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2023_ Datasets and R source code of "Allometry Bird Mitochondrial Bioenergetics"
<p>METHODOLOGICAL INFORMATION</p> <p>This dataset contains mitochondrial bioenergetic data and enzymatic activities of our studies from two tissues: skeletal and cardiac muscles, of 13 bird species ranging from 15 g to 160 kg.<br> Methodology: mitochondrial isolation, respiration, enzyme assays, measurement of body mass<br> All analyses were performed in R version 4.2.1 (R Core Team 2022), using phylogenetic comparative analyses.</p> <p><strong>## Description of the Data and file structure "2023_Data_Allometry Bird mitochondrial bioenergetics"</strong></p> <p>The file contains two sheets: one for the skeletal muscle data and the second for the cardiac muscle. <br> For each section you will find: the name of the species studied, the number of individuals, their body mass (in grams), mitochondrial flux measurements (oxygen consumption, ATP synthesis, ROS generation), ratios (RCR, Slope, Mitochondrial efficiency ATP/O...) and enzymatic activity measurements. </p> <p>Missing data correspond to individuals for whom we were unable to collect data (e.g. no heart samples, not enough tissue for analysis...)</p> <p><strong>## Phylogenetic tree " BirdTree_MCMCglmm "</strong></p> <p>The phylogenetic tree combining the 13 species studied was obtained from the BirdTree.org website (Rubolini et al., 2015).The tree source used was Hackett Sequenced Species: a set of 10 000 trees with 6670 OTUs each (Hackett et al., 2008). We performed 1000 simulations to create the most parsimonious tree. The avian tree was summarized using BEAST (v1.10.4, 2002-2018) to create a target tree usable in nexus format in R version 4.2.1 (R Core Team 2022). The parameters used were: burnin as a number of trees (100), maximum clade credibility tree as target tree type, and common ancestor heights.</p>
Figs 73-84. Pedomyia gen. n., r in Afrotropical Asilidae (Diptera) 25. A key to the genera of the subfamily Stenopogoninae with new synonymy and descriptions of six new genera
Figs 73-84. Pedomyia gen. n., r:J genitalia. 73-75. P. namibia sp. n. paratype (28 km W Outjo). 73. Lateral. 74. Dorsal. 75. Ventral. 76-78. P. simba sp. n. paratype (15 km E Wellington). 76. Lateral. 77. Dorsal. 78. Ventral. 79-81. P. xalllhocera sp. n. paratype (20 km NE Springbok). 79. Lateral. 80. Dorsal. 81. Ventral. 82-84. P. zela sp. n. paratype (10 km N Tulbagh). 82. Lateral. 83. Dorsal. 84. Ventral. Scale lines = I mm.
Additional QCD Background Events for LHCO2020 R&D (signal region only)
<p>These are an additional ~610k QCD dijet background events, in the "signal region" region only (meaning, with mJJ in the range 3.3-3.7 TeV), produced using the same simulation settings as those of the <a href="https://doi.org/10.5281/zenodo.2629072">LHCO2020 R&D Dataset</a>. The features are as described at that link:</p> <p>'pxj1', 'pyj1', 'pzj1', 'mj1', 'tau1j1', 'tau2j1', 'tau3j1', 'pxj2', 'pyj2', 'pzj2', 'mj2', 'tau1j2', 'tau2j2', 'tau3j2'</p> <p>They were used in <a href="https://arxiv.org/abs/2109.00546">CATHODE</a> for training the idealized anomaly detector and supervised classifier, as well as for final evaluation of all the anomaly detection methods. </p> <p><strong>Update September 22, 2023</strong></p> <p>An additional file was uploaded that contains the momentum 3-vectors of all the particles in each event, in addition to the 14 high level features listed above. As in the original LHCO R&D dataset, up to 700 particles are included, with zero padding for events with fewer than 700 particles. So the shape of the dataset is </p> <pre>(612858, 2114)</pre> <p>with the first 2100 entries corresponding to the 3-momenta, in the order px0,py0,pz0,px1,py1,pz1,...,px699,py699,pz699; and the last 14 entries corresponding to the high level features listed above. </p>
R code and datasets for flower-visitor interactions (pollinators, robbers, thieves) and plant traits from Mount Cameroon
<p>Raw data and R code for: <strong>Cheaters among pollinators: Nectar robbing and thieving vary spatiotemporally with floral traits in Afrotropical forests. </strong><i>Ecosphere, 2023</i>. doi: 10.1002/ecs2.4696<br> </p><p>When using the dataset for anything, cite the Sakhalkar et al. <i>Ecosphere </i>paper.</p><p><br>All related information can be found in the cited paper. For additional information, refer to the paper or write to either robert.tropek@gmail.com or sailee.sakha@gmail.com.</p>
Datasets and R code associated with: Acute Health Effects of Wildfire Smoke Exposure During a Compound Event: A Case-Crossover Study of the 2016 Great Smoky Mountain Wildfires
<p>The attached code and csv files accompany the manuscript titled: Acute Health Effects of Wildfire Smoke Exposure During a Compound Event: A Case-Crossover Study of the 2016 Great Smoky Mountain Wildfires by Duncan et al. accepted for publication in the journal GeoHealth in September 2023. </p> <p><a href="https://zenodo.org/api/files/8e030710-b091-48a9-aec4-f9b3de6a0325/Project%20wildfire%20data.csv">Project wildfire data.csv</a> contains a subset wildfire data obtained from:</p> <p>Short, Karen C. 2022. Spatial wildfire occurrence data for the United States, 1992-2020 [FPA_FOD_20221014]. 