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4,694 results for “data analysis”
Data for: Urban form and its impacts on air pollution and access to green space: A global analysis of 462 cities
Open the record for dataset details and reuse information.
Data for a meta-analysis of the effect of kelp forests on fish communities around the world from observational and experimental studies spanning 1983-2020
Data for Pérez-Matus, A., Micheli, F., Konar, B., Shears, N., Low, N., Okamoto, D., Wernberg, T., Krumhansl, K., Ling, S., Kinsgford, M., Navarrete-Fernandez, T., Ruz, C., and Byrnes, J. 2024. Kelp forests as nursery and foundational habitat for reef fish. Ecology. For the definitive analysis, see the paper. Code is at https://github.com/jebyrnes/fish_kelp_meta. This data set concerns the effects of kelp on fish community composition. Data was mined as part of the National Center for Ecological Analysis and Synthesis (NCEAS) working group on "Global impacts of climate change on kelp forest ecosystems." It consists of digitized information from studies searched (see methods) examining fish community composition with and without kelp. To summarize the study, conservation of marine biodiversity requires an understanding of the habitats needed to support and replenish species of interest. It also requires knowledge about the abundance and diversity of multi-species assemblages. Variation in the distribution and composition of kelp forests, one of the most productive marine coastal habitats globally, can have major influences on reef fishes – a group of ecologically and socio-economically important species. In the face of widespread and escalating loss of kelp forests, quantification of these effects is urgently needed to assess and project cascading impacts on biodiversity. Here, we evaluate relationships between kelp forests and associated reef fish populations using a global meta-analysis of experimental kelp removals and comparative surveys of kelp and adjacent non-kelp habitats. These analyses show that kelp forests increase the abundance of reef fishes, though the significance of this effect varied depending on the structural complexity of kelp forests. In experimental studies, kelp forests have a significant positive effect on fish species richness, revealing that kelp act as true foundation species by supporting the diversity of associated multi-species assemblag
Data for a global meta-analysis of passive experimental warming effects on plant traits and community properties
This database contains the data used in a global meta-analysis of warming effects on plants. L0 data are available upon request; they include the raw data from 126 warming experiments. The L1 data are the result of merged L0 data and are cleaned for typos and are standardized names. L1 data contain plant trait and community property measurements in both warmed and ambient conditions. L2 data contain the effect sizes of warming for each study. These data came from 126 warming experiments across the globe.
Marcell Experimental Forest peat core extraction chemical analysis data (DOC, Fe, Ca, Mg, K, P, Al)
This data set reports iron (Fe), dissolved organic carbon (DOC), calcium (Ca), magnesium (Mg), potassium (K), phosphorus (P), and aluminum (Al) measured in extractions of soil cores sampled from two boreal peatlands, the S1 and S2 bogs, in the Marcell Experimental Forest (MEF) in Itasca County, Minnesota. The soil cores were sampled on September 2, 2017. Elements were quantified in extractions with hydrochloric acid, sodium dithionite, sodium sulfate, and sodium dithionite plus hydrochloric acid to examine how iron influences carbon and nutrient cycling in peatlands. The S1 and S2 sites are research catchments instrumented for hydrologic monitoring. The S1 bog is also the location of the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment. These data are used, analyzed, and reported in Curtinrich et al. (2021, Ecosystems).
Plant-mediated root methane emissions and oxidation in a thermokarst bog complex in the Bonanza Creek LTER Experimental Forest V - Raw Microbial Community Analysis Data 2015
Vascular plants are important in the wetland methane cycle but their effect on production, oxidation, and transport has high uncertainty, limiting our ability to predict emissions. Vegetation operated on top of baseline methane emissions, which varied with proximity to the thawing permafrost margin. Emissions from vegetated plots increased over the season, resulting in cumulative seasonal methane emissions that were 4.1-5.2 g m-2 season-1 greater than unvegetated plots. Mass balance calculations signify these greater emissions were due to increased methane production (3.0-3.5 g m-2 season-1) and decreased methane oxidation (1.1-1.6 g m-2 season-1). Minimal oxidation occurred along the plant-transport pathway and oxidation was suppressed outside the plant pathway. Our data indicate suppression of methane oxidation was stimulated by root exudates fueling competition among microbes for electron acceptors. Root exudates are known to fuel methane production and our work provides evidence they also decrease methane oxidation. This dataset contains 2015 results from monthly DNA analyses taken on cores from natural conditions in a bog complex in the Bonanza Creek LTER.
