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Sex-dimorphic and age-dependent organization of 24 hour gene expression rhythms in human
<p>Supplementary data</p>
COMPARATIVE ASSESSMENT OF REPRODUCTIVE INDICATORS DEPENDING ON THE BREED OF CATTLE IN THE ANDIJAN REGION.
Open the record for dataset details and reuse information.
Data, code, and outputs for: groundwater-dependent ecosystem map exposes global dryland protection needs
<p>Contains all data and code used to produce results for:</p> <p>Rohde, M.M.<strong>,</strong> C.M. Albano, X. Huggins, K.R. Klausmeyer, C. Morton, A. Sharman, E. Zaveri, L. Saito, Z. Freed, J.K. Howard, N. Job, H. Richter, K. Toderich, A. Rodella, T. Gleeson, J. Huntington, H.A. Chandanpurkar, A.J. Purdy, J.S. Famiglietti, M.B. Singer, D.A. Roberts, K. Caylor, J.C. Stella. 2024<em>.</em> Groundwater-dependent ecosystem map exposes global dryland protection needs. <em>Nature</em>, doi: 10.1038/s41586-024-07702-8.</p> <p>The resultant global groundwater-dependent ecosystem interactive webmap is available at <a href="https://codefornature.projects.earthengine.app/view/global-gde">https://codefornature.projects.earthengine.app/view/global-gde</a>.</p> <p>The code is also available at <a href="https://github.com/XanderHuggins/global-gde-map">https://github.com/XanderHuggins/global-gde-map</a>.</p>
Supporting data and code for "The scale-dependent effect of environmental filters on species turnover and nestedness in an estuarine benthic community".
<p>R code and dataset for: Menegotto A., Dambros C.S. & Netto S.A. 2019. The scale-dependent effect of environmental filters on species turnover and nestedness in an estuarine benthic community. Ecology, 100, e02721.</p>
Expression of Extraocular opsin Genes and Light-Dependent Basal Activity of Blind Cavefish
<p><strong>Background. </strong>Animals living in well-lit environments utilize optical stimuli for detecting visual information, regulating the homeostatic pacemaker, and controlling patterns of body pigmentation. In contrast, many subterranean animal species without optical stimuli have evolved regressed binocular eyes and body pigmentation. Interestingly, some fossorial and cave-dwelling animals with regressed eyes still respond to light. These light-dependent responses may be simply evolutionary residuals or they may be adaptive, where negative phototaxis provides avoidance of predator-rich surface environments. However, the relationship between these non-ocular light responses and the underlying light-sensing Opsin proteins has not been fully elucidated.</p> <p><strong>Methods. </strong>To highlight the potential functions of opsins in a blind subterranean animal, we used the Mexican cave tetra to investigate opsin gene expression in the eyes and several brain regions of both surface and cave-dwelling adults.<strong> </strong>We performed database surveys, expression analyses by quantitative reverse transcription PCR (RT-qPCR), and light-dependent locomotor activity analysis using pinealectomized fish, one of the high-opsin expressing organs of cavefish.</p> <p><strong>Results. </strong>Based on conservative criteria, we identified 33 opsin genes in the cavefish genome. Surveys of available RNAseq data found 26 of these expressed in the surface fish eye as compared to 24 expressed in cavefish extraocular tissues, 20 of which were expressed in the brain. RT-qPCR of 26 opsins in surface and cavefish eye and brain tissues showed the highest opsin-expressing tissue in cavefish was the pineal organ, which expressed exo-rhodopsin at 72.7 % of the expression levels in surface fish pineal. However, a pinealectomy resulted in no change to the light-dependent locomotor activity in juvenile cavefish and surface fish. Therefore, we conclude that, after 20,000 or more years of evolution in darkness, cavefish light-dependent basal activity is regulated by a non-pineal extraocular organ.</p>
