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556 results for “Meta Data”
Data and code for: Does increasing temperature accentuate disease impacts on fisheries species? A meta-analysis
<p>Rapid warming could drastically alter host-parasite relationships, which is especially important for fisheries crucial to human nutrition and economic livelihoods; yet we lack a synthetic understanding of how warming influences parasite-induced mortality in these systems. We conducted a meta-analysis using 301 effect sizes from 60 empirical papers on harvested aquatic species and determined the relationship between parasite-induced host mortality and temperature and how this relationship was altered by host, parasite and study design traits. Overall, temperature increased parasite-induced host mortality; however, the magnitude and sometimes direction of this relationship varied. Hosts from the order Salmoniformes experienced a greater increase in parasite-induced mortality with temperature than average. Opportunistic parasites were correlated with a greater increase in host mortality with temperature than average, while bacterial parasite-induced mortality was lower than average as temperature increased. Thus, parasites will generally increase host mortality as the environment warms; however, this effect will vary among systems.</p>
Data from: Multi-generation genetic contributions of immigrants reveal cryptic elevated and sex-biased effective gene flow within a natural meta-population
<p>Impacts of immigration on micro-evolution and population dynamics fundamentally depend on net rates and forms of resulting gene flow into recipient populations. Yet, the degrees to which observed rates and sex ratios of physical immigration translate into multi-generational genetic legacies have not been explicitly quantified in natural meta-populations, precluding inference on how movements translate into effective gene flow and eco-evolutionary outcomes. Our analyses of three decades of complete song sparrow (<em>Melospiza melodia</em>) pedigree data show that multi-generational genetic contributions from regular natural immigrants substantially exceeded those from contemporary natives, consistent with heterosis-enhanced introgression. Further, while contributions from female immigrants exceeded those from female natives by up to three-fold, male immigrants' lineages typically went locally extinct soon after arriving. Both the overall magnitude, and the degree of female bias, of effective gene flow therefore greatly exceeded those which would be inferred from observed physical arrivals, reshaping the eco-evolutionary implications of immigration.</p>
Data for article "Personal approach for cancer treatment: a meta-analysis of Phase II Clinical trials"
<p>We conducted systematic review and meta-analysis to provide a comprehensive overview of outcomes in patients who underwent personalized genomics-based versus non-personalized treatment in oncology. The PubMed searches detected 803 studies based on phase II clinical trials’ results published from 2010 to 2021. We selected 50 studies, having 81 arms and 6536 patients for the analysis. We compared Response Rate (RR), medians and 1-year rates of Overall Survival (OS) and Progression-Free Survival (PFS) between genomics-based personalized and non-personalized arms. This repository contains final dataset (Dataset file) and t<span lang="EN-US">he information on 803 studies identified in the literature search (803 studies description file)</span>. </p> <p>The searches, study selection, data extraction and synthesis were performed in accordance to PRISMA (preferred reporting items for systematic review and meta-analysis) guidelines. The research protocol was registered in PROSPERO (International prospective register of systematic reviews, <a href="https://www.crd.york.ac.uk/PROSPERO" rel="nofollow">https://www.crd.york.ac.uk/PROSPERO</a>), record ID CRD42024504021. </p> <p>We performed proportional meta-analysis using the RStudio program, utilizing the R programming language and packages "meta", "metafor," and "tidyverse", the code is available at github: https://github.com/MikhailPot/PreciseOnco_meta-analysis </p>
META-DATA for IEA Wind Task 46 report: Atmospheric drivers of wind turbine blade leading edge erosion: Hydrometeors
<p>The objectives of the work summarized in the report that accompanies this dataset are to:</p> <ul> <li>Describe crucial meteorological parameters for wind turbine blade leading edge erosion</li> <li>Describe technologies appropriate to measurement of hydroclimates and specifically hydrometeor size distributions and phase</li> <li>Identify available data sets that are available to describe hydrometeor size distributions and phase and generate meta-data for data sets available for use in mapping wind turbine blade leading edge erosion potential. This dataset summarizes those meta-data. </li> <li>Identify priority geographic areas for geospatial mapping of wind turbine blade leading edge erosion potential <p> </p> </li> </ul>
Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities: validation cohort meta data and parsed TCR repertoire data
<p>Meta data corresponding the the validation cohort for the paper, "Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities" by Magdalena L Russell, Aisha Souquette, David M Levine, Stefan A Schattgen, E Kaitlynn Allen, Guillermina Kuan, Noah Simon, Angel Balmaseda, Aubree Gordon, Paul G Thomas, Frederick A Matsen IV, and Philip Bradley. These meta data include: </p> <p>(1) SNP genotypes for the two SNPs which overlap with the discovery cohort<br> - (nicaragua_snp_genotypes_ints.tsv) -- SNP genotypes as integers<br> - (nicaragua_snp_genotypes_strings.tsv) -- SNP genotypes as allele strings <br> (2) the ancestry PCs for each individual in the validation cohort (nicaragua_snp_ancestry_PCA.tsv)<br> (3) a file including IMGT genes and sequences used for parsing TCRB repertoire data (human_vj_allele_cdr3_nucseqs.tsv)<br> (4) a file including IMGT genes used for parsing TCRA repertoire data (human_vj_alleles_alpha.tsv)<br> (5) Parsed TCRA repertoire data (nicaragua_parsed_TCRA.tgz)<br> (6) Parsed TCRB repertoire data (nicaragua_parsed_TCRB.tgz) </p> <p><strong>Corresponding raw validation cohort TCR repertoire data is available here:</strong> https://www. ncbi.nlm.nih.gov/bioproject/PRJNA762269 (The BioProject database, accession number: PRJNA762269)</p> <p><strong>Software tools designed to work with these data are available here:</strong> https://github.com/phbradley/tcr-gwas</p>
Data from: The effects of human-altered habitat spatial pattern on frugivory and seed dispersal: a global meta-analysis
<p>Seed dispersal by frugivorous animals is important for plant mobility, regeneration, and persistence. Human-caused landscape change is thought to disrupt seed dispersal, but evidence is scarce. We performed a comprehensive meta-analysis on the effects of habitat spatial pattern on frugivory and seed dispersal. We found 233 effects from 71 studies. At a patch or local scale, altered habitat spatial pattern was measured as declining patch size, increasing patch isolation, or habitat edge (vs. interior). At a landscape scale it was measured as declining amount of habitat, increasing mean patch isolation, increasing number of patches, or increasing habitat edge in the landscape.</p> <p>We found overall negative effects of altered habitat spatial pattern on: (i) the quantity of frugivory or seed dispersal, (ii) the number of species involved in a plant-frugivore interaction, and (iii) seed dispersal distance. Moderator variable analysis was only possible for the first of these. It revealed negative responses of the quantity of frugivory or seed dispersal to habitat loss at both the local scale (declining patch size), and the landscape scale (declining habitat amount), but little evidence for a response to habitat edge at either scale. In addition, altered habitat spatial pattern reduced the quantity of frugivory or seed dispersal more strongly in temperate than tropical areas. Finally, the few-recorded effects of landscape-scale fragmentation per se (increasing patch density or edge density) on the quantity of frugivory or seed dispersal were mixed and weak. Our meta-analysis reinforces the notion that habitat loss is a major threat to frugivory and seed dispersal by animals, and reveals an insufficiency of studies of the effects of habitat fragmentation per se. Thus, based on the current literature, we conclude that maintaining and increasing habitat amount is vital for maintaining seed dispersal by frugivorous animals.</p>
Data for "Meta-analysis of induced anti-herbivore defence traits in plants from 647 manipulative experiments with natural and simulated herbivory"
<p>Data used in analysis in "Meta-analysis of induced anti-herbivore defence traits in plants from 647 manipulative experiments with natural and simulated herbivory" in Journal of Ecology. </p> <p>Code used for analysis are included as Supplementary Material of the main article. </p> <p> </p>
MIntO: a Modular and Scalable Pipeline for Microbiome Metagenomic and Metatranscriptomic Meta-omics Data Integration
<p>To illustrate the use of MIntO, a set of 91 human fecal metagenomes from the Inflammatory Bowel Disease Multi’omics Database was selected (IBDMDB). We selected six participants diagnosed as non-IBD (P6018 (nIBD1), M2072 (nIBD2)); Crohn’s disease (H4006 (CD1) and H4020 (CD2)); and ulcerative colitis (H4019 (UC1) and H4035 (UC2)) that were followed for one year each. </p> <p>Here, we present the results from the <em>genome-based assembly-dependent</em> mode, where we used 91 metagenomic high-quality reads<strong> </strong>to recover 163 high-quality MAGs, which constituted a set of non-redundant genomes.</p>
Overview of COVID-19 individual participant data meta-analyses (IPD-MAs)
