution, and crosstalk in the context of dual isotope MPS. We have developed a comprehensive method for efficiently simulating realistic projections for a realistic population of phantoms in the context of MPS imaging. The new phantom population and realistic database of simulated projections will be useful in performing mathematical and human observer studies to evaluate various acquisition and processing methods such as optimizing the energy window width, investigating the effect of energy resolution on image quality and evaluating compensation methods for degrading factors such as crosstalk in the context of single and dual isotope MPS.

Nuclear-physical analysis methods in medical geology: Assessment of the impact of environmental factors on human health

NASA Astrophysics Data System (ADS)

Gorbunov, A. V.; Lyapunov, S. M.; Okina, O. I.; Frontas'eva, M. V.; Pavlov, S. S.; Il'chenko, I. N.

2015-05-01

The procedure for geomedical studies is outlined, and the niche occupied by the nuclear-physical analysis methods in these studies is pointed out. The necessity of construction of an efficient complex of the most modern analytical methods is demonstrated. The metrological parameters of methods applied in the analysis of natural environments and biological materials are evaluated. The current state of pollution of natural environments with heavy and toxic metals is characterized in two specific industrial hubs: the towns of Gus-Khrustalny and Podolsk. The levels of pollution of diagnostic biological materials (hair and blood) from children living in various urban districts are studied in the light of specific features of the manufacturing industry in these towns and the life environment of child population. The results of studies focused on evaluating the effect of environment on the health of child population are detailed. The actual damage to child health, their neuropsychic development and behavior, and the effect of socioeconomic factors are determined. Preventive problems among the child population exposed to lead and other toxic metals are evaluated, and ways to solve them are proposed. A system of early diagnosis and preventive measures for the mitigation of adverse effect of toxic metals (Pb, Cu, Mn, Zn, Cr, Ni, As, etc.) on the neuropsychic development of children is developed based on an actual ecogeochemical estimation of the state of the region under study.

Approach to prevention of obesity of Roma population in the Region of South Bohemia with focus on selected eating behaviors.

PubMed

Dolák, František; Šedová, Lenka; Nováková, Dita; Olišarová, Věra

2016-12-01

To survey obesity prevention methods for use in the Roma population with a focus on eating behaviors. A semi-structured interview was used to identify potentially useful obesity prevention methods. Basic anthropometric measurements were also gathered at the same time. This study was part of the "Obesity and overweight in the Roma minority in the Region of South Bohemia" research project (grant project 280-COST-LD14114). Participants consisted of members of the Roma minority (302 respondents) as well as the majority (Czech) population for comparisons. Differences in eating behaviors like irregular eating schedules and excessive consumption of fast food were observed. Statistically significant differences between the Roma minority and the majority (Czech/non-Roma) population were found in this area with the help of statistical significance tests. The Chi-square characteristic of independence (χ2) was, in case of this distribution, valued at 30.815 with 5 degrees of freedom, P < 0.001. The analyses, based on the second degree of classification, identified statistically significant differences between the Roma minority and the majority population. Members of the Roma minority attended preventive health check-ups statistically less often than members of the majority population. Differences between the majority and the Roma population were also found in the degree of patient cooperation with general practitioners. The results show that the Roma population is more likely to engage in eating behaviors that can contribute to overweight and obesity than the majority population. Based on the results of a semi-structured interview and on the results of anthropometric measurements, we can say that the Roma population is at a greater health risk, relative to overweight and obesity, than the majority population.

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.

Prevalence and Incidence of Systemic Lupus Erythematosus in a Population-Based Registry of American Indian and Alaska Native People, 2007–2009

PubMed Central

Ferucci, Elizabeth D.; Johnston, Janet M.; Gaddy, Jasmine R.; Sumner, Lisa; Posever, James O.; Choromanski, Tammy L.; Gordon, Caroline; Lim, S. Sam; Helmick, Charles G.

2015-01-01

Objective Few studies have investigated the epidemiology of systemic lupus erythematosus (SLE) in American Indian and Alaska Native populations. The objective of this study was to determine the prevalence and incidence of SLE in the Indian Health Service (IHS) active clinical population in 3 regions of the US. Methods For this population-based registry within the IHS, the denominator consisted of individuals in the IHS active clinical population in 2007, 2008, and/or 2009 and residing in a community in 1 of 3 specified regions. Potential SLE cases were identified based on the presence of a diagnostic code for SLE or related disorder in the IHS National Data Warehouse. Detailed medical record abstraction was performed for each potential case. The primary case definition was documentation in the medical record of ≥4 of the revised American College of Rheumatology criteria for the classification of SLE. Prevalence was calculated for 2007, and the mean annual incidence was calculated for the years 2007 through 2009. Results The age-adjusted prevalence and incidence of SLE according to the primary definition were 178 per 100,000 person-years (95% confidence interval [95% CI] 157–200) and 7.4 per 100,000 person-years (95% CI 5.1–10.4). Among women, the age-adjusted prevalence was 271, and the age-adjusted incidence was 10.4. The prevalence was highest in women ages 50–59 years and in the Phoenix Area IHS. Conclusion The first population-based lupus registry in the US American Indian and Alaska Native population has demonstrated that the prevalence and incidence of SLE are high. Our estimates are as high as or higher than the rates reported in the US black population. PMID:24891315

Pancreatic cancer early detection: Expanding higher-risk group with clinical and metabolomics parameters

PubMed Central

Urayama, Shiro

2015-01-01

Pancreatic ductal adenocarcinoma (PDAC) is the fourth and fifth leading cause of cancer death for each gender in developed countries. With lack of effective treatment and screening scheme available for the general population, the mortality rate is expected to increase over the next several decades in contrast to the other major malignancies such as lung, breast, prostate and colorectal cancers. Endoscopic ultrasound, with its highest level of detection capacity of smaller pancreatic lesions, is the commonly employed and preferred clinical imaging-based PDAC detection method. Various molecular biomarkers have been investigated for characterization of the disease, but none are shown to be useful or validated for clinical utilization for early detection. As seen from studies of a small subset of familial or genetically high-risk PDAC groups, the higher yield and utility of imaging-based screening methods are demonstrated for these groups. Multiple recent studies on the unique cancer metabolism including PDAC, demonstrate the potential for utility of the metabolites as the discriminant markers for this disease. In order to generate an early PDAC detection screening strategy available for a wider population, we propose to expand the population of higher risk PDAC group with combination clinical and metabolomics parameters. PMID:25684935

[Detection and application of PIS genetic deficiency gene in dairy goat].

