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556 results for “Meta Data”
Piburgersee core meta data repository for the publication "Seismic control of large prehistoric rockslides in the Eastern Alps"
<p>This dataset comprises the core meta data of Plansee, which is the basis for the publication Oswald et al. "Seismic control of large prehistoric rockslides in the Eastern Alps".</p> <p>The core meta data belongs to a 8m long sediment core composed of 12 individual core sections (see Plansee_core_data.xlsx). For each individual core section the core image (_coreimage.jpg), the CT data (_CT.rar), XRF data, (_XRF.txt) and multi-sensor core logging data (_MSCL.csv) are provided.</p>
Plansee seismic and core meta data repository for the publication "Seismic control of large prehistoric rockslides in the Eastern Alps"
<p>This dataset comprises the raw seismic data and core meta data of Plansee, which is the basis for the publication Oswald et al. "Seismic control of large prehistoric rockslides in the Eastern Alps".</p> <p>Seismic profiles are provided as .SGY files (Plansee_seismics_SGYfiles.rar)</p> <p>The core meta data belongs to a 7m long sediment core composed of 10 individual core sections (see Plansee_core_data.xlsx). For each individual core section the core image (_coreimage.jpg), the CT data (_CT.rar) and multi-sensor core logging data (_MSCL.csv) are provided.</p>
Trophic-meta-analysis: Second release of tritrophic meta-analysis data, code and appendices
<p>Data, R script and appendices for "Interaction strength and the impact of introduced omnivores: A meta-analysis of introduced aquatic invasive species" submitted to Oikos</p>
Serial Isomorphous Replacement Data -Pilatus3 2M raw images and meta data
<p>Diffraction data collected from the ESRF ID23-EH2 microfocus beamline for the purpose of single isomorphous replacement phasing. These are raw CBF images from a pilatus3 2M detector. The "process" sub directory and CBF headers contain meta data about the experimental setup. Data were collected with the Mesh and Collect workflow and contain partial datasets of ~10 degrees with 0.1 degree oscillations (more detail in the meta data files). </p>
Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities: discovery cohort meta data and parsed TCR repertoire data
<p>Meta data corresponding the the discovery 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) a file mapping the SNP data subject IDs to the TCR repertoire data subject IDs (gwas_id_mapping.tsv)<br> (2) a file including the PCAir PCs, self-reported ancestry, and genomic ancestry for each subject (all_pc_air.txt)<br> (3) a file including the PCAir variance explained by each PC (all_pc_air_variance.txt)<br> (3) a file including the SNP ID, chromosome, hg19 position, allele, rsid, and quality control metrics for each SNP in the SNP array (emerson_snp_rs_data.tsv)<br> (4) a file including IMGT genes and sequences used for parsing TCRB repertoire data (human_vj_allele_cdr3_nucseqs.tsv)<br> (5) a file including predicted TRBD2 allele genotypes for each subject (emerson_trbd2_alleles.tsv)<br> (6) Parsed TCRB repertoire data. These raw data were first published in Emerson et. al, <em>Nature Genetics </em>2017. (emerson_parsed_tcrb.tgz)</p> <p><strong>Corresponding discovery cohort raw TCR repertoire data is available here: </strong>https: //doi.org/10.21417/B7001Z (ImmuneACCESS database)<br> <strong>Corresponding discovery cohort SNP data is available here:</strong> https: //www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001918.v1.p1 (The database of Genotypes and Phenotypes, accession number: phs001918)<br> <br> <strong>Software tools designed to work with these data are available here:</strong> https://github.com/phbradley/tcr-gwas</p>
Data, analytical, and plotting codes needed to reproduce meta-analyses on within-season divorce in birds
<p>This data package contains data (effect sizes and other variables) and analytical codes needed to reproduce three meta-analyses on within-season divorce and breeding success in socially monogamous birds (Culina & Brouwer: No evidence of immediate fitness benefits of within-season divorce in monogamous birds. 2022. Biology Letters.) It also contains codes to reproduce Figures from the main text and from the Supplement. Readme file and Licence are provided too.</p>
Data for "Laplacian-level meta-GGA for the weakly-nonlocal solid and liquid metals"
<p>This dataset contains all VASP inputs and outputs for the paper "Improved Laplacian-level meta-GGA for the weakly-nonlocal solid and liquid metals." For the preprint, see <a href="https://arxiv.org/abs/2203.09403">arXiv:2203.09403</a>, and for the reference densities, fitting routines, and analysis scripts, see the <a href="https://gitlab.com/dhamil/laplacian-level-meta-gga">Gitlab code repository</a>.</p> <p>Description of individual tarballs:</p> <ul> <li>AE6: 6-molecule set of atomization energies</li> <li>ferro: relaxed geometries and magnetic moments for the ferromagnetic solids Fe, Ni, and Co</li> <li>intermetallics: formation energies of three intermetallic solids, HfOs, ScPt, and VPt<sub>2</sub></li> <li>LC20: relaxed geometries and equilibrium bulk moduli for the LC20 set of cubic solids. Equilibrium geometries by equation of state fit. Bandgaps for select insulators are included here.</li> <li>LC20_stress_tensor: same as LC20, but equilibrium geometries found by minimizing forces on unit cell computed with Laplacian-dependent stress tensor</li> <li>LC23: equilibrium geometries, bulk moduli, and cohesive energies for the LC23 set (LC20 + K, Rb, and Cs) found by equation of state fit. Bandgaps for select insulators are included here.</li> <li>Pt_monovac: monovacancy formation energies for Pt, computed in a few different ways described in the text</li> </ul>
