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3,584 results for “population studies”
Aquatic Vertebrate Population Study in Mack Creek, Andrews Experimental Forest, 1987 to present
Populations of Coastal Cutthroat trout (Oncorhynchus clarkii clarkii) in two standard reaches of Mack Creek in the H.J. Andrews Experimental Forest have been monitored since 1987. Monitoring of Coastal Giant Salamanders, Dicamptodon tenebrosus began in 1993. The two standard reaches are in a section of clearcut forest (ca. 1963) and an upstream 500 year old coniferous forest. Sub-reaches are sampled with 2-pass electrofishing, and all captured vertebrates are measured and weighed. Additionally, a set of channel measurements are taken with each sampling. This study constitutes one of the longest continuous records of salmonid populations on record.
Long-term (1935-2019) tree population data from remeasurements of a large network of permanent study plots in old-growth forest, Dukes Research Natural Area, Marquette Co., MI, USA
The Dukes Research Natural Area (Hiawatha National Forest, Marquette Co., MI) amounts to ca. 100 ha of minimally disturbed original forests, including a mix of mesic 'hemlock-northern hardwood' types and peaty wetlands dominated by several species of swamp conifers and black ash (Fraxinus nigra). The RNA hosts a regular grid of 250 0.2-acre (~0.08 ha) permanent monitoring (CFI) plots. This package includes tree censuses for subsets of CFI plots conducted in 1935, 1948, and 1974-1980, and repeated censuses with mapped stems from 1989 to 2019. This 84-year record constitutes one of the longest repeated-measurement, permanent-plot data-sets for old-growth temperate forest.
Variation and overlaps in non-breeding regions of three less-studied breeding populations of the Eurasian Reed Warbler: Figures and datasheet
<p>Non-breeding regions of Eurasian Reed Warbler, <em>Acrocephalus scirpaceus</em> breeding in Finland, Jordan, and Kazakhstan as predicted with hydrogen stable isotope analysis.</p> <p>file name corresponds to the following figure titles:</p> <p>"Fig 2": <strong><span>Figure 2:</span></strong><span> The predicted non-breeding regions of Eurasian Reed Warblers breeding in Finland, Jordan, and Kazakhstan.</span></p> <p><span><span>"Fig 3": <strong><span>Figure </span></strong><span>3: Predicted non-breeding regions for Eurasian Reed Warblers sampled at a breeding site in Finland assigned to isotopic clusters A and </span><span><span>B.</span></span></span></span></p> <p><span><span></span></span><span></span><span><span><span>"Fig 4": </span></span></span><strong><span>Figure 4:</span></strong><span> Predicted within population average non-breeding regions for Eurasian Reed Warblers assigned to clusters A-F breeding in Jordan </span><span>(see Table S1 for details).</span></p> <p><span>Also uploaded is a csv file containing the isotopic signature of the birds. The file name is "data_Acrocephalus_scirpaceus"</span></p>
Long-Term Studies of Huron Mountain Club Small Mammal Populations
These datasets include small mammal population data collected by Richard Manville (1940-1942), Phillip Myers (2003), and Allison Poor (2004-2005). Small mammal traps were initially placed in 8 locations throughout the Huron Mountains in Michigan's Upper Peninsula from 1940-1942 by Richard Manville. Small mammals present in the traps were recorded once each year and twice in 1941. This study was repeated by Phillip Myers and Allison Poor from 2003-2005.
Summer 2007 crab population survey based on crab hole counts in fifty-four GCE LTER Hammock sites and four GCE LTER study sites
Crab abundance was investigated at fifty-four hammock sampling sites and four Georgia Coastal Ecosystems (GCE) LTER study sites in June-July 2007 by counting crab holes as a proxy measurement. Each hammock site had six permanent study plots which were previously laid out. Crab holes were counted within a random location inside those six plots at each hammock. Crab holes were counted within a 625 cm^2 area and species were not differentiated in the count, but noted. This method estimates total crab abundance in each study site.