PubMed

Yang, Bo; Jia, Li-Li; Zhao, De-Chao; Meng, Li-Yun; Liu, Xue-Feng; Zhang, Yan-Jun; Zhang, Wen-Guang; Li, Jin-Quan

2012-07-01

The purpose of this study was to develop a molecular method for detecting polled intersex syndrome (PIS) genetic deficiency gene in dairy goat. Three pairs of primers, PIS-, PIS+, and NEI were designed based on PIS gene sequence (AF404302) to identify the PIS genetic deficiency genotype. For the normal phenotype, the fragments of 141 and 300 bp were obtained for the genotype PIS-PIS-, and 141, 449, and 300 bp for the genotype PIS-PIS+. For the PIS goat with the genotype PIS+PIS+, 449 and 300 bp were obtained. Two hundred and twenty-four dairy goats in one population were tested based on this method. The results showed that there were 150 PIS-PIS+, 70 PIS -PIS-, and 4 PIS+PIS+. The genotype frequency of PIS-PIS+ was 66.9%, and the gene frequency of PIS+ was 35.3% in the population. Therefore, the frequency of PIS offspring was over 12%. This study developed a method to detect PIS genetic deficiency dairy goat. The method could identify buck genotype accurately to avoid the occurrence of PIS genetic deficiency. The ease and accuracy show a strong potential of the method for use in marker assisted selection of dairy goats and healthy development of dairy goat industry.

Fall incidence in Germany: results of two population-based studies, and comparison of retrospective and prospective falls data collection methods.

PubMed

Rapp, Kilian; Freiberger, Ellen; Todd, Chris; Klenk, Jochen; Becker, Clemens; Denkinger, Michael; Scheidt-Nave, Christa; Fuchs, Judith

2014-09-20

Fall incidence differs considerably between studies and countries. Reasons may be differences between study samples or different assessment methods. The aim was to derive estimates of fall incidence from two population-based studies among older community-living people in Germany and compare retrospective and prospective falls data collection methods. Data were derived from the 2008-11 wave of the German health interview and examination survey for adults (DEGS1), and the Activity and Function of the Elderly in Ulm study (ActiFE-Ulm). Data collection took place in community facilities (DEGS1) or participants' homes (ActiFE-Ulm). Participation rates were 42% (newly recruited) and 64% (panel component) in DEGS1 and 19.8% in ActiFE-Ulm. Self-report retrospective fall data covering the previous 12 month period in DEGS1 and ActiFE-Ulm were collected, but only ActiFE-Ulm used prospective 12 month fall calendars. The incidence of 'any fall' and 'recurrent falls' were calculated for both methods. Fall rates increased with age in men but not women. The ActiFE-Ulm prospectively assessed incidence (95% confidence interval) in women and men aged 65- < 90 years were 38.7 (36.9-40.5) and 29.7 (28.1-31.3) fallers/year and 13.7 (12.5-14.9) and 10.9 (9.9-12.0) recurrent fallers/year, respectively. Retrospective and prospective fall incidence in ActiFE-Ulm did not differ.The retrospectively assessed incidence of 'any fall' among persons 65- < 80 years were significantly lower in DEGS1 than ActiFE-Ulm (women: 25.7% (22.4-29.2) versus 37.4% (34.8-39.9); men: 16.3% (13.6-19.3) versus 28.9% (26.6-31.1). Retrospective incidence estimates of recurrent falls were similar in both studies for women (10.4% (8.3-12.9) versus 10.2% (8.5-11.8)) and men (6.1% (4.3-8.5) versus 8.4% (7.1-9.8)). Both studies were population-based, but retrospective self-reported fall incidence differed between studies. Study design influences retrospective reported fall incidence considerably. Costly collection of prospective data gives similar rates to the cheaper retrospective report method.

Diabetic nephropathy in Africa: A systematic review

PubMed Central

Noubiap, Jean Jacques N; Naidoo, Jashira; Kengne, Andre P

2015-01-01

AIM: To determine the prevalence and incidence of diabetic nephropathy in Africa. METHODS: We performed a systematic narrative review of published literature following the MOOSE Guidelines for Meta-Analysis and Systematic Reviews of Observational Studies. We searched PubMed-MEDLINE for all articles published in English and French languages between January 1994 and July 2014 using a predefined strategy based on the combination of relevant terms and the names of each of the 54 African countries and African sub-regions to capture the largest number of studies, and hand-searched the reference lists of retrieved articles. Included studies reported on the prevalence, incidence or determinants of chronic kidney disease (CKD) in people with diabetes within African countries. RESULTS: Overall, we included 32 studies from 16 countries; two being population-based studies and the remaining being clinic-based surveys. Most of the studies (90.6%) were conducted in urban settings. Methods for assessing and classifying CKD varied widely. Measurement of urine protein was the most common method of assessing kidney damage (62.5% of studies). The overall prevalence of CKD varied from 11% to 83.7%. Incident event rates were 94.9% for proteinuria at 10 years of follow-up, 34.7% for end-stage renal disease at 5 years of follow-up and 18.4% for mortality from nephropathy at 20 years of follow-up. Duration of diabetes, blood pressure, advancing age, obesity and glucose control were the common determinants of kidney disease. CONCLUSION: The burden of CKD is important among people with diabetes in Africa. High quality data from large population-based studies with validated measures of kidney function are still needed to better capture the magnitude and characteristics of diabetic nephropathy in Africa. PMID:26069725

Validity of self-reported mechanical demands for occupational epidemiologic research of musculoskeletal disorders

PubMed Central

Barrero, Lope H; Katz, Jeffrey N; Dennerlein, Jack T

2012-01-01

Objectives To describe the relation of the measured validity of self-reported mechanical demands (self-reports) with the quality of validity assessments and the variability of the assessed exposure in the study population. Methods We searched for original articles, published between 1990 and 2008, reporting the validity of self-reports in three major databases: EBSCOhost, Web of Science, and PubMed. Identified assessments were classified by methodological characteristics (eg, type of self-report and reference method) and exposure dimension was measured. We also classified assessments by the degree of comparability between the self-report and the employed reference method, and the variability of the assessed exposure in the study population. Finally, we examined the association of the published validity (r) with this degree of comparability, as well as with the variability of the exposure variable in the study population. Results Of the 490 assessments identified, 75% used observation-based reference measures and 55% tested self-reports of posture duration and movement frequency. Frequently, validity studies did not report demographic information (eg, education, age, and gender distribution). Among assessments reporting correlations as a measure of validity, studies with a better match between the self-report and the reference method, and studies conducted in more heterogeneous populations tended to report higher correlations [odds ratio (OR) 2.03, 95% confidence interval (95% CI) 0.89–4.65 and OR 1.60, 95% CI 0.96–2.61, respectively]. Conclusions The reported data support the hypothesis that validity depends on study-specific factors often not examined. Experimentally manipulating the testing setting could lead to a better understanding of the capabilities and limitations of self-reported information. PMID:19562235

Emotional Symptoms in Inattentive Primary School Children: A Population-Based Study

ERIC Educational Resources Information Center

Sorensen, Lin; Hugdahl, Kenneth; Lundervold, Astri Johansen

2008-01-01

Objective: The present study investigates teacher and parent reports of inattention and emotional symptoms in 6,229 primary school children. Method: The assessment included the Emotional Symptoms subscale and the Impact scale from the Strengths and Difficulties Questionnaire and the inattention items from the Swanson, Nolan, and Pelham IV…

Measuring Personal Growth of New Grandparents: A Practical Tool for Social Workers

ERIC Educational Resources Information Center

Taubman--Ben-Ari, Orit; Ben Shlomo, Shirley

2016-01-01

Objective: Two studies examined the validity of using the Posttraumatic Growth Inventory (PTGI) to assess growth following the transition to grandparenthood as an aid for social workers seeking to promote strengths-based interventions for this population. Method: In Study 1 (n = 210 grandparent/offspring pairs), first-time grandparents'…

Febrile Seizures and Behavioural and Cognitive Outcomes in Preschool Children: The Generation R Study

ERIC Educational Resources Information Center

Visser, Annemarie M.; Jaddoe, Vincent W. V.; Ghassabian, Akhgar; Schenk, Jacqueline J.; Verhulst, Frank C.; Hofman, Albert; Tiemeier, Henning; Moll, Henriette A.; Arts, Willem Frans M.