Data from: Controlled drainage and subirrigation suitability in the United States: A meta-analysis of crop yield and soil moisture effects
<p>Controlled drainage and subirrigation (CDSI) is an important water management strategy in many regions, but the conditions under which CDSI is most likely to increase crop yield and soil moisture are not fully understood. A meta-analysis, consisting of 154 pairwise observations from replicated and randomized trials in 30 peer-reviewed primary research articles on CDSI (6 controlled drainage, 24 CDSI, analyzed together due to data scarcity), was conducted to study the responses of yield and soil moisture to CDSI, and investigate how crop type, soil texture, and cumulative growing season precipitation (PGS) influence these responses. Based on the yield response to these moderating factors, we used a fuzzy-logic approach to map potentially suitable locations for CDSI in the conterminous United States. On average, CDSI increased yield by 8.0% (95% CI = 1.8–14.7%) compared with conventional free drainage. The yield response to CDSI did not differ among crops. However, a greater yield response to CDSI was observed in medium-textured soils (19.4% increase; 95% CI = 12.4–27.0%) than in coarse- or fine-textured soils. The positive effect of CDSI on yield increased with decreasing PGS in coarse- and medium-textured soils. There was no clear effect of CDSI on soil moisture, nor did any moderators influence this relationship, though this may be attributed to the scarcity of studies on CDSI reporting soil moisture. The fuzzy-logic-based approach revealed that while potentially suitable areas are mostly concentrated in the well studied U. S. Midwest, these areas also exist in other regions where CDSI may warrant further study.</p>
Data from: Worldwide impacts of landscape anthropization on mosquito abundance and diversity: a meta-analysis
<p><span>In recent decades, the emergence and resurgence of vector-borne diseases have been well documented </span><span>worldwide</span><span>, especially in tropical regions where protection and defence tools for human populations are still very limited. In this context, the </span><span>dynamics</span><span> of pathogens </span><span>are influenced by</span><span> landscape anthropization (i.e., urbanization, deforestation, and agricultural development)</span><span>,</span><span> and one of the mechanisms through which this occurs is a change in</span><span> the</span><span> abundance and/or diversity of the vectors. An increasing number of empirical studies </span><span>have </span><span>described heterogeneous effects of landscape anthropization on vector communities</span><span>; therefore</span><span>, it is difficult to have an overall picture of these effects on a global scale. Here, we performed a meta-analysis to quantify the impacts of landscape anthropization on a global scale on the presence/abundance and diversity of mosquitoes, the most important arthropods affecting human health. We obtained 338 effect sizes on 132 mosquito species, compiled from 107 studies in 52 countries </span><span>that</span><span> covered almost every part of the world. The results of the meta-analysis showed an overall decline of mosquito presence/abundance and diversity in response to urbanization, deforestation, and </span><span>agricultural</span><span> development, except for a few mosquito species</span><span> </span><span>that have been able to exploit landscape anthropization well. Our results highlighted that these few favoured mosquito species are those of global</span><span> concern. </span><span>They thus provide a better understanding of the overall effect of landscape anthropization on vector communities and</span><span>,</span><span> more importantly, suggest a greater risk of emergence and transmission of vector-borne diseases in human-modified landscapes.</span></p>
LC-MS² meta data for each MassBank (MB) subset
<p>The CSV-file (tab used as separator) provides the Liquid-chromatography (LC) and Tandem-mass spectrometry (MS²) configurations for each MassBank (MB) subset used in the publication: "Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data" by Bach et al. (2022).</p>
Data and code – Effects of climate on salmonid productivity: A global meta-analysis across freshwater ecosystems