Population Study of Geukensia demissa and Ilyanassa obsoleta at the Georgia Coastal Ecosystems LTER site in April 2008
During the dates of April 21-April 23, 2008, we conducted surveys to determine the relative abundance of ribbed mussels (Geukensia demissa) and mud snails (Ilyanassa obsoleta) across Spartina height zones. Surveys were performed at each of the GCE long term sites (GCE1-GCE10) and were comprised of transect and quadrat sampling methods. Quadrats measured 25 cm^2 for mud snails and 1 m^2 for ribbed mussels. Ribbed mussel surveys consisted of both transect and quadrat methods. For ribbed mussels, a total of 10 quadrats were randomly placed in tall-, mid-, and short-form Spartina and number of visible mussels counted. Transects for ribbed mussels measured 50 m x 2 m and were performed in intermediate- and short-form Spartina zones. In each transect, we counted observed number of mussel clumps per transect. For mud snails, a total of 10 quadrats were randomly placed in tall- and intermediate-form Spartina and on mud banks (2 m from Spartina edge along the creek bank) and total number of individuals per quadrat were counted.
General practice characteristics associated with life expectancy of practice populations: a cross-sectional study
<p>The dataset was used to investgate features of general practice associated with life expectancy of general practice populations in England for the period 2015-2019.</p>
Phenome-wide association studies across large population cohorts support drug target validation
<p>Summary-level data generated by Genomics plc as presented in:<br> Diogo, D. et al. Phenome-wide association studies across large population cohorts support drug target validation. Nat. Commun. 9, 4285 (2018). https://doi.org/10.1038/s41467-018-06540-3</p> <p>If you have any questions or comments regarding these files, please contact Genomics plc at <a href="mailto:research@genomicsplc.com">research@genomicsplc.com</a></p> <p>NOTES<br> -----------------------------<br> These analyses were carried out using the interim UK Biobank imputation data release. Analyses were restricted to a subset of "white-British" unrelated samples with a maximum sample size of 112,337 individuals. </p> <p>Case control phenotypes were defined based on categorical datafields as listed in the accompanying file. <br> Quantitative phenotypes were either rank-normalised before analysis, or beta/se values were standardised after analysis using the variance of the phenotype. The normalisation value is indicated in the accompanying file.<br> <br> All analyses included Age at assessment, sex, genotyping chip, and 10 principal components as covariates. </p> <p>We used plink1.9 linear/logistic regression as appropriate. For chromosome X variants males were treated as having 0 or 2 alternative alleles. </p> <p>The results are not adjusted for genomic control.</p> <p>DATA FILE CONTENT DESCRIPTION<br> -----------------------------<br> CHR - Chromosome<br> SNP - Variant rsID<br> ALT - Alternative allele (effect allele)<br> REF - Reference Allele (non-effect allele)<br> BP - Position in base pairs (b37, 1-based)<br> NMISS - Number of samples with non-missing genotypes<br> BETA - Effect size (log odds ratio or standardised effect size)<br> SE - Standard error<br> P - P-value<br> F_MISS - genotype missing rate<br> P_hwe - Hardy-weinberg p-value<br> MAF - ALT allele frequency</p>
Incidences of community onset severe sepsis, Sepsis-3 sepsis, and bacteremia in Sweden – a prospective population-based study.
<p>Sepsis epidemiology study 2011-2012 Sweden</p> <p>Ljungström, Lars; Andersson, Rune; Jacobsson, Gunnar</p> <p> </p> <p>Data collected during the prospective "Sepsis Skaraborg study" performed 2011-2012 in the western region of Sweden. Adult patients admitted to the emergency department for suspicion of a community-onset sepsis were evaluated. The study was approved by the Regional Ethical Review Board of Gothenburg (376-11). The file includes data for patient characteristics, vital signs, biomarker measurements, cases of bacteremia, and patient classifications using Sepsis-2 and Sepsis-3 criteria.</p>
First Study of the Supernova Remnant Population in the Large Magellanic Cloud with eROSITA
<p>Aims. The all-sky survey carried out by the extended Roentgen Survey with an Imaging Telescope Array (eROSITA) on board Spektrum-Roentgen-Gamma (Spektr-RG, SRG) has provided us with spatially and spectrally resolved X-ray data of the entire Large Magellanic Cloud (LMC) and its immediate surroundings in the soft X-ray band down to 0.2 keV with an average angular resolution</p> <p>of 26′′ in the field of view. In this work, we have studied the supernova remnants (SNRs) and candidates in the LMC using data from the first four all-sky surveys (eRASS:4). From the X-ray data in combination with results at other wavelengths, we obtain information about the SNRs, their progenitors, and the surrounding interstellar medium (ISM). The study of the entire population of SNRs in a galaxy helps us to understand the underlying stellar populations, the environments, in which the SNRs are evolving, and the stellar feedback on the ISM.