2012-01-01

Aim: General developmental outcome is known to be good in school-aged children who experienced febrile seizures. We examined cognitive and behavioural outcomes in preschool children with febrile seizures, including language and executive functioning outcomes. Method: This work was performed in the Generation R Study, a population-based cohort…

PHYLOGENETIC ANALYSIS OF 16S RRNA GENE SEQUENCES REVEALS THE PREVALENCE OF MYCOBACTERIA SP., ALPHA-PROTEOBACTERIA, AND UNCULTURED BACTERIA IN DRINKING WATER MICROBIAL COMMUNITIES

EPA Science Inventory

Previous studies have shown that culture-based methods tend to underestimate the densities and diversity of bacterial populations inhabiting water distribution systems (WDS). In this study, the phylogenetic diversity of drinking water bacteria was assessed using sequence analysis...

A comparison of regression methods for model selection in individual-based landscape genetic analysis.

PubMed

Shirk, Andrew J; Landguth, Erin L; Cushman, Samuel A

2018-01-01

Anthropogenic migration barriers fragment many populations and limit the ability of species to respond to climate-induced biome shifts. Conservation actions designed to conserve habitat connectivity and mitigate barriers are needed to unite fragmented populations into larger, more viable metapopulations, and to allow species to track their climate envelope over time. Landscape genetic analysis provides an empirical means to infer landscape factors influencing gene flow and thereby inform such conservation actions. However, there are currently many methods available for model selection in landscape genetics, and considerable uncertainty as to which provide the greatest accuracy in identifying the true landscape model influencing gene flow among competing alternative hypotheses. In this study, we used population genetic simulations to evaluate the performance of seven regression-based model selection methods on a broad array of landscapes that varied by the number and type of variables contributing to resistance, the magnitude and cohesion of resistance, as well as the functional relationship between variables and resistance. We also assessed the effect of transformations designed to linearize the relationship between genetic and landscape distances. We found that linear mixed effects models had the highest accuracy in every way we evaluated model performance; however, other methods also performed well in many circumstances, particularly when landscape resistance was high and the correlation among competing hypotheses was limited. Our results provide guidance for which regression-based model selection methods provide the most accurate inferences in landscape genetic analysis and thereby best inform connectivity conservation actions. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Cross-cultural comparisons of attitudes toward schizophrenia amongst the general population and physicians: a series of web-based surveys in Japan and the United States.

PubMed

Richards, Misty; Hori, Hiroaki; Sartorius, Norman; Kunugi, Hiroshi

2014-02-28

Cross-cultural differences in attitudes toward schizophrenia are suggested, while no studies have compared such attitudes between the United States and Japan. In our previous study in Japan (Hori et al., 2011), 197 subjects in the general population and 112 physicians (excluding psychiatrists) enrolled in a web-based survey using an Internet-based questionnaire format. Utilizing the identical web-based survey method in the United States, the present study enrolled 172 subjects in the general population and 45 physicians. Participants' attitudes toward schizophrenia were assessed with the English version of the 18-item questionnaire used in our previous Japanese survey. Using exploratory factor analysis, we identified four factors labeled "social distance," "belief of dangerousness," "underestimation of patients' abilities," and "skepticism regarding treatment." The two-way multivariate analysis of covariance on the four factors, with country and occupation as the between-subject factors and with potentially confounding demographic variables as the covariates, revealed that the general population in the US scored significantly lower than the Japanese counterparts on the factors "social distance" and "skepticism regarding treatment" and higher on "underestimation of patients' abilities." Our results suggest that culture may have an important role in shaping attitudes toward mental illness. Anti-stigma campaigns that target culture-specific biases are considered important. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

The role of transvaginal ultrasonography for detecting ovarian cancer in an asymptomatic screening population: a systematic review.

PubMed

Buhling, Kai J; Lezon, S; Eulenburg, C; Schmalfeldt, B

2017-05-01

The purpose of this study was to systematically analyze the effect of transvaginal ultrasonography in an asymptomatic female population as an annual screening procedure with regard to mortality data. Studies were evaluated descriptively on their strengths and weaknesses considering the methods and results. We evaluated 632 international studies by selecting only randomized controlled trials (RCTs). Three RCTs concerning transvaginal ultrasonography were found, performed in Japan, the USA, and Great Britain. Currently, no clear recommendation for the screening for ovarian cancer in an asymptomatic population can be given based on these three studies. The authors could not show a change in mortality using transvaginal ultrasonography for annual screening. An annual palpation does not offer a beneficial effect. The development of new ultrasound machines with higher image resolution in combination with a well-standardized algorithm for ovarian cancer in upcoming years might provide an improvement regarding mortality. The current studies do not show a benefit in screening an asymptomatic population annually with transvaginal ultrasonography, but the most recent publication showed a trend toward lower mortality in patients who underwent screening after 7-14 years of follow-up. Nevertheless, all three heterogeneous RCTs had weaknesses in their methods and therefore they neither contradict the general recommendation for screening in an asymptomatic population nor do they support it.

The population approach to falls injury prevention in older people: findings of a two community trial

PubMed Central

2010-01-01

Background There is a sound rationale for the population-based approach to falls injury prevention but there is currently insufficient evidence to advise governments and communities on how they can use population-based strategies to achieve desired reductions in the burden of falls-related injury. The aim of the study was to quantify the effectiveness of a streamlined (and thus potentially sustainable and cost-effective), population-based, multi-factorial falls injury prevention program for people over 60 years of age. Methods Population-based falls-prevention interventions were conducted at two geographically-defined and separate Australian sites: Wide Bay, Queensland, and Northern Rivers, NSW. Changes in the prevalence of key risk factors and changes in rates of injury outcomes within each community were compared before and after program implementation and changes in rates of injury outcomes in each community were also compared with the rates in their respective States. Results The interventions in neither community substantially decreased the rate of falls-related injury among people aged 60 years or older, although there was some evidence of reductions in occurrence of multiple falls reported by women. In addition, there was some indication of improvements in fall-related risk factors, but the magnitudes were generally modest. Conclusions The evidence suggests that low intensity population-based falls prevention programs may not be as effective as those that are intensively implemented. PMID:20167124

Generalizing observational study results: applying propensity score methods to complex surveys.