Sequence data from viral assembly graph analysis of the SERC virome
<p>Various sequence data and details that were used in publishing the manuscript describing assembly graph binning in the SERC viral metagenome. Including: assembled contigs, FASTG, predicted ORFs, two tables describing the assembled contigs and graphs.</p> <p>Also PolA and RNR sequences that were mined from the SERC assembly.</p>
Definitive dataset framework of the Data Analysis on Sutri, HISMAGIS protocol.
<p>Definitive dataset framework of the Data Analysis on Sutri, HISMAGIS protocol.</p> <p>All the feature class, geodatabase and collector carpets have been translated in English.</p>
Head-Neck-Radiomics-HN1 data processed with Pyradiomics ready to use for data analysis
<p>We downloaded <a href="https://wiki.cancerimagingarchive.net/display/Public/Head-Neck-Radiomics-HN1">Head-Neck-Radiomics-HN1, </a>align CT and segmentation images and use PyRadiomics to extract all kind of features for data analysis.</p> <p>CSV contains all the features. Some of them are settings information, setting information should be remove before any data analysis. By using feature extraction algorithm or... by checking values, all the settings have the same values in the columns. Each row is a patient.</p> <p> </p> <p> </p>
Data and Python script for article "A text mining analysis of the climate change literature in industrial ecology'
<p>The data and Python script are part of the forum article "A text mining analysis of the climate change literature in industrial ecology" authored by Dayeen, F.R., Sharma, A.S., and Derrible, S., and published in the <em>Journal of Industrial Ecology</em> in 2020.</p> <p>The Python script and instructions are included in the LiTCoF_v1.00-py.zip file. The original data is available in two formats: .csv and .pkl.</p> <p>Updates of the script will be posted at https://github.com/csunlab/LiTCoF and at https://csun.uic.edu/codes/LiTCoF.html. The data is also available at https://csun.uic.edu/datasets.html#AbstractsIE.</p> <p>Feel free to contact any of the authors for information and questions about the data and code.</p>
Diversification and Management Practices in Selected European Regions. A Data-analysis of Arable Crops Production and soil organic carbon
<p>This data set contains a data-mining performed to assess the impact of intercropping, tillage and fertilizer type on soil organic carbon and crop yield in arable crops from four selected European pedoclimatic regions and typical cropping systems in the Atlantic, Boreal, Mediterranean North, and Mediterranean South regions. A further meta-analysis was performed with these data. </p> <p>These data correspond to the open-access articles:</p> <p>- Diversified Arable Cropping Systems and Management Schemes in Selected European Regions Have Positive Effects on Soil Organic Carbon Content. Agriculture 2019, 9, 261. https://www.mdpi.com/2077-0472/9/12/261?type=check_update&version=2</p> <p>- Diversification and Management Practices in Selected European Regions. A Data-analysis of Arable Crops Production. Agronomy 2020, 10, 297; doi:10.3390/agronomy10020297. https://www.mdpi.com/2073-4395/10/2/297</p> <p>- Deficit Drip Irrigation in Processing Tomato Production in the Mediterranean Basin: A Data Analysis for Italy. Agriculture 2019, 9, 79; doi:10.3390/agriculture9040079. https://www.mdpi.com/2077-0472/9/4/79?type=check_update&version=2</p> <p>The research and publications have been funded by he European Commission Horizon 2020 project Diverfarming [grant agreement 728003]. </p>
Data of "Investigating the potential for genetic improvement of nitrogen and phosphorus efficiency of in a Swiss Large White pigs population using chemical analysis"
<p>Data for article 'Investigating the Potential for Genetic Improvement of Nitrogen and Phosphorus Efficiency in a Swiss Large White Pig Population using Chemical Analysis' (DOI: 10.1111/JBG.12472). Dataset of 294 Swiss Large White pigs for which phenotypes of nitrogen efficiency, phosphorus efficiency (both determined by chemical analysis of N and P content of empty body and carcass as well as the feed ingested over the experiment phase), average daily gain and gain:feed ratio are available. We also provide the pedigree that was used to estimate genetic parameters in animal models and a description of the variables (metadata).</p>
