Baseline Water Demand at Forward Operating Bases

DTIC Science & Technology

2013-09-15

population, often equaling or exceeding the military population: • Brigade: 6000 soldiers • Battalion: 1000 soldiers • Company : 150 soldiers. ERDC/CERL TR...requirements for a company outpost (COP) of 120 personnel (PAX) in the format that the computer tool generates. This tool generates a basic sus...facilities world-wide through several large contractors. One contractor, Kellogg , Brown, and Root (KBR), used a minimum planning factor of 18.4

Identification of two novel glial-restricted cell populations in the embryonic telencephalon arising from unique origins

PubMed Central

Strathmann, Frederick G; Wang, Xi; Mayer-Pröschel, Margot

2007-01-01

Background Considerably less attention has been given to understanding the cellular components of gliogenesis in the telencephalon when compared to neuronogenesis, despite the necessity of normal glial cell formation for neurological function. Early proposals of exclusive ventral oligodendrocyte precursor cell (OPC) generation have been challenged recently with studies revealing the potential of the dorsal telencephalon to also generate oligodendrocytes. The identification of OPCs generated from multiple regions of the developing telencephalon, together with the need of the embryonic telencephalon to provide precursor cells for oligodendrocytes as well as astrocytes in ventral and dorsal areas, raises questions concerning the identity of the precursor cell populations capable of generating macroglial subtypes during multiple developmental windows and in differing locations. Results We have identified progenitor populations in the ventral and dorsal telencephalon restricted to the generation of astrocytes and oligodendrocytes. We further demonstrate that the dorsal glial progenitor cells can be generated de novo from the dorsal telencephalon and we demonstrate their capacity for in vivo production of both myelin-forming oligodendrocytes and astrocytes upon transplantation. Conclusion Based on our results we offer a unifying model of telencephalic gliogenesis, with the generation of both oligodendrocytes and astrocytes from spatially separate, but functionally similar, glial restricted populations at different developmental times in the dorsal and ventral CNS. PMID:17439658

A NEO population generation and observation simulation software tool

NASA Astrophysics Data System (ADS)

Müller, Sven; Gelhaus, Johannes; Hahn, Gerhard; Franco, Raffaella

One of the main targets of ESA's Space Situational Awareness (SSA) program is to build a wide knowledge base about objects that can potentially harm Earth (Near-Earth Objects, NEOs). An important part of this effort is to create the Small Bodies Data Centre (SBDC) which is going to aggregate measurement data from a fully-integrated NEO observation sensor network. Until this network is developed, artificial NEO measurement data is needed in order to validate SBDC algorithms. Moreover, to establish a functioning NEO observation sensor network, it has to be determined where to place sensors, what technical requirements have to be met in order to be able to detect NEOs and which observation strategies work the best. Because of this, a sensor simulation software was needed. This paper presents a software tool which allows users to create and analyse NEO populations and to simulate and analyse population observations. It is a console program written in Fortran and comes with a Graphical User Interface (GUI) written in Java and C. The tool can be distinguished into the components ``Population Generator'' and ``Observation Simulator''. The Population Generator component is responsible for generating and analysing a NEO population. Users can choose between creating fictitious (random) and synthetic populations. The latter are based on one of two models describing the orbital and size distribution of observed NEOs: The existing socalled ``Bottke Model'' (Bottke et al. 2000, 2002) and the new ``Granvik Model'' (Granvik et al. 2014, in preparation) which has been developed in parallel to the tool. Generated populations can be analysed by defining 2D, 3D and scatter plots using various NEO attributes. As a result, the tool creates the appropiate files for the plotting tool ``gnuplot''. The tool's Observation Simulator component yields the Observation Simulation and Observation Analysis functions. Users can define sensor systems using ground- or space-based locations as well as optical or radar sensors and simulate observation campaigns. The tool outputs field-of-view crossings and actual detections of the selected NEO population objects. Using the Observation Analysis users are able to process and plot the results of the Observation Simulation. In order to enable end-users to handle the tool in a user-intuitive and comfortable way, a GUI has been created based on the modular Eclipse Rich Client Platform (RCP) technology. Through the GUI users can easily enter input data for the tool, execute it and view its output data in a clear way. Additionally, the GUI runs gnuplot to create plot pictures and presents them to the user. Furthermore, users can create projects to organise executions of the tool.

Polystyrene microspheres enable 10‐color compensation for immunophenotyping of primary human leukocytes

PubMed Central

Carr, Karen D.; Norman, John C.; Huye, Leslie; Hegde, Meenakshi

2015-01-01

Abstract Compensation is a critical process for the unbiased analysis of flow cytometry data. Numerous compensation strategies exist, including the use of bead‐based products. The purpose of this study was to determine whether beads, specifically polystyrene microspheres (PSMS) compare to the use of primary leukocytes for single color based compensation when conducting polychromatic flow cytometry. To do so, we stained individual tubes of both PSMS and leukocytes with panel specific antibodies conjugated to fluorochromes corresponding to fluorescent channels FL1‐FL10. We compared the matrix generated by PSMS to that generated using peripheral blood mononuclear cells (PBMC). Ideal for compensation is a sample with both a discrete negative population and a bright positive population. We demonstrate that PSMS display autofluorescence properties similar to PBMC. When comparing PSMS to PBMC for compensation PSMS yielded more evenly distributed and discrete negative and positive populations to use for compensation. We analyzed three donors' PBMC stained with our 10‐color T cell subpopulation panel using compensation generated by PSMS vs.PBMC and detected no significant differences in the population distribution. Panel specific antibodies bound to PSMS represent an invaluable valid tool to generate suitable compensation matrices especially when sample material is limited and/or the sample requires analysis of dynamically modulated or rare events. © 2015 The Authors. Cytometry Part A Published by Wiley Periodicals, Inc. PMID:26202733

Induction and transmission of tolerance to the synthetic pesticide emamectin benzoate in field and laboratory populations of diamondback moth.

PubMed

Rahman, M M; Baker, G; Powis, K J; Roush, R T; Schmidt, O

2010-08-01

Field surveys of pest insect pest populations in agroecosystems reveal low but significant levels of tolerance to synthetic and biological pesticides but fail to uncover resistance alleles in test crosses. To study the potential of inducible mechanisms to generate tolerance to synthetic pesticides, we performed baseline susceptibility studies in field and laboratory populations of diamondback moth, Plutella xylostella (L.), to commercial formulations of emamectin benzoate. Pesticide exposure in the field caused elevated levels of tolerance, which decreased in field-collected populations after maintaining insects with pesticide-free diet in the laboratory. Because no significant resistance alleles were identified in back-crossed individuals, the observed increase in tolerance was probably not based on preexisting recessive resistance mechanisms in the population. Instead, the genetic analysis after five and 12 generations is compatible with a transient up-regulation of an immune and metabolic status in tolerant insects that can be transmitted to offspring by a maternal effect. Although the epigenetic effects contributed to incremental increases in tolerance in the first five generations, other resistance mechanisms that are transmitted genetically predominate after 12 generations of increased exposure to the pesticide.

Effectiveness of an image-based sorter to select for kernel color within early segregating hard winter wheat (Triticum aestivum L.) populations

USDA-ARS?s Scientific Manuscript database

Effective mass selection tools are needed to enrich hard winter wheat breeding populations from red wheat × white wheat crosses while maintaining large population sizes in early breeding generations. Tools also are needed to select for white-seeded genotypes or to eliminate white-seeded genotypes wh...

Assessment of economic status in trauma registries: A new algorithm for generating population-specific clustering-based models of economic status for time-constrained low-resource settings.

PubMed

Eyler, Lauren; Hubbard, Alan; Juillard, Catherine

2016-10-01

Low and middle-income countries (LMICs) and the world's poor bear a disproportionate share of the global burden of injury. Data regarding disparities in injury are vital to inform injury prevention and trauma systems strengthening interventions targeted towards vulnerable populations, but are limited in LMICs. We aim to facilitate injury disparities research by generating a standardized methodology for assessing economic status in resource-limited country trauma registries where complex metrics such as income, expenditures, and wealth index are infeasible to assess. To address this need, we developed a cluster analysis-based algorithm for generating simple population-specific metrics of economic status using nationally representative Demographic and Health Surveys (DHS) household assets data. For a limited number of variables, g, our algorithm performs weighted k-medoids clustering of the population using all combinations of g asset variables and selects the combination of variables and number of clusters that maximize average silhouette width (ASW). In simulated datasets containing both randomly distributed variables and "true" population clusters defined by correlated categorical variables, the algorithm selected the correct variable combination and appropriate cluster numbers unless variable correlation was very weak. When used with 2011 Cameroonian DHS data, our algorithm identified twenty economic clusters with ASW 0.80, indicating well-defined population clusters. This economic model for assessing health disparities will be used in the new Cameroonian six-hospital centralized trauma registry. By describing our standardized methodology and algorithm for generating economic clustering models, we aim to facilitate measurement of health disparities in other trauma registries in resource-limited countries. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Voronoi Based Nanocrystalline Generation Algorithm for Atomistic Simulations

DTIC Science & Technology

2016-12-22

the  time  for reviewing instructions, searching existing data sources, gathering and maintaining the  data needed, and completing and reviewing the...taken when generating nanocrystals (left to right): populating cell with grain centers, sphere of atoms with defined crystal structure centered at...nanocrystals (left to right): populating cell with grain centers, sphere of atoms with defined crystal structure centered at each grain center, identifying atoms

Land use as a Driver of Patterns of Rodenticide Exposure in Modeled Kit Fox Populations

EPA Science Inventory

Although rodenticides are increasingly regulated, they nonetheless cause poisonings in many non-target wildlife species. Second-generation anticoagualant rodenticide use is common in agricultural and residential lands. Here, we use an individual-based population model to assess t...

Population Response to Habitat Fragmentation in a Stream-Dwelling Brook Trout Population

PubMed Central

Letcher, Benjamin H.; Nislow, Keith H.; Coombs, Jason A.; O'Donnell, Matthew J.; Dubreuil, Todd L.

2007-01-01

Fragmentation can strongly influence population persistence and expression of life-history strategies in spatially-structured populations. In this study, we directly estimated size-specific dispersal, growth, and survival of stream-dwelling brook trout in a stream network with connected and naturally-isolated tributaries. We used multiple-generation, individual-based data to develop and parameterize a size-class and location-based population projection model, allowing us to test effects of fragmentation on population dynamics at local (i.e., subpopulation) and system-wide (i.e., metapopulation) scales, and to identify demographic rates which influence the persistence of isolated and fragmented populations. In the naturally-isolated tributary, persistence was associated with higher early juvenile survival (∼45% greater), shorter generation time (one-half) and strong selection against large body size compared to the open system, resulting in a stage-distribution skewed towards younger, smaller fish. Simulating barriers to upstream migration into two currently-connected tributary populations caused rapid (2–6 generations) local extinction. These local extinctions in turn increased the likelihood of system-wide extinction, as tributaries could no longer function as population sources. Extinction could be prevented in the open system if sufficient immigrants from downstream areas were available, but the influx of individuals necessary to counteract fragmentation effects was high (7–46% of the total population annually). In the absence of sufficient immigration, a demographic change (higher early survival characteristic of the isolated tributary) was also sufficient to rescue the population from fragmentation, suggesting that the observed differences in size distributions between the naturally-isolated and open system may reflect an evolutionary response to isolation. Combined with strong genetic divergence between the isolated tributary and open system, these results suggest that local adaptation can ‘rescue’ isolated populations, particularly in one-dimensional stream networks where both natural and anthropogenically-mediated isolation is common. However, whether rescue will occur before extinction depends critically on the race between adaptation and reduced survival in response to fragmentation. PMID:18188404

Population response to habitat fragmentation in a stream-dwelling brook trout population

USGS Publications Warehouse

Letcher, B.H.; Nislow, K.H.; Coombs, J.A.; O'Donnell, M. J.; Dubreuil, T.L.

2007-01-01

Fragmentation can strongly influence population persistence and expression of life-history strategies in spatially-structured populations. In this study, we directly estimated size-specific dispersal, growth, and survival of stream-dwelling brook trout in a stream network with connected and naturally-isolated tributaries. We used multiple-generation, individual-based data to develop and parameterize a size-class and location-based population projection model, allowing us to test effects of fragmentation on population dynamics at local (i.e., subpopulation) and system-wide (i.e., metapopulation) scales, and to identify demographic rates which influence the persistence of isolated and fragmented populations. In the naturally-isolated tributary, persistence was associated with higher early juvenile survival (-45% greater), shorter generation time (one-half) and strong selection against large body size compared to the open system, resulting in a stage-distribution skewed towards younger, smaller fish. Simulating barriers to upstream migration into two currently-connected tribuory populations caused rapid (2-6 generations) local extinction. These local extinctions in turn increased the likelihood of system-wide extinction, as tributaries could no longer function as population sources. Extinction could be prevented in the open system if sufficient immigrants from downstream areas were available, but the influx of individuals necessary to counteract fragmentation effects was high (7-46% of the total population annually). In the absence of sufficient immigration, a demographic change (higher early survival characteristic of the isolated tributary) was also sufficient to rescue the population from fragmentation, suggesting that the observed differences in size distributions between the naturally-isolated and open system may reflect an evolutionary response to isolation. Combined with strong genetic divergence between the isolated tributary and open system, these results suggest that local adaptation can 'rescue' isolated populations, particularly in one-dimensional stream networks where both natural and anthropegenically-mediated isolation is common. However, whether rescue will occur before extinction depends critically on the race between adaptation and reduced survival in response to fragmentation.

Health Data Entanglement and artificial intelligence-based analysis: a brand new methodology to improve the effectiveness of healthcare services.

PubMed

Capone, A; Cicchetti, A; Mennini, F S; Marcellusi, A; Baio, G; Favato, G

2016-01-01

Healthcare expenses will be the most relevant policy issue for most governments in the EU and in the USA. This expenditure can be associated with two major key categories: demographic and economic drivers. Factors driving healthcare expenditure were rarely recognised, measured and comprehended. An improvement of health data generation and analysis is mandatory, and in order to tackle healthcare spending growth, it may be useful to design and implement an effective, advanced system to generate and analyse these data. A methodological approach relied upon the Health Data Entanglement (HDE) can be a suitable option. By definition, in the HDE a large amount of data sets having several sources are functionally interconnected and computed through learning machines that generate patterns of highly probable future health conditions of a population. Entanglement concept is borrowed from quantum physics and means that multiple particles (information) are linked together in a way such that the measurement of one particle's quantum state (individual health conditions and related economic requirements) determines the possible quantum states of other particles (population health forecasts to predict their impact). The value created by the HDE is based on the combined evaluation of clinical, economic and social effects generated by health interventions. To predict the future health conditions of a population, analyses of data are performed using self-learning AI, in which sequential decisions are based on Bayesian algorithmic probabilities. HDE and AI-based analysis can be adopted to improve the effectiveness of the health governance system in ways that also lead to better quality of care.

Directory of Experiential Therapy and Adventure-Based Counseling Programs.

ERIC Educational Resources Information Center

Gerstein, Jackie, Ed.

This directory lists 257 organizations with therapeutic adventure and experiential programs for special needs populations. The information was generated from a survey of members of the Association for Experiential Education. Special needs populations include youth-at-risk, persons with addictions, juvenile and adult offenders, inpatient and…

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

PubMed

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

2017-10-03

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

Modeling multilayer x-ray reflectivity using genetic algorithms

NASA Astrophysics Data System (ADS)

Sánchez del Río, M.; Pareschi, G.; Michetschläger, C.

2000-06-01

The x-ray reflectivity of a multilayer is a non-linear function of many parameters (materials, layer thickness, density, roughness). Non-linear fitting of experimental data with simulations requires the use of initial values sufficiently close to the optimum value. This is a difficult task when the topology of the space of the variables is highly structured. We apply global optimization methods to fit multilayer reflectivity. Genetic algorithms are stochastic methods based on the model of natural evolution: the improvement of a population along successive generations. A complete set of initial parameters constitutes an individual. The population is a collection of individuals. Each generation is built from the parent generation by applying some operators (selection, crossover, mutation, etc.) on the members of the parent generation. The pressure of selection drives the population to include "good" individuals. For large number of generations, the best individuals will approximate the optimum parameters. Some results on fitting experimental hard x-ray reflectivity data for Ni/C and W/Si multilayers using genetic algorithms are presented. This method can also be applied to design multilayers optimized for a target application.

An ab initio mechanism for efficient population of triplet states in cytotoxic sulfur substituted DNA bases: the case of 6-thioguanine.

PubMed

Martínez-Fernández, Lara; González, Leticia; Corral, Inés

2012-02-18

The deactivation mechanism of the cytotoxic 6-thioguanine, the 6-sulfur-substituted analogue of the canonical DNA base, is unveiled by ab initio calculations. Oxygen-by-sulfur substitution leads to efficient population of triplet states-the first step for generating singlet oxygen-which is responsible for its cytotoxicity. This journal is © The Royal Society of Chemistry 2012

Unsupervised Ontology Generation from Unstructured Text. CRESST Report 827

ERIC Educational Resources Information Center

Mousavi, Hamid; Kerr, Deirdre; Iseli, Markus R.

2013-01-01

Ontologies are a vital component of most knowledge acquisition systems, and recently there has been a huge demand for generating ontologies automatically since manual or supervised techniques are not scalable. In this paper, we introduce "OntoMiner", a rule-based, iterative method to extract and populate ontologies from unstructured or…

[Prevalence of psychiatric and substance use disorders among three generations of migrants: Results from French population cohort].

PubMed

Guardia, D; Salleron, J; Roelandt, J-L; Vaiva, G

2017-10-01

Mental health of migrant populations has become a major public health issue since these populations more often suffer from mental health problems than host populations. The influence of the migration process on the emergence of these disorders and its impact on future generations is uncertain. This study provides an estimate of the prevalence of mental disorders among three generations of migration. The study was conducted in the general population by the French Collaborating Center of the World Health Organization, in France, on a sample of 37,063 people aged 18 and older. The subjects interviewed were selected by a quota sampling method and, thus, were representative of the general population in the 47 study sites in France. This method develops a sample of subjects with the same characteristics as the general population on predefined issues, such as age, sex, educational level and socioprofessional category. The designation of migrant status was based on the country of birth of the subject, the subject's parents and the subject's grandparents. We defined a migrant as first generation (a subject born abroad; n=1911), second generation (at least one parent born abroad; n=4147), or third generation (at least one grandparent born abroad; n=3763) of migrants. The diagnostic tool used was the Mini International Neuropsychiatric Interview (MINI). The MINI is a brief structured diagnostic interview developed by psychiatrists for ICD-10 and DSM-IVTR psychiatric disorders in the general population. The comparisons by generation of migrants were performed by chi-square test for qualitative variables and by an analysis of variance for quantitative variables. The same tests were used to compare the presence of mental disorders according to the characteristics of the population. Factors with a P-value less than 0.2 were entered in a multivariable logistic regression to assess the relationship between the generation of migrants and the presence of mental disorders, adjusting for the confounding factors. Thirty-eight per cent of migrant subjects have psychological difficulties, versus 30 % in the host population. These results are observed on three successive generations of migrants. Migration status increases risk of depressive disorders (OR=1.555), bipolar disorder (OR=1.597, CI=1.146-2.227), post-traumatic stress disorder (OR=1.615), substance abuse (OR=2.522) and alcohol abuse (OR=1.524), and drug dependence (OR=2.116). This risk is maintained at the second and third generation. The migration process affects mental health of population regardless of socioeconomic status or geographic origin. The consideration of migration and generation of migration shows a specific psychopathological risk profile. This is related to the joint action of a migratory past and precarious socioeconomic situation. Copyright © 2016 L’Encéphale, Paris. Published by Elsevier Masson SAS. All rights reserved.

The Generation R Study: A Review of Design, Findings to Date, and a Study of the 5-HTTLPR by Environmental Interaction from Fetal Life Onward

ERIC Educational Resources Information Center

Tiemeier, Henning; Velders, Fleur P.; Szekely, Eszter; Roza, Sabine J.; Dieleman, Gwen; Jaddoe, Vincent W. V.; Uitterlinden, Andre G.; White, Tonya J. H.; Bakermans-Kranenburg, Marian J.; Hofman, Albert; Van IJzendoorn, Marinus H.; Hudziak, James J.; Verhulst, Frank C.

2012-01-01

Objective: First, we give an overview of child psychiatric research in the Generation R Study, a population-based cohort from fetal life forward. Second, we examine within Generation R whether the functional polymorphism (5-HTTLPR) in the promoter of the serotonin transporter gene interacts with prenatal maternal chronic difficulties, prenatal…

Assessing the variables affecting on the rate of solid waste generation and recycling: An empirical analysis in Prespa Park.

PubMed

Grazhdani, Dorina

2016-02-01

Economic development, urbanization, and improved living standards increase the quantity and complexity of generated solid waste. Comprehensive study of the variables influencing household solid waste production and recycling rate is crucial and fundamental for exploring the generation mechanism and forecasting future dynamics of household solid waste. The present study is employed in the case study of Prespa Park. A model, based on the interrelationships of economic, demographic, housing structure and waste management policy variables influencing the rate of solid waste generation and recycling is developed and employed. The empirical analysis is based on the information derived from a field questionnaire survey conducted in Prespa Park villages for the year 2014. Another feature of this study is to test whether a household's waste generation can be decoupled from its population growth. Descriptive statistics, bivariate correlation analysis and F-tests are used to know the relationship between variables. One-way and two-way fixed effects models data analysis techniques are used to identify variables that determine the effectiveness of waste generation and recycling at household level in the study area. The results reveal that households with heterogeneous characteristics, such as education level, mean building age and income, present different challenges of waste reduction goals. Numerically, an increase of 1% in education level of population corresponds to a waste reduction of 3kg on the annual per capita basis. A village with older buildings, in the case of one year older of the median building age, corresponds to a waste generation increase of 12kg. Other economic and policy incentives such as the mean household income, pay-as-you-throw, percentage of population with access to curbside recycling, the number of drop-off recycling facilities available per 1000 persons and cumulative expenditures on recycling education per capita are also found to be effective measures in waste reduction. The mean expenditure for recycling education spent on a person for years 2010 and 2014 is 12 and 14 cents, respectively and it vary from 0 to €1. For years 2010 and 2014, the mean percentage of population with access to curbside recycling services is 38.6% and 40.3%, and the mean number of drop-off recycling centers per 1000 persons in the population is 0.29 and 0.32, respectively. Empirical evidence suggests that population growth did not necessarily result in increases in waste generation. The results provided are useful when planning, changing or implementing sustainable municipal solid waste management. Copyright © 2015 Elsevier Ltd. All rights reserved.

Demographic responses to multi-generation cadmium exposure in two strains of the freshwater gastropod, Biomphalaria glabrata.

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

Salice, Christopher J.; Miller, Thomas J.; Roesijadi, Guritno

2008-08-20

A life table response experiment (LTRE) was used to quantify the population-level effects of continuous, multi-generation cadmium exposure on two strains of the freshwater gastropod, Biomphalaria glabrata; the parasite resistant BS90 and parasite susceptible NMRI strains. Snails were exposed to waterborne cadmium for three consecutive generations. Survival, growth and reproduction were measured empirically and incorporated into a stage-based, deterministic population model. Cadmium significantly affected hatching success, time to maturity and juvenile and adult survival in both strains. There were significant effects of generation on fecundity, hatching success time to maturity and juvenile survival in NMRI and time to maturity andmore » adult survival in BS90. Cadmium significantly affected the population growth rate, lambda (λ), in BS90. Cadmium, generation and the cadmium x generation interaction had significant effects on λ in NMRI. At the high cadmium exposure, λ for NMRI showed a decrease from generation 1 to generation 2 followed by and increase from generation 2 to 3. Lambda in high cadmium BS90 steadily decreased over the three generations while NMRI at this same concentration was similar to the controls. The results indicated that strain-specific differences in response to multi-generation cadmium exposure are evident in B. glabrata. Moreover, effects seen in the first generation are not necessarily indicative of effects in subsequent generations. Changes in λ over the course of the three-generation exposure suggest that acclimation and/or adaptation to cadmium may have occurred, particularly in NMRI at the high cadmium exposure level.« less

Reproductive biology of Lutzomyia shannoni (Dyar) (Diptera: Psychodidae) under experimental conditions.

PubMed

Cárdenas, E; Ferro, C; Corredor, D; Martínez, O; Munstermann, L E

1999-12-01

Baseline biological growth data of Lutzomyia shannoni (Dyar) were compared under two experimental conditions within insulated styrofoam chests and in standard laboratory incubators. The developmental time from egg to adult was 67 and 52 days, respectively. Based on cohorts of 100 females in each experiment, horizontal life tables were constructed. The following predictive parameters were obtained under each of the two conditions: net rate of reproduction (23.5 and 18.0 females per cohort female), generation time (11.4 and 9.4 weeks), intrinsic rate of population increase (0.27 and 0.30), and finite rate of population increment (1.31 and 1.36). The reproductive value for each class age of the cohort females was calculated. The observed parameters were obtained under each experimental condition: net rate of reproduction (1.9 and 2.5 females per cohort female), generation time (11.7 and 9.6 weeks), intrinsic rate of population increase (0.05 and 0.09), and finite rate of population increment (1.06 and 1.10). Vertical life tables were elaborated and mortality was described for every generation in each cohort. In addition, for two successive generations, additive variance and heritability for fecundity were estimated.

Estimation of a genetically viable population for multigenerational interstellar voyaging: Review and data for project Hyperion

NASA Astrophysics Data System (ADS)

Smith, Cameron M.

2014-04-01

Designing interstellar starships for human migration to exoplanets requires establishing the starship population, which factors into many variables including closed-ecosystem design, architecture, mass and propulsion. I review the central issues of population genetics (effects of mutation, migration, selection and drift) for human populations on such voyages, specifically referencing a roughly 5-generation (c. 150-year) voyage currently in the realm of thought among Icarus Interstellar's Project Hyperion research group. I present several formulae as well as concrete numbers that can be used to help determine populations that could survive such journeys in good health. I find that previously proposed such populations, on the order of a few hundred individuals, are significantly too low to consider based on current understanding of vertebrate (including human) genetics and population dynamics. Population genetics theory, calculations and computer modeling determine that a properly screened and age- and sex-structured total founding population (Nc) of anywhere from roughly 14,000 to 44,000 people would be sufficient to survive such journeys in good health. A safe and well-considered Nc figure is 40,000, an Interstellar Migrant Population (IMP) composed of an Effective Population [Ne] of 23,400 reproductive males and females, the rest being pre- or post-reproductive individuals. This number would maintain good health over five generations despite (a) increased inbreeding resulting from a relatively small human population, (b) depressed genetic diversity due to the founder effect, (c) demographic change through time and (d) expectation of at least one severe population catastrophe over the 5-generation voyage.

Genomic Ancestry of North Africans Supports Back-to-Africa Migrations

PubMed Central

Gravel, Simon; Wang, Wei; Brisbin, Abra; Byrnes, Jake K.; Fadhlaoui-Zid, Karima; Zalloua, Pierre A.; Moreno-Estrada, Andres; Bertranpetit, Jaume; Bustamante, Carlos D.; Comas, David

2012-01-01

North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa. PMID:22253600

Storyboard method of end-user programming with natural language configuration

DOEpatents

Bouchard, Ann M; Osbourn, Gordon C

2013-11-19

A technique for end-user programming includes populating a template with graphically illustrated actions and then invoking a command to generate a screen element based on the template. The screen element is rendered within a computing environment and provides a mechanism for triggering execution of a sequence of user actions. The sequence of user actions is based at least in part on the graphically illustrated actions populated into the template.

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

NASA Astrophysics Data System (ADS)

Ding, R.; He, T.

2017-12-01

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

Population dynamics of Varroa destructor (Acari: Varroidae) in commercial honey bee colonies and implications for control

USDA-ARS?s Scientific Manuscript database

Treatment schedules to maintain low levels of Varroa mites in honey bee colonies were tested in hives started from either package bees or splits of larger colonies. The schedules were developed based on predictions of Varroa population growth generated from a mathematical model of honey bee colony ...

Characterization of the non axial thrust generated by large solid propellant rocket motors in three axis stabilized ascent

NASA Technical Reports Server (NTRS)

Kosmann, W. J.; Dionne, E. R.; Klemetson, R. W.

1978-01-01

Nonaxial thrusts produced by solid rocket motors during three-axis stabilized attitude control have been determined from ascent experience on twenty three Burner II, Burner IIA and Block 5D-1 upper stage vehicles. A data base representing four different rocket motor designs (three spherical and one extended spherical) totaling twenty five three-axis stabilized firings is generated. Solid rocket motor time-varying resultant and lateral side force vector magnitudes, directions and total impulses, and roll torque couple magnitudes, directions, and total impulses are tabulated in the appendix. Population means and three sigma deviations are plotted. Existing applicable ground test side force and roll torque magnitudes and total impulses are evaluated and compared to the above experience data base. Within the spherical motor population, the selected AEDC ground test data consistently underestimated experienced motor side forces, roll torques and total impulses. Within the extended spherical motor population, the selected AEDC test data predicted experienced motor side forces, roll torques, and total impulses, with surprising accuracy considering the very small size of the test and experience populations.

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.

Is urbanisation scrambling the genetic structure of human populations? A case study

PubMed Central

Ashrafian-Bonab, Maziar; Handley, Lori Lawson; Balloux, François

2007-01-01

Recent population expansion and increased migration linked to urbanisation are assumed to be eroding the genetic structure of human populations. We investigated change in population structure over three generations by analysing both demographic and mitochondrial DNA (mtDNA) data from a random sample of 2351 men from twenty-two Iranian populations. Potential changes in genetic diversity (θ) and genetic distance (FST) over the last three generations were analysed by assigning mtDNA sequences to populations based on the individual's place of birth or that of their mother or grandmother. Despite the fact that several areas included cities of over one million inhabitants, we detected no change in genetic diversity, and only a small decrease in population structure, except in the capital city (Tehran), which was characterised by massive immigration, increased θ and a large decrease in FST over time. Our results suggest that recent erosion of human population structure might not be as important as previously thought, except in some large conurbations, and this clearly has important implications for future sampling strategies. PMID:17106453

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…

An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F₂ maize population.

PubMed

Chen, Zongliang; Wang, Baobao; Dong, Xiaomei; Liu, Han; Ren, Longhui; Chen, Jian; Hauck, Andrew; Song, Weibin; Lai, Jinsheng

2014-06-04

Understanding genetic control of tassel and ear architecture in maize (Zea mays L. ssp. mays) is important due to their relationship with grain yield. High resolution QTL mapping is critical for understanding the underlying molecular basis of phenotypic variation. Advanced populations, such as recombinant inbred lines, have been broadly adopted for QTL mapping; however, construction of large advanced generation crop populations is time-consuming and costly. The rapidly declining cost of genotyping due to recent advances in next-generation sequencing technologies has generated new possibilities for QTL mapping using large early generation populations. A set of 708 F2 progeny derived from inbreds Chang7-2 and 787 were generated and genotyped by whole genome low-coverage genotyping-by-sequencing method (average 0.04×). A genetic map containing 6,533 bin-markers was constructed based on the parental SNPs and a sliding-window method, spanning a total genetic distance of 1,396 cM. The high quality and accuracy of this map was validated by the identification of two well-studied genes, r1, a qualitative trait locus for color of silk (chromosome 10) and ba1 for tassel branch number (chromosome 3). Three traits of tassel and ear architecture were evaluated in this population, a total of 10 QTL were detected using a permutation-based-significance threshold, seven of which overlapped with reported QTL. Three genes (GRMZM2G316366, GRMZM2G492156 and GRMZM5G805008) encoding MADS-box domain proteins and a BTB/POZ domain protein were located in the small intervals of qTBN5 and qTBN7 (~800 Kb and 1.6 Mb in length, respectively) and may be involved in patterning of tassel architecture. The small physical intervals of most QTL indicate high-resolution mapping is obtainable with this method. We constructed an ultra-high-dentisy linkage map for the large early generation population in maize. Our study provides an efficient approach for fast detection of quantitative loci responsible for complex trait variation with high accuracy, thus helping to dissect the underlying molecular basis of phenotypic variation and accelerate improvement of crop breeding in a cost-effective fashion.

Theoretical study of dynamic electron-spin-polarization via the doublet-quartet quantum-mixed state and time-resolved ESR spectra of the quartet high-spin state.

PubMed

Teki, Yoshio; Matsumoto, Takafumi

2011-04-07

The mechanism of the unique dynamic electron polarization of the quartet (S = 3/2) high-spin state via a doublet-quartet quantum-mixed state and detail theoretical calculations of the population transfer are reported. By the photo-induced electron transfer, the quantum-mixed charge-separate state is generated in acceptor-donor-radical triad (A-D-R). This mechanism explains well the unique dynamic electron polarization of the quartet state of A-D-R. The generation of the selectively populated quantum-mixed state and its transfer to the strongly coupled pure quartet and doublet states have been treated both by a perturbation approach and by exact numerical calculations. The analytical solutions show that generation of the quantum-mixed states with the selective populations after de-coherence and/or accompanying the (complete) dephasing during the charge-recombination are essential for the unique dynamic electron polarization. Thus, the elimination of the quantum coherence (loss of the quantum information) is the key process for the population transfer from the quantum-mixed state to the quartet state. The generation of high-field polarization on the strongly coupled quartet state by the charge-recombination process can be explained by a polarization transfer from the quantum-mixed charge-separate state. Typical time-resolved ESR patterns of the quantum-mixed state and of the strongly coupled quartet state are simulated based on the generation mechanism of the dynamic electron polarization. The dependence of the spectral pattern of the quartet high-spin state has been clarified for the fine-structure tensor and the exchange interaction of the quantum-mixed state. The spectral pattern of the quartet state is not sensitive towards the fine-structure tensor of the quantum-mixed state, because this tensor contributes only as a perturbation in the population transfer to the spin-sublevels of the quartet state. Based on the stochastic Liouville equation, it is also discussed why the selective population in the quantum-mixed state is generated for the "finite field" spin-sublevels. The numerical calculations of the elimination of the quantum coherence (de-coherence and/or dephasing) are demonstrated. A new possibility of the enhanced intersystem crossing pathway in solution is also proposed.

Exploring Population Admixture Dynamics via Empirical and Simulated Genome-wide Distribution of Ancestral Chromosomal Segments

PubMed Central

Jin, Wenfei; Wang, Sijia; Wang, Haifeng; Jin, Li; Xu, Shuhua

2012-01-01

The processes of genetic admixture determine the haplotype structure and linkage disequilibrium patterns of the admixed population, which is important for medical and evolutionary studies. However, most previous studies do not consider the inherent complexity of admixture processes. Here we proposed two approaches to explore population admixture dynamics, and we demonstrated, by analyzing genome-wide empirical and simulated data, that the approach based on the distribution of chromosomal segments of distinct ancestry (CSDAs) was more powerful than that based on the distribution of individual ancestry proportions. Analysis of 1,890 African Americans showed that a continuous gene flow model, in which the African American population continuously received gene flow from European populations over about 14 generations, best explained the admixture dynamics of African Americans among several putative models. Interestingly, we observed that some African Americans had much more European ancestry than the simulated samples, indicating substructures of local ancestries in African Americans that could have been caused by individuals from some particular lineages having repeatedly admixed with people of European ancestry. In contrast, the admixture dynamics of Mexicans could be explained by a gradual admixture model in which the Mexican population continuously received gene flow from both European and Amerindian populations over about 24 generations. Our results also indicated that recent gene flows from Sub-Saharan Africans have contributed to the gene pool of Middle Eastern populations such as Mozabite, Bedouin, and Palestinian. In summary, this study not only provides approaches to explore population admixture dynamics, but also advances our understanding on population history of African Americans, Mexicans, and Middle Eastern populations. PMID:23103229

Habitat-dependent olfactory discrimination in three-spined sticklebacks (Gasterosteus aculeatus).

PubMed

Hiermes, Meike; Mehlis, Marion; Rick, Ingolf P; Bakker, Theo C M

2015-07-01

The ability to recognize conspecifics is indispensible for differential treatment of particular individuals in social contexts like grouping behavior. The advantages of grouping are multifarious, and there exist numerous additional benefits of joining aggregations of conspecifics. Recognition is based on different signals and transmitted via multiple channels, among others the olfactory channel. The sensory system or the combination of sensory modalities used in recognition processes is highly dependent on the availability and effectiveness of modalities, which are a function of the environmental conditions. Using F1-generations of six three-spined stickleback (Gasterosteus aculeatus) populations from two habitat types (tea-stained and clear-water lakes) from the Outer Hebrides, Scotland, we investigated whether individuals are able to recognize members of their own population solely based on olfactory cues and whether the habitat type an individual originated from had an influence on its recognition abilities. When given the choice (own vs. foreign population) sticklebacks from tea-stained lakes significantly preferred the odor of their own population, whereas fish from clear-water habitats did not show any preference. Moreover, fish from the two habitat types differed significantly in their recognition abilities, indicating that olfactory communication is better developed when visual signaling is disturbed. Thus, the observed odor preferences appear to be the consequence of different selective constraints and adaptations as a result of the differences in environmental conditions that have acted on the parental generations. These adaptations are likely genetically based as the differences are present in the F1-generation that had been reared under identical laboratory conditions.

ICLUS v1.3 Population Projections

EPA Pesticide Factsheets

Climate and land-use change are major components of global environmental change with feedbacks between these components. The consequences of these interactions show that land use may exacerbate or alleviate climate change effects. Based on these findings it is important to use land-use scenarios that are consistent with the specific assumptions underlying climate-change scenarios. The Integrated Climate and Land-Use Scenarios (ICLUS) project developed land-use outputs that are based on a downscaled version of the Intergovernmental Panel on Climate Change (IPCC) Special Report on Emissions Scenarios (SRES) social, economic, and demographic storylines. ICLUS outputs are derived from a pair of models. A demographic model generates county-level population estimates that are distributed by a spatial allocation model (SERGoM v3) as housing density across the landscape. Land-use outputs were developed for the four main SRES storylines and a baseline (base case). The model is run for the conterminous USA and output is available for each scenario by decade to 2100. In addition to housing density at a 1 hectare spatial resolution, this project also generated estimates of impervious surface at a resolution of 1 square kilometer. This shapefile holds population data for all counties of the conterminous USA for all decades (2010-2100) and SRES population growth scenarios (A1, A2, B1, B2), as well as a 'base case' (BC) scenario, for use in the Integrated Climate and Land Use

A Statistical Method to Distinguish Functional Brain Networks

PubMed Central

Fujita, André; Vidal, Maciel C.; Takahashi, Daniel Y.

2017-01-01

One major problem in neuroscience is the comparison of functional brain networks of different populations, e.g., distinguishing the networks of controls and patients. Traditional algorithms are based on search for isomorphism between networks, assuming that they are deterministic. However, biological networks present randomness that cannot be well modeled by those algorithms. For instance, functional brain networks of distinct subjects of the same population can be different due to individual characteristics. Moreover, networks of subjects from different populations can be generated through the same stochastic process. Thus, a better hypothesis is that networks are generated by random processes. In this case, subjects from the same group are samples from the same random process, whereas subjects from different groups are generated by distinct processes. Using this idea, we developed a statistical test called ANOGVA to test whether two or more populations of graphs are generated by the same random graph model. Our simulations' results demonstrate that we can precisely control the rate of false positives and that the test is powerful to discriminate random graphs generated by different models and parameters. The method also showed to be robust for unbalanced data. As an example, we applied ANOGVA to an fMRI dataset composed of controls and patients diagnosed with autism or Asperger. ANOGVA identified the cerebellar functional sub-network as statistically different between controls and autism (p < 0.001). PMID:28261045

A Statistical Method to Distinguish Functional Brain Networks.

PubMed

Fujita, André; Vidal, Maciel C; Takahashi, Daniel Y

2017-01-01

One major problem in neuroscience is the comparison of functional brain networks of different populations, e.g., distinguishing the networks of controls and patients. Traditional algorithms are based on search for isomorphism between networks, assuming that they are deterministic. However, biological networks present randomness that cannot be well modeled by those algorithms. For instance, functional brain networks of distinct subjects of the same population can be different due to individual characteristics. Moreover, networks of subjects from different populations can be generated through the same stochastic process. Thus, a better hypothesis is that networks are generated by random processes. In this case, subjects from the same group are samples from the same random process, whereas subjects from different groups are generated by distinct processes. Using this idea, we developed a statistical test called ANOGVA to test whether two or more populations of graphs are generated by the same random graph model. Our simulations' results demonstrate that we can precisely control the rate of false positives and that the test is powerful to discriminate random graphs generated by different models and parameters. The method also showed to be robust for unbalanced data. As an example, we applied ANOGVA to an fMRI dataset composed of controls and patients diagnosed with autism or Asperger. ANOGVA identified the cerebellar functional sub-network as statistically different between controls and autism ( p < 0.001).

Health Disparities Calculator (HD*Calc) - SEER Software

Cancer.gov

Statistical software that generates summary measures to evaluate and monitor health disparities. Users can import SEER data or other population-based health data to calculate 11 disparity measurements.

[Sex differentiation in plants. Terms and notions].

PubMed

Godin, V N

2007-01-01

There are two methodological approaches to the study of sex in plants: the descriptive and morphological approach and the quantitative approach. The former is based exclusively on external morphological peculiarities of the generative organs of the flower, the latter is based on the functioning of individuals as parents of the coming generation. It has been suggested to recognize three flower types: staminate, pistillate, and complete. Depending on the distribution pattern of the flowers of different sex type, there are monomorphic populations (all individuals form flowers of the same type) and heteromorphic populations (individuals have flowers of different types). Monomorphic populations include monoclinous, monoecious, gynomonoecious, andromonoecious, and polygamomonoecious ones. Among heteromorphic populations, dioecious, polygamodioecious, subdioecious, paradioecious, and trioecious ones are recognized. It is desirable to give up the usage of such terms as "bisexual", "polygamous", "functionally female", and "functionally male" flowers, "temporary dioecy" and some others. The notion "gender" has been established in English-language works for describing the sex quantitavely; two additional terms have been proposed: "phenotypic gender" and "functional gender". The recently developed quantitative approach is at present in the process of accumulating material, and in need of the further elaborating the methodological base for research. Analysis of the principal notions shows the necessity to form their integrated structure and to correct the usage of the existing and new terms.

[Analysis of the population structure of the Black Forest Draught Horse].

PubMed

Aberle, Kerstin; Wrede, Jörn; Distl, Ottmar

2003-01-01

Gene contributions of foreign populations as well as coefficients of inbreeding and relationship were evaluated in 699 Black Forest Draught horses of Baden-Württemberg actually registered in the year 2002. Based on nearly complete 5-generation-pedigrees and after taking into account the remaining incompleteness, the mean coefficient of inbreeding for the total population was 6.5%. The recently by incrossing with different breeds newly established lines of stallions showed significantly lower mean coefficients of inbreeding. High rates of inbreeding of about 1.6% in the last five generations could also be faced by incrossing stallions of foreign coldblooded populations what resulted in a decrease of inbreeding in the last generation. In the total population the mean degree of relationship was 16%. The mean degree of relationships within lines of stallions was between 18.3 and 26.8%. The coefficients of relationships between lines of stallions varied between 5.1 and 16.6%. Especially, the newly established lines of stallions showed a lower mean degree of relationships to the other different lines of stallions. The proportion of purebred Black Forest Draught horses in the total population was nearly 70%. Assuming that most animals of unknown origin were purebred, the proportion of purebred Black Forest Draught horses reached about 90%. Austrian Noric, Swiss Freiberg and South German Coldblood stallions were the most important contributors to the Black Forest Draught horse population.

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

PubMed

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

2016-07-01

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

Similar effects of QTL Haplotypes for Bacterial Cold Water Disease resistance across two generations in a commercial rainbow trout breeding population

USDA-ARS?s Scientific Manuscript database

Previously we have demonstrated that genomic selection (GS) for bacterial cold water disease (BCWD) resistance can double the accuracy of traditional pedigree-based selection in a commercial rainbow trout breeding population. The objective of this study was to evaluate the effectiveness of marker ...

Genotyping single spore isolates of a Pasteuria penetrans population occurring in Florida using SNP-based markers

USDA-ARS?s Scientific Manuscript database

The aim of this study was to examine genotypic variation and virulence characteristics of a population of bacterial parasite of root-knot nematode (RKN), Pasteuria penetrans, isolated from Florida. Six single spore lines (ssp), 16ssp, 17ssp, 18ssp, 25ssp, 26ssp, and 30ssp were generated by infecting...

A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

USDA-ARS?s Scientific Manuscript database

Background: Cotton supplies a great majority of natural fiber for the global textile industry. The negative correlation between yield and fiber quality has hindered breeders’ ability to improve these traits simultaneously. A multi-parent advanced generation inter-cross (MAGIC) population developed t...

Knowledge Data Base for Amorphous Metals

DTIC Science & Technology

2007-07-26

not programmatic, updates. Over 100 custom SQL statements that maintain the domain specific data are attached to the workflow entries in a generic...for the form by populating the SQL and run generation tables. Application data may be prepared in different ways for two steps that invoke the same form...run generation mode). There is a single table of SQL commands. Each record has a user-definable ID, the SQL code, and a comment. The run generation

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.

Linked Patient-Reported Outcomes Data From Patients With Multiple Sclerosis Recruited on an Open Internet Platform to Health Care Claims Databases Identifies a Representative Population for Real-Life Data Analysis in Multiple Sclerosis.

PubMed

Risson, Valery; Ghodge, Bhaskar; Bonzani, Ian C; Korn, Jonathan R; Medin, Jennie; Saraykar, Tanmay; Sengupta, Souvik; Saini, Deepanshu; Olson, Melvin

2016-09-22

An enormous amount of information relevant to public health is being generated directly by online communities. To explore the feasibility of creating a dataset that links patient-reported outcomes data, from a Web-based survey of US patients with multiple sclerosis (MS) recruited on open Internet platforms, to health care utilization information from health care claims databases. The dataset was generated by linkage analysis to a broader MS population in the United States using both pharmacy and medical claims data sources. US Facebook users with an interest in MS were alerted to a patient-reported survey by targeted advertisements. Eligibility criteria were diagnosis of MS by a specialist (primary progressive, relapsing-remitting, or secondary progressive), ≥12-month history of disease, age 18-65 years, and commercial health insurance. Participants completed a questionnaire including data on demographic and disease characteristics, current and earlier therapies, relapses, disability, health-related quality of life, and employment status and productivity. A unique anonymous profile was generated for each survey respondent. Each anonymous profile was linked to a number of medical and pharmacy claims datasets in the United States. Linkage rates were assessed and survey respondents' representativeness was evaluated based on differences in the distribution of characteristics between the linked survey population and the general MS population in the claims databases. The advertisement was placed on 1,063,973 Facebook users' pages generating 68,674 clicks, 3719 survey attempts, and 651 successfully completed surveys, of which 440 could be linked to any of the claims databases for 2014 or 2015 (67.6% linkage rate). Overall, no significant differences were found between patients who were linked and not linked for educational status, ethnicity, current or prior disease-modifying therapy (DMT) treatment, or presence of a relapse in the last 12 months. The frequencies of the most common MS symptoms did not differ significantly between linked patients and the general MS population in the databases. Linked patients were slightly younger and less likely to be men than those who were not linkable. Linking patient-reported outcomes data, from a Web-based survey of US patients with MS recruited on open Internet platforms, to health care utilization information from claims databases may enable rapid generation of a large population of representative patients with MS suitable for outcomes analysis.

Those Perplexing U.S. Fertility Swings. A New Perspective on a 20th Century Puzzle. PRB Report.

ERIC Educational Resources Information Center

Masnick, George S.; McFalls, Joseph A., Jr.

Based on data derived from a study of three generations of black women in Philadelphia in 1975, the report offers a new explanation of fertility differences between generations, population subgroups, and individuals. The authors hypothesize that varying fertility patterns are due to societal norms and circumstances which influence womens'…

Adjusting Limit Setting in Play Therapy with First-Generation Mexican-American Children

ERIC Educational Resources Information Center

Perez, Roxanna; Ramirez, Sylvia Z.; Kranz, Peter L.

2007-01-01

This paper focuses on limit setting in play therapy with first-generation Mexican-American children in two important therapeutic environments that include the traditional indoor playroom and a proposed outdoor play area. The paper is based on a review of the literature and the authors' clinical experiences with this population. They concluded…

DUrable polymer-based sTent CHallenge of Promus ElemEnt versus ReSolute integrity (DUTCH PEERS): rationale and study design of a randomized multicenter trial in a Dutch all-comers population.

PubMed

Tandjung, Kenneth; Basalus, Mounir W Z; Sen, Hanim; Jessurun, Gillian A J; Danse, Peter W; Stoel, Martin; Linssen, Gerard C M; Derks, Anita; van Loenhout, Ton T; Nienhuis, Mark B; Hautvast, Raymond W M; von Birgelen, Clemens

2012-04-01

Drug-eluting stents (DES) are increasingly used for the treatment of coronary artery disease. An optimized DES performance is desirable to successfully treat various challenging coronary lesions in a broad population of patients. In response to this demand, third-generation DES with an improved deliverability were developed. Promus Element (Boston Scientific, Natick, MA) and Resolute Integrity (Medtronic Vascular, Santa Rosa, CA) are 2 novel third-generation DES for which limited clinical data are available. Accordingly, we designed the current multicenter study to investigate in an all-comers population whether the clinical outcome is similar after stenting with Promus Element versus Resolute Integrity. DUTCH PEERS is a multicenter, prospective, single-blinded, randomized trial in a Dutch all-comers population. Patients with all clinical syndromes who require percutaneous coronary interventions with DES implantation are eligible. In these patients, the type of DES implanted will be randomized in a 1:1 ratio between Resolute Integrity versus Promus Element. The trial is powered based on a noninferiority hypothesis. For each stent arm, 894 patients will be enrolled, resulting in a total study population of 1,788 patients. The primary end point is the incidence of target vessel failure at 1-year follow-up. DUTCH PEERS is the first randomized multicenter trial with a head-to-head comparison of Promus Element and Resolute Integrity to investigate the safety and efficacy of these third-generation DES. Copyright © 2012 Mosby, Inc. All rights reserved.

Human Migration Patterns in Yemen and Implications for Reconstructing Prehistoric Population Movements

PubMed Central

Miró-Herrans, Aida T.; Al-Meeri, Ali; Mulligan, Connie J.

2014-01-01

Population migration has played an important role in human evolutionary history and in the patterning of human genetic variation. A deeper and empirically-based understanding of human migration dynamics is needed in order to interpret genetic and archaeological evidence and to accurately reconstruct the prehistoric processes that comprise human evolutionary history. Current empirical estimates of migration include either short time frames (i.e. within one generation) or partial knowledge about migration, such as proportion of migrants or distance of migration. An analysis of migration that includes both proportion of migrants and distance, and direction over multiple generations would better inform prehistoric reconstructions. To evaluate human migration, we use GPS coordinates from the place of residence of the Yemeni individuals sampled in our study, their birthplaces and their parents' and grandparents' birthplaces to calculate the proportion of migrants, as well as the distance and direction of migration events between each generation. We test for differences in these values between the generations and identify factors that influence the probability of migration. Our results show that the proportion and distance of migration between females and males is similar within generations. In contrast, the proportion and distance of migration is significantly lower in the grandparents' generation, most likely reflecting the decreasing effect of technology. Based on our results, we calculate the proportion of migration events (0.102) and mean and median distances of migration (96 km and 26 km) for the grandparent's generation to represent early times in human evolution. These estimates can serve to set parameter values of demographic models in model-based methods of prehistoric reconstruction, such as approximate Bayesian computation. Our study provides the first empirically-based estimates of human migration over multiple generations in a developing country and these estimates are intended to enable more precise reconstruction of the demographic processes that characterized human evolution. PMID:24759992

Human neutral genetic variation and forensic STR data.

PubMed

Silva, Nuno M; Pereira, Luísa; Poloni, Estella S; Currat, Mathias

2012-01-01

The forensic genetics field is generating extensive population data on polymorphism of short tandem repeats (STR) markers in globally distributed samples. In this study we explored and quantified the informative power of these datasets to address issues related to human evolution and diversity, by using two online resources: an allele frequency dataset representing 141 populations summing up to almost 26 thousand individuals; a genotype dataset consisting of 42 populations and more than 11 thousand individuals. We show that the genetic relationships between populations based on forensic STRs are best explained by geography, as observed when analysing other worldwide datasets generated specifically to study human diversity. However, the global level of genetic differentiation between populations (as measured by a fixation index) is about half the value estimated with those other datasets, which contain a much higher number of markers but much less individuals. We suggest that the main factor explaining this difference is an ascertainment bias in forensics data resulting from the choice of markers for individual identification. We show that this choice results in average low variance of heterozygosity across world regions, and hence in low differentiation among populations. Thus, the forensic genetic markers currently produced for the purpose of individual assignment and identification allow the detection of the patterns of neutral genetic structure that characterize the human population but they do underestimate the levels of this genetic structure compared to the datasets of STRs (or other kinds of markers) generated specifically to study the diversity of human populations.

Performance of genomic prediction within and across generations in maritime pine.

PubMed

Bartholomé, Jérôme; Van Heerwaarden, Joost; Isik, Fikret; Boury, Christophe; Vidal, Marjorie; Plomion, Christophe; Bouffier, Laurent

2016-08-11

Genomic selection (GS) is a promising approach for decreasing breeding cycle length in forest trees. Assessment of progeny performance and of the prediction accuracy of GS models over generations is therefore a key issue. A reference population of maritime pine (Pinus pinaster) with an estimated effective inbreeding population size (status number) of 25 was first selected with simulated data. This reference population (n = 818) covered three generations (G0, G1 and G2) and was genotyped with 4436 single-nucleotide polymorphism (SNP) markers. We evaluated the effects on prediction accuracy of both the relatedness between the calibration and validation sets and validation on the basis of progeny performance. Pedigree-based (best linear unbiased prediction, ABLUP) and marker-based (genomic BLUP and Bayesian LASSO) models were used to predict breeding values for three different traits: circumference, height and stem straightness. On average, the ABLUP model outperformed genomic prediction models, with a maximum difference in prediction accuracies of 0.12, depending on the trait and the validation method. A mean difference in prediction accuracy of 0.17 was found between validation methods differing in terms of relatedness. Including the progenitors in the calibration set reduced this difference in prediction accuracy to 0.03. When only genotypes from the G0 and G1 generations were used in the calibration set and genotypes from G2 were used in the validation set (progeny validation), prediction accuracies ranged from 0.70 to 0.85. This study suggests that the training of prediction models on parental populations can predict the genetic merit of the progeny with high accuracy: an encouraging result for the implementation of GS in the maritime pine breeding program.

Diversity Generator Mechanisms Are Essential Components of Biological Systems: The Two Queen Hypothesis

PubMed Central

Muraille, Eric

2018-01-01

Diversity is widely known to fuel adaptation and evolutionary processes and increase robustness at the population, species and ecosystem levels. The Neo-Darwinian paradigm proposes that the diversity of biological entities is the consequence of genetic changes arising spontaneously and randomly, without regard for their usefulness. However, a growing body of evidence demonstrates that the evolutionary process has shaped mechanisms, such as horizontal gene transfer mechanisms, meiosis and the adaptive immune system, which has resulted in the regulated generation of diversity among populations. Though their origins are unrelated, these diversity generator (DG) mechanisms share common functional properties. They (i) contribute to the great unpredictability of the composition and/or behavior of biological systems, (ii) favor robustness and collectivism among populations and (iii) operate mainly by manipulating the systems that control the interaction of living beings with their environment. The definition proposed here for DGs is based on these properties and can be used to identify them according to function. Interestingly, prokaryotic DGs appear to be mainly reactive, as they generate diversity in response to environmental stress. They are involved in the widely described Red Queen/arms race/Cairnsian dynamic. The emergence of multicellular organisms harboring K selection traits (longer reproductive life cycle and smaller population size) has led to the acquisition of a new class of DGs that act anticipatively to stress pressures and generate a distinct dynamic called the “White Queen” here. The existence of DGs leads to the view of evolution as a more “intelligent” and Lamarckian-like process. Their repeated selection during evolution could be a neglected example of convergent evolution and suggests that some parts of the evolutionary process are tightly constrained by ecological factors, such as the population size, the generation time and the intensity of selective pressure. The ubiquity of DGs also suggests that regulated auto-generation of diversity is a fundamental property of life. PMID:29487592

The air quality and regional climate effects of widespread solar power generation under a changing regulatory environment

NASA Astrophysics Data System (ADS)

Millstein, D.; Zhai, P.; Menon, S.

2011-12-01

Over the past decade significant reductions of NOx and SOx emissions from coal burning power plants in the U.S. have been achieved due to regulatory action and substitution of new generation towards natural gas and wind power. Low natural gas prices, ever decreasing solar generation costs, and proposed regulatory changes, such as to the Cross State Air Pollution Rule, promise further long-run coal power plant emission reductions. Reduced power plant emissions have the potential to affect ozone and particulate air quality and influence regional climate through aerosol cloud interactions and visibility effects. Here we investigate, on a national scale, the effects on future (~2030) air quality and regional climate of power plant emission regulations in contrast to and combination with policies designed to aggressively promote solar electricity generation. A sophisticated, economic and engineering based, hourly power generation dispatch model is developed to explore the integration of significant solar generation resources (>10% on an energy basis) at various regions across the county, providing detailed estimates of substitution of solar generation for fossil fuel generation resources. Future air pollutant emissions from all sectors of the economy are scaled based on the U.S. Environmental Protection Agency's National Emission Inventory to account for activity changes based on population and economic projections derived from county level U.S. Census data and the Energy Information Administration's Annual Energy Outlook. Further adjustments are made for technological and regulatory changes applicable within various sectors, for example, emission intensity adjustments to on-road diesel trucking due to exhaust treatment and improved engine design. The future year 2030 is selected for the emissions scenarios to allow for the development of significant solar generation resources. A regional climate and air quality model (Weather Research and Forecasting, WRF model) is used to investigate the effects of the various solar generation scenarios given emissions projections that account for changing regulatory environment, economic and population growth, and technological change. The results will help to quantify the potential air quality benefits of promotion of solar electricity generation in regions containing high penetration of coal-fired power generation. Note current national solar incentives that are based only on solar generation capacity. Further investigation of changes to regional climate due to emission reductions of aerosols and relevant precursors will provide insight into the environmental effects that may occur if solar power generation becomes widespread.

Ancestral Relationships Using Metafounders: Finite Ancestral Populations and Across Population Relationships

PubMed Central

Legarra, Andres; Christensen, Ole F.; Vitezica, Zulma G.; Aguilar, Ignacio; Misztal, Ignacy

2015-01-01

Recent use of genomic (marker-based) relationships shows that relationships exist within and across base population (breeds or lines). However, current treatment of pedigree relationships is unable to consider relationships within or across base populations, although such relationships must exist due to finite size of the ancestral population and connections between populations. This complicates the conciliation of both approaches and, in particular, combining pedigree with genomic relationships. We present a coherent theoretical framework to consider base population in pedigree relationships. We suggest a conceptual framework that considers each ancestral population as a finite-sized pool of gametes. This generates across-individual relationships and contrasts with the classical view which each population is considered as an infinite, unrelated pool. Several ancestral populations may be connected and therefore related. Each ancestral population can be represented as a “metafounder,” a pseudo-individual included as founder of the pedigree and similar to an “unknown parent group.” Metafounders have self- and across relationships according to a set of parameters, which measure ancestral relationships, i.e., homozygozities within populations and relationships across populations. These parameters can be estimated from existing pedigree and marker genotypes using maximum likelihood or a method based on summary statistics, for arbitrarily complex pedigrees. Equivalences of genetic variance and variance components between the classical and this new parameterization are shown. Segregation variance on crosses of populations is modeled. Efficient algorithms for computation of relationship matrices, their inverses, and inbreeding coefficients are presented. Use of metafounders leads to compatibility of genomic and pedigree relationship matrices and to simple computing algorithms. Examples and code are given. PMID:25873631

Estimating inbreeding in large, semi-isolated populations: effects of varying generation lengths and of migration.

PubMed

Pattison, J E

2007-01-01

The purpose of the study reported here was to investigate two important assumptions used in a recently reported new method of estimating inbreeding in large, relatively isolated populations over historic times. The method, based on modeling the genealogical "paradox," produces values of Pearl's coefficients, Z, a measure of inbreeding or genealogical coalescence, as a function of time. In this study, the effects on inbreeding of two important assumptions made in earlier studies, namely those of using a constant generation length and of ignoring migration, have been investigated for the population of Britain. First, by relating the median age of women at childbirth to the development level of various societies, the variation of the generation lengths for different periods in historic Britain were estimated. Values of Z for two types of varying generation lengths were then calculated and compared with the case of constant generation length. Second, the population curve for Britain used in earlier studies was modified to obtain the subpopulation at any time during the past two millennia that was descended from the pre-Roman British Celts. Values of Z for the case with migration were then calculated and compared with the case for no migration. It is shown that these two assumptions may be taken into account if and when required. Both the effect of a varying generation length and the effect of migration on Z were found to be 20-40%, when no known value of inbreeding was used, and 2-5%, when a known value of inbreeding was used.

Parallel approach for bioinspired algorithms

NASA Astrophysics Data System (ADS)

Zaporozhets, Dmitry; Zaruba, Daria; Kulieva, Nina

2018-05-01

In the paper, a probabilistic parallel approach based on the population heuristic, such as a genetic algorithm, is suggested. The authors proposed using a multithreading approach at the micro level at which new alternative solutions are generated. On each iteration, several threads that independently used the same population to generate new solutions can be started. After the work of all threads, a selection operator combines obtained results in the new population. To confirm the effectiveness of the suggested approach, the authors have developed software on the basis of which experimental computations can be carried out. The authors have considered a classic optimization problem – finding a Hamiltonian cycle in a graph. Experiments show that due to the parallel approach at the micro level, increment of running speed can be obtained on graphs with 250 and more vertices.

The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies

PubMed Central

Pham, Nikki T.; Wei, Tong; Schackwitz, Wendy S.; Lipzen, Anna M.; Duong, Phat Q.; Jones, Kyle C.; Ruan, Deling; Bauer, Diane; Peng, Yi; Schmutz, Jeremy

2017-01-01

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations. PMID:28576844

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

Li, Guotian; Jain, Rashmi; Chern, Mawsheng

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportionmore » of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. In conclusion, this work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.« less

The concept and use of elasticity in population viability models [Exercise 13

Treesearch

Carolyn Hull Sieg; Rudy M. King; Fred Van Dyke

2003-01-01

As you have seen in exercise 12, plants, such as the western prairie fringed orchid, typically have distinct life stages and complex life cycles that require the matrix analyses associated with a stage-based population model. Some statistics that can be generated from such matrix analyses can be very informative in determining which variables in the model have the...

Understanding spatial connectivity of individuals with non-uniform population density.

PubMed

Wang, Pu; González, Marta C

2009-08-28

We construct a two-dimensional geometric graph connecting individuals placed in space within a given contact distance. The individuals are distributed using a measured country's density of population. We observe that while large clusters (group of individuals connected) emerge within some regions, they are trapped in detached urban areas owing to the low population density of the regions bordering them. To understand the emergence of a giant cluster that connects the entire population, we compare the empirical geometric graph with the one generated by placing the same number of individuals randomly in space. We find that, for small contact distances, the empirical distribution of population dominates the growth of connected components, but no critical percolation transition is observed in contrast to the graph generated by a random distribution of population. Our results show that contact distances from real-world situations as for WIFI and Bluetooth connections drop in a zone where a fully connected cluster is not observed, hinting that human mobility must play a crucial role in contact-based diseases and wireless viruses' large-scale spreading.

Global optimization and reflectivity data fitting for x-ray multilayer mirrors by means of genetic algorithms

NASA Astrophysics Data System (ADS)

Sanchez del Rio, Manuel; Pareschi, Giovanni

2001-01-01

The x-ray reflectivity of a multilayer is a non-linear function of many parameters (materials, layer thicknesses, densities, roughness). Non-linear fitting of experimental data with simulations requires to use initial values sufficiently close to the optimum value. This is a difficult task when the space topology of the variables is highly structured, as in our case. The application of global optimization methods to fit multilayer reflectivity data is presented. Genetic algorithms are stochastic methods based on the model of natural evolution: the improvement of a population along successive generations. A complete set of initial parameters constitutes an individual. The population is a collection of individuals. Each generation is built from the parent generation by applying some operators (e.g. selection, crossover, mutation) on the members of the parent generation. The pressure of selection drives the population to include 'good' individuals. For large number of generations, the best individuals will approximate the optimum parameters. Some results on fitting experimental hard x-ray reflectivity data for Ni/C multilayers recorded at the ESRF BM5 are presented. This method could be also applied to the help in the design of multilayers optimized for a target application, like for an astronomical grazing-incidence hard X-ray telescopes.

Metabolomics in Population-Based Research

Cancer.gov

Metabolomics is the study of small molecules of both endogenous and exogenous origin, such as metabolic substrates and their products, lipids, small peptides, vitamins and other protein cofactors generated by metabolism, which are downstream from genes.

Feasibility of encoding the Institute for Clinical Systems Improvement Depression Guideline using the Omaha System.

PubMed

Monsen, Karen A; Neely, Claire; Oftedahl, Gary; Kerr, Madeleine J; Pietruszewski, Pam; Farri, Oladimeji

2012-08-01

Evidence-based clinical guidelines are being developed to bridge the gap between research and practice with the goals of improving health care quality and population health. However, disseminating, implementing, and ensuring ongoing use of clinical guidelines in practice settings is challenging. The purpose of this study was to demonstrate the feasibility of encoding evidence-based clinical guidelines using the Omaha System. Clinical documentation with Omaha System-encoded guidelines generates individualized, meaningful data suitable for program evaluation and health care quality research. The use of encoded guidelines within the electronic health record has potential to reinforce use of guidelines, and thus improve health care quality and population health. Research using Omaha System data generated by clinicians has potential to discover new knowledge related to guideline use and effectiveness. Copyright © 2012 Elsevier Inc. All rights reserved.

Life-history traits and effective population size in species with overlapping generations revisited: the importance of adult mortality.

PubMed

Waples, R S

2016-10-01

The relationship between life-history traits and the key eco-evolutionary parameters effective population size (Ne) and Ne/N is revisited for iteroparous species with overlapping generations, with a focus on the annual rate of adult mortality (d). Analytical methods based on populations with arbitrarily long adult lifespans are used to evaluate the influence of d on Ne, Ne/N and the factors that determine these parameters: adult abundance (N), generation length (T), age at maturity (α), the ratio of variance to mean reproductive success in one season by individuals of the same age (φ) and lifetime variance in reproductive success of individuals in a cohort (Vk•). Although the resulting estimators of N, T and Vk• are upwardly biased for species with short adult lifespans, the estimate of Ne/N is largely unbiased because biases in T are compensated for by biases in Vk• and N. For the first time, the contrasting effects of T and Vk• on Ne and Ne/N are jointly considered with respect to d and φ. A simple function of d and α based on the assumption of constant vital rates is shown to be a robust predictor (R(2)=0.78) of Ne/N in an empirical data set of life tables for 63 animal and plant species with diverse life histories. Results presented here should provide important context for interpreting the surge of genetically based estimates of Ne that has been fueled by the genomics revolution.

Dementia Research: Populations, Progress, Problems, and Predictions.

PubMed

Hunter, Sally; Smailagic, Nadja; Brayne, Carol

2018-05-16

Alzheimer's disease (AD) is a clinicopathologically defined syndrome leading to cognitive impairment. Following the recent failures of amyloid-based randomized controlled trials to change the course of AD, there are growing calls for a re-evaluation of basic AD research. Epidemiology offers one approach to integrating the available evidence. Here we examine relationships between evidence from population-based, clinicopathological studies of brain aging and a range of hypotheses from all areas of AD research. We identify various problems, including a lack of systematic approach to measurement of clinical and neuropathological factors associated with dementia in experimental and clinical settings, poor understanding of the strengths and weaknesses of different observational and experimental designs, a lack of clarity in relation to disease definitions from the clinical, neuropathological, and molecular perspectives, inadequate characterization of brain aging in the human population, difficulties in translation between laboratory-based and population-based evidence bases, and a lack of communication between different sections of the dementia research community. Population studies highlight complexity and predict that therapeutic approaches based on single disease features will not be successful. Better characterization of brain aging in the human population is urgently required to select biomarkers and therapeutic targets that are meaningful to human disease. The generation of detailed and reliable evidence must be addressed before progress toward therapeutic interventions can be made.

Genetic diversity of Elaeis oleifera (HBK) Cortes populations using cross species SSRs: implication's for germplasm utilization and conservation.