PubMed

Dugoff, Eva H; Schuler, Megan; Stuart, Elizabeth A

2014-02-01

To provide a tutorial for using propensity score methods with complex survey data. Simulated data and the 2008 Medical Expenditure Panel Survey. Using simulation, we compared the following methods for estimating the treatment effect: a naïve estimate (ignoring both survey weights and propensity scores), survey weighting, propensity score methods (nearest neighbor matching, weighting, and subclassification), and propensity score methods in combination with survey weighting. Methods are compared in terms of bias and 95 percent confidence interval coverage. In Example 2, we used these methods to estimate the effect on health care spending of having a generalist versus a specialist as a usual source of care. In general, combining a propensity score method and survey weighting is necessary to achieve unbiased treatment effect estimates that are generalizable to the original survey target population. Propensity score methods are an essential tool for addressing confounding in observational studies. Ignoring survey weights may lead to results that are not generalizable to the survey target population. This paper clarifies the appropriate inferences for different propensity score methods and suggests guidelines for selecting an appropriate propensity score method based on a researcher's goal. © Health Research and Educational Trust.

From Curves to Trees: A Tree-like Shapes Distance Using the Elastic Shape Analysis Framework.

PubMed

Mottini, A; Descombes, X; Besse, F

2015-04-01

Trees are a special type of graph that can be found in various disciplines. In the field of biomedical imaging, trees have been widely studied as they can be used to describe structures such as neurons, blood vessels and lung airways. It has been shown that the morphological characteristics of these structures can provide information on their function aiding the characterization of pathological states. Therefore, it is important to develop methods that analyze their shape and quantify differences between their structures. In this paper, we present a method for the comparison of tree-like shapes that takes into account both topological and geometrical information. This method, which is based on the Elastic Shape Analysis Framework, also computes the mean shape of a population of trees. As a first application, we have considered the comparison of axon morphology. The performance of our method has been evaluated on two sets of images. For the first set of images, we considered four different populations of neurons from different animals and brain sections from the NeuroMorpho.org open database. The second set was composed of a database of 3D confocal microscopy images of three populations of axonal trees (normal and two types of mutations) of the same type of neurons. We have calculated the inter and intra class distances between the populations and embedded the distance in a classification scheme. We have compared the performance of our method against three other state of the art algorithms, and results showed that the proposed method better distinguishes between the populations. Furthermore, we present the mean shape of each population. These shapes present a more complete picture of the morphological characteristics of each population, compared to the average value of certain predefined features.

Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics

PubMed Central

Pasi, Marco; Maddocks, John H.; Lavery, Richard

2015-01-01

Microsecond molecular dynamics simulations of B-DNA oligomers carried out in an aqueous environment with a physiological salt concentration enable us to perform a detailed analysis of how potassium ions interact with the double helix. The oligomers studied contain all 136 distinct tetranucleotides and we are thus able to make a comprehensive analysis of base sequence effects. Using a recently developed curvilinear helicoidal coordinate method we are able to analyze the details of ion populations and densities within the major and minor grooves and in the space surrounding DNA. The results show higher ion populations than have typically been observed in earlier studies and sequence effects that go beyond the nature of individual base pairs or base pair steps. We also show that, in some special cases, ion distributions converge very slowly and, on a microsecond timescale, do not reflect the symmetry of the corresponding base sequence. PMID:25662221

In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence.

PubMed

Laing, Chad R; Buchanan, Cody; Taboada, Eduardo N; Zhang, Yongxiang; Karmali, Mohamed A; Thomas, James E; Gannon, Victor Pj

2009-06-29

Many approaches have been used to study the evolution, population structure and genetic diversity of Escherichia coli O157:H7; however, observations made with different genotyping systems are not easily relatable to each other. Three genetic lineages of E. coli O157:H7 designated I, II and I/II have been identified using octamer-based genome scanning and microarray comparative genomic hybridization (mCGH). Each lineage contains significant phenotypic differences, with lineage I strains being the most commonly associated with human infections. Similarly, a clade of hyper-virulent O157:H7 strains implicated in the 2006 spinach and lettuce outbreaks has been defined using single-nucleotide polymorphism (SNP) typing. In this study an in silico comparison of six different genotyping approaches was performed on 19 E. coli genome sequences from 17 O157:H7 strains and single O145:NM and K12 MG1655 strains to provide an overall picture of diversity of the E. coli O157:H7 population, and to compare genotyping methods for O157:H7 strains. In silico determination of lineage, Shiga-toxin bacteriophage integration site, comparative genomic fingerprint, mCGH profile, novel region distribution profile, SNP type and multi-locus variable number tandem repeat analysis type was performed and a supernetwork based on the combination of these methods was produced. This supernetwork showed three distinct clusters of strains that were O157:H7 lineage-specific, with the SNP-based hyper-virulent clade 8 synonymous with O157:H7 lineage I/II. Lineage I/II/clade 8 strains clustered closest on the supernetwork to E. coli K12 and E. coli O55:H7, O145:NM and sorbitol-fermenting O157 strains. The results of this study highlight the similarities in relationships derived from multi-locus genome sampling methods and suggest a "common genotyping language" may be devised for population genetics and epidemiological studies. Future genotyping methods should provide data that can be stored centrally and accessed locally in an easily transferable, informative and extensible format based on comparative genomic analyses.

Monitoring population exposure to pesticides based on liquid chromatography-tandem mass spectrometry measurement of their urinary metabolites in urban wastewater: A novel biomonitoring approach.

PubMed

Rousis, Nikolaos I; Zuccato, Ettore; Castiglioni, Sara

2016-11-15

Biomonitoring studies have documented the high exposure of the population to pesticides which are widely used for crop protection, industrial and household purposes. This is the first study which has measured human urinary metabolites of pesticides in urban wastewater as biomarkers of population exposure. A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed to measure fifteen urinary metabolites selected from the major classes of pesticides. Raw wastewater samples were processed by solid phase extraction (SPE) or direct injection into the LC-MS/MS system. Recoveries ranged from 75 to 115% and the limits of quantification were 1-15ng/L for the SPE method and 40-800ng/L for direct injection. The method was employed for the analysis of 44 composite 24-h wastewater samples collected in seven Italian cities. Most of the target substances were detected at concentrations ranging from 1.1ng/L to 1.6μg/L. The highest concentrations were for some common metabolites of alkyl phosphates and pyrethroids and the specific metabolite of chlorpyrifos and chlorpyrifos-methyl (3,5,6-trichloro-2-pyridinol). The frequency of detection and abundance of most of the measured metabolites were in line with the profiles reported in urine biomonitoring studies. This method is therefore proposed as a novel "biomonitoring approach" for obtaining objective, direct information on the levels of exposure of a specific population to pesticides, and current research is addressed to validate the method identifying the most reliable biomarkers. Copyright © 2016 Elsevier B.V. All rights reserved.

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

PubMed Central

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

2006-01-01

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

Molecular diagnosis of strongyloidiasis in a population of an endemic area through nested-PCR.

PubMed

Sharifdini, Meysam; Keyhani, Amir; Eshraghian, Mohammad Reza; Beigom Kia, Eshrat

2018-01-01

This study is aimed to diagnose and analyze strongyloidiasis in a population of an endemic area of Iran using nested-PCR, coupled with parasitological methods. Screening of strongyloidiasis infected people using reliable diagnostic techniques are essential to decrease the mortality and morbidity associated with this infection. Molecular methods have been proved to be highly sensitive and specific for detection of Strongyloides stercoralis in stool samples. A total of 155 fresh single stool samples were randomly collected from residents of north and northwest of Khouzestan Province, Iran. All samples were examined by parasitological methods including formalin-ether concentration and nutrient agar plate culture, and molecular method of nested-PCR. Infections with S. stercoralis were analyzed according to demographic criteria. Based on the results of nested-PCR method 15 cases (9.7%) were strongyloidiasis positive. Nested-PCR was more sensitive than parasitological techniques on single stool sampling. Elderly was the most important population index for higher infectivity with S. stercoralis . In endemic areas of S. stercoralis , old age should be considered as one of the most important risk factors of infection, especially among the immunosuppressed individuals.