</p> <p>Methods. The eROSITA telescopes are the best instruments currently available for the study of extended soft sources like SNRs in an entire galaxy due to their large field of view and high sensitivity in the softer part of the X-ray band. We applied the Gaussian gradient magnitude (GGM) filter to the eROSITA images of the LMC to highlight the edges of the shocked gas in order to find new SNRs. We visually compared the X-ray images with those of their optical and radio counterparts to investigate the true nature of the extended emission. The X-ray emission is evaluated using the contours with respect to the background, while for the optical we used line ratio</p> <p>diagnostics, and non-thermal emission in the radio images. We used the Magellanic Cloud Emission Line Survey (MCELS) for the optical data. For the radio comparison, we used data from the Australian Square Kilometre Array Pathfinder (ASKAP) survey of the LMC. Using the star formation history (SFH) derived from the near-IR photometry of the VISTA survey of the Magellanic Clouds (VMC) we have investigated the possible progenitor type of the new SNRs and SNR candidates in our sample. Results. We present the most updated catalogue of SNRs in the LMC. Previously known SNRs and candidates were detected with 1σ significance down to a surface brightness of Σ [0.2–5.0 keV] = 3.0 × 10−15 erg s−1 cm−2 arcmin−2 and were examined. The eROSITA data have allowed us to confirm one of the previous candidates as an SNR. We confirm three newly detected extended sources as new SNRs, while we propose 13 extended sources as new X-ray SNR candidates. We also present the analysis of the follow-up</p> <p>XMM-Newton observation of MCSNR J0456–6533 discovered with eROSITA. Among the new candidates, we propose J0614–7251 (4eRASSU J061438.1−725112) as the first X-ray SNR candidate in the outskirts of the LMC.</p>
GWAS to single cell: Intersecting single-cell transcriptomics and genome wide association studies identifies crucial cell-populations and candidate genes for atherosclerosis.
<p><strong>Background</strong></p> <p>Genome-wide association studies (GWAS) have discovered hundreds of common genetic variants for atherosclerotic disease and cardiovascular risk factors. The translation of susceptibility loci into biological mechanisms and targets for drug discovery remains challenging. Intersecting genetic and gene expression data has led to identification of candidate genes. However, the assayed tissues are often non-diseased and heterogeneous in cell composition confounding the candidate prioritization. We collected single-cell transcriptomics (scRNA-seq) from atherosclerotic plaques and aimed to identify cell-type-specific expression of disease-associated genes. </p> <p> </p> <p><strong>Methods and Results</strong></p> <p>To identify disease-associated candidate genes, we applied gene-based analyses using GWAS summary statistics from 46 atherosclerotic, cardiometabolic, and other traits. Next we intersected these candidates with single-cell transcriptomics (scRNA-seq) to identify those genes that are specifically expressed in individual cell (sub)populations of atherosclerotic plaques. We derive an enrichment score and show that loci that associated with coronary artery disease demonstrated a prominent substrate in plaque smooth muscle cells (<em>SKI</em>, <em>KANK2</em>, <em>SORT1</em>), endothelial cells (<em>SLC44A1</em>, <em>ATP2B1</em>), and macrophages (<em>APOE</em>, <em>HNRNPUL1</em>). Further sub clustering of SMC-subtypes revealed genes in risk loci for coronary calcification specifically enriched in a synthetic cluster of SMCs. To verify the robustness of our approach, we used liver-derived scRNAseq-data and showed enrichment of circulating lipids-associated loci in hepatocytes.</p> <p><br> <strong>Conclusion</strong></p> <p>We confirm known gene-cell pairs relevant for atherosclerotic disease, and discovered novel pairs pointing to new biological mechanisms amenable for therapy. We present an intuitive single-cell transcriptomics driven workflow rooted in human large-scale genetic studies to identify putative candidate genes and affected cells associated with cardiovascular traits.</p> <p> </p>
Population-level health and economic impacts of introducing Vaccae vaccination in China: A modeling study
<p>Supplementary to "Population-level health and economic impacts of introducing Vaccae vaccination in China: A modeling study"</p>
State of the art of studies on earthworm populations in the state of Paraná