Input data for the analysis of changes in functional structures of Japanese tree species by species loss simulation
<p>The dataset was used in Kusumoto, Shiono & Kubota (2020). It includes functional structure indices (community means, functional richness, and Rao's quadratic entropy) for 514 Japanese timber and non-timber tree species at 10-km grid cell level. The community means were based on specific leaf area and leaf nitrogen content, respectively. Functional richness and Rao's Q were based on wood density and tree height. There functional metrics were calculated for the observed species assemblages and simulated assemblages at 10-km grid cell level. The simulated assemblages were computed by removing species in each grid cell at 5 levels of species loss (10%, 20%, 30%, 40% and 50%) with two scenarios: random loss and ordered loss depending on species successional niche score (i.e. later successinal species are preferentially lost). See "README" sheet for detailed explanations of the contents.</p> <p>Kusumoto, Shiono & Kubota (2020) Ethnobotany-informed trait ecology: measuring vulnerability of timber provisioning services across forest biomes in Japan. Biodiversity and Conservation. DOI: 10.1007/s10531-020-01974-y</p>
Microbiota data analysis lesson datasets
<p>Datasets to be used in the Carpentry-style lesson on [microbiota data analysis](https://scienceparkstudygroup.github.io/microbiome-lesson/).</p> <p>Datasets from the paper: Zancarini, A., Echenique-Subiabre, I., Debroas, D. <em>et al.</em> Deciphering biodiversity and interactions between bacteria and microeukaryotes within epilithic biofilms from the Loue River, France. <em>Sci Rep</em> <strong>7, </strong>4344 (2017). https://doi.org/10.1038/s41598-017-04016-w. <a href="https://rdcu.be/b3CZh">https://rdcu.be/b3CZh</a></p>
ZENODO TEST: ALE Variant Analysis data and scripts
<p>ALE Variant Analysis data and scripts</p>
Dataset used for "Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data"
<p>Each simulated dataset was generated using the AbSim R package (version 0.2.6) in a B cell single-lineage fashion. Each B cell clone simulation begins with a random selection from sets of IGHV, IGHD, and IGHJ germline sequences to produce a unique V(D)J recombination event. Then, clones are made by introducing mutations using a local nucleotide context-dependent model (S5F model) along a phylogenetic tree in which branching events occur stochastically. </p>
Data from NanoSIMS analysis, software LANS_LeKieffre et al. 2020_ Proceedings B
<p>Data extracted from NanoSIMS analysis with the software <a href="mailto:Look@NanoSIMS">Look@NanoSIMS</a> (Polerecky et al. 2012). Different foraminiferal cytoplasmic compartments and the symbiotic dinoflagellates were analyzed for their 13C/12C and 15N/14N isotopic ratios. Three experiments were made: incubations with (1) 13C-bicarbonate and 15N-ammonium, (2) 13C-bicarbonate and 15N-nitrate, and (3) feeding with 13C- and 15N-labeled food. Details can be found in the manuscript:<br> LeKieffre C. et al. 2020. Ammonium is the preferred source of nitrogen for planktonic foraminifer and their dinoflagellate symbionts. Proceedings of the Royal Society B.</p>
In-hospital patient safety events, healthcare costs and utilization: an analysis of data from the incident reporting system in an academic medical center
<p>Raw Datasets for the study 'In-hospital patient safety events, healthcare costs and utilization: an analysis of data from the incident reporting system in an academic medical center'.</p>
MarTREC Data Set for Report: Developing and Applying an Analysis Methodology to Identify Flow Generation Influences between Vessel and Truck Shipments