PubMed

Ithnin, Maizura; Teh, Chee-Keng; Ratnam, Wickneswari

2017-04-19

The Elaeis oleifera genetic materials were assembled from its center of diversity in South and Central America. These materials are currently being preserved in Malaysia as ex situ living collections. Maintaining such collections is expensive and requires sizable land. Information on the genetic diversity of these collections can help achieve efficient conservation via maintenance of core collection. For this purpose, we have applied fourteen unlinked microsatellite markers to evaluate 532 E. oleifera palms representing 19 populations distributed across Honduras, Costa Rica, Panama and Colombia. In general, the genetic diversity decreased from Costa Rica towards the north (Honduras) and south-east (Colombia). Principle coordinate analysis (PCoA) showed a single cluster indicating low divergence among palms. The phylogenetic tree and STRUCTURE analysis revealed clusters based on country of origin, indicating considerable gene flow among populations within countries. Based on the values of the genetic diversity parameters, some genetically diverse populations could be identified. Further, a total of 34 individual palms that collectively captured maximum allelic diversity with reduced redundancy were also identified. High pairwise genetic differentiation (Fst > 0.250) among populations was evident, particularly between the Colombian populations and those from Honduras, Panama and Costa Rica. Crossing selected palms from highly differentiated populations could generate off-springs that retain more genetic diversity. The results attained are useful for selecting palms and populations for core collection. The selected materials can also be included into crossing scheme to generate offsprings that capture greater genetic diversity for selection gain in the future.

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

PubMed Central

FUNK, W. CHRIS; LOVICH, ROBERT E.; HOHENLOHE, PAUL A.; HOFMAN, COURTNEY A.; MORRISON, SCOTT A.; SILLETT, T. SCOTT; GHALAMBOR, CAMERON K.; MALDONADO, JESUS E.; RICK, TORBEN C.; DAY, MITCH D.; POLATO, NICHOLAS R.; FITZPATRICK, SARAH W.; COONAN, TIMOTHY J.; CROOKS, KEVIN R.; DILLON, ADAM; GARCELON, DAVID K.; KING, JULIE L.; BOSER, CHRISTINA L.; GOULD, NICHOLAS; ANDELT, WILLIAM F.

2016-01-01

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of 6 subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland gray foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness, and reduced adaptive potential. PMID:26992010

Hubble's Next Generation Spectral Library

NASA Astrophysics Data System (ADS)

Heap, Sara R.; Lindler, D.

2008-03-01

Spectroscopic surveys of galaxies at z 1 or more bring the rest-frame ultraviolet into view of large, ground-based telescopes. This spectral region is rich in diagnostics, but these diagnostics have not yet been calibrated in terms of the properties of the responsible stellar population(s). Such calibrations are now possible with Hubble's Next Generation Spectral Library (NGSL). This library contains UV-optical spectra (0.2-1.0 microns) of 378 stars having a wide range in temperature, luminosity, and metallicity. We have derived the basic stellar parameters from the optical spectral region (0.35 - 1.0 microns) and are using them to calibrate UV spectral diagnostic indices and colors.

A two-stage cluster sampling method using gridded population data, a GIS, and Google Earth(TM) imagery in a population-based mortality survey in Iraq.

PubMed

Galway, Lp; Bell, Nathaniel; Sae, Al Shatari; Hagopian, Amy; Burnham, Gilbert; Flaxman, Abraham; Weiss, Wiliam M; Rajaratnam, Julie; Takaro, Tim K

2012-04-27

Mortality estimates can measure and monitor the impacts of conflict on a population, guide humanitarian efforts, and help to better understand the public health impacts of conflict. Vital statistics registration and surveillance systems are rarely functional in conflict settings, posing a challenge of estimating mortality using retrospective population-based surveys. We present a two-stage cluster sampling method for application in population-based mortality surveys. The sampling method utilizes gridded population data and a geographic information system (GIS) to select clusters in the first sampling stage and Google Earth TM imagery and sampling grids to select households in the second sampling stage. The sampling method is implemented in a household mortality study in Iraq in 2011. Factors affecting feasibility and methodological quality are described. Sampling is a challenge in retrospective population-based mortality studies and alternatives that improve on the conventional approaches are needed. The sampling strategy presented here was designed to generate a representative sample of the Iraqi population while reducing the potential for bias and considering the context specific challenges of the study setting. This sampling strategy, or variations on it, are adaptable and should be considered and tested in other conflict settings.

A two-stage cluster sampling method using gridded population data, a GIS, and Google EarthTM imagery in a population-based mortality survey in Iraq

PubMed Central

2012-01-01

Background Mortality estimates can measure and monitor the impacts of conflict on a population, guide humanitarian efforts, and help to better understand the public health impacts of conflict. Vital statistics registration and surveillance systems are rarely functional in conflict settings, posing a challenge of estimating mortality using retrospective population-based surveys. Results We present a two-stage cluster sampling method for application in population-based mortality surveys. The sampling method utilizes gridded population data and a geographic information system (GIS) to select clusters in the first sampling stage and Google Earth TM imagery and sampling grids to select households in the second sampling stage. The sampling method is implemented in a household mortality study in Iraq in 2011. Factors affecting feasibility and methodological quality are described. Conclusion Sampling is a challenge in retrospective population-based mortality studies and alternatives that improve on the conventional approaches are needed. The sampling strategy presented here was designed to generate a representative sample of the Iraqi population while reducing the potential for bias and considering the context specific challenges of the study setting. This sampling strategy, or variations on it, are adaptable and should be considered and tested in other conflict settings. PMID:22540266

Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress.

PubMed

Fernández, Jesús; Toro, Miguel Á; Sonesson, Anna K; Villanueva, Beatriz

2014-01-01

The success of an aquaculture breeding program critically depends on the way in which the base population of breeders is constructed since all the genetic variability for the traits included originally in the breeding goal as well as those to be included in the future is contained in the initial founders. Traditionally, base populations were created from a number of wild strains by sampling equal numbers from each strain. However, for some aquaculture species improved strains are already available and, therefore, mean phenotypic values for economically important traits can be used as a criterion to optimize the sampling when creating base populations. Also, the increasing availability of genome-wide genotype information in aquaculture species could help to refine the estimation of relationships within and between candidate strains and, thus, to optimize the percentage of individuals to be sampled from each strain. This study explores the advantages of using phenotypic and genome-wide information when constructing base populations for aquaculture breeding programs in terms of initial and subsequent trait performance and genetic diversity level. Results show that a compromise solution between diversity and performance can be found when creating base populations. Up to 6% higher levels of phenotypic performance can be achieved at the same level of global diversity in the base population by optimizing the selection of breeders instead of sampling equal numbers from each strain. The higher performance observed in the base population persisted during 10 generations of phenotypic selection applied in the subsequent breeding program.

Evolution of a research prototype expert system for endemic populations of mountain pine beetle in lodgepole pine forests

Treesearch

Dale L. Bartos; Kent B. Downing

1989-01-01

A knowledge acquisition program was written to aid in obtaining knowledge from the experts concerning endemic populations of mountain pine beetle in lodgepole pine forest. An application expert system is then automatically generated by the knowledge acquisition program that contains the codified base of expert knowledge. Data can then be entered into the expert system...

An Updating System for the Gridded Population Database of China Based on Remote Sensing, GIS and Spatial Database Technologies.

PubMed

Yang, Xiaohuan; Huang, Yaohuan; Dong, Pinliang; Jiang, Dong; Liu, Honghui

2009-01-01

The spatial distribution of population is closely related to land use and land cover (LULC) patterns on both regional and global scales. Population can be redistributed onto geo-referenced square grids according to this relation. In the past decades, various approaches to monitoring LULC using remote sensing and Geographic Information Systems (GIS) have been developed, which makes it possible for efficient updating of geo-referenced population data. A Spatial Population Updating System (SPUS) is developed for updating the gridded population database of China based on remote sensing, GIS and spatial database technologies, with a spatial resolution of 1 km by 1 km. The SPUS can process standard Moderate Resolution Imaging Spectroradiometer (MODIS L1B) data integrated with a Pattern Decomposition Method (PDM) and an LULC-Conversion Model to obtain patterns of land use and land cover, and provide input parameters for a Population Spatialization Model (PSM). The PSM embedded in SPUS is used for generating 1 km by 1 km gridded population data in each population distribution region based on natural and socio-economic variables. Validation results from finer township-level census data of Yishui County suggest that the gridded population database produced by the SPUS is reliable.

Constructing stage-structured matrix population models from life tables: comparison of methods

PubMed Central

Diaz-Lopez, Jasmin

2017-01-01

A matrix population model is a convenient tool for summarizing per capita survival and reproduction rates (collectively vital rates) of a population and can be used for calculating an asymptotic finite population growth rate (λ) and generation time. These two pieces of information can be used for determining the status of a threatened species. The use of stage-structured population models has increased in recent years, and the vital rates in such models are often estimated using a life table analysis. However, potential bias introduced when converting age-structured vital rates estimated from a life table into parameters for a stage-structured population model has not been assessed comprehensively. The objective of this study was to investigate the performance of methods for such conversions using simulated life histories of organisms. The underlying models incorporate various types of life history and true population growth rates of varying levels. The performance was measured by comparing differences in λ and the generation time calculated using the Euler-Lotka equation, age-structured population matrices, and several stage-structured population matrices that were obtained by applying different conversion methods. The results show that the discretization of age introduces only small bias in λ or generation time. Similarly, assuming a fixed age of maturation at the mean age of maturation does not introduce much bias. However, aggregating age-specific survival rates into a stage-specific survival rate and estimating a stage-transition rate can introduce substantial bias depending on the organism’s life history type and the true values of λ. In order to aggregate survival rates, the use of the weighted arithmetic mean was the most robust method for estimating λ. Here, the weights are given by survivorship curve after discounting with λ. To estimate a stage-transition rate, matching the proportion of individuals transitioning, with λ used for discounting the rate, was the best approach. However, stage-structured models performed poorly in estimating generation time, regardless of the methods used for constructing the models. Based on the results, we recommend using an age-structured matrix population model or the Euler-Lotka equation for calculating λ and generation time when life table data are available. Then, these age-structured vital rates can be converted into a stage-structured model for further analyses. PMID:29085763

Constructing stage-structured matrix population models from life tables: comparison of methods.

PubMed

Fujiwara, Masami; Diaz-Lopez, Jasmin

2017-01-01

A matrix population model is a convenient tool for summarizing per capita survival and reproduction rates (collectively vital rates) of a population and can be used for calculating an asymptotic finite population growth rate ( λ ) and generation time. These two pieces of information can be used for determining the status of a threatened species. The use of stage-structured population models has increased in recent years, and the vital rates in such models are often estimated using a life table analysis. However, potential bias introduced when converting age-structured vital rates estimated from a life table into parameters for a stage-structured population model has not been assessed comprehensively. The objective of this study was to investigate the performance of methods for such conversions using simulated life histories of organisms. The underlying models incorporate various types of life history and true population growth rates of varying levels. The performance was measured by comparing differences in λ and the generation time calculated using the Euler-Lotka equation, age-structured population matrices, and several stage-structured population matrices that were obtained by applying different conversion methods. The results show that the discretization of age introduces only small bias in λ or generation time. Similarly, assuming a fixed age of maturation at the mean age of maturation does not introduce much bias. However, aggregating age-specific survival rates into a stage-specific survival rate and estimating a stage-transition rate can introduce substantial bias depending on the organism's life history type and the true values of λ . In order to aggregate survival rates, the use of the weighted arithmetic mean was the most robust method for estimating λ . Here, the weights are given by survivorship curve after discounting with λ . To estimate a stage-transition rate, matching the proportion of individuals transitioning, with λ used for discounting the rate, was the best approach. However, stage-structured models performed poorly in estimating generation time, regardless of the methods used for constructing the models. Based on the results, we recommend using an age-structured matrix population model or the Euler-Lotka equation for calculating λ and generation time when life table data are available. Then, these age-structured vital rates can be converted into a stage-structured model for further analyses.

Ancestral Relationships Using Metafounders: Finite Ancestral Populations and Across Population Relationships.

PubMed

Legarra, Andres; Christensen, Ole F; Vitezica, Zulma G; Aguilar, Ignacio; Misztal, Ignacy

2015-06-01

Recent use of genomic (marker-based) relationships shows that relationships exist within and across base population (breeds or lines). However, current treatment of pedigree relationships is unable to consider relationships within or across base populations, although such relationships must exist due to finite size of the ancestral population and connections between populations. This complicates the conciliation of both approaches and, in particular, combining pedigree with genomic relationships. We present a coherent theoretical framework to consider base population in pedigree relationships. We suggest a conceptual framework that considers each ancestral population as a finite-sized pool of gametes. This generates across-individual relationships and contrasts with the classical view which each population is considered as an infinite, unrelated pool. Several ancestral populations may be connected and therefore related. Each ancestral population can be represented as a "metafounder," a pseudo-individual included as founder of the pedigree and similar to an "unknown parent group." Metafounders have self- and across relationships according to a set of parameters, which measure ancestral relationships, i.e., homozygozities within populations and relationships across populations. These parameters can be estimated from existing pedigree and marker genotypes using maximum likelihood or a method based on summary statistics, for arbitrarily complex pedigrees. Equivalences of genetic variance and variance components between the classical and this new parameterization are shown. Segregation variance on crosses of populations is modeled. Efficient algorithms for computation of relationship matrices, their inverses, and inbreeding coefficients are presented. Use of metafounders leads to compatibility of genomic and pedigree relationship matrices and to simple computing algorithms. Examples and code are given. Copyright © 2015 by the Genetics Society of America.

Using GIS to generate spatially balanced random survey designs for natural resource applications.

PubMed

Theobald, David M; Stevens, Don L; White, Denis; Urquhart, N Scott; Olsen, Anthony R; Norman, John B

2007-07-01

Sampling of a population is frequently required to understand trends and patterns in natural resource management because financial and time constraints preclude a complete census. A rigorous probability-based survey design specifies where to sample so that inferences from the sample apply to the entire population. Probability survey designs should be used in natural resource and environmental management situations because they provide the mathematical foundation for statistical inference. Development of long-term monitoring designs demand survey designs that achieve statistical rigor and are efficient but remain flexible to inevitable logistical or practical constraints during field data collection. Here we describe an approach to probability-based survey design, called the Reversed Randomized Quadrant-Recursive Raster, based on the concept of spatially balanced sampling and implemented in a geographic information system. This provides environmental managers a practical tool to generate flexible and efficient survey designs for natural resource applications. Factors commonly used to modify sampling intensity, such as categories, gradients, or accessibility, can be readily incorporated into the spatially balanced sample design.

Population aging and international development: addressing competing claims of distributive justice.

PubMed

Engelman, Michal; Johnson, Summer

2007-04-01

To date, bioethics and health policy scholarship has given little consideration to questions of aging and intergenerational justice in the developing world. Demographic changes are precipitating rapid population aging in developing nations, however, and ethical issues regarding older people's claim to scarce healthcare resources must be addressed. This paper posits that the traditional arguments about generational justice and age-based rationing of healthcare resources, which were developed primarily in more industrialized nations, fail to adequately address the unique challenges facing older persons in developing nations. Existing philosophical approaches to age-based resource allocation underemphasize the importance of older persons for developing countries and fail to adequately consider the rights and interests of older persons in these settings. Ultimately, the paper concludes that the most appropriate framework for thinking about generational justice in developing nations is a rights-based approach that allows for the interests of all age groups, including the oldest, to be considered in the determination of health resource allocation.

Quasideterministic generation of maximally entangled states of two mesoscopic atomic ensembles by adiabatic quantum feedback

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

Di Lisi, Antonio; De Siena, Silvio; Illuminati, Fabrizio

2005-09-15

We introduce an efficient, quasideterministic scheme to generate maximally entangled states of two atomic ensembles. The scheme is based on quantum nondemolition measurements of total atomic populations and on adiabatic quantum feedback conditioned by the measurements outputs. The high efficiency of the scheme is tested and confirmed numerically for ideal photodetection as well as in the presence of losses.

Veterans' informal caregivers in the "sandwich generation": a systematic review toward a resilience model.

PubMed

Smith-Osborne, Alexa; Felderhoff, Brandi

2014-01-01

Social work theory advanced the formulation of the construct of the sandwich generation to apply to the emerging generational cohort of caregivers, most often middle-aged women, who were caring for maturing children and aging parents simultaneously. This systematic review extends that focus by synthesizing the literature on sandwich generation caregivers for the general aging population with dementia and for veterans with dementia and polytrauma. It develops potential protective mechanisms based on empirical literature to support an intervention resilience model for social work practitioners. This theoretical model addresses adaptive coping of sandwich- generation families facing ongoing challenges related to caregiving demands.

Long-PCR based next generation sequencing of the whole mitochondrial genome of the peacock skate Pavoraja nitida (Elasmobranchii: Arhynchobatidae).

PubMed

Yang, Lei; Naylor, Gavin J P

2016-01-01

We determined the complete mitochondrial genome sequence (16,760 bp) of the peacock skate Pavoraja nitida using a long-PCR based next generation sequencing method. It has 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region in the typical vertebrate arrangement. Primers, protocols, and procedures used to obtain this mitogenome are provided. We anticipate that this approach will facilitate rapid collection of mitogenome sequences for studies on phylogenetic relationships, population genetics, and conservation of cartilaginous fishes.

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.

Optimization of PV/WIND/DIESEL Hybrid Power System in HOMER for Rural Electrification

NASA Astrophysics Data System (ADS)

Hassan, Q.; Jaszczur, M.; Abdulateef, J.

2016-09-01

A large proportion of the world's population lives in remote rural areas that are geographically isolated and sparsely populated. The present study is based on modeling, computer simulation and optimization of hybrid power generation system in the rural area in Muqdadiyah district of Diyala state, Iraq. Two renewable resources, namely, solar photovoltaic (PV) and wind turbine (WT) are considered. The HOMER software is used to study and design the proposed hybrid energy system model. Based on simulation results, it has been found that renewable energy sources perhaps replace the conventional energy sources and would be a feasible solution for the generation of electric power at remote locations with a reasonable investment. The hybrid power system solution to electrify the selected area resulted in a least-cost combination of the hybrid power system that can meet the demand in a dependable manner at a cost about (0.321/kWh). If the wind resources in the study area at the lower stage, it's not economically viable for a wind turbine to generate the electricity.

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.

Genetic structure of cougar populations across the Wyoming basin: Metapopulation or megapopulation

USGS Publications Warehouse

Anderson, C.R.; Lindzey, F.G.; McDonald, D.B.

2004-01-01

We examined the genetic structure of 5 Wyoming cougar (Puma concolor) populations surrounding the Wyoming Basin, as well as a population from southwestern Colorado. When using 9 microsatellite DNA loci, observed heterozygosity was similar among populations (HO = 0.49-0.59) and intermediate to that of other large carnivores. Estimates of genetic structure (FST = 0.028, RST = 0.029) and number of migrants per generation (Nm) suggested high gene flow. Nm was lowest between distant populations and highest among adjacent populations. Examination of these data, plus Mantel test results of genetic versus geographic distance (P ??? 0.01), suggested both isolation by distance and an effect of habitat matrix. Bayesian assignment to population based on individual genotypes showed that cougars in this region were best described as a single panmictic population. Total effective population size for cougars in this region ranged from 1,797 to 4,532 depending on mutation model and analytical method used. Based on measures of gene flow, extinction risk in the near future appears low. We found no support for the existence of metapopulation structure among cougars in this region.

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.

The utilization of neural nets in populating an object-oriented database

NASA Technical Reports Server (NTRS)

Campbell, William J.; Hill, Scott E.; Cromp, Robert F.

1989-01-01

Existing NASA supported scientific data bases are usually developed, managed and populated in a tedious, error prone and self-limiting way in terms of what can be described in a relational Data Base Management System (DBMS). The next generation Earth remote sensing platforms (i.e., Earth Observation System, (EOS), will be capable of generating data at a rate of over 300 Mbs per second from a suite of instruments designed for different applications. What is needed is an innovative approach that creates object-oriented databases that segment, characterize, catalog and are manageable in a domain-specific context and whose contents are available interactively and in near-real-time to the user community. Described here is work in progress that utilizes an artificial neural net approach to characterize satellite imagery of undefined objects into high-level data objects. The characterized data is then dynamically allocated to an object-oriented data base where it can be reviewed and assessed by a user. The definition, development, and evolution of the overall data system model are steps in the creation of an application-driven knowledge-based scientific information system.

PAGER--Rapid assessment of an earthquake?s impact

USGS Publications Warehouse

Wald, D.J.; Jaiswal, K.; Marano, K.D.; Bausch, D.; Hearne, M.

2010-01-01

PAGER (Prompt Assessment of Global Earthquakes for Response) is an automated system that produces content concerning the impact of significant earthquakes around the world, informing emergency responders, government and aid agencies, and the media of the scope of the potential disaster. PAGER rapidly assesses earthquake impacts by comparing the population exposed to each level of shaking intensity with models of economic and fatality losses based on past earthquakes in each country or region of the world. Earthquake alerts--which were formerly sent based only on event magnitude and location, or population exposure to shaking--now will also be generated based on the estimated range of fatalities and economic losses.

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

PubMed Central

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

2015-01-01

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

Projecting pest population dynamics under global warming: the combined effect of inter- and intra-annual variations.

PubMed

Zidon, Royi; Tsueda, Hirotsugu; Morin, Efrat; Morin, Shai

2016-06-01

The typical short generation length of insects makes their population dynamics highly sensitive not only to mean annual temperatures but also to their intra-annual variations. To consider the combined effect of both thermal factors under global warming, we propose a modeling framework that links general circulation models (GCMs) with a stochastic weather generator and population dynamics models to predict species population responses to inter- and intra-annual temperature changes. This framework was utilized to explore future changes in populations of Bemisia tabaci, an invasive insect pest-species that affects multiple agricultural systems in the Mediterranean region. We considered three locations representing different pest status and climatic conditions: Montpellier (France), Seville (Spain), and Beit-Jamal (Israel). We produced ensembles of local daily temperature realizations representing current and future (mid-21st century) climatic conditions under two emission scenarios for the three locations. Our simulations predicted a significant increase in the average number of annual generations and in population size, and a significant lengthening of the growing season in all three locations. A negative effect was found only in Seville for the summer season, where future temperatures lead to a reduction in population size. High variability in population size was observed between years with similar annual mean temperatures, suggesting a strong effect of intra-annual temperature variation. Critical periods were from late spring to late summer in Montpellier and from late winter to early summer in Seville and Beit-Jamal. Although our analysis suggested that earlier seasonal activity does not necessarily lead to increased populations load unless an additional generation is produced, it is highly likely that the insect will become a significant pest of open-fields at Mediterranean latitudes above 40° during the next 50 years. Our simulations also implied that current predictions based on mean temperature anomalies are relatively conservative and it is better to apply stochastic tools to resolve complex responses to climate change while taking natural variability into account. In summary, we propose a modeling framework capable of determining distinct intra-annual temperature patterns leading to large or small population sizes, for pest risk assessment and management planning of both natural and agricultural ecosystems.

Optimizing digital elevation models (DEMs) accuracy for planning and design of mobile communication networks

NASA Astrophysics Data System (ADS)

Hassan, Mahmoud A.

2004-02-01

Digital elevation models (DEMs) are important tools in the planning, design and maintenance of mobile communication networks. This research paper proposes a method for generating high accuracy DEMs based on SPOT satellite 1A stereo pair images, ground control points (GCP) and Erdas OrthoBASE Pro image processing software. DEMs with 0.2911 m mean error were achieved for the hilly and heavily populated city of Amman. The generated DEM was used to design a mobile communication network resulted in a minimum number of radio base transceiver stations, maximum number of covered regions and less than 2% of dead zones.

A multiple-alignment based primer design algorithm for genetically highly variable DNA targets

PubMed Central

2013-01-01

Background Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to population diversity and primer localization in relatively conserved regions, in addition to recognized constraints typically considered in primer design. Results Design constraints include degenerate sites to maximize population coverage, matching of melting temperatures, optimizing de novo sequence length, finding optimal bio-barcodes to allow efficient downstream analyses, and minimizing risk of dimerization. To facilitate primer design addressing these and other constraints, we created a novel computer program (PrimerDesign) that automates this complex procedure. We show its powers and limitations and give examples of successful designs for the analysis of HIV-1 populations. Conclusions PrimerDesign is useful for researchers who want to design DNA primers and probes for analyzing highly variable DNA populations. It can be used to design primers for PCR, RT-PCR, Sanger sequencing, next-generation sequencing, and other experimental protocols targeting highly variable DNA samples. PMID:23965160

Population-genetic properties of differentiated copy number variations in cattle.

PubMed

Xu, Lingyang; Hou, Yali; Bickhart, Derek M; Zhou, Yang; Hay, El Hamidi Abdel; Song, Jiuzhou; Sonstegard, Tad S; Van Tassell, Curtis P; Liu, George E

2016-03-23

While single nucleotide polymorphism (SNP) is typically the variant of choice for population genetics, copy number variation (CNV) which comprises insertion, deletion and duplication of genomic sequence, is an informative type of genetic variation. CNVs have been shown to be both common in mammals and important for understanding the relationship between genotype and phenotype. However, CNV differentiation, selection and its population genetic properties are not well understood across diverse populations. We performed a population genetics survey based on CNVs derived from the BovineHD SNP array data of eight distinct cattle breeds. We generated high resolution results that show geographical patterns of variations and genome-wide admixture proportions within and among breeds. Similar to the previous SNP-based studies, our CNV-based results displayed a strong correlation of population structure and geographical location. By conducting three pairwise comparisons among European taurine, African taurine, and indicine groups, we further identified 78 unique CNV regions that were highly differentiated, some of which might be due to selection. These CNV regions overlapped with genes involved in traits related to parasite resistance, immunity response, body size, fertility, and milk production. Our results characterize CNV diversity among cattle populations and provide a list of lineage-differentiated CNVs.

Automatic Generation of English-Japanese Translation Pattern Utilizing Genetic Programming Technique

NASA Astrophysics Data System (ADS)

Matsumura, Koki; Tamekuni, Yuji; Kimura, Shuhei

There are a lot of constructional differences in an English-Japanese phrase template, and that often makes the act of translation difficult. Moreover, there exist various and tremendous phrase templates and sentence to be refered to. It is not easy to prepare the corpus that covers the all. Therefore, it is very significant to generate the translation pattern of the sentence pattern automatically from a viewpoint of the translation success rate and the capacity of the pattern dictionary. Then, for the purpose of realizing the automatic generation of the translation pattern, this paper proposed the new method for the generation of the translation pattern by using the genetic programming technique (GP). The technique tries to generate the translation pattern of various sentences which are not registered in the phrase template dictionary automatically by giving the genetic operation to the parsing tree of a basic pattern. The tree consists of the pair of the English-Japanese sentence generated as the first stage population. The analysis tree data base with 50,100,150,200 pairs was prepared as the first stage population. And this system was applied and executed for an English input of 1,555 sentences. As a result, the analysis tree increases from 200 to 517, and the accuracy rate of the translation pattern has improved from 42.57% to 70.10%. And, 86.71% of the generated translations was successfully done, whose meanings are enough acceptable and understandable. It seemed that this proposal technique became a clue to raise the translation success rate, and to find the possibility of the reduction of the analysis tree data base.

Evaluation of the influence of the definition of an isolated hip fracture as an exclusion criterion for trauma system benchmarking: a multicenter cohort study.

PubMed

Tiao, J; Moore, L; Porgo, T V; Belcaid, A

2016-06-01

To assess whether the definition of an IHF used as an exclusion criterion influences the results of trauma center benchmarking. We conducted a multicenter retrospective cohort study with data from an integrated Canadian trauma system. The study population included all patients admitted between 1999 and 2010 to any of the 57 adult trauma centers. Seven definitions of IHF based on diagnostic codes, age, mechanism of injury, and secondary injuries, identified in a systematic review, were used. Trauma centers were benchmarked using risk-adjusted mortality estimates generated using the Trauma Risk Adjustment Model. The agreement between benchmarking results generated under different IHF definitions was evaluated with correlation coefficients on adjusted mortality estimates. Correlation coefficients >0.95 were considered to convey acceptable agreement. The study population consisted of 172,872 patients before exclusion of IHF and between 128,094 and 139,588 patients after exclusion. Correlation coefficients between risk-adjusted mortality estimates generated in populations including and excluding IHF varied between 0.86 and 0.90. Correlation coefficients of estimates generated under different definitions of IHF varied between 0.97 and 0.99, even when analyses were restricted to patients aged ≥65 years. Although the exclusion of patients with IHF has an influence on the results of trauma center benchmarking based on mortality, the definition of IHF in terms of diagnostic codes, age, mechanism of injury and secondary injury has no significant impact on benchmarking results. Results suggest that there is no need to obtain formal consensus on the definition of IHF for benchmarking activities.

The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies.

PubMed

Li, Guotian; Jain, Rashmi; Chern, Mawsheng; Pham, Nikki T; Martin, Joel A; Wei, Tong; Schackwitz, Wendy S; Lipzen, Anna M; Duong, Phat Q; Jones, Kyle C; Jiang, Liangrong; Ruan, Deling; Bauer, Diane; Peng, Yi; Barry, Kerrie W; Schmutz, Jeremy; Ronald, Pamela C

2017-06-01

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake ( Oryza sativa ssp japonica ), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations. © 2017 American Society of Plant Biologists. All rights reserved.

Suicide among immigrant population in Norway: a national register-based study.

PubMed

Puzo, Q; Mehlum, L; Qin, P

2017-06-01

To investigate differences in suicide risk among immigrant population in Norway compared with native Norwegians, with respect to associated country group of origin. Based on the entire national population, a nested case-control design was adopted using Norwegian national longitudinal registers to obtain 23 073 suicide cases having occurred in 1969-2012 and 373 178 controls. Odds ratios (ORs) for suicide were estimated using conditional logistic regression analysis adjusting for socio-economic factors. Compared with native Norwegians, suicide risk was significantly lower in first- and second-generation immigrants but higher in Norwegian-born with one foreign-born parent and foreign-born individuals with at least one Norwegian-born parent. When stratifying data by country group of origin, first-generation immigrants had lower ORs in most of the strata. Subjects born in Asia and in Central and South America with at least one Norwegian-born parent had a significantly higher risk of suicide. The observed results remained mostly unchanged in the analyses controlled for socio-economic status. Suicide risk is lower in first- and second-generation immigrants but higher in subjects born in Norway with one foreign-born parent and those born abroad with at least one Norwegian-born parent, with notable differences by country group of origin. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies

DOE PAGES

Li, Guotian; Jain, Rashmi; Chern, Mawsheng; ...

2017-06-02

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportionmore » of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. In conclusion, this work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.« less

Neural Population Dynamics during Reaching Are Better Explained by a Dynamical System than Representational Tuning

PubMed Central

Dann, Benjamin

2016-01-01

Recent models of movement generation in motor cortex have sought to explain neural activity not as a function of movement parameters, known as representational models, but as a dynamical system acting at the level of the population. Despite evidence supporting this framework, the evaluation of representational models and their integration with dynamical systems is incomplete in the literature. Using a representational velocity-tuning based simulation of center-out reaching, we show that incorporating variable latency offsets between neural activity and kinematics is sufficient to generate rotational dynamics at the level of neural populations, a phenomenon observed in motor cortex. However, we developed a covariance-matched permutation test (CMPT) that reassigns neural data between task conditions independently for each neuron while maintaining overall neuron-to-neuron relationships, revealing that rotations based on the representational model did not uniquely depend on the underlying condition structure. In contrast, rotations based on either a dynamical model or motor cortex data depend on this relationship, providing evidence that the dynamical model more readily explains motor cortex activity. Importantly, implementing a recurrent neural network we demonstrate that both representational tuning properties and rotational dynamics emerge, providing evidence that a dynamical system can reproduce previous findings of representational tuning. Finally, using motor cortex data in combination with the CMPT, we show that results based on small numbers of neurons or conditions should be interpreted cautiously, potentially informing future experimental design. Together, our findings reinforce the view that representational models lack the explanatory power to describe complex aspects of single neuron and population level activity. PMID:27814352

Neural Population Dynamics during Reaching Are Better Explained by a Dynamical System than Representational Tuning.

PubMed

Michaels, Jonathan A; Dann, Benjamin; Scherberger, Hansjörg

2016-11-01

Recent models of movement generation in motor cortex have sought to explain neural activity not as a function of movement parameters, known as representational models, but as a dynamical system acting at the level of the population. Despite evidence supporting this framework, the evaluation of representational models and their integration with dynamical systems is incomplete in the literature. Using a representational velocity-tuning based simulation of center-out reaching, we show that incorporating variable latency offsets between neural activity and kinematics is sufficient to generate rotational dynamics at the level of neural populations, a phenomenon observed in motor cortex. However, we developed a covariance-matched permutation test (CMPT) that reassigns neural data between task conditions independently for each neuron while maintaining overall neuron-to-neuron relationships, revealing that rotations based on the representational model did not uniquely depend on the underlying condition structure. In contrast, rotations based on either a dynamical model or motor cortex data depend on this relationship, providing evidence that the dynamical model more readily explains motor cortex activity. Importantly, implementing a recurrent neural network we demonstrate that both representational tuning properties and rotational dynamics emerge, providing evidence that a dynamical system can reproduce previous findings of representational tuning. Finally, using motor cortex data in combination with the CMPT, we show that results based on small numbers of neurons or conditions should be interpreted cautiously, potentially informing future experimental design. Together, our findings reinforce the view that representational models lack the explanatory power to describe complex aspects of single neuron and population level activity.

Analysis and forecasting of municipal solid waste in Nankana City using geo-spatial techniques.

PubMed

Mahmood, Shakeel; Sharif, Faiza; Rahman, Atta-Ur; Khan, Amin U

2018-04-11

The objective of this study was to analyze and forecast municipal solid waste (MSW) in Nankana City (NC), District Nankana, Province of Punjab, Pakistan. The study is based on primary data acquired through a questionnaire, Global Positioning System (GPS), and direct waste sampling and analysis. Inverse distance weighting (IDW) technique was applied to geo-visualize the spatial trend of MSW generation. Analysis revealed that the total MSW generated was 12,419,636 kg/annum (12,419.64 t) or 34,026.4 kg/day (34.03 t), or 0.46 kg/capita/day (kg/cap/day). The average wastes generated per day by studied households, clinics, hospitals, and hotels were 3, 7.5, 20, and 15 kg, respectively. The residential sector was the top producer with 95.5% (32,511 kg/day) followed by commercial sector 1.9% (665 kg/day). On average, high-income and low-income households were generating waste of 4.2 kg/household/day (kg/hh/day) and 1.7 kg/hh/day, respectively. Similarly, large-size families were generating more (4.4 kg/hh/day) waste than small-size families (1.8 kg/hh/day). The physical constituents of MSW generated in the study area with a population of about 70,000 included paper (7%); compostable matter (61%); plastics (9%); fine earth, ashes, ceramics, and stones (20.4%); and others (2.6%).The spatial trend of MSW generation varies; city center has a high rate of generation and towards periphery generation lowers. Based on the current population growth and MSW generation rate, NC is expected to generate 2.8 times more waste by the year 2050.This is imperative to develop a proper solid waste management plan to reduce the risk of environmental degradation and protect human health. This study provides insights into MSW generation rate, physical composition, and forecasting which are vital in its management strategies.

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).

PubMed

Funk, W Chris; Lovich, Robert E; Hohenlohe, Paul A; Hofman, Courtney A; Morrison, Scott A; Sillett, T Scott; Ghalambor, Cameron K; Maldonado, Jesus E; Rick, Torben C; Day, Mitch D; Polato, Nicholas R; Fitzpatrick, Sarah W; Coonan, Timothy J; Crooks, Kevin R; Dillon, Adam; Garcelon, David K; King, Julie L; Boser, Christina L; Gould, Nicholas; Andelt, William F

2016-05-01

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential. © 2016 John Wiley & Sons Ltd.

Experimental Estimation of Mutation Rates in a Wheat Population With a Gene Genealogy Approach

PubMed Central

Raquin, Anne-Laure; Depaulis, Frantz; Lambert, Amaury; Galic, Nathalie; Brabant, Philippe; Goldringer, Isabelle

2008-01-01

Microsatellite markers are extensively used to evaluate genetic diversity in natural or experimental evolving populations. Their high degree of polymorphism reflects their high mutation rates. Estimates of the mutation rates are therefore necessary when characterizing diversity in populations. As a complement to the classical experimental designs, we propose to use experimental populations, where the initial state is entirely known and some intermediate states have been thoroughly surveyed, thus providing a short timescale estimation together with a large number of cumulated meioses. In this article, we derived four original gene genealogy-based methods to assess mutation rates with limited bias due to relevant model assumptions incorporating the initial state, the number of new alleles, and the genetic effective population size. We studied the evolution of genetic diversity at 21 microsatellite markers, after 15 generations in an experimental wheat population. Compared to the parents, 23 new alleles were found in generation 15 at 9 of the 21 loci studied. We provide evidence that they arose by mutation. Corresponding estimates of the mutation rates ranged from 0 to 4.97 × 10−3 per generation (i.e., year). Sequences of several alleles revealed that length polymorphism was only due to variation in the core of the microsatellite. Among different microsatellite characteristics, both the motif repeat number and an independent estimation of the Nei diversity were correlated with the novel diversity. Despite a reduced genetic effective size, global diversity at microsatellite markers increased in this population, suggesting that microsatellite diversity should be used with caution as an indicator in biodiversity conservation issues. PMID:18689900

Experimental estimation of mutation rates in a wheat population with a gene genealogy approach.

PubMed

Raquin, Anne-Laure; Depaulis, Frantz; Lambert, Amaury; Galic, Nathalie; Brabant, Philippe; Goldringer, Isabelle

2008-08-01

Microsatellite markers are extensively used to evaluate genetic diversity in natural or experimental evolving populations. Their high degree of polymorphism reflects their high mutation rates. Estimates of the mutation rates are therefore necessary when characterizing diversity in populations. As a complement to the classical experimental designs, we propose to use experimental populations, where the initial state is entirely known and some intermediate states have been thoroughly surveyed, thus providing a short timescale estimation together with a large number of cumulated meioses. In this article, we derived four original gene genealogy-based methods to assess mutation rates with limited bias due to relevant model assumptions incorporating the initial state, the number of new alleles, and the genetic effective population size. We studied the evolution of genetic diversity at 21 microsatellite markers, after 15 generations in an experimental wheat population. Compared to the parents, 23 new alleles were found in generation 15 at 9 of the 21 loci studied. We provide evidence that they arose by mutation. Corresponding estimates of the mutation rates ranged from 0 to 4.97 x 10(-3) per generation (i.e., year). Sequences of several alleles revealed that length polymorphism was only due to variation in the core of the microsatellite. Among different microsatellite characteristics, both the motif repeat number and an independent estimation of the Nei diversity were correlated with the novel diversity. Despite a reduced genetic effective size, global diversity at microsatellite markers increased in this population, suggesting that microsatellite diversity should be used with caution as an indicator in biodiversity conservation issues.

Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history.

PubMed

Zhu, Yuan O; Aw, Pauline P K; de Sessions, Paola Florez; Hong, Shuzhen; See, Lee Xian; Hong, Lewis Z; Wilm, Andreas; Li, Chen Hao; Hue, Stephane; Lim, Seng Gee; Nagarajan, Niranjan; Burkholder, William F; Hibberd, Martin

2017-10-27

Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies. To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key. In particular, long-range haplotype information for thousands of individual viruses is critical; yet generating this information is non-trivial. Popular deep sequencing methods generate relatively short reads that do not preserve linkage information, while third generation sequencing methods have higher error rates that make detection of low frequency mutations a bioinformatics challenge. Here we applied BAsE-Seq, an Illumina-based single-virion sequencing technology, to eight samples from four chronic hepatitis B (CHB) patients - once before antiviral treatment and once after viral rebound due to resistance. With single-virion sequencing, we obtained 248-8796 single-virion sequences per sample, which allowed us to find evidence for both hard and soft selective sweeps. We were able to reconstruct population demographic history that was independently verified by clinically collected data. We further verified four of the samples independently through PacBio SMRT and Illumina Pooled deep sequencing. Overall, we showed that single-virion sequencing yields insight into viral evolution and population dynamics in an efficient and high throughput manner. We believe that single-virion sequencing is widely applicable to the study of viral evolution in the context of drug resistance and host adaptation, allows differentiation between soft or hard selective sweeps, and may be useful in the reconstruction of intra-host viral population demographic history.

Revived STIS. II. Properties of Stars in the Next Generation Spectral Library

NASA Technical Reports Server (NTRS)

Heap, Sara R.; Lindler, D.

2010-01-01

Spectroscopic surveys of galaxies at high redshift will bring the rest-frame ultraviolet into view of large, ground-based telescopes. The UV-blue spectral region is rich in diagnostics, but these diagnostics have not yet been calibrated in terms of the properties of the responsible stellar population(s). Such calibrations are now possible with Hubble's Next Generation Spectral Library (NGSL). The NGSL contains UV-optical spectra (0.2 - 1.0 microns) of 374 stars having a wide range in temperature, luminosity, and metallicity. We will describe our work to derive basic stellar parameters from NGSL spectra using modern model spectra and to use these stellar parameters to develop UV-blue spectral diagnostics.

Conservation status of polar bears (Ursus maritimus) in relation to projected sea-ice declines

NASA Astrophysics Data System (ADS)

Laidre, K. L.; Regehr, E. V.; Akcakaya, H. R.; Amstrup, S. C.; Atwood, T.; Lunn, N.; Obbard, M.; Stern, H. L., III; Thiemann, G.; Wiig, O.

2016-12-01

Loss of Arctic sea ice due to climate change is the most serious threat to polar bears (Ursus maritimus) throughout their circumpolar range. We performed a data-based sensitivity analysis with respect to this threat by evaluating the potential response of the global polar bear population to projected sea-ice conditions. We conducted 1) an assessment of generation length for polar bears, 2) developed of a standardized sea-ice metric representing important habitat characteristics for the species; and 3) performed population projections over three generations, using computer simulation and statistical models representing alternative relationships between sea ice and polar bear abundance. Using three separate approaches, the median percent change in mean global population size for polar bears between 2015 and 2050 ranged from -4% (95% CI = -62%, 50%) to -43% (95% CI = -76%, -20%). Results highlight the potential for large reductions in the global population if sea-ice loss continues. They also highlight the large amount of uncertainty in statistical projections of polar bear abundance and the sensitivity of projections to plausible alternative assumptions. The median probability of a reduction in the mean global population size of polar bears greater than 30% over three generations was approximately 0.71 (range 0.20-0.95. The median probability of a reduction greater than 50% was approximately 0.07 (range 0-0.35), and the probability of a reduction greater than 80% was negligible.

Genotyping of single spore isolates of a Pasteuria penetrans population occurring in Florida using SNP-based markers.

PubMed

Joseph, S; Schmidt, L M; Danquah, W B; Timper, P; Mekete, T

2017-02-01

To generate single spore lines of a population of bacterial parasite of root-knot nematode (RKN), Pasteuria penetrans, isolated from Florida and examine genotypic variation and virulence characteristics exist within the population. Six single spore lines (SSP), 16SSP, 17SSP, 18SSP, 25SSP, 26SSP and 30SSP were generated. Genetic variability was evaluated by comparing single-nucleotide polymorphisms (SNPs) in six protein-coding genes and the 16S rRNA gene. An average of one SNP was observed for every 69 bp in the 16S rRNA, whereas no SNPs were observed in the protein-coding sequences. Hierarchical cluster analysis of 16S rRNA sequences placed the clones into three distinct clades. Bio-efficacy analysis revealed significant heterogeneity in the level virulence and host specificity between the individual clones. The SNP markers developed to the 5' hypervariable region of the 16S rRNA gene may be useful in biotype differentiation within a population of P. penetrans. This study demonstrates an efficient method for generating single spore lines of P. penetrans and gives a deep insight into genetic heterogeneity and varying level of virulence exists within a population parasitizing a specific Meloidogyne sp. host. The results also suggest that the application of generalist spore lines in nematode management may achieve broad RKN control. © 2016 The Society for Applied Microbiology.

Statistical aspects of evolution under natural selection, with implications for the advantage of sexual reproduction.

PubMed

Crouch, Daniel J M

2017-10-27

The prevalence of sexual reproduction remains mysterious, as it poses clear evolutionary drawbacks compared to reproducing asexually. Several possible explanations exist, with one of the most likely being that finite population size causes linkage disequilibria to randomly generate and impede the progress of natural selection, and that these are eroded by recombination via sexual reproduction. Previous investigations have either analysed this phenomenon in detail for small numbers of loci, or performed population simulations for many loci. Here we present a quantitative genetic model for fitness, based on the Price Equation, in order to examine the theoretical consequences of randomly generated linkage disequilibria when there are many loci. In addition, most previous work has been concerned with the long-term consequences of deleterious linkage disequilibria for population fitness. The expected change in mean fitness between consecutive generations, a measure of short-term evolutionary success, is shown under random environmental influences to be related to the autocovariance in mean fitness between the generations, capturing the effects of stochastic forces such as genetic drift. Interaction between genetic drift and natural selection, due to randomly generated linkage disequilibria, is demonstrated to be one possible source of mean fitness autocovariance. This suggests a possible role for sexual reproduction in reducing the negative effects of genetic drift, thereby improving the short-term efficacy of natural selection. Copyright © 2017 Elsevier Ltd. All rights reserved.

Population growth enhances the mean fixation time of neutral mutations and the persistence of neutral variation.

PubMed

Waxman, D

2012-06-01

A fundamental result of population genetics states that a new mutation, at an unlinked neutral locus in a randomly mating diploid population, has a mean time of fixation of ∼4N(e) generations, where N(e) is the effective population size. This result is based on an assumption of fixed population size, which does not universally hold in natural populations. Here, we analyze such neutral fixations in populations of changing size within the framework of the diffusion approximation. General expressions are derived for the mean and variance of the fixation time in changing populations. Some explicit results are given for two cases: (i) the effective population size undergoes a sudden change, representing a sudden population expansion or a sudden bottleneck; (ii) the effective population changes linearly for a limited period of time and then remains constant. Additionally, a lower bound for the mean time of fixation is obtained for an effective population size that increases with time, and this is applied to exponentially growing populations. The results obtained in this work show, among other things, that for populations that increase in size, the mean time of fixation can be enhanced, sometimes substantially so, over 4N(e,0) generations, where N(e,0) is the effective population size at the time the mutation arises. Such an enhancement is associated with (i) an increased probability of neutral polymorphism in a population and (ii) an enhanced persistence of high-frequency neutral variation, which is the variation most likely to be observed.

Low incidence of inbreeding in a long-lived primate population isolated for 75 years.

PubMed

Widdig, Anja; Muniz, Laura; Minkner, Mirjam; Barth, Yvonne; Bley, Stefanie; Ruiz-Lambides, Angelina; Junge, Olaf; Mundry, Roger; Kulik, Lars

2017-01-01

When close relatives mate, offspring are expected to suffer fitness consequences due to inbreeding depression. Inbreeding has previously been quantified in two ways: using a sufficiently large panel of markers or deep and complete pedigrees over several generations. However, the application of both approaches is still limited by the challenge of compiling such data for species with long generation times, such as primates. Here, we assess inbreeding in rhesus macaques living on Cayo Santiago (Puerto Rico), a population genetically isolated since 1938, but descendant of a large set of presumably unrelated founders. Using comprehensive genetic data, we calculated inbreeding coefficients ( F ) for 2669 individuals with complete three generation pedigrees and 609 individuals with complete four generation pedigrees. We found that 0.79 and 7.39% of individuals had an F  > 0 when using data from three and four generation pedigrees, respectively. No evidence of an increase in inbreeding over the study period (up to 23 years) was found. Furthermore, the observed mean relatedness of breeding pairs differed significantly from the distribution of parental relatedness expected as simulated based on previous reproductive data, suggesting that kin generally avoid breeding with each other. Finally, inbreeding was not a predictor of early mortality measured as survival until weaning and sexual maturation, respectively. Our results remain consistent with three estimators of inbreeding (standardized heterozygosity, internal relatedness, and homozygosity by loci) using up to 42 highly polymorphic microsatellites for the same set of individuals. Together, our results demonstrate that close inbreeding may not be prevalent even in populations isolated over long periods when mechanisms of inbreeding avoidance can operate. When close relatives mate, offspring may suffer from such inbreeding, e.g., via lower survival and/or fertility. Using (i) a large panel of genetic markers and (ii) complete three or four generation pedigrees, respectively, we show that incidences of inbreeding in a long-lived primate population are rare, even after genetic isolation for 75 years. Moreover, our simulations suggest that kin in our population generally avoid breeding with each other. Finally, the few inbred individuals detected in our large sample did not suffer from lower survival. Given that many animal species face dramatic habitat loss combined with critical population declines, our study provides important implications for conservation biology in general and for population management in particular.

Exploring Agricultural Livelihood Transitions with an Agent-Based Virtual Laboratory: Global Forces to Local Decision-Making

PubMed Central

Magliocca, Nicholas R.; Brown, Daniel G.; Ellis, Erle C.

2013-01-01

Rural populations are undergoing rapid changes in both their livelihoods and land uses, with associated impacts on ecosystems, global biogeochemistry, and climate change. A primary challenge is, thus, to explain these shifts in terms of the actors and processes operating within a variety of land systems in order to understand how land users might respond locally to future changes in broader-scale environmental and economic conditions. Using ‘induced intensification’ theory as a benchmark, we develop a generalized agent-based model to investigate mechanistic explanations of relationships between agricultural intensity and population density, environmental suitability, and market influence. Land-use and livelihood decisions modeled from basic micro-economic theories generated spatial and temporal patterns of agricultural intensification consistent with predictions of induced intensification theory. Further, agent actions in response to conditions beyond those described by induced intensification theory were explored, revealing that interactions among environmental constraints, population pressure, and market influence may produce transitions to multiple livelihood regimes of varying market integration. The result is new hypotheses that could modify and enrich understanding of the classic relationship between agricultural intensity and population density. The strength of this agent-based model and the experimental results is the generalized form of the decision-making processes underlying land-use and livelihood transitions, creating the prospect of a virtual laboratory for systematically generating hypotheses of how agent decisions and interactions relate to observed land-use and livelihood patterns across diverse land systems. PMID:24039892

Phasic Firing in Vasopressin Cells: Understanding Its Functional Significance through Computational Models

PubMed Central

MacGregor, Duncan J.; Leng, Gareth

2012-01-01

Vasopressin neurons, responding to input generated by osmotic pressure, use an intrinsic mechanism to shift from slow irregular firing to a distinct phasic pattern, consisting of long bursts and silences lasting tens of seconds. With increased input, bursts lengthen, eventually shifting to continuous firing. The phasic activity remains asynchronous across the cells and is not reflected in the population output signal. Here we have used a computational vasopressin neuron model to investigate the functional significance of the phasic firing pattern. We generated a concise model of the synaptic input driven spike firing mechanism that gives a close quantitative match to vasopressin neuron spike activity recorded in vivo, tested against endogenous activity and experimental interventions. The integrate-and-fire based model provides a simple physiological explanation of the phasic firing mechanism involving an activity-dependent slow depolarising afterpotential (DAP) generated by a calcium-inactivated potassium leak current. This is modulated by the slower, opposing, action of activity-dependent dendritic dynorphin release, which inactivates the DAP, the opposing effects generating successive periods of bursting and silence. Model cells are not spontaneously active, but fire when perturbed by random perturbations mimicking synaptic input. We constructed one population of such phasic neurons, and another population of similar cells but which lacked the ability to fire phasically. We then studied how these two populations differed in the way that they encoded changes in afferent inputs. By comparison with the non-phasic population, the phasic population responds linearly to increases in tonic synaptic input. Non-phasic cells respond to transient elevations in synaptic input in a way that strongly depends on background activity levels, phasic cells in a way that is independent of background levels, and show a similar strong linearization of the response. These findings show large differences in information coding between the populations, and apparent functional advantages of asynchronous phasic firing. PMID:23093929

Pedigree-based estimation of covariance between dominance deviations and additive genetic effects in closed rabbit lines considering inbreeding and using a computationally simpler equivalent model.

PubMed

Fernández, E N; Legarra, A; Martínez, R; Sánchez, J P; Baselga, M

2017-06-01

Inbreeding generates covariances between additive and dominance effects (breeding values and dominance deviations). In this work, we developed and applied models for estimation of dominance and additive genetic variances and their covariance, a model that we call "full dominance," from pedigree and phenotypic data. Estimates with this model such as presented here are very scarce both in livestock and in wild genetics. First, we estimated pedigree-based condensed probabilities of identity using recursion. Second, we developed an equivalent linear model in which variance components can be estimated using closed-form algorithms such as REML or Gibbs sampling and existing software. Third, we present a new method to refer the estimated variance components to meaningful parameters in a particular population, i.e., final partially inbred generations as opposed to outbred base populations. We applied these developments to three closed rabbit lines (A, V and H) selected for number of weaned at the Polytechnic University of Valencia. Pedigree and phenotypes are complete and span 43, 39 and 14 generations, respectively. Estimates of broad-sense heritability are 0.07, 0.07 and 0.05 at the base versus 0.07, 0.07 and 0.09 in the final generations. Narrow-sense heritability estimates are 0.06, 0.06 and 0.02 at the base versus 0.04, 0.04 and 0.01 at the final generations. There is also a reduction in the genotypic variance due to the negative additive-dominance correlation. Thus, the contribution of dominance variation is fairly large and increases with inbreeding and (over)compensates for the loss in additive variation. In addition, estimates of the additive-dominance correlation are -0.37, -0.31 and 0.00, in agreement with the few published estimates and theoretical considerations. © 2017 Blackwell Verlag GmbH.

Alien Genetic Algorithm for Exploration of Search Space

NASA Astrophysics Data System (ADS)

Patel, Narendra; Padhiyar, Nitin

2010-10-01

Genetic Algorithm (GA) is a widely accepted population based stochastic optimization technique used for single and multi objective optimization problems. Various versions of modifications in GA have been proposed in last three decades mainly addressing two issues, namely increasing convergence rate and increasing probability of global minima. While both these. While addressing the first issue, GA tends to converge to a local optima and addressing the second issue corresponds the large computational efforts. Thus, to reduce the contradictory effects of these two aspects, we propose a modification in GA by adding an alien member in the population at every generation. Addition of an Alien member in the current population at every generation increases the probability of obtaining global minima at the same time maintaining higher convergence rate. With two test cases, we have demonstrated the efficacy of the proposed GA by comparing with the conventional GA.

Inference for multivariate regression model based on multiply imputed synthetic data generated via posterior predictive sampling

NASA Astrophysics Data System (ADS)

Moura, Ricardo; Sinha, Bimal; Coelho, Carlos A.

2017-06-01

The recent popularity of the use of synthetic data as a Statistical Disclosure Control technique has enabled the development of several methods of generating and analyzing such data, but almost always relying in asymptotic distributions and in consequence being not adequate for small sample datasets. Thus, a likelihood-based exact inference procedure is derived for the matrix of regression coefficients of the multivariate regression model, for multiply imputed synthetic data generated via Posterior Predictive Sampling. Since it is based in exact distributions this procedure may even be used in small sample datasets. Simulation studies compare the results obtained from the proposed exact inferential procedure with the results obtained from an adaptation of Reiters combination rule to multiply imputed synthetic datasets and an application to the 2000 Current Population Survey is discussed.

Human Neural Cell-Based Biosensor

DTIC Science & Technology

2011-03-11

following areas: (1) neural progenitor isolation from induced pluripotent stem cells , (2) directed differentiation of progenitors into dopaminergic...from induced pluripotent stem cells , (2) directed differentiation of progenitors into dopaminergic neurons, motoneurons and astrocytes using defined...progenitors from mixed populations, such as induced pluripotent stem cells (iPSCs). We also developed lentiviral based methods to generate iPSCs in

Next-Generation CBE: Designing Competency-Based Education for Underprepared College Learners

ERIC Educational Resources Information Center

Girardi, Amy; Crew, Rachel

2016-01-01

Competency-based education (CBE) is widely viewed as an innovative alternative to traditional higher education, yet most programs serve only a narrow slice of the postsecondary population. Few are intended for adults who need to boost basic skills in order to succeed in college coursework. However, if designed with the needs of a broader range of…

Stochastic foundations in nonlinear density-regulation growth

NASA Astrophysics Data System (ADS)

Méndez, Vicenç; Assaf, Michael; Horsthemke, Werner; Campos, Daniel

2017-08-01

In this work we construct individual-based models that give rise to the generalized logistic model at the mean-field deterministic level and that allow us to interpret the parameters of these models in terms of individual interactions. We also study the effect of internal fluctuations on the long-time dynamics for the different models that have been widely used in the literature, such as the theta-logistic and Savageau models. In particular, we determine the conditions for population extinction and calculate the mean time to extinction. If the population does not become extinct, we obtain analytical expressions for the population abundance distribution. Our theoretical results are based on WKB theory and the probability generating function formalism and are verified by numerical simulations.

Life tables and reproductive parameters of Lutzomyia spinicrassa (Diptera: Psychodidae) under laboratory conditions.

PubMed

Escovar, Jesús; Bello, Felio J; Morales, Alberto; Moncada, Ligia; Cárdenas, Estrella

2004-10-01

Lutzomyia spinicrassa is a vector of Leishmania braziliensis in Colombia. This sand fly has a broad geographical distribution in Colombia and Venezuela and it is found mainly in coffee plantations. Baseline biological growth data of L. spinicrassa were obtained under experimental laboratory conditions. The development time from egg to adult ranged from 59 to 121 days, with 12.74 weeks in average. Based on cohorts of 100 females, horizontal life table was constructed. The following predictive parameters were obtained: net rate of reproduction (8.4 females per cohort female), generation time (12.74 weeks), intrinsic rate of population increase (0.17), and finite rate of population increment (1.18). The reproductive value for each class age of the cohort females was calculated. Vertical life tables were elaborated and mortality was described for the generation obtained of the field cohort. In addition, for two successive generations, additive variance and heritability for fecundity were estimated.

Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy.

PubMed

Ahmad, Meraj; Sinha, Anubhav; Ghosh, Sreya; Kumar, Vikrant; Davila, Sonia; Yajnik, Chittaranjan S; Chandak, Giriraj R

2017-07-27

Imputation is a computational method based on the principle of haplotype sharing allowing enrichment of genome-wide association study datasets. It depends on the haplotype structure of the population and density of the genotype data. The 1000 Genomes Project led to the generation of imputation reference panels which have been used globally. However, recent studies have shown that population-specific panels provide better enrichment of genome-wide variants. We compared the imputation accuracy using 1000 Genomes phase 3 reference panel and a panel generated from genome-wide data on 407 individuals from Western India (WIP). The concordance of imputed variants was cross-checked with next-generation re-sequencing data on a subset of genomic regions. Further, using the genome-wide data from 1880 individuals, we demonstrate that WIP works better than the 1000 Genomes phase 3 panel and when merged with it, significantly improves the imputation accuracy throughout the minor allele frequency range. We also show that imputation using only South Asian component of the 1000 Genomes phase 3 panel works as good as the merged panel, making it computationally less intensive job. Thus, our study stresses that imputation accuracy using 1000 Genomes phase 3 panel can be further improved by including population-specific reference panels from South Asia.

Generative inference for cultural evolution.

PubMed

Kandler, Anne; Powell, Adam

2018-04-05

One of the major challenges in cultural evolution is to understand why and how various forms of social learning are used in human populations, both now and in the past. To date, much of the theoretical work on social learning has been done in isolation of data, and consequently many insights focus on revealing the learning processes or the distributions of cultural variants that are expected to have evolved in human populations. In population genetics, recent methodological advances have allowed a greater understanding of the explicit demographic and/or selection mechanisms that underlie observed allele frequency distributions across the globe, and their change through time. In particular, generative frameworks-often using coalescent-based simulation coupled with approximate Bayesian computation (ABC)-have provided robust inferences on the human past, with no reliance on a priori assumptions of equilibrium. Here, we demonstrate the applicability and utility of generative inference approaches to the field of cultural evolution. The framework advocated here uses observed population-level frequency data directly to establish the likely presence or absence of particular hypothesized learning strategies. In this context, we discuss the problem of equifinality and argue that, in the light of sparse cultural data and the multiplicity of possible social learning processes, the exclusion of those processes inconsistent with the observed data might be the most instructive outcome. Finally, we summarize the findings of generative inference approaches applied to a number of case studies.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'. © 2018 The Author(s).

Early induction of a prechondrogenic population allows efficient generation of stable chondrocytes from human induced pluripotent stem cells.

PubMed

Lee, Jieun; Taylor, Sarah E B; Smeriglio, Piera; Lai, Janice; Maloney, William J; Yang, Fan; Bhutani, Nidhi

2015-08-01

Regeneration of human cartilage is inherently inefficient; an abundant autologous source, such as human induced pluripotent stem cells (hiPSCs), is therefore attractive for engineering cartilage. We report a growth factor-based protocol for differentiating hiPSCs into articular-like chondrocytes (hiChondrocytes) within 2 weeks, with an overall efficiency >90%. The hiChondrocytes are stable and comparable to adult articular chondrocytes in global gene expression, extracellular matrix production, and ability to generate cartilage tissue in vitro and in immune-deficient mice. Molecular characterization identified an early SRY (sex-determining region Y) box (Sox)9(low) cluster of differentiation (CD)44(low)CD140(low) prechondrogenic population during hiPSC differentiation. In addition, 2 distinct Sox9-regulated gene networks were identified in the Sox9(low) and Sox9(high) populations providing novel molecular insights into chondrogenic fate commitment and differentiation. Our findings present a favorable method for generating hiPSC-derived articular-like chondrocytes. The hiChondrocytes are an attractive cell source for cartilage engineering because of their abundance, autologous nature, and potential to generate articular-like cartilage rather than fibrocartilage. In addition, hiChondrocytes can be excellent tools for modeling human musculoskeletal diseases in a dish and for rapid drug screening. © FASEB.

Intake-to-delivered-energy ratios for central station and distributed electricity generation in California

NASA Astrophysics Data System (ADS)

Heath, Garvin A.; Nazaroff, William W.

In previous work, we showed that the intake fraction (iF) for nonreactive primary air pollutants was 20 times higher in central tendency for small-scale, urban-sited distributed electricity generation (DG) sources than for large-scale, central station (CS) power plants in California [Heath, G.A., Granvold, P.W., Hoats, A.S., Nazaroff, W.W., 2006. Intake fraction assessment of the air pollutant exposure implications of a shift toward distributed electricity generation. Atmospheric Environment 40, 7164-7177]. The present paper builds on that study, exploring pollutant- and technology-specific aspects of population inhalation exposure from electricity generation. We compare California's existing CS-based system to one that is more reliant on DG units sited in urban areas. We use Gaussian plume modeling and a GIS-based exposure analysis to assess 25 existing CSs and 11 DG sources hypothetically located in the downtowns of California's most populous cities. We consider population intake of three pollutants—PM 2.5, NO x and formaldehyde—directly emitted by five DG technologies—natural gas (NG)-fired turbines, NG internal combustion engines (ICE), NG microturbines, diesel ICEs, and fuel cells with on-site NG reformers. We also consider intake of these pollutants from existing CS facilities, most of which use large NG turbines, as well as from hypothetical facilities located at these same sites but meeting California's best-available control technology standards. After systematically exploring the sensitivity of iF to pollutant decay rate, the iFs for each of the three pollutants for all DG and CS cases are estimated. To efficiently compare the pollutant- and technology-specific exposure potential on an appropriate common basis, a new metric is introduced and evaluated: the intake-to-delivered-energy ratio (IDER). The IDER expresses the mass of pollutant inhaled by an exposed population owing to emissions from an electricity generation unit per quantity of electric energy delivered to the place of use. We find that the central tendency of IDER is much greater for almost every DG technology evaluated than for existing CS facilities in California.

RNAbrowse: RNA-Seq de novo assembly results browser.

PubMed

Mariette, Jérôme; Noirot, Céline; Nabihoudine, Ibounyamine; Bardou, Philippe; Hoede, Claire; Djari, Anis; Cabau, Cédric; Klopp, Christophe

2014-01-01

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse.

Retention in the allied health workforce: boomers, generation X, and generation Y.

PubMed

Dodd, Jenny; Saggers, Sherry; Wildy, Helen

2009-01-01

The recruitment and retention of allied health workers present challenges for organizations in Australia and internationally. Australia, in common with other developed countries, faces the prospect of a rapidly aging population and the high turnover of younger allied health workers (the majority of whom are female) from employing organizations. Emphases on the individual characteristics of Boomer, Generation X, and Generation Y workers may provide a useful starting base for recruitment and retention strategies, but our study shows that these need to be contextualized within broader political, social, and structural factors that take account of gender and the changing needs of workers over their life span.

India Allele Finder: a web-based annotation tool for identifying common alleles in next-generation sequencing data of Indian origin.

PubMed

Zhang, Jimmy F; James, Francis; Shukla, Anju; Girisha, Katta M; Paciorkowski, Alex R

2017-06-27

We built India Allele Finder, an online searchable database and command line tool, that gives researchers access to variant frequencies of Indian Telugu individuals, using publicly available fastq data from the 1000 Genomes Project. Access to appropriate population-based genomic variant annotation can accelerate the interpretation of genomic sequencing data. In particular, exome analysis of individuals of Indian descent will identify population variants not reflected in European exomes, complicating genomic analysis for such individuals. India Allele Finder offers improved ease-of-use to investigators seeking to identify and annotate sequencing data from Indian populations. We describe the use of India Allele Finder to identify common population variants in a disease quartet whole exome dataset, reducing the number of candidate single nucleotide variants from 84 to 7. India Allele Finder is freely available to investigators to annotate genomic sequencing data from Indian populations. Use of India Allele Finder allows efficient identification of population variants in genomic sequencing data, and is an example of a population-specific annotation tool that simplifies analysis and encourages international collaboration in genomics research.

Population size predicts technological complexity in Oceania

PubMed Central

Kline, Michelle A.; Boyd, Robert

2010-01-01

Much human adaptation depends on the gradual accumulation of culturally transmitted knowledge and technology. Recent models of this process predict that large, well-connected populations will have more diverse and complex tool kits than small, isolated populations. While several examples of the loss of technology in small populations are consistent with this prediction, it found no support in two systematic quantitative tests. Both studies were based on data from continental populations in which contact rates were not available, and therefore these studies do not provide a test of the models. Here, we show that in Oceania, around the time of early European contact, islands with small populations had less complicated marine foraging technology. This finding suggests that explanations of existing cultural variation based on optimality models alone are incomplete because demography plays an important role in generating cumulative cultural adaptation. It also indicates that hominin populations with similar cognitive abilities may leave very different archaeological records, a conclusion that has important implications for our understanding of the origin of anatomically modern humans and their evolved psychology. PMID:20392733

Time delay generation at high frequency using SOA based slow and fast light.

PubMed

Berger, Perrine; Bourderionnet, Jérôme; Bretenaker, Fabien; Dolfi, Daniel; Alouini, Mehdi

2011-10-24

We show how Up-converted Coherent Population Oscillations (UpCPO) enable to get rid of the intrinsic limitation of the carrier lifetime, leading to the generation of time delays at any high frequencies in a single SOA device. The linear dependence of the RF phase shift with respect to the RF frequency is theoretically predicted and experimentally evidenced at 16 and 35 GHz. © 2011 Optical Society of America

Genetic polymorphisms of nine X-STR loci in four population groups from Inner Mongolia, China.

PubMed

Hou, Qiao-Fang; Yu, Bin; Li, Sheng-Bin

2007-02-01

Nine short tandem repeat (STR) markers on the X chromosome (DXS101, DXS6789, DXS6799, DXS6804, DXS7132, DXS7133, DXS7423, DXS8378, and HPRTB) were analyzed in four population groups (Mongol, Ewenki, Oroqen, and Daur) from Inner Mongolia, China, in order to learn about the genetic diversity, forensic suitability, and possible genetic affinities of the populations. Frequency estimates, Hardy-Weinberg equilibrium, and other parameters of forensic interest were computed. The results revealed that the nine markers have a moderate degree of variability in the population groups. Most heterozygosity values for the nine loci range from 0.480 to 0.891, and there are evident differences of genetic variability among the populations. A UPGMA tree constructed on the basis of the generated data shows very low genetic distance between Mongol and Han (Xi'an) populations. Our results based on genetic distance analysis are consistent with the results of earlier studies based on linguistics and the immigration history and origin of these populations. The minisatellite loci on the X chromosome studied here are not only useful in showing significant genetic variation between the populations, but also are suitable for human identity testing among Inner Mongolian populations.

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

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

PubMed Central

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

2015-01-01

Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (FROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13–0.91 and 0.12–0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations. PMID:26074948

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

PubMed

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

2015-01-01

Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (F ROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13-0.91 and 0.12-0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.