<p>Individual participant data meta-analyses (IPD-MAs), which include harmonising and analysing participant-level data from related studies, provide several advantages over aggregate data meta-analyses, which pool study-level findings. IPD-MAs inform the design and conduct of randomised clinical trials and have informed the research and public health responses to COVID-19. To identify areas of overlap, we conducted a rapid systematic review of completed or ongoing COVID-19 IPD-MAs. We identified 31 COVID-19 related IPD-MAs, including 5 living IPD-MAs, and found several areas of overlap in study designs, populations, exposures, and outcomes of interest. Details of the 31 identified COVID-19 IPD-MAs are presented in this dataset. </p>
Data set from "Absolute Treatment Effects for the Primary Outcome and All-cause Mortality in the Cardiovascular Outcome Trials of New Antidiabetic Drugs – A Meta-Analysis of Digitalized Individual Patient Data"
<p>This data set contains the complete digitalized individual patient data that are used in the manuscript "Absolute Treatment Effects for the Primary Outcome and All-cause Mortality in the Cardiovascular Outcome Trials of New Antidiabetic Drugs – A Meta-Analysis of Digitalized Individual Patient Data", which is accepted from "Acta Diabetologica".<br> The data file is in CSV format and contains the five variables "OutcomeType" (with values "AllcauseMortality" or "PrimaryOutcome"), "Study" (denoting the respective cardiovascular outcome trial), "Treatment" (denoting the respective study treatment or placebo), "Event" (denoting if the respective has been observed (Event=1) or not (Event=0)), and "SurvivalTimeMonths" (denoting the respective time to the event or censoring in months).</p>
Data for meta-analysis of the soil greenhouse gas emissions
<p><span>Exploring the </span><span>responses of greenhouse gases (GHGs) emissions to land use conversion or reversion is significant for taking effective land use measures to alleviate global warming.</span> <span>A global meta-analysis was conducted to analyze the responses of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) emissions to land use conversion or reversion, and determine their temporal evolution, driving factors and potential mechanisms. Our results showed that CH4 and N2O responded positively to land use conversion while CO2 responded negatively to the changes from natural herb and secondary forest to plantation. By comparison, CH4 responded negatively to land use reversion and N2O also showed negative response to the reversion from agricultural land to forest. The conversion of land use weakened the function of natural forest and grassland as CH4 sink and the artificial nitrogen (N) addition for plantation increased N source for N2O release from soil, while the reversion of land use could alleviate them to some degree. Besides, soil carbon would impact CO2 emission for a long time after land use conversion, and secondary forest reached the methane uptake level similar to that of primary forest after over 40 years. N2O responses had negative relationships with time interval under the conversions from forest to plantation, secondary forest and pasture. In addition, meta-regression indicated that CH4 had correlations with several environmental variables, and carbon-nitrogen ratio had contrary relationships with N2O emission responses to land use conversion and reversion.</span> <span>And the importance of driving factors displayed that CO2, CH4 and </span><span>N2O</span><span> response to land use conversion and reversion were easily affected by NH4+ and soil moisture, </span><span>mean annual temperature</span><span> and NO3-, total nitrogen and </span><span>mean annual temperature</span><span>, respectively.</span> <span>This study would provide enlightenment for scientific land management and reducing of GHG emissions.</span></p>
Baltic Sea stable isotope ecology meta-data collection
<p>Stable isotope analysis (SIA) has become a pivotal method in food web and ecological research, leading to the establishment of the research field "stable isotope ecology". We conducted the first systematic review of stable isotope studies in this field in the Baltic Sea macro-region (Eglite et al. 2022). The meta-data collection provided here includes the information extracted from all 164 studies identified in the systematic review across various dimensions (topic, space, time, taxonomic, and technical focus), but not primary stable isotope data. The first published version of this meta-data collection represents the status as of July 10, 2021, and was used to filter and extract meta-data to produce the figures and tables in the review by Eglite et al. (2022). The meta-data collection is a resource for both experienced isotope ecologists and newcomers to grasp and access all published Baltic Sea SIA work on any fundamental or applied research topic, sub-region, taxon, or trophic group of interest. It also represents an ideal foundation for an envisioned "Baltic Isobank" database of primary stable isotope data, following the vision outlined in Eglite et al. (2022). We will provide regular updates of the meta-data collection in the Dryad repository, based on new runs of the systematic review query and including any additions of research papers and corrections received from the stable isotope ecology community. For this purpose, we encourage researchers to inform us about newly published research papers employing stable isotopes in the Baltic Sea ecology field by sending an e-mail with the publication reference to baltic-isobank@geomar.de.</p>