Dataset for 'Context-dependent dispersal mutualisms mediate coexistence of unequal competitors in a metapopulation'
<div> <div>This repo contains code and data for manuscript titled 'Context-dependent dispersal mutualisms mediate coexistence of unequal competitors in a metapopulation'.</div> <div>Mutualisms are context-dependent interactions, with their costs and benefits fluctuating in space and time. Due to their impact on species growth, mutualisms can mediate the coexistence of competing species. One such context-dependent mutualism is endozoochory, where frugivores acquire nutrition by predating on fruits while dispersing their seeds via excretion. The presence of costs and benefits in these mutualisms at different spatial scales and of different currencies (i.e. local predation vs global dispersal) necessitates developing mechanistic models to understand their dynamics. Here, we study how frugivory could engender coexistence between two competing plant species across connected habitats. By combining local population dynamics with ideas from metapopulation theory, we decipher the conditions under which dispersive mutualisms engender competitive coexistence across habitats. We find that frugivore dispersal, fruit consumption rates, and degree of specialisation all contribute to shaping the coexistence of competing fruiting plant species across patches.</div> </div>
Figure 4 in The web amount and quality of web spiders (Agelenidae, Pholcidae), Agelena labyrinthica (Clerck, 1757) and Holocnemus pluchei (Scopoli, 1763), depending on food and temperature
Figure 4. Temperature change related to the amount of food in Agelena labyrinthica.
Metaproteogenomics resolution of a high-CO2 aquifer community reveals a complex cellular adaptation of groundwater Gracilibacteria to a host-dependent lifestyle
<p>This dataset contains the Supplementary files S1 and S2 of the publication "Metaproteogenomics resolution of a high-CO2 aquifer community reveals a complex cellular adaptation of groundwater Gracilibacteria to a host-dependent lifestyle". The first of the datasets is a protein sequence database used as a reference for metaproteomics in the study (with simplified unique headers compatible with the software). The metadata file contains reference names to convert ProteinIDs from the fasta file to their original GeneID as well as further Metadata (such as the functional and taxonomic annotation of the protein identifiers). For more information, please read the publication, currently available as a preprint at https://www.biorxiv.org/content/10.1101/2023.12.18.572140v2 .</p>
Figure 9 in Biogeography of marine tintinnid ciliates (Ciliophora, Tintinnida): a Scale-Dependent Model
Figure 9. Species accumulation curve for tintinnid ciliates diversity in the Atlantic Ocean.
Figure 11 in Biogeography of marine tintinnid ciliates (Ciliophora, Tintinnida): a Scale-Dependent Model
Figure 11. Species accumulation curve for tintinnid ciliates diversity in the Pacific Ocean.
Figure 13 in Biogeography of marine tintinnid ciliates (Ciliophora, Tintinnida): a Scale-Dependent Model
Figure 13. Species accumulation curve for tintinnid ciliates diversity in the Indian Ocean.
Eq 1 from: Pellegrini TG, Sales LP, Aguiar P, Ferreira RL (2016) Linking spatial scale dependence of land-use descriptors and invertebrate cave community composition. Subterranean Biology 18: 17-38. https://doi.org/10.3897/subtbiol.18.8335
Eq 1 -
Thickness Dependent Electronic Properties of Pt Dichalcogenides – PtX2 (X = S, Se, and Te)
<p>POSCAR files of all the calculated systems for the study entitled, "Thickness Dependent Electronic Properties of Pt Dichalcogenides – PtX<sub>2</sub> (X = S, Se, and Te)".</p>
Graph of the dependence of the temperature of welding of the leather tissue of sheepskins during the canning process
<p>Graph of the dependence of the temperature of welding of the leather tissue of sheepskins during the canning process</p>
Morphology-Dependent Influences on the Performance of Battery Cells with a Hierarchically Structured Positive Electrode
<p><i>Raw data for the publication:</i></p><p><i> </i>NAUMANN, Johanna, et al. Morphology‐Dependent Influences on the Performance of Battery Cells with a Hierarchically Structured Positive Electrode. <i>Batteries & Supercaps</i>, 2023, S. e202300264.</p><p><a href="https://doi.org/10.1002/batt.202300264">https://doi.org/10.1002/batt.202300264</a></p>
Determination of the best point of entry of percutaneous insertion of sacroiliac screws depending on patient positioning for surgery: a cadaveric study
<p>Supplemental file, including raw data analysed in the manucript titled <em>Determination of the best point of entry of percutaneous insertion of sacroiliac screws depending on patient positioning for surgery: a cadaveric study.</em></p>
All raw data for "Tributary mitigates river discontinuity by dam depending on the distance from dam to the tributary confluence"
<p>All raw data for "Tributary mitigates river discontinuity by dam depending on the distance from dam to the tributary confluence". The units of the variables were shown in the paper. "quadrate" means the number of each quadrate site in each study reach for measuring the variables.</p>
Varied effects of tobacco smoke and e-cigarette vapor suggest that nicotine does not affect endothelium-dependent relaxation and nitric oxide signaling
<p>Chronic smoking causes dysfunction of vascular endothelial cells, evident as a reduction of flow-mediated dilation in smokers, but the role of nicotine is still controversial. Given the increasing use of e-cigarettes and other nicotine products, it appears essential to clarify this issue. We studied extracts from cigarette smoke (CSE) and vapor from e-cigarettes (EVE) and heated tobacco (HTE) for their effects on vascular relaxation, endothelial nitric oxide signaling, and the activity of soluble guanylyl cyclase. The average nicotine concentrations of CSE, EVE, and HTE were 164, 800, and 85 µM, respectively. At a dilution of 1:3, CSE almost entirely inhibited the relaxation of rat aortas and porcine coronary arteries to acetylcholine and bradykinin, respectively, while undiluted EVE, with a 15-fold higher nicotine concentration, had no significant effect. With about 50% inhibition at 1:2 dilution, the effect of HTE was between CSE and EVE. Neither extract affected endothelium-independent relaxation to an NO donor. At the dilutions tested, CSE was not toxic to cultured endothelial cells but, in contrast to EVE, impaired NO signaling and inhibited NO stimulation of soluble guanylyl cyclase. Our results demonstrate that nicotine does not mediate the impaired endothelium-dependent vascular relaxation caused by smoking.</p>
Occurrence dataset for Sales & Parrott (2023): "The owls are coming: positive effects of climate change in Northern ecosystems depend on grassland protection"
<p>Records from virtual databases were downloaded using the function occ() from the R package spocc. All occurrences were thoroughly assessed for their completeness and reliability. Occurrence records located exactly over centroids of municipalities and political polygons were removed from the dataset, in addition to duplicates, incomplete coordinates, and those from museums, using the suite of clean_coordinates functions from R package CoordinateCleaner. Occurrences with spatial autocorrelation structures widely divergent from the rest of the dataset coupled with coordinates outside the known extent of occurrence of the species, taken from the International Union for the Conservation of Nature, were also removed. Maintaining the contemporaneity with the climatic dataset, we also removed records dated before the year 1970.<br> </p>
Dependency Practices for Vulnerability Mitigation
<p>This is the replication package for our paper on dependency practices for mitigating vulnerabilities.</p> <p>Here is a short description of what is contained in this package:</p> <p><strong>Vul. Extraction</strong></p> <p>The code to extract vulnerability info from the npm advisories in json format.</p> <p><strong>Data</strong></p> <p>The preliminary datasets curated for the project. The raw data can be extracted from libraries.io and the npm advisories on github.com.</p> <p><strong>Model Code</strong></p> <p>The code for feature extraction, feature preprocessing and model training.</p> <p><strong>Visualization Scripts</strong></p> <p>The visualizer.py file includes the visualization scripts used for the paper.</p> <p><strong>Analysis Code</strong></p> <p>The analysis code used for findings of RQ1.</p> <p><strong>Survey Responses</strong></p> <p>The raw anonymized survey responses for RQ3.</p>
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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.