Trans-generational influences of sulfamethoxazole on lifespan, reproduction and population growth of Caenorhabditis elegans.

PubMed

Yu, Zhenyang; Sun, Guohua; Liu, Yanjun; Yin, Daqiang; Zhang, Jing

2017-01-01

Trans-generational effects are increasingly used to indicate long-term influences of environmental pollutants. However, such studies can be complex and yield inconclusive results. In this study, the trans-generational effects of sulfamethoxazole (SMX) on Caenorhabditis elegans on lifespan, reproduction and population growth were tested for 7 consecutive generations, which included gestating generation (F0), embryo-exposed generation (F1), germline-exposed generation (F2), the first non-exposed generation (F3) and the three following generations (F4-F6). Results showed that lifespan was significantly affected by embryo exposure (F1) at 400µm SMX with a value as low as 47% of the control. The reproduction (a total brood size as 49% of the control) and population growth (81% of the control) were significantly affected in germline exposure (F2). Lifespan and reproduction were severely inhibited in non-exposed generations, confirming the real trans-generational effects. Notably, initial reproduction and reproduction duration showed opposite generation-related changes, indicating their interplay in the overall brood size. The population growth rate was well correlated with median lethal time, brood size and initial reproduction, which indicated that the population would increase when the nematodes lived longer and reproduced more offspring within shorter duration. Copyright © 2016 Elsevier Inc. All rights reserved.

First genealogy for a wild marine fish population reveals multigenerational philopatry.

PubMed

Salles, Océane C; Pujol, Benoit; Maynard, Jeffrey A; Almany, Glenn R; Berumen, Michael L; Jones, Geoffrey P; Saenz-Agudelo, Pablo; Srinivasan, Maya; Thorrold, Simon R; Planes, Serge

2016-11-15

Natal philopatry, the return of individuals to their natal area for reproduction, has advantages and disadvantages for animal populations. Natal philopatry may generate local genetic adaptation, but it may also increase the probability of inbreeding that can compromise persistence. Although natal philopatry is well documented in anadromous fishes, marine fish may also return to their birth site to spawn. How philopatry shapes wild fish populations is, however, unclear because it requires constructing multigenerational pedigrees that are currently lacking for marine fishes. Here we present the first multigenerational pedigree for a marine fish population by repeatedly genotyping all individuals in a population of the orange clownfish (Amphiprion percula) at Kimbe Island (Papua New Guinea) during a 10-y period. Based on 2927 individuals, our pedigree analysis revealed that longitudinal philopatry was recurrent over five generations. Progeny tended to settle close to their parents, with related individuals often sharing the same colony. However, successful inbreeding was rare, and genetic diversity remained high, suggesting occasional inbreeding does not impair local population persistence. Local reproductive success was dependent on the habitat larvae settled into, rather than the habitat they came from. Our study suggests that longitudinal philopatry can influence both population replenishment and local adaptation of marine fishes. Resolving multigenerational pedigrees during a relatively short period, as we present here, provides a framework for assessing the ability of marine populations to persist and adapt to accelerating climate change.

First genealogy for a wild marine fish population reveals multigenerational philopatry

PubMed Central

Salles, Océane C.; Pujol, Benoit; Maynard, Jeffrey A.; Almany, Glenn R.; Berumen, Michael L.; Jones, Geoffrey P.; Saenz-Agudelo, Pablo; Srinivasan, Maya; Thorrold, Simon R.; Planes, Serge

2016-01-01

Natal philopatry, the return of individuals to their natal area for reproduction, has advantages and disadvantages for animal populations. Natal philopatry may generate local genetic adaptation, but it may also increase the probability of inbreeding that can compromise persistence. Although natal philopatry is well documented in anadromous fishes, marine fish may also return to their birth site to spawn. How philopatry shapes wild fish populations is, however, unclear because it requires constructing multigenerational pedigrees that are currently lacking for marine fishes. Here we present the first multigenerational pedigree for a marine fish population by repeatedly genotyping all individuals in a population of the orange clownfish (Amphiprion percula) at Kimbe Island (Papua New Guinea) during a 10-y period. Based on 2927 individuals, our pedigree analysis revealed that longitudinal philopatry was recurrent over five generations. Progeny tended to settle close to their parents, with related individuals often sharing the same colony. However, successful inbreeding was rare, and genetic diversity remained high, suggesting occasional inbreeding does not impair local population persistence. Local reproductive success was dependent on the habitat larvae settled into, rather than the habitat they came from. Our study suggests that longitudinal philopatry can influence both population replenishment and local adaptation of marine fishes. Resolving multigenerational pedigrees during a relatively short period, as we present here, provides a framework for assessing the ability of marine populations to persist and adapt to accelerating climate change. PMID:27799530

Comparison of facial morphologies between adult Chinese and Houstonian Caucasian populations using three-dimensional imaging.

PubMed

Wirthlin, J; Kau, C H; English, J D; Pan, F; Zhou, H

2013-09-01

The objective of this study was to compare the facial morphologies of an adult Chinese population to a Houstonian white population. Three-dimensional (3D) images were acquired via a commercially available stereophotogrammetric camera system, 3dMDface™. Using the system, 100 subjects from a Houstonian population and 71 subjects from a Chinese population were photographed. A complex mathematical algorithm was performed to generate a composite facial average (one for males and one for females) for each subgroup. The computer-generated facial averages were then superimposed based on a previously validated superimposition method. The facial averages were evaluated for differences. Distinct facial differences were evident between the subgroups evaluated. These areas included the nasal tip, the peri-orbital area, the malar process, the labial region, the forehead, and the chin. Overall, the mean facial difference between the Chinese and Houstonian female averages was 2.73±2.20mm, while the difference between the Chinese and Houstonian males was 2.83±2.20mm. The percent similarity for the female population pairings and male population pairings were 10.45% and 12.13%, respectively. The average adult Chinese and Houstonian faces possess distinct differences. Different populations and ethnicities have different facial features and averages that should be considered in the planning of treatment. Copyright © 2013 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Ecological extension of the theory of evolution by natural selection from a perspective of Western and Eastern holistic philosophy.

PubMed

Nakajima, Toshiyuki

2017-12-01

Evolution by natural selection requires the following conditions: (1) a particular selective environment; (2) variation of traits in the population; (3) differential survival/reproduction among the types of organisms; and (4) heritable traits. However, the traditional (standard) model does not clearly explain how and why these conditions are generated or determined. What generates a selective environment? What generates new types? How does a certain type replace, or coexist with, others? In this paper, based on the holistic philosophy of Western and Eastern traditions, I focus on the ecosystem as a higher-level system and generator of conditions that induce the evolution of component populations; I also aim to identify the ecosystem processes that generate those conditions. In particular, I employ what I call the scientific principle of dependent-arising (SDA), which is tailored for scientific use and is based on Buddhism principle called "pratītya-samutpāda" in Sanskrit. The SDA principle asserts that there exists a higher-level system, or entity, which includes a focal process of a system as a part within it; this determines or generates the conditions required for the focal process to work in a particular way. I conclude that the ecosystem generates (1) selective environments for component species through ecosystem dynamics; (2) new genetic types through lateral gene transfer, hybridization, and symbiogenesis among the component species of the ecosystem; (3) mechanistic processes of replacement of an old type with a new one. The results of this study indicate that the ecological extension of the theoretical model of adaptive evolution is required for better understanding of adaptive evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Determination of HIV Status in African Adults With Discordant HIV Rapid Tests.

PubMed

Fogel, Jessica M; Piwowar-Manning, Estelle; Donohue, Kelsey; Cummings, Vanessa; Marzinke, Mark A; Clarke, William; Breaud, Autumn; Fiamma, Agnès; Donnell, Deborah; Kulich, Michal; Mbwambo, Jessie K K; Richter, Linda; Gray, Glenda; Sweat, Michael; Coates, Thomas J; Eshleman, Susan H

2015-08-01

In resource-limited settings, HIV infection is often diagnosed using 2 rapid tests. If the results are discordant, a third tie-breaker test is often used to determine HIV status. This study characterized samples with discordant rapid tests and compared different testing strategies for determining HIV status in these cases. Samples were previously collected from 173 African adults in a population-based survey who had discordant rapid test results. Samples were classified as HIV positive or HIV negative using a rigorous testing algorithm that included two fourth-generation tests, a discriminatory test, and 2 HIV RNA tests. Tie-breaker tests were evaluated, including rapid tests (1 performed in-country), a third-generation enzyme immunoassay, and two fourth-generation tests. Selected samples were further characterized using additional assays. Twenty-nine samples (16.8%) were classified as HIV positive and 24 of those samples (82.8%) had undetectable HIV RNA. Antiretroviral drugs were detected in 1 sample. Sensitivity was 8.3%-43% for the rapid tests; 24.1% for the third-generation enzyme immunoassay; 95.8% and 96.6% for the fourth-generation tests. Specificity was lower for the fourth-generation tests than the other tests. Accuracy ranged from 79.5% to 91.3%. In this population-based survey, most HIV-infected adults with discordant rapid tests were virally suppressed without antiretroviral drugs. Use of individual assays as tie-breaker tests was not a reliable method for determining HIV status in these individuals. More extensive testing algorithms that use a fourth-generation screening test with a discriminatory test and HIV RNA test are preferable for determining HIV status in these cases.

Ex vivo generation of dendritic cells from cryopreserved, post-induction chemotherapy, mobilized leukapheresis from pediatric patients with medulloblastoma.

PubMed

Nair, Smita K; Driscoll, Timothy; Boczkowski, David; Schmittling, Robert; Reynolds, Renee; Johnson, Laura A; Grant, Gerald; Fuchs, Herbert; Bigner, Darell D; Sampson, John H; Gururangan, Sridharan; Mitchell, Duane A

2015-10-01

Generation of patient-derived, autologous dendritic cells (DCs) is a critical component of cancer immunotherapy with ex vivo-generated, tumor antigen-loaded DCs. An important factor in the ability to generate DCs is the potential impact of prior therapies on DC phenotype and function. We investigated the ability to generate DCs using cells harvested from pediatric patients with medulloblastoma for potential evaluation of DC-RNA based vaccination approach in this patient population. Cells harvested from medulloblastoma patient leukapheresis following induction chemotherapy and granulocyte colony stimulating factor mobilization were cryopreserved prior to use in DC generation. DCs were generated from the adherent CD14+ monocytes using standard procedures and analyzed for cell recovery, phenotype and function. To summarize, 4 out of 5 patients (80%) had sufficient monocyte recovery to permit DC generation, and we were able to generate DCs from 3 out of these 4 patient samples (75%). Overall, we successfully generated DCs that met phenotypic requisites for DC-based cancer therapy from 3 out of 5 (60%) patient samples and met both phenotypic and functional requisites from 2 out of 5 (40%) patient samples. This study highlights the potential to generate functional DCs for further clinical treatments from refractory patients that have been heavily pretreated with myelosuppressive chemotherapy. Here we demonstrate the utility of evaluating the effect of the currently employed standard-of-care therapies on the ex vivo generation of DCs for DC-based clinical studies in cancer patients.

Concordance of the ForenSeq™ system and characterisation of sequence-specific autosomal STR alleles across two major population groups.

PubMed

Devesse, Laurence; Ballard, David; Davenport, Lucinda; Riethorst, Immy; Mason-Buck, Gabriella; Syndercombe Court, Denise

2018-05-01

By using sequencing technology to genotype loci of forensic interest it is possible to simultaneously target autosomal, X and Y STRs as well as identity, ancestry and phenotypic informative SNPs, resulting in a breadth of data obtained from a single run that is considerable when compared to that generated with standard technologies. It is important however that this information aligns with the genotype data currently obtained using commercially available kits for CE-based investigations such that results are compatible with existing databases and hence can be of use to the forensic community. In this work, 400 samples were typed using commercially available STR kits and CE, as well as using the Ilumina ForenSeq™ DNA Signature Prep Kit and MiSeq ® FGx to assess concordance of autosomal STRs and population variability. Results show a concordance rate between the two technologies exceeding 99.98% while numerous novel sequence based alleles are described. In order to make use of the sequence variation observed, sequence specific allele frequencies were generated for White British and British Chinese populations. Copyright © 2017 Elsevier B.V. All rights reserved.

Leveraging Hierarchical Population Structure in Discrete Association Studies

PubMed Central

Carlson, Jonathan; Kadie, Carl; Mallal, Simon; Heckerman, David

2007-01-01

Population structure can confound the identification of correlations in biological data. Such confounding has been recognized in multiple biological disciplines, resulting in a disparate collection of proposed solutions. We examine several methods that correct for confounding on discrete data with hierarchical population structure and identify two distinct confounding processes, which we call coevolution and conditional influence. We describe these processes in terms of generative models and show that these generative models can be used to correct for the confounding effects. Finally, we apply the models to three applications: identification of escape mutations in HIV-1 in response to specific HLA-mediated immune pressure, prediction of coevolving residues in an HIV-1 peptide, and a search for genotypes that are associated with bacterial resistance traits in Arabidopsis thaliana. We show that coevolution is a better description of confounding in some applications and conditional influence is better in others. That is, we show that no single method is best for addressing all forms of confounding. Analysis tools based on these models are available on the internet as both web based applications and downloadable source code at http://atom.research.microsoft.com/bio/phylod.aspx. PMID:17611623

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

Effects of number of training generations on genomic prediction for various traits in a layer chicken population.

PubMed

Weng, Ziqing; Wolc, Anna; Shen, Xia; Fernando, Rohan L; Dekkers, Jack C M; Arango, Jesus; Settar, Petek; Fulton, Janet E; O'Sullivan, Neil P; Garrick, Dorian J

2016-03-19

Genomic estimated breeding values (GEBV) based on single nucleotide polymorphism (SNP) genotypes are widely used in animal improvement programs. It is typically assumed that the larger the number of animals is in the training set, the higher is the prediction accuracy of GEBV. The aim of this study was to quantify genomic prediction accuracy depending on the number of ancestral generations included in the training set, and to determine the optimal number of training generations for different traits in an elite layer breeding line. Phenotypic records for 16 traits on 17,793 birds were used. All parents and some selection candidates from nine non-overlapping generations were genotyped for 23,098 segregating SNPs. An animal model with pedigree relationships (PBLUP) and the BayesB genomic prediction model were applied to predict EBV or GEBV at each validation generation (progeny of the most recent training generation) based on varying numbers of immediately preceding ancestral generations. Prediction accuracy of EBV or GEBV was assessed as the correlation between EBV and phenotypes adjusted for fixed effects, divided by the square root of trait heritability. The optimal number of training generations that resulted in the greatest prediction accuracy of GEBV was determined for each trait. The relationship between optimal number of training generations and heritability was investigated. On average, accuracies were higher with the BayesB model than with PBLUP. Prediction accuracies of GEBV increased as the number of closely-related ancestral generations included in the training set increased, but reached an asymptote or slightly decreased when distant ancestral generations were used in the training set. The optimal number of training generations was 4 or more for high heritability traits but less than that for low heritability traits. For less heritable traits, limiting the training datasets to individuals closely related to the validation population resulted in the best predictions. The effect of adding distant ancestral generations in the training set on prediction accuracy differed between traits and the optimal number of necessary training generations is associated with the heritability of traits.

The Cohesive Population Genetics of Molecular Drive

PubMed Central

Ohta, Tomoko; Dover, Gabriel A.

1984-01-01

The long-term population genetics of multigene families is influenced by several biased and unbiased mechanisms of nonreciprocal exchanges (gene conversion, unequal exchanges, transposition) between member genes, often distributed on several chromosomes. These mechanisms cause fluctuations in the copy number of variant genes in an individual and lead to a gradual replacement of an original family of n genes (A) in N number of individuals by a variant gene (a). The process for spreading a variant gene through a family and through a population is called molecular drive. Consideration of the known slow rates of nonreciprocal exchanges predicts that the population variance in the copy number of gene a per individual is small at any given generation during molecular drive. Genotypes at a given generation are expected only to range over a small section of all possible genotypes from one extreme (n number of A) to the other (n number of a). A theory is developed for estimating the size of the population variance by using the concept of identity coefficients. In particular, the variance in the course of spreading of a single mutant gene of a multigene family was investigated in detail, and the theory of identity coefficients at the state of steady decay of genetic variability proved to be useful. Monte Carlo simulations and numerical analysis based on realistic rates of exchange in families of known size reveal the correctness of the theoretical prediction and also assess the effect of bias in turnover. The population dynamics of molecular drive in gradually increasing the mean copy number of a variant gene without the generation of a large variance (population cohesion) is of significance regarding potential interactions between natural selection and molecular drive. PMID:6500260

The cohesive population genetics of molecular drive.

PubMed

Ohta, T; Dover, G A

1984-10-01

The long-term population genetics of multigene families is influenced by several biased and unbiased mechanisms of nonreciprocal exchanges (gene conversion, unequal exchanges, transposition) between member genes, often distributed on several chromosomes. These mechanisms cause fluctuations in the copy number of variant genes in an individual and lead to a gradual replacement of an original family of n genes (A) in N number of individuals by a variant gene (a). The process for spreading a variant gene through a family and through a population is called molecular drive. Consideration of the known slow rates of nonreciprocal exchanges predicts that the population variance in the copy number of gene a per individual is small at any given generation during molecular drive. Genotypes at a given generation are expected only to range over a small section of all possible genotypes from one extreme (n number of A) to the other (n number of a). A theory is developed for estimating the size of the population variance by using the concept of identity coefficients. In particular, the variance in the course of spreading of a single mutant gene of a multigene family was investigated in detail, and the theory of identity coefficients at the state of steady decay of genetic variability proved to be useful. Monte Carlo simulations and numerical analysis based on realistic rates of exchange in families of known size reveal the correctness of the theoretical prediction and also assess the effect of bias in turnover. The population dynamics of molecular drive in gradually increasing the mean copy number of a variant gene without the generation of a large variance (population cohesion) is of significance regarding potential interactions between natural selection and molecular drive.

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

Forest-based biomass supply in Massachusetts: How much is there and how much is available

Treesearch

Marla Markowski-Lindsay; Paul Catanzaro; David Damery; David B. Kittredge; Brett J. Butler; Thomas Stevens

2012-01-01

Forest owners in Massachusetts (U.S.) live in a densely populated state and near forestland that is under pressure of development and characterized by small parcel size. Forest-based biomass harvesting in Massachusetts is a renewable energy topic generating a great deal of discussion among all constituents. To provide perspective on these discussions, our analysis asks...

Differences between genomic-based and pedigree-based relationships in a chicken population, as a function of quality control and pedigree links among individuals.

PubMed

Wang, H; Misztal, I; Legarra, A

2014-12-01

This work studied differences between expected (calculated from pedigree) and realized (genomic, from markers) relationships in a real population, the influence of quality control on these differences, and their fit to current theory. Data included 4940 pure line chickens across five generations genotyped for 57,636 SNP. Pedigrees (5762 animals) were available for the five generations, pedigree starting on the first one. Three levels of quality control were used. With no quality control, mean difference between realized and expected relationships for different type of relationships was ≤ 0.04 with standard deviation ≤ 0.10. With strong quality control (call rate ≥ 0.9, parent-progeny conflicts, minor allele frequency and use of only autosomal chromosomes), these numbers reduced to ≤ 0.02 and ≤ 0.04, respectively. While the maximum difference was 1.02 with the complete data, it was only 0.18 with the latest three generations of genotypes (but including all pedigrees). Variation of expected minus realized relationships agreed with theoretical developments and suggests an effective number of loci of 70 for this population. When the pedigree is complete and as deep as the genotypes, the standard deviation of difference between the expected and realized relationships is around 0.04, all categories confounded. Standard deviation of differences larger than 0.10 suggests bad quality control, mistakes in pedigree recording or genotype labelling, or insufficient depth of pedigree. © 2014 Blackwell Verlag GmbH.

Comparing predictions of extinction risk using models and subjective judgement

NASA Astrophysics Data System (ADS)

McCarthy, Michael A.; Keith, David; Tietjen, Justine; Burgman, Mark A.; Maunder, Mark; Master, Larry; Brook, Barry W.; Mace, Georgina; Possingham, Hugh P.; Medellin, Rodrigo; Andelman, Sandy; Regan, Helen; Regan, Tracey; Ruckelshaus, Mary

2004-10-01

Models of population dynamics are commonly used to predict risks in ecology, particularly risks of population decline. There is often considerable uncertainty associated with these predictions. However, alternatives to predictions based on population models have not been assessed. We used simulation models of hypothetical species to generate the kinds of data that might typically be available to ecologists and then invited other researchers to predict risks of population declines using these data. The accuracy of the predictions was assessed by comparison with the forecasts of the original model. The researchers used either population models or subjective judgement to make their predictions. Predictions made using models were only slightly more accurate than subjective judgements of risk. However, predictions using models tended to be unbiased, while subjective judgements were biased towards over-estimation. Psychology literature suggests that the bias of subjective judgements is likely to vary somewhat unpredictably among people, depending on their stake in the outcome. This will make subjective predictions more uncertain and less transparent than those based on models.

Retention of Ag-specific memory CD4+ T cells in the draining lymph node indicates lymphoid tissue resident memory populations.

PubMed

Marriott, Clare L; Dutton, Emma E; Tomura, Michio; Withers, David R

2017-05-01

Several different memory T-cell populations have now been described based upon surface receptor expression and migratory capabilities. Here we have assessed murine endogenous memory CD4 + T cells generated within a draining lymph node and their subsequent migration to other secondary lymphoid tissues. Having established a model response targeting a specific peripheral lymph node, we temporally labelled all the cells within draining lymph node using photoconversion. Tracking of photoconverted and non-photoconverted Ag-specific CD4 + T cells revealed the rapid establishment of a circulating memory population in all lymph nodes within days of immunisation. Strikingly, a resident memory CD4 + T cell population became established in the draining lymph node and persisted for several months in the absence of detectable migration to other lymphoid tissue. These cells most closely resembled effector memory T cells, usually associated with circulation through non-lymphoid tissue, but here, these cells were retained in the draining lymph node. These data indicate that lymphoid tissue resident memory CD4 + T-cell populations are generated in peripheral lymph nodes following immunisation. © 2017 The Authors. European Journal of Immunology published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Consequences of harvesting for genetic diversity in American ginseng (Panax quinquefolius L.): A simulation study

USGS Publications Warehouse

Cruse-Sanders, J. M.; Hamrick, J.L.; Ahumada, J.A.

2005-01-01

American ginseng, Panax quinquefolius L., is one of the most heavily traded medicinal plants in North America. The effect of harvest on genetic diversity in ginseng was measured with a single generation culling simulation program. Culling scenarios included random harvest at varying levels, legal limit random harvest and legal limit mature plant harvest. The legal limit was determined by the proportion of legally harvestable plants per population (% mature plants per population). Random harvest at varying levels resulted in significant loss of genetic diversity, especially allelic richness. Relative to initial levels, average within-population genetic diversity (H e) was significantly lower when plants were culled randomly at the legal limit (Mann-Whitney U = 430, p < 0.001) or when only mature plants were culled (Mann-Whitney U = 394, p < 0.01). Within-population genetic diversity was significantly higher with legal limit mature plant harvest (H e = 0.068) than when plants were culled randomly at the legal limit (H e = 0.064; U = 202, p < 0.01). Based on these simulations of harvest over one generation, we recommend that harvesting fewer than the proportion of mature plants could reduce the negative genetic effects of harvest on ginseng populations. ?? Springer 2005.

Individual-based models for adaptive diversification in high-dimensional phenotype spaces.

PubMed

Ispolatov, Iaroslav; Madhok, Vaibhav; Doebeli, Michael

2016-02-07

Most theories of evolutionary diversification are based on equilibrium assumptions: they are either based on optimality arguments involving static fitness landscapes, or they assume that populations first evolve to an equilibrium state before diversification occurs, as exemplified by the concept of evolutionary branching points in adaptive dynamics theory. Recent results indicate that adaptive dynamics may often not converge to equilibrium points and instead generate complicated trajectories if evolution takes place in high-dimensional phenotype spaces. Even though some analytical results on diversification in complex phenotype spaces are available, to study this problem in general we need to reconstruct individual-based models from the adaptive dynamics generating the non-equilibrium dynamics. Here we first provide a method to construct individual-based models such that they faithfully reproduce the given adaptive dynamics attractor without diversification. We then show that a propensity to diversify can be introduced by adding Gaussian competition terms that generate frequency dependence while still preserving the same adaptive dynamics. For sufficiently strong competition, the disruptive selection generated by frequency-dependence overcomes the directional evolution along the selection gradient and leads to diversification in phenotypic directions that are orthogonal to the selection gradient. Copyright © 2015 Elsevier Ltd. All rights reserved.

Historical pedigree reconstruction from extant populations using PArtitioning of RElatives (PREPARE).

PubMed

Shem-Tov, Doron; Halperin, Eran

2014-06-01

Recent technological improvements in the field of genetic data extraction give rise to the possibility of reconstructing the historical pedigrees of entire populations from the genotypes of individuals living today. Current methods are still not practical for real data scenarios as they have limited accuracy and assume unrealistic assumptions of monogamy and synchronized generations. In order to address these issues, we develop a new method for pedigree reconstruction, [Formula: see text], which is based on formulations of the pedigree reconstruction problem as variants of graph coloring. The new formulation allows us to consider features that were overlooked by previous methods, resulting in a reconstruction of up to 5 generations back in time, with an order of magnitude improvement of false-negatives rates over the state of the art, while keeping a lower level of false positive rates. We demonstrate the accuracy of [Formula: see text] compared to previous approaches using simulation studies over a range of population sizes, including inbred and outbred populations, monogamous and polygamous mating patterns, as well as synchronous and asynchronous mating.

Initial characterisation of low and high seed dormancy populations of Lolium rigidum produced by repeated selection.

PubMed

Goggin, Danica E; Emery, R J Neil; Powles, Stephen B; Steadman, Kathryn J

2010-10-15

The physiological and biochemical bases of seed dormancy in Lolium rigidum (annual ryegrass) are largely unknown, and study of this process is complicated by the outcrossing nature of the species and the strong influence of environment on seed dormancy. In order to identify heritable biochemical factors contributing to seed dormancy in L. rigidum, seeds from a field-collected population were used to select sub-populations with consistently low or high seed dormancy over four generations. Low-dormancy seeds showed constitutive alpha-amylase activity prior to imbibition, higher concentrations of polyphenols and cis-zeatin, and lower abscisic acid and cis-zeatin riboside concentrations than high-dormancy seeds. Selection for high dormancy was associated with a reduction in response to dark-stratification for 21d at 20 degrees C (an effective means of releasing dormancy in the original, unselected population) over successive generations, but fluridone remained effective in breaking dormancy. Crossing of low- and high-dormancy populations indicated that dormancy level was not dependent upon the maternal genotype of the seed, and that the constitutive alpha-amylase activity and high seed anthocyanin concentrations characteristic of the low-dormancy populations were not correlated to high basal germination ability. Copyright (c) 2010 Elsevier GmbH. All rights reserved.

An Ecohydrological Approach to the Resiliency and Stability of Ecosystems

NASA Astrophysics Data System (ADS)

Peña Alzate, S.; Canon Barriga, J. E.

2013-12-01

We introduce a simplified ecohydrological model to quantitatively assess the resiliency and stability of ecosystems. The proposed model couples a hydrological soil moisture balance with a set of spatiotemporal dynamics of systems and agent-based algorithms to represent the interactions among several plant populations in a gridded area under different water, soil and temperature constraints. The model also allows disturbances, representing mostly the effects of deforestation practices. The simulated ecosystem, composed by a set of plant populations, includes allometric rules (i.e., power laws for generational and reproductive times, linear approximations for water and temperature gains, losses and optimal values and a set of intra and interspecific interaction rules based on high, optimal and low competition responses among the populations). Disturbances are determined by a clearance of populations in a defined area within the model's domain. The effects of climate variability can be also incorporated through precipitation and temperature time series that exhibit trends and heteroskedasticity. Resiliency and stability are calculated with modified indices that are used in hydrology, in this case to determine the ability of the ecosystem to recover from a disturbance. The model represents different types of plant phenotypes showing exponential growth in the first steps of the simulations. The indices, evaluated on each population and over the structure of the entire ecosystem, show how different populations respond differently to disturbances, following behaviors similar to those expected in nature, like high reproduction rates on gregarious plants with short generation times, and low densities in plants with high generations times. The selection of plant populations was mainly focused on the concept of biodiversity with emphasis on tropical regions. The model can represent the spatial and temporal succession of the ecosystem after being disturbed. The model also shows the differences between a disturbed and undisturbed ecosystem in a temporal scale, and how the differences in the phenotypical characteristics of plant populations can be advantageous or disadvantageous when they are disturbed. This ecohydrological model is intended to be used as an aid for making decisions about restoration and conservation practices, and also to help understanding resilience and stability of ecosystems, especially in tropical forests under climate change scenarios. Acknowledgements: authors thank the financial support of COLCIENCIAS (program Jovenes Investigadores e innovadores 2012), GAIA group and Universidad de Antioquia through its Sustainability Program 2011-2012.

Quantification of the genetic change in the transition of Rhodnius pallescens Barber, 1932 (Hemiptera: Reduviidae) from field to laboratory.

PubMed

Gómez-Sucerquia, Leysa Jackeline; Triana-Chávez, Omar; Jaramillo-Ocampo, Nicolás

2009-09-01

Previous studies have reported genetic differences between wild-caught sylvatic, domestic and laboratory pop-ulations of several Triatominae species. The differences between sylvatic and laboratory colonies parallel are similar to the differences observed between sylvatic and domestic populations. Laboratory colonies are frequently used as references for field populations, but the consequences of founder events on the genetic makeup of laboratory or domestic populations are rarely quantified. Our goal was to quantify the genetic change in Rhodnius pallescens populations artificially submitted to founder effects via laboratory colonization. We compared the genetic makeup of two sylvatic populations and their laboratory descendants using a panel of 10 microsatellite markers. Both sylvatic populations were initially collected from palm trees, but the colonies differed in the number of founder insects and amount of time kept in the laboratory. We evaluated allelic polymorphism, differences between expected and observed heterozygosity, estimates of population differentiation (Fst) and inbreeding (Fis, Fit) and cluster analyses based on Nei's distances. We found a unique genetic structure for each sample population, with significant differentiation between the field insects and each of the laboratory generations. These analyses showed strong founder effects and showed that genetic drift had led to a genetic equilibrium over several generations of isolation. Our results suggest that laboratory colonies of R. pallescens have a different genetic structure than their wild relatives and similar processes likely affect other Triatominae laboratory stocks.

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

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

Longiaru, S.; Bhattacharyya, T.

1985-01-01

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

Generation time and effective population size in Polar Eskimos.

PubMed

Matsumura, Shuichi; Forster, Peter

2008-07-07

North Greenland Polar Eskimos are the only hunter-gatherer population, to our knowledge, who can offer precise genealogical records spanning several generations. This is the first report from Eskimos on two key parameters in population genetics, namely, generation time (T) and effective population size (Ne). The average mother-daughter and father-son intervals were 27 and 32 years, respectively, roughly similar to the previously published generation times obtained from recent agricultural societies across the world. To gain an insight for the generation time in our distant ancestors, we calculated maternal generation time for two wild chimpanzee populations. We also provide the first comparison among three distinct approaches (genealogy, variance and life table methods) for calculating Ne, which resulted in slightly differing values for the Eskimos. The ratio of the effective to the census population size is estimated as 0.6-0.7 for autosomal and X-chromosomal DNA, 0.7-0.9 for mitochondrial DNA and 0.5 for Y-chromosomal DNA. A simulation of alleles along the genealogy suggested that Y-chromosomal DNA may drift a little faster than mitochondrial DNA in this population, in contrast to agricultural Icelanders. Our values will be useful not only in prehistoric population inference but also in understanding the shaping of our genome today.

həli?dxw/Healthy Hearts Across Generations: Development and Evaluation Design of a Tribally Based Cardiovascular Disease Prevention Intervention for American Indian Families

PubMed Central

LaMarr, June; Levy, Rona L.; Pearson, Cynthia; Maresca, Teresa; Mohammed, Selina A.; Simoni, Jane M.; Evans-Campbell, Teresa; Fredriksen-Goldsen, Karen; Fryberg, Sheryl; Jobe, Jared B.

2012-01-01

American Indian and Alaska Native (AIAN) populations are disproportionately at risk for cardiovascular disease (CVD), diabetes, and obesity, compared with the general US population. This article describes the həli?dxw/Healthy Hearts Across Generations project, an AIAN-run, tribally based randomized controlled trial (January 2010–June 2012) designed to evaluate a culturally appropriate CVD risk prevention program for AI parents residing in the Pacific Northwest of the United States. At-risk AIAN adults (n = 135) were randomly assigned to either a CVD prevention intervention arm or a comparison arm focusing on increasing family cohesiveness, communication, and connectedness. Both year-long conditions included 1 month of motivational interviewing counseling followed by personal coach contacts and family life-skills classes. Blood chemistry, blood pressure, body mass index, food intake, and physical activity were measured at baseline and at 4- and 12-month follow-up times. PMID:22965622

Project həli?dx(w)/Healthy Hearts Across Generations: development and evaluation design of a tribally based cardiovascular disease prevention intervention for American Indian families.

PubMed

Walters, Karina L; LaMarr, June; Levy, Rona L; Pearson, Cynthia; Maresca, Teresa; Mohammed, Selina A; Simoni, Jane M; Evans-Campbell, Teresa; Fredriksen-Goldsen, Karen; Fryberg, Sheryl; Jobe, Jared B

2012-08-01

American Indian and Alaska Native (AIAN) populations are disproportionately at risk for cardiovascular disease (CVD), diabetes, and obesity, compared with the general US population. This article describes the həli?dx(w)/Healthy Hearts Across Generations project, an AIAN-run, tribally based randomized controlled trial (January 2010-June 2012) designed to evaluate a culturally appropriate CVD risk prevention program for AI parents residing in the Pacific Northwest of the United States. At-risk AIAN adults (n = 135) were randomly assigned to either a CVD prevention intervention arm or a comparison arm focusing on increasing family cohesiveness, communication, and connectedness. Both year-long conditions included 1 month of motivational interviewing counseling followed by personal coach contacts and family life-skills classes. Blood chemistry, blood pressure, body mass index, food intake, and physical activity were measured at baseline and at 4- and 12-month follow-up times.

Comparison of drug utilization patterns in observational data: antiepileptic drugs in pediatric patients

PubMed Central

Bourgeois, Florence T; Olson, Karen L; Poduri, Annapurna; Mandl, Kenneth D

2015-01-01

Purpose Physicians require information on the comparative benefits and harms of medications for optimal treatment decisions. However, this type of data is limited, especially for pediatric patients. Objective Our aim was to use observational data to measure and compare medication utilization patterns in a pediatric patient population. Methods Using pharmacy claims data from a large, national-scale insurance program in the US, we identified all patients with a diagnosis of epilepsy treated with a first-generation (carabamazepine, ethosuximide, phenobarbital, phenytoin, valproate) or second-generation (carbamazepine XR, gabapentin, lamotrigine, levetiracetam, oxcarbazepine, tiagabine, topiramate, valproate XR, zonisamide) antiepileptic drug. Treatment periods were defined based on prescription fill dates and medication days supplied. Medication use was measured for individual antiepileptic drugs and for first-generation and second-generation drugs as groups. Results There were 2527 (54%) patients who initiated therapy with first-generation and 2139 (46%) with second-generation antiepileptics. First- and second-generation drugs had the same one-year retention rates (26% [95%CI 24–28] and 26% [95%CI 25–28], respectively). A total of 26% (95%CI 25–28) and 29% (95%CI 27–31) of patients who started on a first- or second-generation antiepileptic medication, respectively, resumed treatment with the initial drug after discontinuation. Overall, 73% (95%CI 71–74) of patients were treated with only one antiepileptic drug, with similar rates for patients started on first- and second-generation drugs (71% [95%CI 69–73] vs 74% [95%CI 72–76]). Conclusions Comparing drug utilization patterns in a pediatric population using observational data, we found similar rates of retention and therapeutic changes. These findings are consistent with available comparative data and demonstrate an approach that could be extended to other drug classes and conditions in pediatric populations to examine drug effectiveness. PMID:26070280

In silico evaluation of gadofosveset pharmacokinetics in different population groups using the Simcyp® simulator platform.

PubMed

Spanakis, Marios; Marias, Kostas

2014-12-01

Gadofosveset is a Gd-based contrast agent used for magnetic resonance imaging (MRI). Gadolinium kinetic distribution models are implemented in T1-weighted dynamic contrast-enhanced perfusion MRI for characterization of lesion sites in the body. Physiology changes in a disease state potentially can influence the pharmacokinetics of drugs and to this respect modify the distribution properties of contrast agents. This work focuses on the in silico modelling of pharmacokinetic properties of gadofosveset in different population groups through the application of physiologically-based pharmacokinetic models (PBPK) embedded in Simcyp® population pharmacokinetics platform. Physicochemical and pharmacokinetic properties of gadofosveset were introduced into Simcyp® simulator platform and a min-PBPK model was applied. In silico clinical trials were generated simulating the administration of the recommended dose for the contrast agent (i.v., 30 mg/kg) in population cohorts of healthy volunteers, obese, renal and liver impairment, and in a generated virtual oncology population. Results were evaluated regarding basic pharmacokinetic parameters of Cmax, AUC and systemic CL and differences were assessed through ANOVA and estimation of ratio of geometric mean between healthy volunteers and the other population groups. Simcyp® predicted a mean Cmax = 551.60 mg/l, a mean AUC = 4079.12 mg/L*h and a mean systemic CL = 0.56 L/h for the virtual population of healthy volunteers. Obese population showed a modulation in Cmax and CL, attributed to increased administered dose. In renal and liver impairment cohorts a significant modulation in Cmax, AUC and CL of gadofosveset is predicted. Oncology population exhibited statistical significant differences regarding AUC when compared with healthy volunteers. This work employed Simcyp® population pharmacokinetics platform in order to compute gadofosveset's pharmacokinetic profiles through PBPK models and in silico clinical trials and evaluate possible differences between population groups. The approach showed promising results that could provide new insights regarding administration of contrast agents in special population cohorts. In silico pharmacokinetics could further be used for evaluating of possible toxicity, interpretation of MRI PK image maps and development of novel contrast agents.

The impact of selection on population genetic structure in the clam Meretrix petechialis revealed by microsatellite markers.

PubMed

Lu, Xia; Wang, Hongxia; Li, Yan; Liu, Baozhong

2016-02-01

The aim of our work is to evaluate the impact of mass selection on genetic structure in artificially closed populations of the clam Meretrix petechialis. In the present study, we performed mass selection over four generations (from 2004 to 2010) on two clam populations [shell features of purple lines (SP) and black dots (SB)] and analyzed their temporal genetic variation and structure using microsatellite makers. The two closed populations originated from the natural Shandong population (SD); thus, a natural SD population (10SD) was used to detect the current genetic structure after 6 years of natural selection. The results showed that the genetic diversity of the four generations of SB and SP was gradually reduced but remained at relatively high levels (SB, A = 18.9.4-16.8, Ho = 0.7389-0.6971, and He = 0.8897-0.8591; SP, A = 20.0-17.8, Ho = 0.7512-0.7043, and He = 0.8938-0.8625), which has not been reduced compared with that of the 10SD population (A = 17.8, Ho = 0.6803, and He = 0.8302). The Ne estimates for the two populations were almost at the same levels as the actual numbers of parental individuals. In addition, a low inbreeding coefficient was detected in the two populations (SB, 0.00201-0.00639; SP, 0.00176-0.00541). Based on the results, the present mass selection has not made a large impact on the population genetic structure of the closed populations. The present investigation provides important information for the development of management strategies for genetic breeding of the clam.

Modelling Feedback Excitation, Pacemaker Properties and Sensory Switching of Electrically Coupled Brainstem Neurons Controlling Rhythmic Activity

PubMed Central

Hull, Michael J.; Soffe, Stephen R.; Willshaw, David J.; Roberts, Alan

2016-01-01

What cellular and network properties allow reliable neuronal rhythm generation or firing that can be started and stopped by brief synaptic inputs? We investigate rhythmic activity in an electrically-coupled population of brainstem neurons driving swimming locomotion in young frog tadpoles, and how activity is switched on and off by brief sensory stimulation. We build a computational model of 30 electrically-coupled conditional pacemaker neurons on one side of the tadpole hindbrain and spinal cord. Based on experimental estimates for neuron properties, population sizes, synapse strengths and connections, we show that: long-lasting, mutual, glutamatergic excitation between the neurons allows the network to sustain rhythmic pacemaker firing at swimming frequencies following brief synaptic excitation; activity persists but rhythm breaks down without electrical coupling; NMDA voltage-dependency doubles the range of synaptic feedback strengths generating sustained rhythm. The network can be switched on and off at short latency by brief synaptic excitation and inhibition. We demonstrate that a population of generic Hodgkin-Huxley type neurons coupled by glutamatergic excitatory feedback can generate sustained asynchronous firing switched on and off synaptically. We conclude that networks of neurons with NMDAR mediated feedback excitation can generate self-sustained activity following brief synaptic excitation. The frequency of activity is limited by the kinetics of the neuron membrane channels and can be stopped by brief inhibitory input. Network activity can be rhythmic at lower frequencies if the neurons are electrically coupled. Our key finding is that excitatory synaptic feedback within a population of neurons can produce switchable, stable, sustained firing without synaptic inhibition. PMID:26824331

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.

Full spectrum of psychiatric disorders related to foreign migration: a Danish population-based cohort study.

PubMed

Cantor-Graae, Elizabeth; Pedersen, Carsten B

2013-04-01

Although increased risk for schizophrenia among immigrants is well established, knowledge of the broader spectrum of psychiatric disorders associated with a foreign migration background is lacking. To examine the full range of psychiatric disorders associated with any type of foreign migration background among persons residing in Denmark, including foreign-born adoptees, first- and second-generation immigrants, native Danes with a history of foreign residence, and persons born abroad to Danish expatriates. Danish population-based cohort study. Persons were followed up from their 10th birthday for the development of mental disorders based on outpatient and inpatient data. All persons born between January 1, 1971, and December 31, 2000 (N = 1 859 419) residing in Denmark by their 10th birthday with follow-up data to December 31, 2010. Incidence rate ratios (IRRs) and cumulative incidences for psychiatric outcomes. All categories of foreign migration background, except persons born abroad to Danish expatriates, were associated with increased risk for at least 1 psychiatric disorder. Foreign-born adoptees had increased IRRs for all psychiatric disorders and had the highest IRRs for these disorders compared with other foreign migration categories. First- and second-generation immigrants having 2 foreign-born parents had significantly increased IRRs for schizophrenia and schizophrenia spectrum disorders and had similar risk magnitudes. Second-generation immigrants having 1 foreign-born parent had significantly increased IRRs for all psychiatric disorders. Native Danes with a history of foreign residence had increased IRRs for bipolar affective disorder, affective disorders, personality disorders, and schizophrenia spectrum disorders. The extent to which a background of foreign migration confers an increased risk for the broad spectrum of psychiatric disorders varies according to parental origin, with greatest risks for foreign-born adoptees. The spectrum of psychiatric disorders showed greater variation within the second-generation immigrant group than between first-generation vs second-generation immigrants, and the spectrum differed according to whether individuals had 1 or 2 foreign-born parents.

Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle

PubMed Central

da Silva, Joaquim Manoel; Giachetto, Poliana Fernanda; da Silva, Luiz Otávio Campos; Cintra, Leandro Carrijo; Paiva, Samuel Rezende; Caetano, Alexandre Rodrigues; Yamagishi, Michel Eduardo Beleza

2015-01-01

High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus) samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production. PMID:26305794

Weighted social networks for a large scale artificial society

NASA Astrophysics Data System (ADS)

Fan, Zong Chen; Duan, Wei; Zhang, Peng; Qiu, Xiao Gang

2016-12-01

The method of artificial society has provided a powerful way to study and explain how individual behaviors at micro level give rise to the emergence of global social phenomenon. It also creates the need for an appropriate representation of social structure which usually has a significant influence on human behaviors. It has been widely acknowledged that social networks are the main paradigm to describe social structure and reflect social relationships within a population. To generate social networks for a population of interest, considering physical distance and social distance among people, we propose a generation model of social networks for a large-scale artificial society based on human choice behavior theory under the principle of random utility maximization. As a premise, we first build an artificial society through constructing a synthetic population with a series of attributes in line with the statistical (census) data for Beijing. Then the generation model is applied to assign social relationships to each individual in the synthetic population. Compared with previous empirical findings, the results show that our model can reproduce the general characteristics of social networks, such as high clustering coefficient, significant community structure and small-world property. Our model can also be extended to a larger social micro-simulation as an input initial. It will facilitate to research and predict some social phenomenon or issues, for example, epidemic transition and rumor spreading.

RNAbrowse: RNA-Seq De Novo Assembly Results Browser

PubMed Central

Mariette, Jérôme; Noirot, Céline; Nabihoudine, Ibounyamine; Bardou, Philippe; Hoede, Claire; Djari, Anis; Cabau, Cédric; Klopp, Christophe

2014-01-01

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse. PMID:24823498

A Micro-Level Data-Calibrated Agent-Based Model: The Synergy between Microsimulation and Agent-Based Modeling.

PubMed

Singh, Karandeep; Ahn, Chang-Won; Paik, Euihyun; Bae, Jang Won; Lee, Chun-Hee

2018-01-01

Artificial life (ALife) examines systems related to natural life, its processes, and its evolution, using simulations with computer models, robotics, and biochemistry. In this article, we focus on the computer modeling, or "soft," aspects of ALife and prepare a framework for scientists and modelers to be able to support such experiments. The framework is designed and built to be a parallel as well as distributed agent-based modeling environment, and does not require end users to have expertise in parallel or distributed computing. Furthermore, we use this framework to implement a hybrid model using microsimulation and agent-based modeling techniques to generate an artificial society. We leverage this artificial society to simulate and analyze population dynamics using Korean population census data. The agents in this model derive their decisional behaviors from real data (microsimulation feature) and interact among themselves (agent-based modeling feature) to proceed in the simulation. The behaviors, interactions, and social scenarios of the agents are varied to perform an analysis of population dynamics. We also estimate the future cost of pension policies based on the future population structure of the artificial society. The proposed framework and model demonstrates how ALife techniques can be used by researchers in relation to social issues and policies.

Monte Carlo simulation models of breeding-population advancement.

Treesearch

J.N. King; G.R. Johnson

1993-01-01

Five generations of population improvement were modeled using Monte Carlo simulations. The model was designed to address questions that are important to the development of an advanced generation breeding population. Specifically we addressed the effects on both gain and effective population size of different mating schemes when creating a recombinant population for...

Size and sequence polymorphisms in the glutamate-rich protein gene of the human malaria parasite Plasmodium falciparum in Thailand.

PubMed

Pattaradilokrat, Sittiporn; Trakoolsoontorn, Chawinya; Simpalipan, Phumin; Warrit, Natapot; Kaewthamasorn, Morakot; Harnyuttanakorn, Pongchai

2018-01-22

The glutamate-rich protein (GLURP) of the malaria parasite Plasmodium falciparum is a key surface antigen that serves as a component of a clinical vaccine. Moreover, the GLURP gene is also employed routinely as a genetic marker for malarial genotyping in epidemiological studies. While extensive size polymorphisms in GLURP are well recorded, the extent of the sequence diversity of this gene is rarely investigated. The present study aimed to explore the genetic diversity of GLURP in natural populations of P. falciparum. The polymorphic C-terminal repetitive R2 region of GLURP sequences from 65 P. falciparum isolates in Thailand were generated and combined with the data from 103 worldwide isolates to generate a GLURP database. The collection was comprised of 168 alleles, encoding 105 unique GLURP subtypes, characterized by 18 types of amino acid repeat units (AAU). Of these, 28 GLURP subtypes, formed by 10 AAU types, were detected in P. falciparum in Thailand. Among them, 19 GLURP subtypes and 2 AAU types are described for the first time in the Thai parasite population. The AAU sequences were highly conserved, which is likely due to negative selection. Standard Fst analysis revealed the shared distributions of GLURP types among the P. falciparum populations, providing evidence of gene flow among the different demographic populations. Sequence diversity causing size variations in GLURP in Thai P. falciparum populations were detected, and caused by non-synonymous substitutions in repeat units and some insertion/deletion of aspartic acid or glutamic acid codons between repeat units. The P. falciparum population structure based on GLURP showed promising implications for the development of GLURP-based vaccines and for monitoring vaccine efficacy.

Variations in population vulnerability to tectonic and landslide-related tsunami hazards in Alaska

USGS Publications Warehouse

Wood, Nathan J.; Peters, Jeff

2015-01-01

Effective tsunami risk reduction requires an understanding of how at-risk populations are specifically vulnerable to tsunami threats. Vulnerability assessments primarily have been based on single hazard zones, even though a coastal community may be threatened by multiple tsunami sources that vary locally in terms of inundation extents and wave arrival times. We use the Alaskan coastal communities of Cordova, Kodiak, Seward, Valdez, and Whittier (USA), as a case study to explore population vulnerability to multiple tsunami threats. We use anisotropic pedestrian evacuation models to assess variations in population exposure as a function of travel time out of hazard zones associated with tectonic and landslide-related tsunamis (based on scenarios similar to the 1964 M w9.2 Good Friday earthquake and tsunami disaster). Results demonstrate that there are thousands of residents, employees, and business customers in tsunami hazard zones associated with tectonically generated waves, but that at-risk individuals will likely have sufficient time to evacuate to high ground before waves are estimated to arrive 30–60 min after generation. Tsunami hazard zones associated with submarine landslides initiated by a subduction zone earthquake are smaller and contain fewer people, but many at-risk individuals may not have enough time to evacuate as waves are estimated to arrive in 1–2 min and evacuations may need to occur during earthquake ground shaking. For all hazard zones, employees and customers at businesses far outnumber residents at their homes and evacuation travel times are highest on docks and along waterfronts. Results suggest that population vulnerability studies related to tsunami hazards should recognize non-residential populations and differences in wave arrival times if emergency managers are to develop realistic preparedness and outreach efforts.

Effects of ethanol-based fuel contamination: microbial community changes, production of regulated compounds, and methane generation.

PubMed

Nelson, Denice K; Lapara, Timothy M; Novak, Paige J

2010-06-15

Ethanol-based fuels are becoming more heavily used, increasing the likelihood of ethanol-based fuel spills during transportation and storage. Although ethanol is well-known to be readily biodegradable, very little is known about the effects that such a spill might have on an indigenous microbial community. Of particular concern is that ethanol contamination could stimulate the growth of organisms that can generate regulated compounds and/or produce explosive quantities of methane gas. A column-based study was performed to elucidate the potential impacts of ethanol-based fuel (E85) on the indigenous microbial community during a simulated fuel spill. A continuous dilute supply of E85 resulted in profound shifts in both the bacterial and archaeal communities. The shift was accompanied by the production of high concentrations of volatile fatty acids and butanol, a compound that is regulated in groundwater by some states. Results also indicated that a continuous feed of dilute E85 generated explosive levels of methane within one month of column operation. Quantitative PCR data showed a statistically significant increase in methanogenic populations when compared to a control column. The elevated population numbers correlated to areas of the column receiving a sustained carbon load. Toxicity data indicated that microbial growth was completely inhibited (as evidenced by absence of ethanol breakdown products) at ethanol levels above 6% (v/v). These data suggest that ethanol from ethanol-based fuel can be readily degraded, but can also produce metabolic products that are regulated as well as explosive levels of methane. The core of an E85 spill may serve as a long-term source of contamination as it cannot be degraded until significant dilution has occurred.

USING GIS TO GENERATE SPATIALLY-BALANCED RANDOM SURVEY DESIGNS FOR NATURAL RESOURCE APPLICATIONS

EPA Science Inventory

Sampling of a population is frequently required to understand trends and patterns in natural resource management because financial and time constraints preclude a complete census. A rigorous probability-based survey design specifies where to sample so that inferences from the sam...

Is population structure sufficient to generate area-level inequalities in influenza rates? An examination using agent-based models.

PubMed

Kumar, Supriya; Piper, Kaitlin; Galloway, David D; Hadler, James L; Grefenstette, John J

2015-09-23

In New Haven County, CT (NHC), influenza hospitalization rates have been shown to increase with census tract poverty in multiple influenza seasons. Though multiple factors have been hypothesized to cause these inequalities, including population structure, differential vaccine uptake, and differential access to healthcare, the impact of each in generating observed inequalities remains unknown. We can design interventions targeting factors with the greatest explanatory power if we quantify the proportion of observed inequalities that hypothesized factors are able to generate. Here, we ask if population structure is sufficient to generate the observed area-level inequalities in NHC. To our knowledge, this is the first use of simulation models to examine the causes of differential poverty-related influenza rates. Using agent-based models with a census-informed, realistic representation of household size, age-structure, population density in NHC census tracts, and contact rates in workplaces, schools, households, and neighborhoods, we measured poverty-related differential influenza attack rates over the course of an epidemic with a 23 % overall clinical attack rate. We examined the role of asthma prevalence rates as well as individual contact rates and infection susceptibility in generating observed area-level influenza inequalities. Simulated attack rates (AR) among adults increased with census tract poverty level (F = 30.5; P < 0.001) in an epidemic caused by a virus similar to A (H1N1) pdm09. We detected a steeper, earlier influenza rate increase in high-poverty census tracts-a finding that we corroborate with a temporal analysis of NHC surveillance data during the 2009 H1N1 pandemic. The ratio of the simulated adult AR in the highest- to lowest-poverty tracts was 33 % of the ratio observed in surveillance data. Increasing individual contact rates in the neighborhood did not increase simulated area-level inequalities. When we modified individual susceptibility such that it was inversely proportional to household income, inequalities in AR between high- and low-poverty census tracts were comparable to those observed in reality. To our knowledge, this is the first study to use simulations to probe the causes of observed inequalities in influenza disease patterns. Knowledge of the causes and their relative explanatory power will allow us to design interventions that have the greatest impact on reducing inequalities. Differential exposure due to population structure in our realistic simulation model explains a third of the observed inequality. Differential susceptibility to disease due to prevailing chronic conditions, vaccine uptake, and smoking should be considered in future models in order to quantify the role of additional factors in generating influenza inequalities.

Development of next-generation mapping populations: Multi-parent Advanced Generation Inter-Cross (MAGIC) and Marker-Assisted Recurrent Selection (MARS) populations in peanut

USDA-ARS?s Scientific Manuscript database

Generation Inter-Cross (MAGIC) and Marker-Assisted Recurrent Selection (MARS) have been proposed and used in many crops to dissect complex traits or QTL. MAGIC allows for dissecting genomic structure, and for improving breeding populations by integrating multiple alleles from different parents. MAR...

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.

Utilization and costs of antipsychotic agents: a Canadian population-based study, 1996-2006.

PubMed

Alessi-Severini, Silvia; Biscontri, Robert G; Collins, David M; Kozyrskyj, Anita; Sareen, Jitender; Enns, Murray W

2008-05-01

This study evaluated the prescribing patterns and costs for antipsychotic agents in the population of the Canadian province of Manitoba over the past decade. A population-based study of antipsychotic utilization and costs was conducted on data collected from the administrative databases of the Manitoba Population Health Data Repository and the Statistics Canada census between index years 1996 and 2006 (April 1, 1995, through March 31, 2006). The total annual number of antipsychotic prescriptions dispensed in Manitoba increased by 227% between 1996 and 2006, and the prevalence of antipsychotic users increased by 62% over the same time interval. The fastest-growing segment of antipsychotic users in Manitoba appears to be young males, who increased from .16% in 1996 to .88% in 2006. The highest numbers of prescriptions were reported for schizophrenia, dementia, and conduct disorder. Annual expenditures for antipsychotics increased from $1.7 million in 1996 to $22.0 million in 2006 (expenditures are in Canadian dollars). The cost of second-generation agents reached 80% of total antipsychotic expenditures in 2006; risperidone was the most prescribed agent in all age groups of patients. The per-patient annual cost of antipsychotic pharmacotherapy increased by approximately 680% between 1996 and 2006 in Manitoba. The number of antipsychotic prescriptions and the prevalence of users of antipsychotic medications increased significantly in Manitoba over the study period, despite a steady-state population of approximately 1.2 million. Incremental costs relative to the use of antipsychotic medications can be explained by the market penetration of the second-generation agents and their expanded use in the treatment of various diagnoses.

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.

Bioethics and Populism: How Should Our Field Respond?

PubMed

Solomon, Mildred Z; Jennings, Bruce

2017-03-01

Across the world, an authoritarian and exclusionary form of populism is gaining political traction. Historically, some populist movements have been democratic and based on a sense of inclusive justice and the common good. But the populism on the rise at present speaks and acts otherwise. It is challenging constitutional democracies. The polarization seen in authoritarian populism goes beyond the familiar left-right political spectrum and generates disturbing forms of extremism, including the so-called alternative right in the United States and similar ethnic and nationalistic political movements in other countries. The field of bioethics will be profoundly affected if authoritarian populism displaces constitutional democracy. But the field has a significant contribution to make to rebuilding the communal and civic foundations upon which constitutional democracy rests. © 2017 The Hastings Center.

Lineage Tracking for Probing Heritable Phenotypes at Single-Cell Resolution

PubMed Central

Cottinet, Denis; Condamine, Florence; Bremond, Nicolas; Griffiths, Andrew D.; Rainey, Paul B.; de Visser, J. Arjan G. M.; Baudry, Jean; Bibette, Jérôme

2016-01-01

Determining the phenotype and genotype of single cells is central to understand microbial evolution. DNA sequencing technologies allow the detection of mutants at high resolution, but similar approaches for phenotypic analyses are still lacking. We show that a drop-based millifluidic system enables the detection of heritable phenotypic changes in evolving bacterial populations. At time intervals, cells were sampled and individually compartmentalized in 100 nL drops. Growth through 15 generations was monitored using a fluorescent protein reporter. Amplification of heritable changes–via growth–over multiple generations yields phenotypically distinct clusters reflecting variation relevant for evolution. To demonstrate the utility of this approach, we follow the evolution of Escherichia coli populations during 30 days of starvation. Phenotypic diversity was observed to rapidly increase upon starvation with the emergence of heritable phenotypes. Mutations corresponding to each phenotypic class were identified by DNA sequencing. This scalable lineage-tracking technology opens the door to large-scale phenotyping methods with special utility for microbiology and microbial population biology. PMID:27077662

Lineage Tracking for Probing Heritable Phenotypes at Single-Cell Resolution.

PubMed

Cottinet, Denis; Condamine, Florence; Bremond, Nicolas; Griffiths, Andrew D; Rainey, Paul B; de Visser, J Arjan G M; Baudry, Jean; Bibette, Jérôme

2016-01-01

Determining the phenotype and genotype of single cells is central to understand microbial evolution. DNA sequencing technologies allow the detection of mutants at high resolution, but similar approaches for phenotypic analyses are still lacking. We show that a drop-based millifluidic system enables the detection of heritable phenotypic changes in evolving bacterial populations. At time intervals, cells were sampled and individually compartmentalized in 100 nL drops. Growth through 15 generations was monitored using a fluorescent protein reporter. Amplification of heritable changes-via growth-over multiple generations yields phenotypically distinct clusters reflecting variation relevant for evolution. To demonstrate the utility of this approach, we follow the evolution of Escherichia coli populations during 30 days of starvation. Phenotypic diversity was observed to rapidly increase upon starvation with the emergence of heritable phenotypes. Mutations corresponding to each phenotypic class were identified by DNA sequencing. This scalable lineage-tracking technology opens the door to large-scale phenotyping methods with special utility for microbiology and microbial population biology.

A network-based approach for resistance transmission in bacterial populations.

PubMed

Gehring, Ronette; Schumm, Phillip; Youssef, Mina; Scoglio, Caterina

2010-01-07

Horizontal transfer of mobile genetic elements (conjugation) is an important mechanism whereby resistance is spread through bacterial populations. The aim of our work is to develop a mathematical model that quantitatively describes this process, and to use this model to optimize antimicrobial dosage regimens to minimize resistance development. The bacterial population is conceptualized as a compartmental mathematical model to describe changes in susceptible, resistant, and transconjugant bacteria over time. This model is combined with a compartmental pharmacokinetic model to explore the effect of different plasma drug concentration profiles. An agent-based simulation tool is used to account for resistance transfer occurring when two bacteria are adjacent or in close proximity. In addition, a non-linear programming optimal control problem is introduced to minimize bacterial populations as well as the drug dose. Simulation and optimization results suggest that the rapid death of susceptible individuals in the population is pivotal in minimizing the number of transconjugants in a population. This supports the use of potent antimicrobials that rapidly kill susceptible individuals and development of dosage regimens that maintain effective antimicrobial drug concentrations for as long as needed to kill off the susceptible population. Suggestions are made for experiments to test the hypotheses generated by these simulations.

Increased cadmium excretion in metal-adapted populations of the midge Chironomus riparius (Diptera)

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

Postma, J.F.; Nugteren, P. van; Buckert-De Jong, M.B.

1996-03-01

Cadmium kinetics were studied in cadmium-adapted and nonadapted field populations of the midge Chironomus riparius. Accumulation and elimination experiments were carried out using first-generation laboratory-reared animals. Differences between populations were, therefore, assumed to have a genetic basis. Larvae were dissected to analyze the guts and the remainder of the larvae separately. First-order one-compartment models were not always successful in describing accumulation processes, probably due to acclimation. No interpopulation differences were observed in larval development based on dry weights, whereas some differences existed based on pupation rate. In most cases more than 80% of the total amount of cadmium was foundmore » in the guts of all populations. Larvae from cadmium-adapted populations showed a decreased net accumulation rate as well as higher equilibrium values (15--20%) compared to nonadapted populations. In addition, cadmium excretion efficiency was increased for cadmium-adapted larvae, which was due to an increased elimination rate from the guts. It was concluded that exposure to high cadmium concentrations in the field resulted in populations of C. riparius with an increased storage capability and an increased excretion efficiency, especially regarding the guts.« less

Differential-Evolution Control Parameter Optimization for Unmanned Aerial Vehicle Path Planning

PubMed Central

Kok, Kai Yit; Rajendran, Parvathy

2016-01-01

The differential evolution algorithm has been widely applied on unmanned aerial vehicle (UAV) path planning. At present, four random tuning parameters exist for differential evolution algorithm, namely, population size, differential weight, crossover, and generation number. These tuning parameters are required, together with user setting on path and computational cost weightage. However, the optimum settings of these tuning parameters vary according to application. Instead of trial and error, this paper presents an optimization method of differential evolution algorithm for tuning the parameters of UAV path planning. The parameters that this research focuses on are population size, differential weight, crossover, and generation number. The developed algorithm enables the user to simply define the weightage desired between the path and computational cost to converge with the minimum generation required based on user requirement. In conclusion, the proposed optimization of tuning parameters in differential evolution algorithm for UAV path planning expedites and improves the final output path and computational cost. PMID:26943630

Development of germ-line-specific CRISPR-Cas9 systems to improve the production of heritable gene modifications in Arabidopsis

PubMed Central

Mao, Yanfei; Zhang, Zhengjing; Feng, Zhengyan; Wei, Pengliang; Zhang, Hui; Botella, José Ramón; Zhu, Jian-Kang

2017-01-01

Summary The Streptococcus-derived CRISPR/Cas9 system is being widely used to perform targeted gene modifications in plants. This customized endonuclease system has two components, the single-guide RNA (sgRNA) for target DNA recognition and the CRISPR-associated protein 9 (Cas9) for DNA cleavage. Ubiquitously expressed CRISPR/Cas9 systems (UC) generate targeted gene modifications with high efficiency but only those produced in reproductive cells are transmitted to the next generation. We report the design and characterization of a germ-line-specific Cas9 system (GSC) for Arabidopsis gene modification in male gametocytes, constructed using a SPOROCYTELESS (SPL) genomic expression cassette. Four loci in two endogenous genes were targeted by both systems for comparative analysis. Mutations generated by the GSC system were rare in T1 plants but were abundant (30%) in the T2 generation. The vast majority (70%) of the T2 mutant population generated using the UC system were chimeras while the newly developed GSC system produced only 29% chimeras, with 70% of the T2 mutants being heterozygous. Analysis of two loci in the T2 population showed that the abundance of heritable gene mutations was 37% higher in the GSC system compared to the UC system and the level of polymorphism of the mutations was also dramatically increased with the GSC system. Two additional systems based on germ-line-specific promoters (pDD45-GT and pLAT52-GT) were also tested, and one of them was capable of generating heritable homozygous T1 mutant plants. Our results suggest that future application of the described GSC system will facilitate the screening for targeted gene modifications, especially lethal mutations in the T2 population. PMID:26360626

Robust Identification of Local Adaptation from Allele Frequencies

PubMed Central

Günther, Torsten; Coop, Graham

2013-01-01

Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of “standardized allele frequencies” that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools—a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org. PMID:23821598

Risk of disability pension in first and second generation immigrants: the role of age and region of birth in a prospective population-based study from Sweden.

PubMed

Di Thiene, D; Helgesson, M; Alexanderson, K; La Torre, G; Tiihonen, J; Mittendorfer-Rutz, E

2017-12-04

In several countries, immigrants have higher disability pension (DP) rates than natives. Reasons for this are poorly understood. The aim of this study was to investigate if the risk of diagnosis-specific DP differed in first, second, and second/intermediate generation immigrants compared to natives, in general and across regions of birth, and stratified by age. A population-based prospective cohort study of all 3,507,055 individuals aged 19-50 years and living in Sweden in 2004 with a 6-year follow-up period. Hazard ratios (HR) and 95% confidence intervals (CI) for mental and somatic DP were estimated by Cox regression for first, second, and second/intermediate generation immigrants compared to natives, across regions of birth and stratified by age. After multivariate adjustment, HRs for both mental and somatic DP were higher at follow-up in the first generation compared to natives: mental HR 1.17 (CI 1.12-1.22) and somatic 1.15 (1.09-1.22) for individuals <35 years; 1.74 (1.69-1.79) and 1.70 (1.66-1.74) ≥35 years (median), respectively. Immigrants born in Europe outside EU25, and countries outside Europe had particularly elevated HRs. Also in the second generation, HRs were higher in mental 1.29 (1.21-1.37) and somatic DP: 1.30 (1.19-1.42) in those <35 years; and 1.18 (1.10-1.27); and 1.10 (1.03-1.17) for those ≥35 years, respectively. Among second generation immigrants there were no strong differences in HRs between regions of birth. Compared to natives, the risk of DP was higher in first and second generation immigrants. Higher estimates were seen for immigrants from Europe outside EU25 and from the rest of the world in the first generation. No considerable differences in estimates regarding mental or somatic DP diagnoses were found.

Modeling of plug-in electric vehicle travel patterns and charging load based on trip chain generation

NASA Astrophysics Data System (ADS)

Wang, Dai; Gao, Junyu; Li, Pan; Wang, Bin; Zhang, Cong; Saxena, Samveg

2017-08-01

Modeling PEV travel and charging behavior is the key to estimate the charging demand and further explore the potential of providing grid services. This paper presents a stochastic simulation methodology to generate itineraries and charging load profiles for a population of PEVs based on real-world vehicle driving data. In order to describe the sequence of daily travel activities, we use the trip chain model which contains the detailed information of each trip, namely start time, end time, trip distance, start location and end location. A trip chain generation method is developed based on the Naive Bayes model to generate a large number of trips which are temporally and spatially coupled. We apply the proposed methodology to investigate the multi-location charging loads in three different scenarios. Simulation results show that home charging can meet the energy demand of the majority of PEVs in an average condition. In addition, we calculate the lower bound of charging load peak on the premise of lowest charging cost. The results are instructive for the design and construction of charging facilities to avoid excessive infrastructure.

Alternative Constraint Handling Technique for Four-Bar Linkage Path Generation

NASA Astrophysics Data System (ADS)

Sleesongsom, S.; Bureerat, S.

2018-03-01

This paper proposes an extension of a new concept for path generation from our previous work by adding a new constraint handling technique. The propose technique was initially designed for problems without prescribed timing by avoiding the timing constraint, while remain constraints are solving with a new constraint handling technique. The technique is one kind of penalty technique. The comparative study is optimisation of path generation problems are solved using self-adaptive population size teaching-learning based optimization (SAP-TLBO) and original TLBO. In this study, two traditional path generation test problem are used to test the proposed technique. The results show that the new technique can be applied with the path generation problem without prescribed timing and gives better results than the previous technique. Furthermore, SAP-TLBO outperforms the original one.