Code and data for directed emission from uniformly excited non-Hermitian photonic meta-structures
<p>Wolfram Mathematica notebook (.nb) used to generate figures, data, and confirm analytical results presented in the main work. Data generated from the notebook is included here as separate text files (.dat) as well.</p>
Extracted data for meta-analysis: Distal versus proximal radial access in coronary angiography
<p>Data base underlying quantitative meta-analysis in the manuscript titled "Distal versus proximal radial access in coronary angiography: A meta-analysis" by Lueg, Schulze, Stöhr, & Leistner.</p> <p>Data allows meta-analysis of primary endpoint (RAO), secondary endpoints, meta-regression for moderator analysis, and publication bias analysis.</p>
Data from: Tamm Review: a meta-analysis of thinning, prescribed fire, and wildfire effects on subsequent wildfire severity in conifer dominated forests of the Western US
<p>Increased understanding of how active forest management (i.e., mechanical thinning, prescribed burning, and managed wildfire) affects subsequent wildfire severity is urgently needed as people and forests face a growing wildfire crisis. In response, we reviewed scientific literature for the US West and completed a meta-analysis that answered three questions: (1) How much do treatments reduce wildfire severity within treated areas? (2) How do the effects vary with treatment type, treatment age, and forest type? (3) How does fire weather moderate the effects of treatments? We found overwhelming evidence that mechanical thinning with prescribed burning, mechanical thinning with pile burning, and prescribed burning only are effective at reducing subsequent wildfire severity, resulting in reductions in severity from 62% to 72% relative to untreated areas. In comparison, thinning only was less effective – underscoring the importance of treating surface fuels when mitigating wildfire severity is the management goal. The efficacy of these treatments did not vary among forest types assessed in this study and was high across a range of fire weather conditions. Prior wildfire had more complex impacts on subsequent wildfire severity, which varied with forest type and initial wildfire severity. Across treatment types, we found that effectiveness of treatments declined over time, with the mean reduction in wildfire severity decreasing nearly threefold when wildfire occurred greater than 10 years after initial treatment. Our meta-analysis provides up-to-date information on the extent to which active forest management reduces wildfire severity and facilitates better outcomes for people and forests during future wildfire events. </p>
Effect size data for the meta-analysis article ""Effects of vegetation management intensity on biodiversity and ecosystem services in vineyards: a meta-analysis"
<p>This Exel file includes the effect size dataset used for the statistical analysis for the paper "Effect of vegetation management intensity on biodiversity and ecosystem services in vineyards: a meta-analysis", which will be published in the Journal of Applied Ecology in 2018.</p> <p>This meta-analysis was conducted in the course of the project VineDivers (<a href="http://www.vinedivers.eu/">www.vinedivers.eu</a>) funded through the 2013-2014 BiodivERsA/FACCE-JPI joint call for research proposals, with the national funders: Austrian Science Fund (FWF), Spanish Ministry for Economy and Competitiveness (MINECO), French National Research Agency (ANR), Romanian Executive Agency for Higher Education, Research, Development and Innovation Funding (UEFISCDI) and Federal Ministry of Education and Research (BMBF/Germany). P. Batáry was supported by the German Research Foundation (DFG BA4438/2-1) and by the Economic Development and Innovation Operational Programme of Hungary (GINOP–2.3.2–15–2016–00019).</p> <p> </p>
Summary-level data from meta-analysis of fat distribution phenotypes in UK Biobank and GIANT
<p>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</p> <p>Summary-level data as presented in:</p> <p>"Meta-analysis of genome-wide association studies for body fat distribution in 694,649 individuals of European ancestry." Pulit, SL et al. bioRxiv, 2018. https://www.biorxiv.org/content/early/2018/04/18/304030</p> <p>**If you use these data, please cite the above preprint.</p> <p>If you have any questions or comments regarding these files, please contact me:</p> <p>Sara L Pulit<br> spulit@well.ox.ac.uk or s.l.pulit@umcutrecht.nl</p> <p>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</p> <p><strong>(1) Data files</strong></p> <p><em>i. whradjbmi.giant-ukbb.meta-analysis.combined.23May2018.txt</em><br> Meta-analysis of waist-to-hip ratio adjusted for body mass index (whradjbmi) in UK Biobank and GIANT data. Combined set of samples, max N = 694,649.