<p>In this review, we included all the studies performed in the state of Paraná, Brazil, which had data on earthworms. We reviewed the literature for all publications (journal articles, dissertations, theses, conference proceedings, book chapters) carried out in the state of Paraná, Brazil, which had data on earthworms. The period evaluated ranged from 1986 (earliest date in the state) to 2020. Searches were performed in online databases including Sicence Direct, Scielo, CAPES and the digital collection of dissertations and theses from Brazilian Universities (BDTD). </p> <p>Overall 51 publications had earthworm data, including abundance, biomass, species, richness or just presence/absence. Data were extracted from these publications and compiled into an excel file. The dataset contains information gathered from 62 of the 399 municipalities in Paraná, and includes separation in ten geopolitical regions (IBGE 2010), as well as topographic regions and climate (Köppen, 1931). The ten geopolitical mesoregions are: West (WE), Northwest (NW), Center West (CW), Center North (CN), North Pioneer (NP), Center East (CE), Metropolitan (MT), Center South (CS), Southeast (SE) and Southwest (SW). The three topographic regions include the First, Second and Third Plateaus, and the Coastal Lowland. </p> <p>Earthworm data are presented as total abundance (number of individual m<sup>-2</sup>), fresh biomass (in g m<sup>-2</sup>) and species richness (total number). We also provide information on each species encountered, its ecological category, and whether it is native or exotic to the state of Paraná. For earthworm species, ecological category information follows the classification of Bouché (1977), including the intermediate categories: e.g., anecic, epigeic, endogeic, polyhumic endogeic, mesohumic endogeic, epi-endogeic, endo-epigeic. For each species, full names (when available), and species author(s) and year of the description are provided.</p> <p>Geographic location is provided when possible, with latitude, longitude and altitude, soil types according to the Sistema Brasileiro de Classificação de Solos - SiBCS (Santos et al. 2018). Sampling date and season are also provided, when available.</p> <p>When known, the sampling method(s) used were given. These included quantitative methods involving handsorting, such as 1) the standard Tropical Soil Biology and Fertility (TSBF) Programme method (Anderson & Ingram 1993), in which soils are handsorted from monoliths 25x25 cm square to depths ranging from 10 to 40 cm (identified as TSBF in the spreadsheets); or 2) other monolith dimensions like 20x20, 40x40 and 50x50 cm (identified as Handsorting in the spreadsheets). Qualitative sampling (e.g. Bartz et al. 2014) included: 1) collecting in various niches like deeper soil layers, litter, under rocks, in and under rotting logs, next to water bodies like streams, lakes and swamps; 2) chemical extraction using a diluted formalin solution (usually over an area 50x50 cm), following recommendations of ISO 23611-1 (2017), and pouring of the solution either on the soil surface, or at the bottom of the pit; 3) electrical extraction using a modifed apparatus (Azevedo et al. 2010), based on the Octet-Method (Thielemann 1986).</p> <p>The determination of LUS was based on Nadolny et al. (2020), which characterized Native Vegetation, Forest Plantation (including forest with <em>Pinus</em> sp. and <em>Eucalyptus</em> sp.), Pasture, Integrated Systems (e.g., agropastoral, silvopastoral or agrosilvopastoral systems) and agricultural areas (Conventional Tillage, No-Tillage and Minimum Tillage). In addition to these, Perennial Crops, Grass Lawns and Agroforestry Systems were included.</p> <p>The soil chemical and physical analysis data were included in the dataset when performed in the same places as the earthworm sampling. Chemical data included: pH, H+Al, K, Ca, Mg, P, C, sum of Bases, CEC, Base saturation, N, Na. Physical data included: sand, clay and silt proportions, texture, porosity, density and resistance to penetration.</p> <p>All data are provided in excel format and include 5 tabs: Readme, Legend, Earthworms + environment, Species distribution and References. The Readme tab provides information on the associated publication in the Revista Brasileira de Ciência do Solo authored by Dudas et al. (see https://doi.org/10.36783/18069657rbcs20220159). The Legend tab provides a description of the variables used in the other (data) tabs. Earthworms + environment has information on the sampling methods used, the earthworm abundance, biomass and richness found at the different sampling sites in Paraná, and the data on soil and environmental variables. The Species distribution tab provides information on the species found, places of origin, ecological category, sampling method used and LUS. The References tab provides detailed bibliographic information on the sources of the data used to build the tables and the dataset.</p> <p>Overall, in the state of Paraná, 90 species of earthworms were found in 51 counties of the state, of which 66 were native and 24 were exotic. A large number of species (46) are likely new and still must be formally described. Higher species richness was found in native vegetation, which also had a higher proportion of native species (75%). The other LUS with more native species were: Forest Plantation (FP) and No-Tillage (NT), while Conventional Tillage (CT) sites had only 17% native species. Earthworm abundance and biomass were highest in less disturbed LUS such as agroforestry systems, native vegetation, forestry plantation,<br> grass lawns, and permanent crops, compared to the highest disturbance LUS including soil preparation (MT and CT), where the lowest abundance and biomass were found. However, as only 16% of the 399 counties in Paraná have been sampled so far, much further research is needed in order to adequately assess the relationships between earthworms and land use. </p>