<p>Salmonids are of immense socio-economic importance in much of the world but are threatened by climate change. This has generated a substantial literature documenting effects of climate variation on salmonid productivity in freshwater ecosystems, but there has been no global quantitative synthesis across studies. We conducted a systematic review and meta-analysis to gain quantitative insight into key factors shaping the effects of climate on salmonid productivity, ultimately collecting 1,321 correlations from 156 studies, representing 23 species across 24 countries. Fisher's Z was used as the standardized effect size, and a series of weighted mixed-effects models were compared to identify covariates that best explained variation in effects. Patterns in climate effects were complex, and were driven by spatial (latitude, elevation), temporal (time-period, age-class), and biological (range, habitat type, anadromy) variation within and among study populations. These trends were often consistent with predictions based on salmonid thermal tolerances. Namely, warming and decreased precipitation tended to reduce productivity when high temperatures challenged upper thermal limits, while opposite patterns were common when cold temperatures limited productivity. Overall, variable climate impacts on salmonids suggest that future declines in some locations may be counterbalanced by gains in others. In particular, we suggest that future warming should (1) increase salmonid productivity at high latitudes and elevations (especially >60° and >1,500m), (2) reduce productivity in populations experiencing hotter and dryer growing season conditions, (3) favor non-native over native salmonids, and (4) impact lentic populations less negatively than lotic ones. These patterns should help conservation and management organizations identify populations most vulnerable to climate change, which can then be prioritized for protective measures. Our framework enables broad inferences about future productivity that can inform decision-making under climate change for salmonids and other taxa, but more widespread, standardized, and hypothesis-driven research is needed to expand current knowledge.</p>
Meta-analysis of diurnal transcriptomics reveals strong patterns of concordance and discordance in mouse liver: processed data
<p>The accumulation of public transcriptomic timeseries data enables robust meta-analyses that were not possible until recently. To assess the consistency of biological rhythms across studies, 43 public mouse liver tissue timeseries totaling 805 RNA-seq samples were obtained and analyzed. Only the control groups of each study were included, to create comparable data. Technical factors in RNA-seq library preparation were the largest contributors to transcriptome-level differences, beyond biological or experiment-specific factors such as lighting conditions. Core clock genes were remarkably consistent in phase across all studies, while phase distributions of other periodic genes were generally less consistent. Overlap of genes identified as rhythmic across studies was generally low, with around 50% between some of the highest sample count studies. Distributions of phases of significant genes were remarkably inconsistent across studies, but genes consistently identified as rhythmic clustered near ZT0 and ZT12 in acrophase. Data was integrated across studies in a JIVE analysis, which showed that the top two components of joint within-study variation are determined by time of day. A shape-invariant model with random effects was fit to the genes to identify the underlying shape of the rhythms, consistent across all studies. This revealed the extent of asymmetric and multimodal genes.<br> <br> This supplemental file provides preprocessed RNA-seq quantifications of all reviewed datasets, as well as results of multiple analyses.</p>
Data and code for "Salomon et al. 2024: Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to Daphnia - a meta-analysis."
<div> <p>All data and R code for</p> <p><strong>Salomon S, Grubmüller E, Kropf P, Nickl E, Rühl A, Weigel S, Becker F, Antonio Vital AL, Laforsch C, Schott M, Mair MM. (2024). Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to <em>Daphnia</em> - a meta-analysis. <em>Microplastics and Nanoplastics</em>. (<a href="https://doi.org/10.1186/s43591-024-00088-4" target="_blank" rel="noopener">https://doi.org/10.1186/s43591-024-00088-4</a>)</strong></p> <p><em>Abstract</em></p> <p>Effects of micro- and nanoplastic particles (MNP) on organisms have been increasingly reported in recent years, with a large number of studies conducted on water fleas of the genus <em>Daphnia</em>. Most of the available studies used pristine particles that have not been exposed to the environment or to organic substances. In natural environments, however, organic substances like dissolved organic matter (DOM) attach to the MNP, forming an ecocorona on the particles’ surface. How the formation of an ecocorona influences MNP toxicity is still uncertain. While some studies suggest that DOM can mitigate the negative effects of MNP on organisms, other studies did not find such associations. In addition, it is unclear whether the DOM attached to the particles’ surface is attenuating the effects of MNP directly or whether co-exposure with DOM solved in the medium attenuates MNP toxicity indirectly, for instance by increasing Daphnia‘s resilience to stressors in general. To draw more solid conclusions about the direction and size of the mediating effect of DOM on MNP-associated immobilization in <em>Daphnia</em> spp., we synthesized evidence from the published literature and compiled 305 data points from 13 independent studies. The results of our meta-analysis show that the toxic effects of MNP are likely reduced in the presence of certain types of DOM in the exposure media. We found similar mediating effects when MNP were incubated in media containing DOM before the exposure experiments, although to a lesser extent. Future studies designed to disentangle the effects of DOM attached to the MNP from the general effects of DOM in the exposure medium will contribute to a deeper mechanistic understanding of MNP toxicity in nature and enhance the reliability of MNP risk assessment.</p> </div>