Turing patterns and a stochastic individual-based model for predator-prey systems

NASA Astrophysics Data System (ADS)

Nagano, Seido

2012-02-01

Reaction-diffusion theory has played a very important role in the study of pattern formations in biology. However, a group of individuals is described by a single state variable representing population density in reaction-diffusion models and interaction between individuals can be included only phenomenologically. Recently, we have seamlessly combined individual-based models with elements of reaction-diffusion theory. To include animal migration in the scheme, we have adopted a relationship between the diffusion and the random numbers generated according to a two-dimensional bivariate normal distribution. Thus, we have observed the transition of population patterns from an extinction mode, a stable mode, or an oscillatory mode to the chaotic mode as the population growth rate increases. We show our phase diagram of predator-prey systems and discuss the microscopic mechanism for the stable lattice formation in detail.

Use of Computer Kiosks for Breast Cancer Education in Five Community Settings

ERIC Educational Resources Information Center

Kreuter, Matthew W.; Black, Wynona J.; Friend, LaBraunna; Booker, Angela C.; Klump, Paula; Bobra, Sonal; Holt, Cheryl L.

2006-01-01

Finding ways to bring effective computer-based behavioral interventions to those with limited access to technology is a continuing challenge for health educators. Computer kiosks placed in community settings may help reach such populations. The "Reflections of You" kiosk generates individually tailored magazines on breast cancer and…

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…

Application of population sequencing (POPSEQ) for ordering and inputting genotyping-by-sequencing markers in hexaploid wheat

USDA-ARS?s Scientific Manuscript database

The advancement of next-generation sequencing technologies in conjunction with new bioinformatics tools enabled fine-tuning of sequence-based high resolution mapping strategies for complex genomes. Although genotyping-by-sequencing (GBS) provides a large number of markers, its application for assoc...

ESTIMATING CHILDREN'S DERMAL AND NON-DIETARY INGESTION EXPOSURE AND DOSE WITH EPA'S SHEDS MODEL

EPA Science Inventory

A physically-based stochastic model (SHEDS) has been developed to estimate pesticide exposure and dose to children via dermal residue contact and non-dietary ingestion. Time-location-activity data are sampled from national survey results to generate a population of simulated ch...

Realized gain from breeding Eucalyptus grandis in Florida

Treesearch

George Meskimen

1983-01-01

E. grandis is in the fourth generation of selection in southwest Florida. The breeding strategy combines a provenance trial, genetic base population, seedling seed orchard, and progeny test in a single plantation where all families are completely randomized in single-tree plots. That planting configuration closely predicted the magnitude of genetic...

Higher Education and Adult Demography.

ERIC Educational Resources Information Center

Brazziel, William F.

This paper examines the changing demographics of American society and the impact of these changes on higher education. Discussions include a historical background of early American demography, the building and expansion of the population base, and census changes through various generations of the baby boom years and beyond. Next, the report…

MAPPING THE DISTRIBUTION OF HARVESTED ESTUARINE BIVALVES WITH NATURAL HISTORY-BASED HABITAT SUITABILITY MODELS

EPA Science Inventory

Maps of harvested bivalve populations are invaluable for the management of fisheries species, yet the cost to produce them typically limits their availability. Here, we demonstrate a relatively low-cost approach to generate habitat maps for five species of bivalves found in many ...

Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps

USDA-ARS?s Scientific Manuscript database

Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental populations are typically unrepli...

[Strategy of development, use and evaluation of the efficiency of biologically active food supplements].

PubMed

Tutel'ian, V A

1996-01-01

Analytical reviews discussed of theoretical bases and principal problems in creation, usage and evaluation of biological active food supplements (BAFS)-nutriceuticals and pharmaceuticals. Need of use the BAFS by population is grounded by data on dietary intake showing deficiency of some nutrients. Treatment and prevention of chronic diseases are other important points of BAFS using. Classification of BAFS are presented taking into consideration the resources and regulative effects. Wide using of BAFS among population is grounded by decreasing of food consumption and nutrient intake in dietary intake of modern population. Importance of BAFS in nutrition of generations of XXI century is discussed.

Population momentum across vertebrate life histories

USGS Publications Warehouse

Koons, D.N.; Grand, J.B.; Arnold, J.M.

2006-01-01

Population abundance is critically important in conservation, management, and demographic theory. Thus, to better understand how perturbations to the life history affect long-term population size, we examined population momentum for four vertebrate classes with different life history strategies. In a series of demographic experiments we show that population momentum generally has a larger effect on long-term population size for organisms with long generation times than for organisms with short generation times. However, patterns between population momentum and generation time varied across taxonomic groups and according to the life history parameter that was changed. Our findings indicate that momentum may be an especially important aspect of population dynamics for long-lived vertebrates, and deserves greater attention in life history studies. Further, we discuss the importance of population momentum in natural resource management, pest control, and conservation arenas. ?? 2006 Elsevier B.V. All rights reserved.

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

Sequence-Based Genotyping of Expressed Swine Leukocyte Antigen Class I Alleles by Next-Generation Sequencing Reveal Novel Swine Leukocyte Antigen Class I Haplotypes and Alleles in Belgian, Danish, and Kenyan Fattening Pigs and Göttingen Minipigs.

PubMed

Sørensen, Maria Rathmann; Ilsøe, Mette; Strube, Mikael Lenz; Bishop, Richard; Erbs, Gitte; Hartmann, Sofie Bruun; Jungersen, Gregers

2017-01-01

The need for typing of the swine leukocyte antigen (SLA) is increasing with the expanded use of pigs as models for human diseases and organ-transplantation experiments, their use in infection studies, and for design of veterinary vaccines. Knowledge of SLA sequences is furthermore a prerequisite for the prediction of epitope binding in pigs. The low number of known SLA class I alleles and the limited knowledge of their prevalence in different pig breeds emphasizes the need for efficient SLA typing methods. This study utilizes an SLA class I-typing method based on next-generation sequencing of barcoded PCR amplicons. The amplicons were generated with universal primers and predicted to resolve 68-88% of all known SLA class I alleles dependent on amplicon size. We analyzed the SLA profiles of 72 pigs from four different pig populations; Göttingen minipigs and Belgian, Kenyan, and Danish fattening pigs. We identified 67 alleles, nine previously described haplotypes and 15 novel haplotypes. The highest variation in SLA class I profiles was observed in the Danish pigs and the lowest among the Göttingen minipig population, which also have the highest percentage of homozygote individuals. Highlighting the fact that there are still numerous unknown SLA class I alleles to be discovered, a total of 12 novel SLA class I alleles were identified. Overall, we present new information about known and novel alleles and haplotypes and their prevalence in the tested pig populations.

Quality of the Exotic Parasitoid Cotesia flavipes (Hymenoptera: Braconidae) Does Not Show Deleterious Effects after Inbreeding for 10 Generations.

PubMed

Trevisan, Maíra; De Bortoli, Sergio A; Vacari, Alessandra M; Laurentis, Valéria L; Ramalho, Dagmara G

2016-01-01

Although the parasitoid Cotesia flavipes (Cameron) has proven effective in controlling sugarcane borer Diatraea saccharalis (Fabricius) for many years, concern has arisen over the quality of individuals produced at large scales. The parasitoid has been reared in laboratories in Brazil for more than 40 years, with no new introductions of new populations during that period. Since the quality of the parasitoids was not verified at the time of the species' introduction in Brazil, we do not know if there has been any reduction in quality so far. However, it is possible to determine whether the parasitoid could reduce in quality in future generations. Thus, the objective of this research was to assess the quality of these insects over 10 generations and look for evidence of any loss in quality. We used two populations: one from a biofactory that has been maintained in the laboratory for over 40 years, and an inbred laboratory population. Both were bred, and compared for 10 generations. We wanted to determine what happened to the quality of the parasitoid after 10 generations in an extreme inbreeding situation. To assure inbreeding, newly emerged females were forced to mate with a sibling. Individual females were then allowed to parasitize larvae of D. saccharalis. We performed evaluations for each generation until the tenth generation, and recorded the sex ratio, percentage emergence, number of offspring/females, and longevity of both males and females. Results of the measurements of biological characteristics demonstrated random significant differences between populations; best results were obtained intermittently for both the biofactory population and the inbred population. No significant differences across generations for the same population were observed. Thus, rearing of a C. flavipes population subjected to inbreeding for 10 generations was not sufficient to reveal any deleterious effects of inbreeding.

Characterisation of 12 microsatellite loci in the Vietnamese commercial clam Lutraria rhynchaena Jonas 1844 (Heterodonta: Bivalvia: Mactridae) through next-generation sequencing.

PubMed

Thai, Binh Thanh; Tan, Mun Hua; Lee, Yin Peng; Gan, Han Ming; Tran, Trang Thi; Austin, Christopher M

2016-05-01

The marine clam Lutraria rhynchaena is gaining popularity as an aquaculture species in Asia. Lutraria populations are present in the wild throughout Vietnam and several stocks have been established and translocated for breeding and aquaculture grow-out purposes. In this study, we demonstrate the feasibility of utilising Illumina next-generation sequencing technology to streamline the identification and genotyping of microsatellite loci from this clam species. Based on an initial partial genome scan, 48 microsatellite markers with similar melting temperatures were identified and characterised. The 12 most suitable polymorphic loci were then genotyped using 51 individuals from a population in Quang Ninh Province, North Vietnam. Genetic variation was low (mean number of alleles per locus = 2.6; mean expected heterozygosity = 0.41). Two loci showed significant deviation from Hardy-Weinberg equilibrium (HWE) and the presence of null alleles, but there was no evidence of linkage disequilibrium among loci. Three additional populations were screened (n = 7-36) to test the geographic utility of the 12 loci, which revealed 100 % successful genotyping in two populations from central Vietnam (Nha Trang). However, a second population from north Vietnam (Co To) could not be successfully genotyped and morphological evidence and mitochondrial variation suggests that this population represents a cryptic species of Lutraria. Comparisons of the Qang Ninh and Nha Trang populations, excluding the 2 loci out of HWE, revealed statistically significant allelic variation at 4 loci. We reported the first microsatellite loci set for the marine clam Lutraria rhynchaena and demonstrated its potential in differentiating clam populations. Additionally, a cryptic species population of Lutraria rhynchaena was identified during initial loci development, underscoring the overlooked diversity of marine clam species in Vietnam and the need to genetically characterise population representatives prior to microsatellite development. The rapid identification and validation of microsatellite loci using next-generation sequencing technology warrant its integration into future microsatellite loci development for key aquaculture species in Vietnam and more generally, aquaculture countries in the South East Asia region.

Facial morphologies of an adult Egyptian population and an adult Houstonian white population compared using 3D imaging.

PubMed

Seager, Dennis Craig; Kau, Chung How; English, Jeryl D; Tawfik, Wael; Bussa, Harry I; Ahmed, Abou El Yazeed M

2009-09-01

To compare the facial morphologies of an adult Egyptian population with those of a Houstonian white population. The three-dimensional (3D) images were acquired via a commercially available stereophotogrammetric camera capture system. The 3dMDface System photographed 186 subjects from two population groups (Egypt and Houston). All of the participants from both population groups were between 18 and 30 years of age and had no apparent facial anomalies. All facial images were overlaid and superimposed, and a complex mathematical algorithm was performed to generate a composite facial average (one male and one female) for each subgroup (EGY-M: Egyptian male subjects; EGY-F: Egyptian female subjects; HOU-M: Houstonian male subjects; and HOU-F: Houstonian female subjects). The computer-generated facial averages were superimposed based on a previously validated superimposition method, and the facial differences were evaluated and quantified. Distinct facial differences were evident between the subgroups evaluated, involving various regions of the face including the slant of the forehead, and the nasal, malar, and labial regions. Overall, the mean facial differences between the Egyptian and Houstonian female subjects were 1.33 +/- 0.93 mm, while the differences in Egyptian and Houstonian male subjects were 2.32 +/- 2.23 mm. The range of differences for the female population pairings and the male population pairings were 14.34 mm and 13.71 mm, respectively. The average adult Egyptian and white Houstonian face possess distinct differences. Different populations and ethnicities have different facial features and averages.

Techniques of contributing-area delineation for analysis of nonpoint-source contamination of Long Island, New York

USGS Publications Warehouse

Misut, P.

1995-01-01

Ninety shallow monitoring wells on Long Island, N.Y., were used to test the hypothesis that the correlation between the detection of volatile organic compounds (VOC's) at a well and explanatory variables representing land use, population density, and hydrogeologic conditions around the well is affected by the size and shape of the area defined as the contributing area. Explanatory variables are quantified through overlay of various specified contributing areas on 1:24 000-scale landuse and population-density geographic information system (GIS) coverages. Four methods of contributing-area delineation were used: (a) centering a circle of selected radius on the well site, (b) orienting a triangular area along the direction of horizontal ground-water flow to the well, (c) generating a shaped based on direction and magnitude of horizontal flow to the well, and (d) generating a shape based on three-dimensional particle pathlines backtracked from the well screen to the water table. The strongest correlations with VOC detections were obtained from circles of 400- to 1 000-meter radius. Improvement in correlation through delineations based on ground-water flow would require geographic overlay on more highly detailed GIS coverages than those used in the study.

The temporal spectrum of adult mosquito population fluctuations: conceptual and modeling implications.

PubMed

Jian, Yun; Silvestri, Sonia; Brown, Jeff; Hickman, Rick; Marani, Marco

2014-01-01

An improved understanding of mosquito population dynamics under natural environmental forcing requires adequate field observations spanning the full range of temporal scales over which mosquito abundance fluctuates in natural conditions. Here we analyze a 9-year daily time series of uninterrupted observations of adult mosquito abundance for multiple mosquito species in North Carolina to identify characteristic scales of temporal variability, the processes generating them, and the representativeness of observations at different sampling resolutions. We focus in particular on Aedes vexans and Culiseta melanura and, using a combination of spectral analysis and modeling, we find significant population fluctuations with characteristic periodicity between 2 days and several years. Population dynamical modelling suggests that the observed fast fluctuations scales (2 days-weeks) are importantly affected by a varying mosquito activity in response to rapid changes in meteorological conditions, a process neglected in most representations of mosquito population dynamics. We further suggest that the range of time scales over which adult mosquito population variability takes place can be divided into three main parts. At small time scales (indicatively 2 days-1 month) observed population fluctuations are mainly driven by behavioral responses to rapid changes in weather conditions. At intermediate scales (1 to several month) environmentally-forced fluctuations in generation times, mortality rates, and density dependence determine the population characteristic response times. At longer scales (annual to multi-annual) mosquito populations follow seasonal and inter-annual environmental changes. We conclude that observations of adult mosquito populations should be based on a sub-weekly sampling frequency and that predictive models of mosquito abundance must include behavioral dynamics to separate the effects of a varying mosquito activity from actual changes in the abundance of the underlying population.

The risk of elevated prolactin levels in pediatric patients exposed to antipsychotics for the treatment of schizophrenia and schizophrenia spectrum disorders: protocol for a systematic review and meta-analysis

PubMed Central

2014-01-01

Background Antipsychotic medications, particularly second-generation antipsychotics, are increasingly being used to alleviate the symptoms of schizophrenia and other severe mental disorders in the pediatric population. While evidence-based approaches examining efficacy and safety outcomes have been reported, no review has evaluated prolactin-based adverse events for antipsychotic treatments in schizophrenia and schizophrenia spectrum disorders. Methods/design Searches involving MEDLINE, EMBASE, CENTRAL, PsycINFO, and clinical trial registries (ClinicalTrials.gov, Drug Industry Document Archive [DIDA], International Clinical Trials Registry Platform [ICTRP]) will be used to identify relevant studies. Two reviewers will independently screen abstracts and relevant full-text articles of the papers identified by the initial search according to the prospectively defined eligibility criteria. Data extraction will be conducted in duplicate independently. Pairwise random effects meta-analyses and network meta-analyses will be conducted on individual drug and class effects where appropriate. Discussion This systematic review will evaluate prolactin-based adverse events of first- and second-generation antipsychotics in the pediatric population with schizophrenia and schizophrenia spectrum disorders. It will also seek to strengthen the evidence base of the safety of antipsychotics by incorporating both randomized controlled trials and observational studies. Systematic review registration PROSPERO CRD42014009506 PMID:25312992

A Study of the Multiple Populations in M10

NASA Astrophysics Data System (ADS)

Gerber, Jeffrey M.; Friel, Eileen D.; Vesperini, Enrico

2017-06-01

We present an analysis of CN and CH band strengths which allow the identification of multiple populations in red giant stars in the globular cluster M10. Our measurements come from low-resolution spectroscopy obtained for ~140 red and asymptotic giant branch stars over two observation runs using Hydra on the WIYN 3.5m telescope. We sort the stars into nitrogen normal and enhanced populations based on the distribution of CN band strength as a function of magnitude. Once the stars are sorted into first and second generation (CN normal and enhanced, respectively), we compare this analysis to other ways of determining multiple stellar populations such as with the light elements Na and O and photometric indicators, particularly the UV photometry from the Hubble Space Telescope. C and N abundances are determined by matching observed CN and CH band measurements with those produced by synthetic spectra created with the Synthetic Spectrum Generator (SSG). The large sample size also allows us to study characteristics like radial distribution, and evolutionary effects such as the depletion of carbon (and subsequent nitrogen enrichment) as a star climbs the red giant branch. We find a rate of carbon depletion as a function of time for both populations in M10 and compare our result to M13, a cluster similar in metallicity.

FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations

PubMed Central

Delaney, Nigel F.; Marx, Christopher J.

2012-01-01

Understanding evolutionary dynamics within microbial populations requires the ability to accurately follow allele frequencies through time. Here we present a rapid, cost-effective method (FREQ-Seq) that leverages Illumina next-generation sequencing for localized, quantitative allele frequency detection. Analogous to RNA-Seq, FREQ-Seq relies upon counts from the >105 reads generated per locus per time-point to determine allele frequencies. Loci of interest are directly amplified from a mixed population via two rounds of PCR using inexpensive, user-designed oligonucleotides and a bar-coded bridging primer system that can be regenerated in-house. The resulting bar-coded PCR products contain the adapters needed for Illumina sequencing, eliminating further library preparation. We demonstrate the utility of FREQ-Seq by determining the order and dynamics of beneficial alleles that arose as a microbial population, founded with an engineered strain of Methylobacterium, evolved to grow on methanol. Quantifying allele frequencies with minimal bias down to 1% abundance allowed effective analysis of SNPs, small in-dels and insertions of transposable elements. Our data reveal large-scale clonal interference during the early stages of adaptation and illustrate the utility of FREQ-Seq as a cost-effective tool for tracking allele frequencies in populations. PMID:23118913

Potential and limits for rapid genetic adaptation to warming in a Great Barrier Reef coral.

PubMed

Matz, Mikhail V; Treml, Eric A; Aglyamova, Galina V; Bay, Line K

2018-04-01

Can genetic adaptation in reef-building corals keep pace with the current rate of sea surface warming? Here we combine population genomics, biophysical modeling, and evolutionary simulations to predict future adaptation of the common coral Acropora millepora on the Great Barrier Reef (GBR). Genomics-derived migration rates were high (0.1-1% of immigrants per generation across half the latitudinal range of the GBR) and closely matched the biophysical model of larval dispersal. Both genetic and biophysical models indicated the prevalence of southward migration along the GBR that would facilitate the spread of heat-tolerant alleles to higher latitudes as the climate warms. We developed an individual-based metapopulation model of polygenic adaptation and parameterized it with population sizes and migration rates derived from the genomic analysis. We find that high migration rates do not disrupt local thermal adaptation, and that the resulting standing genetic variation should be sufficient to fuel rapid region-wide adaptation of A. millepora populations to gradual warming over the next 20-50 coral generations (100-250 years). Further adaptation based on novel mutations might also be possible, but this depends on the currently unknown genetic parameters underlying coral thermal tolerance and the rate of warming realized. Despite this capacity for adaptation, our model predicts that coral populations would become increasingly sensitive to random thermal fluctuations such as ENSO cycles or heat waves, which corresponds well with the recent increase in frequency of catastrophic coral bleaching events.

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

Turbine Control of a Tidal and River Power Generator

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

Muljadi, Eduard; Wright, Alan; Gevorgian, Vahan

As renewable generation has become less expensive during recent decades, and it becomes more accepted by the global population, the focus on renewable generation has expanded to include new types with promising future applications, such as river and tidal generation. The input variations to these types of resources are slower but also steadier than wind or solar generation. The level of water turbulent flow may vary from one place to another, however, the control algorithm can be adjusted to local environment. This paper describes the hydrokinetic aspects of river and tidal generation based on a river and tidal generator. Althoughmore » the information given in this paper is not that of an exact generator deployed on site, the data used is representative of a typical river or tidal generator. In this paper, the hydrokinetic and associated electrical controller of the system were not included; however, the focus of this paper is on the hydrodynamic control.« less

Turbine Control of a Tidal and River Power Generator: Preprint

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

Muljadi, Eduard; Gevorgian, Vahan; Wright, Alan

As renewable generation has become less expensive during recent decades, and it becomes more accepted by the global population, the focus on renewable generation has expanded to include new types with promising future applications, such as river and tidal generation. The input variations to these types of resources are slower but also steadier than wind or solar generation. The level of water turbulent flow may vary from one place to another, however, the control algorithm can be adjusted to local environment. This paper describes the hydrokinetic aspects of river and tidal generation based on a river and tidal generator. Althoughmore » the information given in this paper is not that of an exact generator deployed on site, the data used is representative of a typical river or tidal generator. In this paper, the hydrokinetic and associated electrical controller of the system were not included; however, the focus of this paper is on the hydrodynamic control.« less

Propagating Neural Source Revealed by Doppler Shift of Population Spiking Frequency

PubMed Central

Zhang, Mingming; Shivacharan, Rajat S.; Chiang, Chia-Chu; Gonzalez-Reyes, Luis E.

2016-01-01

Electrical activity in the brain during normal and abnormal function is associated with propagating waves of various speeds and directions. It is unclear how both fast and slow traveling waves with sometime opposite directions can coexist in the same neural tissue. By recording population spikes simultaneously throughout the unfolded rodent hippocampus with a penetrating microelectrode array, we have shown that fast and slow waves are causally related, so a slowly moving neural source generates fast-propagating waves at ∼0.12 m/s. The source of the fast population spikes is limited in space and moving at ∼0.016 m/s based on both direct and Doppler measurements among 36 different spiking trains among eight different hippocampi. The fact that the source is itself moving can account for the surprising direction reversal of the wave. Therefore, these results indicate that a small neural focus can move and that this phenomenon could explain the apparent wave reflection at tissue edges or multiple foci observed at different locations in neural tissue. SIGNIFICANCE STATEMENT The use of novel techniques with an unfolded hippocampus and penetrating microelectrode array to record and analyze neural activity has revealed the existence of a source of neural signals that propagates throughout the hippocampus. The source itself is electrically silent, but its location can be inferred by building isochrone maps of population spikes that the source generates. The movement of the source can also be tracked by observing the Doppler frequency shift of these spikes. These results have general implications for how neural signals are generated and propagated in the hippocampus; moreover, they have important implications for the understanding of seizure generation and foci localization. PMID:27013678

Direct estimate of the spontaneous germ line mutation rate in African green monkeys.

PubMed

Pfeifer, Susanne P

2017-12-01

Here, I provide the first direct estimate of the spontaneous mutation rate in an Old World monkey, using a seven individual, three-generation pedigree of African green monkeys. Eight de novo mutations were identified within ∼1.5 Gbp of accessible genome, corresponding to an estimated point mutation rate of 0.94 × 10 -8 per site per generation, suggesting an effective population size of ∼12000 for the species. This estimation represents a significant improvement in our knowledge of the population genetics of the African green monkey, one of the most important nonhuman primate models in biomedical research. Furthermore, by comparing mutation rates in Old World monkeys with the only other direct estimates in primates to date-humans and chimpanzees-it is possible to uniquely address how mutation rates have evolved over longer time scales. While the estimated spontaneous mutation rate for African green monkeys is slightly lower than the rate of 1.2 × 10 -8 per base pair per generation reported in chimpanzees, it is similar to the lower range of rates of 0.96 × 10 -8 -1.28 × 10 -8 per base pair per generation recently estimated from whole genome pedigrees in humans. This result suggests a long-term constraint on mutation rate that is quite different from similar evidence pertaining to recombination rate evolution in primates. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

An Untapped Resource for Increasing College Attainment: Estimating the Population of Potential First-Generation Students in Wisconsin. WISCAPE Policy Brief

ERIC Educational Resources Information Center

Lazenby, Sara

2011-01-01

Potential first-generation students make up a large segment of Wisconsin's teenage population. To increase the pool of educated workers in Wisconsin, policymakers must work to recruit, retain, and graduate these students. Estimates of the size of the first-generation student population in the state are crucial for these efforts. This brief…

Assessing Coverage of Population-Based and Targeted Fortification Programs with the Use of the Fortification Assessment Coverage Toolkit (FACT): Background, Toolkit Development, and Supplement Overview.

PubMed

Friesen, Valerie M; Aaron, Grant J; Myatt, Mark; Neufeld, Lynnette M

2017-05-01

Food fortification is a widely used approach to increase micronutrient intake in the diet. High coverage is essential for achieving impact. Data on coverage is limited in many countries, and tools to assess coverage of fortification programs have not been standardized. In 2013, the Global Alliance for Improved Nutrition developed the Fortification Assessment Coverage Toolkit (FACT) to carry out coverage assessments in both population-based (i.e., staple foods and/or condiments) and targeted (e.g., infant and young child) fortification programs. The toolkit was designed to generate evidence on program coverage and the use of fortified foods to provide timely and programmatically relevant information for decision making. This supplement presents results from FACT surveys that assessed the coverage of population-based and targeted food fortification programs across 14 countries. It then discusses the policy and program implications of the findings for the potential for impact and program improvement.

Incorporating GIS building data and census housing statistics for sub-block-level population estimation

USGS Publications Warehouse

Wu, S.-S.; Wang, L.; Qiu, X.

2008-01-01

This article presents a deterministic model for sub-block-level population estimation based on the total building volumes derived from geographic information system (GIS) building data and three census block-level housing statistics. To assess the model, we generated artificial blocks by aggregating census block areas and calculating the respective housing statistics. We then applied the model to estimate populations for sub-artificial-block areas and assessed the estimates with census populations of the areas. Our analyses indicate that the average percent error of population estimation for sub-artificial-block areas is comparable to those for sub-census-block areas of the same size relative to associated blocks. The smaller the sub-block-level areas, the higher the population estimation errors. For example, the average percent error for residential areas is approximately 0.11 percent for 100 percent block areas and 35 percent for 5 percent block areas.

Neural-like computing with populations of superparamagnetic basis functions.

PubMed

Mizrahi, Alice; Hirtzlin, Tifenn; Fukushima, Akio; Kubota, Hitoshi; Yuasa, Shinji; Grollier, Julie; Querlioz, Damien

2018-04-18

In neuroscience, population coding theory demonstrates that neural assemblies can achieve fault-tolerant information processing. Mapped to nanoelectronics, this strategy could allow for reliable computing with scaled-down, noisy, imperfect devices. Doing so requires that the population components form a set of basis functions in terms of their response functions to inputs, offering a physical substrate for computing. Such a population can be implemented with CMOS technology, but the corresponding circuits have high area or energy requirements. Here, we show that nanoscale magnetic tunnel junctions can instead be assembled to meet these requirements. We demonstrate experimentally that a population of nine junctions can implement a basis set of functions, providing the data to achieve, for example, the generation of cursive letters. We design hybrid magnetic-CMOS systems based on interlinked populations of junctions and show that they can learn to realize non-linear variability-resilient transformations with a low imprint area and low power.

Diversity and distribution of Wolbachia in relation to geography, host plant affiliation and life cycle of a heterogonic gall wasp.

PubMed

Schuler, Hannes; Egan, Scott P; Hood, Glen R; Busbee, Robert W; Driscoe, Amanda L; Ott, James R

2018-03-27

The maternally inherited endosymbiont Wolbachia is widespread in arthropods and nematodes and can play an important role in the ecology and evolution of its host through reproductive manipulation. Here, we survey Wolbachia in Belonocnema treatae, a widely distributed North American cynipid gall forming wasp that exhibits regional host specialization on three species of oaks and alternation of sexually and asexually reproducing generations. We investigated whether patterns of Wolbachia infection and diversity in B. treatae are associated with the insect's geographic distribution, host plant association, life cycle, and mitochondrial evolutionary history. Screening of 463 individuals from 23 populations including sexual and asexual generations from all three host plants across the southern U.S. showed an average infection rate of 56% with three common Wolbachia strains: wTre1-3 and an additional rare variant wTre4. Phylogenetic analysis based on wsp showed that these strains are unrelated and likely independently inherited. We found no difference in Wolbachia infection frequency among host plant associated populations or between the asexual and sexual generations, or between males and females of the sexual generation. Partially incomplete Wolbachia transmission rates might explain the occurrence of uninfected individuals. A parallel analysis of the mitochondrial cytochrome oxidase I gene in B. treatae showed high mtDNA haplotype diversity in both infected and uninfected populations suggesting an ancestral infection by Wolbachia as well as a clear split between eastern and western B. treatae mtDNA clades with a sequence divergence of > 6%. The strain wTre1 was present almost exclusively in the western clade while wTre2 and wTre3 occur almost exclusively in eastern populations. In contrast, the same strains co-occur as double-infections in Georgia and triple-infections in two populations in central Florida. The diversity of Wolbachia across geographically and genetically distinct populations of B. treatae and the co-occurrence of the same strains within three populations highlights the complex infection dynamics in this system. Moreover, the association of distinct Wolbachia strains with mitochondrial haplotypes of its host in populations infected by different Wolbachia strains suggests a potential role of the endosymbiont in reproductive isolation in B. treatae.

Controlling the Growth of Future LEO Debris Populations with Active Debris Removal

NASA Technical Reports Server (NTRS)

Liou, J.-C.; Johnson, N. L.; Hill, N. M.

2008-01-01

Active debris removal (ADR) was suggested as a potential means to remediate the low Earth orbit (LEO) debris environment as early as the 1980s. The reasons ADR has not become practical are due to its technical difficulties and the high cost associated with the approach. However, as the LEO debris populations continue to increase, ADR may be the only option to preserve the near-Earth environment for future generations. An initial study was completed in 2007 to demonstrate that a simple ADR target selection criterion could be developed to reduce the future debris population growth. The present paper summarizes a comprehensive study based on more realistic simulation scenarios, including fragments generated from the 2007 Fengyun-1C event, mitigation measures, and other target selection options. The simulations were based on the NASA long-term orbital debris projection model, LEGEND. A scenario, where at the end of mission lifetimes, spacecraft and upper stages were moved to 25-year decay orbits, was adopted as the baseline environment for comparison. Different annual removal rates and different ADR target selection criteria were tested, and the resulting 200-year future environment projections were compared with the baseline scenario. Results of this parametric study indicate that (1) an effective removal strategy can be developed based on the mass and collision probability of each object as the selection criterion, and (2) the LEO environment can be stabilized in the next 200 years with an ADR removal rate of five objects per year.

A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells

PubMed Central

2012-01-01

Background CD4+ T cells have several subsets of functional phenotypes, which play critical yet diverse roles in the immune system. Pathogen-driven differentiation of these subsets of cells is often heterogeneous in terms of the induced phenotypic diversity. In vitro recapitulation of heterogeneous differentiation under homogeneous experimental conditions indicates some highly regulated mechanisms by which multiple phenotypes of CD4+ T cells can be generated from a single population of naïve CD4+ T cells. Therefore, conceptual understanding of induced heterogeneous differentiation will shed light on the mechanisms controlling the response of populations of CD4+ T cells under physiological conditions. Results We present a simple theoretical framework to show how heterogeneous differentiation in a two-master-regulator paradigm can be governed by a signaling network motif common to all subsets of CD4+ T cells. With this motif, a population of naïve CD4+ T cells can integrate the signals from their environment to generate a functionally diverse population with robust commitment of individual cells. Notably, two positive feedback loops in this network motif govern three bistable switches, which in turn, give rise to three types of heterogeneous differentiated states, depending upon particular combinations of input signals. We provide three prototype models illustrating how to use this framework to explain experimental observations and make specific testable predictions. Conclusions The process in which several types of T helper cells are generated simultaneously to mount complex immune responses upon pathogenic challenges can be highly regulated, and a simple signaling network motif can be responsible for generating all possible types of heterogeneous populations with respect to a pair of master regulators controlling CD4+ T cell differentiation. The framework provides a mathematical basis for understanding the decision-making mechanisms of CD4+ T cells, and it can be helpful for interpreting experimental results. Mathematical models based on the framework make specific testable predictions that may improve our understanding of this differentiation system. PMID:22697466

Modern spandrels: the roles of genetic drift, gene flow and natural selection in the evolution of parallel clines.

PubMed

Santangelo, James S; Johnson, Marc T J; Ness, Rob W

2018-05-16

Urban environments offer the opportunity to study the role of adaptive and non-adaptive evolutionary processes on an unprecedented scale. While the presence of parallel clines in heritable phenotypic traits is often considered strong evidence for the role of natural selection, non-adaptive evolutionary processes can also generate clines, and this may be more likely when traits have a non-additive genetic basis due to epistasis. In this paper, we use spatially explicit simulations modelled according to the cyanogenesis (hydrogen cyanide, HCN) polymorphism in white clover ( Trifolium repens ) to examine the formation of phenotypic clines along urbanization gradients under varying levels of drift, gene flow and selection. HCN results from an epistatic interaction between two Mendelian-inherited loci. Our results demonstrate that the genetic architecture of this trait makes natural populations susceptible to decreases in HCN frequencies via drift. Gradients in the strength of drift across a landscape resulted in phenotypic clines with lower frequencies of HCN in strongly drifting populations, giving the misleading appearance of deterministic adaptive changes in the phenotype. Studies of heritable phenotypic change in urban populations should generate null models of phenotypic evolution based on the genetic architecture underlying focal traits prior to invoking selection's role in generating adaptive differentiation. © 2018 The Author(s).

Population specific fitness response of Drosophila subobscura to lead pollution.

PubMed

Kenig, Bojan; Stamenković-Radak, Marina; Andelković, Marko

2013-04-01

Differences in heavy metal tolerance among separate populations of the same species have often been interpreted as local adaptation. Persistence of differences after removing the stressor indicates that mechanisms responsible for the increased tolerance were genetically determined. Drosophila subobscura Collin (Diptera: Drosophilidae) populations were sampled from two localities with different history of heavy metal pollution, and reared for eight generations in the laboratory on a standard medium and on media with different concentrations of lead (Pb). To determine whether flies from different natural populations exposed to the Pb-contaminated media in the laboratory show population specific variability in fitness components over generations, experimental groups with different concentrations of lead were assayed in three generations (F2 , F5 , and F8 ) for fecundity, developmental time, and egg-to-adult viability. On the contaminated medium, fecundity was reduced in later generations and viability was increased, irrespective of the environmental origin of populations. For both populations, developmental time showed a tendency of slowing down on media with lead. Faster development was observed in later generations. Preadaptation to contamination, meaning higher fecundity, higher viability, and faster egg to adult development in all studied generations, was found in D. subobscura originating from the locality with a higher level of heavy metal pollution. © 2012 The Authors Insect Science © 2012 Institute of Zoology, Chinese Academy of Sciences.

Genomic variation in macrophage-cultured European porcine reproductive and respiratory syndrome virus Olot/91 revealed using ultra-deep next generation sequencing.

PubMed

Lu, Zen H; Brown, Alexander; Wilson, Alison D; Calvert, Jay G; Balasch, Monica; Fuentes-Utrilla, Pablo; Loecherbach, Julia; Turner, Frances; Talbot, Richard; Archibald, Alan L; Ait-Ali, Tahar

2014-03-04

Porcine Reproductive and Respiratory Syndrome (PRRS) is a disease of major economic impact worldwide. The etiologic agent of this disease is the PRRS virus (PRRSV). Increasing evidence suggest that microevolution within a coexisting quasispecies population can give rise to high sequence heterogeneity in PRRSV. We developed a pipeline based on the ultra-deep next generation sequencing approach to first construct the complete genome of a European PRRSV, strain Olot/9, cultured on macrophages and then capture the rare variants representative of the mixed quasispecies population. Olot/91 differs from the reference Lelystad strain by about 5% and a total of 88 variants, with frequencies as low as 1%, were detected in the mixed population. These variants included 16 non-synonymous variants concentrated in the genes encoding structural and nonstructural proteins; including Glycoprotein 2a and 5. Using an ultra-deep sequencing methodology, the complete genome of Olot/91 was constructed without any prior knowledge of the sequence. Rare variants that constitute minor fractions of the heterogeneous PRRSV population could successfully be detected to allow further exploration of microevolutionary events.

An assessment of total and leachable contaminants in zebra mussels (Dreissena polymorpha) from Lake Erie

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

Doherty, F.G.; Evans, D.W.; Neuhauser, E.F.

Samples of zebra mussels, Dreissena polymorpha, from populations infesting two power generating stations on Lake Erie were subjected to tests assessing the potential for leaching of metals and other (inorganic and organic) contaminants from mussel waste destined for disposal in conventional landfills. These tests revealed that mussels collected from Ontario Hydro's Nanticoke Thermal Generating Station and Niagara Mohawk Power Corporation's Dunkirk Steam Station did not release hazardous materials in excess of limits set forth in Canadian and U.S. regulations, respectively. A variety of metals and inorganic materials leached from Nanticoke mussels at levels significantly lower than the registration limits formore » those analytes. Detectable levels of chloroform (0.080 mg/liter) and barium (3.3 mg/liter) leached from Dunkirk mussels at > 30-fold lower levels than U.S. regulatory action limits for those materials. Whole body analyses revealed a lack of detectable levels of herbicides and pesticides in either population with a variety of metals and inorganic constituents in all samples from both populations. The physiological condition of Dunkirk mussels appeared to be consistent with that of other Lake Erie populations based on percentage water and total fat content of soft tissues.« less

An assessment of total and leachable contaminants in zebra mussels (Dreissena polymorpha) from Lake Erie.

PubMed

Doherty, F G; Evans, D W; Neuhauser, E F

1993-06-01

Samples of zebra mussels, Dreissena polymorpha, from populations infesting two power generating stations on Lake Erie were subjected to tests assessing the potential for leaching of metals and other (inorganic and organic) contaminants from mussel waste destined for disposal in conventional landfills. These tests revealed that mussels collected from Ontario Hydro's Nanticoke Thermal Generating Station and Niagara Mohawk Power Corporation's Dunkirk Steam Station did not release hazardous materials in excess of limits set forth in Canadian and U.S. regulations, respectively. A variety of metals and inorganic materials leached from Nanticoke mussels at levels significantly lower than the registration limits for those analytes. Detectable levels of chloroform (0.080 mg/liter) and barium (3.3 mg/liter) leached from Dunkirk mussels at > 30-fold lower levels than U.S. regulatory action limits for those materials. Whole body analyses revealed a lack of detectable levels of herbicides and pesticides in either population with a variety of metals and inorganic constituents in all samples from both populations. The physiological condition of Dunkirk mussels appeared to be consistent with that of other Lake Erie populations based on percentage water and total fat content of soft tissues.

A multi-parent advanced generation inter-cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.).

PubMed

Huynh, Bao-Lam; Ehlers, Jeffrey D; Huang, Bevan Emma; Muñoz-Amatriaín, María; Lonardi, Stefano; Santos, Jansen R P; Ndeve, Arsenio; Batieno, Benoit J; Boukar, Ousmane; Cisse, Ndiaga; Drabo, Issa; Fatokun, Christian; Kusi, Francis; Agyare, Richard Y; Guo, Yi-Ning; Herniter, Ira; Lo, Sassoum; Wanamaker, Steve I; Xu, Shizhong; Close, Timothy J; Roberts, Philip A

2018-03-01

Multi-parent advanced generation inter-cross (MAGIC) populations are an emerging type of resource for dissecting the genetic structure of traits and improving breeding populations. We developed a MAGIC population for cowpea (Vigna unguiculata L. Walp.) from eight founder parents. These founders were genetically diverse and carried many abiotic and biotic stress resistance, seed quality and agronomic traits relevant to cowpea improvement in the United States and sub-Saharan Africa, where cowpea is vitally important in the human diet and local economies. The eight parents were inter-crossed using structured matings to ensure that the population would have balanced representation from each parent, followed by single-seed descent, resulting in 305 F 8 recombinant inbred lines each carrying a mosaic of genome blocks contributed by all founders. This was confirmed by single nucleotide polymorphism genotyping with the Illumina Cowpea Consortium Array. These lines were on average 99.74% homozygous but also diverse in agronomic traits across environments. Quantitative trait loci (QTLs) were identified for several parental traits. Loci with major effects on photoperiod sensitivity and seed size were also verified by biparental genetic mapping. The recombination events were concentrated in telomeric regions. Due to its broad genetic base, this cowpea MAGIC population promises breakthroughs in genetic gain, QTL and gene discovery, enhancement of breeding populations and, for some lines, direct releases as new varieties. © 2018 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

Genetic algorithms with memory- and elitism-based immigrants in dynamic environments.

PubMed

Yang, Shengxiang

2008-01-01

In recent years the genetic algorithm community has shown a growing interest in studying dynamic optimization problems. Several approaches have been devised. The random immigrants and memory schemes are two major ones. The random immigrants scheme addresses dynamic environments by maintaining the population diversity while the memory scheme aims to adapt genetic algorithms quickly to new environments by reusing historical information. This paper investigates a hybrid memory and random immigrants scheme, called memory-based immigrants, and a hybrid elitism and random immigrants scheme, called elitism-based immigrants, for genetic algorithms in dynamic environments. In these schemes, the best individual from memory or the elite from the previous generation is retrieved as the base to create immigrants into the population by mutation. This way, not only can diversity be maintained but it is done more efficiently to adapt genetic algorithms to the current environment. Based on a series of systematically constructed dynamic problems, experiments are carried out to compare genetic algorithms with the memory-based and elitism-based immigrants schemes against genetic algorithms with traditional memory and random immigrants schemes and a hybrid memory and multi-population scheme. The sensitivity analysis regarding some key parameters is also carried out. Experimental results show that the memory-based and elitism-based immigrants schemes efficiently improve the performance of genetic algorithms in dynamic environments.

Interacting effects of genetic variation for seed dormancy and flowering time on phenology, life history, and fitness of experimental Arabidopsis thaliana populations over multiple generations in the field.

PubMed

Taylor, Mark A; Cooper, Martha D; Sellamuthu, Reena; Braun, Peter; Migneault, Andrew; Browning, Alyssa; Perry, Emily; Schmitt, Johanna

2017-10-01

Major alleles for seed dormancy and flowering time are well studied, and can interact to influence seasonal timing and fitness within generations. However, little is known about how this interaction controls phenology, life history, and population fitness across multiple generations in natural seasonal environments. To examine how seed dormancy and flowering time shape annual plant life cycles over multiple generations, we established naturally dispersing populations of recombinant inbred lines of Arabidopsis thaliana segregating early and late alleles for seed dormancy and flowering time in a field experiment. We recorded seasonal phenology and fitness of each genotype over 2 yr and several generations. Strong seed dormancy suppressed mid-summer germination in both early- and late-flowering genetic backgrounds. Strong dormancy and late-flowering genotypes were both necessary to confer a winter annual life history; other genotypes were rapid-cycling. Strong dormancy increased within-season fecundity in an early-flowering background, but decreased it in a late-flowering background. However, there were no detectable differences among genotypes in population growth rates. Seasonal phenology, life history, and cohort fitness over multiple generations depend strongly upon interacting genetic variation for dormancy and flowering. However, similar population growth rates across generations suggest that different life cycle genotypes can coexist in natural populations. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform

PubMed Central

Suyama, Yoshihisa; Matsuki, Yu

2015-01-01

Restriction-enzyme (RE)-based next-generation sequencing methods have revolutionized marker-assisted genetic studies; however, the use of REs has limited their widespread adoption, especially in field samples with low-quality DNA and/or small quantities of DNA. Here, we developed a PCR-based procedure to construct reduced representation libraries without RE digestion steps, representing de novo single-nucleotide polymorphism discovery, and its genotyping using next-generation sequencing. Using multiplexed inter-simple sequence repeat (ISSR) primers, thousands of genome-wide regions were amplified effectively from a wide variety of genomes, without prior genetic information. We demonstrated: 1) Mendelian gametic segregation of the discovered variants; 2) reproducibility of genotyping by checking its applicability for individual identification; and 3) applicability in a wide variety of species by checking standard population genetic analysis. This approach, called multiplexed ISSR genotyping by sequencing, should be applicable to many marker-assisted genetic studies with a wide range of DNA qualities and quantities. PMID:26593239

Epigenetic and Genetic Contributions to Adaptation in Chlamydomonas.

PubMed

Kronholm, Ilkka; Bassett, Andrew; Baulcombe, David; Collins, Sinéad

2017-09-01

Epigenetic modifications, such as DNA methylation or histone modifications, can be transmitted between cellular or organismal generations. However, there are no experiments measuring their role in adaptation, so here we use experimental evolution to investigate how epigenetic variation can contribute to adaptation. We manipulated DNA methylation and histone acetylation in the unicellular green alga Chlamydomonas reinhardtii both genetically and chemically to change the amount of epigenetic variation generated or transmitted in adapting populations in three different environments (salt stress, phosphate starvation, and high CO2) for two hundred asexual generations. We find that reducing the amount of epigenetic variation available to populations can reduce adaptation in environments where it otherwise happens. From genomic and epigenomic sequences from a subset of the populations, we see changes in methylation patterns between the evolved populations over-represented in some functional categories of genes, which is consistent with some of these differences being adaptive. Based on whole genome sequencing of evolved clones, the majority of DNA methylation changes do not appear to be linked to cis-acting genetic mutations. Our results show that transgenerational epigenetic effects play a role in adaptive evolution, and suggest that the relationship between changes in methylation patterns and differences in evolutionary outcomes, at least for quantitative traits such as cell division rates, is complex. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Art meets science: The Cosmopolitan Chicken Research Project.

PubMed

Stinckens, A; Vereijken, A; Ons, E; Konings, P; Van As, P; Cuppens, H; Moreau, Y; Sakai, R; Aerts, J; Goddeeris, B; Buys, N; Vanmechelen, K; Cassiman, J J

2015-01-01

The Cosmopolitan Chicken Project is an artistic undertaking of renowned artist Koen Vanmechelen. In this project, the artist interbreeds domestic chickens from different countries aiming at the creation of a true Cosmopolitan Chicken as a symbol for global diversity. The unifying theme is the chicken and the egg, symbols that link scientific, political, philosophical and ethical issues. The Cosmopolitan Chicken Research Project is the scientific component of this artwork. Based on state of the art genomic techniques, the project studies the effect of the crossing of chickens on the genetic diversity. Also, this research is potentially applicable to the human population. The setup of the CC®P is quite different from traditional breeding experiments: starting from the crossbreed of two purebred chickens (Mechelse Koekoek x Poule de Bresse), every generation is crossed with a few animals from another breed. For 26 of these purebred and crossbred populations, genetic diversity was measured (1) under the assumption that populations were sufficiently large to maintain all informative SNP within a generation and (2) under the circumstances of the CCP breeding experiment. Under the first assumption, a steady increase in genetic diversity was witnessed over the consecutive generations, thus indeed indicating the creation of a "Cosmopolitan Chicken Genome". However, under the conditions of the CCP, which reflects the reality within the human population, diversity is seen to fluctuate within given boundaries instead of steadily increasing. A reflection on this might be that this is because, in humans, an evolutionary optimum in genetic diversity is reached. Key words.

Genetic determinants of freckle occurrence in the Spanish population: Towards ephelides prediction from human DNA samples.

PubMed

Hernando, Barbara; Ibañez, Maria Victoria; Deserio-Cuesta, Julio Alberto; Soria-Navarro, Raquel; Vilar-Sastre, Inca; Martinez-Cadenas, Conrado

2018-03-01

Prediction of human pigmentation traits, one of the most differentiable externally visible characteristics among individuals, from biological samples represents a useful tool in the field of forensic DNA phenotyping. In spite of freckling being a relatively common pigmentation characteristic in Europeans, little is known about the genetic basis of this largely genetically determined phenotype in southern European populations. In this work, we explored the predictive capacity of eight freckle and sunlight sensitivity-related genes in 458 individuals (266 non-freckled controls and 192 freckled cases) from Spain. Four loci were associated with freckling (MC1R, IRF4, ASIP and BNC2), and female sex was also found to be a predictive factor for having a freckling phenotype in our population. After identifying the most informative genetic variants responsible for human ephelides occurrence in our sample set, we developed a DNA-based freckle prediction model using a multivariate regression approach. Once developed, the capabilities of the prediction model were tested by a repeated 10-fold cross-validation approach. The proportion of correctly predicted individuals using the DNA-based freckle prediction model was 74.13%. The implementation of sex into the DNA-based freckle prediction model slightly improved the overall prediction accuracy by 2.19% (76.32%). Further evaluation of the newly-generated prediction model was performed by assessing the model's performance in a new cohort of 212 Spanish individuals, reaching a classification success rate of 74.61%. Validation of this prediction model may be carried out in larger populations, including samples from different European populations. Further research to validate and improve this newly-generated freckle prediction model will be needed before its forensic application. Together with DNA tests already validated for eye and hair colour prediction, this freckle prediction model may lead to a substantially more detailed physical description of unknown individuals from DNA found at the crime scene. Copyright © 2017 Elsevier B.V. All rights reserved.

Social-ecological interactions, management panaceas, and the future of wild fish populations

PubMed Central

van Poorten, Brett T.; Arlinghaus, Robert; Daedlow, Katrin; Haertel-Borer, Susanne S.

2011-01-01

We explored the social and ecological outcomes associated with emergence of a management panacea designed to govern a stochastic renewable natural resource. To that end, we constructed a model of a coupled social-ecological system of recreational fisheries in which a manager supports naturally fluctuating stocks by stocking fish in response to harvest-driven satisfaction of resource users. The realistic assumption of users remembering past harvest experiences when exploiting a stochastically fluctuating fish population facilitates the emergence of a stocking-based management panacea over time. The social benefits of panacea formation involve dampening natural population fluctuations and generating stability of user satisfaction. It also maintains the resource but promotes the eventual replacement of wild fish by hatchery-descended fish. Our analyses show this outcome is particularly likely when hatchery-descended fish are reasonably fit (e.g., characterized by similar survival relative to wild fish) and/or when natural recruitment of the wild population is low (e.g., attributable to habitat deterioration), which leaves the wild population with little buffer against competition by stocked fish. The potential for release-based panacea formation is particularly likely under user-based management regimes and should be common in a range of social-ecological systems (e.g., fisheries, forestry), whenever user groups are entitled to engage in release or replanting strategies. The net result will be the preservation of a renewable resource through user-based incentives, but the once natural populations are likely to be altered and to host nonnative genotypes. This risks other ecosystem services and the future of wild populations. PMID:21742983

Correlations between U.S. county annual cancer incidence and population density.

PubMed

Vares, David Ae; St-Pierre, Linda S; Persinger, Michael A

2015-01-01

Population density implicitly involves specific distances between living individuals who exhibit biophysical forces and energies. Objective was to investigate major data bases of cancer incidence and population data to help understand the emergent properties of diseases that become apparent only when large populations and areas are considered. Correlation analyses of the annual incidence (years 2007 to 2011) of cancer in counties (2,885) of the U.S. and population densities were convergent with these quantitative predictions and suggested an inflection threshold around 50 people per square mile. The potential role of subtle or even "non-local" factors coupled to averaged population density in the viability and mortality of the human species may serve as alternative explanations to the attribution of malignancy to "chance" factors. Calculations indicated average distances between the electric force dipole of the brains or bodies of human beings generate forces known to affect DNA extension and when distributed over the Compton wavelength of the electron could produce energies sufficient to affect the binding of base nucleotides. An inclusive science of human ecology might benefit from considering subtle forces and energies associated with the individual members within the habitat that could determine the probability of cellular anomalies.

Whole genome sequencing and imputation in isolated populations identify genetic associations with medically-relevant complex traits

PubMed Central

Southam, Lorraine; Gilly, Arthur; Süveges, Dániel; Farmaki, Aliki-Eleni; Schwartzentruber, Jeremy; Tachmazidou, Ioanna; Matchan, Angela; Rayner, Nigel W.; Tsafantakis, Emmanouil; Karaleftheri, Maria; Xue, Yali; Dedoussis, George; Zeggini, Eleftheria

2017-01-01

Next-generation association studies can be empowered by sequence-based imputation and by studying founder populations. Here we report ∼9.5 million variants from whole-genome sequencing (WGS) of a Cretan-isolated population, and show enrichment of rare and low-frequency variants with predicted functional consequences. We use a WGS-based imputation approach utilizing 10,422 reference haplotypes to perform genome-wide association analyses and observe 17 genome-wide significant, independent signals, including replicating evidence for association at eight novel low-frequency variant signals. Two novel cardiometabolic associations are at lead variants unique to the founder population sequences: chr16:70790626 (high-density lipoprotein levels beta −1.71 (SE 0.25), P=1.57 × 10−11, effect allele frequency (EAF) 0.006); and rs145556679 (triglycerides levels beta −1.13 (SE 0.17), P=2.53 × 10−11, EAF 0.013). Our findings add empirical support to the contribution of low-frequency variants in complex traits, demonstrate the advantage of including population-specific sequences in imputation panels and exemplify the power gains afforded by population isolates. PMID:28548082

Patterns of genetic diversity in the polymorphic ground snake (Sonora semiannulata).

PubMed

Cox, Christian L; Chippindale, Paul T

2014-08-01

We evaluated the genetic diversity of a snake species with color polymorphism to understand the evolutionary processes that drive genetic structure across a large geographic region. Specifically, we analyzed genetic structure of the highly polymorphic ground snake, Sonora semiannulata, (1) among populations, (2) among color morphs (3) at regional and local spatial scales, using an amplified fragment length polymorphism dataset and multiple population genetic analyses, including FST-based and clustering analytical techniques. Based upon these methods, we found that there was moderate to low genetic structure among populations. However, this diversity was not associated with geographic locality at either spatial scale. Similarly, we found no evidence for genetic divergence among color morphs at either spatial scale. These results suggest that despite dramatic color polymorphism, this phenotypic diversity is not a major driver of genetic diversity within or among populations of ground snakes. We suggest that there are two mechanisms that could explain existing genetic diversity in ground snakes: recent range expansion from a genetically diverse founder population and current or recent gene flow among populations. Our findings have further implications for the types of color polymorphism that may generate genetic diversity in snakes.

Improving production efficiency in the presence of genotype by environment interactions in pig genomic selection breeding programmes.

PubMed

Nirea, K G; Meuwissen, T H E

2017-04-01

We simulated a genomic selection pig breeding schemes containing nucleus and production herds to improve feed efficiency of production pigs that were cross-breed. Elite nucleus herds had access to high-quality feed, and production herds were fed low-quality feed. Feed efficiency in the nucleus herds had a heritability of 0.3 and 0.25 in the production herds. It was assumed the genetic relationships between feed efficiency in the nucleus and production were low (r g  = 0.2), medium (r g  = 0.5) and high (r g  = 0.8). In our alternative breeding schemes, different proportion of production animals were recorded for feed efficiency and genotyped with high-density panel of genetic markers. Genomic breeding value of the selection candidates for feed efficiency was estimated based on three different approaches. In one approach, genomic breeding value was estimated including nucleus animals in the reference population. In the second approach, the reference population was containing a mixture of nucleus and production animals. In the third approach, the reference population was only consisting of production herds. Using a mixture reference population, we generated 40-115% more genetic gain in the production environment as compared to only using nucleus reference population that were fed high-quality feed sources when the production animals were offspring of the nucleus animals. When the production animals were grand offspring of the nucleus animals, 43-104% more genetic gain was generated. Similarly, a higher genetic gain generated in the production environment when mixed reference population was used as compared to only using production animals. This was up to 19 and 14% when the production animals were offspring and grand offspring of nucleus animals, respectively. Therefore, in genomic selection pig breeding programmes, feed efficiency traits could be improved by properly designing the reference population. © 2016 Blackwell Verlag GmbH.

AN INTEGRATION OF COPEPOD-BASED BAFS, LIFECYCLE TOXICITY TESTING, AND ENDOCRINE DISRUPTION METHODOLOGIES FOR RAPID POPULATION-LEVEL RISK ASSESSMENT OF PERSISTENT BIOACCUMULATIVE TOXICANTS

EPA Science Inventory

Extensive multi-generational microplate culturing (copepod hatching stage through two broods) experiments were completed with the POPs lindane, DDD and fipronil sulfide.  Identical tandem microplate experiments were run concurrently to yield sufficient copepod biomass for li...

Personalized Surgical Risk Assessment Using Population-Based Data Analysis

ERIC Educational Resources Information Center

AbuSalah, Ahmad Mohammad

2013-01-01

The volume of information generated by healthcare providers is growing at a relatively high speed. This tremendous growth has created a gap between knowledge and clinical practice that experts say could be narrowed with the proper use of healthcare data to guide clinical decisions and tools that support rapid information availability at the…

Toward a better understanding of the impact of mass transit air pollutants on human health

USDA-ARS?s Scientific Manuscript database

Modern mass transit systems, based on roads, rail, water, and air, generate toxic airborne pollutants throughout the developed world. This has become one of the leading concerns about the use of modern transportation, particularly in densely-populated urban areas where their use is enormous and inc...

Examining Continuity of Early Expressive Vocabulary Development: The Generation R Study

ERIC Educational Resources Information Center

Henrichs, Jens; Rescorla, Leslie; Schenk, Jacqueline J.; Schmidt, Henk G.; Jaddoe, Vincent W. V.; Hofman, Albert; Raat, Hein; Verhulst, Frank C.; Tiemeier, Henning

2011-01-01

Purpose: The authors investigated continuity and discontinuity of vocabulary skills in a population-based cohort in the Netherlands. Method: Mothers of 3,759 children completed the Dutch version of the MacArthur Short Form Vocabulary Checklist (Zink & Lejaegere, 2003) at 18 months and a Dutch translation of the Language Development Survey…

Environmental Education and Training in Brazil. Discussion Paper No. 84.

ERIC Educational Resources Information Center

Bruan, Ricardo

Brazilian environmental education and training experience is recent but has a concrete base of generating awareness among all levels of the population and also aims to train people to protect, control and manage the use of environmental resources. Several visits were made by the author to organizations, enterprises and institutions from federal,…

Older People of Tomorrow: A Psychosocial Profile.

ERIC Educational Resources Information Center

Silverstone, Barbara

1996-01-01

Attempts to narrow the scope of present uncertainties about the older population by sketching a psychosocial profile of the older people of tomorrow based on what is known today. Focuses on the baby boom generation and the interplay between personal attributes they could bring to late life and the social and physical environment in which they…

Mapping genes underlying ethnic differences in disease risk by linkage disequilibrium in recently admixed populations.

PubMed Central

McKeigue, P M

1997-01-01

Where recent admixture has occurred between two populations that have different disease rates for genetic reasons, family-based association studies can be used to map the genes underlying these differences, if the ancestry of the alleles at each locus examined can be assigned to one of the two founding populations. This article explores the statistical power and design requirements of this approach. Markers suitable for assigning the ancestry of genomic regions could be defined by grouping alleles at closely spaced microsatellite loci into haplotypes, or generated by representational difference analysis. For a given relative risk between populations, the sample size required to detect a disease locus that accounts for this relative risk by linkage-disequilibrium mapping in an admixed population is not critically dependent on assumptions about genotype penetrances or allele frequencies. Using the transmission-disequilibrium test to search the genome for a locus that accounts for a relative risk of between 2 and 3 in a high-risk population, compared with a low-risk population, generally requires between 150 and 800 case-parent pairs of mixed descent. The optimal strategy is to conduct an initial study using markers spaced at < or = 10 cM with cases from the second and third generations of mixed descent, and then to map the disease loci more accurately in a subsequent study of a population with a longer history of admixture. This approach has greater statistical power than allele-sharing designs and has obvious applications to the genetics of hypertension, non-insulin-dependent diabetes, and obesity. PMID:8981962

Assessing alternative measures of wealth in health research.

PubMed

Cubbin, Catherine; Pollack, Craig; Flaherty, Brian; Hayward, Mark; Sania, Ayesha; Vallone, Donna; Braveman, Paula

2011-05-01

We assessed whether it would be feasible to replace the standard measure of net worth with simpler measures of wealth in population-based studies examining associations between wealth and health. We used data from the 2004 Survey of Consumer Finances (respondents aged 25-64 years) and the 2004 Health and Retirement Survey (respondents aged 50 years or older) to construct logistic regression models relating wealth to health status and smoking. For our wealth measure, we used the standard measure of net worth as well as 9 simpler measures of wealth, and we compared results among the 10 models. In both data sets and for both health indicators, models using simpler wealth measures generated conclusions about the association between wealth and health that were similar to the conclusions generated by models using net worth. The magnitude and significance of the odds ratios were similar for the covariates in multivariate models, and the model-fit statistics for models using these simpler measures were similar to those for models using net worth. Our findings suggest that simpler measures of wealth may be acceptable in population-based studies of health.

Detecting and modelling delayed density-dependence in abundance time series of a small mammal (Didelphis aurita)

NASA Astrophysics Data System (ADS)

Brigatti, E.; Vieira, M. V.; Kajin, M.; Almeida, P. J. A. L.; de Menezes, M. A.; Cerqueira, R.

2016-02-01

We study the population size time series of a Neotropical small mammal with the intent of detecting and modelling population regulation processes generated by density-dependent factors and their possible delayed effects. The application of analysis tools based on principles of statistical generality are nowadays a common practice for describing these phenomena, but, in general, they are more capable of generating clear diagnosis rather than granting valuable modelling. For this reason, in our approach, we detect the principal temporal structures on the bases of different correlation measures, and from these results we build an ad-hoc minimalist autoregressive model that incorporates the main drivers of the dynamics. Surprisingly our model is capable of reproducing very well the time patterns of the empirical series and, for the first time, clearly outlines the importance of the time of attaining sexual maturity as a central temporal scale for the dynamics of this species. In fact, an important advantage of this analysis scheme is that all the model parameters are directly biologically interpretable and potentially measurable, allowing a consistency check between model outputs and independent measurements.

Epigenetics and Future Generations.

PubMed

Del Savio, Lorenzo; Loi, Michele; Stupka, Elia

2015-10-01

Recent evidence of intergenerational epigenetic programming of disease risk broadens the scope of public health preventive interventions to future generations, i.e. non existing people. Due to the transmission of epigenetic predispositions, lifestyles such as smoking or unhealthy diet might affect the health of populations across several generations. While public policy for the health of future generations can be justified through impersonal considerations, such as maximizing aggregate well-being, in this article we explore whether there are rights-based obligations supervening on intergenerational epigenetic programming despite the non-identity argument, which challenges this rationale in case of policies that affect the number and identity of future people. We propose that rights based obligations grounded in the interests of non-existing people might fall upon existing people when generations overlap. In particular, if environmental exposure in F0 (i.e. existing people) will affect the health of F2 (i.e. non-existing people) through epigenetic programming, then F1 (i.e. existing and overlapping with both F0 and F2) might face increased costs to address F2's condition in the future: this might generate obligations upon F0 from various distributive principles, such as the principle of equal opportunity for well being. © 2015 John Wiley & Sons Ltd.

Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population.

PubMed

Hirata, Satoshi; Kojima, Kaname; Misawa, Kazuharu; Gervais, Olivier; Kawai, Yosuke; Nagasaki, Masao

2018-05-01

Forensic DNA typing is widely used to identify missing persons and plays a central role in forensic profiling. DNA typing usually uses capillary electrophoresis fragment analysis of PCR amplification products to detect the length of short tandem repeat (STR) markers. Here, we analyzed whole genome data from 1,070 Japanese individuals generated using massively parallel short-read sequencing of 162 paired-end bases. We have analyzed 843,473 STR loci with two to six basepair repeat units and cataloged highly polymorphic STR loci in the Japanese population. To evaluate the performance of the cataloged STR loci, we compared 23 STR loci, widely used in forensic DNA typing, with capillary electrophoresis based STR genotyping results in the Japanese population. Seventeen loci had high correlations and high call rates. The other six loci had low call rates or low correlations due to either the limitations of short-read sequencing technology, the bioinformatics tool used, or the complexity of repeat patterns. With these analyses, we have also purified the suitable 218 STR loci with four basepair repeat units and 53 loci with five basepair repeat units both for short read sequencing and PCR based technologies, which would be candidates to the actual forensic DNA typing in Japanese population.

The I2 dissociation mechanisms in the chemical oxygen-iodine laser revisited.

PubMed

Waichman, K; Barmashenko, B D; Rosenwaks, S

2012-06-28

The recently suggested mechanism of I(2) dissociation in the chemical oxygen-iodine laser (COIL) [K. Waichman, B. D. Barmashenko, and S. Rosenwaks, J. Appl. Phys. 106, 063108 (2009); and J. Chem. Phys. 133, 084301 (2010)] was largely based on the suggestion of V. N. Azyazov, S. Yu. Pichugin, and M. C. Heaven [J. Chem. Phys. 130, 104306 (2009)] that the vibrational population of O(2)(a) produced in the chemical generator is high enough to play an essential role in the dissociation. The results of model calculations based on this mechanism agreed very well with measurements of the small signal gain g, I(2) dissociation fraction F, and temperature T in the COIL. This mechanism is here revisited, following the recent experiments of M. V. Zagidullin [Quantum Electron. 40, 794 (2010)] where the observed low population of O(2)(b, v = 1) led to the conclusion that the vibrational population of O(2)(a) at the outlet of the generator is close to thermal equilibrium value. This value corresponds to a very small probability, ∼0.05, of O(2)(a) energy pooling to the states O(2)(X,a,b, v > 0). We show that the dissociation mechanism can reproduce the experimentally observed values of g, F, and T in the COIL only if most of the energy released in the processes of O(2)(a) energy pooling and O(2)(b) quenching by H(2)O ends up as vibrational energy of the products, O(2)(X,a,b), where the vibrational states v = 2 and 3 are significantly populated. We discuss possible reasons for the differences in the suggested vibrational population and explain how these differences can be reconciled.

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.

Patterns of population subdivision, gene flow and genetic variability in the African wild dog (Lycaon pictus).

PubMed

Girman, D J; Vilà, C; Geffen, E; Creel, S; Mills, M G; McNutt, J W; Ginsberg, J; Kat, P W; Mamiya, K H; Wayne, R K

2001-07-01

African wild dogs are large, highly mobile carnivores that are known to disperse over considerable distances and are rare throughout much of their geographical range. Consequently, genetic variation within and differentiation between geographically separated populations is predicted to be minimal. We determined the genetic diversity of mitochondrial DNA (mtDNA) control region sequences and microsatellite loci in seven populations of African wild dogs. Analysis of mtDNA nucleotide diversity suggests that, historically, wild dog populations have been small relative to other large carnivores. However, population declines due to recent habitat loss have not caused a dramatic reduction in genetic diversity. We found one historical and eight recent mtDNA genotypes in 280 individuals that defined two highly divergent clades. In contrast to a previous, more limited, mtDNA analysis, sequences from these clades are not geographically restricted to eastern or southern African populations. Rather, we found a large admixture zone spanning populations from Botswana, Zimbabwe and south-eastern Tanzania. Mitochondrial and microsatellite differentiation between populations was significant and unique mtDNA genotypes and alleles characterized the populations. However, gene flow estimates (Nm) based on microsatellite data were generally greater than one migrant per generation. In contrast, gene flow estimates based on the mtDNA control region were lower than expected given differences in the mode of inheritance of mitochondrial and nuclear markers which suggests a male bias in long-distance dispersal.

Human judgment vs. quantitative models for the management of ecological resources.

PubMed

Holden, Matthew H; Ellner, Stephen P

2016-07-01

Despite major advances in quantitative approaches to natural resource management, there has been resistance to using these tools in the actual practice of managing ecological populations. Given a managed system and a set of assumptions, translated into a model, optimization methods can be used to solve for the most cost-effective management actions. However, when the underlying assumptions are not met, such methods can potentially lead to decisions that harm the environment and economy. Managers who develop decisions based on past experience and judgment, without the aid of mathematical models, can potentially learn about the system and develop flexible management strategies. However, these strategies are often based on subjective criteria and equally invalid and often unstated assumptions. Given the drawbacks of both methods, it is unclear whether simple quantitative models improve environmental decision making over expert opinion. In this study, we explore how well students, using their experience and judgment, manage simulated fishery populations in an online computer game and compare their management outcomes to the performance of model-based decisions. We consider harvest decisions generated using four different quantitative models: (1) the model used to produce the simulated population dynamics observed in the game, with the values of all parameters known (as a control), (2) the same model, but with unknown parameter values that must be estimated during the game from observed data, (3) models that are structurally different from those used to simulate the population dynamics, and (4) a model that ignores age structure. Humans on average performed much worse than the models in cases 1-3, but in a small minority of scenarios, models produced worse outcomes than those resulting from students making decisions based on experience and judgment. When the models ignored age structure, they generated poorly performing management decisions, but still outperformed students using experience and judgment 66% of the time. © 2016 by the Ecological Society of America.