Using spatial capture–recapture to elucidate population processes and space-use in herpetological studies

USGS Publications Warehouse

Muñoz, David J.; Miller, David A.W.; Sutherland, Chris; Grant, Evan H. Campbell

2016-01-01

The cryptic behavior and ecology of herpetofauna make estimating the impacts of environmental change on demography difficult; yet, the ability to measure demographic relationships is essential for elucidating mechanisms leading to the population declines reported for herpetofauna worldwide. Recently developed spatial capture–recapture (SCR) methods are well suited to standard herpetofauna monitoring approaches. Individually identifying animals and their locations allows accurate estimates of population densities and survival. Spatial capture–recapture methods also allow estimation of parameters describing space-use and movement, which generally are expensive or difficult to obtain using other methods. In this paper, we discuss the basic components of SCR models, the available software for conducting analyses, and the experimental designs based on common herpetological survey methods. We then apply SCR models to Red-backed Salamander (Plethodon cinereus), to determine differences in density, survival, dispersal, and space-use between adult male and female salamanders. By highlighting the capabilities of SCR, and its advantages compared to traditional methods, we hope to give herpetologists the resource they need to apply SCR in their own systems.

Use of experience sampling method to understand the wilderness experience

Treesearch

Lynn Anderson

2002-01-01

There is a growing body of research documenting the benefits of outdoor adventure and wilderness-based programs with a variety of special populations. Criticisms of this body of research are that it is not grounded in theory and it is outcome-based, with no investigation into the processes causing the behavior change in individuals. This study attempted to investigate...

Relationship between Eating Behavior, Breakfast Consumption, and Obesity among Finnish and Greek Adolescents

ERIC Educational Resources Information Center

Veltsista, Alexandra; Laitinen, Jaana; Sovio, Ulla; Roma, Eleftheria; Jarvelin, Marjo-Ritta; Bakoula, Chryssa

2010-01-01

Objective: To investigate the relationship between eating-related behaviors, particularly breakfast consumption, and weight status in Finnish and Greek adolescents. Methods: A total of 6,468 16-year-old Finnish adolescents and 2,842 17- and 18-year-old Greek adolescents, based on the latest follow-up of 2 population-based cohorts, were studied.…

The Effect of Self-Reported and Performance-Based Functional Impairment on Future Hospital Costs of Community-Dwelling Older Persons

ERIC Educational Resources Information Center

Reuben, David B.; Seeman, Teresa E.; Keeler, Emmett; Hayes, Risa P.; Bowman, Lee; Sewall, Ase; Hirsch, Susan H.; Wallace, Robert B.; Guralnik, Jack M.

2004-01-01

Purpose: We determined the prognostic value of self-reported and performance-based measurement of function, including functional transitions and combining different measurement approaches, on utilization. Design and Methods: Our cohort study used the 6th, 7th, and 10th waves of three sites of the Established Populations for Epidemiologic Studies…

Population-based breast cancer screening in a primary care network

PubMed Central

Atlas, Steven J.; Ashburner, Jeffrey M.; Chang, Yuchiao; Lester, William T.; Barry, Michael J.; Grant, Richard W.

2013-01-01

Objective To assess up to 3-year follow-up of a health information technology system that facilitated population-based breast cancer screening. Study Design Cohort study with 2-year follow-up after completing a 1-year cluster randomized trial. Methods Women 42-69 years old receiving care within a 12-practice primary care network. The trial tested an integrated, non-visit-based population management informatics system that: 1) identified women overdue for mammograms, 2) connected them to primary care providers using a Web-based tool, 3) created automatically-generated outreach letters for patients specified by providers, 4) monitored for subsequent mammography scheduling and completion, and 5) provided practice delegates a list of women remaining unscreened for reminder phone calls. All practices also provided visit-based cancer screening reminders. Eligible women overdue for a mammogram during a one-year study period included those overdue at study start (prevalent cohort) or becoming overdue during follow-up (incident cohort). The main outcome measure was mammography completion rates over three years. Results Among 32,688 eligible women, 9,795 (30%) were overdue for screening including 4,487 in intervention and 5,308 in control practices. Intervention patients were somewhat younger, more likely to be non-Hispanic white, and have health insurance compared to control patients. Among patients in the prevalent cohort (n=6,697), adjusted completion rates were significantly higher among intervention compared to control patients after 3 years (51.7% vs. 45.8%, p=0.002). For patients in the incident cohort (n=3,098), adjusted completion rates after 2 years were 53.8% vs. 48.7%, p=0.052, respectively. Conclusions Population-based informatics systems can enable sustained increases in mammography screening rates beyond that seen with office-based visit reminders. PMID:23286611

Evaluation of Selection Bias in an Internet-based Study of Pregnancy Planners

PubMed Central

Hatch, Elizabeth E.; Hahn, Kristen A.; Wise, Lauren A.; Mikkelsen, Ellen M.; Kumar, Ramya; Fox, Matthew P.; Brooks, Daniel R.; Riis, Anders H.; Sorensen, Henrik Toft; Rothman, Kenneth J.

2016-01-01

Selection bias is a potential concern in all epidemiologic studies, but it is usually difficult to assess. Recently, concerns have been raised that internet-based prospective cohort studies may be particularly prone to selection bias. Although use of the internet is efficient and facilitates recruitment of subjects that are otherwise difficult to enroll, any compromise in internal validity would be of great concern. Few studies have evaluated selection bias in internet-based prospective cohort studies. Using data from the Danish Medical Birth Registry from 2008 to 2012, we compared six well-known perinatal associations (e.g., smoking and birth weight) in an inter-net-based preconception cohort (Snart Gravid n = 4,801) with the total population of singleton live births in the registry (n = 239,791). We used log-binomial models to estimate risk ratios (RRs) and 95% confidence intervals (CIs) for each association. We found that most results in both populations were very similar. For example, maternal obesity was associated with an increased risk of delivering a macrosomic infant in Snart Gravid (RR = 1.5; 95% CI: 1.2, 1.7) and the total population (RR = 1.5; 95% CI: 1.45, 1.53), and maternal smoking of >10 cigarettes per day was associated with a higher risk of low birth weight (RR = 2.7; 95% CI: 1.2, 5.9 vs. RR = 2.9; 95% CI: 2.6, 3.1) in Snart Gravid and the total population, respectively. We cannot be certain that our results would apply to other associations or different populations. Nevertheless, our results suggest that recruitment of reproductive aged women via the internet may be no more prone to selection bias than traditional methods of recruitment. PMID:26484423

A Population-based study of dementia in the oldest old: the Monzino 80-plus Study