<p>Truck activity is logically connected to vessel activity at a port. In turn, vessel activity is also influenced by truck shipments. Although one might expect a direct and straightforward relation between these two types of shipments, that is rarely the case. For instance, many maritime containers carry consolidated cargos that have multiple and different final destinations. Also, different truck capacities, customs clearance and regulations play a critical role in determining the actual relation between these two types of shipments. This project aims at shedding light on the nuances of maritime and roadway flow relations by quantitatively analyzing the linkages between these two types of shipments.</p> <p>The study performed a statistical analysis to determine the probability distributions of vessel and truck activity, and then explore the correlation of each activity with the other. The analysis yielded coefficients that function as explanatory values for specific truck flows.</p> <p>The ultimate purpose of this study is to provide a clearer and quantitative understanding of the relationship between maritime and truck shipments, and by doing so, to provide tools to develop a system for managing trucks that maximizes efficiency for industry, while minimizing industry’s negative impacts on a region.</p> <p>For this purpose, the study selected the Port Freeport as a case study.</p>
Data from: Single cell RNA-seq analysis reveals that prenatal arsenic exposure results in long-term, adverse effects on immune gene expression in response to Influenza A infection
<p>Arsenic exposure via drinking water is a serious environmental health concern. Epidemiological studies suggest a strong association between prenatal<i> </i>arsenic exposure and subsequent childhood respiratory infections, as well as morbidity from respiratory diseases in adulthood, long after systemic clearance of arsenic.<i> </i>We investigated the impact of exclusive prenatal arsenic exposure on the inflammatory immune response and respiratory health after an adult influenza A (IAV) lung infection. C57BL/6J mice were exposed to 100 ppb sodium arsenite<i> in utero,</i> and subsequently infected with IAV (H1N1) after maturation to adulthood. Assessment of lung tissue and bronchoalveolar lavage fluid (BALF) at various time points post IAV infection reveals greater lung damage and inflammation in arsenic exposed mice versus control mice. Single-cell RNA sequencing analysis of immune cells harvested from IAV infected lungs suggests that the enhanced inflammatory response is mediated by dysregulation of innate immune function of monocyte derived macrophages, neutrophils, NK cells, and alveolar macrophages. Our results suggest that prenatal arsenic exposure results in lasting effects on the adult host innate immune response to IAV infection, long after exposure to arsenic, leading to greater immunopathology. This study provides the first direct evidence that exclusive prenatal exposure to arsenic in drinking water causes predisposition to a hyperinflammatory response to IAV infection in adult mice, which is associated with significant lung damage.</p>
Data from Mehra et al. (2020-05-29), "Hydroxychloroquine or chloroquine with or without a macrolide for treatment of COVID-19: a multinational registry analysis"
<p>Recent <a href="http://doi.org/dw8t">reports</a> have identified errors and implausible results in the <a href="http://doi.org/ggwzsb">title paper</a>, few of which have been corrected to date. To facilitate analysis, I provide a spreadsheet containing all data from tables in the corrected version (2020-05-29), from both the main text (html) and supporting information (PDF).</p> <p><br> The data is uploaded to this publicly-funded repository with the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7255293/">permission</a> of the copyright holder: <em>"Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories ... with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source."</em> Text and data mining are also <a href="http://web.archive.org/web/20200602210529/https://www.elsevier.com/connect/coronavirus-information-center">permitted</a>: <em>"These articles are also available to download with rights for full text and data mining, re-use and analyses for as long as needed."</em></p>
ScienceDex guides
Understand access before you commit
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.