Genetic analysis of a red tilapia (Oreochromis spp.) population undergoing three generations of selection for increased body weight at harvest.

PubMed

Hamzah, Azhar; Thoa, Ngo Phu; Nguyen, Nguyen Hong

2017-11-01

Quantitative genetic analysis was performed on 10,919 data records collected over three generations from the selection programme for increased body weight at harvest in red tilapia (Oreochromis spp.). They were offspring of 224 sires and 226 dams (50 sires and 60 dams per generation, on average). Linear mixed models were used to analyse body traits (weight, length, width and depth), whereas threshold generalised models assuming probit distribution were employed to examine genetic inheritance of survival rate, sexual maturity and body colour. The estimates of heritability for traits studied (body weight, standard length, body width, body depth, body colour, early sexual maturation and survival) across statistical models were moderate to high (0.13-0.45). Genetic correlations among body traits and survival were high and positive (0.68-0.96). Body length and width exhibited negative genetic correlations with body colour (- 0.47 to - 0.25). Sexual maturity was genetically correlated positively with measurements of body traits (weight and length). Direct and correlated genetic responses to selection were measured as estimated breeding values in each generation and expressed in genetic standard deviation units (σ G ). The cumulative improvement achieved for harvest body weight was 1.72 σ G after three generations or 12.5% per generation when the gain was expressed as a percentage of the base population. Selection for improved body weight also resulted in correlated increase in other body traits (length, width and depth) and survival rate (ranging from 0.25 to 0.81 genetic standard deviation units). Avoidance of black spot parent matings also improved the overall red colour of the selected population. It is concluded that the selective breeding programme for red tilapia has succeeded in achieving significant genetic improvement for a range of commercially important traits in this species, and the large genetic variation in body colour and survival also shows that there are prospects for future improvement of these traits in this population of red tilapia.

Selection for fertility in mice - the selection plateau and how to overcome it.

PubMed

Schüler, L

1985-04-01

A long-term experiment for increasing the traits first day litter size (LS1) and litter weight (LW1) was conducted with two populations for 33 generations. The selection plateau was reached in population DU-C (selection and estrus synchronization (h(2) = 0.02±0.01); in population DU-K (selection) the plateau (h(2) = 0.05±0.2) was nearly reached. Selection progress per generation was in LS1 b = 0.11±0.02; b = 0.12±0.04 (1st to 18th generation DU-K, DU-C) and b = 0.10±0.03; b = 0.07±0.05 (19th to 33rd generation, DU-K, DU-C) in LW1 b = 0.16±0.04 g; 0.19±0.07 g (DU-K, DU-C) b = 0.20±0.09 g; 0.001±0.09 g (DU-K, DU-C). Reverse and relaxe selection as well as systematic inbreeding was applied for 10 generations. Reverse selection yielded h(2) = 0.28±0.11 (R-DU-K) and h(2) = 0.17±0.05 (R-DU-C) and showed that there was still additive genetic variance. Relaxe selection did not cause alterations in the selection parameters, whereas inbreeding lead to inbred depressions (b = LS1 = -0.42±0.15; -0.45±0.12; b = LW1 = -1.13±0.20; -0.82±0.18 I-DU-K, I-DU-C). The plateau was based upon the heterozygote advantage. Several methods for overcoming the plateau were applied. A new selective useful variance could be created by crossing the plateau populations (h(2) = 0.14±0.04). A short-term progress in overcoming the plateau (1st to 3rd generation) could be obtained by litter size standardization (LS = 388). Tandem selection (selection for body weight - BW42) as well as crossing of inbred strains were not suitable for overcoming the selection plateau. Altering the environmental conditions as a possibility for overcoming the plateau has been discussed.

Evaluation of Residual Static Corrections by Hybrid Genetic Algorithm Steepest Ascent Autostatics Inversion.Application southern Algerian fields

NASA Astrophysics Data System (ADS)

Eladj, Said; bansir, fateh; ouadfeul, sid Ali

2016-04-01

The application of genetic algorithm starts with an initial population of chromosomes representing a "model space". Chromosome chains are preferentially Reproduced based on Their fitness Compared to the total population. However, a good chromosome has a Greater opportunity to Produce offspring Compared To other chromosomes in the population. The advantage of the combination HGA / SAA is the use of a global search approach on a large population of local maxima to Improve Significantly the performance of the method. To define the parameters of the Hybrid Genetic Algorithm Steepest Ascent Auto Statics (HGA / SAA) job, we Evaluated by testing in the first stage of "Steepest Ascent," the optimal parameters related to the data used. 1- The number of iterations "Number of hill climbing iteration" is equal to 40 iterations. This parameter defines the participation of the algorithm "SA", in this hybrid approach. 2- The minimum eigenvalue for SA '= 0.8. This is linked to the quality of data and S / N ratio. To find an implementation performance of hybrid genetic algorithms in the inversion for estimating of the residual static corrections, tests Were Performed to determine the number of generation of HGA / SAA. Using the values of residual static corrections already calculated by the Approaches "SAA and CSAA" learning has Proved very effective in the building of the cross-correlation table. To determine the optimal number of generation, we Conducted a series of tests ranging from [10 to 200] generations. The application on real seismic data in southern Algeria allowed us to judge the performance and capacity of the inversion with this hybrid method "HGA / SAA". This experience Clarified the influence of the corrections quality estimated from "SAA / CSAA" and the optimum number of generation hybrid genetic algorithm "HGA" required to have a satisfactory performance. Twenty (20) generations Were enough to Improve continuity and resolution of seismic horizons. This Will allow us to achieve a more accurate structural interpretation Key words: Hybrid Genetic Algorithm, number of generations, model space, local maxima, Number of hill climbing iteration, Minimum eigenvalue, cross-correlation table

Translating effects of inbreeding depression on component vital rates to overall population growth in endangered bighorn sheep.

PubMed

Johnson, Heather E; Mills, L Scott; Wehausen, John D; Stephenson, Thomas R; Luikart, Gordon

2011-12-01

Evidence of inbreeding depression is commonly detected from the fitness traits of animals, yet its effects on population growth rates of endangered species are rarely assessed. We examined whether inbreeding depression was affecting Sierra Nevada bighorn sheep (Ovis canadensis sierrae), a subspecies listed as endangered under the U.S. Endangered Species Act. Our objectives were to characterize genetic variation in this subspecies; test whether inbreeding depression affects bighorn sheep vital rates (adult survival and female fecundity); evaluate whether inbreeding depression may limit subspecies recovery; and examine the potential for genetic management to increase population growth rates. Genetic variation in 4 populations of Sierra Nevada bighorn sheep was among the lowest reported for any wild bighorn sheep population, and our results suggest that inbreeding depression has reduced adult female fecundity. Despite this population sizes and growth rates predicted from matrix-based projection models demonstrated that inbreeding depression would not substantially inhibit the recovery of Sierra Nevada bighorn sheep populations in the next approximately 8 bighorn sheep generations (48 years). Furthermore, simulations of genetic rescue within the subspecies did not suggest that such activities would appreciably increase population sizes or growth rates during the period we modeled (10 bighorn sheep generations, 60 years). Only simulations that augmented the Mono Basin population with genetic variation from other subspecies, which is not currently a management option, predicted significant increases in population size. Although we recommend that recovery activities should minimize future losses of genetic variation, genetic effects within these endangered populations-either negative (inbreeding depression) or positive (within subspecies genetic rescue)-appear unlikely to dramatically compromise or stimulate short-term conservation efforts. The distinction between detecting the effects of inbreeding depression on a component vital rate (e.g., fecundity) and the effects of inbreeding depression on population growth underscores the importance of quantifying inbreeding costs relative to population dynamics to effectively manage endangered populations. ©2011 Society for Conservation Biology.

Primary healthcare usage and use of medications among immigrant children according to age of arrival to Norway: a population-based study

PubMed Central

Diaz, Esperanza

2017-01-01

Background Morbidity, use of healthcare and medication use have been reported to vary across groups of migrants and according to the different phases of migration, but little is known about children with immigrant background. In this study, we investigate whether the immigrant children's age of arrival predicts differences in usage of primary healthcare (PHC) and in use of prescribed medication. Methods This nationwide, population-based study used information for children under 18 years of age in 2008 from three linked registers in Norway. Use of medication was assessed with logistic regression analyses presented with ORs with 95% CIs. Results Of 1 168 365 children, 119 251 had immigrant background. The mean number of PHC visits among children aged 10–18 years, was 1.19 for non-immigrants, 1.17 among second generation immigrants, 1.12, 1.05 and 0.83 among first immigrant children who were <5, 5–9 and ≥10 years at arrival in Norway, respectively. Patterns were similar for younger immigrants, and were confirmed with regression models adjusting for age and sex. First generation immigrant children used less of nearly all groups of prescribed medication compared to non-immigrants when adjusting for age and sex (overall OR 0.48 (0.47 to 0.49)), and medication was also generally less used among second generation immigrant children (overall OR 0.92 (0.91 to 0.94)). Conclusions Age of arrival predicted PHC usage among children among first-generation children. First-generation immigrant children, particularly those arriving later in adolescence, used PHC less than age corresponding non-immigrant children. Immigrant children used less prescribed medication compared to non-immigrants after adjustment for age and sex. PMID:28148537

Changes in Sexual Behavior and Attitudes Across Generations and Gender Among a Population-Based Probability Sample From an Urbanizing Province in Thailand.

PubMed

Techasrivichien, Teeranee; Darawuttimaprakorn, Niphon; Punpuing, Sureeporn; Musumari, Patou Masika; Lukhele, Bhekumusa Wellington; El-Saaidi, Christina; Suguimoto, S Pilar; Feldman, Mitchell D; Ono-Kihara, Masako; Kihara, Masahiro

2016-02-01

Thailand has undergone rapid modernization with implications for changes in sexual norms. We investigated sexual behavior and attitudes across generations and gender among a probability sample of the general population of Nonthaburi province located near Bangkok in 2012. A tablet-based survey was performed among 2,138 men and women aged 15-59 years identified through a three-stage, stratified, probability proportional to size, clustered sampling. Descriptive statistical analysis was carried out accounting for the effects of multistage sampling. Relationship of age and gender to sexual behavior and attitudes was analyzed by bivariate analysis followed by multivariate logistic regression analysis to adjust for possible confounding. Patterns of sexual behavior and attitudes varied substantially across generations and gender. We found strong evidence for a decline in the age of sexual initiation, a shift in the type of the first sexual partner, and a greater rate of acceptance of adolescent premarital sex among younger generations. The study highlighted profound changes among young women as evidenced by a higher number of lifetime sexual partners as compared to older women. In contrast to the significant gender gap in older generations, sexual profiles of Thai young women have evolved to resemble those of young men with attitudes gradually converging to similar sexual standards. Our data suggest that higher education, being never-married, and an urban lifestyle may have been associated with these changes. Our study found that Thai sexual norms are changing dramatically. It is vital to continue monitoring such changes, considering the potential impact on the HIV/STIs epidemic and unintended pregnancies.

The study of in vivo quantification of aluminum (Al) in human bone with a compact DD generator-based neutron activation analysis (NAA) system.

PubMed

Byrne, Patrick; Mostafaei, Farshad; Liu, Yingzi; Blake, Scott P; Koltick, David; Nie, Linda H

2016-05-01

The feasibility and methodology of using a compact DD generator-based neutron activation analysis system to measure aluminum in hand bone has been investigated. Monte Carlo simulations were used to simulate the moderator, reflector, and shielding assembly and to estimate the radiation dose. A high purity germanium (HPGe) detector was used to detect the Al gamma ray signals. The minimum detectable limit (MDL) was found to be 11.13 μg g(-1) dry bone (ppm). An additional HPGe detector would improve the MDL by a factor of 1.4, to 7.9 ppm. The equivalent dose delivered to the irradiated hand was calculated by Monte Carlo to be 11.9 mSv. In vivo bone aluminum measurement with the DD generator was found to be feasible among general population with an acceptable dose to the subject.

Integrating mechanistic and polymorphism data to characterize human genetic susceptibility for environmental chemical risk assessment in the 21st century

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

Mortensen, Holly M., E-mail: mortensen.holly@epa.gov; Euling, Susan Y.

Response to environmental chemicals can vary widely among individuals and between population groups. In human health risk assessment, data on susceptibility can be utilized by deriving risk levels based on a study of a susceptible population and/or an uncertainty factor may be applied to account for the lack of information about susceptibility. Defining genetic susceptibility in response to environmental chemicals across human populations is an area of interest in the NAS' new paradigm of toxicity pathway-based risk assessment. Data from high-throughput/high content (HT/HC), including -omics (e.g., genomics, transcriptomics, proteomics, metabolomics) technologies, have been integral to the identification and characterization ofmore » drug target and disease loci, and have been successfully utilized to inform the mechanism of action for numerous environmental chemicals. Large-scale population genotyping studies may help to characterize levels of variability across human populations at identified target loci implicated in response to environmental chemicals. By combining mechanistic data for a given environmental chemical with next generation sequencing data that provides human population variation information, one can begin to characterize differential susceptibility due to genetic variability to environmental chemicals within and across genetically heterogeneous human populations. The integration of such data sources will be informative to human health risk assessment.« less

Value-based resource management: a model for best value nursing care.

PubMed

Caspers, Barbara A; Pickard, Beth

2013-01-01

With the health care environment shifting to a value-based payment system, Catholic Health Initiatives nursing leadership spearheaded an initiative with 14 hospitals to establish best nursing care at a lower cost. The implementation of technology-enabled business processes at point of care led to a new model for best value nursing care: Value-Based Resource Management. The new model integrates clinical patient data from the electronic medical record and embeds the new information in care team workflows for actionable real-time decision support and predictive forecasting. The participating hospitals reported increased patient satisfaction and cost savings in the reduction of overtime and improvement in length of stay management. New data generated by the initiative on nursing hours and cost by patient and by population (Medicare severity diagnosis-related groups), and patient health status outcomes across the acute care continuum expanded business intelligence for a value-based population health system.

Selection for long and short sleep duration in Drosophila melanogaster reveals the complex genetic network underlying natural variation in sleep

PubMed Central

2017-01-01

Why do some individuals need more sleep than others? Forward mutagenesis screens in flies using engineered mutations have established a clear genetic component to sleep duration, revealing mutants that convey very long or short sleep. Whether such extreme long or short sleep could exist in natural populations was unknown. We applied artificial selection for high and low night sleep duration to an outbred population of Drosophila melanogaster for 13 generations. At the end of the selection procedure, night sleep duration diverged by 9.97 hours in the long and short sleeper populations, and 24-hour sleep was reduced to 3.3 hours in the short sleepers. Neither long nor short sleeper lifespan differed appreciably from controls, suggesting little physiological consequences to being an extreme long or short sleeper. Whole genome sequence data from seven generations of selection revealed several hundred thousand changes in allele frequencies at polymorphic loci across the genome. Combining the data from long and short sleeper populations across generations in a logistic regression implicated 126 polymorphisms in 80 candidate genes, and we confirmed three of these genes and a larger genomic region with mutant and chromosomal deficiency tests, respectively. Many of these genes could be connected in a single network based on previously known physical and genetic interactions. Candidate genes have known roles in several classic, highly conserved developmental and signaling pathways—EGFR, Wnt, Hippo, and MAPK. The involvement of highly pleiotropic pathway genes suggests that sleep duration in natural populations can be influenced by a wide variety of biological processes, which may be why the purpose of sleep has been so elusive. PMID:29240764

Selection for long and short sleep duration in Drosophila melanogaster reveals the complex genetic network underlying natural variation in sleep.

PubMed

Harbison, Susan T; Serrano Negron, Yazmin L; Hansen, Nancy F; Lobell, Amanda S

2017-12-01

Why do some individuals need more sleep than others? Forward mutagenesis screens in flies using engineered mutations have established a clear genetic component to sleep duration, revealing mutants that convey very long or short sleep. Whether such extreme long or short sleep could exist in natural populations was unknown. We applied artificial selection for high and low night sleep duration to an outbred population of Drosophila melanogaster for 13 generations. At the end of the selection procedure, night sleep duration diverged by 9.97 hours in the long and short sleeper populations, and 24-hour sleep was reduced to 3.3 hours in the short sleepers. Neither long nor short sleeper lifespan differed appreciably from controls, suggesting little physiological consequences to being an extreme long or short sleeper. Whole genome sequence data from seven generations of selection revealed several hundred thousand changes in allele frequencies at polymorphic loci across the genome. Combining the data from long and short sleeper populations across generations in a logistic regression implicated 126 polymorphisms in 80 candidate genes, and we confirmed three of these genes and a larger genomic region with mutant and chromosomal deficiency tests, respectively. Many of these genes could be connected in a single network based on previously known physical and genetic interactions. Candidate genes have known roles in several classic, highly conserved developmental and signaling pathways-EGFR, Wnt, Hippo, and MAPK. The involvement of highly pleiotropic pathway genes suggests that sleep duration in natural populations can be influenced by a wide variety of biological processes, which may be why the purpose of sleep has been so elusive.

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

Multidimensional data analysis in immunophenotyping.

PubMed

Loken, M R

2001-05-01

The complexity of cell populations requires careful selection of reagents to detect cells of interest and distinguish them from other types. Additional reagents are frequently used to provide independent criteria for cell identification. Two or three monoclonal antibodies in combination with forward and right-angle light scatter generate a data set that is difficult to visualize because the data must be represented in four- or five-dimensional space. The separation between cell populations provided by the multiple characteristics is best visualized by multidimensional analysis using all parameters simultaneously to identify populations within the resulting hyperspace. Groups of cells are distinguished based on a combination of characteristics not apparent in any usual two-dimensional representation of the data.

Simulating a base population in honey bee for molecular genetic studies

PubMed Central

2012-01-01

Background Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor) is one of the main causes. Selective breeding of resistant bees can help to prevent losses due to the parasite, but it requires that a robust breeding program and genetic evaluation are implemented. Genomic selection has emerged as an important tool in animal breeding programs and simulation studies have shown that it yields more accurate breeding value estimates, higher genetic gain and low rates of inbreeding. Since genomic selection relies on marker data, simulations conducted on a genomic dataset are a pre-requisite before selection can be implemented. Although genomic datasets have been simulated in other species undergoing genetic evaluation, simulation of a genomic dataset specific to the honey bee is required since this species has a distinct genetic and reproductive biology. Our software program was aimed at constructing a base population by simulating a random mating honey bee population. A forward-time population simulation approach was applied since it allows modeling of genetic characteristics and reproductive behavior specific to the honey bee. Results Our software program yielded a genomic dataset for a base population in linkage disequilibrium. In addition, information was obtained on (1) the position of markers on each chromosome, (2) allele frequency, (3) χ2 statistics for Hardy-Weinberg equilibrium, (4) a sorted list of markers with a minor allele frequency less than or equal to the input value, (5) average r2 values of linkage disequilibrium between all simulated marker loci pair for all generations and (6) average r2 value of linkage disequilibrium in the last generation for selected markers with the highest minor allele frequency. Conclusion We developed a software program that takes into account the genetic and reproductive biology specific to the honey bee and that can be used to constitute a genomic dataset compatible with the simulation studies necessary to optimize breeding programs. The source code together with an instruction file is freely accessible at http://msproteomics.org/Research/Misc/honeybeepopulationsimulator.html PMID:22520469

Simulating a base population in honey bee for molecular genetic studies.

PubMed

Gupta, Pooja; Conrad, Tim; Spötter, Andreas; Reinsch, Norbert; Bienefeld, Kaspar

2012-06-27

Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor) is one of the main causes. Selective breeding of resistant bees can help to prevent losses due to the parasite, but it requires that a robust breeding program and genetic evaluation are implemented. Genomic selection has emerged as an important tool in animal breeding programs and simulation studies have shown that it yields more accurate breeding value estimates, higher genetic gain and low rates of inbreeding. Since genomic selection relies on marker data, simulations conducted on a genomic dataset are a pre-requisite before selection can be implemented. Although genomic datasets have been simulated in other species undergoing genetic evaluation, simulation of a genomic dataset specific to the honey bee is required since this species has a distinct genetic and reproductive biology. Our software program was aimed at constructing a base population by simulating a random mating honey bee population. A forward-time population simulation approach was applied since it allows modeling of genetic characteristics and reproductive behavior specific to the honey bee. Our software program yielded a genomic dataset for a base population in linkage disequilibrium. In addition, information was obtained on (1) the position of markers on each chromosome, (2) allele frequency, (3) χ(2) statistics for Hardy-Weinberg equilibrium, (4) a sorted list of markers with a minor allele frequency less than or equal to the input value, (5) average r(2) values of linkage disequilibrium between all simulated marker loci pair for all generations and (6) average r2 value of linkage disequilibrium in the last generation for selected markers with the highest minor allele frequency. We developed a software program that takes into account the genetic and reproductive biology specific to the honey bee and that can be used to constitute a genomic dataset compatible with the simulation studies necessary to optimize breeding programs. The source code together with an instruction file is freely accessible at http://msproteomics.org/Research/Misc/honeybeepopulationsimulator.html.

Let's jump in: A phylogenetic study of the great basin springfishes and poolfishes, Crenichthys and Empetrichthys (Cyprinodontiformes: Goodeidae)

PubMed Central

2017-01-01

North America’s Great Basin has long been of interest to biologists due to its high level of organismal endemicity throughout its endorheic watersheds. One example of such a group is the subfamily Empetricthyinae. In this paper, we analyzed the relationships of the Empetrichtyinae and assessed the validity of the subspecies designations given by Williams and Wilde within the group using concatenated phylogenetic tree estimation and species tree estimation. Samples from 19 populations were included covering the entire distribution of the three extant species of Empetricthyinae–Crenichthys nevadae, Crenichthys baileyi and Empetricthys latos. Three nuclear introns (S8 intron 4, S7 intron 1, and P0 intron 1) and one mitochondrial gene (Cytb) were sequenced for phylogenetic analysis. Using these sequences, we generated two separate hypotheses of the evolutionary relationships of Empetrichtyinae- one based on the mitochondrial data and one based on the nuclear data using Bayesian phylogenetics. Haplotype networks were also generated to look at the relationships of the populations within Empetrichthyinae. After comparing the two phylogenetic hypotheses, species trees were generated using *BEAST with the nuclear data to further test the validity of the subspecies within Empetrichthyinae. The mitochondrial analyses supported four lineages within C. baileyi and 2 within C. nevadae. The concatenated nuclear tree was more conserved, supporting one clade and an unresolved polytomy in both species. The species tree analysis supported the presence of two species within both C. baileyi and C. nevadae. Based on the results of these analyses, the subspecies designations of Williams and Wilde are not valid, rather a conservative approach suggests there are two species within C. nevadae and two species within C. baileyi. No structure was found for E. latos or the populations of Empetricthyinae. This study represents one of many demonstrating the invalidity of subspecies and their detriment to species identification, conservation, and understanding. PMID:29077708

Human Prostate Side Population Cells Demonstrate Stem Cell Properties in Recombination with Urogenital Sinus Mesenchyme

PubMed Central

Foster, Barbara A.; Gangavarapu, Kalyan J.; Mathew, Grinu; Azabdaftari, Gissou; Morrison, Carl D.; Miller, Austin; Huss, Wendy J.

2013-01-01

Stem cell enrichment provides a tool to examine prostate stem cells obtained from benign and malignant tissue. Functional assays can enrich stem cells based on common stem cell phenotypes, such as high ATP binding cassette (ABC) transporter mediated efflux of Hoechst substrates (side population assay). This functional assay is based upon mechanisms that protect cells from environmental insult thus contributing to the survival and protection of the stem cell population. We have isolated and analyzed cells digested from twelve clinical prostate specimens based on the side population assay. Prostate stem cell properties of the isolated cells were tested by serial recombination with rat urogenital mesenchyme. Recombinants with side population cells demonstrate an increase in the frequency of human ductal growth and the number of glands per recombinant when compared to recombinants with non-side population cells. Isolated cells were capable of prostatic growth for up to three generations in the recombination assay with as little as 125 sorted prostate cells. The ability to reproducibly use cells isolated by fluorescence activated cell sorting from human prostate tissue is an essential step to a better understanding of human prostate stem cell biology. ABC transporter G2 (ABCG2) was expressed in recombinants from side population cells indicating the side population cells have self-renewal properties. Epithelial cell differentiation of recombinants was determined by immunohistochemical analysis for expression of the basal, luminal, and neuroendocrine markers, p63, androgen receptor, prostate specific antigen, and chromogranin A, respectively. Thus, the ABCG2 expressing side population demonstrates multipotency and self-renewal properties indicating stem cells are within this population. PMID:23383057

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

PubMed

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

2017-01-01

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

Examining the impact of migrant status on ethnic differences in mental health service use preceding a first diagnosis of schizophrenia.

PubMed

Anderson, Kelly K; McKenzie, Kwame J; Kurdyak, Paul

2017-08-01

Some ethnic groups have more negative contacts with health services for first-episode psychosis, likely arising from a complex interaction between ethnicity, socio-economic factors, and immigration status. Using population-based health administrative data, we sought to examine the effects of ethnic group and migrant status on patterns of health service use preceding a first diagnosis of schizophrenia or schizoaffective disorder among people aged 14-35 over a 10-year period. We compared access to care and intensity of service use for first-generation ethnic minority groups to the general population of Ontario. To control for migrant status, we restricted the sample to first-generation migrants and compared service use indicators for ethnic minority groups to the European migrant group. Our cohort included 18,080 people with a first diagnosis of schizophrenia or schizoaffective disorder, of whom 14.4% (n = 2607) were the first-generation migrants. Our findings suggest that the magnitude of ethnic differences in health service use is reduced and no longer statistically significant when the sample is restricted to first-generation migrants. Of exception, nearly, all migrant groups have lower intensity of primary care use, and Caribbean migrants are consistently less likely to use psychiatric services. We observed fewer ethnic differences in health service use preceding the first diagnosis of psychosis when patterns are compared among first-generation migrants, rather than to the general population, suggesting that the choice of reference group influences ethnic patterning of health service use. We need a comprehensive understanding of the mechanisms behind observed differences for minority groups to adequately address disparities in access to care.

Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing

PubMed Central

2011-01-01

Background The recent development of next generation sequencing technologies has made it possible to generate very large amounts of sequence data in species with little or no genome information. Combined with the large phenotypic databases available for wild and non-model species, these data will provide an unprecedented opportunity to "genomicise" ecological model organisms and establish the genetic basis of quantitative traits in natural populations. Results This paper describes the sequencing, de novo assembly and analysis from the transcriptome of eight tissues of ten wild great tits. Approximately 4.6 million sequences and 1.4 billion bases of DNA were generated and assembled into 95,979 contigs, one third of which aligned with known Taeniopygia guttata (zebra finch) and Gallus gallus (chicken) transcripts. The majority (78%) of the remaining contigs aligned within or very close to regions of the zebra finch genome containing known genes, suggesting that they represented precursor mRNA rather than untranscribed genomic DNA. More than 35,000 single nucleotide polymorphisms and 10,000 microsatellite repeats were identified. Eleven percent of contigs were expressed in every tissue, while twenty one percent of contigs were expressed in only one tissue. The function of those contigs with strong evidence for tissue specific expression and contigs expressed in every tissue was inferred from the gene ontology (GO) terms associated with these contigs; heart and pancreas had the highest number of highly tissue specific GO terms (21.4% and 28.5% respectively). Conclusions In summary, the transcriptomic data generated in this study will contribute towards efforts to assemble and annotate the great tit genome, as well as providing the markers required to perform gene mapping studies in wild populations. PMID:21635727

Orthopedic implant devices: prevalence and sociodemographic findings from the 1988 National Health Interview Survey.

PubMed

Moore, R M; Hamburger, S; Jeng, L L; Hamilton, P M

1991-01-01

National population-based estimates on the magnitude and distribution of orthopedic implant devices in the United States have not been available to date. The Food and Drug Administration's Center for Devices and Radiological Health (FDA/CDRH) collaborated with the Centers for Disease Control's National Center for Health Statistics (CDC/NCHS) in the design and conduct of a nationwide medical device implant survey to generate the first national population-based prevalence estimates of orthopedic implant devices. A Medical Device Implant Supplement to the 1988 National Health Interview Survey was administered in personal household interviews to a national sample of 47,485 households, which included 122,310 individuals. An estimated 6.5 million orthopedic implants were in use in the general US population in 1988, including 1.6 million artificial joints and 4.9 million fixation devices. As a group, orthopedic implants comprised nearly half of all medical device implants in use, 43.4%. The majority of artificial joint recipients were 65 years of age or older, white, and male. The majority of fixation device recipients were less than 45 years of age, white, and male. The limitations and strengths of these population-based estimates are discussed.

Spectral analysis of a two-species competition model: Determining the effects of extreme conditions on the color of noise generated from simulated time series

NASA Astrophysics Data System (ADS)

Golinski, M. R.

2006-07-01

Ecologists have observed that environmental noise affects population variance in the logistic equation for one-species growth. Interactions between deterministic and stochastic dynamics in a one-dimensional system result in increased variance in species population density over time. Since natural populations do not live in isolation, the present paper simulates a discrete-time two-species competition model with environmental noise to determine the type of colored population noise generated by extreme conditions in the long-term population dynamics of competing populations. Discrete Fourier analysis is applied to the simulation results and the calculated Hurst exponent ( H) is used to determine how the color of population noise for the two species corresponds to extreme conditions in population dynamics. To interpret the biological meaning of the color of noise generated by the two-species model, the paper determines the color of noise generated by three reference models: (1) A two-dimensional discrete-time white noise model (0⩽ H<1/2); (2) A two-dimensional fractional Brownian motion model (H=1/2); and (3) A two-dimensional discrete-time model with noise for unbounded growth of two uncoupled species (1/2< H⩽1).

[Impact of cardiovascular risk factors on the consumption of resources in Primary Care according to Clinical Risk Groups].

PubMed

Millá Perseguer, Magdalena; Guadalajara Olmeda, Natividad; Vivas Consuelo, David

2018-06-13

To analyze the prevalence of Cardiovascular Risk Factors (CVRF) in the context of a Basic Health Area and the impact they generate on morbidity and consumption of healthcare resources in the stratified population according to the Clinical System Risk Groups (CRG) in Primary Care, with the purpose of identifying the population with multimorbidity to apply preventive measures, as well as the one that generates the highest care burden and social needs. Observational, cross-sectional and population-based study for a basic health area during 2013. Department of Health 2 (Castellón), Comunidad Valenciana (CV). Includes outpatient care in Primary Care and specialized. All citizens registered in the Population Information System, N=32,667. From the computerized system Abucasis we obtained the demographic, clinical and consumption variables of health resources. We consider the prevalence of CVRF based on the presence or absence of the ICD.9.MC diagnostic codes. The relationship of the CVRF with the 9 CRG health states was analyzed and a predictive analysis was performed with the logistic regression model to evaluate the explanatory capacity of each variable. In addition, an explanatory model of ambulatory pharmaceutical expenditure was obtained through multivariate regression. The population of health status CRG4 and above had multimorbidity. The CRG7 and 6 health states have a higher prevalence of CVRF; it was predictive that the higher the morbidity, the greater the consumption of resources through OR above the mean, p<0.05 and the 95% confidence intervals. It was observed that 59.8% of ambulatory pharmaceutical expenditure was explained by the CRG system and all the CVRF (p<0.05 and R 2 corrected=0.598). Regarding the effect of the CVRF on the CRG health states, there was a significant association (p<0.05) for the alteration of blood glucose, dyslipidemia and HBP in all the CRG states. The study of CVRF in a stratified population using the CRG system identifies and predicts where the greatest impact on morbidity and consumption of healthcare resources is generated. It allows us to know the groups of patients where to develop prevention and chronicity strategies. At the level of clinical practice, a new concept of multimorbidity is provided, defined from the state of health CRG 4 and above. Publicado por Elsevier España, S.L.U.

Examining the Relationship between Pre-Malignant Breast Lesions, Carcinogenesis and Tumor Evolution in the Mammary Epithelium Using an Agent-Based Model.

PubMed

Chapa, Joaquin; An, Gary; Kulkarni, Swati A

2016-01-01

Breast cancer, the product of numerous rare mutational events that occur over an extended time period, presents numerous challenges to investigators interested in studying the transformation from normal breast epithelium to malignancy using traditional laboratory methods, particularly with respect to characterizing transitional and pre-malignant states. Dynamic computational modeling can provide insight into these pathophysiological dynamics, and as such we use a previously validated agent-based computational model of the mammary epithelium (the DEABM) to investigate the probabilistic mechanisms by which normal populations of ductal cells could transform into states replicating features of both pre-malignant breast lesions and a diverse set of breast cancer subtypes. The DEABM consists of simulated cellular populations governed by algorithms based on accepted and previously published cellular mechanisms. Cells respond to hormones, undergo mitosis, apoptosis and cellular differentiation. Heritable mutations to 12 genes prominently implicated in breast cancer are acquired via a probabilistic mechanism. 3000 simulations of the 40-year period of menstrual cycling were run in wild-type (WT) and BRCA1-mutated groups. Simulations were analyzed by development of hyperplastic states, incidence of malignancy, hormone receptor and HER-2 status, frequency of mutation to particular genes, and whether mutations were early events in carcinogenesis. Cancer incidence in WT (2.6%) and BRCA1-mutated (45.9%) populations closely matched published epidemiologic rates. Hormone receptor expression profiles in both WT and BRCA groups also closely matched epidemiologic data. Hyperplastic populations carried more mutations than normal populations and mutations were similar to early mutations found in ER+ tumors (telomerase, E-cadherin, TGFB, RUNX3, p < .01). ER- tumors carried significantly more mutations and carried more early mutations in BRCA1, c-MYC and genes associated with epithelial-mesenchymal transition. The DEABM generates diverse tumors that express tumor markers consistent with epidemiologic data. The DEABM also generates non-invasive, hyperplastic populations, analogous to atypia or ductal carcinoma in situ (DCIS), via mutations to genes known to be present in hyperplastic lesions and as early mutations in breast cancers. The results demonstrate that agent-based models are well-suited to studying tumor evolution through stages of carcinogenesis and have the potential to be used to develop prevention and treatment strategies.

How Well Do Molecular and Pedigree Relatedness Correspond, in Populations with Diverse Mating Systems, and Various Types and Quantities of Molecular and Demographic Data?

PubMed

Kopps, Anna M; Kang, Jungkoo; Sherwin, William B; Palsbøll, Per J

2015-06-30

Kinship analyses are important pillars of ecological and conservation genetic studies with potentially far-reaching implications. There is a need for power analyses that address a range of possible relationships. Nevertheless, such analyses are rarely applied, and studies that use genetic-data-based-kinship inference often ignore the influence of intrinsic population characteristics. We investigated 11 questions regarding the correct classification rate of dyads to relatedness categories (relatedness category assignments; RCA) using an individual-based model with realistic life history parameters. We investigated the effects of the number of genetic markers; marker type (microsatellite, single nucleotide polymorphism SNP, or both); minor allele frequency; typing error; mating system; and the number of overlapping generations under different demographic conditions. We found that (i) an increasing number of genetic markers increased the correct classification rate of the RCA so that up to >80% first cousins can be correctly assigned; (ii) the minimum number of genetic markers required for assignments with 80 and 95% correct classifications differed between relatedness categories, mating systems, and the number of overlapping generations; (iii) the correct classification rate was improved by adding additional relatedness categories and age and mitochondrial DNA data; and (iv) a combination of microsatellite and single-nucleotide polymorphism data increased the correct classification rate if <800 SNP loci were available. This study shows how intrinsic population characteristics, such as mating system and the number of overlapping generations, life history traits, and genetic marker characteristics, can influence the correct classification rate of an RCA study. Therefore, species-specific power analyses are essential for empirical studies. Copyright © 2015 Kopps et al.

Combining real-time PCR and next-generation DNA sequencing to provide quantitative comparisons of fungal aerosol populations

NASA Astrophysics Data System (ADS)

Dannemiller, Karen C.; Lang-Yona, Naama; Yamamoto, Naomichi; Rudich, Yinon; Peccia, Jordan

2014-02-01

We examined fungal communities associated with the PM10 mass of Rehovot, Israel outdoor air samples collected in the spring and fall seasons. Fungal communities were described by 454 pyrosequencing of the internal transcribed spacer (ITS) region of the fungal ribosomal RNA encoding gene. To allow for a more quantitative comparison of fungal exposure in humans, the relative abundance values of specific taxa were transformed to absolute concentrations through multiplying these values by the sample's total fungal spore concentration (derived from universal fungal qPCR). Next, the sequencing-based absolute concentrations for Alternaria alternata, Cladosporium cladosporioides, Epicoccum nigrum, and Penicillium/Aspergillus spp. were compared to taxon-specific qPCR concentrations for A. alternata, C. cladosporioides, E. nigrum, and Penicillium/Aspergillus spp. derived from the same spring and fall aerosol samples. Results of these comparisons showed that the absolute concentration values generated from pyrosequencing were strongly associated with the concentration values derived from taxon-specific qPCR (for all four species, p < 0.005, all R > 0.70). The correlation coefficients were greater for species present in higher concentrations. Our microbial aerosol population analyses demonstrated that fungal diversity (number of fungal operational taxonomic units) was higher in the spring compared to the fall (p = 0.02), and principal coordinate analysis showed distinct seasonal differences in taxa distribution (ANOSIM p = 0.004). Among genera containing allergenic and/or pathogenic species, the absolute concentrations of Alternaria, Aspergillus, Fusarium, and Cladosporium were greater in the fall, while Cryptococcus, Penicillium, and Ulocladium concentrations were greater in the spring. The transformation of pyrosequencing fungal population relative abundance data to absolute concentrations can improve next-generation DNA sequencing-based quantitative aerosol exposure assessment.

A coccidioidomycosis outbreak following the Northridge, Calif, earthquake

USGS Publications Warehouse

Schneider, E.; Hajjeh, R.A.; Spiegel, R.A.; Jibson, R.W.; Harp, E.L.; Marshall, G.A.; Gunn, R.A.; McNeil, M.M.; Pinner, R.W.; Baron, R.C.; Burger, R.C.; Hutwagner, L.C.; Crump, C.; Kaufman, L.; Reef, S.E.; Feldman, G.M.; Pappagianis, D.; Werner, S.B.

1997-01-01

Objective. - To describe a coccidioidomycosis outbreak in Ventura County following the January 1994 earthquake, centered in Northridge, Calif, and to identify factors that increased the risk for acquiring acute coccidioidomycosis infection. Design. - Epidemic investigation, population- based skin test survey, and case-control study. Setting. - Ventura County, California. Results. - In Ventura County, between January 24 and March 15, 1994, 203 outbreak-associated coccidioidomycosis cases, including 3 fatalities, were identified (attack rate [AR], 30 cases per 100 000 population). The majority of cases (56%) and the highest AR (114 per 100 000 population) occurred in the town of Simi Valley, a community located at the base of a mountain range that experienced numerous landslides associated with the earthquake. Disease onset for cases peaked 2 weeks after the earthquake. The AR was 2.8 times greater for persons 40 years of age and older than for younger persons (relative risk, 2.8; 95% confidence interval [CI], 2.1-3.7; P<.001). Environmental data indicated that large dust clouds, generated by landslides following the earthquake and strong aftershocks in the Santa Susana Mountains north of Simi Valley, were dispersed into nearby valleys by northeast winds. Simi Valley case-control study data indicated that physically being in a dust cloud (odds ratio, 3.0; 95% CI, 1.6-5.4; P<.001) and time spent in a dust cloud (P<.001) significantly increased the risk for being diagnosed with acute coccidioidomycosis. Conclusions. - Both the location and timing of cases strongly suggest that the coccidioidomycosis outbreak in Ventura County was caused when arthrospores were spread in dust clouds generated by the earthquake. This is the first report of a coccidioidomycosis outbreak following an earthquake. Public and physician awareness, especially in endemic areas following similar dust cloud- generating events, may result in prevention and early recognition of acute coccidioidomycosis.

A Fire Department Community Health Intervention to Prevent Carbon Monoxide Poisoning Following a Hurricane

PubMed Central

Levy, Matthew; Jenkins, J Lee; Seaman, Kevin

2014-01-01

Portable generators are commonly used during electrical service interruptions that occur following large storms such as hurricanes. Nearly all portable generators use carbon based fuels and produce deadly carbon monoxide gas. Despite universal warnings to operate these generators outside only, the improper placement of generators makes these devices the leading cause of engine related carbon monoxide deaths in the United States. The medical literature reports many cases of Carbon Monoxide (CO) toxicity associated with generator use following hurricanes and other weather events. This paper describes how Howard County, Maryland Fire and Rescue (HCFR) Services implemented a public education program that focused on prevention of Carbon Monoxide poisoning from portable generator use in the wake of events where electrical service interruptions occurred or had the potential to occur. A major challenge faced was communication with those members of the population who were almost completely dependent upon electronic and wireless technologies and were without redundancies. HCFR utilized several tactics to overcome this challenge including helicopter based surveillance and the use of geocoded information from the electrical service provider to identify outage areas. Once outage areas were identified, HCFR personnel conducted a door-to-door canvasing of effected communities, assessing for hazards and distributing information flyers about the dangers of generator use. This effort represents one of the first reported examples of a community-based endeavor by a fire department to provide proactive interventions designed to prevent carbon monoxide illness. PMID:24596660

GONe: Software for estimating effective population size in species with generational overlap

USGS Publications Warehouse

Coombs, J.A.; Letcher, B.H.; Nislow, K.H.

2012-01-01

GONe is a user-friendly, Windows-based program for estimating effective size (N e) in populations with overlapping generations. It uses the Jorde-Ryman modification to the temporal method to account for age structure in populations. This method requires estimates of age-specific survival and birth rate and allele frequencies measured in two or more consecutive cohorts. Allele frequencies are acquired by reading in genotypic data from files formatted for either GENEPOP or TEMPOFS. For each interval between consecutive cohorts, N e is estimated at each locus and over all loci. Furthermore, N e estimates are output for three different genetic drift estimators (F s, F c and F k). Confidence intervals are derived from a chi-square distribution with degrees of freedom equal to the number of independent alleles. GONe has been validated over a wide range of N e values, and for scenarios where survival and birth rates differ between sexes, sex ratios are unequal and reproductive variances differ. GONe is freely available for download at. ?? 2011 Blackwell Publishing Ltd.

Isolation and characterization of 14 tetranucleotide microsatellite loci for the cannonball jellyfish (Stomolophus sp.) by next generation sequencing.

PubMed

Getino-Mamet, Leandro Nicolás; Valdivia-Carrillo, Tania; Gómez Daglio, Liza; García-De León, Francisco Javier

2017-04-01

The Cannonball jellyfish (Stomolophus sp.) is a species of jellyfish with high relevance in artisanal fishing. Studies of their populations do not extend beyond the morphological descriptions knowing that presents a great morphological variability. However, there are no genetic studies to determine the number of independent populations, so microsatellite markers become a suitable option. Since there are no species-specific microsatellite loci, in this paper, 14 new microsatellite loci are characterized. Microsatellite loci were isolated de novo through next generation sequencing, by two runs on Illumina MiSeq. A total of 506,771,269 base pair were obtained, from which 142,616 were microsatellite loci, and 1546 of them could design primers. We tested 14 primer pairs on 32 individuals from Bahía de La Paz, Gulf of California. We observed low genetic variation among loci (mean number of alleles per locus = 4.33, mean observed heterozygosity 0.381, mean expected heterozygosity 0.501). These loci are the first ones described for the species and will be helpful to carry out genetic diversity and population genetics studies.

Knowledge, attitudes and intention regarding mHealth in generation Y: evidence from a population based cross sectional study in Chakaria, Bangladesh

PubMed Central

Rahman, M Shafiqur; Hanifi, Syed; Khatun, Fatema; Iqbal, Mohammad; Rasheed, Sabrina; Ahmed, Tanvir; Hoque, Shahidul; Sharmin, Tamanna; Khan, Nazib-Uz Zaman; Mahmood, Shehrin Shaila; Bhuiya, Abbas

2017-01-01

Background and objectives mHealth offers a new opportunity to ensure access to qualified healthcare providers. Therefore, to better understand its potential in Bangladesh, it is important to understand how young people use mobile phones for healthcare. Here we examine the knowledge, attitudes and intentions to use mHealth services among young population. Design Population based cross sectional household survey. Setting and participants A total of 4909 respondents, aged 18 years and above, under the Chakaria Health and Demographic Surveillance System (HDSS) area, were interviewed during the period November 2012 to April 2013. Methods Participants younger than 30 years of age were defined as young (or generation Y). To examine the level of knowledge about and intention towards mHealth services in generation Y compared with their older counterparts, the percentage of the respective outcome measure from a 2×2 contingency table and adjusted odds ratio (aOR), which controls for potential confounders such as mobile ownership, sex, education, occupation and socioeconomic status, were estimated. The aOR was estimated using both the Cochran–Mantel–Haenszel approach and multivariable logistic regression models controlling for confounders. Results Generation Y had significantly greater access to mobile phones (50%vs40%) and better knowledge about its use for healthcare (37.8%vs27.5%;aOR 1.6 (95% CI1.3 to 2.0)). Furthermore, the level of knowledge about two existing mHealth services in generation Y was significantly higher compared with their older counterparts, with aOR values of 3.2 (95% CI 2.6 to 5.5) and 1.5 (95% CI 1.1 to 1.8), respectively. Similarly, generation Y showed significantly greater intention towards future use of mHealth services compared with their older counterparts (aOR 1.3 (95% CI 1.1 to 1.4)). The observed associations were not modified by sociodemographic factors. Conclusion There is a greater potential for mHealth services in the future among young people compared with older age groups. However, given the low overall use of mHealth, appropriate policy measures need to be formulated to enhance availability, access, utilisation and effectiveness of mHealth services. PMID:29146634

Knowledge, attitudes and intention regarding mHealth in generation Y: evidence from a population based cross sectional study in Chakaria, Bangladesh.

PubMed

Rahman, M Shafiqur; Hanifi, Syed; Khatun, Fatema; Iqbal, Mohammad; Rasheed, Sabrina; Ahmed, Tanvir; Hoque, Shahidul; Sharmin, Tamanna; Khan, Nazib-Uz Zaman; Mahmood, Shehrin Shaila; Bhuiya, Abbas

2017-11-15

mHealth offers a new opportunity to ensure access to qualified healthcare providers. Therefore, to better understand its potential in Bangladesh, it is important to understand how young people use mobile phones for healthcare. Here we examine the knowledge, attitudes and intentions to use mHealth services among young population. Population based cross sectional household survey. A total of 4909 respondents, aged 18 years and above, under the Chakaria Health and Demographic Surveillance System (HDSS) area, were interviewed during the period November 2012 to April 2013. Participants younger than 30 years of age were defined as young (or generation Y). To examine the level of knowledge about and intention towards mHealth services in generation Y compared with their older counterparts, the percentage of the respective outcome measure from a 2×2 contingency table and adjusted odds ratio (aOR), which controls for potential confounders such as mobile ownership, sex, education, occupation and socioeconomic status, were estimated. The aOR was estimated using both the Cochran-Mantel-Haenszel approach and multivariable logistic regression models controlling for confounders. Generation Y had significantly greater access to mobile phones (50%vs40%) and better knowledge about its use for healthcare (37.8%vs27.5%;aOR 1.6 (95% CI1.3 to 2.0)). Furthermore, the level of knowledge about two existing mHealth services in generation Y was significantly higher compared with their older counterparts, with aOR values of 3.2 (95% CI 2.6 to 5.5) and 1.5 (95% CI 1.1 to 1.8), respectively. Similarly, generation Y showed significantly greater intention towards future use of mHealth services compared with their older counterparts (aOR 1.3 (95% CI 1.1 to 1.4)). The observed associations were not modified by sociodemographic factors. There is a greater potential for mHealth services in the future among young people compared with older age groups. However, given the low overall use of mHealth, appropriate policy measures need to be formulated to enhance availability, access, utilisation and effectiveness of mHealth services. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Results from six generations of selection for intramuscular fat in Duroc swine using real-time ultrasound. I. Direct and correlated phenotypic responses to selection.

PubMed

Schwab, C R; Baas, T J; Stalder, K J; Nettleton, D

2009-09-01

A study was conducted to evaluate the efficacy of selection for intramuscular fat (IMF) in a population of purebred Duroc swine using real-time ultrasound. Forty gilts were purchased from US breeders and randomly mated for 2 generations to boars available in regional boar studs, resulting in a base population of 56 litters. Littermate pairs of gilts from this population were randomly assigned to a select line (SL) or control line (CL) and mated to the same sire to establish genetic ties between lines. At an average BW of 114 kg, a minimum of 4 longitudinal ultrasound images were collected 7 cm off-midline across the 10th to 13th ribs of all pigs for the prediction of IMF (UIMF). At least 1 barrow or gilt was slaughtered from each litter, and carcass data were collected. A sample of the LM from the 10th to 11th rib interface was analyzed for carcass IMF (CIMF). Breeding values for IMF were estimated by fitting a 2-trait (UIMF and CIMF) animal model in MATVEC. In the SL, selection in each subsequent generation was based on EBV for IMF with the top 10 boars and top 75 gilts used to produce the next generation. One boar from each sire family and 50 to 60 gilts representing all sire families were randomly selected to maintain the CL. Through 6 generations of selection, an 88% improvement in IMF has been realized (4.53% in SL vs. 2.41% in CL). Results of this study revealed no significant correlated responses in measures of growth performance. However, 6 generations of selection for IMF have yielded correlated effects of decreased loin muscle area and increased backfat. Additionally, the SL obtained more desirable objective measures of tenderness and sensory evaluations of flavor and off-flavor. Meat quality characteristics of pH, water holding capacity, and percent cooking loss were not significantly affected by selection for IMF. Selection for IMF using real-time ultrasound is effective but may be associated with genetic ramifications for carcass composition traits. Intramuscular fat may be used in purebred Duroc swine breeding programs as an indicator trait for sensory traits that influence consumer acceptance; however, rapid improvement should not be expected when simultaneous improvement in other trait categories is also pursued.

Monitoring Dolphins in an Urban Marine System: Total and Effective Population Size Estimates of Indo-Pacific Bottlenose Dolphins in Moreton Bay, Australia

PubMed Central

Ansmann, Ina C.; Lanyon, Janet M.; Seddon, Jennifer M.; Parra, Guido J.

2013-01-01

Moreton Bay, Queensland, Australia is an area of high biodiversity and conservation value and home to two sympatric sub-populations of Indo-Pacific bottlenose dolphins (Tursiops aduncus). These dolphins live in close proximity to major urban developments. Successful management requires information regarding their abundance. Here, we estimate total and effective population sizes of bottlenose dolphins in Moreton Bay using photo-identification and genetic data collected during boat-based surveys in 2008–2010. Abundance (N) was estimated using open population mark-recapture models based on sighting histories of distinctive individuals. Effective population size (Ne) was estimated using the linkage disequilibrium method based on nuclear genetic data at 20 microsatellite markers in skin samples, and corrected for bias caused by overlapping generations (Nec). A total of 174 sightings of dolphin groups were recorded and 365 different individuals identified. Over the whole of Moreton Bay, a population size N of 554±22.2 (SE) (95% CI: 510–598) was estimated. The southern bay sub-population was small at an estimated N = 193±6.4 (SE) (95% CI: 181–207), while the North sub-population was more numerous, with 446±56 (SE) (95% CI: 336–556) individuals. The small estimated effective population size of the southern sub-population (Nec = 56, 95% CI: 33–128) raises conservation concerns. A power analysis suggested that to reliably detect small (5%) declines in size of this population would require substantial survey effort (>4 years of annual mark-recapture surveys) at the precision levels achieved here. To ensure that ecological as well as genetic diversity within this population of bottlenose dolphins is preserved, we consider that North and South sub-populations should be treated as separate management units. Systematic surveys over smaller areas holding locally-adapted sub-populations are suggested as an alternative method for increasing ability to detect abundance trends. PMID:23755197

Recapitulation of Human Retinal Development from Human Pluripotent Stem Cells Generates Transplantable Populations of Cone Photoreceptors.

PubMed

Gonzalez-Cordero, Anai; Kruczek, Kamil; Naeem, Arifa; Fernando, Milan; Kloc, Magdalena; Ribeiro, Joana; Goh, Debbie; Duran, Yanai; Blackford, Samuel J I; Abelleira-Hervas, Laura; Sampson, Robert D; Shum, Ian O; Branch, Matthew J; Gardner, Peter J; Sowden, Jane C; Bainbridge, James W B; Smith, Alexander J; West, Emma L; Pearson, Rachael A; Ali, Robin R

2017-09-12

Transplantation of rod photoreceptors, derived either from neonatal retinae or pluripotent stem cells (PSCs), can restore rod-mediated visual function in murine models of inherited blindness. However, humans depend more upon cone photoreceptors that are required for daylight, color, and high-acuity vision. Indeed, macular retinopathies involving loss of cones are leading causes of blindness. An essential step for developing stem cell-based therapies for maculopathies is the ability to generate transplantable human cones from renewable sources. Here, we report a modified 2D/3D protocol for generating hPSC-derived neural retinal vesicles with well-formed ONL-like structures containing cones and rods bearing inner segments and connecting cilia, nascent outer segments, and presynaptic structures. This differentiation system recapitulates human photoreceptor development, allowing the isolation and transplantation of a pure population of stage-matched cones. Purified human long/medium cones survive and become incorporated within the adult mouse retina, supporting the potential of photoreceptor transplantation for treating retinal degeneration. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Electromagnetic fields and the public: EMF standards and estimation of risk

NASA Astrophysics Data System (ADS)

Grigoriev, Yury

2010-04-01

Mobile communications are a relatively new and additional source of electromagnetic exposure for the population. Standard daily mobile-phone use is known to increase RF-EMF (radiofrequency electromagnetic field) exposure to the brains of users of all ages, whilst mobile-phone base stations, and base station units for cordless phones, can regularly increase the exposures of large numbers of the population to RF-EMF radiation in everyday life. The need to determine appropriate standards stipulating the maximum acceptable short-term and long-term RF-EMF levels encountered by the public, and set such levels as general guidelines, is of great importance in order to help preserve the general public's health and that of the next generation of humanity.

Resolving species delimitation within the genus Bunopus Blanford, 1874 (Squamata: Gekkonidae) in Iran using DNA barcoding approach.

PubMed

Khosravani, Azar; Rastegar-Pouyani, Eskandar; Rastegar-Pouyani, Nasrullah; Oraie, Hamzeh; Papenfuss, Theodore J

2017-12-19

Mitochondrial COI sequences were used to investigate species delimitation within the genus Bunopus in Iran. A dataset with a final sequence length of 633 nucleotides including 100 specimens from 31 geographically distant localities across Iran were generated. The result demonstrated that two major clades with strong support can be identified within the genus Bunopus in Iran. Clade A includes Bunopus crassicaudus and two new entities, eastern populations (subclade A2,1) and Shahdad populations (subclade A2,2). The second clade comprises western and southwestern populations (subclade B1,1), Arabian populations (subclade B1,2) and south and southeast populations in Iran, to which Bunopus tuberculatus (subclade B2) is assigned. In addition to Bunopus crassicaudus and B. tuberculatus, three new candidate species in Iran can easily be identified based on the DNA barcoding approach.

Population health and social governance: analyzing the mainstream incorporation of ethnography.

PubMed

O'Byrne, Patrick

2012-06-01

Recently, health care workers (researchers, academics, policy writers, clinicians) have begun to view ethnography as an acceptable research methodology for informing public health work. This corresponds with a change in public health practice toward population health, wherein identifiable groups are examined to identify the group-level and contextual factors that affect their health statuses. Although population health-based methodological and outcomes-focused examinations have already occurred regarding ethnography, no extant literature scrutinizes the incorporation of ethnography into mainstream public and population health work from a sociopolitical viewpoint. Consequently, such an investigation occurs here using Foucault's concepts of discipline and Lupton's advancement of Foucault's ideas about the imperative of health. The outcome of this investigation is the assertion that ethnography is a strategic method for disciplining populations that do not respect the imperative of health. In other words, ethnography helps generate the data that can be used to normalize large groups of people.

Creating targeted initial populations for genetic product searches in heterogeneous markets

NASA Astrophysics Data System (ADS)

Foster, Garrett; Turner, Callaway; Ferguson, Scott; Donndelinger, Joseph

2014-12-01

Genetic searches often use randomly generated initial populations to maximize diversity and enable a thorough sampling of the design space. While many of these initial configurations perform poorly, the trade-off between population diversity and solution quality is typically acceptable for small-scale problems. Navigating complex design spaces, however, often requires computationally intelligent approaches that improve solution quality. This article draws on research advances in market-based product design and heuristic optimization to strategically construct 'targeted' initial populations. Targeted initial designs are created using respondent-level part-worths estimated from discrete choice models. These designs are then integrated into a traditional genetic search. Two case study problems of differing complexity are presented to illustrate the benefits of this approach. In both problems, targeted populations lead to computational savings and product configurations with improved market share of preferences. Future research efforts to tailor this approach and extend it towards multiple objectives are also discussed.

A nonparametric method to generate synthetic populations to adjust for complex sampling design features.

PubMed

Dong, Qi; Elliott, Michael R; Raghunathan, Trivellore E

2014-06-01

Outside of the survey sampling literature, samples are often assumed to be generated by a simple random sampling process that produces independent and identically distributed (IID) samples. Many statistical methods are developed largely in this IID world. Application of these methods to data from complex sample surveys without making allowance for the survey design features can lead to erroneous inferences. Hence, much time and effort have been devoted to develop the statistical methods to analyze complex survey data and account for the sample design. This issue is particularly important when generating synthetic populations using finite population Bayesian inference, as is often done in missing data or disclosure risk settings, or when combining data from multiple surveys. By extending previous work in finite population Bayesian bootstrap literature, we propose a method to generate synthetic populations from a posterior predictive distribution in a fashion inverts the complex sampling design features and generates simple random samples from a superpopulation point of view, making adjustment on the complex data so that they can be analyzed as simple random samples. We consider a simulation study with a stratified, clustered unequal-probability of selection sample design, and use the proposed nonparametric method to generate synthetic populations for the 2006 National Health Interview Survey (NHIS), and the Medical Expenditure Panel Survey (MEPS), which are stratified, clustered unequal-probability of selection sample designs.

A nonparametric method to generate synthetic populations to adjust for complex sampling design features

PubMed Central

Dong, Qi; Elliott, Michael R.; Raghunathan, Trivellore E.

2017-01-01

Outside of the survey sampling literature, samples are often assumed to be generated by a simple random sampling process that produces independent and identically distributed (IID) samples. Many statistical methods are developed largely in this IID world. Application of these methods to data from complex sample surveys without making allowance for the survey design features can lead to erroneous inferences. Hence, much time and effort have been devoted to develop the statistical methods to analyze complex survey data and account for the sample design. This issue is particularly important when generating synthetic populations using finite population Bayesian inference, as is often done in missing data or disclosure risk settings, or when combining data from multiple surveys. By extending previous work in finite population Bayesian bootstrap literature, we propose a method to generate synthetic populations from a posterior predictive distribution in a fashion inverts the complex sampling design features and generates simple random samples from a superpopulation point of view, making adjustment on the complex data so that they can be analyzed as simple random samples. We consider a simulation study with a stratified, clustered unequal-probability of selection sample design, and use the proposed nonparametric method to generate synthetic populations for the 2006 National Health Interview Survey (NHIS), and the Medical Expenditure Panel Survey (MEPS), which are stratified, clustered unequal-probability of selection sample designs. PMID:29200608

Pattern formation in individual-based systems with time-varying parameters

NASA Astrophysics Data System (ADS)

Ashcroft, Peter; Galla, Tobias

2013-12-01

We study the patterns generated in finite-time sweeps across symmetry-breaking bifurcations in individual-based models. Similar to the well-known Kibble-Zurek scenario of defect formation, large-scale patterns are generated when model parameters are varied slowly, whereas fast sweeps produce a large number of small domains. The symmetry breaking is triggered by intrinsic noise, originating from the discrete dynamics at the microlevel. Based on a linear-noise approximation, we calculate the characteristic length scale of these patterns. We demonstrate the applicability of this approach in a simple model of opinion dynamics, a model in evolutionary game theory with a time-dependent fitness structure, and a model of cell differentiation. Our theoretical estimates are confirmed in simulations. In further numerical work, we observe a similar phenomenon when the symmetry-breaking bifurcation is triggered by population growth.

Computational hybrid anthropometric paediatric phantom library for internal radiation dosimetry

NASA Astrophysics Data System (ADS)

Xie, Tianwu; Kuster, Niels; Zaidi, Habib

2017-04-01

Hybrid computational phantoms combine voxel-based and simplified equation-based modelling approaches to provide unique advantages and more realism for the construction of anthropomorphic models. In this work, a methodology and C++ code are developed to generate hybrid computational phantoms covering statistical distributions of body morphometry in the paediatric population. The paediatric phantoms of the Virtual Population Series (IT’IS Foundation, Switzerland) were modified to match target anthropometric parameters, including body mass, body length, standing height and sitting height/stature ratio, determined from reference databases of the National Centre for Health Statistics and the National Health and Nutrition Examination Survey. The phantoms were selected as representative anchor phantoms for the newborn, 1, 2, 5, 10 and 15 years-old children, and were subsequently remodelled to create 1100 female and male phantoms with 10th, 25th, 50th, 75th and 90th body morphometries. Evaluation was performed qualitatively using 3D visualization and quantitatively by analysing internal organ masses. Overall, the newly generated phantoms appear very reasonable and representative of the main characteristics of the paediatric population at various ages and for different genders, body sizes and sitting stature ratios. The mass of internal organs increases with height and body mass. The comparison of organ masses of the heart, kidney, liver, lung and spleen with published autopsy and ICRP reference data for children demonstrated that they follow the same trend when correlated with age. The constructed hybrid computational phantom library opens up the prospect of comprehensive radiation dosimetry calculations and risk assessment for the paediatric population of different age groups and diverse anthropometric parameters.

Prediction of Spatiotemporal Patterns of Neural Activity from Pairwise Correlations

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

Marre, O.; El Boustani, S.; Fregnac, Y.

We designed a model-based analysis to predict the occurrence of population patterns in distributed spiking activity. Using a maximum entropy principle with a Markovian assumption, we obtain a model that accounts for both spatial and temporal pairwise correlations among neurons. This model is tested on data generated with a Glauber spin-glass system and is shown to correctly predict the occurrence probabilities of spatiotemporal patterns significantly better than Ising models only based on spatial correlations. This increase of predictability was also observed on experimental data recorded in parietal cortex during slow-wave sleep. This approach can also be used to generate surrogatesmore » that reproduce the spatial and temporal correlations of a given data set.« less

Single nucleotide polymorphism discovery in cutthroat trout subspecies using genome reduction, barcoding, and 454 pyro-sequencing

PubMed Central

2012-01-01

Background Salmonids are popular sport fishes, and as such have been subjected to widespread stocking throughout western North America. Historically, stocking was done with little regard for genetic variation among populations and has resulted in genetic mixing among species and subspecies in many areas, thus putting the genetic integrity of native salmonid populations at risk and creating a need to assess the genetic constitution of native salmonid populations. Cutthroat trout is a salmonid species with pronounced geographic structure (there are 10 extant subspecies) and a recent history of hybridization with introduced rainbow trout in many populations. Genetic admixture has also occurred among cutthroat trout subspecies in areas where introductions have brought two or more subspecies into contact. Consequently, management agencies have increased their efforts to evaluate the genetic composition of cutthroat trout populations to identify populations that remain uncompromised and manage them accordingly, but additional genetic markers are needed to do so effectively. Here we used genome reduction, MID-barcoding, and 454-pyrosequencing to discover single nucleotide polymorphisms that differentiate cutthroat trout subspecies and can be used as a rapid, cost-effective method to characterize the genetic composition of cutthroat trout populations. Results Thirty cutthroat and six rainbow trout individuals were subjected to genome reduction and next-generation sequencing. A total of 1,499,670 reads averaging 379 base pairs in length were generated by 454-pyrosequencing, resulting in 569,060,077 total base pairs sequenced. A total of 43,558 putative SNPs were identified, and of those, 125 SNP primers were developed that successfully amplified 96 cutthroat trout and rainbow trout individuals. These SNP loci were able to differentiate most cutthroat trout subspecies using distance methods and Structure analyses. Conclusions Genomic and bioinformatic protocols were successfully implemented to identify 125 nuclear SNPs that are capable of differentiating most subspecies of cutthroat trout from one another. The ability to use this suite of SNPs to identify individuals of unknown genetic background to subspecies can be a valuable tool for management agencies in their efforts to evaluate the genetic structure of cutthroat trout populations prior to constructing and implementing conservation plans. PMID:23259499

Genome-wide population structure and evolutionary history of the Frizarta dairy sheep.

PubMed

Kominakis, A; Hager-Theodorides, A L; Saridaki, A; Antonakos, G; Tsiamis, G

2017-10-01

In the present study, we used genomic data, generated with a medium density single nucleotide polymorphisms (SNP) array, to acquire more information on the population structure and evolutionary history of the synthetic Frizarta dairy sheep. First, two typical measures of linkage disequilibrium (LD) were estimated at various physical distances that were then used to make inferences on the effective population size at key past time points. Population structure was also assessed by both multidimensional scaling analysis and k-means clustering on the distance matrix obtained from the animals' genomic relationships. The Wright's fixation F ST index was also employed to assess herds' genetic homogeneity and to indirectly estimate past migration rates. The Wright's fixation F IS index and genomic inbreeding coefficients based on the genomic relationship matrix as well as on runs of homozygosity were also estimated. The Frizarta breed displays relatively low LD levels with r 2 and |D'| equal to 0.18 and 0.50, respectively, at an average inter-marker distance of 31 kb. Linkage disequilibrium decayed rapidly by distance and persisted over just a few thousand base pairs. Rate of LD decay (β) varied widely among the 26 autosomes with larger values estimated for shorter chromosomes (e.g. β=0.057, for OAR6) and smaller values for longer ones (e.g. β=0.022, for OAR2). The inferred effective population size at the beginning of the breed's formation was as high as 549, was then reduced to 463 in 1981 (end of the breed's formation) and further declined to 187, one generation ago. Multidimensional scaling analysis and k-means clustering suggested a genetically homogenous population, F ST estimates indicated relatively low genetic differentiation between herds, whereas a heat map of the animals' genomic kinship relationships revealed a stratified population, at a herd level. Estimates of genomic inbreeding coefficients suggested that most recent parental relatedness may have been a major determinant of the current effective population size. A denser than the 50k SNP panel may be more beneficial when performing genome wide association studies in the breed.

Functional genetic divergence in high CO2 adapted Emiliania huxleyi populations.

PubMed

Lohbeck, Kai T; Riebesell, Ulf; Collins, Sinéad; Reusch, Thorsten B H

2013-07-01

Predicting the impacts of environmental change on marine organisms, food webs, and biogeochemical cycles presently relies almost exclusively on short-term physiological studies, while the possibility of adaptive evolution is often ignored. Here, we assess adaptive evolution in the coccolithophore Emiliania huxleyi, a well-established model species in biological oceanography, in response to ocean acidification. We previously demonstrated that this globally important marine phytoplankton species adapts within 500 generations to elevated CO2 . After 750 and 1000 generations, no further fitness increase occurred, and we observed phenotypic convergence between replicate populations. We then exposed adapted populations to two novel environments to investigate whether or not the underlying basis for high CO2 -adaptation involves functional genetic divergence, assuming that different novel mutations become apparent via divergent pleiotropic effects. The novel environment "high light" did not reveal such genetic divergence whereas growth in a low-salinity environment revealed strong pleiotropic effects in high CO2 adapted populations, indicating divergent genetic bases for adaptation to high CO2 . This suggests that pleiotropy plays an important role in adaptation of natural E. huxleyi populations to ocean acidification. Our study highlights the potential mutual benefits for oceanography and evolutionary biology of using ecologically important marine phytoplankton for microbial evolution experiments. © 2012 The Author(s). Evolution © 2012 The Society for the Study of Evolution.

Reproductive adaptation in Drosophila exposed to oxygen-enriched atmospheres

NASA Technical Reports Server (NTRS)

Kloek, G.; Winkle, L.

1979-01-01

Ten successive generations of a Drosophila melanogaster population were exposed to an atmospheric mix of 50% oxygen/50% nitrogen at standard pressure. This atmospheric mix has been shown to be toxic to this species and causes significantly shortened life span. By the fifth generation, survivorship and life span for the first 25-30 days were identical to control populations and total life span was shorter by only a few days. Egg-laying rates were stable in the experimental populations but below those of the controls. Hatching success was identical between experimental and control populations. Even though the egg-laying rates were lower in 50% oxygen, it was concluded that the population had adapted and could maintain a stable population in these conditions. The near-normal life spans, normal hatching rates, and overall population stability, exhibited following five generations of adaptation, were considered sufficient to allow continued reproduction in spite of a reduced egg-laying rate.