PubMed Central

2011-01-01

Background Despite being the fastest growing and the most cognitively impaired age group, the oldest olds are under-represented in clinical research. The purpose of this study was to describe the design, methods, and baseline characteristics of the survey population and investigate possible differences in demographic, cognitive, functional, and behavioral characteristics between oldest old with and without any performance on cognitive tests and between oldest old alive and those deceased prior to the interview. Methods The Monzino 80-plus Study is a prospective door-to-door population-based survey among 80 years or older residents in the municipalities in the province of Varese, Italy. Dementia cases were identified with a one-phase design. Trained psychologists interviewed both the subject and a proxy informant. The interview included a comprehensive standardized questionnaire together with an array of rating scales and a multidomain cognitive battery to assess cognitive and functional ability, behavioral disturbances and mood. Results Information was available for 2,139 of the 2,428 registered individuals aged 80 years or older. Main baseline characteristics of the population are reported and discussed. In comparison with those living, elderly persons who had died before the first visit were older, had twice the rate of institutionalization, poorer cognitive performance and competence, and significantly greater instrumental and basic functional disability. The percentage of elderly persons, alive at baseline, without Mini-Mental State Examination rose rather evenly with age. Moreover, they had significantly worse cognitive competence and functional ability, and reported higher prevalences of depressive symptoms and problem behaviors than those with Mini-Mental State Examination. Conclusions Prospective investigation of a large population of oldest old can contribute significantly to understanding the relations between age, cognitive decline, and dementia occurrence. Use of informant-based instruments in surveys in the oldest old is crucial in assessing everyday functioning and changes, especially in participants with no cognitive test performance available. Failure to include information on deceased elderly would underestimate, increasingly with age, the prevalence of cognitive and functional disability in the elderly population. PMID:21612585

Recurrent bottlenecks in the malaria life cycle obscure signals of positive selection.

PubMed

Chang, Hsiao-Han; Hartl, Daniel L

2015-02-01

Detecting signals of selection in the genome of malaria parasites is a key to identify targets for drug and vaccine development. Malaria parasites have a unique life cycle alternating between vector and host organism with a population bottleneck at each transition. These recurrent bottlenecks could influence the patterns of genetic diversity and the power of existing population genetic tools to identify sites under positive selection. We therefore simulated the site-frequency spectrum of a beneficial mutant allele through time under the malaria life cycle. We investigated the power of current population genetic methods to detect positive selection based on the site-frequency spectrum as well as temporal changes in allele frequency. We found that a within-host selective advantage is difficult to detect using these methods. Although a between-host transmission advantage could be detected, the power is decreased when compared with the classical Wright-Fisher (WF) population model. Using an adjusted null site-frequency spectrum that takes the malaria life cycle into account, the power of tests based on the site-frequency spectrum to detect positive selection is greatly improved. Our study demonstrates the importance of considering the life cycle in genetic analysis, especially in parasites with complex life cycles.

Visual aggregate analysis of eligibility features of clinical trials.

PubMed

He, Zhe; Carini, Simona; Sim, Ida; Weng, Chunhua

2015-04-01

To develop a method for profiling the collective populations targeted for recruitment by multiple clinical studies addressing the same medical condition using one eligibility feature each time. Using a previously published database COMPACT as the backend, we designed a scalable method for visual aggregate analysis of clinical trial eligibility features. This method consists of four modules for eligibility feature frequency analysis, query builder, distribution analysis, and visualization, respectively. This method is capable of analyzing (1) frequently used qualitative and quantitative features for recruiting subjects for a selected medical condition, (2) distribution of study enrollment on consecutive value points or value intervals of each quantitative feature, and (3) distribution of studies on the boundary values, permissible value ranges, and value range widths of each feature. All analysis results were visualized using Google Charts API. Five recruited potential users assessed the usefulness of this method for identifying common patterns in any selected eligibility feature for clinical trial participant selection. We implemented this method as a Web-based analytical system called VITTA (Visual Analysis Tool of Clinical Study Target Populations). We illustrated the functionality of VITTA using two sample queries involving quantitative features BMI and HbA1c for conditions "hypertension" and "Type 2 diabetes", respectively. The recruited potential users rated the user-perceived usefulness of VITTA with an average score of 86.4/100. We contributed a novel aggregate analysis method to enable the interrogation of common patterns in quantitative eligibility criteria and the collective target populations of multiple related clinical studies. A larger-scale study is warranted to formally assess the usefulness of VITTA among clinical investigators and sponsors in various therapeutic areas. Copyright © 2015 Elsevier Inc. All rights reserved.

Snow mapping and land use studies in Switzerland

NASA Technical Reports Server (NTRS)

Haefner, H. (Principal Investigator)

1977-01-01

The author has identified the following significant results. A system was developed for operational snow and land use mapping, based on a supervised classification method using various classification algorithms and representation of the results in maplike form on color film with a photomation system. Land use mapping, under European conditions, was achieved with a stepwise linear discriminant analysis by using additional ratio variables. On fall images, signatures of built-up areas were often not separable from wetlands. Two different methods were tested to correlate the size of settlements and the population with an accuracy for the densely populated Swiss Plateau between +2 or -12%.

A framework for the assessment of the spatial and temporal patterns of threatened coastal delphinids

NASA Astrophysics Data System (ADS)

Wang, Jingzhen; Yang, Yingting; Yang, Feng; Li, Yuelin; Li, Lianjie; Lin, Derun; He, Tangtian; Liang, Bo; Zhang, Tao; Lin, Yao; Li, Ping; Liu, Wenhua

2016-01-01

The massively accelerated biodiversity loss rate in the Anthropocene calls for an efficient and effective way to identify the spatial and temporal dynamics of endangered species. To this end, we developed a useful identification framework based on a case study of locally endangered Sousa chinensis by combining both LEK (local ecological knowledge) evaluation and regional boat-based survey methods. Our study investigated the basic ecological information of Sousa chinensis in the estuaries of eastern Guangdong that had previously been neglected, which could guide the future study and conservation. Based on the statistical testing of reported spatial and temporal dolphins sighting data from fishermen and the ecological monitoring analyses, including sighting rate, site fidelity and residence time estimations, some of the current Sousa chinensis units are likely to be geographically isolated and critically endangered, which calls for much greater conservation efforts. Given the accelerated population extinction rate and increasing budgetary constraints, our survey pattern can be applied in a timely and economically acceptable manner to the spatial and temporal assessment of other threatened coastal delphinids, particularly when population distributions are on a large scale and traditional sampling methods are difficult to implement.

A framework for the assessment of the spatial and temporal patterns of threatened coastal delphinids.

PubMed

Wang, Jingzhen; Yang, Yingting; Yang, Feng; Li, Yuelin; Li, Lianjie; Lin, Derun; He, Tangtian; Liang, Bo; Zhang, Tao; Lin, Yao; Li, Ping; Liu, Wenhua

2016-01-25

The massively accelerated biodiversity loss rate in the Anthropocene calls for an efficient and effective way to identify the spatial and temporal dynamics of endangered species. To this end, we developed a useful identification framework based on a case study of locally endangered Sousa chinensis by combining both LEK (local ecological knowledge) evaluation and regional boat-based survey methods. Our study investigated the basic ecological information of Sousa chinensis in the estuaries of eastern Guangdong that had previously been neglected, which could guide the future study and conservation. Based on the statistical testing of reported spatial and temporal dolphins sighting data from fishermen and the ecological monitoring analyses, including sighting rate, site fidelity and residence time estimations, some of the current Sousa chinensis units are likely to be geographically isolated and critically endangered, which calls for much greater conservation efforts. Given the accelerated population extinction rate and increasing budgetary constraints, our survey pattern can be applied in a timely and economically acceptable manner to the spatial and temporal assessment of other threatened coastal delphinids, particularly when population distributions are on a large scale and traditional sampling methods are difficult to implement.