</p> <p><em>ii. whradjbmi.giant-ukbb.meta-analysis.females.23May2018.txt</em><br> Meta-analysis of whradjbmi in UK Biobank and GIANT data. Female samples only, max N = 379,501.</p> <p><em>iii. whradjbmi.giant-ukbb.meta-analysis.males.23May2018.txt</em><br> Meta-analysis of whradjbmi in UK Biobank and GIANT data. Male samples only, max N = 315,284.</p> <p><em>iv. whr.giant-ukbb.meta-analysis.combined.23May2018.txt</em><br> Meta-analysis of waist-to-hip ratio (whr) in UK Biobank and GIANT data. Combined set of samples, max N = 697,734.</p> <p><em>v. whr.giant-ukbb.meta-analysis.females.23May2018.txt</em><br> Meta-analysis of whr in UK Biobank and GIANT data. Female samples only, max N = 381,152.</p> <p><em>vi. whr.giant-ukbb.meta-analysis.males.23May2018.txt</em><br> Meta-analysis of whr in UK Biobank and GIANT data. Male samples only, max N = 316,772.</p> <p><em>vii. bmi.giant-ukbb.meta-analysis.combined.23May2018.txt</em><br> Meta-analysis of body mass index (bmi) in UK Biobank and GIANT data. Combined set of samples, max N = 806,834.</p> <p><em>viii. bmi.giant-ukbb.meta-analysis.females.23May2018.txt</em><br> Meta-analysis of bmi in UK Biobank and GIANT data. Female samples only, max N = 434,794.</p> <p><em>ix. bmi.giant-ukbb.meta-analysis.males.23May2018.txt</em><br> Meta-analysis of bmi in UK Biobank and GIANT data. Male samples only, max N = 374,756.</p> <p><strong>(2) Data file format</strong></p> <p>CHR: Chromosome</p> <p>POS: Chromosomal position of the SNP, build hg19</p> <p>SNP: the dbSNP151 identifier of the SNP, followed by the first allele and second allele of the SNP, delimited with a colon. A small number of SNPs (<9,000) from the GIANT data had no dbSNP151 identifier, and are left as just an rsID. Note that these SNPs are also missing chromosome and position information (not provided in the GIANT data).</p> <p>Tested_Allele: the allele for which all association statistics are reported</p> <p>Other_Allele: the other allele at the SNP</p> <p>Freq_Tested_Allele: frequency of the tested allele</p> <p>BETA: the effect size of the tested allele</p> <p>SE: the standard error of the beta</p> <p>P: the p-value of the SNP, as reported from the inverse variance-weighted fixed effects meta-analysis</p> <p>N: the total sample size for this SNP</p> <p>INFO: the imputation quality (info score) of the SNP, as reported by UK Biobank. A number between 0 and 1 indicating quality of imputation (0, poor quality; 1, high quality or genotyped). Note that the summary-level GIANT data does not report info score, so SNPs appearing only in the GIANT analysis do not have info scores.</p>
The Effects of Cycle and Treadmill Desks on Work Performance and Cognitive Function in Sedentary Workers: data repository of a review and meta-analysis.
<p>This repository contains additional files related to the review and meta-analysis. The first dataset contains list of search terms. The second dataset contains list od studies included in the meta-analysis. The third dataset contains study evaluation using PEDro scale tool. The fourth dataset contains two additional forrest plots (Effect of cycle and treadmill desks on typing errors and Effect of cycle and treadmill desks on congruent Eriksen Flanker test).</p>
Meta-data and coding for Resilience of Coastal Communities Nexus Evidence Map
<p>Data extracted and coded for studies relevant to the Evidence Map associated with the manuscript "Mapping research at the nexus of resilience, wellbeing and environmental sustainability in UK marine systems"</p>
Data from: Plant-type dominates fine-root C:N:P stoichiometry across China: a meta-analysis
<p>Aim: Fine roots play an important role in biogeochemical cycling in terrestrial ecosystems. However, our understanding of large scale biogeographic patterns and drivers of fine-root C:N:P stoichiometry is extremely limited.</p> <p>Location: China.</p> <p>Methods: We compiled data for fine-root carbon (C), nitrogen (N) and phosphorus (P) concentrations at 165 sites across China to explore large-scale biogeographic patterns and drivers of fine-root C:N:P stoichiometry.</p> <p>Results: The geometric means of fine-root C, N, and P concentrations were 448.81 mg g-1, 10.73 mg g-1, and 0.9 mg g-1, respectively, whereas C:N, C:P and N:P ratios were 41.84, 508.32 and 11.73, respectively. The fine-root elemental concentrations and their ratios varied widely among plant groups and biomes, and showed clear latitudinal and longitudinal trends, as a consequence of differences in climate, soil and plant-type. However, plant-type was the largest contributor to the total variance in fine-root C, N, and P and their ratios compared to climate factors or soil features.</p> <p>Main conclusions: The data reveal the existence of broad biogeographic patterns of fine-root C:N:P stoichiometry in China. These results advance our knowledge about the biogeochemical cycling of fine roots.</p>
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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.