Reproductive adaptation in Drosophila exposed to oxygen-enriched atmospheres.

PubMed

Kloek, G; Winkle, L

1979-04-01

Ten successive generations of a Drosophila melanogaster population were exposed to an atmospheric mix of 50% oxygen/50% nitrogen at standard pressure. This atmospheric mix has been shown to be toxic to this species and causes significantly shortened life span. By the fifth generation, survivorship and life span for the first 25-30 days were identical to control populations and total life span was shorter by only a few days. Egg-laying rates were stable in the experimental populations but below those of the controls. Hatching success was identical between experimental and control populations. Even though the egg-laying rates were lower in 50% oxygen, it was concluded that the population had adapted and could maintain a stable population in these conditions. The near-normal life spans, normal hatching rates, and overall population stability, exhibited following five generations of adaptation, were considered sufficient to allow continued reproduction in spite of a reduced egg-laying rate.

The Geography of Happiness: Connecting Twitter Sentiment and Expression, Demographics, and Objective Characteristics of Place

PubMed Central

Mitchell, Lewis; Frank, Morgan R.; Harris, Kameron Decker; Dodds, Peter Sheridan; Danforth, Christopher M.

2013-01-01

We conduct a detailed investigation of correlations between real-time expressions of individuals made across the United States and a wide range of emotional, geographic, demographic, and health characteristics. We do so by combining (1) a massive, geo-tagged data set comprising over 80 million words generated in 2011 on the social network service Twitter and (2) annually-surveyed characteristics of all 50 states and close to 400 urban populations. Among many results, we generate taxonomies of states and cities based on their similarities in word use; estimate the happiness levels of states and cities; correlate highly-resolved demographic characteristics with happiness levels; and connect word choice and message length with urban characteristics such as education levels and obesity rates. Our results show how social media may potentially be used to estimate real-time levels and changes in population-scale measures such as obesity rates. PMID:23734200

A multigenerational view of inequality.

PubMed

Mare, Robert D

2011-02-01

The study of intergenerational mobility and most population research are governed by a two-generation (parent-to-offspring) view of intergenerational influence, to the neglect of the effects of grandparents and other ancestors and nonresident contemporary kin. While appropriate for some populations in some periods, this perspective may omit important sources of intergenerational continuity of family-based social inequality. Social institutions, which transcend individual lives, help support multigenerational influence, particularly at the extreme top and bottom of the social hierarchy, but to some extent in the middle as well. Multigenerational influence also works through demographic processes because families influence subsequent generations through differential fertility and survival, migration, and marriage patterns, as well as through direct transmission of socioeconomic rewards, statuses, and positions. Future research should attend more closely to multigenerational effects; to the tandem nature of demographic and socioeconomic reproduction; and to data, measures, and models that transcend co-resident nuclear families.

Marine pollution. Plastic waste inputs from land into the ocean.

PubMed

Jambeck, Jenna R; Geyer, Roland; Wilcox, Chris; Siegler, Theodore R; Perryman, Miriam; Andrady, Anthony; Narayan, Ramani; Law, Kara Lavender

2015-02-13

Plastic debris in the marine environment is widely documented, but the quantity of plastic entering the ocean from waste generated on land is unknown. By linking worldwide data on solid waste, population density, and economic status, we estimated the mass of land-based plastic waste entering the ocean. We calculate that 275 million metric tons (MT) of plastic waste was generated in 192 coastal countries in 2010, with 4.8 to 12.7 million MT entering the ocean. Population size and the quality of waste management systems largely determine which countries contribute the greatest mass of uncaptured waste available to become plastic marine debris. Without waste management infrastructure improvements, the cumulative quantity of plastic waste available to enter the ocean from land is predicted to increase by an order of magnitude by 2025. Copyright © 2015, American Association for the Advancement of Science.

Uncertainty quantification and validation of combined hydrological and macroeconomic analyses.

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

Hernandez, Jacquelynne; Parks, Mancel Jordan; Jennings, Barbara Joan

2010-09-01

Changes in climate can lead to instabilities in physical and economic systems, particularly in regions with marginal resources. Global climate models indicate increasing global mean temperatures over the decades to come and uncertainty in the local to national impacts means perceived risks will drive planning decisions. Agent-based models provide one of the few ways to evaluate the potential changes in behavior in coupled social-physical systems and to quantify and compare risks. The current generation of climate impact analyses provides estimates of the economic cost of climate change for a limited set of climate scenarios that account for a small subsetmore » of the dynamics and uncertainties. To better understand the risk to national security, the next generation of risk assessment models must represent global stresses, population vulnerability to those stresses, and the uncertainty in population responses and outcomes that could have a significant impact on U.S. national security.« less

The geography of happiness: connecting twitter sentiment and expression, demographics, and objective characteristics of place.

PubMed

Mitchell, Lewis; Frank, Morgan R; Harris, Kameron Decker; Dodds, Peter Sheridan; Danforth, Christopher M

2013-01-01

We conduct a detailed investigation of correlations between real-time expressions of individuals made across the United States and a wide range of emotional, geographic, demographic, and health characteristics. We do so by combining (1) a massive, geo-tagged data set comprising over 80 million words generated in 2011 on the social network service Twitter and (2) annually-surveyed characteristics of all 50 states and close to 400 urban populations. Among many results, we generate taxonomies of states and cities based on their similarities in word use; estimate the happiness levels of states and cities; correlate highly-resolved demographic characteristics with happiness levels; and connect word choice and message length with urban characteristics such as education levels and obesity rates. Our results show how social media may potentially be used to estimate real-time levels and changes in population-scale measures such as obesity rates.

Proposals for enhanced health risk assessment and stratification in an integrated care scenario

PubMed Central

Dueñas-Espín, Ivan; Vela, Emili; Pauws, Steffen; Bescos, Cristina; Cano, Isaac; Cleries, Montserrat; Contel, Joan Carles; de Manuel Keenoy, Esteban; Garcia-Aymerich, Judith; Gomez-Cabrero, David; Kaye, Rachelle; Lahr, Maarten M H; Lluch-Ariet, Magí; Moharra, Montserrat; Monterde, David; Mora, Joana; Nalin, Marco; Pavlickova, Andrea; Piera, Jordi; Ponce, Sara; Santaeugenia, Sebastià; Schonenberg, Helen; Störk, Stefan; Tegner, Jesper; Velickovski, Filip; Westerteicher, Christoph; Roca, Josep

2016-01-01

Objectives Population-based health risk assessment and stratification are considered highly relevant for large-scale implementation of integrated care by facilitating services design and case identification. The principal objective of the study was to analyse five health-risk assessment strategies and health indicators used in the five regions participating in the Advancing Care Coordination and Telehealth Deployment (ACT) programme (http://www.act-programme.eu). The second purpose was to elaborate on strategies toward enhanced health risk predictive modelling in the clinical scenario. Settings The five ACT regions: Scotland (UK), Basque Country (ES), Catalonia (ES), Lombardy (I) and Groningen (NL). Participants Responsible teams for regional data management in the five ACT regions. Primary and secondary outcome measures We characterised and compared risk assessment strategies among ACT regions by analysing operational health risk predictive modelling tools for population-based stratification, as well as available health indicators at regional level. The analysis of the risk assessment tool deployed in Catalonia in 2015 (GMAs, Adjusted Morbidity Groups) was used as a basis to propose how population-based analytics could contribute to clinical risk prediction. Results There was consensus on the need for a population health approach to generate health risk predictive modelling. However, this strategy was fully in place only in two ACT regions: Basque Country and Catalonia. We found marked differences among regions in health risk predictive modelling tools and health indicators, and identified key factors constraining their comparability. The research proposes means to overcome current limitations and the use of population-based health risk prediction for enhanced clinical risk assessment. Conclusions The results indicate the need for further efforts to improve both comparability and flexibility of current population-based health risk predictive modelling approaches. Applicability and impact of the proposals for enhanced clinical risk assessment require prospective evaluation. PMID:27084274

Variation in Generational Perceptions of Child Health and Well-being.

PubMed

Freed, Gary L; Davis, Matthew M; Singer, Dianne C; Gebremariam, Acham; Schultz, Sara L; Matos-Moreno, Amilcar; Wietecha, Mark

To assess adults' perceptions regarding the health and well-being of children today relative to their own health and well-being as youth and the potential for intergenerational differences in those perceptions. A cross-sectional, Internet-based survey of a nationally representative household sample was conducted using GfK Custom Research's Web-enabled KnowledgePanel, a probability-based panel representative of the US population. We assessed perceptions of children's health and well-being today compared to when respondents were growing up, including physical and mental health; and children's education, exercise, diet, health care, safety of communities, and emotional support from families, groups, and organizations. Overall, 1330 (65%) of 2047 adult respondents completed the survey. Only 26% of respondents believed that the current physical health of children, and 14% that the current mental health of children, is better today than when they were growing up. There was a significant trend among generations, with a greater proportion of older generations perceiving the physical health of children to be better today. Only 15% of respondents reported the chances for a child to grow up with good mental health in the future are "better" now than when they were growing up. Adults across all generations in the United States today view children's health as unlikely to meet the goals of the American Dream of continuous improvement. Although demographic changes require continued focus on our aging population, we must equally recognize the importance of advancing a healthy future for our nation's children, who will assume the mantle of our future. Copyright © 2017 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

Qualitatively and quantitatively evaluating harm-reduction goal setting among chronically homeless individuals with alcohol dependence

PubMed Central

Collins, Susan E.; Grazioli, Véronique S.; Torres, Nicole I.; Taylor, Emily M.; Jones, Connor B.; Hoffman, Gail E.; Haelsig, Laura; Zhu, Mengdan D.; Hatsukami, Alyssa S.; Koker, Molly J.; Herndon, Patrick; Greenleaf, Shawna M.; Dean, Parker E.

2015-01-01

Most treatment programs for alcohol dependence have prioritized alcohol abstinence as the primary treatment goal. However, abstinence-based goals are not always considered desirable or attainable by more severely affected populations, such as chronically homeless people with alcohol dependence. Because these individuals comprise a multimorbid and high-utilizing population, they are in need of more focused research attention that elucidates their preferred treatment goals. The aim of this secondary study was therefore to qualitatively and quantitatively document participant-generated treatment goals. Participants were currently or formerly chronically homeless individuals (N=31) with alcohol dependence who participated in a pilot of extended-release naltrexone and harm-reduction counseling. Throughout the treatment period, study interventionists elicited participants’ goals and recorded them on an open-ended grid. In subsequent weeks, progress towards and achievement of goals was obtained via self-report and recorded by study interventionists. Conventional content analysis was performed to classify participant-generated treatment goals. Representation of the three top categories remained stable over the course of treatment. In the order of their frequency, they included drinking-related goals, quality-of-life goals and health-related goals. Within the category of drinking-related goals, participants consistently endorsed reducing drinking and alcohol-related consequences ahead of abstinence-based goals. Quantitative analyses indicated participants generated an increasing number of goals over the course of treatment. Proportions of goals achieved and progressed toward kept pace with this increase. Findings confirmed hypotheses that chronically homeless people with alcohol dependence can independently generate and achieve treatment goals toward alcohol harm reduction and quality-of-life improvement. PMID:25697724

Women with high early pregnancy urinary iodine levels have an increased risk of hyperthyroid newborns: the population-based Generation R Study.

PubMed

Medici, Marco; Ghassabian, Akhgar; Visser, Willy; de Muinck Keizer-Schrama, Sabine M P F; Jaddoe, Vincent W V; Visser, W Edward; Hooijkaas, Herbert; Hofman, Albert; Steegers, Eric A P; Bongers-Schokking, Jacoba J; Ross, H Alec; Tiemeier, Henning; Visser, Theo J; de Rijke, Yolanda B; Peeters, Robin P

2014-04-01

Iodine deficiency during pregnancy results in thyroid dysfunction and has been associated with adverse obstetric and foetal effects, leading to worldwide salt iodization programmes. As nowadays 69% of the world's population lives in iodine-sufficient regions, we investigated the effects of variation in iodine status on maternal and foetal thyroid (dys)function in an iodine-sufficient population. Urinary iodine, serum TSH, free T4 (FT4) and TPO-antibody levels were determined in early pregnancy (13·3 (1·9) week; mean (SD)) in 1098 women from the population-based Generation R Study. Newborn cord serum TSH and FT4 levels were determined at birth. The median urinary iodine level was 222·5 μg/l, indicating an iodine-sufficient population. 30·8% and 11·5% had urinary iodine levels <150 and >500 μg/l, respectively. When comparing mothers with urinary iodine levels <150 vs ≥150 μg/l, and >500 vs ≤500 μg/l, there were no differences in the risk of maternal increased or decreased TSH, hypothyroxinaemia or hyperthyroidism. Mothers with urinary iodine levels >500 μg/l had a higher risk of a newborn with decreased cord TSH levels (5·6 ± 1·4 (mean ± SE) vs 2·1 ± 0·5%, P = 0·04), as well as a higher risk of a hyperthyroid newborn (3·1 ± 0·9 vs 0·6 ± 0·3%, P = 0·02). These mothers had newborns with higher cord FT4 levels (21·7 ± 0·3 vs 21·0 ± 0·1 pm, P = 0·04). Maternal urinary iodine levels <150 μg/l were not associated with newborn thyroid dysfunction. In an iodine-sufficient population, higher maternal urinary iodine levels are associated with an increased risk of a hyperthyroid newborn. © 2013 John Wiley & Sons Ltd.

Change in genetic size of small-closed populations: Lessons from a domestic mammal population.

PubMed

Ghafouri-Kesbi, Farhad

2010-10-01

The aim of this study was to monitor changes in genetic size of a small-closed population of Iranian Zandi sheep, by using pedigree information from animals born between 1991 and 2005. The genetic size was assessed by using measures based on the probability of identity-by-descend of genes (coancestry, f, and effective population size, N(e) ), as well as measures based on probability of gene origin (effective number of founders, f(e) , effective number of founder genomes, f(g) , and effective number of non-founder genomes, f(ne) ). Average coancestry, or the degree of genetic similarity of individuals, increased from 0.81% to 1.44% during the period 1993 to 2005, at the same time that N(e) decreased from 263 to 93. The observed trend for f(e) was irregular throughout the experiment in a way that f(e) was 68, 87, 77, 92, and 80 in 1993, 1996, 1999, 2002, and 2005, respectively. Simultaneously, f(g) , the most informative effective number, decreased from 61 to 35. The index of genetic diversity (GD) which was obtained from estimates of f(g) , decreased about 2% throughout the period studied. In addition, a noticeable reduction was observed in the estimates of f(ne) from 595 in 1993 to 61 in 2005. The higher than 1 ratio of f(e) to f(g) indicated the presence of bottlenecks and genetic drift in the development of this population of Zandi sheep. From 1993 to 1999, f(ne) was much higher than f(e) , thereby indicating that with respect to loss of genetic diversity, the unequal contribution of founders was more important than the random genetic drift in non-founder generations. Subsequently, random genetic drift in non-founder generations was the major reason for f(e) > f(ne) . The minimization of average coancestry in new reproductive individuals was recommended as a means of preserving the population against a further loss in genetic diversity.

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.

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.

Evaluating the Impact of an Accountable Care Organization on Population Health: The Quasi-Experimental Design of the German Gesundes Kinzigtal.

PubMed

Pimperl, Alexander; Schulte, Timo; Mühlbacher, Axel; Rosenmöller, Magdalena; Busse, Reinhard; Groene, Oliver; Rodriguez, Hector P; Hildebrandt, Helmut

2017-06-01

A central goal of accountable care organizations (ACOs) is to improve the health of their accountable population. No evidence currently links ACO development to improved population health. A major challenge to establishing the evidence base for the impact of ACOs on population health is the absence of a theoretically grounded, robust, operationally feasible, and meaningful research design. The authors present an evaluation study design, provide an empirical example, and discuss considerations for generating the evidence base for ACO implementation. A quasi-experimental study design using propensity score matching in combination with small-scale exact matching is implemented. Outcome indicators based on claims data were constructed and analyzed. Population health is measured by using a range of mortality indicators: mortality ratio, age at time of death, years of potential life lost/gained, and survival time. The application is assessed using longitudinal data from Gesundes Kinzigtal, one of the leading population-based ACOs in Germany. The proposed matching approach resulted in a balanced control of observable differences between the intervention (ACO) and control groups. The mortality indicators used indicate positive results. For example, 635.6 fewer years of potential life lost (2005.8 vs. 2641.4; t-test: sig. P < 0.05*) in the ACO intervention group (n = 5411) attributable to the ACO, also after controlling for a potential (indirect) immortal time bias by excluding the first half year after enrollment from the outcome measurement. This empirical example of the impact of a German ACO on population health can be extended to the evaluation of ACOs and other integrated delivery models of care.

Sublethal effects of imidacloprid on the fecundity, longevity, and enzyme activity of Sitobion avenae (Fabricius) and Rhopalosiphum padi (Linnaeus).

PubMed

Lu, Y-H; Zheng, X-S; Gao, X-W

2016-08-01

The aphid species Sitobion avenae and Rhopalosiphum padi are the most important pests in wheat growing regions of many countries. In this study, we investigated the sublethal effects of imidacloprid on fecundity, longevity, and enzyme activity in both aphid species by comparing 3-h exposure for one or three generations. Our results indicated that 3-h exposure to sublethal doses of imidacloprid for one generation had no discernible effect on the survival, fecundity, longevity, or enzyme activity levels of aphids. However, when pulse exposures to imidacloprid were sustained over three generations, both fecundity and longevity were significantly decreased in both S. avenae and R. padi. Interestingly, the fecundity of R. padi had almost recovered by the F5 generation, but its longevity was still deleteriously affected. These results indicated that R. padi laid eggs in shorter time lags and has a more fast resilience. The change in reproduction behavior may be a phenomenon of R. padi to compensate its early death. If this is stable for the next generation, it means that the next generation is more competitive than unexposed populations, which could be the reason underlying population outbreaks that occur after longer-term exposure to an insecticide. This laboratory-based study highlights the sublethal effects of imidacloprid on the longevity and fecundity of descendants and provides an empirical basis from which to consider management decisions for chemical control in the field.

Digital Badges for STEM Learning in Secondary Contexts: A Mixed Methods Study

NASA Astrophysics Data System (ADS)

Elkordy, Angela

The deficit in STEM skills is a matter of concern for national economies and a major focus for educational policy makers. The development of Information and Communications Technologies (ICT) has resulted in a rapidly changing workforce of global scale. In addition, ICT have fostered the growth of digital and mobile technologies which have been the learning context, formal and informal, for a generation of youth. The purpose of this study was to design an intervention based upon a competency-based, digitally-mediated, learning intervention: digital badges for learning STEM habits of mind and practices. Designed purposefully, digital badge learning trajectories and criteria can be flexible tools for scaffolding, measuring, and communicating the acquisition of knowledge, skills, or competencies. One of the most often discussed attributes of digital badges, is the ability of badges to motivate learners. However, the research base to support this claim is in its infancy; there is little empirical evidence. A skills-based digital badge intervention was designed to demonstrate mastery learning in key, age-appropriate, STEM competencies aligned with Next Generation Science Standards (NGSS) and other educational standards. A mixed methods approach was used to study the impact of a digital badge intervention in the sample middle and high school population. Among the findings were statistically significant measures which substantiate that in this student population, the digital badges increased perceived competence and motivated learners to persist at task.

Empirical population and public health ethics: A review and critical analysis to advance robust empirical-normative inquiry.

PubMed

Knight, Rod

2016-05-01

The field of population and public health ethics (PPHE) has yet to fully embrace the generation of evidence as an important project. This article reviews the philosophical debates related to the 'empirical turn' in clinical bioethics, and critically analyses how PPHE has and can engage with the philosophical implications of generating empirical data within the task of normative inquiry. A set of five conceptual and theoretical issues pertaining to population health that are unresolved and could potentially benefit from empirical PPHE approaches to normative inquiry are discussed. Each issue differs from traditional empirical bioethical approaches, in that they emphasize (1) concerns related to the population, (2) 'upstream' policy-relevant health interventions - within and outside of the health care system and (3) the prevention of illness and disease. Within each theoretical issue, a conceptual example from population and public health approaches to HIV prevention and health promotion is interrogated. Based on the review and critical analysis, this article concludes that empirical-normative approaches to population and public health ethics would be most usefully pursued as an iterative project (rather than as a linear project), in which the normative informs the empirical questions to be asked and new empirical evidence constantly directs conceptualizations of what constitutes morally robust public health practices. Finally, a conceptualization of an empirical population and public health ethics is advanced in order to open up new interdisciplinary 'spaces', in which empirical and normative approaches to ethical inquiry are transparently (and ethically) integrated. © The Author(s) 2015.

Mapping in an apple (Malus x domestica) F1 segregating population based on physical clustering of differentially expressed genes

USDA-ARS?s Scientific Manuscript database

Background: Apple tree breeding is slow and difficult due to long generation times, self incompatibility, and complex genetics. The identification of molecular markers linked to traits of interest is a way to expedite the breeding process. In the present study, we aimed to identify genes whose stead...

Two fern species new to New Hampshire, with comments on the generation of calcareous-like habitat by base-poor rocks

Treesearch

Scott W. Bailey

2013-01-01

Incidental to other field investigations, I happened upon small populations of two fern species not previously reported from New Hampshire: Pellaea atropurpurea (L.) Link and Dryopteris filix-mas (L.) Schott. Both species are typically associated with calcareous habitats, although limestone and marble are nearly absent from New...

Population Policies for a New Economic Era. Worldwatch Paper 53.

ERIC Educational Resources Information Center

Brown, Lester R.

After a generation of unprecedented economic growth, the world economy appears to be losing momentum. Double-digit inflation, high interest rates, and soaring deficits are often cited as causes of the global economic slowdown, but these are more symptom than cause. More fundamental is the depletion of the global resource base that allowed the…

The Intersection of Inquiry-Based Science and Language: Preparing Teachers for ELL Classrooms

ERIC Educational Resources Information Center

Weinburgh, Molly; Silva, Cecilia; Smith, Kathy Horak; Groulx, Judy; Nettles, Jenesta

2014-01-01

As teacher educators, we are tasked with preparing prospective teachers to enter a field that has undergone significant changes in student population and policy since we were K-12 teachers. With the emphasis placed on connections, mathematics integration, and communication by the New Generation Science Standards (NGSS) (Achieve in Next generation…

The Effect on Non-Normal Distributions on the Integrated Moving Average Model of Time-Series Analysis.

ERIC Educational Resources Information Center

Doerann-George, Judith

The Integrated Moving Average (IMA) model of time series, and the analysis of intervention effects based on it, assume random shocks which are normally distributed. To determine the robustness of the analysis to violations of this assumption, empirical sampling methods were employed. Samples were generated from three populations; normal,…

Strengthening the Validity of Population-Based Suicide Rate Comparisons: An Illustration Using U.S. Military and Civilian Data

ERIC Educational Resources Information Center

Eaton, Karen M.; Messer, Stephen C.; Garvey Wilson, Abigail L.; Hoge, Charles W.

2006-01-01

The objectives of this study were to generate precise estimates of suicide rates in the military while controlling for factors contributing to rate variability such as demographic differences and classification bias, and to develop a simple methodology for the determination of statistically derived thresholds for detecting significant rate…

Diversity and relatedness in a black walnut seed orchard

Treesearch

Keith Woeste; Doug Mersman

2003-01-01

Geneticists and silviculturists have selected over 450 black walnut clones for inclusion in the black walnut breeding program at Purdue University over the past 35 years. Most of the selections were from Indiana; a few were from other states in the Central Hardwoods Region. Selection of second and third generation clones out of this founder population was based...

A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar

USDA-ARS?s Scientific Manuscript database

A small fast neutron mutant population has been established from Phaseolus vulgaris cv. Red Hawk. We leveraged the available P. vulgaris genome sequence and high throughput next generation DNA sequencing to examine the genomic structure of five Phaseolus vulgaris cv. Red Hawk fast neutron mutants wi...

Parental Family Stress during Pregnancy and Cognitive Functioning in Early Childhood: The Generation R Study

ERIC Educational Resources Information Center

Henrichs, Jens; Schenk, Jacqueline J.; Kok, Rianne; Ftitache, Bouchra; Schmidt, Henk G.; Hofman, Albert; Jaddoe, Vincent W. V.; Verhulst, Frank C.; Tiemeier, Henning

2011-01-01

We investigated whether parental family stress during pregnancy is associated with cognitive functioning in early childhood in a population-based cohort (n = 3139). Family stress was assessed using the Family Assessment Device at the 20th week of pregnancy and was reported by mothers and fathers. Mothers completed the MacArthur Communicative…

Publishing web-based guidelines using interactive decision models.

PubMed

Sanders, G D; Nease, R F; Owens, D K

2001-05-01

Commonly used methods for guideline development and dissemination do not enable developers to tailor guidelines systematically to specific patient populations and update guidelines easily. We developed a web-based system, ALCHEMIST, that uses decision models and automatically creates evidence-based guidelines that can be disseminated, tailored and updated over the web. Our objective was to demonstrate the use of this system with clinical scenarios that provide challenges for guideline development. We used the ALCHEMIST system to develop guidelines for three clinical scenarios: (1) Chlamydia screening for adolescent women, (2) antiarrhythmic therapy for the prevention of sudden cardiac death; and (3) genetic testing for the BRCA breast-cancer mutation. ALCHEMIST uses information extracted directly from the decision model, combined with the additional information from the author of the decision model, to generate global guidelines. ALCHEMIST generated electronic web-based guidelines for each of the three scenarios. Using ALCHEMIST, we demonstrate that tailoring a guideline for a population at high-risk for Chlamydia changes the recommended policy for control of Chlamydia from contact tracing of reported cases to a population-based screening programme. We used ALCHEMIST to incorporate new evidence about the effectiveness of implantable cardioverter defibrillators (ICD) and demonstrate that the cost-effectiveness of use of ICDs improves from $74 400 per quality-adjusted life year (QALY) gained to $34 500 per QALY gained. Finally, we demonstrate how a clinician could use ALCHEMIST to incorporate a woman's utilities for relevant health states and thereby develop patient-specific recommendations for BRCA testing; the patient-specific recommendation improved quality-adjusted life expectancy by 37 days. The ALCHEMIST system enables guideline developers to publish both a guideline and an interactive decision model on the web. This web-based tool enables guideline developers to tailor guidelines systematically, to update guidelines easily, and to make the underlying evidence and analysis transparent for users.

Patterns of death in the first and second generation immigrants from selected Middle Eastern countries in California.

PubMed

Nasseri, Kiumarss; Moulton, Lawrence H

2011-04-01

Migrant studies in the United States (US) have rarely covered the Middle Eastern population (ME), and have never distinguished the first and second generations born in the US. This study aims to describe the mortality patterns of ME immigrants by origin, acculturation, and generation. Death certificates issued from 1997 through 2004 were used to calculate, for Middle Eastern immigrants, the proportional odds ratios (POR) for major causes of death, with comparison to non-Hispanic Whites born in the US to US-born parents. First generation immigrants had higher odds for colorectal cancers, diabetes, and diseases of the heart, while their odds for chronic obstructive pulmonary disease (COPD) and suicide were lower. Men had higher odds for all cancers combined, cancers of the lymphatics, and pancreas. Women had lower odds for lung cancer, and dementia, and higher odds for breast cancer. The second generation men had higher odds for all cancers combined, and diseases of the heart, whereas women had lower odds for lung cancer and cerebrovascular accidents. Higher odds for colorectal cancers and lower odds for COPD were noted in both sexes. Some of the observed differences may be based on ethnic characteristics, including genetic makeup, early exposures, and culturally determined values. Time since immigration is associated with convergence of most odds to that of the native population.

Generalization and dilution of association results from European GWAS in populations of non-European ancestry: the PAGE study.

PubMed

Carlson, Christopher S; Matise, Tara C; North, Kari E; Haiman, Christopher A; Fesinmeyer, Megan D; Buyske, Steven; Schumacher, Fredrick R; Peters, Ulrike; Franceschini, Nora; Ritchie, Marylyn D; Duggan, David J; Spencer, Kylee L; Dumitrescu, Logan; Eaton, Charles B; Thomas, Fridtjof; Young, Alicia; Carty, Cara; Heiss, Gerardo; Le Marchand, Loic; Crawford, Dana C; Hindorff, Lucia A; Kooperberg, Charles L

2013-09-01

The vast majority of genome-wide association study (GWAS) findings reported to date are from populations with European Ancestry (EA), and it is not yet clear how broadly the genetic associations described will generalize to populations of diverse ancestry. The Population Architecture Using Genomics and Epidemiology (PAGE) study is a consortium of multi-ancestry, population-based studies formed with the objective of refining our understanding of the genetic architecture of common traits emerging from GWAS. In the present analysis of five common diseases and traits, including body mass index, type 2 diabetes, and lipid levels, we compare direction and magnitude of effects for GWAS-identified variants in multiple non-EA populations against EA findings. We demonstrate that, in all populations analyzed, a significant majority of GWAS-identified variants have allelic associations in the same direction as in EA, with none showing a statistically significant effect in the opposite direction, after adjustment for multiple testing. However, 25% of tagSNPs identified in EA GWAS have significantly different effect sizes in at least one non-EA population, and these differential effects were most frequent in African Americans where all differential effects were diluted toward the null. We demonstrate that differential LD between tagSNPs and functional variants within populations contributes significantly to dilute effect sizes in this population. Although most variants identified from GWAS in EA populations generalize to all non-EA populations assessed, genetic models derived from GWAS findings in EA may generate spurious results in non-EA populations due to differential effect sizes. Regardless of the origin of the differential effects, caution should be exercised in applying any genetic risk prediction model based on tagSNPs outside of the ancestry group in which it was derived. Models based directly on functional variation may generalize more robustly, but the identification of functional variants remains challenging.

Generalization and Dilution of Association Results from European GWAS in Populations of Non-European Ancestry: The PAGE Study

PubMed Central

Carlson, Christopher S.; Matise, Tara C.; North, Kari E.; Haiman, Christopher A.; Fesinmeyer, Megan D.; Buyske, Steven; Schumacher, Fredrick R.; Peters, Ulrike; Franceschini, Nora; Ritchie, Marylyn D.; Duggan, David J.; Spencer, Kylee L.; Dumitrescu, Logan; Eaton, Charles B.; Thomas, Fridtjof; Young, Alicia; Carty, Cara; Heiss, Gerardo; Le Marchand, Loic; Crawford, Dana C.; Hindorff, Lucia A.; Kooperberg, Charles L.

2013-01-01

The vast majority of genome-wide association study (GWAS) findings reported to date are from populations with European Ancestry (EA), and it is not yet clear how broadly the genetic associations described will generalize to populations of diverse ancestry. The Population Architecture Using Genomics and Epidemiology (PAGE) study is a consortium of multi-ancestry, population-based studies formed with the objective of refining our understanding of the genetic architecture of common traits emerging from GWAS. In the present analysis of five common diseases and traits, including body mass index, type 2 diabetes, and lipid levels, we compare direction and magnitude of effects for GWAS-identified variants in multiple non-EA populations against EA findings. We demonstrate that, in all populations analyzed, a significant majority of GWAS-identified variants have allelic associations in the same direction as in EA, with none showing a statistically significant effect in the opposite direction, after adjustment for multiple testing. However, 25% of tagSNPs identified in EA GWAS have significantly different effect sizes in at least one non-EA population, and these differential effects were most frequent in African Americans where all differential effects were diluted toward the null. We demonstrate that differential LD between tagSNPs and functional variants within populations contributes significantly to dilute effect sizes in this population. Although most variants identified from GWAS in EA populations generalize to all non-EA populations assessed, genetic models derived from GWAS findings in EA may generate spurious results in non-EA populations due to differential effect sizes. Regardless of the origin of the differential effects, caution should be exercised in applying any genetic risk prediction model based on tagSNPs outside of the ancestry group in which it was derived. Models based directly on functional variation may generalize more robustly, but the identification of functional variants remains challenging. PMID:24068893

Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps.

PubMed

Garud, Nandita R; Messer, Philipp W; Buzbas, Erkan O; Petrov, Dmitri A

2015-02-01

Adaptation from standing genetic variation or recurrent de novo mutation in large populations should commonly generate soft rather than hard selective sweeps. In contrast to a hard selective sweep, in which a single adaptive haplotype rises to high population frequency, in a soft selective sweep multiple adaptive haplotypes sweep through the population simultaneously, producing distinct patterns of genetic variation in the vicinity of the adaptive site. Current statistical methods were expressly designed to detect hard sweeps and most lack power to detect soft sweeps. This is particularly unfortunate for the study of adaptation in species such as Drosophila melanogaster, where all three confirmed cases of recent adaptation resulted in soft selective sweeps and where there is evidence that the effective population size relevant for recent and strong adaptation is large enough to generate soft sweeps even when adaptation requires mutation at a specific single site at a locus. Here, we develop a statistical test based on a measure of haplotype homozygosity (H12) that is capable of detecting both hard and soft sweeps with similar power. We use H12 to identify multiple genomic regions that have undergone recent and strong adaptation in a large population sample of fully sequenced Drosophila melanogaster strains from the Drosophila Genetic Reference Panel (DGRP). Visual inspection of the top 50 candidates reveals that in all cases multiple haplotypes are present at high frequencies, consistent with signatures of soft sweeps. We further develop a second haplotype homozygosity statistic (H2/H1) that, in combination with H12, is capable of differentiating hard from soft sweeps. Surprisingly, we find that the H12 and H2/H1 values for all top 50 peaks are much more easily generated by soft rather than hard sweeps. We discuss the implications of these results for the study of adaptation in Drosophila and in species with large census population sizes.

The Solid Rocket Motor Slag Population: Results of a Radar-Based Regressive Statistical Evaluation

NASA Technical Reports Server (NTRS)

Horstman, Matthew F.; Xu, Yu-Lin

2008-01-01

Solid rocket motor (SRM) slag has been identified as a potential source of man-made orbital debris. The possibility that SRMs (in addition to generating dust particles in the sub-millimeter range) may generate particles up to centimeters in size has caused concern regarding their contribution to the debris environment. Returned surfaces from space do not have sufficient area or exposure time to provide a clear picture of the SRM millimeter and centimeter debris population. Currently, radar observation is probably the only way to collect data showing the debris contribution from SRMs. Such observation is used to sample the debris environment, but it is difficult to obtain accurate orbital elements for the detected debris objects. NASA has developed several models to describe the different orbital debris populations, based on assumed debris production mechanisms to create clouds of debris objects that can be propagated in time. The NASA model, LEGEND (LEO-to-GEO Environment Debris), functions as a time-tested debris model for most debris sources. However, the current LEGEND model does not include contributions from the SRM population. An SRM model has recently been developed by NASA, based on purely theoretical details of SRM production and known SRM launches, but verification with hard data is needed. Because the detections of individual SRM objects cannot be deterministically separated from the total debris observed by radar, the validation of the SRM model can only be done by combining it with the LEGEND breakup model and comparing it with data. By applying observational constraints, the degree of SRM slag contribution to the environment may be estimated. This serves as an observationally sound method from which to calibrate a purely theoretical model into something more realistic. For this study, we use the populations observed by the Haystack radar from 1996 to present. For the SRM debris, we use a historical database of SRM launches, propellant masses, and estimated locations and times of tailoff to produce and propagate the SRM debris clouds. Comparisons with radar data from the ensuing years were made, and the SRM model was altered with respect to size and mass production of slag particles to reflect the populations estimated from the data. The result is a model SRM population that fits within the bounds of the observed environment and estimates of the production and contribution of SRM debris to the environment.

Single neuron firing properties impact correlation-based population coding

PubMed Central

Hong, Sungho; Ratté, Stéphanie; Prescott, Steven A.; De Schutter, Erik

2012-01-01

Correlated spiking has been widely observed but its impact on neural coding remains controversial. Correlation arising from co-modulation of rates across neurons has been shown to vary with the firing rates of individual neurons. This translates into rate and correlation being equivalently tuned to the stimulus; under those conditions, correlated spiking does not provide information beyond that already available from individual neuron firing rates. Such correlations are irrelevant and can reduce coding efficiency by introducing redundancy. Using simulations and experiments in rat hippocampal neurons, we show here that pairs of neurons receiving correlated input also exhibit correlations arising from precise spike-time synchronization. Contrary to rate co-modulation, spike-time synchronization is unaffected by firing rate, thus enabling synchrony- and rate-based coding to operate independently. The type of output correlation depends on whether intrinsic neuron properties promote integration or coincidence detection: “ideal” integrators (with spike generation sensitive to stimulus mean) exhibit rate co-modulation whereas “ideal” coincidence detectors (with spike generation sensitive to stimulus variance) exhibit precise spike-time synchronization. Pyramidal neurons are sensitive to both stimulus mean and variance, and thus exhibit both types of output correlation proportioned according to which operating mode is dominant. Our results explain how different types of correlations arise based on how individual neurons generate spikes, and why spike-time synchronization and rate co-modulation can encode different stimulus properties. Our results also highlight the importance of neuronal properties for population-level coding insofar as neural networks can employ different coding schemes depending on the dominant operating mode of their constituent neurons. PMID:22279226

Long prereproductive selection and divergence by depth in a Caribbean candelabrum coral

PubMed Central

Prada, Carlos; Hellberg, Michael E.

2013-01-01

Long-lived corals, the foundation of modern reefs, often follow ecological gradients, so that populations or sister species segregate by habitat. Adaptive divergence maintains sympatric congeners after secondary contact or may even generate species by natural selection in the face of gene flow. Such ecological divergence, initially between alternative phenotypes within populations, may be aided by immigrant inviability, especially when a long period separates larval dispersal and the onset of reproduction, during which selection can sort lineages to match different habitats. Here, we evaluate the strength of one ecological factor (depth) to isolate populations by comparing the genes and morphologies of pairs of depth-segregated populations of the candelabrum coral Eunicea flexuosa across the Caribbean. Eunicea is endemic to the Caribbean and all sister species co-occur. Eunicea flexuosa is widespread both geographically and across reef habitats. Our genetic analysis revealed two depth-segregated lineages. Field survivorship data, combined with estimates of selection coefficients based on transplant experiments, suggest that selection is strong enough to segregate these two lineages. Genetic exchange between the Shallow and Deep lineages occurred either immediately after divergence or the two have diverged with gene flow. Migration occurs asymmetrically from the Shallow to Deep lineage. Limited recruitment to reproductive age, even under weak annual selection advantage, is sufficient to generate habitat segregation because of the cumulative prolonged prereproductive selection. Ecological factors associated with depth can act as filters generating strong barriers to gene flow, altering morphologies, and contributing to the potential for speciation in the sea. PMID:23359716

[Disease numbers in pneumology - a projection to 2060].

PubMed

Pritzkuleit, R; Beske, F; Katalinic, A

2010-09-01

The demographic change leads to a change in the age-composition of the population. We have calculated a status quo projection of the absolute numbers for five diagnoses of the lung (COPD, CAP, lung cancer, bronchial asthma and tuberculosis) for Germany up to 2060. Based on the 12 (th) coordinated population prediction of the Federal Statistics Office, we transferred age- and sex-specific incidence and prevalence rates, respectively, to the expected population. All described developments are based solely on demographic changes. The absolute numbers of bronchial asthma and tuberculosis will experience a minor decrease. We expect at first increasing and later decreasing case numbers for COPD and lung cancer. A major increase of the case numbers for CAP will be probable. By reason of a decreasing population, the rates (burden of disease for the population) will increase considerably. The demographic change is mainly caused by increasing life expectancy, constantly low birth rates, and the entry of the baby-boom generation into the age of higher disease risks. A discussion about prioritisation of health care is needed because of the rising burdens for the health system, including diseases of the lung. Copyright Georg Thieme Verlag KG Stuttgart . New York.

A parallel implementation of an off-lattice individual-based model of multicellular populations

NASA Astrophysics Data System (ADS)

Harvey, Daniel G.; Fletcher, Alexander G.; Osborne, James M.; Pitt-Francis, Joe

2015-07-01

As computational models of multicellular populations include ever more detailed descriptions of biophysical and biochemical processes, the computational cost of simulating such models limits their ability to generate novel scientific hypotheses and testable predictions. While developments in microchip technology continue to increase the power of individual processors, parallel computing offers an immediate increase in available processing power. To make full use of parallel computing technology, it is necessary to develop specialised algorithms. To this end, we present a parallel algorithm for a class of off-lattice individual-based models of multicellular populations. The algorithm divides the spatial domain between computing processes and comprises communication routines that ensure the model is correctly simulated on multiple processors. The parallel algorithm is shown to accurately reproduce the results of a deterministic simulation performed using a pre-existing serial implementation. We test the scaling of computation time, memory use and load balancing as more processes are used to simulate a cell population of fixed size. We find approximate linear scaling of both speed-up and memory consumption on up to 32 processor cores. Dynamic load balancing is shown to provide speed-up for non-regular spatial distributions of cells in the case of a growing population.

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.

Precision medicine: does ethnicity information complement genotype-based prescribing decisions?

PubMed Central

Shah, Rashmi R.; Gaedigk, Andrea

2017-01-01

Inter-ethnic differences in drug response are all too well known. These are underpinned by a number of factors, including pharmacogenetic differences across various ethnic populations. Precision medicine relies on genotype-based prescribing decisions with the aim of maximizing efficacy and mitigating the risks. When there is no access to genotyping tests, ethnicity is frequently regarded as a proxy of the patient’s probable genotype on the basis of overall population-based frequency of genetic variations in the ethnic group the patient belongs to, with some variations being ethnicity-specific. However, ever-increasing transcontinental migration of populations and the resulting admixing of populations have undermined the utility of self-identified ethnicity in predicting the genetic ancestry, and therefore the genotype, of the patient. An example of the relevance of genetic ancestry of a patient is the inadequate performance of European-derived pharmacogenetic dosing algorithms of warfarin in African Americans, Brazilians and Caribbean Hispanics. Consequently, genotyping a patient potentially requires testing for all known clinically actionable variants that the patient may harbour, and new variants that are likely to be identified using state-of the art next-generation sequencing-based methods. Furthermore, self-identified ethnicity is associated with a number of ethnicity-related attributes and non-genetic factors that potentially influence the risk of phenoconversion (genotype–phenotype discordance), which may adversely impact the success of genotype-based prescribing decisions. Therefore, while genotype-based prescribing decisions are important in implementing precision medicine, ethnicity should not be disregarded. PMID:29318005

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

Inability of populations of Callosobruchus maculatus to develop tolerance to exposures of acute gamma irradiation

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

Brower, J.H.

1974-03-01

The reproductive capacity and resistance to an acute dose of gamma irradiation were determined for populations of Callosobruchus maculatus treated with substerilizing doses of irradiation each generation for 30 generations. Reproductive capacity was decreased by an ancestral history of irradiation, the reduction being positively correlated with both the size of dose per generation and the number of ancestral generations treated. Irradiation of the selected populations with an acute dose revealed no increase in tolerance, even after 30 generations. In general, the greater the amount of accumulated ancestral exposure to irradiation, the greater the sensitivity to further irradiation. The ability tomore » develop a tolerance to ionizing irradiation may not be a general phenomenon in insects. (auth)« less

Factors Affecting the Biology and Pathogenicity of Heterodera schachtii on Sugarbeet.

PubMed

Griffin, G D

1988-07-01

A direct relationship exists between soil temperature and Heterodera schachtii development. The average developmental period of two nematode populations from Lewiston, Utah, and Rupert, Idaho, from J2 to J3, J4, adult, and the next generation J2 at soil temperatures of 18-28 C were 100, 140,225, and 399 degree-days (base 8 C), respectively. There was a positive relationship (P < 0.05) between nematode Pi, nematode generations, and sugarbeet yields. The greatest sugarbeet growth inhibition (87%) occurred when sugarbeets were exposed to a Pi of 12 eggs/cm(3) soil for five generations (1,995 degree-days), compared with a 47% inhibition when plants were exposed to the same Pi for two generations. There was a negative correlation (P < 0.05) between the Pi, Pf, and sugarbeet yield for each population threshold. The smaller the Pi, the greater the sugarbeet yields and the greater the Pf. Root yields were 80 and 29 t /ha and Pf were 8.4 and 3.6 eggs/cm(3) soil when sugarbeet seeds were planted at Pi of 0.4 and 7.9 eggs/cm(3). respectively, at a soil temperature of 8 C. The number of years rotation with a nonhost crop required to reduce the nematode population density below a damage threshold level of 2 eggs/cm(3) depends on the Pi. A Pi of 33.8 eggs/cm(3) soil required a 5-year crop rotation, whereas a Pi of 8.4 eggs/cm(3) soil required a 2-year crop rotation.

Factors Affecting the Biology and Pathogenicity of Heterodera schachtii on Sugarbeet

PubMed Central

Griffin, G. D.

1988-01-01

A direct relationship exists between soil temperature and Heterodera schachtii development. The average developmental period of two nematode populations from Lewiston, Utah, and Rupert, Idaho, from J2 to J3, J4, adult, and the next generation J2 at soil temperatures of 18-28 C were 100, 140,225, and 399 degree-days (base 8 C), respectively. There was a positive relationship (P < 0.05) between nematode Pi, nematode generations, and sugarbeet yields. The greatest sugarbeet growth inhibition (87%) occurred when sugarbeets were exposed to a Pi of 12 eggs/cm³ soil for five generations (1,995 degree-days), compared with a 47% inhibition when plants were exposed to the same Pi for two generations. There was a negative correlation (P < 0.05) between the Pi, Pf, and sugarbeet yield for each population threshold. The smaller the Pi, the greater the sugarbeet yields and the greater the Pf. Root yields were 80 and 29 t /ha and Pf were 8.4 and 3.6 eggs/cm³ soil when sugarbeet seeds were planted at Pi of 0.4 and 7.9 eggs/cm³. respectively, at a soil temperature of 8 C. The number of years rotation with a nonhost crop required to reduce the nematode population density below a damage threshold level of 2 eggs/cm³ depends on the Pi. A Pi of 33.8 eggs/cm³ soil required a 5-year crop rotation, whereas a Pi of 8.4 eggs/cm³ soil required a 2-year crop rotation. PMID:19290229

An Agent-Based Modeling Template for a Cohort of Veterans with Diabetic Retinopathy.

PubMed

Day, Theodore Eugene; Ravi, Nathan; Xian, Hong; Brugh, Ann

2013-01-01

Agent-based models are valuable for examining systems where large numbers of discrete individuals interact with each other, or with some environment. Diabetic Veterans seeking eye care at a Veterans Administration hospital represent one such cohort. The objective of this study was to develop an agent-based template to be used as a model for a patient with diabetic retinopathy (DR). This template may be replicated arbitrarily many times in order to generate a large cohort which is representative of a real-world population, upon which in-silico experimentation may be conducted. Agent-based template development was performed in java-based computer simulation suite AnyLogic Professional 6.6. The model was informed by medical data abstracted from 535 patient records representing a retrospective cohort of current patients of the VA St. Louis Healthcare System Eye clinic. Logistic regression was performed to determine the predictors associated with advancing stages of DR. Predicted probabilities obtained from logistic regression were used to generate the stage of DR in the simulated cohort. The simulated cohort of DR patients exhibited no significant deviation from the test population of real-world patients in proportion of stage of DR, duration of diabetes mellitus (DM), or the other abstracted predictors. Simulated patients after 10 years were significantly more likely to exhibit proliferative DR (P<0.001). Agent-based modeling is an emerging platform, capable of simulating large cohorts of individuals based on manageable data abstraction efforts. The modeling method described may be useful in simulating many different conditions where course of disease is described in categorical stages.

Development of germ-line-specific CRISPR-Cas9 systems to improve the production of heritable gene modifications in Arabidopsis.

PubMed

Mao, Yanfei; Zhang, Zhengjing; Feng, Zhengyan; Wei, Pengliang; Zhang, Hui; Botella, José Ramón; Zhu, Jian-Kang

2016-02-01

The Streptococcus-derived CRISPR/Cas9 system is being widely used to perform targeted gene modifications in plants. This customized endonuclease system has two components, the single-guide RNA (sgRNA) for target DNA recognition and the CRISPR-associated protein 9 (Cas9) for DNA cleavage. Ubiquitously expressed CRISPR/Cas9 systems (UC) generate targeted gene modifications with high efficiency but only those produced in reproductive cells are transmitted to the next generation. We report the design and characterization of a germ-line-specific Cas9 system (GSC) for Arabidopsis gene modification in male gametocytes, constructed using a SPOROCYTELESS (SPL) genomic expression cassette. Four loci in two endogenous genes were targeted by both systems for comparative analysis. Mutations generated by the GSC system were rare in T1 plants but were abundant (30%) in the T2 generation. The vast majority (70%) of the T2 mutant population generated using the UC system were chimeras while the newly developed GSC system produced only 29% chimeras, with 70% of the T2 mutants being heterozygous. Analysis of two loci in the T2 population showed that the abundance of heritable gene mutations was 37% higher in the GSC system compared to the UC system and the level of polymorphism of the mutations was also dramatically increased with the GSC system. Two additional systems based on germ-line-specific promoters (pDD45-GT and pLAT52-GT) were also tested, and one of them was capable of generating heritable homozygous T1 mutant plants. Our results suggest that future application of the described GSC system will facilitate the screening for targeted gene modifications, especially lethal mutations in the T2 population. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Risk of eating disorders in immigrant populations.

PubMed

Mustelin, L; Hedman, A M; Thornton, L M; Kuja-Halkola, R; Keski-Rahkonen, A; Cantor-Graae, E; Almqvist, C; Birgegård, A; Lichtenstein, P; Mortensen, P B; Pedersen, C B; Bulik, C M

2017-08-01

The risk of certain psychiatric disorders is elevated among immigrants. To date, no population studies on immigrant health have addressed eating disorders. We examined whether risk of eating disorders in first- and second-generation immigrants differs from native-born Danes and Swedes. All individuals born 1984-2002 (Danish cohort) and 1989-1999 (Swedish cohort) and residing in the respective country on their 10th birthday were included. They were followed up for the development of eating disorders based on out-patient and in-patient data. The risks of all eating disorder types were lower among first-generation immigrants compared to the native populations: Incidence-rate ratio (95% confidence interval) was 0.39 (0.29, 0.51) for anorexia nervosa, 0.60 (0.42, 0.83) for bulimia nervosa, and 0.62 (0.47, 0.79) for other eating disorders in Denmark and 0.27 (0.21, 0.34) for anorexia nervosa, 0.30 (0.18, 0.51) for bulimia nervosa, and 0.39 (0.32, 0.47) for other eating disorders in Sweden. Likewise, second-generation immigrants by both parents were at lower risk, whereas those with only one foreign-born parent were not. The decreased risk of eating disorders among immigrants is opposite to what has been observed for other psychiatric disorders, particularly schizophrenia. Possible explanations include buffering sociocultural factors and underdetection in health care. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Dispersal Timing: Emigration of Insects Living in Patchy Environments.

PubMed

Lakovic, Milica; Poethke, Hans-Joachim; Hovestadt, Thomas

2015-01-01

Dispersal is a life-history trait affecting dynamics and persistence of populations; it evolves under various known selective pressures. Theoretical studies on dispersal typically assume 'natal dispersal', where individuals emigrate right after birth. But emigration may also occur during a later moment within a reproductive season ('breeding dispersal'). For example, some female butterflies first deposit eggs in their natal patch before migrating to other site(s) to continue egg-laying there. How breeding compared to natal dispersal influences the evolution of dispersal has not been explored. To close this gap we used an individual-based simulation approach to analyze (i) the evolution of timing of breeding dispersal in annual organisms, (ii) its influence on dispersal (compared to natal dispersal). Furthermore, we tested (iii) its performance in direct evolutionary contest with individuals following a natal dispersal strategy. Our results show that evolution should typically result in lower dispersal under breeding dispersal, especially when costs of dispersal are low and population size is small. By distributing offspring evenly across two patches, breeding dispersal allows reducing direct sibling competition in the next generation whereas natal dispersal can only reduce trans-generational kin competition by producing highly dispersive offspring in each generation. The added benefit of breeding dispersal is most prominent in patches with small population sizes. Finally, the evolutionary contests show that a breeding dispersal strategy would universally out-compete natal dispersal.

Raised incidence rates of all psychoses among migrant groups: findings from the East London first episode psychosis study.

PubMed

Coid, Jeremy W; Kirkbride, James B; Barker, Dave; Cowden, Fiona; Stamps, Rebekah; Yang, Min; Jones, Peter B

2008-11-01

Certain black and minority ethnic groups are at increased risk for psychoses. It is unknown whether risk for second- and later-generation black and minority ethnic groups in the United Kingdom is universally increased or varies by ethnicity, population structure, or diagnostic category. To examine whether excess risk in black and minority ethnic groups varies by generation status and to determine whether this is explained solely by an excess of broadly defined schizophrenia. Population-based epidemiological survey of first-onset psychoses during a 2-year study period. Three inner-city boroughs in East London, England. Patients Four hundred eighty-four patients with first-episode psychosis aged 18 to 64 years. Nonaffective or affective psychoses according to the DSM-IV. Raised incidence of both nonaffective and affective psychoses were found for all of the black and minority ethnic subgroups compared with white British individuals. The risk of nonaffective psychoses for first and second generations varied by ethnicity (likelihood ratio test, P = .06). Only black Caribbean second-generation individuals were at significantly greater risk compared with their first-generation counterparts (incidence rate ratio, 2.2; 95% confidence interval, 1.1-4.2) [corrected]. No significant differences between first and second generations were observed in other ethnic groups. Asian women but not men of both generations were at increased risk for psychoses compared with white British individuals. Patterns were broadly upheld for the affective psychoses. Both first- and second-generation immigrants were at elevated risk for both nonaffective and affective psychoses, but this varied by ethnicity. Our results suggest that given the same age structure, the risk of psychoses in first and second generations of the same ethnicity will be roughly equal. We suggest that socioenvironmental factors operate differentially by ethnicity but not generation status, even if the exact specification of these stressors differs across generations. Research should focus on differential rates of psychoses by ethnicity rather than between generations.

Developing metapopulation connectivity criteria from genetic and habitat data to recover the endangered Mexican wolf.

PubMed

Carroll, Carlos; Fredrickson, Richard J; Lacy, Robert C

2014-02-01

Restoring connectivity between fragmented populations is an important tool for alleviating genetic threats to endangered species. Yet recovery plans typically lack quantitative criteria for ensuring such population connectivity. We demonstrate how models that integrate habitat, genetic, and demographic data can be used to develop connectivity criteria for the endangered Mexican wolf (Canis lupus baileyi), which is currently being restored to the wild from a captive population descended from 7 founders. We used population viability analysis that incorporated pedigree data to evaluate the relation between connectivity and persistence for a restored Mexican wolf metapopulation of 3 populations of equal size. Decreasing dispersal rates greatly increased extinction risk for small populations (<150-200), especially as dispersal rates dropped below 0.5 genetically effective migrants per generation. We compared observed migration rates in the Northern Rocky Mountains (NRM) wolf metapopulation to 2 habitat-based effective distance metrics, least-cost and resistance distance. We then used effective distance between potential primary core populations in a restored Mexican wolf metapopulation to evaluate potential dispersal rates. Although potential connectivity was lower in the Mexican wolf versus the NRM wolf metapopulation, a connectivity rate of >0.5 genetically effective migrants per generation may be achievable via natural dispersal under current landscape conditions. When sufficient data are available, these methods allow planners to move beyond general aspirational connectivity goals or rules of thumb to develop objective and measurable connectivity criteria that more effectively support species recovery. The shift from simple connectivity rules of thumb to species-specific analyses parallels the previous shift from general minimum-viable-population thresholds to detailed viability modeling in endangered species recovery planning. © 2013 Society for Conservation Biology.

LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants.

PubMed

Machiela, Mitchell J; Chanock, Stephen J

2015-11-01

Assessing linkage disequilibrium (LD) across ancestral populations is a powerful approach for investigating population-specific genetic structure as well as functionally mapping regions of disease susceptibility. Here, we present LDlink, a web-based collection of bioinformatic modules that query single nucleotide polymorphisms (SNPs) in population groups of interest to generate haplotype tables and interactive plots. Modules are designed with an emphasis on ease of use, query flexibility, and interactive visualization of results. Phase 3 haplotype data from the 1000 Genomes Project are referenced for calculating pairwise metrics of LD, searching for proxies in high LD, and enumerating all observed haplotypes. LDlink is tailored for investigators interested in mapping common and uncommon disease susceptibility loci by focusing on output linking correlated alleles and highlighting putative functional variants. LDlink is a free and publically available web tool which can be accessed at http://analysistools.nci.nih.gov/LDlink/. mitchell.machiela@nih.gov. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

Epidemiology of cognitive aging and Alzheimer's disease: contributions of the cache county utah study of memory, health and aging.

PubMed

Hayden, Kathleen M; Welsh-Bohmer, Kathleen A

2012-01-01

Epidemiological studies of Alzheimer's disease (AD) provide insights into changing public health trends and their contribution to disease incidence. The current chapter considers how the population-based approach has contributed to our understanding of lifetime exposures that contribute to later disease risk and may act to modify onset of symptoms. We focus on the findings from a recent survey of an exceptionally long-lived population, the Cache County Utah Study of Memory, Health, and Aging. This study is confined to a single geographic population has allowed estimation of the genetic and environmental influences on AD expression across the expected human lifespan of 95+ years. Given the emphasis of this text on the behavioral neurosciences of aging, we highlight within the current chapter the particular contributions of this population-based study to the neuropsychology of aging and AD. We also discuss hypotheses generated from this survey with respect to factors that may either accelerate or delay symptom onset in AD and the conditions that appear to be associated with successful cognitive aging.

Analysis of spatio-temporal patterns of African swine fever cases in Russian wild boar does not reveal an endemic situation.

PubMed

Lange, M; Siemen, H; Blome, S; Thulke, H-H

2014-11-15

African swine fever (ASF) is a highly lethal viral disease of domestic pigs and wild boar. ASF was introduced into the southern Russian Federation in 2007 and is now reported to be spreading in populations of wild and domestic suids. An endemic situation in the local wild boar population would significantly complicate management of the disease in the livestock population. To date no sound method exists for identifying the characteristic pattern of an endemic situation, which describes infection persisting from generation to generation in the same population. To support urgent management decisions at the wildlife-livestock interface, a new algorithm was constructed to test the hypothesis of an endemic disease situation in wildlife on the basis of case reports. The approach described here uses spatial and temporal associations between observed diagnostic data to discriminate between endemic and non-endemic patterns of case occurrence. The algorithm was validated with data from an epidemiological simulation model and applied to ASF case data from southern Russia. Based on the algorithm and the diagnostic data available, the null hypothesis of an endemic situation of ASF in wild boar of the region was rejected. Copyright © 2014 Elsevier B.V. All rights reserved.

Tychoparthenogenesis and mixed mating in natural populations of the mayfly Stenonema femoratum.

PubMed

Ball, S L

2001-09-01

Tychoparthenogenesis is a breeding system characterized by low population mean hatching success (usually < 10%) of unfertilized eggs from females of typically sexually reproducing species. I used progeny-array analysis to estimate outcrossing and parthenogenetic rates for two tychoparthenogenetic populations of the mayfly, Stenonema femoratum. Based on multilocus outcrossing rate estimates (t(m)), populations exhibited moderate rates of tychoparthenogenetic reproduction (population LD: 1 - t(m)=0.266; population RBG: 1 - t(m)=0.495). Differences between multilocus and average single-locus outcrossing rates indicated some biparental inbreeding in population LD, but not in population RBG. Family outcrossing rates ranged from 0 to 1.0, indicating mixed mating in which some females generated a mixture of sexually and parthenogenetically produced offspring. Outcrossing rates showed substantial heterogeneity among families. Correlation with paternity was high, indicating that outcrossed sibs within families were sired by the same father. Progeny-array sex ratios were significantly female biased for both populations and did not differ significantly between populations. However, family outcrossing rate was not significantly correlated with family sex ratio. Results indicate that substantial amounts of parthenogenetic reproduction are occurring in these natural S. femoratum populations and that some females produce mixed broods of sexually and parthenogenetically produced offspring.

Recombinant and epitope-based vaccines on the road to the market and implications for vaccine design and production.

PubMed

Oyarzún, Patricio; Kobe, Bostjan

2016-03-03

Novel vaccination approaches based on rational design of B- and T-cell epitopes - epitope-based vaccines - are making progress in the clinical trial pipeline. The epitope-focused recombinant protein-based malaria vaccine (termed RTS,S) is a next-generation approach that successfully reached phase-III trials, and will potentially become the first commercial vaccine against a human parasitic disease. Progress made on methods such as recombinant DNA technology, advanced cell-culture techniques, immunoinformatics and rational design of immunogens are driving the development of these novel concepts. Synthetic recombinant proteins comprising both B- and T-cell epitopes can be efficiently produced through modern biotechnology and bioprocessing methods, and can enable the induction of large repertoires of immune specificities. In particular, the inclusion of appropriate CD4+ T-cell epitopes is increasingly considered a key vaccine component to elicit robust immune responses, as suggested by results coming from HIV-1 clinical trials. In silico strategies for vaccine design are under active development to address genetic variation in pathogens and several broadly protective "universal" influenza and HIV-1 vaccines are currently at different stages of clinical trials. Other methods focus on improving population coverage in target populations by rationally considering specificity and prevalence of the HLA proteins, though a proof-of-concept in humans has not been demonstrated yet. Overall, we expect immunoinformatics and bioprocessing methods to become a central part of the next-generation epitope-based vaccine development and production process.

Multigenerational Exposure of the Estuarine Sheepshead Minnow (Cyprinodon variegatus) to 17β-estradiol. II. Population-Level Effects Through Two Life Cycles

EPA Science Inventory

The evaluation of multi-generation, population-level impacts is particularly important in the risk assessment of endocrine disrupting compounds (EDCs) because adverse effects may not be evident during the first generation of exposure. Population models were developed for the shee...

Age and Time Population Differences: Young Adults, Gen Xers, and Millennials

ERIC Educational Resources Information Center

Menard, Lauren A.

2013-01-01

Age and Time disparities in young adult research populations are common because young adults are defined by varying age spans; members of Generation X and Millennial generations may both be considered young adults; study years vary, affecting populations; and qualitative methods with limited age/year samples are frequently utilized. The current…

Population-based pediatric reference intervals for general clinical chemistry analytes on the Abbott Architect ci8200 instrument.

PubMed

Ridefelt, Peter; Aldrimer, Mattias; Rödöö, Per-Olof; Niklasson, Frank; Jansson, Leif; Gustafsson, Jan; Hellberg, Dan

2012-02-29

Reference intervals are crucial decision-making tools aiding clinicians in differentiating between healthy and diseased populations. However, for children such values often are lacking or incomplete. Blood samples were obtained from 692 healthy children, aged 6 months to 18 years, recruited in daycare centers and schools. Twelve common general clinical chemistry analytes were measured on the Abbott Architect ci8200 platform; sodium, potassium, chloride, calcium, albumin-adjusted calcium, phosphate, magnesium, creatinine (Jaffe and enzymatic), cystatin C, urea and uric acid. Age- and gender specific pediatric reference intervals were defined by calculating the 2.5th and 97.5th percentiles. The data generated is primarily applicable to a Caucasian population when using the Abbott Architect platform, but could be used by any laboratory if validated for the local patient population.

Investigation into Differences in Level of Knowledge about Hypertension between High School Students and Elderly People.

PubMed

Sanagawa, Akimasa; Ogasawara, Misa; Kusahara, Yuri; Yasumoto, Miki; Iwaki, Soichiro; Fujii, Satoshi

2017-01-01

As a major chronic non-communicable disease, hypertension is the most important risk factor for cardiovascular disease, chronic kidney disease, stroke and, if not treated appropriately, premature death. A population-based approach aimed at decreasing high blood pressure among the general population is an important component of any comprehensive plan to prevent hypertension. However, few studies have investigated generational differences in knowledge about, and consciousness of, hypertension. Thus, we conducted a questionnaire survey about hypertension, with the aim of clarifying differences of understanding about hypertension between high school students and elderly people. The results of this investigation suggested that there is indeed a generational difference: knowledge about hypertension, and awareness of its relationship with salt intake, was higher in elderly people than in high school students. Furthermore, our study showed that among high school students, salt intake consciousness correlated with a family history of hypertension. By contrast, in elderly people, salt intake consciousness is related to age and to an awareness of recommended daily salt intake. This study strongly showed that knowledge and consciousness of hypertension varied among generations, with the elderly being more aware and conscientious about salt intake. Acknowledgement of this generational diversity is critical to developing an effective overall preventive strategy for hypertension.

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

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

PubMed

Meyer, Melanie

2017-12-01

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

Excavating past population structures by surname-based sampling: the genetic legacy of the Vikings in northwest England

PubMed Central

Bowden, Georgina R.; Balaresque, Patricia; King, Turi E.; Hansen, Ziff; Lee, Andrew C.; Pergl-Wilson, Giles; Hurley, Emma; Roberts, Stephen J.; Waite, Patrick; Jesch, Judith; Jones, Abigail L.; Thomas, Mark G.; Harding, Stephen E.; Jobling, Mark A.

2009-01-01

The genetic structures of past human populations are obscured by recent migrations and expansions, and can been observed only indirectly by inference from modern samples. However, the unique link between a heritable cultural marker, the patrilineal surname, and a genetic marker, the Y chromosome, provides a means to target sets of modern individuals that might resemble populations at the time of surname establishment. As a test case, we studied samples from the Wirral peninsula and West Lancashire, in northwest England. Place names and archaeology show clear evidence of a past Viking presence, but heavy immigration and population growth since the Industrial Revolution are likely to have weakened the genetic signal of a thousand-year-old Scandinavian contribution. Samples ascertained on the basis of two generations of residence were compared with independent samples based on known ancestry in the region, plus the possession of a surname known from historical records to have been present there in medieval times. The Y-chromosomal haplotypes of these two sets of samples are significantly different, and in admixture analyses the surname-ascertained samples show markedly greater Scandinavian ancestry proportions, supporting the idea that northwest England was once heavily populated by Scandinavian settlers. The method of historical surname-based ascertainment promises to allow investigation of the influence of migration and drift over the last few centuries in changing the population structure of Britain, and will have general utility in other regions where surnames are patrilineal and suitable historical records survive. PMID:18032405

Population delimitation across contrasting evolutionary clines in deer mice (Peromyscus maniculatus)

PubMed Central

Yang, D-S; Kenagy, G

2011-01-01

Despite current interest in population genetics, a concrete definition of a “population” remains elusive. Multiple ecologically and evolutionarily based definitions of population are in current use, which focus, respectively, on demographic and genetic interactions. Accurate population delimitation is crucial for not only evolutionary and ecological population biology, but also for conservation of threatened populations. Along the Pacific Coast of North America, two contrasting patterns of geographic variation in deer mice (Peromyscus maniculatus) converge within the state of Oregon. Populations of these mice diverge morphologically across an east–west axis, and they diverge in mitochondrial DNA haplotypes across a north–south axis. In this study, we investigate these geographically contrasting patterns of differentiation in the context of ecological and evolutionary definitions (paradigms) of populations. We investigate these patterns using a new and geographically expansive sample that integrates data on morphology, mitochondrial DNA, and nuclear DNA. We found no evidence of nuclear genetic differentiation between the morphologically and mitochondrially distinct populations, thus indicating the occurrence of gene flow across Oregon. Under the evolutionary paradigm, Oregon populations can be considered a single population, whereas morphological and mitochondrial differentiations do not indicate distinct populations. In contrast, under the ecological paradigm morphological differentiation indicates distinct populations based on the low likelihood of demographic interactions between geographically distant individuals. The two sympatric but mitochondrially distinct haplogroups form a single population under the ecological paradigm. Hence, we find that the difference between evolutionary and ecological paradigms is the time-scale of interest, and we believe that the more chronologically inclusive evolutionary paradigm may be preferable except in cases where only a single generation is of interest. PMID:22393480

[Study of the growth and development of Chlorella on "Kosmos-1887"].

PubMed

Sychev, V N; Levinskikh, M A; Livanskaia, O G

1989-01-01

The growth, development and population characteristics of Chlorella cells flown for 13 days in space were investigated during their postflight cultivation. The growth rate of flown algae did not differ from that of ground-based controls in terms of increases in the cell number and biomass. All basic parameters of the specimens (generation time, number of developing autospores, time ratio of developmental phases) were ontogentically normal. Exposure of the algae to space flight as a component of the algobacterial cenosis--fish autotrophic-heterotrophic system produced no significant effect of the population or individual specimens during their postflight cultivation.

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.

Effects of population outcrossing on rotifer fitness

PubMed Central

2010-01-01

Background Outcrossing between populations can exert either positive or negative effects on offspring fitness. Cyclically parthenogenetic rotifers, like other continental zooplankters, show high genetic differentiation despite their high potential for passive dispersal. Within this context, the effects of outcrossing may be relevant in modulating gene flow between populations through selection for or against interpopulation hybrids. Nevertheless, these effects remain practically unexplored in rotifers. Here, the consequences of outcrossing on the rotifer Brachionus plicatilis were investigated. Cross-mating experiments were performed between a reference population and three alternative populations that differed in their genetic distance with regard to the former. Two offspring generations were obtained: F1 and BC ('backcross'). Fitness of the outcrossed offspring was compared with fitness of the offspring of the reference population for both generations and for three different between-population combinations. Four fitness components were measured throughout the rotifer life cycle: the diapausing egg-hatching proportion, clone viability (for the clones originating from diapausing eggs), initial net growth rate R for each viable clone, and the proportion of male-producing clones. Additionally, both the parental fertilisation proportion and a compound fitness measure, integrating the complete life cycle, were estimated. Results In the F1 generation, hybrid vigour was detected for the diapausing egg-hatching proportion, while R was lower in the outcrossed offspring than in the offspring of the reference population. Despite these contrasting results, hybrid vigour was globally observed for the compound measure of fitness. Moreover, there was evidence that this vigour could increase with the genetic differentiation of the outcrossed populations. In the BC generation, the hybrid vigour detected for the egg-hatching proportion in the F1 generation reverted to outbreeding depression. By contrast, signs of hybrid vigour were observed for clone viability and R. The opposing trends observed for different life-cycle stages yielded a global pattern of hybrid vigour in the BC generation for two out of the three between-population comparisons. Conclusions Results suggest that outbreeding depression does not constitute a barrier to gene flow. In newly-founded populations, where the population size is still small, dilution of immigrants should be low. Thus, a lack of outbreeding depression would allow gene flow to have an impact on the genetic composition of these populations. PMID:20955598

Generating para-water from para-hydrogen: A Gedankenexperiment.

PubMed

Ivanov, Konstantin L; Bodenhausen, Geoffrey

2018-07-01

A novel conceptual approach is described that is based on the transfer of hyperpolarization from para-hydrogen in view of generating a population imbalance between the two spin isomers of H 2 O. The approach is analogous to SABRE (Signal Amplification By Reversible Exchange) and makes use of the transfer of spin order from para-hydrogen to H 2 O in a hypothetical organometallic complex. The spin order transfer is expected to be most efficient at avoided level crossings. The highest achievable enrichment levels of para- and ortho-water are discussed. Copyright © 2018 Elsevier Inc. All rights reserved.

Holocaust exposure and disordered eating: a study of multi-generational transmission.

PubMed

Zohar, Ada H; Giladi, Lotem; Givati, Timor

2007-01-01

To test the hypothesis that disordered eating in second- and third-generation women would be related to their levels of Holocaust exposure and family dysfunction. One hundred eight mother-daughter dyads were ascertained through the daughters, all Israeli college students 18-35 years of age. Mothers and daughters assessed themselves on family function, Holocaust exposure and disordered eating. The disordered eating of women of the third generation was partially predicted by their mothers' disordered eating and by their mothers' Holocaust exposure. The second generation reported more maternal over-protection and emotional over-involvement than did the third generation. Contrary to expectation, the third-generation women were more Holocaust exposed than were the second generation. The nature of Holocaust exposure for second and third generations needs further study and clarification in relation to disordered eating. There is considerable disparity between the results of clinical and qualitative studies which tend to find a strong relationship between Holocaust exposure and psychopathology, and population-based quantitative studies which tend to find a much weaker relationship. 2006 John Wiley & Sons, Ltd and Eating Disorders Association

Home educating in an extended family culture and aging society may fare best during a pandemic.

PubMed

Dawson, Wayne; Yamamoto, Kenji

2009-09-28

Large cities can contain populations that move rapidly from one section to another in an efficient transportation network. An emerging air-borne or contact based pathogen could use these transportation routes to rapidly spread an infection throughout an entire population in a short time. Further, in many developed countries, the aging population is increasing. The family structure in these societies may also affect the course of a disease. To help understand the impact of an epidemic on family structure in a networked population, an individual based computer model that randomly generates networked cities with a specified range of population and disease characteristics and individual schedules, infectivity, transmission and hygiene factors was developed. Several salient issues emerged. First, a city of highly active individuals may in fact diminish the number of fatalities because the average duration of the interactions between agents is reduced. Second, home schooling can significantly improve survival because the institutional clustering of weak individuals is minimized. Third, the worst scenario for an aging population is the nuclear family where the aged population is confined to large housing facilities. Naturally, hygiene is the first barrier to infection. The results suggest that societies where extended families and small groups manage most of their own affairs may also be the most suitable for defense against a pandemic. This may prove applicable in city planning and policy making.

The Use of a Poisson Regression to Evaluate Antihistamines and Fatal Aircraft Mishaps in Instrument Meteorological Conditions.

PubMed

Gildea, Kevin M; Hileman, Christy R; Rogers, Paul; Salazar, Guillermo J; Paskoff, Lawrence N

2018-04-01

Research indicates that first-generation antihistamine usage may impair pilot performance by increasing the likelihood of vestibular illusions, spatial disorientation, and/or cognitive impairment. Second- and third-generation antihistamines generally have fewer impairing side effects and are approved for pilot use. We hypothesized that toxicological findings positive for second- and third-generation antihistamines are less likely to be associated with pilots involved in fatal mishaps than first-generation antihistamines. The evaluated population consisted of 1475 U.S. civil pilots fatally injured between September 30, 2008, and October 1, 2014. Mishap factors evaluated included year, weather conditions, airman rating, recent airman flight time, quarter of year, and time of day. Due to the low prevalence of positive antihistamine findings, a count-based model was selected, which can account for rare outcomes. The means and variances were close for both regression models supporting the assumption that the data follow a Poisson distribution; first-generation antihistamine mishap airmen (N = 582, M = 0.17, S2 = 0.17) with second- and third-generation antihistamine mishap airmen (N = 116, M = 0.20, S2 = 0.18). The data indicate fewer airmen with second- and third-generation antihistamines than first-generation antihistamines in their system are fatally injured while flying in IMC conditions. Whether the lower incidence is a factor of greater usage of first-generation antihistamines versus second- and third-generation antihistamines by the pilot population or fewer deleterious side effects with second- and third-generation antihistamines is unclear. These results engender cautious optimism, but additional research is necessary to determine why these differences exist.Gildea KM, Hileman CR, Rogers P, Salazar GJ, Paskoff LN. The use of a Poisson regression to evaluate antihistamines and fatal aircraft mishaps in instrument meteorological conditions. Aerosp Med Hum Perform. 2018; 89(4):389-395.

Genetic polymorphisms, forensic efficiency and phylogenetic analysis of 15 autosomal STR loci in the Kazak population of Ili Kazak Autonomous Prefecture, northwestern China.

PubMed

Feng, Chunmei; Wang, Xin; Wang, Xiaolong; Yu, Hao; Zhang, Guohua

2018-03-01

We investigated the frequencies of 15 autosomal STR loci in the Kazak population of the Ili Kazak Autonomous Prefecture with the aim of expanding the available population information in human genetic databases and for forensic DNA analysis. Genetic polymorphisms of 15 autosomal short tandem repeat (STR) loci were analysed in 456 individuals of the Kazak population from Ili Kazakh Autonomous Prefecture, northwestern China. A total of 173 alleles at 15 autosomal STR loci were found; the allele frequencies ranged from 0.5022-0.0011. The combined power of discrimination and exclusion statistics for the 15 STR loci were 0.999 999 999 85 and 0.999 998 800 65, respectively. In addition, phylogenetic analysis involving the Ili Uygur population and other relevant populations was carried out. A neighbour-joining tree and multidimensional scaling plot were generated based on Nei's standard genetic distance. Results of the population comparison indicated that the Ili Uygur population was most closely related genetically to the Uygur populations from other regions in China. These findings are consistent with the historical and geographic backgrounds of these populations.

Reconstructing a Large-Scale Population for Social Simulation

NASA Astrophysics Data System (ADS)

Fan, Zongchen; Meng, Rongqing; Ge, Yuanzheng; Qiu, Xiaogang

The advent of social simulation has provided an opportunity to research on social systems. More and more researchers tend to describe the components of social systems in a more detailed level. Any simulation needs the support of population data to initialize and implement the simulation systems. However, it's impossible to get the data which provide full information about individuals and households. We propose a two-step method to reconstruct a large-scale population for a Chinese city according to Chinese culture. Firstly, a baseline population is generated through gathering individuals into households one by one; secondly, social relationships such as friendship are assigned to the baseline population. Through a case study, a population of 3,112,559 individuals gathered in 1,133,835 households is reconstructed for Urumqi city, and the results show that the generated data can respect the real data quite well. The generated data can be applied to support modeling of some social phenomenon.

Influence of harvesting pressure on demographic tactics: Implications for wildlife management

USGS Publications Warehouse

Servanty, S.; Gaillard, J.-M.; Ronchi, F.; Focardi, S.; Baubet, E.; Gimenez, O.

2011-01-01

Demographic tactics within animal populations are shaped by selective pressures. Exploitation exerts additional pressures so that differing demographic tactics might be expected among populations with differences in levels of exploitation. Yet little has been done so far to assess the possible consequences of exploitation on the demographic tactics of mammals, even though such information could influence the choice of effective management strategies. Compared with similar-sized ungulate species, wild boar Sus scrofa has high reproductive capabilities, which complicates population management. Using a perturbation analysis, we investigated how population growth rates (??) and critical life-history stages differed between two wild boar populations monitored for several years, one of which was heavily harvested and the other lightly harvested. Asymptotic ?? was 1??242 in the lightly hunted population and 1??115 in the heavily hunted population, while the ratio between the elasticity of adult survival and juvenile survival was 2??63 and 1??27, respectively. A comparative analysis including 21 other ungulate species showed that the elasticity ratio in the heavily hunted population was the lowest ever observed. Compared with expected generation times of similar-sized ungulates (more than 6years), wild boar has a fast life-history speed, especially when facing high hunting pressure. This is well illustrated by our results, where generation times were 3??6years in the lightly hunted population and only 2??3years in the heavily hunted population. High human-induced mortality combined with non-limiting food resources accounted for the accelerated life history of the hunted population because of earlier reproduction. Synthesis and applications. For wild boar, we show that when a population is facing a high hunting pressure, increasing the mortality in only one age-class (e.g. adults or juveniles) may not allow managers to limit population growth. We suggest that simulations of management strategies based on context-specific demographic models are useful for selecting interventions for population control. This type of approach allows the assessment of population response to exploitation by considering a range of plausible scenarios, improving the chance of selecting appropriate management actions. ?? 2011 The Authors. Journal of Applied Ecology ?? 2011 British Ecological Society.

Seroprevalence of hepatitis E virus differs in Dutch and first generation migrant populations in Amsterdam, the Netherlands: a cross-sectional study.

PubMed

Sadik, S; van Rijckevorsel, G G C; van Rooijen, M S; Sonder, G J B; Bruisten, S M

2016-11-08

In the last decade hepatitis E virus (HEV) is increasingly recognized as a cause of acute viral hepatitis in developed countries. HEV is transmitted via the fecal-oral route. In countries like the Netherlands, HEV infection is suspected to be a zoonosis but HEV may also be introduced by migrants. We studied the seroprevalence of HEV among different migrants, mainly Moroccans and Turks, and compared this to that of the native Dutch population in Amsterdam, the Netherlands. Data were obtained from a cross-sectional survey of the adult Amsterdam population performed in 2004; the Amsterdam Health Monitor. A total of 1199 plasma samples were tested for IgG-and IgM antibodies to HEV using the Wantai kit according to instructions of the manufacturer. Basic demographic data (gender, age, country of birth, and age at immigration) were used in the analyses. Hepatitis A virus (HAV) serology data were available from a previous study. The total weighted anti-HEV IgG seroprevalence in the overall Amsterdam population was 26.7 %, based on 1199 samples. In the study population (not-weighted) this HEV seroprevalence was 157/426 (36.9 %) for the Dutch participants and it was 161/257 (62.6 %) for Moroccans, 99/296 (33.4 %) for Turks and 42/220 (19.1 %) for other ethnicities. HEV seroprevalence increased significantly with age. First-generation Moroccan migrants (44.0 %) had a significantly higher weighted HEV seroprevalence than the Dutch participants (29.7 %). In the first generation Turks (20.3 %) and first generation migrants from other countries (16.7 %) this weighted seroprevalence was lower, but this was only significant for the 'other ethnicities'. The median age of migration was significantly higher in the Moroccan and Turkish migrants who were HEV IgG positive versus HEV IgG negative. However, when stratifying for age at time of study, median migration age was only significantly different for HEV sero-status for younger Turks and younger 'other ethnicities'. HEV IgM antibodies were found in 0.6 % (n = 7) of participants and none were positive for HEV RNA, showing that there were no acute infections. Despite the common route of fecal-oral transmission for both viruses, there was no relation between HEV and HAV seropositivity. Within the multi-ethnical capital city of Amsterdam the HEV seroprevalence in first generation migrant populations differed from each other and from the autochthonous Dutch population. The relation between being HEV seropositive and a higher median age of migration suggests that younger migrants got more often infected in their country of origin than in the Netherlands.

The Latino Male Educational Trajectory: A Precollege Econometric Model and 21st Century Implications

ERIC Educational Resources Information Center

Ortiz, Ramon, Jr.

2017-01-01

The twin challenges of aging demographics in the United States and the need for higher levels of education to compete in the new technology-based economy is creating a socioeconomic paradox (Friedman, 2005). As the Baby Boomer generation retires, those replacing them are increasingly a non-White population. This demographic shift is inevitable and…

Selective functionalization of carbon nanotubes

NASA Technical Reports Server (NTRS)

Strano, Michael S. (Inventor); Usrey, Monica (Inventor); Barone, Paul (Inventor); Dyke, Christopher A. (Inventor); Tour, James M. (Inventor); Kittrell, W. Carter (Inventor); Hauge, Robert H. (Inventor); Smalley, Richard E. (Inventor)

2009-01-01

The present invention is directed toward methods of selectively functionalizing carbon nanotubes of a specific type or range of types, based on their electronic properties, using diazonium chemistry. The present invention is also directed toward methods of separating carbon nanotubes into populations of specific types or range(s) of types via selective functionalization and electrophoresis, and also to the novel compositions generated by such separations.

Evidence-based medical oncology and interventional radiology paradigms for liver-dominant colorectal cancer metastases

PubMed Central

Sag, Alan Alper; Selcukbiricik, Fatih; Mandel, Nil Molinas

2016-01-01

Colorectal cancer metastasizes predictably, with liver predominance in most cases. Because liver involvement has been shown to be a major determinant of survival in this population, liver-directed therapies are increasingly considered even in cases where there is (limited) extrahepatic disease. Unfortunately, these patients carry a known risk of recurrence in the liver regardless of initial therapy choice. Therefore, there is a demand for minimally invasive, non-surgical, personalized cancer treatments to preserve quality of life in the induction, consolidation, and maintenance phases of cancer therapy. This report aims to review evidence-based conceptual, pharmacological, and technological paradigm shifts in parenteral and percutaneous treatment strategies as well as forthcoming evidence regarding next-generation systemic, locoregional, and local treatment approaches for this patient population. PMID:27003990

Small meteoroids' major contribution to Mercury's exosphere

NASA Astrophysics Data System (ADS)

Grotheer, E. B.; Livi, S. A.

2014-01-01

The contribution of the meteoroid population to the generation of Mercury's exosphere is analyzed to determine which segment contributes most greatly to exospheric refilling via the process of meteoritic impact vaporization. For the meteoroid data, a differential mass distribution based on work by Grün et al. (Grün, E., Zook, H.A., Fechtig, H., Giese, R.H. [1985]. Icarus 62(2), 244-272) and a differential velocity distribution based on the work of Zook (Zook, H.A. [1975]. In: 6th Lunar Science Conference, vol. 2. Pergamon Press, Inc., Houston, TX, pp. 1653-1672) is used. These distributions are then evaluated using the method employed by Cintala (Cintala, M.J. [1992]. J. Geophys. Res. 97(E1), 947-974) to determine impact rates for selected mass and velocity segments of the meteoroid population.

Multiscale musculoskeletal modelling, data–model fusion and electromyography-informed modelling

PubMed Central

Zhang, J.; Heidlauf, T.; Sartori, M.; Besier, T.; Röhrle, O.; Lloyd, D.

2016-01-01

This paper proposes methods and technologies that advance the state of the art for modelling the musculoskeletal system across the spatial and temporal scales; and storing these using efficient ontologies and tools. We present population-based modelling as an efficient method to rapidly generate individual morphology from only a few measurements and to learn from the ever-increasing supply of imaging data available. We present multiscale methods for continuum muscle and bone models; and efficient mechanostatistical methods, both continuum and particle-based, to bridge the scales. Finally, we examine both the importance that muscles play in bone remodelling stimuli and the latest muscle force prediction methods that use electromyography-assisted modelling techniques to compute musculoskeletal forces that best reflect the underlying neuromuscular activity. Our proposal is that, in order to have a clinically relevant virtual physiological human, (i) bone and muscle mechanics must be considered together; (ii) models should be trained on population data to permit rapid generation and use underlying principal modes that describe both muscle patterns and morphology; and (iii) these tools need to be available in an open-source repository so that the scientific community may use, personalize and contribute to the database of models. PMID:27051510

MendeLIMS: a web-based laboratory information management system for clinical genome sequencing.

PubMed

Grimes, Susan M; Ji, Hanlee P

2014-08-27

Large clinical genomics studies using next generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate laboratory information management systems to manage the thousands of patient samples that are subject to this type of genetic analysis. To meet the needs of clinical population studies using genome sequencing, we developed a web-based laboratory information management system (LIMS) with a flexible configuration that is adaptable to continuously evolving experimental protocols of next generation DNA sequencing technologies. Our system is referred to as MendeLIMS, is easily implemented with open source tools and is also highly configurable and extensible. MendeLIMS has been invaluable in the management of our clinical genome sequencing studies. We maintain a publicly available demonstration version of the application for evaluation purposes at http://mendelims.stanford.edu. MendeLIMS is programmed in Ruby on Rails (RoR) and accesses data stored in SQL-compliant relational databases. Software is freely available for non-commercial use at http://dna-discovery.stanford.edu/software/mendelims/.

Argentine stem weevil ( Listronotus bonariensis, Coleoptera: Curculionidae) population dynamics in Canterbury, New Zealand dryland pasture.

PubMed

Goldson, S L; Barron, M C; Kean, J M; van Koten, C

2011-06-01

The Argentine stem weevil (Listronotus bonariensis) was an economically important pest in New Zealand pastures until the release of the parasitoid Microctonus hyperodae. This contribution uses historical data to investigate the regulation of the pest populations prior to, and somewhat during, the establishment of this parasitoid in dryland Canterbury, New Zealand. Thus, a significant goal of this study is to provide an L. bonariensis population dynamics baseline for any future work that aims to analyse the full effects of M. hyperodae on the weevil, now that equilibrium with the weevil host has been reached.The population dynamics of L. bonariensis, based on a life-table approach, were investigated using data collected regularly for eight years from populations in Canterbury, New Zealand. The key factor affecting end-of-season L. bonariensis density was found to be variation in second generation fourth instar prepupal and pupal mortality. This may have been caused by arrested development and ongoing mortality resulting from the onset of cooler autumnal conditions.A compensatory response was found in recruitment to the second summer weevil generation, whereby the realised fecundity of the emergent first summer generation of weevils was found to be negatively related to the density of adult weevils per ryegrass tiller. This is the first time that this has been found via long-term population analysis of L. bonariensis, although indications of this have been found elsewhere in caging, pot and small plot experiments.In this study, the effect of the parasitoid biocontrol agent Microctonus hyperodae on L. bonariensis population dynamics was unclear, as the analysis covered a period when the parasitoid Microctonus hyperodae was introduced and still establishing. It does, however, raise important questions for future analysis in terms of the interaction between parasitism and unrealised fecundity.The results in this contribution also highlighted regional differences. Overwintering mortality of adult weevils in Canterbury was constant between years, whilst earlier studies in the North Island Waikato region indicated this mortality was density dependent. In addition, the availability of tillers in endophyte-free ryegrass pastures in Canterbury had no influence on egg and early-instar larval survival, which contrasts with the finding from endophytic Waikato pastures.

The importance of information on relatives for the prediction of genomic breeding values and the implications for the makeup of reference data sets in livestock breeding schemes.

PubMed

Clark, Samuel A; Hickey, John M; Daetwyler, Hans D; van der Werf, Julius H J

2012-02-09

The theory of genomic selection is based on the prediction of the effects of genetic markers in linkage disequilibrium with quantitative trait loci. However, genomic selection also relies on relationships between individuals to accurately predict genetic value. This study aimed to examine the importance of information on relatives versus that of unrelated or more distantly related individuals on the estimation of genomic breeding values. Simulated and real data were used to examine the effects of various degrees of relationship on the accuracy of genomic selection. Genomic Best Linear Unbiased Prediction (gBLUP) was compared to two pedigree based BLUP methods, one with a shallow one generation pedigree and the other with a deep ten generation pedigree. The accuracy of estimated breeding values for different groups of selection candidates that had varying degrees of relationships to a reference data set of 1750 animals was investigated. The gBLUP method predicted breeding values more accurately than BLUP. The most accurate breeding values were estimated using gBLUP for closely related animals. Similarly, the pedigree based BLUP methods were also accurate for closely related animals, however when the pedigree based BLUP methods were used to predict unrelated animals, the accuracy was close to zero. In contrast, gBLUP breeding values, for animals that had no pedigree relationship with animals in the reference data set, allowed substantial accuracy. An animal's relationship to the reference data set is an important factor for the accuracy of genomic predictions. Animals that share a close relationship to the reference data set had the highest accuracy from genomic predictions. However a baseline accuracy that is driven by the reference data set size and the overall population effective population size enables gBLUP to estimate a breeding value for unrelated animals within a population (breed), using information previously ignored by pedigree based BLUP methods.

Improving the Rank Precision of Population Health Measures for Small Areas with Longitudinal and Joint Outcome Models

PubMed Central

Athens, Jessica K.; Remington, Patrick L.; Gangnon, Ronald E.

2015-01-01

Objectives The University of Wisconsin Population Health Institute has published the County Health Rankings since 2010. These rankings use population-based data to highlight health outcomes and the multiple determinants of these outcomes and to encourage in-depth health assessment for all United States counties. A significant methodological limitation, however, is the uncertainty of rank estimates, particularly for small counties. To address this challenge, we explore the use of longitudinal and pooled outcome data in hierarchical Bayesian models to generate county ranks with greater precision. Methods In our models we used pooled outcome data for three measure groups: (1) Poor physical and poor mental health days; (2) percent of births with low birth weight and fair or poor health prevalence; and (3) age-specific mortality rates for nine age groups. We used the fixed and random effects components of these models to generate posterior samples of rates for each measure. We also used time-series data in longitudinal random effects models for age-specific mortality. Based on the posterior samples from these models, we estimate ranks and rank quartiles for each measure, as well as the probability of a county ranking in its assigned quartile. Rank quartile probabilities for univariate, joint outcome, and/or longitudinal models were compared to assess improvements in rank precision. Results The joint outcome model for poor physical and poor mental health days resulted in improved rank precision, as did the longitudinal model for age-specific mortality rates. Rank precision for low birth weight births and fair/poor health prevalence based on the univariate and joint outcome models were equivalent. Conclusion Incorporating longitudinal or pooled outcome data may improve rank certainty, depending on characteristics of the measures selected. For measures with different determinants, joint modeling neither improved nor degraded rank precision. This approach suggests a simple way to use existing information to improve the precision of small-area measures of population health. PMID:26098858

Inferring the demographic history from DNA sequences: An importance sampling approach based on non-homogeneous processes.

PubMed

Ait Kaci Azzou, S; Larribe, F; Froda, S

2016-10-01

In Ait Kaci Azzou et al. (2015) we introduced an Importance Sampling (IS) approach for estimating the demographic history of a sample of DNA sequences, the skywis plot. More precisely, we proposed a new nonparametric estimate of a population size that changes over time. We showed on simulated data that the skywis plot can work well in typical situations where the effective population size does not undergo very steep changes. In this paper, we introduce an iterative procedure which extends the previous method and gives good estimates under such rapid variations. In the iterative calibrated skywis plot we approximate the effective population size by a piecewise constant function, whose values are re-estimated at each step. These piecewise constant functions are used to generate the waiting times of non homogeneous Poisson processes related to a coalescent process with mutation under a variable population size model. Moreover, the present IS procedure is based on a modified version of the Stephens and Donnelly (2000) proposal distribution. Finally, we apply the iterative calibrated skywis plot method to a simulated data set from a rapidly expanding exponential model, and we show that the method based on this new IS strategy correctly reconstructs the demographic history. Copyright © 2016. Published by Elsevier Inc.

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

PubMed Central

Nowicka, Malgorzata; Krieg, Carsten; Weber, Lukas M.; Hartmann, Felix J.; Guglietta, Silvia; Becher, Burkhard; Levesque, Mitchell P.; Robinson, Mark D.

2017-01-01

High dimensional mass and flow cytometry (HDCyto) experiments have become a method of choice for high throughput interrogation and characterization of cell populations.Here, we present an R-based pipeline for differential analyses of HDCyto data, largely based on Bioconductor packages. We computationally define cell populations using FlowSOM clustering, and facilitate an optional but reproducible strategy for manual merging of algorithm-generated clusters. Our workflow offers different analysis paths, including association of cell type abundance with a phenotype or changes in signaling markers within specific subpopulations, or differential analyses of aggregated signals. Importantly, the differential analyses we show are based on regression frameworks where the HDCyto data is the response; thus, we are able to model arbitrary experimental designs, such as those with batch effects, paired designs and so on. In particular, we apply generalized linear mixed models to analyses of cell population abundance or cell-population-specific analyses of signaling markers, allowing overdispersion in cell count or aggregated signals across samples to be appropriately modeled. To support the formal statistical analyses, we encourage exploratory data analysis at every step, including quality control (e.g. multi-dimensional scaling plots), reporting of clustering results (dimensionality reduction, heatmaps with dendrograms) and differential analyses (e.g. plots of aggregated signals). PMID:28663787

Developing a systems-based framework of the factors influencing dietary and physical activity behaviours in ethnic minority populations living in Europe - a DEDIPAC study.

PubMed

Holdsworth, Michelle; Nicolaou, Mary; Langøien, Lars Jørun; Osei-Kwasi, Hibbah Araba; Chastin, Sebastien F M; Stok, F Marijn; Capranica, Laura; Lien, Nanna; Terragni, Laura; Monsivais, Pablo; Mazzocchi, Mario; Maes, Lea; Roos, Gun; Mejean, Caroline; Powell, Katie; Stronks, Karien

2017-11-07

Some ethnic minority populations have a higher risk of non-communicable diseases than the majority European population. Diet and physical activity behaviours contribute to this risk, shaped by a system of inter-related factors. This study mapped a systems-based framework of the factors influencing dietary and physical activity behaviours in ethnic minority populations living in Europe, to inform research prioritisation and intervention development. A concept mapping approach guided by systems thinking was used: i. Preparation (protocol and terminology); ii. Generating a list of factors influencing dietary and physical activity behaviours in ethnic minority populations living in Europe from evidence (systematic mapping reviews) and 'eminence' (89 participants from 24 academic disciplines via brainstorming, an international symposium and expert review) and; iii. Seeking consensus on structuring, rating and clustering factors, based on how they relate to each other; and iv. Interpreting/utilising the framework for research and interventions. Similar steps were undertaken for frameworks developed for the majority European population. Seven distinct clusters emerged for dietary behaviour (containing 85 factors) and 8 for physical activity behaviours (containing 183 factors). Four clusters were similar across behaviours: Social and cultural environment; Social and material resources; Psychosocial; and Migration context. Similar clusters of factors emerged in the frameworks for diet and physical activity behaviours of the majority European population, except for 'migration context'. The importance of factors across all clusters was acknowledged, but their relative importance differed for ethnic minority populations compared with the majority population. This systems-based framework integrates evidence from both expert opinion and published literature, to map the factors influencing dietary and physical activity behaviours in ethnic minority groups. Our findings illustrate that innovative research and complex interventions need to be developed that are sensitive to the needs of ethnic minority populations. A systems approach that encompasses the complexity of the inter-related factors that drive behaviours may inform a more holistic public health paradigm to more effectively reach ethnic minorities living in Europe, as well as the majority host population.

Bio optofluidics cell sorter: cell-BOCS concept and applications

NASA Astrophysics Data System (ADS)

Roth, Tue; Glückstad, Jesper

2012-03-01

The cell-BOCS is a novel microfluidics based cell-sorting instrument utilizing next generation optical trapping technology developed at the Technical University of Denmark. It is targeted emerging bio-medical research and diagnostics markets where it for certain applications offers a number of advantages over conventional fluorescence activated cell-sorting (FACSTM) technology. Advantages include gentle handling of cells, sterile sorting, easy operation, small footprint and lower cost allowing out-of-core-facility use. Application examples are found within sorting of fragile transfected cells, high value samples and primary cell lines, where traditional FACS technology has limited application due to it's droplet-based approach to cell-sorting. In the diagnostics field, in particular applying the cell-BOCS for isolating pure populations of circulating tumor cells is an area that has generated a lot of interest.

Innovative paths for providing green energy for sustainable global economic growth

NASA Astrophysics Data System (ADS)

Singh, Rajendra; Alapatt, G. F.

2012-10-01

According to United Nation, world population may reach 10.1 billion by the year 2100. The fossil fuel based global economy is not sustainable. For sustainable global green energy scenario we must consider free fuel based energy conversion, environmental concerns and conservation of water. Photovoltaics (PV) offers a unique opportunity to solve the 21st century's electricity generation because solar energy is essentially unlimited and PV systems provide electricity without any undesirable impact on the environment. Innovative paths for green energy conversion and storage are proposed in areas of R and D, manufacturing and system integration, energy policy and financing. With existing silicon PV system manufacturing, the implementation of new innovative energy policies and new innovative business model can provide immediately large capacity of electricity generation to developed, emerging and underdeveloped economies.

Evaluating mortality rates with a novel integrated framework for nonmonogamous species.

PubMed

Tenan, Simone; Iemma, Aaron; Bragalanti, Natalia; Pedrini, Paolo; De Barba, Marta; Randi, Ettore; Groff, Claudio; Genovart, Meritxell

2016-12-01

The conservation of wildlife requires management based on quantitative evidence, and especially for large carnivores, unraveling cause-specific mortalities and understanding their impact on population dynamics is crucial. Acquiring this knowledge is challenging because it is difficult to obtain robust long-term data sets on endangered populations and, usually, data are collected through diverse sampling strategies. Integrated population models (IPMs) offer a way to integrate data generated through different processes. However, IPMs are female-based models that cannot account for mate availability, and this feature limits their applicability to monogamous species only. We extended classical IPMs to a two-sex framework that allows investigation of population dynamics and quantification of cause-specific mortality rates in nonmonogamous species. We illustrated our approach by simultaneously modeling different types of data from a reintroduced, unhunted brown bear (Ursus arctos) population living in an area with a dense human population. In a population mainly driven by adult survival, we estimated that on average 11% of cubs and 61% of adults died from human-related causes. Although the population is currently not at risk, adult survival and thus population dynamics are driven by anthropogenic mortality. Given the recent increase of human-bear conflicts in the area, removal of individuals for management purposes and through poaching may increase, reversing the positive population growth rate. Our approach can be generalized to other species affected by cause-specific mortality and will be useful to inform conservation decisions for other nonmonogamous species, such as most large carnivores, for which data are scarce and diverse and thus data integration is highly desirable. © 2016 Society for Conservation Biology.

Estimating a Preference-Based Index from the Clinical Outcomes in Routine Evaluation–Outcome Measure (CORE-OM)

PubMed Central

Brazier, John E.; Rowen, Donna; Barkham, Michael

2013-01-01

Background. The Clinical Outcomes in Routine Evaluation–Outcome Measure (CORE-OM) is used to evaluate the effectiveness of psychological therapies in people with common mental disorders. The objective of this study was to estimate a preference-based index for this population using CORE-6D, a health state classification system derived from the CORE-OM consisting of a 5-item emotional component and a physical item, and to demonstrate a novel method for generating states that are not orthogonal. Methods. Rasch analysis was used to identify 11 emotional health states from CORE-6D that were frequently observed in the study population and are, thus, plausible (in contrast, conventional statistical design might generate implausible states). Combined with the 3 response levels of the physical item of CORE-6D, they generate 33 plausible health states, 18 of which were selected for valuation. A valuation survey of 220 members of the public in South Yorkshire, United Kingdom, was undertaken using the time tradeoff (TTO) method. Regression analysis was subsequently used to predict values for all possible states described by CORE-6D. Results. A number of multivariate regression models were built to predict values for the 33 health states of CORE-6D, using the Rasch logit value of the emotional state and the response level of the physical item as independent variables. A cubic model with high predictive value (adjusted R2 = 0.990) was selected to predict TTO values for all 729 CORE-6D health states. Conclusion. The CORE-6D preference-based index will enable the assessment of cost-effectiveness of interventions for people with common mental disorders using existing and prospective CORE-OM data sets. The new method for generating states may be useful for other instruments with highly correlated dimensions. PMID:23178639

Fitness effects of a selfish gene (the Mus t complex) are revealed in an ecological context.

PubMed

Carroll, Lara S; Meagher, Shawn; Morrison, Linda; Penn, Dustin J; Potts, Wayne K

2004-06-01

In wild house mice, genes linked to the t transmission distortion complex cause meiotic drive by sabotaging wild-type gametes. The t complex is consequently inherited at frequencies higher than 90%. Yet, for unclear reasons, in wild mouse populations this selfish DNA is found at frequencies much lower than expected. Here, we examine selection on the t complex in 10 seminatural populations of wild mice based on data from 234 founders and nearly 2000 progeny. Eight of the 10 populations decreased in t frequency over one generation, and the overall frequency of t haplotypes across all 10 populations was 48.5% below expectations based on transmission distortion and 34.3% below Mendelian (or Hardy-Weinberg) expectations. Behavioral and reproductive data were collected for 10 months for each population, and microsatellite genotyping was performed on seven of the populations to determine parentage. These combined data show t-associated fitness declines in both males and females. This is the first study to show evidence for a reduction in the ability of +/t males to maintain territories. Because females tend to mate with dominant males, impairment of territorial success can explain much of the selection against t observed in our populations. In nature, selection against heterozygote carriers of the t complex helps solve the puzzlingly low t frequencies found in wild populations. This ecological approach for determining fitness consequences of genetic variants has broad application for the discovery of gene function in general.

Earth's Most Powerful Natural Particle Accelerator

NASA Technical Reports Server (NTRS)

Rowland, Doug

2012-01-01

Thunderstorms launch antimatter, gamma rays, and highly energetic electrons and neutrons to the edge of space. This witches' brew of radiation is generated at the edge of the stratopause, by the strong electric fields associated with lightning discharges. In less than a quarter millisecond, an explosive feedback process takes an initial seed population of electrons, perhaps produced by cosmic rays from dying stars, and amplifies them a billion billion-fold in the rarefied air over high altitude thunderheads. The electrons generate gamma radiation as they travel through the stratosphere and lower mesosphere, momentarily brighter and of harder spectrum than cosmic gamma ray bursts. These electrons ultimately are absorbed by the atmosphere, but the gamma rays continue on, into the upper reaches of the atmosphere, where they in turn generate a new population of electrons, positrons, and energetic neutrons. These secondary electrons and positrons move along the magnetic field, and can reach near-earth space, streaming through the inner radiation belts, and possibly contributing to the trapped populations there. First postulated by Wilson in 1925, and serendipitously discovered by the Compton Gamma Ray Observatory in 1994 [Fishman et al.], these events, known as "Terrestrial Gamma ray Flashes" (TGFs), represent the most intense episodes of particle acceleration on or near the Earth, resulting in electrons with energies up to 100 MeV. Recent observations by the RHESSI [Smith et al., 2004], Fermi [Briggs et al., 2010], and AGILE [Tavani et al., 2011] satellites, and theoretical and computational modeling, have suggested that the relativistic runaway electron avalanche (RREA) mechanism [Gurevich, 1992], and important modifications, such as the relativistic feedback discharge (RFD) model [Dwyer 2012] can best explain the observations at present. In these models, strong thunderstorm electric fields drive seed electrons, generated from cosmic ray interactions, into a runaway discharge, in which the seed electrons continually gain energy from the electric field, creating a host of secondaries as they interact with the background atmospheric gas. The feedback mechanisms include backwards-propagating positrons and gamma rays, which then can generate new "seed" electrons at the base of the acceleration region, and themselves generate further avalanche chain reactions, greatly amplifying the initial seed population. All these processes happen in the stratosphere, in the altitude range near 15-20 km, where the electric fields and mean free paths are appropriate to allow the discharge to develop.

On the Observability of Individual Population III Stars and Their Stellar-mass Black Hole Accretion Disks through Cluster Caustic Transits

NASA Astrophysics Data System (ADS)

Windhorst, Rogier A.; Timmes, F. X.; Wyithe, J. Stuart B.; Alpaslan, Mehmet; Andrews, Stephen K.; Coe, Daniel; Diego, Jose M.; Dijkstra, Mark; Driver, Simon P.; Kelly, Patrick L.; Kim, Duho

2018-02-01

We summarize panchromatic Extragalactic Background Light data to place upper limits on the integrated near-infrared surface brightness (SB) that may come from Population III stars and possible accretion disks around their stellar-mass black holes (BHs) in the epoch of First Light, broadly taken from z ≃ 7–17. Theoretical predictions and recent near-infrared power spectra provide tighter constraints on their sky signal. We outline the physical properties of zero-metallicity Population III stars from MESA stellar evolution models through helium depletion and of BH accretion disks at z≳ 7. We assume that second-generation non-zero-metallicity stars can form at higher multiplicity, so that BH accretion disks may be fed by Roche-lobe overflow from lower-mass companions. We use these near-infrared SB constraints to calculate the number of caustic transits behind lensing clusters that the James Webb Space Telescope and the next-generation ground-based telescopes may observe for both Population III stars and their BH accretion disks. Typical caustic magnifications can be μ ≃ {10}4{--}{10}5, with rise times of hours and decline times of ≲ 1 year for cluster transverse velocities of {v}T≲ 1000 km s‑1. Microlensing by intracluster-medium objects can modify transit magnifications but lengthen visibility times. Depending on BH masses, accretion-disk radii, and feeding efficiencies, stellar-mass BH accretion-disk caustic transits could outnumber those from Population III stars. To observe Population III caustic transits directly may require monitoring 3–30 lensing clusters to {AB}≲ 29 mag over a decade.

New insights into the correlation structure of DSM-IV depression symptoms in the general population v. subsamples of depressed individuals.

PubMed

Foster, S; Mohler-Kuo, M

2018-06-01

Previous research failed to uncover a replicable dimensional structure underlying the symptoms of depression. We aimed to examine two neglected methodological issues in this research: (a) adjusting symptom correlations for overall depression severity; and (b) analysing general population samples v. subsamples of currently depressed individuals. Using population-based cross-sectional and longitudinal data from two nations (Switzerland, 5883 young men; USA, 2174 young men and 2244 young women) we assessed the dimensions of the nine DSM-IV depression symptoms in young adults. In each general-population sample and each subsample of currently depressed participants, we conducted a standardised process of three analytical steps, based on exploratory and confirmatory factor and bifactor analysis, to reveal any replicable dimensional structure underlying symptom correlations while controlling for overall depression severity. We found no evidence of a replicable dimensional structure across samples when adjusting symptom correlations for overall depression severity. In the general-population samples, symptoms correlated strongly and a single dimension of depression severity was revealed. Among depressed participants, symptom correlations were surprisingly weak and no replicable dimensions were identified, regardless of severity-adjustment. First, caution is warranted when considering studies assessing dimensions of depression because general population-based studies and studies of depressed individuals generate different data that can lead to different conclusions. This problem likely generalises to other models based on the symptoms' inter-relationships such as network models. Second, whereas the overall severity aligns individuals on a continuum of disorder intensity that allows non-affected individuals to be distinguished from affected individuals, the clinical evaluation and treatment of depressed individuals should focus directly on each individual's symptom profile.

Population-based prevention of eating disorders: an application of the Rose prevention model.

PubMed

Austin, S B

2001-03-01

Several decades of concerted research on eating disorders have generated a broad range of proposed causal influences, but much of this etiologic research does not elucidate practical avenues for preventive interventions. Translating etiologic theory into community health interventions depends on the identification of key leverage points, factors that are amenable to public health intervention and provide an opportunity to maximize impact on the outcome of interest. Population-based preventive strategies, elaborated by epidemiologist Geoffrey Rose, can maximize the impact of public health interventions. In the case of eating disorders, Rose's model is instructive: Dieting stands out as risk behavior that may both fit Rose's model well and be a key leverage point for preventive intervention. Grounded in Rose's work, this article lodges a theoretical argument for the population-based prevention of eating disorders. In the introductory section, existing research on the epidemiology of dieting is reviewed, showing that it is extremely common among adolescent girls and women and that the behavior has been implicated as a causal factor for disordered eating. Next, new evidence is offered to build a case for how a population-wide reduction in dieting may be an effective strategy for prevention of eating pathology. Finally Rose's prevention framework is used to introduce a unique and provocative perspective on the prevention of eating disorders. Dieting is a normative behavior in our culture with psychological and physiological effects in the causal chain leading to eating pathology. This behavior may represent an ideal target for population-based prevention. Theoretical and empirical evidence suggests that a population-wide reduction in dieting may be a justifiable and effective strategy for prevention of eating pathology. Copyright 2001 American Health Foundation and Academic Press.

Inequalities in neighbourhood socioeconomic characteristics: potential evidence-base for neighbourhood health planning

PubMed Central

Odoi, Agricola; Wray, Ron; Emo, Marion; Birch, Stephen; Hutchison, Brian; Eyles, John; Abernathy, Tom

2005-01-01

Background Population health planning aims to improve the health of the entire population and to reduce health inequities among population groups. Socioeconomic factors are increasingly being recognized as major determinants of many aspects of health and causes of health inequities. Knowledge of socioeconomic characteristics of neighbourhoods is necessary to identify their unique health needs and enhance identification of socioeconomically disadvantaged populations. Careful integration of this knowledge into health planning activities is necessary to ensure that health planning and service provision are tailored to unique neighbourhood population health needs. In this study, we identify unique neighbourhood socioeconomic characteristics and classify the neighbourhoods based on these characteristics. Principal components analysis (PCA) of 18 socioeconomic variables was used to identify the principal components explaining most of the variation in socioeconomic characteristics across the neighbourhoods. Cluster analysis was used to classify neighbourhoods based on their socioeconomic characteristics. Results Results of the PCA and cluster analysis were similar but the latter were more objective and easier to interpret. Five neighbourhood types with distinguishing socioeconomic and demographic characteristics were identified. The methodology provides a more complete picture of the neighbourhood socioeconomic characteristics than when a single variable (e.g. income) is used to classify neighbourhoods. Conclusion Cluster analysis is useful for generating neighbourhood population socioeconomic and demographic characteristics that can be useful in guiding neighbourhood health planning and service provision. This study is the first of a series of studies designed to investigate health inequalities at the neighbourhood level with a view to providing evidence-base for health planners, service providers and policy makers to help address health inequity issues at the neighbourhood level. Subsequent studies will investigate inequalities in health outcomes both within and across the neighbourhood types identified in the current study. PMID:16092969

Transgenerational effects and recovery of microplastics exposure in model populations of the freshwater cladoceran Daphnia magna Straus.

PubMed

Martins, Alexandra; Guilhermino, Lúcia

2018-08-01

The environmental contamination by microplastics is a global challenge to ecosystem and human health, and the knowledge on the long-term effects of such particles is limited. Thus, the effects of microplastics and post-exposure recovery were investigated over 4 generations (F 0 , F 1 , F 2 , F 3 ) using Daphnia magna as model. Effect criteria were parental mortality, growth, several reproductive parameters, and population growth rate. Microplastics exposure (0.1mg/l of pristine polymer microspheres 1-5μm diameter) caused parental mortality (10-100%), and significantly (p≤0.05) decreased growth, reproduction, and population growth rate leading to the extinction of the microplastics-exposed model population in the F 1 generation. Females descending from those exposed to microplastics in F 0 and exposed to clean medium presented some recovery but up to the F 3 generation they still had significantly (p≤0.05) reduced growth, reproduction, and population growth rate. Overall, these results indicate that D. magna recovery from chronic exposure to microplastics may take several generations, and that the continuous exposure over generations to microplastics may cause population extinction. These findings have implications to aquatic ecosystem functioning and services, and raise concern on the long-term animal and human exposure to microplastics through diverse routes. Copyright © 2018. Published by Elsevier B.V.

Climate change, renewable energy and population impact on future energy demand for Burkina Faso build environment

NASA Astrophysics Data System (ADS)

Ouedraogo, B. I.

This research addresses the dual challenge faced by Burkina Faso engineers to design sustainable low-energy cost public buildings and domestic dwellings while still providing the required thermal comfort under warmer temperature conditions caused by climate change. It was found base don climate change SRES scenario A2 that predicted mean temperature in Burkina Faso will increase by 2oC between 2010 and 2050. Therefore, in order to maintain a thermally comfortable 25oC inside public buildings, the projected annual energy consumption for cooling load will increase by 15%, 36% and 100% respectively for the period between 2020 to 2039, 2040 to 2059 and 2070 to 2089 when compared to the control case. It has also been found that a 1% increase in population growth will result in a 1.38% and 2.03% increase in carbon emission from primary energy consumption and future electricity consumption respectively. Furthermore, this research has investigated possible solutions for adaptation to the severe climate change and population growth impact on energy demand in Burkina Faso. Shading devices could potentially reduce the cooling load by up to 40%. Computer simulation programming of building energy consumption and a field study has shown that adobe houses have the potential of significantly reducing energy demand for cooling and offer a formidable method for climate change adaptation. Based on the Net Present Cost, hybrid photovoltaic (PV) and Diesel generator energy production configuration is the most cost effective local electricity supply system, for areas without electricity at present, with a payback time of 8 years when compared to diesel generator stand-alone configuration. It is therefore a viable solution to increase electricity access to the majority of the population.

Efficacy of insecticide residues on adult Halyomorpha halys (Stål) (Hemiptera: Pentatomidae) mortality and injury in apple and peach orchards.

PubMed

Leskey, Tracy C; Short, Brent D; Lee, Doo-Hyung

2014-07-01

The primary threat from Halyomorpha halys (Stål) (Hemiptera: Pentatomidae) originates from populations continuously dispersing from and among wild and cultivated hosts, so many individuals may not be directly sprayed with insecticides. Limited information exists regarding field-based residual activity of insecticides for management of H. halys in tree fruit. Thus, we conducted field-based bioassays in apple and peach orchards to evaluate residual activity of insecticides commonly applied against H. halys. Adults used in these trials were collected from wild and cultivated hosts less than one week prior to testing to more accurately reflect the susceptibility of wild H. halys populations in the field throughout the season. Significantly higher mortality rates of Halyomorpha halys were observed early in the growing season, when overwintered adults were prevalent, compared with populations present later in the growing season that included new generation adults. Significantly higher mortality was recorded for adults exposed to fresh insecticide applications compared with three- and seven-day old residues. Typically, the addition of an adjuvant did not enhance efficacy or residual activity of insecticides. Significantly fewer injury sites were recorded on apples treated with dinotefuran and fenpropathrin compared with the untreated apples for all residue ages. Overwintered Halyomorpha halys populations are easier to kill with insecticide applications than the first and second generation which are present in the field during the mid- to late-season. Residual activity of nearly all insecticides decreased significantly three days after application and adjuvants generally did not increase residual activity. These factors should be considered in developing season-long programs for management of this invasive species in tree fruit. © 2013 Society of Chemical Industry.

HIV, HCV, HBV, and syphilis among transgender women from Brazil: Assessing different methods to adjust infection rates of a hard-to-reach, sparse population.

PubMed

Bastos, Francisco I; Bastos, Leonardo Soares; Coutinho, Carolina; Toledo, Lidiane; Mota, Jurema Corrêa; Velasco-de-Castro, Carlos Augusto; Sperandei, Sandro; Brignol, Sandra; Travassos, Tamiris Severino; Dos Santos, Camila Mattos; Malta, Monica Siqueira

2018-05-01

Different sampling strategies, analytic alternatives, and estimators have been proposed to better assess the characteristics of different hard-to-reach populations and their respective infection rates (as well as their sociodemographic characteristics, associated harms, and needs) in the context of studies based on respondent-driven sampling (RDS). Despite several methodological advances and hundreds of empirical studies implemented worldwide, some inchoate findings and methodological challenges remain. The in-depth assessment of the local structure of networks and the performance of the available estimators are particularly relevant when the target populations are sparse and highly stigmatized. In such populations, bottlenecks as well as other sources of biases (for instance, due to homophily and/or too sparse or fragmented groups of individuals) may be frequent, affecting the estimates.In the present study, data were derived from a cross-sectional, multicity RDS study, carried out in 12 Brazilian cities with transgender women (TGW). Overall, infection rates for HIV and syphilis were very high, with some variation between different cities. Notwithstanding, findings are of great concern, considering the fact that female TGW are not only very hard-to-reach but also face deeply-entrenched prejudice and have been out of the reach of most therapeutic and preventive programs and projects.We cross-compared findings adjusted using 2 estimators (the classic estimator usually known as estimator II, originally proposed by Volz and Heckathorn) and a brand new strategy to adjust data generated by RDS, partially based on Bayesian statistics, called for the sake of this paper, the RDS-B estimator. Adjusted prevalence was cross-compared with estimates generated by non-weighted analyses, using what has been called by us a naïve estimator or rough estimates.

The Luminosity Function of Star Clusters in 20 Star-Forming Galaxies Based on Hubble Legacy Archive Photometry

NASA Astrophysics Data System (ADS)

Bowers, Ariel; Whitmore, B. C.; Chandar, R.; Larsen, S. S.

2014-01-01

Luminosity functions have been determined for star cluster populations in 20 nearby (4 - 30 Mpc), star-forming galaxies based on ACS source lists generated by the Hubble Legacy Archive (http://hla.stsci.edu). These cluster catalogs provide one of the largest sets of uniform, automatically-generated cluster candidates available in the literature at present. Comparisons are made with other recently generated cluster catalogs demonstrating that the HLA-generated catalogs are of similar quality, but in general do not go as deep. A typical cluster luminosity function can be approximated by a power-law, dN/dL ∝ Lα, with an average value for α of -2.37 and rms scatter = 0.18. A comparison of fitting results based on methods which use binned and unbinned data shows good agreement, although there may be a systematic tendency for the unbinned (maximum-likelihood) method to give slightly more negative values of α for galaxies with steper luminosity functions. Our uniform database results in a small scatter (0.5 magnitude) in the correlation between the magnitude of the brightest cluster (Mbrightest) and Log of the number of clusters brighter than MI = -9 (Log N). We also examine the magnitude of the brightest cluster vs. Log SFR for a sample including LIRGS and ULIRGS.

Rewriting the narrative of the epidemiology of HIV in sub-Saharan Africa.

PubMed

Baral, Stefan; Phaswana-Mafuya, Nancy

2012-01-01

The fight against HIV remains complicated with contracting donor resources and high burden of HIV among reproductive age adults still often limiting independent economic development. In the widespread HIV epidemics of sub-Saharan Africa (SSA), it is proposed that key populations with specific HIV acquisition and transmission risk factors, such as men who have sex with men (MSM), female sex workers (FSW), and people who use drugs (PUD), are less relevant because HIV transmission is sustained in the general population with average HIV acquisition and transmission risks. However, the understanding that key populations are less relevant in the epidemics of Africa is based on the surveillance system from which these populations are mostly excluded. Outside of SSA, the epidemics of HIV are generally concentrated in the same populations that are excluded from the primary HIV surveillance systems in SSA. The manuscripts included in this special issue present convincing data that FSW, MSM, and PUD carry disproportionate burdens of HIV wherever studied in SSA, are underrepresented in HIV programs and research, and require specific HIV prevention services. These manuscripts collectively suggest that the only effective path forward is one that transcends denial and stigma and focuses on systematically collecting data on all populations at risk for HIV. In addition, there is a need to move to a third generation of HIV surveillance as the current one inadvertently devalues HIV surveillance among key populations in the context of widespread HIV epidemics. Overall, the data reviewed here demonstrate that the dynamics of HIV in Africa are complex and achieving an AIDS-free generation necessitates acceptance of that complexity in all HIV surveillance, research, and prevention, treatment, and care programs.

Does Population Density and Neighborhood Deprivation Predict Schizophrenia? A Nationwide Swedish Family-Based Study of 2.4 Million Individuals

PubMed Central

Sariaslan, Amir; Larsson, Henrik; D’Onofrio, Brian; Långström, Niklas; Fazel, Seena; Lichtenstein, Paul

2015-01-01

People living in densely populated and socially disorganized areas have higher rates of psychiatric morbidity, but the potential causal status of such factors is uncertain. We used nationwide Swedish longitudinal registry data to identify all children born 1967–1989 (n = 2361585), including separate datasets for all cousins (n = 1715059) and siblings (n = 1667894). The nature of the associations between population density and neighborhood deprivation and individual risk for a schizophrenia diagnosis was investigated while adjusting for unobserved familial risk factors (through cousin and sibling comparisons) and then compared with similar associations for depression. We generated familial pedigree structures using the Multi-Generation Registry and identified study participants with schizophrenia and depression using the National Patient Registry. Fixed-effects logistic regression models were used to study within-family estimates. Population density, measured as ln(population size/km2), at age 15 predicted subsequent schizophrenia in the population (OR = 1.10; 95% CI: 1.09; 1.11). Unobserved familial risk factors shared by cousins within extended families attenuated the association (1.06; 1.03; 1.10), and the link disappeared entirely within nuclear families (1.02; 0.97; 1.08). Similar results were found for neighborhood deprivation as predictor and for depression as outcome. Sensitivity tests demonstrated that timing and accumulation effects of the exposures (mean scores across birth, ages 1–5, 6–10, and 11–15 years) did not alter the findings. Excess risks of psychiatric morbidity, particularly schizophrenia, in densely populated and socioeconomically deprived Swedish neighborhoods appear, therefore, to result primarily from unobserved familial selection factors. Previous studies may have overemphasized the etiological importance of these environmental factors. PMID:25053652

Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure

PubMed Central

Basu, Analabha; Sarkar-Roy, Neeta; Majumder, Partha P.

2016-01-01

India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform. PMID:26811443

A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds.

PubMed

Manunza, Arianna; Noce, Antonia; Serradilla, Juan Manuel; Goyache, Félix; Martínez, Amparo; Capote, Juan; Delgado, Juan Vicente; Jordana, Jordi; Muñoz, Eva; Molina, Antonio; Landi, Vincenzo; Pons, Agueda; Balteanu, Valentin; Traoré, Amadou; Vidilla, Montse; Sánchez-Rodríguez, Manuel; Sànchez, Armand; Cardoso, Tainã Figueiredo; Amills, Marcel

2016-07-25

The main goal of the current work was to infer the demographic history of seven Spanish goat breeds (Malagueña, Murciano-Granadina, Florida, Palmera, Mallorquina, Bermeya and Blanca de Rasquera) based on genome-wide diversity data generated with the Illumina Goat SNP50 BeadChip (population size, N = 176). Five additional populations from Europe (Saanen and Carpathian) and Africa (Tunisian, Djallonké and Sahel) were also included in this analysis (N = 80) for comparative purposes. Our results show that the genetic background of Spanish goats traces back mainly to European breeds although signs of North African admixture were detected in two Andalusian breeds (Malagueña and Murciano-Granadina). In general, observed and expected heterozygosities were quite similar across the seven Spanish goat breeds under analysis irrespective of their population size and conservation status. For the Mallorquina and Blanca de Rasquera breeds, which have suffered strong population declines during the past decades, we observed increased frequencies of large-sized (ROH), a finding that is consistent with recent inbreeding. In contrast, a substantial part of the genome of the Palmera goat breed comprised short ROH, which suggests a strong and ancient founder effect. Admixture with African goats, genetic drift and inbreeding have had different effects across the seven Spanish goat breeds analysed in the current work. This has generated distinct patterns of genome-wide diversity that provide new clues about the demographic history of these populations.

A Scalable System for Production of Functional Pancreatic Progenitors from Human Embryonic Stem Cells

PubMed Central

Schulz, Thomas C.; Young, Holly Y.; Agulnick, Alan D.; Babin, M. Josephine; Baetge, Emmanuel E.; Bang, Anne G.; Bhoumik, Anindita; Cepa, Igor; Cesario, Rosemary M.; Haakmeester, Carl; Kadoya, Kuniko; Kelly, Jonathan R.; Kerr, Justin; Martinson, Laura A.; McLean, Amanda B.; Moorman, Mark A.; Payne, Janice K.; Richardson, Mike; Ross, Kelly G.; Sherrer, Eric S.; Song, Xuehong; Wilson, Alistair Z.; Brandon, Eugene P.; Green, Chad E.; Kroon, Evert J.; Kelly, Olivia G.; D’Amour, Kevin A.; Robins, Allan J.

2012-01-01

Development of a human embryonic stem cell (hESC)-based therapy for type 1 diabetes will require the translation of proof-of-principle concepts into a scalable, controlled, and regulated cell manufacturing process. We have previously demonstrated that hESC can be directed to differentiate into pancreatic progenitors that mature into functional glucose-responsive, insulin-secreting cells in vivo. In this study we describe hESC expansion and banking methods and a suspension-based differentiation system, which together underpin an integrated scalable manufacturing process for producing pancreatic progenitors. This system has been optimized for the CyT49 cell line. Accordingly, qualified large-scale single-cell master and working cGMP cell banks of CyT49 have been generated to provide a virtually unlimited starting resource for manufacturing. Upon thaw from these banks, we expanded CyT49 for two weeks in an adherent culture format that achieves 50–100 fold expansion per week. Undifferentiated CyT49 were then aggregated into clusters in dynamic rotational suspension culture, followed by differentiation en masse for two weeks with a four-stage protocol. Numerous scaled differentiation runs generated reproducible and defined population compositions highly enriched for pancreatic cell lineages, as shown by examining mRNA expression at each stage of differentiation and flow cytometry of the final population. Islet-like tissue containing glucose-responsive, insulin-secreting cells was generated upon implantation into mice. By four- to five-months post-engraftment, mature neo-pancreatic tissue was sufficient to protect against streptozotocin (STZ)-induced hyperglycemia. In summary, we have developed a tractable manufacturing process for the generation of functional pancreatic progenitors from hESC on a scale amenable to clinical entry. PMID:22623968

Simulated Models Suggest That Price per Calorie Is the Dominant Price Metric That Low-Income Individuals Use for Food Decision Making123

PubMed Central

2016-01-01

Background: The price of food has long been considered one of the major factors that affects food choices. However, the price metric (e.g., the price of food per calorie or the price of food per gram) that individuals predominantly use when making food choices is unclear. Understanding which price metric is used is especially important for studying individuals with severe budget constraints because food price then becomes even more important in food choice. Objective: We assessed which price metric is used by low-income individuals in deciding what to eat. Methods: With the use of data from NHANES and the USDA Food and Nutrient Database for Dietary Studies, we created an agent-based model that simulated an environment representing the US population, wherein individuals were modeled as agents with a specific weight, age, and income. In our model, agents made dietary food choices while meeting their budget limits with the use of 1 of 3 different metrics for decision making: energy cost (price per calorie), unit price (price per gram), and serving price (price per serving). The food consumption patterns generated by our model were compared to 3 independent data sets. Results: The food choice behaviors observed in 2 of the data sets were found to be closest to the simulated dietary patterns generated by the price per calorie metric. The behaviors observed in the third data set were equidistant from the patterns generated by price per calorie and price per serving metrics, whereas results generated by the price per gram metric were further away. Conclusions: Our simulations suggest that dietary food choice based on price per calorie best matches actual consumption patterns and may therefore be the most salient price metric for low-income populations. PMID:27655757

Simulated Models Suggest That Price per Calorie Is the Dominant Price Metric That Low-Income Individuals Use for Food Decision Making.

PubMed

Beheshti, Rahmatollah; Igusa, Takeru; Jones-Smith, Jessica

2016-11-01

The price of food has long been considered one of the major factors that affects food choices. However, the price metric (e.g., the price of food per calorie or the price of food per gram) that individuals predominantly use when making food choices is unclear. Understanding which price metric is used is especially important for studying individuals with severe budget constraints because food price then becomes even more important in food choice. We assessed which price metric is used by low-income individuals in deciding what to eat. With the use of data from NHANES and the USDA Food and Nutrient Database for Dietary Studies, we created an agent-based model that simulated an environment representing the US population, wherein individuals were modeled as agents with a specific weight, age, and income. In our model, agents made dietary food choices while meeting their budget limits with the use of 1 of 3 different metrics for decision making: energy cost (price per calorie), unit price (price per gram), and serving price (price per serving). The food consumption patterns generated by our model were compared to 3 independent data sets. The food choice behaviors observed in 2 of the data sets were found to be closest to the simulated dietary patterns generated by the price per calorie metric. The behaviors observed in the third data set were equidistant from the patterns generated by price per calorie and price per serving metrics, whereas results generated by the price per gram metric were further away. Our simulations suggest that dietary food choice based on price per calorie best matches actual consumption patterns and may therefore be the most salient price metric for low-income populations. © 2016 American Society for Nutrition.

Science as a Classed and Gendered Endeavor: Persistence of Two White Female First-Generation College Students within an Undergraduate Science Context

ERIC Educational Resources Information Center

Wilson, Rachel E.; Kittleson, Julie

2013-01-01

As colleges and universities aim for greater diversity in their undergraduate populations, one population researchers consider is first-generation students, or students whose parents do not have a college education. The research reported here addresses first-generation college students' discipline of study (e.g., biology) and its impact on…

A calibration protocol for population-specific accelerometer cut-points in children.

PubMed

Mackintosh, Kelly A; Fairclough, Stuart J; Stratton, Gareth; Ridgers, Nicola D

2012-01-01

To test a field-based protocol using intermittent activities representative of children's physical activity behaviours, to generate behaviourally valid, population-specific accelerometer cut-points for sedentary behaviour, moderate, and vigorous physical activity. Twenty-eight children (46% boys) aged 10-11 years wore a hip-mounted uniaxial GT1M ActiGraph and engaged in 6 activities representative of children's play. A validated direct observation protocol was used as the criterion measure of physical activity. Receiver Operating Characteristics (ROC) curve analyses were conducted with four semi-structured activities to determine the accelerometer cut-points. To examine classification differences, cut-points were cross-validated with free-play and DVD viewing activities. Cut-points of ≤ 372, >2160 and >4806 counts • min(-1) representing sedentary, moderate and vigorous intensity thresholds, respectively, provided the optimal balance between the related needs for sensitivity (accurately detecting activity) and specificity (limiting misclassification of the activity). Cross-validation data demonstrated that these values yielded the best overall kappa scores (0.97; 0.71; 0.62), and a high classification agreement (98.6%; 89.0%; 87.2%), respectively. Specificity values of 96-97% showed that the developed cut-points accurately detected physical activity, and sensitivity values (89-99%) indicated that minutes of activity were seldom incorrectly classified as inactivity. The development of an inexpensive and replicable field-based protocol to generate behaviourally valid and population-specific accelerometer cut-points may improve the classification of physical activity levels in children, which could enhance subsequent intervention and observational studies.

Quantifying aggregated uncertainty in Plasmodium falciparum malaria prevalence and populations at risk via efficient space-time geostatistical joint simulation.

PubMed

Gething, Peter W; Patil, Anand P; Hay, Simon I

2010-04-01

Risk maps estimating the spatial distribution of infectious diseases are required to guide public health policy from local to global scales. The advent of model-based geostatistics (MBG) has allowed these maps to be generated in a formal statistical framework, providing robust metrics of map uncertainty that enhances their utility for decision-makers. In many settings, decision-makers require spatially aggregated measures over large regions such as the mean prevalence within a country or administrative region, or national populations living under different levels of risk. Existing MBG mapping approaches provide suitable metrics of local uncertainty--the fidelity of predictions at each mapped pixel--but have not been adapted for measuring uncertainty over large areas, due largely to a series of fundamental computational constraints. Here the authors present a new efficient approximating algorithm that can generate for the first time the necessary joint simulation of prevalence values across the very large prediction spaces needed for global scale mapping. This new approach is implemented in conjunction with an established model for P. falciparum allowing robust estimates of mean prevalence at any specified level of spatial aggregation. The model is used to provide estimates of national populations at risk under three policy-relevant prevalence thresholds, along with accompanying model-based measures of uncertainty. By overcoming previously unchallenged computational barriers, this study illustrates how MBG approaches, already at the forefront of infectious disease mapping, can be extended to provide large-scale aggregate measures appropriate for decision-makers.

Endocrine disruption in aquatic systems: up-scaling research to address ecological consequences.

PubMed

Windsor, Fredric M; Ormerod, Steve J; Tyler, Charles R

2018-02-01

Endocrine-disrupting chemicals (EDCs) can alter biological function in organisms at environmentally relevant concentrations and are a significant threat to aquatic biodiversity, but there is little understanding of exposure consequences for populations, communities and ecosystems. The pervasive nature of EDCs within aquatic environments and their multiple sub-lethal effects make assessments of their impact especially important but also highly challenging. Herein, we review the data on EDC effects in aquatic systems focusing on studies assessing populations and ecosystems, and including how biotic and abiotic processes may affect, and be affected by, responses to EDCs. Recent research indicates a significant influence of behavioural responses (e.g. enhancing feeding rates), transgenerational effects and trophic cascades in the ecological consequences of EDC exposure. In addition, interactions between EDCs and other chemical, physical and biological factors generate uncertainty in our understanding of the ecological effects of EDCs within aquatic ecosystems. We illustrate how effect thresholds for EDCs generated from individual-based experimental bioassays of the types commonly applied using chemical test guidelines [e.g. Organisation for Economic Co-operation and Development (OECD)] may not necessarily reflect the hazards associated with endocrine disruption. We argue that improved risk assessment for EDCs in aquatic ecosystems urgently requires more ecologically oriented research as well as field-based assessments at population-, community- and food-web levels. © 2017 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

Machine Vision Within The Framework Of Collective Neural Assemblies

NASA Astrophysics Data System (ADS)

Gupta, Madan M.; Knopf, George K.

1990-03-01

The proposed mechanism for designing a robust machine vision system is based on the dynamic activity generated by the various neural populations embedded in nervous tissue. It is postulated that a hierarchy of anatomically distinct tissue regions are involved in visual sensory information processing. Each region may be represented as a planar sheet of densely interconnected neural circuits. Spatially localized aggregates of these circuits represent collective neural assemblies. Four dynamically coupled neural populations are assumed to exist within each assembly. In this paper we present a state-variable model for a tissue sheet derived from empirical studies of population dynamics. Each population is modelled as a nonlinear second-order system. It is possible to emulate certain observed physiological and psychophysiological phenomena of biological vision by properly programming the interconnective gains . Important early visual phenomena such as temporal and spatial noise insensitivity, contrast sensitivity and edge enhancement will be discussed for a one-dimensional tissue model.

An Epidemiological Model for Examining Marijuana Use over the Life Course

PubMed Central

Paddock, Susan M.; Kilmer, Beau; Caulkins, Jonathan P.; Booth, Marika J.; Pacula, Rosalie L.

2012-01-01

Trajectories of drug use are usually studied empirically by following over time persons sampled from either the general population (most often youth and young adults) or from heavy or problematic users (e.g., arrestees or those in treatment). The former, population-based samples, describe early career development, but miss the years of use that generate the greatest social costs. The latter, selected populations, help to summarize the most problematic use, but cannot easily explain how people become problem users nor are they representative of the population as a whole. This paper shows how microsimulation can synthesize both sorts of data within a single analytical framework, while retaining heterogeneous influences that can impact drug use decisions over the life course. The RAND Marijuana Microsimulation Model is constructed for marijuana use, validated, and then used to demonstrate how such models can be used to evaluate alternative policy options aimed at reducing use over the life course. PMID:23236590

Assessing and forecasting population health: integrating knowledge and beliefs in a comprehensive framework.

PubMed

Van Meijgaard, Jeroen; Fielding, Jonathan E; Kominski, Gerald F

2009-01-01

A comprehensive population health-forecasting model has the potential to interject new and valuable information about the future health status of the population based on current conditions, socioeconomic and demographic trends, and potential changes in policies and programs. Our Health Forecasting Model uses a continuous-time microsimulation framework to simulate individuals' lifetime histories by using birth, risk exposures, disease incidence, and death rates to mark changes in the state of the individual. The model generates a reference forecast of future health in California, including details on physical activity, obesity, coronary heart disease, all-cause mortality, and medical expenditures. We use the model to answer specific research questions, inform debate on important policy issues in public health, support community advocacy, and provide analysis on the long-term impact of proposed changes in policies and programs, thus informing stakeholders at all levels and supporting decisions that can improve the health of populations.

Extinction phase transitions in a model of ecological and evolutionary dynamics

NASA Astrophysics Data System (ADS)

Barghathi, Hatem; Tackkett, Skye; Vojta, Thomas

2017-07-01

We study the non-equilibrium phase transition between survival and extinction of spatially extended biological populations using an agent-based model. We especially focus on the effects of global temporal fluctuations of the environmental conditions, i.e., temporal disorder. Using large-scale Monte-Carlo simulations of up to 3 × 107 organisms and 105 generations, we find the extinction transition in time-independent environments to be in the well-known directed percolation universality class. In contrast, temporal disorder leads to a highly unusual extinction transition characterized by logarithmically slow population decay and enormous fluctuations even for large populations. The simulations provide strong evidence for this transition to be of exotic infinite-noise type, as recently predicted by a renormalization group theory. The transition is accompanied by temporal Griffiths phases featuring a power-law dependence of the life time on the population size.

Analysis of persistent changes to γ-aminobutyric acid receptor gene expression in Plutella xylostella subjected to sublethal amounts of spinosad.

PubMed

Yin, X-H; Wu, Q-J; Zhang, Y-J; Long, Y-H; Wu, X-M; Li, R-Y; Wang, M; Tian, X-L; Jiao, X-G

2016-07-25

A multi-generational approach was used to investigate the persistent effects of a sub-lethal dose of spinosad in Plutella xylostella. The susceptibility of various sub-populations of P. xylostella to spinosad and the effects of the insecticide on the gene expression of γ-aminobutyric acid receptor (GABAR) were determined. The results of a leaf dip bioassay showed that the sensitivity of P. xylostella to spinosad decreased across generations. The sub-strains had been previously selected based on a determined LC25 of spinosad. Considering that GABA-gated chloride channels are the primary targets of spinosad, the cDNA of P. xylostella was used to clone GABARα by using reverse transcription-polymerase chain reaction (RT-PCR). The mature peptide cDNA was 1477-bp long and contained a 1449-bp open reading frame encoding a protein of 483 amino acids. The resulting amino acid sequence was used to generate a neighbor-joining dendrogram, and homology search was conducted using NCBI BLAST. The protein had high similarity with the known GABAR sequence from P. xylostella. Subsequent semi-quantitative RT-PCR and real-time PCR analyses indicated that the GABAR transcript levels in the spinosad-resistant strain (RR, 145.82-fold) and in Sub1 strain (selected with LC25 spinosad for one generation) were the highest, followed by those in the spinosad-susceptible strain, the Sub10 strain (selected for ten generations), and the Sub5 strain (selected for five generations). This multi-generational study found significant correlations between spinosad susceptibility and GABAR gene expression, providing insights into the long-term effects of sub-lethal insecticide exposure and its potential to lead to the development of insecticide-resistant insect populations.

Singapore Indian Eye Study-2: methodology and impact of migration on systemic and eye outcomes.

PubMed

Sabanayagam, Charumathi; Yip, Wanfen; Gupta, Preeti; Mohd Abdul, Riswana Bb; Lamoureux, Ecosse; Kumari, Neelam; Cheung, Gemmy Cm; Cheung, Carol Y; Wang, Jie Jin; Cheng, Ching-Yu; Wong, Tien Yin

2017-11-01

Asian Indians are the fastest growing migration groups in the world. Studies evaluating the impact of migration on disease outcomes in this population are rare. We describe the methodology of the Singapore Indian Eye Study-2 (SINDI-2) aimed to evaluate the impact of migration status on diabetic retinopathy and other major age-related eye diseases in Asian Indians living in an urban environment. Population-based cohort study. A total of 2200 adults had participated in baseline SINDI (2007-2009, mean age [range] = 57.8 [42.7-84.1] years) and SINDI-2 (2013-2015, 56.5 [48.4-90.2] years). Participants were classified as 'first generation' if they were Indian residents born outside of Singapore and as 'second-generation' immigrants (59.7% in SINDI vs. 63.6% in SINDI-2) if they were born in Singapore. Response rate, participant characteristics and prevalence of systemic diseases were stratified by migration status. Of the 2914 eligible SINDI participants invited to participate, 2200 participated in SINDI-2 (response rate of 75.2%). In both SINDI and SINDI-2, compared with first-generation immigrants, second-generation immigrants were younger, less likely to have income <1000 SGD, had lower levels of pulse pressure, higher levels of high-density lipoprotein cholesterol, had lower prevalence of hypertension and chronic kidney disease and had higher prevalence of current smoking and obesity (all P < 0.05). In both SINDI and SINDI-2, second-generation immigrants had lower prevalence of cardiovascular risk factors except smoking and obesity compared with first-generation immigrants. The final report will confirm if these differences between generations are evident with regard to eye diseases. © 2017 Royal Australian and New Zealand College of Ophthalmologists.

Cosmic transcendence, loneliness, and exchange of emotional support with adult children: a study among older parents in The Netherlands.

PubMed

Sadler, E A; Braam, A W; Broese van Groenou, M I; Deeg, D J H; van der Geest, S

2006-09-01

Gerotranscendence defines a shift in meta-perspective from earlier materialistic and pragmatic concerns, toward more cosmic and transcendent ones in later life. Population-based studies that have empirically examined this concept using Tornstam's gerotranscendence scale, highlight cosmic transcendence as a core component, which includes a sense of belongingness with past and future generations. Such generative concerns may increase expectations regarding the quality of the bond with one's children in later life. This study examined whether the association between emotional support exchanged with children and feelings of loneliness later in life varied by the degree of cosmic transcendence of the older parent. Data from 1,845 older parents participating in a population-based study living in The Netherlands were analyzed from the 1995/1996 cycle of the Longitudinal Aging Study Amsterdam. Interviews included self-report measures of cosmic transcendence, loneliness, emotional support exchanged with children, health indicators, and marital status. Results indicated that a negative association between loneliness and level of emotional support exchanged with children was more pronounced among older parents with higher cosmic transcendence scores, in particular among the married. It is argued that cosmic transcendence reflects a sense of generativity and an increased emotional dependency on children in later life. Under favorable social conditions (supportive relationships with children and being married) cosmic transcendent views had a positive impact on social well-being in later life. When children no longer met emotional needs of older parents, cosmic transcendence increased feelings of loneliness.

Seasonal migration to high latitudes results in major reproductive benefits in an insect

PubMed Central

Chapman, Jason W.; Bell, James R.; Burgin, Laura E.; Reynolds, Donald R.; Pettersson, Lars B.; Hill, Jane K.; Bonsall, Michael B.; Thomas, Jeremy A.

2012-01-01

Little is known of the population dynamics of long-range insect migrants, and it has been suggested that the annual journeys of billions of nonhardy insects to exploit temperate zones during summer represent a sink from which future generations seldom return (the “Pied Piper” effect). We combine data from entomological radars and ground-based light traps to show that annual migrations are highly adaptive in the noctuid moth Autographa gamma (silver Y), a major agricultural pest. We estimate that 10–240 million immigrants reach the United Kingdom each spring, but that summer breeding results in a fourfold increase in the abundance of the subsequent generation of adults, all of which emigrate southward in the fall. Trajectory simulations show that 80% of emigrants will reach regions suitable for winter breeding in the Mediterranean Basin, for which our population dynamics model predicts a winter carrying capacity only 20% of that of northern Europe during the summer. We conclude not only that poleward insect migrations in spring result in major population increases, but also that the persistence of such species is dependent on summer breeding in high-latitude regions, which requires a fundamental change in our understanding of insect migration. PMID:22927392

Genetic variability and heritability on Kipas Putih soybean mutant lines using gamma rays irradiation (M3 generation)

NASA Astrophysics Data System (ADS)

Nilahayati; Rosmayati; Hanafiah, D. S.; Harahap, F.

2018-02-01

The objective of the research was to determine the selection criteria in Kipas Putih Soybean with gamma rays irradiation in M3 generation. In this study there are four populations namely population 0 Gray (control), 100 Gray, 200 Gray and 300 Gray. The results showed that high genotypic coefficient of variation (GCV) was obtained on the number of pods and seed weight per plant in population 200 Gy, number of branches on 100 Gy and 300 Gy, number of pods and seed weight per plants 100 and 200 Gy, moderate GCV in number of branches on 100 and 300 Gy while other characters such as plant height, numbers of branches on 200 Gy, flowering and harvest age have narrow GCV criteria. High heritability values are found in 300 Gy on plant height, number of branches 300 Gy, number of pods and seed weight per plant 200 Gy, days to flower 200 Gy and 300 Gy and days to harvest of all doses. Based on the genetic variabiliy and heritability, characters that can be used as selection criteria in this study is number of pods and seeds weight per plant, days to flower and days to harvest.

Density-dependent natural selection and trade-offs in life history traits.

PubMed

Mueller, L D; Guo, P Z; Ayala, F J

1991-07-26

Theories of density-dependent natural selection state that at extreme population densities evolution produces alternative life histories due to trade-offs. The trade-offs are presumed to arise because those genotypes with highest fitness at high population densities will not also have high fitness at low density and vice-versa. These predictions were tested by taking samples from six populations of Drosophila melanogaster kept at low population densities (r-populations) for nearly 200 generations and placing them in crowded cultures (K-populations). After 25 generations in the crowded cultures, the derived K-populations showed growth rate and productivity that at high densities were elevated relative to the controls, but at low density were depressed.

Population-based study on the seroprevalence of hepatitis A, B, and C virus infection in Amsterdam, 2004.

PubMed

Baaten, G G G; Sonder, G J B; Dukers, N H T M; Coutinho, R A; Van den Hoek, J A R

2007-12-01

In order to enhance screening and preventive strategies, this study investigated the seroprevalence of hepatitis A, B, and C in the general adult urban population and in subgroups. In 2004, sera from 1,364 adult residents of Amsterdam were tested for viral markers. Sociodemographic characteristics were collected using a standardized questionnaire. For hepatitis A, 57.0% was immune. Of first-generation immigrants from Turkey and Morocco, 100% was immune. Of all Western persons and second-generation non-Western immigrants, approximately half was still susceptible. For hepatitis B, 9.9% had antibodies to hepatitis B core antigen (anti-HBc) and 0.4% had hepatitis B surface antigen. Anti-HBc seroprevalences were highest among first-generation immigrants from Surinam, Morocco, and Turkey, and correlated with age at the time of immigration, and among men with a sexual preference for men. Seroprevalence among second-generation immigrants was comparable to Western persons. The seroprevalence of hepatitis C virus antibodies was 0.6%. In conclusion, a country with overall low endemicity for viral hepatitis can show higher endemicity in urban regions, indicating the need for differentiated regional studies and prevention strategies. More prevention efforts in cities like Amsterdam are warranted, particularly for hepatitis A and B among second-generation immigrants, for hepatitis B among men with a sexual preference for men, and for hepatitis C. Active case finding strategies are needed for both hepatitis B and C. (c) Wiley-Liss, Inc.

The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape

PubMed Central

Busby, George B.J.; Hellenthal, Garrett; Montinaro, Francesco; Tofanelli, Sergio; Bulayeva, Kazima; Rudan, Igor; Zemunik, Tatijana; Hayward, Caroline; Toncheva, Draga; Karachanak-Yankova, Sena; Nesheva, Desislava; Anagnostou, Paolo; Cali, Francesco; Brisighelli, Francesca; Romano, Valentino; Lefranc, Gerard; Buresi, Catherine; Ben Chibani, Jemni; Haj-Khelil, Amel; Denden, Sabri; Ploski, Rafal; Krajewski, Pawel; Hervig, Tor; Moen, Torolf; Herrera, Rene J.; Wilson, James F.; Myers, Simon; Capelli, Cristian

2015-01-01

Summary Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient humans across West Eurasia, demonstrating the presence of large-scale, dynamic population movements over the last 10,000 years, such that ancestry across present-day populations is likely to be a mixture of several ancient groups [1, 2, 3, 4, 5, 6, 7]. While these efforts are bringing the details of West Eurasian prehistory into increasing focus, studies aimed at understanding the processes behind the generation of the current West Eurasian genetic landscape have been limited by the number of populations sampled or have been either too regional or global in their outlook [8, 9, 10, 11]. Here, using recently described haplotype-based techniques [11], we present the results of a systematic survey of recent admixture history across Western Eurasia and show that admixture is a universal property across almost all groups. Admixture in all regions except North Western Europe involved the influx of genetic material from outside of West Eurasia, which we date to specific time periods. Within Northern, Western, and Central Europe, admixture tended to occur between local groups during the period 300 to 1200 CE. Comparisons of the genetic profiles of West Eurasians before and after admixture show that population movements within the last 1,500 years are likely to have maintained differentiation among groups. Our analysis provides a timeline of the gene flow events that have generated the contemporary genetic landscape of West Eurasia. PMID:26387712

Rethinking the influence of hydroelectric development on gene flow in a long-lived fish, the Lake Sturgeon Acipenser fulvescens

PubMed Central

McDougall, Craig A.; Welsh, Amy B.; Gosselin, Thierry; Anderson, W. Gary; Nelson, Patrick A.

2017-01-01

Many hydroelectric dams have been in place for 50 - >100 years, which for most fish species means that enough generations have passed for fragmentation induced divergence to have accumulated. However, for long-lived species such as Lake Sturgeon, Acipenser fulvescens, it should be possible to discriminate between historical population structuring and contemporary gene flow and improve the broader understanding of anthropogenic influence. On the Winnipeg River, Manitoba, two hypotheses were tested: 1) Measureable quantities of former reservoir dwelling Lake Sturgeon now reside downstream of the Slave Falls Generating Station, and 2) genetically differentiated populations of Lake Sturgeon occur upstream and downstream, a result of historical structuring. Genetic methods based on ten microsatellite markers were employed, and simulations were conducted to provide context. With regards to contemporary upstream to downstream contributions, the inclusion of length-at-age data proved informative. Both pairwise relatedness and Bayesian clustering analysis substantiated that fast-growing outliers, apparently entrained after residing in the upstream reservoir for several years, accounted for ~15% of the Lake Sturgeon 525–750 mm fork length captured downstream. With regards to historical structuring, upstream and downstream populations were found to be differentiated (FST = 0.011, and 0.013–0.014 when fast-growing outliers were excluded), and heterozygosity metrics were higher for downstream versus upstream juveniles. Historical asymmetric (downstream) gene flow in the vicinity of the generating station was the most logical explanation for the observed genetic structuring. In this section of the Winnipeg River, construction of a major dam does not appear to have fragmented a previously panmictic Lake Sturgeon population, but alterations to habitat may be influencing upstream to downstream contributions in unexpected ways. PMID:28329005

Rethinking the influence of hydroelectric development on gene flow in a long-lived fish, the Lake Sturgeon Acipenser fulvescens.

PubMed

McDougall, Craig A; Welsh, Amy B; Gosselin, Thierry; Anderson, W Gary; Nelson, Patrick A

2017-01-01

Many hydroelectric dams have been in place for 50 - >100 years, which for most fish species means that enough generations have passed for fragmentation induced divergence to have accumulated. However, for long-lived species such as Lake Sturgeon, Acipenser fulvescens, it should be possible to discriminate between historical population structuring and contemporary gene flow and improve the broader understanding of anthropogenic influence. On the Winnipeg River, Manitoba, two hypotheses were tested: 1) Measureable quantities of former reservoir dwelling Lake Sturgeon now reside downstream of the Slave Falls Generating Station, and 2) genetically differentiated populations of Lake Sturgeon occur upstream and downstream, a result of historical structuring. Genetic methods based on ten microsatellite markers were employed, and simulations were conducted to provide context. With regards to contemporary upstream to downstream contributions, the inclusion of length-at-age data proved informative. Both pairwise relatedness and Bayesian clustering analysis substantiated that fast-growing outliers, apparently entrained after residing in the upstream reservoir for several years, accounted for ~15% of the Lake Sturgeon 525-750 mm fork length captured downstream. With regards to historical structuring, upstream and downstream populations were found to be differentiated (FST = 0.011, and 0.013-0.014 when fast-growing outliers were excluded), and heterozygosity metrics were higher for downstream versus upstream juveniles. Historical asymmetric (downstream) gene flow in the vicinity of the generating station was the most logical explanation for the observed genetic structuring. In this section of the Winnipeg River, construction of a major dam does not appear to have fragmented a previously panmictic Lake Sturgeon population, but alterations to habitat may be influencing upstream to downstream contributions in unexpected ways.

Impact of reduced marker set estimation of genomic relationship matrices on genomic selection for feed efficiency in Angus cattle.

PubMed

Rolf, Megan M; Taylor, Jeremy F; Schnabel, Robert D; McKay, Stephanie D; McClure, Matthew C; Northcutt, Sally L; Kerley, Monty S; Weaber, Robert L

2010-04-19

Molecular estimates of breeding value are expected to increase selection response due to improvements in the accuracy of selection and a reduction in generation interval, particularly for traits that are difficult or expensive to record or are measured late in life. Several statistical methods for incorporating molecular data into breeding value estimation have been proposed, however, most studies have utilized simulated data in which the generated linkage disequilibrium may not represent the targeted livestock population. A genomic relationship matrix was developed for 698 Angus steers and 1,707 Angus sires using 41,028 single nucleotide polymorphisms and breeding values were estimated using feed efficiency phenotypes (average daily feed intake, residual feed intake, and average daily gain) recorded on the steers. The number of SNPs needed to accurately estimate a genomic relationship matrix was evaluated in this population. Results were compared to estimates produced from pedigree-based mixed model analysis of 862 Angus steers with 34,864 identified paternal relatives but no female ancestors. Estimates of additive genetic variance and breeding value accuracies were similar for AFI and RFI using the numerator and genomic relationship matrices despite fewer animals in the genomic analysis. Bootstrap analyses indicated that 2,500-10,000 markers are required for robust estimation of genomic relationship matrices in cattle. This research shows that breeding values and their accuracies may be estimated for commercially important sires for traits recorded in experimental populations without the need for pedigree data to establish identity by descent between members of the commercial and experimental populations when at least 2,500 SNPs are available for the generation of a genomic relationship matrix.

A cost-effectiveness analysis of a proactive management strategy for the Sprint Fidelis recall: a probabilistic decision analysis model.

PubMed

Bashir, Jamil; Cowan, Simone; Raymakers, Adam; Yamashita, Michael; Danter, Matthew; Krahn, Andrew; Lynd, Larry D

2013-12-01

The management of the recall is complicated by the competing risks of lead failure and complications that can occur with lead revision. Many of these patients are currently undergoing an elective generator change--an ideal time to consider lead revision. To determine the cost-effectiveness of a proactive management strategy for the Sprint Fidelis recall. We obtained detailed clinical outcomes and costing data from a retrospective analysis of 341 patients who received the Sprint Fidelis lead in British Columbia, where patients younger than 60 years were offered lead extraction when undergoing generator replacement. These population-based data were used to construct and populate a probabilistic Markov model in which a proactive management strategy was compared to a conservative strategy to determine the incremental cost per lead failure avoided. In our population, elective lead revisions were half the cost of emergent revisions and had a lower complication rate. In the model, the incremental cost-effectiveness ratio of proactive lead revision versus a recommended monitoring strategy was $12,779 per lead failure avoided. The proactive strategy resulted in 21 fewer failures per 100 patients treated and reduced the chance of an additional complication from an unexpected surgery. Cost-effectiveness analysis suggests that prospective lead revision should be considered when patients with a Sprint Fidelis lead present for pulse generator change. Elective revision of the lead is justified even when 25% of the population is operated on per year, and in some scenarios, it is both less costly and provides a better outcome. © 2013 Heart Rhythm Society Published by Heart Rhythm Society All rights reserved.

Genetic trend in economic traits in Iranian native fowl.

PubMed

Ghorbani, S H; Kamali, M A

2007-09-15

Genetic parameters were estimated in base population of a closed experimental strain fowl, from data issued from 13 successive generations of selection. This population had been selected for body weight at 12 weeks of age (BW12) and egg number during the first 12 weeks of laying period (EN), mean egg weight at 28th, 30th, 32nd weeks and Age at Sexual Maturity (ASM). Data were obtained on 35461 Iranian native hens belonging to breeding center for Fars province in Iran. The method of multi-traits restricted maximum likelihood with an animal model was used to estimate genetic parameters. Resulting heritabilities for BW12, EN, EW and ASM were 0.58, 0.34, 0.62 and 0.49, respectively. Genetic correlations between BW12 and EN, EW and ASM were -0.06, 0.49 and 0.02, respectively. Genetic correlations between EN and EW and ASM were -0.26 and-0.77, respectively, while between EW and ASM, it was 0.20. The overall predicted genetic gains, after 13 generations of selection, estimated by the regression coefficients of the breeding value on generation number were equal to 9.55, 0.99, 0.05 and -1.66, for BW12, EN, EW and ASM, respectively.

Geospatial techniques for developing a sampling frame of watersheds across a region

USGS Publications Warehouse

Gresswell, Robert E.; Bateman, Douglas S.; Lienkaemper, George; Guy, T.J.

2004-01-01

Current land-management decisions that affect the persistence of native salmonids are often influenced by studies of individual sites that are selected based on judgment and convenience. Although this approach is useful for some purposes, extrapolating results to areas that were not sampled is statistically inappropriate because the sampling design is usually biased. Therefore, in recent investigations of coastal cutthroat trout (Oncorhynchus clarki clarki) located above natural barriers to anadromous salmonids, we used a methodology for extending the statistical scope of inference. The purpose of this paper is to apply geospatial tools to identify a population of watersheds and develop a probability-based sampling design for coastal cutthroat trout in western Oregon, USA. The population of mid-size watersheds (500-5800 ha) west of the Cascade Range divide was derived from watershed delineations based on digital elevation models. Because a database with locations of isolated populations of coastal cutthroat trout did not exist, a sampling frame of isolated watersheds containing cutthroat trout had to be developed. After the sampling frame of watersheds was established, isolated watersheds with coastal cutthroat trout were stratified by ecoregion and erosion potential based on dominant bedrock lithology (i.e., sedimentary and igneous). A stratified random sample of 60 watersheds was selected with proportional allocation in each stratum. By comparing watershed drainage areas of streams in the general population to those in the sampling frame and the resulting sample (n = 60), we were able to evaluate the how representative the subset of watersheds was in relation to the population of watersheds. Geospatial tools provided a relatively inexpensive means to generate the information necessary to develop a statistically robust, probability-based sampling design.

The Rare-Variant Generalized Disequilibrium Test for Association Analysis of Nuclear and Extended Pedigrees with Application to Alzheimer Disease WGS Data.

PubMed

He, Zongxiao; Zhang, Di; Renton, Alan E; Li, Biao; Zhao, Linhai; Wang, Gao T; Goate, Alison M; Mayeux, Richard; Leal, Suzanne M

2017-02-02

Whole-genome and exome sequence data can be cost-effectively generated for the detection of rare-variant (RV) associations in families. Causal variants that aggregate in families usually have larger effect sizes than those found in sporadic cases, so family-based designs can be a more powerful approach than population-based designs. Moreover, some family-based designs are robust to confounding due to population admixture or substructure. We developed a RV extension of the generalized disequilibrium test (GDT) to analyze sequence data obtained from nuclear and extended families. The GDT utilizes genotype differences of all discordant relative pairs to assess associations within a family, and the RV extension combines the single-variant GDT statistic over a genomic region of interest. The RV-GDT has increased power by efficiently incorporating information beyond first-degree relatives and allows for the inclusion of covariates. Using simulated genetic data, we demonstrated that the RV-GDT method has well-controlled type I error rates, even when applied to admixed populations and populations with substructure. It is more powerful than existing family-based RV association methods, particularly for the analysis of extended pedigrees and pedigrees with missing data. We analyzed whole-genome sequence data from families affected by Alzheimer disease to illustrate the application of the RV-GDT. Given the capability of the RV-GDT to adequately control for population admixture or substructure and analyze pedigrees with missing genotype data and its superior power over other family-based methods, it is an effective tool for elucidating the involvement of RVs in the etiology of complex traits. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Chain pooling to minimize prediction error in subset regression. [Monte Carlo studies using population models

NASA Technical Reports Server (NTRS)

Holms, A. G.

1974-01-01

Monte Carlo studies using population models intended to represent response surface applications are reported. Simulated experiments were generated by adding pseudo random normally distributed errors to population values to generate observations. Model equations were fitted to the observations and the decision procedure was used to delete terms. Comparison of values predicted by the reduced models with the true population values enabled the identification of deletion strategies that are approximately optimal for minimizing prediction errors.

G1738R is a BRCA1 founder mutation in Greek breast/ovarian cancer patients: evaluation of its pathogenicity and inferences on its genealogical history.

PubMed

Anagnostopoulos, Theodore; Pertesi, Maroulio; Konstantopoulou, Irene; Armaou, Sofia; Kamakari, Smaragda; Nasioulas, George; Athanasiou, Athanassios; Dobrovic, Alex; Young, Mary-Anne; Goldgar, David; Fountzilas, George; Yannoukakos, Drakoulis

2008-07-01

We have performed screening in 287 breast/ovarian cancer families in Greece which has revealed that approximately 12% (8/65) of all index patients-carriers of a deleterious mutation in BRCA1 and BRCA2 genes, contain the base substitution G to A at position 5331 of BRCA1 gene. This generates the amino acid change G1738R for which based on a combination of genetic, in silico and histopathological analysis there are strong suggestions that it is a causative mutation. In this paper, we present further evidence suggesting the pathogenicity of this variant. Forty breast/ovarian cancer patients were reported in 11 Greek families: the above eight living in Greece, two living in Australia and one in USA, all containing G1738R. Twenty of these patients were screened and were all found to be carriers of the same base substitution. In addition, we have detected the same base change in five breast/ovarian cancer patients after screening 475 unselected patient samples with no apparent family history. The mean age of onset for all the above patients was 39.4 and 53.6 years for breast and ovarian cancer cases, respectively. A multi-factorial likelihood model for classification of unclassified variants in BRCA1 and BRCA2 developed previously was applied on G1738R and the odds of it being a deleterious mutation was estimated to be 11470:1. In order to explain the prevalence of this mutation mainly in the Greek population, its genealogical history was examined. DNA samples were collected from 11 carrier families living in Greece, Australia and USA. Screening of eight intragenic SNPs, three intragenic and seven extragenic microsatellite markers and comparison with control individuals, suggested a common origin for the mutation while the time to its most recent common ancestor was estimated to be 11 generations (about 275 years assuming a generational interval of 25 years) with a 1-lod support interval of 4-24 generations (100-600 years). Considering the large degree of genetic heterogeneity in the Greek population, the identification of a frequent founder mutation greatly facilitates genetic screening.

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.

Genetic diversity and genetic structure of consecutive breeding generations of golden mandarin fish (Siniperca scherzeri Steindachner) using microsatellite markers.

PubMed

Luo, X N; Yang, M; Liang, X F; Jin, K; Lv, L Y; Tian, C X; Yuan, Y C; Sun, J

2015-09-25

In this study, 12 polymorphic microsatellites were inves-tigated to determine the genetic diversity and structure of 5 consecu-tive selected populations of golden mandarin fish (Siniperca scherzeri Steindachner). The total numbers of alleles, average heterozyosity, and average polymorphism information content showed that the genetic diversity of these breeding populations was decreasing. Additionally, pairwise fixation index FST values among populations and Da values in-creased from F1 generation to subsequent generations (FST values from 0.0221-0.1408; Da values from 0.0608-0.1951). Analysis of molecular variance indicated that most genetic variations arise from individuals within populations (about 92.05%), while variation among populations accounted for only 7.95%. The allele frequency of the loci SC75-220 and SC101-222 bp changed regularly in the 5 breeding generations. Their frequencies were gradually increased and showed an enrichment trend, indicating that there may be genetic correlations between these 2 loci and breeding traits. Our study indicated that microsatellite markers are effective for assessing the genetic variability in the golden mandarin fish breeding program.

Microsatellite variation suggests a recent fine-scale population structure of Drosophila sechellia, a species endemic of the Seychelles archipelago.

PubMed

Legrand, Delphine; Vautrin, Dominique; Lachaise, Daniel; Cariou, Marie-Louise

2011-07-01

Drosophila sechellia is closely related to the cosmopolitan and widespread model species, D. simulans. This species, endemic to the Seychelles archipelago, is specialized on the fruits of Morinda citrifolia, and harbours the lowest overall genetic diversity compared to other species of Drosophila. This low diversity is associated with a small population size. In addition, no obvious population structure has been evidenced so far across islands of the Seychelles archipelago. Here, a microsatellite panel of 17 loci in ten populations from nine islands of the Seychelles was used to assess the effect of the D. sechellia's fragmented distribution on the fine-scale population genetic structure, the migration pattern, as well as on the demography of the species. Contrary to previous results, also based on microsatellites, no evidence for population contraction in D. sechellia was found. The results confirm previous studies based on gene sequence polymorphism that showed a long-term stable population size for this species. Interestingly, a pattern of Isolation By Distance which had not been described yet in D. sechellia was found, with evidence of first-generation migrants between some neighbouring islands. Bayesian structuring algorithm results were consistent with a split of D. sechellia into two main groups of populations: Silhouette/Mahé versus all the other islands. Thus, microsatellites suggest that variability in D. sechellia is most likely explained by local genetic exchanges between neighbouring islands that have recently resulted in slight differentiation of the two largest island populations from all the others.

Vancouver Coastal Health's Second Generation Health Strategy: A need for a reboot?

PubMed

Masuda, Jeffrey R; Chan, Sophy

2017-03-01

In this commentary, we consider the motivations and implications of Vancouver Coastal Health's place-based population health strategy called the Downtown Eastside Second Generation Health Strategy (2GHS) in light of a broader historical view of shifting values in population and public health and structural health reforms in Canada over the past three decades. We argue that the tone and content of the 2GHS signals a shift towards a neoliberal clientelist model of health that treats people as patients and the DTES as a site of clinical encounter rather than as a community in its own right. In its clinical emphasis, the 2GHS fails to recognize the political dimension of health and well-being in the DTES, a community that faces compounding health risks associated with colonialism, gentrification, human displacement, the criminalization of poverty, sex work, and the street economy. Furthermore, we suggest that in its emphasis on allocating funding based on a rationalist model of health system access, the 2GHS undermines well-established insights and best practices from community-driven health initiatives. Our aim is to provide a provocation that will encourage public health policy-makers to embrace community-based leadership as well as the broader structural health determinants that are at the root of the current circumstances of people in the DTES and other marginalized communities in Canada.

Guidelines for Adapting Manualized Interventions for New Target Populations: A Step-Wise Approach Using Anger Management as a Model

PubMed Central

Goldstein, Naomi E. S.; Kemp, Kathleen A.; Leff, Stephen S.; Lochman, John E.

2014-01-01

The use of manual-based interventions tends to improve client outcomes and promote replicability. With an increasingly strong link between funding and the use of empirically supported prevention and intervention programs, manual development and adaptation have become research priorities. As a result, researchers and scholars have generated guidelines for developing manuals from scratch, but there are no extant guidelines for adapting empirically supported, manualized prevention and intervention programs for use with new populations. Thus, this article proposes step-by-step guidelines for the manual adaptation process. It also describes two adaptations of an extensively researched anger management intervention to exemplify how an empirically supported program was systematically and efficiently adapted to achieve similar outcomes with vastly different populations in unique settings. PMID:25110403

Projection of Big Cities Waste Management and Cost Based on Economic and Demographic Factors in Indonesia

NASA Astrophysics Data System (ADS)

Prajati, Gita; Padmi, Tri; Benno Rahardyan, dan

2017-12-01

Nowadays, solid waste management continues to be a major challenge in urban areas, especially in developing country. It is triggered by population growth, economic growth, industrialization and urbanization. Indonesia itselfs categorized into developing country. Indonesia's government has many program in order to increase the economic growth. One of them is MP3EI (Masterplan Percepatan dan Perluasan Pembangunan Ekonomi Indonesia. This program should be suppported by right waste management system. If Indonesia's waste management system can't afford the economic growth, it will trigger health and environmental problems. This study's purpose is to develop the socio-economic-environment model that can be used as a basis planning for the facility and cost of waste management systems. In this paper we used the development of Khajuria model test method. This method used six variables, which are GDP, population, population density, illiteracy, school's period and economic growth. The result showed that development of Khajuria test could explained the influence of economic and demographic factors to waste generation, 65.6%. The projection of waste generation shows that Pangkalpinang, Pekanbaru and Serang are the cities with the highest waste generation for the next five years. The number of dump truck and TPS in DKI Jakarata is the highest within another city, which is 39.37%. For the next five years, the waste management system in our study areas cost maximum 0.8% from GDP (Gross Domestic Products).

Sequential Insertion Heuristic with Adaptive Bee Colony Optimisation Algorithm for Vehicle Routing Problem with Time Windows

PubMed Central

Jawarneh, Sana; Abdullah, Salwani

2015-01-01

This paper presents a bee colony optimisation (BCO) algorithm to tackle the vehicle routing problem with time window (VRPTW). The VRPTW involves recovering an ideal set of routes for a fleet of vehicles serving a defined number of customers. The BCO algorithm is a population-based algorithm that mimics the social communication patterns of honeybees in solving problems. The performance of the BCO algorithm is dependent on its parameters, so the online (self-adaptive) parameter tuning strategy is used to improve its effectiveness and robustness. Compared with the basic BCO, the adaptive BCO performs better. Diversification is crucial to the performance of the population-based algorithm, but the initial population in the BCO algorithm is generated using a greedy heuristic, which has insufficient diversification. Therefore the ways in which the sequential insertion heuristic (SIH) for the initial population drives the population toward improved solutions are examined. Experimental comparisons indicate that the proposed adaptive BCO-SIH algorithm works well across all instances and is able to obtain 11 best results in comparison with the best-known results in the literature when tested on Solomon’s 56 VRPTW 100 customer instances. Also, a statistical test shows that there is a significant difference between the results. PMID:26132158

Temporal trends in prevalence, incidence, and mortality for rheumatoid arthritis in Quebec, Canada: a population-based study.

PubMed

Jean, Sonia; Hudson, Marie; Gamache, Philippe; Bessette, Louis; Fortin, Paul R; Boire, Gilles; Bernatsky, Sasha

2017-12-01

Health administrative data are a potentially efficient resource to conduct population-based research and surveillance, including trends in incidence and mortality over time. Our objective was to explore time trends in incidence and mortality for rheumatoid arthritis (RA), as well as estimating period prevalence. Our RA case definition was based on one or more hospitalizations with a RA diagnosis code, or three or more RA physician-billing codes, over 2 years, with at least one RA billing code by a rheumatologist, orthopedic surgeon, or internist. To identify incident cases, a "run-in" period of 5 years (1996-2000) was used to exclude prevalent cases. Crude age and sex-specific incidence rates were calculated (using data from 2001 to 2015), and sex-specific incidence rates were also standardized to the 2001 age structure of the Quebec population. We linked the RA cohort (both prevalent and incident patients) to the vital statistics registry, and standardized mortality rate ratios were generated. Negative binomial regression was used to test for linear change in standardized incidence rates and mortality ratios. The linear trends in standardized incidence rates did not show significant change over the study period. Mortality in RA was significantly higher than the general population and this remained true throughout the study period. Our prevalence estimate suggested 0.8% of the Quebec population may be affected by RA. RA incidence appeared relatively stable, and mortality was substantially higher in RA versus the general population and remained so over the study period. This suggests the need to optimize long-term RA outcomes.

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K.

PubMed

Kopelman, Naama M; Mayzel, Jonathan; Jakobsson, Mattias; Rosenberg, Noah A; Mayrose, Itay

2015-09-01

The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population-genetic data analysis. Application of model-based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present Clumpak (Cluster Markov Packager Across K), a method that automates the postprocessing of results of model-based population structure analyses. For analysing multiple independent runs at a single K value, Clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software Clumpp. Next, Clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in Clumpp and simplifying the comparison of clustering results across different K values. Clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. Clumpak, available at http://clumpak.tau.ac.il, simplifies the use of model-based analyses of population structure in population genetics and molecular ecology. © 2015 John Wiley & Sons Ltd.

Canada's population: growth and dualism.

PubMed

Beaujot, R P

1978-04-01

In Canada the current 1.3% population growth rate is causing some concern. Those concerned argue that such a rate of growth in combination with high levels of consumption could jeopardize the country's resource base and its comfortable style of living. Many Canadians are questioning high levels of immigration, for now that the fertility level is below replacement level, net immigration contributes substantially to population growth (over 1/3 in 1976). The growing proportion of non-Europeans among recent immigrants is causing resentment, and, in a tight job market, immigrants are regarded as threats to the World War 2 baby boom cohort who are now at working ages. The baby boom generation also puts stress on housing and health services, and it will increase the need for pension checks as it ages. Although French fertility is no longer high and immigration is no longer dominated by the British, the French group's 200-year struggle to preserve its identity continues on in the current effort of the Quebec government to enforce the use of French language by law within that province. Geography and climate dictate another demographic fact that divides the country and pervades its history. In addition to intense regionalism, uneven population distribution is responsible for 2 other concerns: the rapid growth of several already large cities and depopulation of many small communities. Focus in this discussion is on Canada's population growth in the past and as projected for the future, historical and current fertility, mortality and immigration trends, the search for a new immigration policy, the impact of the baby boom generation on the population's age structure and the problems this creates, and recent shifts in population distribution and in the country's ethnic and linguistic makeup. The population policy proposals evolved thus far involve to a great extent the use of immigration as a lever for achieving given population objectives.

Admixture and genetic relationships of Mexican Mestizos regarding Latin American and Caribbean populations based on 13 CODIS-STRs.

PubMed

Salazar-Flores, J; Zuñiga-Chiquette, F; Rubi-Castellanos, R; Álvarez-Miranda, J L; Zetina-Hérnandez, A; Martínez-Sevilla, V M; González-Andrade, F; Corach, D; Vullo, C; Álvarez, J C; Lorente, J A; Sánchez-Diz, P; Herrera, R J; Cerda-Flores, R M; Muñoz-Valle, J F; Rangel-Villalobos, H

2015-02-01

Short tandem repeats (STRs) of the combined DNA index system (CODIS) are probably the most employed markers for human identification purposes. STR databases generated to interpret DNA profiles are also helpful for anthropological purposes. In this work, we report admixture, population structure, and genetic relationships of Mexican Mestizos with respect to Latin American and Caribbean populations based on 13 CODIS-STRs. In addition, new STR population data were included from Tijuana, Baja California (Northwest, Mexico), which represents an interesting case of elevated genetic flow as a bordering city with the USA. Inter-population analyses included CODIS-STR data from 11 Mexican Mestizo, 12 Latin American and four Caribbean populations, in addition to European, Amerindian, and African genetic pools as ancestral references. We report allele frequencies and statistical parameters of forensic interest (PD, PE, Het, PIC, typical PI), for 15 STRs in Tijuana, Baja California. This Mexican border city was peculiar by the increase of African ancestry, and by presenting three STRs in Hardy-Weinberg disequilibrium, probably explained by recurrent gene flow. The Amerindian ancestry in Central and Southeast of Mexico was the greatest in Latin America (50.9-68.6%), only comparable with the North of Central America and Ecuador (48.8-56.4%), whereas the European ancestry was prevalent in South America (66.7-75%). The African ancestry in Mexico was the smallest (2.2-6.3%) in Latin America (≥ 2.6%), particularly regarding Brazil (21%), Honduras (62%), and the Caribbean (43.2-65.2%). CODIS-STRs allowed detecting significant population structure in Latin America based on greater presence of European, Amerindian, and African ancestries in Central/South America, Mexican Mestizos, and the Caribbean, respectively. Copyright © 2014 Elsevier GmbH. All rights reserved.

Student Technology Use in the Information-Seeking and Information-Gathering Process: A Critical Incident Approach for Benchmarking Performance

ERIC Educational Resources Information Center

Cordes, Sean

2012-01-01

This article is an exploratory study of student behavior using online tools to do project-based work for a library science course at a mid-sized Midwestern public university. The population was 22 net generation students aged 18-24, who were enrolled in an Introduction to Information Resources course. The study was designed to better understand…

Methods for selective functionalization and separation of carbon nanotubes

NASA Technical Reports Server (NTRS)

Strano, Michael S. (Inventor); Usrey, Monica (Inventor); Barone, Paul (Inventor); Dyke, Christopher A. (Inventor); Tour, James M. (Inventor); Kittrell, W. Carter (Inventor); Hauge, Robert H (Inventor); Smalley, Richard E. (Inventor); Marek, legal representative, Irene Marie (Inventor)

2011-01-01

The present invention is directed toward methods of selectively functionalizing carbon nanotubes of a specific type or range of types, based on their electronic properties, using diazonium chemistry. The present invention is also directed toward methods of separating carbon nanotubes into populations of specific types or range(s) of types via selective functionalization and electrophoresis, and also to the novel compositions generated by such separations.

Rural Land Use: Patterns and Proposals for Reform.

ERIC Educational Resources Information Center

Erickson, Ronald P.

In a world where the population is increasing at an annual rate of 76 million, where food is in short supply, and where agricultural production is one of our largest capital generating sources, U.S. agriculture and the land base supporting it are vital. Rural America has been losing land at a rate of one and a half million acres a year due to soil…

Developing and Evaluating the Impact of an Extension-Based Train-the-Trainer Model for Effectively Disseminating Food Safety Education to Middle School Students

ERIC Educational Resources Information Center

Richards, Jennifer; Pratt, Carrie; Skolits, Gary J.; Burney, Janie

2012-01-01

Adolescents are an understudied, but meaningful, population when it comes to food safety education. With the proliferation of pathogenic microbes and changes in eating habits of Americans, today's youth are more at risk of contracting a foodborne illness than previous generations. Hands On: Real World Lessons for Middle School Classrooms provides…

Experience with a third-generation parathyroid hormone assay (BIO-PTH) in the diagnosis of primary hyperparathyroidism in a Brazilian population.

PubMed

Bonanséa, Teresa Cristina P; Ohe, Monique Nakayama; Brandão, Cynthia; Ferrer, Cláudia de Francischi; Santos, Lívia Marcela; Lazaretti-Castro, Marise; Vieira, José Gilberto Henriques

2016-10-01

To evaluate the usefulness of a third-generation PTH assay in the diagnosis of primary hyperparathyroidism (PHPT). Forty-one PHPT patients (4 men and 37 women) with 61.2 ± 10.9 (mean ± SD) years, were studied and had PTH levels measured with two different methods using the same immunochemiluminescent assay plataform (Elecsys 2010 System, Roche). We compared a second-generation assay (I-PTH) with a third-generation PTH assay (Bio-PTH). Two populations of 423 and 120 healthy adults with serum 25OHD levels above 25 ng/mL were used to define normal values in the I-PTH and Bio-PTH assays respectively. Normal PTH values based in the healthy adults population were 24.2-78.0 pg/mL for the I-PTH assay and 19.9-58.5 pg/mL for Bio-PTH assay. In PHPT patients, PTH values ranged from 67 to 553 pg/mL (median: 168 pg/mL) using the I-PTH assay and from 55 to 328 pg/mL (median: 111 pg/mL) using the Bio-PTH assay. Results obtained with the Bio-PTH assay were significantly lower (p < 0.0001, Wilcoxon). In general I-PTH and Bio-PTH showed highly significant correlation (r = 0.952, p < 0.0001). Passing-Bablok analysis gave a regression equation of Bio PTH = 13.44 + 0.59 x intact PTH. PHPT patients had 25OHD levels ranging from 4 to 36 ng/mL (mean 16.2 ng/mL); 35 subjects (85.3%) had values bellow 25 ng/mL. Our results demonstrate that both second and third generation PTH methods are strongly correlated in PHPT patients and control subjects. Lower results with Bio-PTH tests are expected in function of the assay specificity determined by the amino-terminal antibody used.

Medium term municipal solid waste generation prediction by autoregressive integrated moving average

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

Younes, Mohammad K.; Nopiah, Z. M.; Basri, Noor Ezlin A.

2014-09-12

Generally, solid waste handling and management are performed by municipality or local authority. In most of developing countries, local authorities suffer from serious solid waste management (SWM) problems and insufficient data and strategic planning. Thus it is important to develop robust solid waste generation forecasting model. It helps to proper manage the generated solid waste and to develop future plan based on relatively accurate figures. In Malaysia, solid waste generation rate increases rapidly due to the population growth and new consumption trends that characterize the modern life style. This paper aims to develop monthly solid waste forecasting model using Autoregressivemore » Integrated Moving Average (ARIMA), such model is applicable even though there is lack of data and will help the municipality properly establish the annual service plan. The results show that ARIMA (6,1,0) model predicts monthly municipal solid waste generation with root mean square error equals to 0.0952 and the model forecast residuals are within accepted 95% confident interval.« less

The Alzheimer's Prevention Initiative Generation Program: Evaluating CNP520 Efficacy in the Prevention of Alzheimer's Disease.

PubMed

Lopez Lopez, C; Caputo, A; Liu, F; Riviere, M E; Rouzade-Dominguez, M-L; Thomas, R G; Langbaum, J B; Lenz, R; Reiman, E M; Graf, A; Tariot, P N

2017-01-01

Alzheimer's disease pathology begins decades before the onset of clinical symptoms. This provides an opportunity for interventional clinical trials to potentially delay or prevent the onset of cognitive impairment or dementia. CNP520 (a beta-site-amyloid precursor protein-cleaving enzyme inhibitor) is in clinical development for the treatment of preclinical Alzheimer's disease under the Alzheimer's Prevention Initiative Generation Program. The Alzheimer's Prevention Initiative is a public-private partnership intended to accelerate the evaluation of Alzheimer's disease prevention therapies. The Generation Program comprises two pivotal phase II/III studies with similar designs to assess the efficacy and safety of investigational treatments in a cognitively unimpaired population at increased risk for developing Alzheimer's disease based on age and apolipoprotein E (APOE) genotype (i.e., presence of the APOE ε4 allele). The program has been designed to maximize benefit to Alzheimer's disease research. Generation Study 1 (NCT02565511) and Generation Study 2 (NCT03131453) are currently enrolling; their key features are presented here.

Medium term municipal solid waste generation prediction by autoregressive integrated moving average

NASA Astrophysics Data System (ADS)

Younes, Mohammad K.; Nopiah, Z. M.; Basri, Noor Ezlin A.; Basri, Hassan

2014-09-01

Generally, solid waste handling and management are performed by municipality or local authority. In most of developing countries, local authorities suffer from serious solid waste management (SWM) problems and insufficient data and strategic planning. Thus it is important to develop robust solid waste generation forecasting model. It helps to proper manage the generated solid waste and to develop future plan based on relatively accurate figures. In Malaysia, solid waste generation rate increases rapidly due to the population growth and new consumption trends that characterize the modern life style. This paper aims to develop monthly solid waste forecasting model using Autoregressive Integrated Moving Average (ARIMA), such model is applicable even though there is lack of data and will help the municipality properly establish the annual service plan. The results show that ARIMA (6,1,0) model predicts monthly municipal solid waste generation with root mean square error equals to 0.0952 and the model forecast residuals are within accepted 95% confident interval.

Responses of three successive generations of beet armyworm, Spodoptera exigua, fed exclusively on different levels of gossypol in cotton leaves.

PubMed

Wu, Gang; Guo, Jian-Ying; Wan, Fang-Hao; Xiao, Neng-Wen

2010-01-01

The beet armyworm, Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae), is an important pest of numerous crops, and it causes economic damage in China. Use of secondary metabolic compounds in plants is an important method used to control this insect as a part of integrated pest management. In this study the growth, development, and food utilization of three successive generations of S. exigua fed on three cotton gossypol cultivars were examined. Significantly longer larval life-spans were observed in S. exigua fed on high gossypol cultivar M9101 compared with those fed on two low gossypol cultivars, ZMS13 and HZ401. The pupal weight of the first generation was significantly lower than that of the latter two generations fed on ZMS13 group. Significantly lower fecundity was observed in the second and third generations of S. exigua fed on M9101 compared with S. exigua fed on ZMS13 and HZ401. The efficiency of conversion was significantly higher in the first and third generations fed on HZ401 compared with those fed on ZMS13 and M9101. A significantly lower relative growth rate was observed in the three successive generations fed on M9101 compared with those fed on ZMS13 and HZ401. Cotton cultivars significantly affected the growth, development, and food utilization indices of S. exigua, except for frass and approximate digestibility. Development of S. exigua was significantly affected by relative consumption rate and efficiency of conversion of ingested food, but not by relative growth rate or approximate digestibility, suggesting that diet-utilization efficiency was different based on food quality and generation. Measuring the development and food utilization of S. exigua at the individual and population levels over more than one generation provided more meaningful predictions of long-term population dynamics.

Dyslipidemia and reference values for fasting plasma lipid concentrations in Danish/North-European White children and adolescents.

PubMed

Nielsen, Tenna Ruest Haarmark; Lausten-Thomsen, Ulrik; Fonvig, Cilius Esmann; Bøjsøe, Christine; Pedersen, Lise; Bratholm, Palle Skov; Hansen, Torben; Pedersen, Oluf; Holm, Jens-Christian

2017-04-28

Dyslipidemia is reported in 27 - 43% of children and adolescents with overweight/obesity and tracks into adulthood, increasing the risk of cardiovascular morbidity. Cut-off values for fasting plasma lipid concentrations are typically set at fixed levels throughout childhood. The objective of this cross-sectional study was to generate fasting plasma lipid references for a Danish/North-European White population-based cohort of children and adolescents, and investigate the prevalence of dyslipidemia in this cohort as well as in a cohort with overweight/obesity. A population-based cohort of 2141 (1275 girls) children and adolescents aged 6 - 19 (median 11.5) years was recruited from 11 municipalities in Denmark. Additionally, a cohort of children and adolescents of 1421 (774 girls) with overweight/obesity aged 6 - 19 years (median 11.8) was recruited for the study. Height, weight, and fasting plasma lipid concentrations were measured on all participants. Smoothed reference curves and percentiles were generated using the Generalized Additive Models for Location Scale and Shape package in the statistical software R. In the population-based cohort, plasma concentrations of total cholesterol (TC) (P < 0.05), low-density lipoprotein cholesterol (LDL) (P < 0.005), and high-density lipoprotein cholesterol (HDL) (P < 0.005) were higher in the youngest compared to the oldest tertile. Fasting plasma levels of triglycerides (TG) (P < 0.005) increased with age in both sexes. In boys, non-HDL was lower in the oldest compared to the youngest tertile (P < 0.0005). Concentrations of TC, LDL, non-HDL, and TG were higher (P < 0.05), and HDL lower (P < 0.05) in the cohort with overweight/obesity in both sexes and for all ages except for TC in the youngest girls. The overall prevalence of dyslipidemia was 6.4% in the population-based cohort and 28.0% in the cohort with overweight/obesity. The odds ratio for exhibiting dyslipidemia in the cohort with overweight/obesity compared with the population-based cohort was 6.2 (95% CI: 4.9 - 8.1, P < 2*10 -16 ). Fasting plasma lipid concentrations change during childhood and adolescence and differ with sex and age. Children and adolescents with obesity have increased concentrations of circulating lipids and exhibit an increased prevalence of dyslipidemia. The study is part of The Danish Childhood Obesity Biobank; ClinicalTrials.gov ID-no.: NCT00928473 retrospectively registered on June 25th 2009.

Predicting rates of inbreeding in populations undergoing selection.

PubMed Central

Woolliams, J A; Bijma, P

2000-01-01

Tractable forms of predicting rates of inbreeding (DeltaF) in selected populations with general indices, nonrandom mating, and overlapping generations were developed, with the principal results assuming a period of equilibrium in the selection process. An existing theorem concerning the relationship between squared long-term genetic contributions and rates of inbreeding was extended to nonrandom mating and to overlapping generations. DeltaF was shown to be approximately (1)/(4)(1 - omega) times the expected sum of squared lifetime contributions, where omega is the deviation from Hardy-Weinberg proportions. This relationship cannot be used for prediction since it is based upon observed quantities. Therefore, the relationship was further developed to express DeltaF in terms of expected long-term contributions that are conditional on a set of selective advantages that relate the selection processes in two consecutive generations and are predictable quantities. With random mating, if selected family sizes are assumed to be independent Poisson variables then the expected long-term contribution could be substituted for the observed, providing (1)/(4) (since omega = 0) was increased to (1)/(2). Established theory was used to provide a correction term to account for deviations from the Poisson assumptions. The equations were successfully applied, using simple linear models, to the problem of predicting DeltaF with sib indices in discrete generations since previously published solutions had proved complex. PMID:10747074

Dynamic Models Applied to Landslides: Study Case Angangueo, MICHOACÁN, MÉXICO.

NASA Astrophysics Data System (ADS)

Torres Fernandez, L.; Hernández Madrigal, V. M., , Dr; Capra, L.; Domínguez Mota, F. J., , Dr

2017-12-01

Most existing models for landslide zonification are static type, do not consider the dynamic behavior of the trigger factor. This results in a limited representation of the actual zonation of slope instability, present a short-term validity, cańt be applied for the design of early warning systems, etc. Particularly in Mexico, these models are static because they do not consider triggering factor such as precipitation. In this work, we present a numerical evaluation to know the landslide susceptibility, based on probabilistic methods. Which are based on the generation of time series, which are generated from the meteorological stations, having limited information an interpolation is made to generate the simulation of the precipitation in the zone. The obtained information is integrated in PCRaster and in conjunction with the conditioning factors it is possible to generate a dynamic model. This model will be applied for landslide zoning in the municipality of Angangueo, characterized by frequent logging of debris and mud flow, translational and rotational landslides, detonated by atypical precipitations, such as those recorded in 2010. These caused economic losses and humans. With these models, it would be possible to generate probable scenarios that help the Angangueo's population to reduce the risks and to carry out actions of constant resilience activities.

Density dependence in demography and dispersal generates fluctuating invasion speeds

PubMed Central

Li, Bingtuan; Miller, Tom E. X.

2017-01-01

Density dependence plays an important role in population regulation and is known to generate temporal fluctuations in population density. However, the ways in which density dependence affects spatial population processes, such as species invasions, are less understood. Although classical ecological theory suggests that invasions should advance at a constant speed, empirical work is illuminating the highly variable nature of biological invasions, which often exhibit nonconstant spreading speeds, even in simple, controlled settings. Here, we explore endogenous density dependence as a mechanism for inducing variability in biological invasions with a set of population models that incorporate density dependence in demographic and dispersal parameters. We show that density dependence in demography at low population densities—i.e., an Allee effect—combined with spatiotemporal variability in population density behind the invasion front can produce fluctuations in spreading speed. The density fluctuations behind the front can arise from either overcompensatory population growth or density-dependent dispersal, both of which are common in nature. Our results show that simple rules can generate complex spread dynamics and highlight a source of variability in biological invasions that may aid in ecological forecasting. PMID:28442569

Generating functionals and Gaussian approximations for interruptible delay reactions

NASA Astrophysics Data System (ADS)

Brett, Tobias; Galla, Tobias

2015-10-01

We develop a generating functional description of the dynamics of non-Markovian individual-based systems in which delay reactions can be terminated before completion. This generalizes previous work in which a path-integral approach was applied to dynamics in which delay reactions complete with certainty. We construct a more widely applicable theory, and from it we derive Gaussian approximations of the dynamics, valid in the limit of large, but finite, population sizes. As an application of our theory we study predator-prey models with delay dynamics due to gestation or lag periods to reach the reproductive age. In particular, we focus on the effects of delay on noise-induced cycles.

Asymmetric competition causes multimodal size distributions in spatially structured populations

PubMed Central

Velázquez, Jorge; Allen, Robert B.; Coomes, David A.; Eichhorn, Markus P.

2016-01-01

Plant sizes within populations often exhibit multimodal distributions, even when all individuals are the same age and have experienced identical conditions. To establish the causes of this, we created an individual-based model simulating the growth of trees in a spatially explicit framework, which was parametrized using data from a long-term study of forest stands in New Zealand. First, we demonstrate that asymmetric resource competition is a necessary condition for the formation of multimodal size distributions within cohorts. By contrast, the legacy of small-scale clustering during recruitment is transient and quickly overwhelmed by density-dependent mortality. Complex multi-layered size distributions are generated when established individuals are restricted in the spatial domain within which they can capture resources. The number of modes reveals the effective number of direct competitors, while the separation and spread of modes are influenced by distances among established individuals. Asymmetric competition within local neighbourhoods can therefore generate a range of complex size distributions within even-aged cohorts. PMID:26817778

Correlations in fertility across generations: can low fertility persist?

PubMed

Kolk, Martin; Cownden, Daniel; Enquist, Magnus

2014-03-22

Correlations in family size across generations could have a major influence on human population size in the future. Empirical studies have shown that the associations between the fertility of parents and the fertility of children are substantial and growing over time. Despite their potential long-term consequences, intergenerational fertility correlations have largely been ignored by researchers. We present a model of the fertility transition as a cultural process acting on new lifestyles associated with fertility. Differences in parental and social influences on the acquisition of these lifestyles result in intergenerational correlations in fertility. We show different scenarios for future population size based on models that disregard intergenerational correlations in fertility, models with fertility correlations and a single lifestyle, and models with fertility correlations and multiple lifestyles. We show that intergenerational fertility correlations will result in an increase in fertility over time. However, present low-fertility levels may persist if the rapid introduction of new cultural lifestyles continues into the future.

CFD-PBM coupled simulation of a nanobubble generator with honeycomb structure

NASA Astrophysics Data System (ADS)

Ren, F.; Noda, N. A.; Ueda, T.; Sano, Y.; Takase, Y.; Umekage, T.; Yonezawa, Y.; Tanaka, H.

2018-06-01

In recent years, nanobubble technologies have drawn great attention due to their wide applications in many fields of science and technology. The nitrogen nanobubble water circulation can be used to slow the progressions of oxidation and spoilage for the seafood long- term storage. From previous studies, a kind of honeycomb structure for high-efficiency nanobubble generation has been proposed. In this paper, the bubbly flow in the honeycomb structure was studied. The numerical simulations of honeycomb structure were performed by using a computational fluid dynamics–population balance model (CFD-PBM) coupled model. The numerical model was based on the Eulerian multiphase model and the population balance model (PBM) was used to calculate the gas bubble size distribution. The bubble coalescence and breakage were included. Considering the effect of bubble diameter on the fluid flow, the phase interactions were coupled with the PBM. The bubble size distributions in the honeycomb structure under different work conditions were predicted. The experimental results were compared with the simulation predictions.

Correlations in fertility across generations: can low fertility persist?

PubMed Central

Kolk, Martin; Cownden, Daniel; Enquist, Magnus

2014-01-01

Correlations in family size across generations could have a major influence on human population size in the future. Empirical studies have shown that the associations between the fertility of parents and the fertility of children are substantial and growing over time. Despite their potential long-term consequences, intergenerational fertility correlations have largely been ignored by researchers. We present a model of the fertility transition as a cultural process acting on new lifestyles associated with fertility. Differences in parental and social influences on the acquisition of these lifestyles result in intergenerational correlations in fertility. We show different scenarios for future population size based on models that disregard intergenerational correlations in fertility, models with fertility correlations and a single lifestyle, and models with fertility correlations and multiple lifestyles. We show that intergenerational fertility correlations will result in an increase in fertility over time. However, present low-fertility levels may persist if the rapid introduction of new cultural lifestyles continues into the future. PMID:24478294

The dark side of high-frequency oscillations in the developing brain.

PubMed

Le Van Quyen, Michel; Khalilov, Ilgam; Ben-Ari, Yehezkel

2006-07-01

Adult brain networks generate a wide range of oscillations. Some of these are behaviourally relevant, whereas others occur during seizures and other pathological conditions. This raises the question of how physiological oscillations differ from pathogenic ones. In this review, this issue is discussed from a developmental standpoint. Indeed, both epileptic and physiological high-frequency oscillations (HFOs) appear progressively during maturation, and it is therefore possible to determine how this program corresponds to maturation of the neuronal populations that generate these oscillations. We review here important differences in the development of neuronal populations that might contribute to their different oscillatory properties. In particular, at an early stage, the density of glutamatergic synapses is too low for physiological HFOs but an additional drive can be provided by excitatory GABA, triggering epileptic HFOs and the cascades involved in long-lasting epileptogenic transformations. This review is part of the INMED/TINS special issue "Nature and nurture in brain development and neurological disorders", based on presentations at the annual INMED/TINS symposium (http://inmednet.com/).

Intrinsically active and pacemaker neurons in pluripotent stem cell-derived neuronal populations.

PubMed

Illes, Sebastian; Jakab, Martin; Beyer, Felix; Gelfert, Renate; Couillard-Despres, Sébastien; Schnitzler, Alfons; Ritter, Markus; Aigner, Ludwig

2014-03-11

Neurons generated from pluripotent stem cells (PSCs) self-organize into functional neuronal assemblies in vitro, generating synchronous network activities. Intriguingly, PSC-derived neuronal assemblies develop spontaneous activities that are independent of external stimulation, suggesting the presence of thus far undetected intrinsically active neurons (IANs). Here, by using mouse embryonic stem cells, we provide evidence for the existence of IANs in PSC-neuronal networks based on extracellular multielectrode array and intracellular patch-clamp recordings. IANs remain active after pharmacological inhibition of fast synaptic communication and possess intrinsic mechanisms required for autonomous neuronal activity. PSC-derived IANs are functionally integrated in PSC-neuronal populations, contribute to synchronous network bursting, and exhibit pacemaker properties. The intrinsic activity and pacemaker properties of the neuronal subpopulation identified herein may be particularly relevant for interventions involving transplantation of neural tissues. IANs may be a key element in the regulation of the functional activity of grafted as well as preexisting host neuronal networks.

Intrinsically Active and Pacemaker Neurons in Pluripotent Stem Cell-Derived Neuronal Populations

PubMed Central

Illes, Sebastian; Jakab, Martin; Beyer, Felix; Gelfert, Renate; Couillard-Despres, Sébastien; Schnitzler, Alfons; Ritter, Markus; Aigner, Ludwig

2014-01-01

Summary Neurons generated from pluripotent stem cells (PSCs) self-organize into functional neuronal assemblies in vitro, generating synchronous network activities. Intriguingly, PSC-derived neuronal assemblies develop spontaneous activities that are independent of external stimulation, suggesting the presence of thus far undetected intrinsically active neurons (IANs). Here, by using mouse embryonic stem cells, we provide evidence for the existence of IANs in PSC-neuronal networks based on extracellular multielectrode array and intracellular patch-clamp recordings. IANs remain active after pharmacological inhibition of fast synaptic communication and possess intrinsic mechanisms required for autonomous neuronal activity. PSC-derived IANs are functionally integrated in PSC-neuronal populations, contribute to synchronous network bursting, and exhibit pacemaker properties. The intrinsic activity and pacemaker properties of the neuronal subpopulation identified herein may be particularly relevant for interventions involving transplantation of neural tissues. IANs may be a key element in the regulation of the functional activity of grafted as well as preexisting host neuronal networks. PMID:24672755

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

Background Selection in Partially Selfing Populations

PubMed Central

Roze, Denis

2016-01-01

Self-fertilizing species often present lower levels of neutral polymorphism than their outcrossing relatives. Indeed, selfing automatically increases the rate of coalescence per generation, but also enhances the effects of background selection and genetic hitchhiking by reducing the efficiency of recombination. Approximations for the effect of background selection in partially selfing populations have been derived previously, assuming tight linkage between deleterious alleles and neutral loci. However, loosely linked deleterious mutations may have important effects on neutral diversity in highly selfing populations. In this article, I use a general method based on multilocus population genetics theory to express the effect of a deleterious allele on diversity at a linked neutral locus in terms of moments of genetic associations between loci. Expressions for these genetic moments at equilibrium are then computed for arbitrary rates of selfing and recombination. An extrapolation of the results to the case where deleterious alleles segregate at multiple loci is checked using individual-based simulations. At high selfing rates, the tight linkage approximation underestimates the effect of background selection in genomes with moderate to high map length; however, another simple approximation can be obtained for this situation and provides accurate predictions as long as the deleterious mutation rate is not too high. PMID:27075726

First-Generation Women and Identity Intersectionality

ERIC Educational Resources Information Center

Kouzoukas, Georgia

2017-01-01

With a considerable focus to increase America's degree completion rates amongst our diverse population, higher education policymakers and researchers have examined the college access, persistence, and completion rates of first-generation students. However, minimal research has addressed the heterogeneous student population through a gendered or…

The impact of tourism on municipal solid waste generation: the case of Menorca Island (Spain).

PubMed

Mateu-Sbert, Josep; Ricci-Cabello, Ignacio; Villalonga-Olives, Ester; Cabeza-Irigoyen, Elena

2013-12-01

Tourism can sustain high levels of employment and income, but the sector is a source of environmental and health impacts. One of the most important is the generation of municipal solid waste (MSW). However, there is a lack of studies which quantify how much the tourist population engages in total MSW and separately collected recyclables. The aim of this paper is to estimate the impact of the tourist population on MSW, both total and separately collected, for the period 1998-2010, for the Mediterranean island of Menorca (Spain). We use dynamic regressions models, including data for monthly stocks of tourists. The results show that, on average, a 1% increase in the tourist population in Menorca causes an overall MSW increase of 0.282% and one more tourist in Menorca generates 1.31 kg day(-1) (while one more resident generates 1.48 kg day(-1)). This result could be useful to better estimate the seasonal population of different regions, since intrannual fluctuation of MSW is used as a proxy measure of actual population (the sum of residents and tourists). Moreover, an increase of 1% in the tourist population causes an increase of 0.232% in separately collected recyclables and an additional tourist generates 0.160 kg day(-1). One resident selectively collects on average 47.3% more than one tourist. These results can help in the planning of waste infrastructure and waste collection services in tourist areas. Copyright © 2013 Elsevier Ltd. All rights reserved.

A continuously growing web-based interface structure databank

NASA Astrophysics Data System (ADS)

Erwin, N. A.; Wang, E. I.; Osysko, A.; Warner, D. H.

2012-07-01

The macroscopic properties of materials can be significantly influenced by the presence of microscopic interfaces. The complexity of these interfaces coupled with the vast configurational space in which they reside has been a long-standing obstacle to the advancement of true bottom-up material behavior predictions. In this vein, atomistic simulations have proven to be a valuable tool for investigating interface behavior. However, before atomistic simulations can be utilized to model interface behavior, meaningful interface atomic structures must be generated. The generation of structures has historically been carried out disjointly by individual research groups, and thus, has constituted an overlap in effort across the broad research community. To address this overlap and to lower the barrier for new researchers to explore interface modeling, we introduce a web-based interface structure databank (www.isdb.cee.cornell.edu) where users can search, download and share interface structures. The databank is intended to grow via two mechanisms: (1) interface structure donations from individual research groups and (2) an automated structure generation algorithm which continuously creates equilibrium interface structures. In this paper, we describe the databank, the automated interface generation algorithm, and compare a subset of the autonomously generated structures to structures currently available in the literature. To date, the automated generation algorithm has been directed toward aluminum grain boundary structures, which can be compared with experimentally measured population densities of aluminum polycrystals.

Viewpoints of working sandwich generation women and occupational therapists on role balance strategies.

PubMed

Evans, Kiah L; Girdler, Sonya J; Falkmer, Torbjorn; Richmond, Janet E; Wagman, Petra; Millsteed, Jeannine; Falkmer, Marita

2017-09-01

Occupational therapists need to be cognizant of evidence-based role balance advice and strategies that women with multigenerational caring responsibilities can implement independently or with minimal assistance, as role balance may not be the primary goal during many encounters with this population. Hence, this study aimed to identify the viewpoints on the most helpful role balance strategies for working sandwich generation women, both from their own perspectives and from the perspective of occupational therapists. This was achieved through a Q methodology study, where 54 statements were based on findings from interviews, sandwich generation literature and occupational therapy literature. In total, 31 working sandwich generation women and 42 occupational therapists completed the Q sort through either online or paper administration. The data were analysed using factor analysis with varimax rotation and were interpreted through collaboration with experts in the field. The findings revealed similarities between working sandwich generation women and occupational therapists, particularly in terms of advocating strategies related to sleep, rest and seeking practical assistance from support networks. Differences were also present, with working sandwich generation women viewpoints tending to emphasize strategies related to coping with a busy lifestyle attending to multiple responsibilities. In contrast, occupational therapy viewpoints prioritized strategies related to the occupational therapy process, such as goal setting, activity focused interventions, monitoring progress and facilitating sustainable outcomes.