Data from: Meta-analytical evidence for frequency-dependent selection across the tree of life
<p>Explaining the maintenance of genetic variation in fitness related traits within populations is a fundamental challenge in ecology and evolutionary biology. Frequency-dependent selection (FDS) is one mechanism that can maintain such variation, especially when selection favours rare variants (negative FDS). However, our general knowledge about the occurrence of FDS, its strength and direction remain fragmented, limiting general inferences about this important evolutionary process. We systematically reviewed the published literature on FDS and assembled a database of 747 effect sizes from 101 studies to analyse the occurrence, strength, and direction of FDS, and the factors that could explain heterogeneity in FDS. Using a meta-analysis, we found that overall, FDS is more commonly negative, although not significantly when accounting for phylogeny. An analysis of absolute values of effect sizes, however, revealed the widespread occurrence of modest FDS. However, negative FDS was only significant in laboratory experiments and non-significant in mesocosms and field-based studies. Moreover, negative FDS was stronger in studies measuring fecundity and involving resource competition over studies using other fitness components or focused on other ecological interactions. Our study unveils key general patterns of FDS and points in future promising research directions that can help us understand a long-standing fundamental problem in evolutionary biology and its consequences for demography and ecological dynamics.</p>
A METAS VNA Tools project which contains S-parameter data of a CPW containing 3000 Josephson Junctions operated at 4 Kelvin, 10 Kelvin and 25 Kelvin with currents up to 200 mA
<p>A METAS VNA Tools project which contains S-parameter data of a CPW containing 3000 Josephson Junctions on a 1cmx1cm silicon chip made from intrinsic silicon. The chip is operated at 4 Kelvin, 10 Kelvin and 25 Kelvin with currents up to 200 mA for further heating injected. The temperature, current and DC resistance are noted in each filename.</p>
Data for: A systematic review and meta-analysis of Drosophila short-term-memory genetics: robust reproducibility, but little independent replication
<p>All the data, code, analyses, and figures used in the study entitled: "A systematic review and meta-analysis of Drosophila short-term-memory genetics: robust reproducibility, but little independent replication" <em>(doi: https://doi.org/<a href="http://bb2sz3ek3z.search.serialssolutions.com/?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&__char_set=utf8&rft_id=info:doi/10.1101/247650&rfr_id=info:sid/libx&rft.genre=article">10.1101/247650</a>)</em></p> <p><strong>Abstract</strong></p> <p>Geneticists have long used olfactory conditioning techniques in <em>Drosophila</em> to identify the neurons and genes that mediate learning. While this method has characterized an abundance of memory-related genes, little is known about how these genes induce short-term memory (STM) via signaling pathways; characterizing these networks will be essential to developing mechanistic models of memory formation. Here, we investigated why elucidating the STM pathways has been relatively slow. One possibility is that the STM evidence base is weak due to publication of poorly reproducible results, as has been observed in other fields. We examined this hypothesis by performing a systematic review and subsequent meta-analysis of the STM genetics field. Using several metrics to quantify the variation between discovery articles and follow-up studies, we found that seven genes were highly replicated, showed no publication bias, and had generally high reproducibility. However, the remaining ~80% memory genes have not been replicated since their initial discovery. Although we observed only a few studies that investigated gene interactions, the reviewed genes could together account for >1000% memory. This large summed effect size indicates either that some of the gene findings are not reproducible, that many memory genes participate in shared pathways, or that current protocols lack the specificity needed to identify core plasticity memory genes. Mechanistic theories of memory and cognition will require the convergence of evidence from system, circuit, cellular, molecular, and genetic experiments. As this study demonstrates, systematic data synthesis is an essential tool for this integrated brain science.</p>
A Meta-Analysis on the Reliability of Comparative Judgement Data