Towards a Global Water Scarcity Risk Assessment Framework: Incorporation of Probability Distributions and Hydro-Climatic Variability

NASA Technical Reports Server (NTRS)

Veldkamp, T. I. E.; Wada, Y.; Aerts, J. C. J. H.; Ward, P. J.

2016-01-01

Changing hydro-climatic and socioeconomic conditions increasingly put pressure on fresh water resources and are expected to aggravate water scarcity conditions towards the future. Despite numerous calls for risk-based water scarcity assessments, a global-scale framework that includes UNISDR's definition of risk does not yet exist. This study provides a first step towards such a risk based assessment, applying a Gamma distribution to estimate water scarcity conditions at the global scale under historic and future conditions, using multiple climate change and population growth scenarios. Our study highlights that water scarcity risk, expressed in terms of expected annual exposed population, increases given all future scenarios, up to greater than 56.2% of the global population in 2080. Looking at the drivers of risk, we find that population growth outweigh the impacts of climate change at global and regional scales. Using a risk-based method to assess water scarcity, we show the results to be less sensitive than traditional water scarcity assessments to the use of fixed threshold to represent different levels of water scarcity. This becomes especially important when moving from global to local scales, whereby deviations increase up to 50% of estimated risk levels.

Methodological flaws introduce strong bias into molecular analysis of microbial populations.

PubMed

Krakat, N; Anjum, R; Demirel, B; Schröder, P

2017-02-01

In this study, we report how different cell disruption methods, PCR primers and in silico analyses can seriously bias results from microbial population studies, with consequences for the credibility and reproducibility of the findings. Our results emphasize the pitfalls of commonly used experimental methods that can seriously weaken the interpretation of results. Four different cell lysis methods, three commonly used primer pairs and various computer-based analyses were applied to investigate the microbial diversity of a fermentation sample composed of chicken dung. The fault-prone, but still frequently used, amplified rRNA gene restriction analysis was chosen to identify common weaknesses. In contrast to other studies, we focused on the complete analytical process, from cell disruption to in silico analysis, and identified potential error rates. This identified a wide disagreement of results between applied experimental approaches leading to very different community structures depending on the chosen approach. The interpretation of microbial diversity data remains a challenge. In order to accurately investigate the taxonomic diversity and structure of prokaryotic communities, we suggest a multi-level approach combining DNA-based and DNA-independent techniques. The identified weaknesses of commonly used methods to study microbial diversity can be overcome by a multi-level approach, which produces more reliable data about the fate and behaviour of microbial communities of engineered habitats such as biogas plants, so that the best performance can be ensured. © 2016 The Society for Applied Microbiology.

[Chromosome as a chronicler: Genetic dating, historical events, and DNA-genealogic temptation].

PubMed

Balanovsky, O P; Zaporozhchenko, V V

2016-07-01

Nonrecombinant portions of the genome, Y chromosome and mitochondrial DNA, are widely used for research on human population gene pools and reconstruction of their history. These systems allow the genetic dating of clusters of emerging haplotypes. The main method for age estimations is ρ statistics, which is an average number of mutations from founder haplotype to all modern-day haplotypes. A researcher can estimate the age of the cluster by multiplying this number by the mutation rate. The second method of estimation, ASD, is used for STR haplotypes of the Y chromosome and is based on the squared difference in the number of repeats. In addition to the methods of calculation, methods of Bayesian modeling assume a new significance. They have greater computational cost and complexity, but they allow obtaining an a posteriori distribution of the value of interest that is the most consistent with experimental data. The mutation rate must be known for both calculation methods and modeling methods. It can be determined either during the analysis of lineages or by providing calibration points based on populations with known formation time. These two approaches resulted in rate estimations for Y-chromosomal STR haplotypes with threefold difference. This contradiction was only recently refuted through the use of sequence data for the complete Y chromosome; “whole-genomic” rates of single nucleotide mutations obtained by both methods are mutually consistent and mark the area of application for different rates of STR markers. An issue even more crucial than that of the rates is correlation of the reconstructed history of the haplogroup (a cluster of haplotypes) and the history of the population. Although the need for distinguishing “lineage history” and “population history” arose in the earliest days of phylogeographic research, reconstructing the population history using genetic dating requires a number of methods and conditions. It is known that population history events leave distinct traces in the history of haplogroups only under certain demographic conditions. Direct identification of national history with the history of its occurring haplogroups is inappropriate and is avoided in population genetic studies, although because of its simplicity and attractiveness it is a constant temptation for researchers. An example of DNA genealogy, an amateur field that went beyond the borders of even citizen science and is consistently using the principle of equating haplogroup with lineage and population, which leads to absurd results (e.g., Eurasia as an origin of humankind), can serve as a warning against a simplified approach for interpretation of genetic dating results.

The 10-year Absolute Risk of Cardiovascular (CV) Events in Northern Iran: a Population Based Study

PubMed Central

Motamed, Nima; Mardanshahi, Alireza; Saravi, Benyamin Mohseni; Siamian, Hasan; Maadi, Mansooreh; Zamani, Farhad

2015-01-01

Background: The present study was conducted to estimate 10-year cardiovascular disease events (CVD) risk using three instruments in northern Iran. Material and methods: Baseline data of 3201 participants 40-79 of a population based cohort which was conducted in Northern Iran were analyzed. Framingham risk score (FRS), World Health Organization (WHO) risk prediction charts and American college of cardiovascular / American heart association (ACC/AHA) tool were applied to assess 10-year CVD events risk. The agreement values between the risk assessment instruments were determined using the kappa statistics. Results: Our study estimated 53.5%of male population aged 40-79 had a 10 –year risk of CVD events≥10% based on ACC/AHA approach, 48.9% based on FRS and 11.8% based on WHO risk charts. A 10 –year risk≥10% was estimated among 20.1% of women using the ACC/AHA approach, 11.9%using FRS and 5.7%using WHO tool. ACC/AHA and Framingham tools had closest agreement in the estimation of 10-year risk≥10% (κ=0.7757) in meanwhile ACC/AHA and WHO approaches displayed highest agreement (κ=0.6123) in women. Conclusion: Different estimations of 10-year risk of CVD event were provided by ACC/AHA, FRS and WHO approaches. PMID:26236160

Evidence for the effect of disease management: is $1 billion a year a good investment?