6th Edition. Fort Collins, CO: Forest Service Research Data Archive. https://doi.org/10.2737/RDS-2013-0009.6</p> <p><a href="https://zenodo.org/api/files/8e030710-b091-48a9-aec4-f9b3de6a0325/Modeled%20PM2.5%20data_clean.csv">Modeled PM2.5 data_clean.csv</a> includes modeled PM<sub>2.5</sub> concentrations used to make Figure 2. Model results can be obtained from <a href="https://www.epa.gov/hesc/rsig-related-downloadable-data-files">EPA's Fused Air Quality Surfaces Using Downscaling Tool</a>. <a href="https://zenodo.org/api/files/8e030710-b091-48a9-aec4-f9b3de6a0325/plot_Modeled.R">plot_Modeled.R</a> contains the R code to generate this figure. </p> <p><a href="https://zenodo.org/api/files/8e030710-b091-48a9-aec4-f9b3de6a0325/ORs%20all%20Counties.csv">ORs all Counties.csv</a> contains the odds ratios, confidence intervals, and p-values used to make Figures 3, 4, and 5.<a href="https://zenodo.org/api/files/8e030710-b091-48a9-aec4-f9b3de6a0325/PM2.5%2035ug-m3%20ORs.csv">PM2.5 35ug-m3 ORs.csv</a> contains the odds ratios, confidence intervals, and p-values used to make Figure S1. <a href="https://zenodo.org/api/files/8e030710-b091-48a9-aec4-f9b3de6a0325/Wildfire_Forest.R">Wildfire_Forest.R</a> contains the R code to generate these figures. </p>
"It was recorded on Sunday, morning of the 28th of September as some of the slower runners of the Berlin Marathon made it past Torstrasse near my flat. Iwas out to buy some bread for breakfast, but Iusually bring a camera and my Edirol R-1 recorder whenever Igo out. Since Iwas freshly returned to Berlin Iguess Iwas sensitive to the more antiquated sounds which still survive there, like that of the organ grinder. Iam generally interested in how human beings are replacing the presence of Nature with an artificial environment made entirely by human hands (and thus far more understandable, it is hoped). In this new Human Nature, the sounds of Nature are also Human made. Iwrite about these things, but Ialso use the sounds in my videos and my interactive and generative media work, so generally Iam wandering around building up my archive of media documents for use as material in future works." [Baruch/ gottlieb]17 in Collecting Sounds. Online Sharing of Field Recordings as Cultural Practice
"It was recorded on Sunday, morning of the 28th of September as some of the slower runners of the Berlin Marathon made it past Torstrasse near my flat. Iwas out to buy some bread for breakfast, but Iusually bring a camera and my Edirol R-1 recorder whenever Igo out. Since Iwas freshly returned to Berlin Iguess Iwas sensitive to the more antiquated sounds which still survive there, like that of the organ grinder. Iam generally interested in how human beings are replacing the presence of Nature with an artificial environment made entirely by human hands (and thus far more understandable, it is hoped). In this new Human Nature, the sounds of Nature are also Human made. Iwrite about these things, but Ialso use the sounds in my videos and my interactive and generative media work, so generally Iam wandering around building up my archive of media documents for use as material in future works." [Baruch/ gottlieb]17
Study of Efficacy and Safety of MBG453 in Combination With Azacitidine in Subjects With Intermediate, High or Very High Risk Myelodysplastic Syndrome (MDS) as Per IPSS-R, or Chronic Myelomonocytic Leu
ClinicalTrials.gov study NCT04266301. IPD Sharing: YES. Countries: 36. Publications: 1.
A Study of MBG453 in Combination With Hypomethylating Agents in Subjects With IPSS-R Intermediate, High or Very High Risk Myelodysplastic Syndrome (MDS).
ClinicalTrials.gov study NCT03946670. IPD Sharing: YES. Countries: 17. Publications: 1.
(QuANTUM-R): An Open-label Study of Quizartinib Monotherapy vs. Salvage Chemotherapy in Acute Myeloid Leukemia (AML) Subjects Who Are FLT3-ITD Positive
ClinicalTrials.gov study NCT02039726. IPD Sharing: YES. Countries: 19. Publications: 3.
Data for: rtrees: An R package to assemble phylogenetic trees from megatrees
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Key Biodiversity Areas (KBAs) R package, KBAscope, application to Greece
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Data from: Ppgm: an R package for integrating neontological, palaeontological, and climate data in a phylogenetic comparative framework
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R code for differential gene expression and enrichment analyses
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SSP: An R package to estimate sampling effort in studies of ecological communities
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R scripts, input and output data for: Season of death, pathogen persistence and wildlife behaviour alter number of anthrax secondary infections from environmental reservoirs
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Area and Timing data and R script for: 3D scanning as a tool to measure growth rates of live coral microfragments used for coral reef restoration
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Data and R code used for the GLMM and NBDA analyses in 'Captive Asian short-clawed otters (Aonyx cinereus) learn to exploit unfamiliar natural prey'
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funspace: an R package to build, analyze and plot functional trait spaces
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R code for: Following regulation, imidacloprid persists and flupyradifurone increases in non-target wildlife
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Data and R code used in: Plant geographic distribution influences chemical defenses in native and introduced Plantago lanceolata populations
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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.