<p>This is the data and R analysis script with the article "A Meta-Analysis on the Reliability of Comparative Judgement"</p>
Patients data for meta-analysis of genotype-phenotype associations in Bardet-Biedl Syndrome
<p>Data used for metaanalysis of the genotype-phenotype relationship in Bardet Biedl Syndrome.</p> <p>File "EV table 1 literature.xlsx" describes studies that were included in the metaanalysis. File "EV table 2 dataset.xlsx" contains individual patient data. Each row corresponds to a patient. If the same patient was reported in more than 1 study, their data were merged into one row. The columns are as follows:</p> <p>* source - a citation to the study the patient originated in</p> <p>* FamilyID - randomly generated ID of a family (unique over the dataset), two persons with the same FamilyID are related.</p> <p>* source case n. - A unique identifier of the patient within the study</p> <p>* gene - A gene carrying the principal BBSome related mutation</p> <p>* nucleotide change (allele 1,2) - description of the mutations in DNA individual alleles of the gene, in HGVS nomenclature</p> <p>* protein change (allele 1,2) - description of how the mutations in DNA change the resulting protein, in HGVS nomenclature</p> <p>* type of mut allele 1,2 - whether the given mutation is considered missense (MS) or large truncation (trunc)</p> <p>* mut/mut - combination of mutations for both alleles</p> <p>* additional mutations - mutations in other BBSome-related genes. Format is "gene: DNA mutation, protein mutation"</p> <p>* sex - "F" or "M" (where reported)</p> <p>* age group - age group (where reported)</p> <p>* age - age in years. Contains fractions, decimal values and "5 month"</p> <p>* RD, OBE, PD, CI, REP, REN, HEART, LIV, DD - presense or absence of phenotypes, if reported. RD – retinal dystrophy, OBE – obesity, PD – polydactyly, CI – cognitive impairment , REP – reproductive system anomalies, REN – renal anomalies, HRT – heart disease, LIV – liver anomalies, DD - Developmental delay. Values are "" (not reported), "0" (no phenotype), "1" (phenotype present), "1!" conflicting reports of phenotype in multiple studies (some patients were involved in multiple studies)</p> <p>* ethnicity - ethnicity of the patient, if reported</p> <p>* ethinc group - grouping of the ethnicities into 8 larger groups (see paper for details)</p> <p>* note - miscellanous text, in particular contains notes on patients merged from multiple studies</p> <p>====</p> <p>The protocol for this meta-analysis was pre-registered with PROSPERO (CRD42018096099).</p> <p>PubMed and Google Scholar databases were searched in May 2018 for the following keywords: [bardet-biedl syndrome AND (genotype phenotype OR cohort)]. Other suitable records were identified by snowball searching, in particular, by retrieving relevant articles from the references of the studied full-texts. In addition, all the references included in the publicly available Euro-Wabb database (<a href="https://lovd.euro-wabb.org/home.php">https://lovd.euro-wabb.org/home.php</a>) were covered. Our search was limited to the literature published in English language and covered the period from the inception of each database to the 21st of May 2018.</p>
Data used in meta-analysis of debris-covered glacier melt
<p>The data used in the study Accuracy of Empirical Models of Debris-Covered Glaciers, A Winter-Billington, RD Moore and R Dadic, in prep. for submission to the Journal of Glaciology.</p>
Data set for AYUSH interventions for COVID-19- A Living Systematic Review and Meta-analysis
<p>The COVID-19 pandemic has put a huge strain on governments and medical professionals all across the world.<br> To identify acceptable treatments, many clinical studies from the Indian system of Traditional Medicines [Ayurveda, Yoga and Naturopathy, Unani, Siddha, and Homoeopathy (AYUSH)] have been conducted. Objective of the study is determine the efficiency of the Traditional System of Indian Medicine (AYUSH system) in lowering the incidence, duration, and severity of COVID-19 through a living systematic review and meta-analysis. We will search the following databases e.g; Pubmed; the Cochrane central register of controlled trials (CENTRAL); the Clinical Trials Registry - India (CTRI); Digital Helpline for Ayurveda Research Articles (DHARA): AYUSH research portal; WHO COVID-19 database etc. Clinical improvement, WHO ordinal scale, viral clearance, incidences of COVID-19 infection, and mortality will be considered as primary outcomes. Secondary outcomes will be use of O2 therapy or mechanical ventilator, admission to high dependency unit or emergency unit, duration of hospitalization, the time to symptom resolution, and adverse events. The review will be updated bi-monthly with two updates. It will provide practitioners, guideline developers, and authorities with up-to-date syntheses on interventions on a regular basis to help them make health-care decisions about AYUSH therapies for COVID-19 management. Study is supported by World Health Organization, South East Asia Regional Office, New Delhi, India. Here, we shared the result of our search strategy of our project and data extraction tool developed.</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.