PubMed

Mattke, Soeren; Seid, Michael; Ma, Sai

2007-12-01

To assess the evidence for the effect of disease management on quality of care, disease control, and cost, with a focus on population-based programs. Literature review. We conducted a literature search for and a structured review of studies on population-based disease management programs, as well as for reviews and meta-analyses of disease management interventions. We identified 3 evaluations of large-scale population-based programs, as well as 10 meta-analyses and 16 systematic reviews, covering 317 unique studies. We found consistent evidence that disease management improves processes of care and disease control but no conclusive support for its effect on health outcomes. Overall, disease management does not seem to affect utilization except for a reduction in hospitalization rates among patients with congestive heart failure and an increase in outpatient care and prescription drug use among patients with depression. When the costs of the intervention were appropriately accounted for and subtracted from any savings, there was no conclusive evidence that disease management leads to a net reduction of direct medical costs. Although disease management seems to improve quality of care, its effect on cost is uncertain. Most of the evidence to date addresses small-scale programs targeting high-risk individuals, while only 3 studies evaluate large population-based interventions, implying that little is known about their effect. Payers and policy makers should remain skeptical about vendor claims and should demand supporting evidence based on transparent and scientifically sound methods.

DNA Barcoding of Recently Diverged Species: Relative Performance of Matching Methods

PubMed Central

van Velzen, Robin; Weitschek, Emanuel; Felici, Giovanni; Bakker, Freek T.

2012-01-01

Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a ‘barcode gap’ and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75%) than for older species (∼97%) (P<0.00001). Similarity-based and diagnostic methods significantly outperform tree-based methods, when applied to simulated DNA barcode data (P<0.00001). The diagnostic method BLOG had highest correct query identification rate based on simulated (86.2%) as well as empirical data (93.1%), indicating that it is a consistently better method overall. Another advantage of BLOG is that it offers species-level information that can be used outside the realm of DNA barcoding, for instance in species description or molecular detection assays. Even though we can confirm that identification success based on DNA barcoding is generally high in our data, recently diverged species remain difficult to identify. Nevertheless, our results contribute to improved solutions for their accurate identification. PMID:22272356

DNA barcoding of recently diverged species: relative performance of matching methods.

PubMed

van Velzen, Robin; Weitschek, Emanuel; Felici, Giovanni; Bakker, Freek T

2012-01-01

Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a 'barcode gap' and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75%) than for older species (∼97%) (P<0.00001). Similarity-based and diagnostic methods significantly outperform tree-based methods, when applied to simulated DNA barcode data (P<0.00001). The diagnostic method BLOG had highest correct query identification rate based on simulated (86.2%) as well as empirical data (93.1%), indicating that it is a consistently better method overall. Another advantage of BLOG is that it offers species-level information that can be used outside the realm of DNA barcoding, for instance in species description or molecular detection assays. Even though we can confirm that identification success based on DNA barcoding is generally high in our data, recently diverged species remain difficult to identify. Nevertheless, our results contribute to improved solutions for their accurate identification.

A method for determining weights for excess relative risk and excess absolute risk when applied in the calculation of lifetime risk of cancer from radiation exposure.

PubMed

Walsh, Linda; Schneider, Uwe

2013-03-01

Radiation-related risks of cancer can be transported from one population to another population at risk, for the purpose of calculating lifetime risks from radiation exposure. Transfer via excess relative risks (ERR) or excess absolute risks (EAR) or a mixture of both (i.e., from the life span study (LSS) of Japanese atomic bomb survivors) has been done in the past based on qualitative weighting. Consequently, the values of the weights applied and the method of application of the weights (i.e., as additive or geometric weighted means) have varied both between reports produced at different times by the same regulatory body and also between reports produced at similar times by different regulatory bodies. Since the gender and age patterns are often markedly different between EAR and ERR models, it is useful to have an evidence-based method for determining the relative goodness of fit of such models to the data. This paper identifies a method, using Akaike model weights, which could aid expert judgment and be applied to help to achieve consistency of approach and quantitative evidence-based results in future health risk assessments. The results of applying this method to recent LSS cancer incidence models are that the relative EAR weighting by cancer solid cancer site, on a scale of 0-1, is zero for breast and colon, 0.02 for all solid, 0.03 for lung, 0.08 for liver, 0.15 for thyroid, 0.18 for bladder and 0.93 for stomach. The EAR weighting for female breast cancer increases from 0 to 0.3, if a generally observed change in the trend between female age-specific breast cancer incidence rates and attained age, associated with menopause, is accounted for in the EAR model. Application of this method to preferred models from a study of multi-model inference from many models fitted to the LSS leukemia mortality data, results in an EAR weighting of 0. From these results it can be seen that lifetime risk transfer is most highly weighted by EAR only for stomach cancer. However, the generalization and interpretation of radiation effect estimates based on the LSS cancer data, when projected to other populations, are particularly uncertain if considerable differences exist between site-specific baseline rates in the LSS and the other populations of interest. Definitive conclusions, regarding the appropriate method for transporting cancer risks, are limited by a lack of knowledge in several areas including unknown factors and uncertainties in biological mechanisms and genetic and environmental risk factors for carcinogenesis; uncertainties in radiation dosimetry; and insufficient statistical power and/or incomplete follow-up in data from radio-epidemiological studies.

CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins

PubMed Central

Londin, Eric R.; Keller, Margaret A.; Maista, Cathleen; Smith, Gretchen; Mamounas, Laura A.; Zhang, Ran; Madore, Steven J.; Gwinn, Katrina; Corriveau, Roderick A.

2010-01-01

Background Genetic ancestry is known to impact outcomes of genotype-phenotype studies that are designed to identify risk for common diseases in human populations. Failure to control for population stratification due to genetic ancestry can significantly confound results of disease association studies. Moreover, ancestry is a critical factor in assessing lifetime risk of disease, and can play an important role in optimizing treatment. As modern medicine moves towards using personal genetic information for clinical applications, it is important to determine genetic ancestry in an accurate, cost-effective and efficient manner. Self-identified race is a common method used to track and control for population stratification; however, social constructs of race are not necessarily informative for genetic applications. The use of ancestry informative markers (AIMs) is a more accurate method for determining genetic ancestry for the purposes of population stratification. Methodology/Principal Findings Here we introduce a novel panel of 36 microsatellite (MSAT) AIMs that determines continental admixture proportions. This panel, which we have named Continental Ancestry Informative Markers or CoAIMs, consists of MSAT AIMs that were chosen based upon their measure of genetic variance (Fst), allele frequencies and their suitability for efficient genotyping. Genotype analysis using CoAIMs along with a Bayesian clustering method (STRUCTURE) is able to discern continental origins including Europe/Middle East (Caucasians), East Asia, Africa, Native America, and Oceania. In addition to determining continental ancestry for individuals without significant admixture, we applied CoAIMs to ascertain admixture proportions of individuals of self declared race. Conclusion/Significance CoAIMs can be used to efficiently and effectively determine continental admixture proportions in a sample set. The CoAIMs panel is a valuable resource for genetic researchers performing case-control genetic association studies, as it can control for the confounding effects of population stratification. The MSAT-based approach used here has potential for broad applicability as a cost effective tool toward determining admixture proportions. PMID:20976178

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 savings can be achieved using the new approach and a monetary cost analysis provides a practical measure of its utility. PMID:24699269

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 can be achieved using the new approach and a monetary cost analysis provides a practical measure of its utility.

Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions.

PubMed

Najibi, Seyed Morteza; Maadooliat, Mehdi; Zhou, Lan; Huang, Jianhua Z; Gao, Xin

2017-01-01

Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction.