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637 results for “Population analysis”
Multi-Generational Black Hole Population Analysis with an Astrophysically Informed Mass Function
<p>We analyze the population statistics of black holes in the LIGO/Virgo/KAGRA GWTC-3 catalog using a parametric mass function derived from simulations of massive stars experiencing pulsational pair-instability supernovae (PPISN). Our formalism enables us to separate the black hole mass function into sub-populations corresponding to mergers between objects formed via different astrophysical pathways, allowing us to infer the properties of black holes formed from stellar collapse and black holes formed via prior mergers separately. Applying this formalism, we find that this model fits the data better than the powerlaw+peak model with Bayes factor 9.7±0.1. We measure the location of the lower edge of the upper black hole mass gap to be 84.05<sub>-12.88</sub><sup>+17.19</sup> M<sub>☉</sub>, providing evidence that the 35M<sub>☉</sub> Gaussian peak detected in the data using other models is not associated with the PPISN pile-up predicted to precede this gap. Incorporating spin, we find that the normalized spins of stellar remnant black holes are close to zero while those of higher generation black holes tend to larger values. All of these results are in accordance with the predictions of stellar structure theory and black hole merger scenarios. Finally, we combine our mass function with the spectral siren method for measuring the Hubble constant to find H₀=36.19<sub>-10.91</sub><sup>+17.50</sup> km/s/Mpc and discuss potential explanations of this low value. Our results demonstrate how astrophysically-informed mass functions can facilitate the interpretation of gravitational wave catalog data to provide information about black hole formation and cosmology. Future data releases will improve the precision of our measurements.</p>
Fig. 2 in Repeatability Analysis Of Egg Shape In A Wild Tree Sparrow (Passer Montanus) Population: A Sensitive Method For Egg Shape Description
Fig. 2. Data collecting method results in 22 co-ordinates of each eggs
Fig. 1 in Repeatability Analysis Of Egg Shape In A Wild Tree Sparrow (Passer Montanus) Population: A Sensitive Method For Egg Shape Description
Fig. 1. Differently shaped eggs characterised with the same egg shape index (ES = 0.7)
Figure 2 in Comparative analysis of brain in relation to the body length and weight of common carp (Cyprinus carpio) in captive (hatchery) and wild (river system) populations
Figure 2. brain of common carps in wild environment.
Figure 1 in Comparative analysis of brain in relation to the body length and weight of common carp (Cyprinus carpio) in captive (hatchery) and wild (river system) populations
Figure 1. brain of common carps in captive environment.
Dataset of the Volkswagen Fond Project no. 90 216 " Early mounted nomads and their vessels Ceramic analysis project aimed at supporting the reconstruction of socio-economic conditions in mobile populations north of the Black Sea between 1100 and 600 BC"
<p>The Excel-Sheet contains information (location of the site, chronological position, type of site, archaeological culture, literature, photographies and drawings, analysis made, results of the analysis, etc.) about the samples taken in the Volkswagen Fond Project no. 90 216 "Early mounted nomads and their vessels Ceramic analysis project aimed at supporting the reconstruction of socio-economic conditions in mobile populations north of the Black Sea between 1100 and 600 BC".</p> <p>The project itself focuses on contacts and interactions between groups with different material culture remains in two vegetation zones to the north of the Black Sea.The investigation takes a complex archaeometric approach to characterise the pottery of communities that lived in the forest steppe zone and steppe zone to the north of the Black Sea between the Dniester and Dnieper rivers between 1100 and 600 BC. By using an multidisciplinary approach to study the material culture of these communities with mobile lifeways, this project will allow the comparison of the natural science and archaeological data for the first time.</p> <p>The Excel-Sheet presents the results of various analyses performed during the project and serves as the database for publications of the project members.</p>
Fig. 4 in Population analysis of white grubs (Coleoptera: Melolonthidae) throughout the Brazilian Pampa biome
Fig. 4. Melolonthidae species and number of locations that each species was found.
Silva, Harder et al. Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history Data
<p>Dataset used in the "Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history" paper by Silva, Harder et al.</p> <p>This dataset includes Fasta files for Simulated dataset and VCF files for both Empirical and Simulated datasets.</p>
Vortex input files -- Linking habitat and population viability analysis models of a metapopulation of Florida scrub-jays
<p>Vortex input files for manuscript "<span>Linking </span><span><span>habitat and population viability analysis models to account for <span>vegetation dynamics, habitat fragmentation, and social behavior of a metapopulation of Florida scrub-jays</span></span></span>" by R. C. Lacy, D. B. Breininger, et al. </p>
A Modeling Framework for Near-Road Population Exposure to Traffic-Related PM2.5 and Environmental Equity Analysis: A Case Study in Atlanta, Georgia
<p>This is the dataset for the NCST project <em>"A Modeling Framework for Near-Road Population Exposure to Traffic-Related PM2.5 and Environmental Equity Analysis: A Case Study in Atlanta, Georgia"</em> by the Georgia Tech research team.</p> <p> </p> <p>Here is the abstract of the research: </p> <p>In this study, a modeling framework for population exposure to traffic-related PM2.5 with high spatiotemporal resolution is proposed and applied to the I-575/I-75 Northwest Corridor (NWC) in Atlanta, GA, for environmental equity analysis. The analyses retrieved trip data from the Atlanta Regional Commission’s (ARC) Activity-Based Model 2020 (ABM2020), after implementing path retention algorithms (Zhao, et al., 2019) to generate individual travel paths for more than 20 million predicted vehicle trips. Emission rates for each link were retrieved from MOVES-Matrix given the ABM link speed and facility type, the ARC’s county-level fleet composition data, and regional fuel properties and I&M program parameters. High-resolution downwind concentration profiles were predicted using EPA’s AERMOD microscale dispersion model with AERMET meteorology profiles for a huge array of receptors. Trip-end locations were derived from the ABM trip data, and the on-road trajectories for each person-trip (vehicle trace data) were derived from the travel paths through network. ABM synthetic household and person data were used in demographic assessment, and linked to representative household latitude and longitude locations in the Epsilon 2019 household demographic dataset. Individual exposure to traffic-related PM2.5 in time and space (average hourly concentration) was assessed by overlaying the second-by-second person location profiles (for 24 hours) against the hourly predicted PM2.5 concentration profiles. The analyses summarize the results across 16 demographic groups and the aggregate population exposure are compared to assess potential impact differences across demographics. High-income households in the corridor were exposed to less traffic-related air pollution as they tended to live further from the freeways. The analyses did not reveal large disproportionate negative impacts on low income groups along this specific corridor, but lager disproportionate negative impacts are expected elsewhere in the metro area due to the spatial clustering of income groups along other corridors. Overall, the research demonstrates the applicability of the modeling framework and describes how the various elements (e.g., link screening, dispersion modeling, path tracing, etc.) are optimized on the supercomputing cluster.</p>
pgHMA: Application of the Heteroduplex mobility assay analysis in phylogenetics and population genetics
<p><span><span><span><span><span><span><span><span><span><span><span>The Heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for phylogenetics and population genetic analyses (pgHMA). We show how commonly applied techniques in phylogenetics and population genetics have equivalents with pgHMA: phylogenetic reconstruction with bootstrapping, skyline plots, and mismatch distribution analysis. We assess the performance and accuracy of pgHMA by comparing the results obtained against those obtained using standard methods of analyses applied to sequencing data. The resulting comparisons demonstrate that: (1) there is a significant linear relationship (R = 0.992) between heteroduplex mobility and genetic distance; (2) phylogenetic trees obtained by HMA and nucleotide sequences present nearly identical topologies; (3) clades with high pgHMA parametric bootstrap support also have high bootstrap support on nucleotide phylogenies; (4) skyline plots estimated from the UPGMA trees of HMA and Bayesian trees of nucleotide data reveal similar trends, especially for the median trend estimate of effective population size; and (5) optimized mismatch distributions of HMA are closely fitted to the mismatch distributions of nucleotide sequences. In summary, pgHMA is an easily-applied method for approximating phylogenetic diversity and population trends.</span></span></span></span></span></span></span></span></span></span></span></p>
Grey model analysis of vehicle population, road transport energy consumption, and vehicular emissions
<p>The files provide additional information to the paper “Grey model analysis of vehicle population, road transport energy consumption, and vehicular emissions". The supporting data file contains excel sheets of data used in the analysis, and the supporting information file provides some assumptions, background information and other results not included in the paper</p>
Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
<p><span>Recently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (<em>Galemys</em> <em>pyrenaicus</em>). For this, we used the ddRADseq technique, which generated 1,421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research.</span></p>
Antibiotic versus surgery in the treatment of acute appendicitis in the pregnant population: A systematic review and meta-analysis
<p>Antibiotic versus surgery in the treatment of acute appendicitis in the pregnant population: A systematic review and meta-analysis</p>
Survival analysis after vertebral compression fractures in population over 65 years old
<p><strong>Background: </strong>Mortality in vertebral compression fractures (VCF) is rarely directly associated with the fracture. Lower mortality has been demonstrated when fractures are treated surgically (vertebral augmentation) versus conservatively. However, the exact mechanism that justifies this increased survival is unknown. This study aims to analyze overall survival in elderly patients who have suffered a non-pathological VCF, its causes, and the relationship with different factors.</p> <p><strong>Methods: </strong>All patients over 65 years old diagnosed with acute, non-pathologic thoracic or lumbar VCF, treated consecutively in our center from January 2017 to December 2020, were retrospectively selected for analysis. Those patients with follow-ups under two years or who required arthrodesis due to poor fracture evolution were excluded. Only the first process was considered for patients who presented a second VCF in the first three months.</p> <p><strong>Results: </strong>A total of 509 consecutive fractures were registered. Seventeen were excluded, leaving 492 cases for final analysis. The mean age was 78.9 years old. Overall mortality was 36.2%. Survival rate at 1-, 12-, 24-, 48-, and 60-month follow-up was 97.4%, 86.6%, 78.0%, 64.4%, and 59.4%, respectively. The independent factors associated with a higher mortality risk were age, male, oncologic history, non-traumatic mechanism, and co-morbidity during hospitalization. No statistical differences were found when comparing the two survival curves by treatment (vertebral augmentation vs. conservative management) over time. No benefit was observed in those patients with comprehensive outpatient geriatric care. </p> <p><strong>Conclusion: </strong>Age, male sex, history of oncological disease, non-traumatic mechanism of the fracture, and any comorbidity during hospitalization were identified as variables independently associated with a higher risk of mortality following a VCF in the elderly. Vertebral augmentation and comprehensive outpatient geriatric care showed no benefit in overall survival.</p>
Effects of global change on bird and beetle populations in boreal forest landscape: an assemblage dissimilarity analysis
Aim <p>Despite an increasing number of studies highlighting the impacts of climate change on boreal species, the main factors that will drive changes in species assemblages remain ambiguous. We study how species community composition would change following anthropogenic and natural disturbances. We determine the main drivers of assemblage dissimilarity for bird and beetle communities.</p> Location <p>Côte-Nord, Québec, Canada.</p> Methods <p>We quantify two climate-induced pathways based on direct and indirect effects on species occurrence under different harvest management scenarios. The direct climate effects illustrate the impact of climate variables while the indirect effects are reflected through habitat-based climate change. We develop empirical models to predict the distribution of more than 100 species over the next century. We analyze the regional and the latitudinal species assemblage dissimilarity by decomposing it into<em> </em>'balanced variation in species occupancy and occurrence' and 'occupancy and occurrence gradient'. </p> Results <p>Both pathways increased dissimilarity in species assemblage. At the regional scale, both effects have an impact on decreasing the number of winning species. Yet, responses are much larger in magnitude under mixed climate effects (a mixture of direct and indirect effects). Regional assemblage dissimilarity reached 0.77 and 0.69 under mixed effects versus 0.09 and 0.10 under indirect effects for beetles and birds, respectively, between RCP8.5 and baseline climate scenarios when considering harvesting. Latitudinally, assemblage dissimilarity increased following the climate conditions pattern. </p> Main conclusions <p>The two pathways are complementary and alter biodiversity, mainly caused by species turnover. Yet, responses are much larger in magnitude under mixed climate effects. Therefore, the inclusion of climatic variables considers aspects other than just those related to forest landscapes, such as life cycles of animal species. Moreover, we expect differences in occupancy between the two studied taxa. This could indicate the potential range of change in boreal species concerning novel environmental conditions.</p>
Data from: Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in sage grouse Centrocercus urophasianus
<p><span>Sex ratio, and the extent to which it varies over time, is an important factor in the demography, management, and conservation of wildlife populations. We estimated pre-breeding sex ratio of greater sage-grouse (Centrocercus urophasianus) in a peripheral, geographically isolated population in northwestern Colorado during two consecutive winters using closed-population, robust-design, multi-state, genetic mark-recapture models in program MARK (White and Burnham 1999). This data release includes the data files (.inp format) used in those models, as described in Shyvers et al. 2023. The data include capture histories and auxiliary data for individual greater sage-grouse collected during two study seasons: Season 1 (winter 2012-2013) and Season 2 (winter 2013-2014) and are readable using program MARK or notepad. Each data row includes the unique bird identification number (GMR-ID); the bird's encounter history for n= sampling occasions coded as a static state (M = male, F = female); the group ID; and a region covariate (0 = North, 1 = South). The data were adapted from those originally developed for Shyvers et al. 2020 and applied using Closed Robust Design Multi-state (CRDMS) Huggins' p and c w/state probabilities in program MARK to obtain estimates of Omega, enabling estimation of sex ratio with associated confidence intervals (see Shyvers et al. 2023).</span></p> <p>References:</p> <p>Shyvers, J.E., Walker, B.L., Oyler-McCance, S.J., Fike, J.A. and Noon, B.R. 2023. Genetic mark-recapture analysis reveals large annual variation in pre-breeding sex ratio of greater sage-grouse. Wildlife Biology (https://doi.org/10.1002/wlb3.01085)</p> <p>Shyvers, J.E., Walker, B.L., Oyler‐McCance, S.J., Fike, J.A. and Noon, B.R., 2020. Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in Sage Grouse Centrocercus urophasianus. Ibis, 162(3), pp.749-765.</p> <p>White, G. C., and K. P. Burnham. 1999. Program Mark: survival estimation from populations of marked animals. – Bird Study 46:120–139.</p>