Population pharmacokinetic studies of critically ill adults receiving beta-lactam antimicrobials: covariate dataset
<p>A dataset of reported covariates from a systematic review of population pharmacokinetic studies of critically ill adults receiving beta-lactam antimicrobials, including R script of statistical and graphical analyses</p>
A scalable, accurate, and universal analysis framework using individual-level allele frequency for large-scale genetic association studies in an admixed population
<p>Inclusion of individuals with diverse or admixed genetic ancestries is crucial to discover novel findings that may be missed by genomics analyses rooted solely in Caucasian population. Here, we present an analysis framework, SPAmix, which is scalable to a large-scale biobank data analysis including hundreds of thousands of admixed individuals and is universally applicable to various types of complex traits including binary trait, quantitative trait, time-to-event trait, longitudinal traits, etc. For each genetic variant, SPAmix uses genotype data and genetic principal components (PCs) to estimate individual-level allele frequency, which is subsequently used to calibrate p values via a retrospective analysis. A hybrid strategy including saddlepoint approximation (SPA) can greatly increase the accuracy to analyze rare genetic variants, especially if the phenotypic distribution is unbalanced or extremely unbalanced. Compared to Tractor, SPAmix does not require local ancestry information and can be straightforwardly applicable to a multi-way admixed population. Meanwhile, SPAmix can also be extended to SPAmix<sub>local</sub> in which the local ancestry can be incorporated if available. In addition, we propose SPAmix<sub>CCT</sub> to combine the p values of SPAmix and SPAmix<sub>local</sub> via Cauchy combination (CCT). SPAmix<sub>local</sub> performs close to Tractor when analyzing quantitative traits and is more accurate when analyzing binary traits with an unbalanced case-control ratio. And SPAmix<sub>CCT </sub>is an optimal unified approach for various cross-ancestry genetic architectures. Extensive simulation studies and real data analyses of 369,314 UK Biobank individuals from multiple ancestries demonstrated that SPAmix is scalable and can discover novel hits while controlling type I error rates well.</p>
Baltimore Ecosystem Study: Estimates of population in focal watersheds based on 2010 census
This dataset includes population estimates for eight focal sub-watersheds in the Baltimore Ecosystem Study based on the proportion of 2010 census blocks located within the watershed. These data can facilitate per capita calculations of watershed fluxes.
Figure 2 in Taxonomic study and population variation of scale insects (Hemiptera: Coccidae and Diaspididae) and associated parasitoids (Hymenoptera: Chalcidoidea) in an olive grove at Rio Grande do Sul, Brazil
Figure 2. Population variation of Hemiberlesia lataniae (Hemiptera: Diaspididae) on different varieties of Olea europaea (Arbequina, Arbosana and Koroneiki), at different times of sampling, in Barra do Ribeiro (30°30′54.95″S, 51°30′20.84″W), Rio Grande do Sul, Brazil.
Figure 1 in Taxonomic study and population variation of scale insects (Hemiptera: Coccidae and Diaspididae) and associated parasitoids (Hymenoptera: Chalcidoidea) in an olive grove at Rio Grande do Sul, Brazil
Figure 1. Population variation of Hemiberlesia lataniae (Hemiptera: Diaspididae) in an Olea europaea multivarietal olive grove (Arbequina, Arbosana and Koroneiki), at different sampling times, considering different phases and stage of development in Barra do Ribeiro (30°30′54.95″S, 51°30′20.84″W), Rio Grande do Sul, Brazil.
Fig. 4 in Connecting systematic and ecological studies using DNA barcoding in a population survey of Drosophilidae (Diptera) from Mt Oku (Cameroon)
Fig. 4. Phylogenetic analysis of the subgenus Sophophora and Lissocephala aff. diola Tsacas & Lachaise, 1979. Conventions as for Fig. 3.
Fig. 2 in Connecting systematic and ecological studies using DNA barcoding in a population survey of Drosophilidae (Diptera) from Mt Oku (Cameroon)
Fig. 2. Percent divergence of the morphospecies DNA barcode from the closest neighbor found in the barcode database.
ScienceDex guides
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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.