Axiom canine microarray data from Australian dingoes and domestic dogs for admixture and population structure analysis
<p>Admixture between species is a cause for concern in wildlife management. Canids are particularly vulnerable to inter-specific hybridisation, and genetic admixture has shaped their evolutionary history. Microsatellite DNA testing, relying on a small number of genetic markers and geographically restricted reference populations, has identified extensive domestic dog admixture in Australian dingoes and driven conservation management policy. There has been concern that geographic variation in dingo genotypes could confound ancestry analyses that use a small number of genetic markers. Here we apply genome-wide single nucleotide polymorphism (SNP) genotyping to a set of 385 wild and captive dingoes from across Australia and then carry out comparisons to domestic dogs, and perform ancestry modelling and biogeographic analyses to characterize population structure in dingoes and investigate the extent of admixture between dingoes and dogs in different regions of the continent. We show that there are at least five distinct dingo populations across Australia. We observed limited evidence of dog admixture in wild dingoes, challenging previous reports regarding the occurrence and extent of dog admixture in dingoes, as our ancestry analyses show that previous assessments severely overestimate the degree of domestic dog admixture in dingo populations, particularly in southeastern Australia. These findings strongly support the use of genome-wide SNP genotyping as a refined method for wildlife managers and policy makers to assess and inform dingo management policy and legislation moving forwards.</p>
Sources of coaster brook trout (Salvelinus fontinalis) revealed by genomic analysis of brook trout populations along Minnesota's shoreline with Lake Superior
<p>Knowledge of population-level relationships and how these relationships pertain to different life history forms is critical to developing effective management plans for native trout, char, and salmon. In the Lake Superior basin, identifying effective restoration strategies for coaster brook trout (<em>Salvelinus</em> <em>fontinalis</em>), a lake-inhabiting form of brook trout, is hampered by limited information on genetic connectivity and source-sink dynamics among brook trout populations. Here, we infer these relationships by surveying 8,178 single nucleotide polymorphisms in 234 brook trout from seven rivers along the Minnesota shoreline with Lake Superior, including from reaches above and below natural waterfalls that prevent upstream movement. We identified well-differentiated above-barrier populations that supply brook trout to below-barrier reaches. We also compared within-river brook trout to 26 coaster brook trout from Lake Superior. We identified at least four source populations for these coaster brook trout, three of which were located within rivers. Additionally, we estimated N<sub>E</sub> for within-river populations and detected a decline across recent generations, with the most recent estimates approaching critical thresholds. Finally, comparisons with 94 domestic brook trout representing nine hatchery strains revealed a lack of domestic introgression into wild populations, demonstrating the importance of natural reproduction to population persistence. Our results offer novel insights into sources of coaster brook trout and highlight the role of within-river populations in supporting the coaster life history. Management efforts focused on instream restoration may be more important to rehabilitating coaster brook trout than previously thought, and are urgently needed given the population-level conservation status reported here.</p>
Population genomic analysis of an emerging pathogen Lonsdalea quercina affecting various species of oaks in western North America
<p>Previously unrecognized diseases continue to threaten the health of forest ecosystems globally. Understanding processes leading to disease emergence is important for effective disease management and prevention of future epidemics. Utilizing whole genome sequencing, we studied the phylogenetic relationship and within diversity of two populations of the bacterial oak pathogen <em>Lonsdalea</em> <em>quercina</em> from western North America (Colorado and California) and compared these populations to other <em>Lonsdalea</em> species found worldwide. Phylogenetic analysis separated Colorado and California populations into two well-supported clades within the genus <em>Lonsdalea</em>, with an average nucleotide identity between them near species boundaries (95.31%) for bacteria, suggesting long isolation. Populations comprise distinct patterns in genetic structure and distribution. Genotypes collected from different host species and habitats were randomly distributed within the California cluster, while most Colorado isolates from introduced planted trees were distinct from isolates collected from a natural stand of CO native <em>Q. gambelii,</em> indicating the presence of cryptic population structure. The distribution of clones in California varied, while Colorado clones were always collected from neighboring trees. Despite its recent emergence, the Colorado population had higher nucleotide diversity, possibly due to migrants moving with nursery stock. Overall results suggest independent pathogen emergence in two states likely driven by changes in host-microbe interactions due to ecosystem conditions changing. To our knowledge, this is the first study on <em>L. quercina</em> population structure. Further studies are warranted to understand evolutionary relationships among <em>L. quercina</em> populations from different areas, including the native habitat of red oak in northeastern USA.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.