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Data_supplemental figure 3_Enzymatic interconversion of the oxysterols 7β,25 dihydroxycholesterol and 7-keto,25-hydroxycholesterol by 11β-hydroxysteroid dehydrogenase type 1 and 2
<p>Data of supplemental figure 3 from Enzymatic interconversion of the oxysterols 7β,25 dihydroxycholesterol and 7-keto,25-hydroxycholesterol by 11β-hydroxysteroid dehydrogenase type 1 and 2</p> <p>Dataset (doi:<a href="https://doi.org/10.1016/j.jsbmb.2019.03.011">10.1016/j.jsbmb.2019.03.011</a>) contains the original figure as PNG format (<a href="https://doi.org/10.1016/j.jsbmb.2019.03.011">10.1016/j.jsbmb.2019.03.011</a>_FigS3). Corresponding raw data obtained from liquid scintillation analysis provided as three files in CSV format (31003A-179400_date_name_27Oxysterol_11_7_1-3). All further experiment related information and subsequent data analysis provided as meta-data-file (31003A-179400_date_name_25Oxysterol_11_7_M) as TXT format.</p>
Data_supplemental figure 1_Enzymatic interconversion of the oxysterols 7β,25 dihydroxycholesterol and 7-keto,25-hydroxycholesterol by 11β-hydroxysteroid dehydrogenase type 1 and 2
<p>Data of supplemental figure 1 Enzymatic interconversion of the oxysterols 7β,25 dihydroxycholesterol and 7-keto,25-hydroxycholesterol by 11β-hydroxysteroid dehydrogenase type 1 and 2</p> <p>Dataset (doi:<a href="https://doi.org/10.1016/j.jsbmb.2019.03.011">10.1016/j.jsbmb.2019.03.011</a>) contains the original figure as PNG format (<a href="https://doi.org/10.1016/j.jsbmb.2019.03.011">10.1016/j.jsbmb.2019.03.011</a>_FigS1). Data obtained from LC-MS/MS measurements subsequent data analysis (31003A-179400_date_name_25Oxysterol_4_7_1) provided as one CSV file and meta-data-files (31003A-179400_date_name_25Oxysterol_4_7_M_1) as PDF format.</p>
Data Supplement: U.S. state-level projections of the spatial distribution of population consistent with Shared Socioeconomic Pathways.
<p>These data are to supplement the following in-press publication: </p> <p>Zoraghein, H., and O'Neill B. (2020). U.S. state-level projections of the spatial distribution of population consistent with Shared Socioeconomic Pathways. Sustainability.</p> <p>The data herein were generated using the `population_gravity` model which can be found here: <a href="https://github.com/IMMM-SFA/population_gravity">https://github.com/IMMM-SFA/population_gravity</a></p> <p>CONTENTS:</p> <p><strong>zoraghein-oneill_population_gravity_inputs_outputs.zip</strong></p> <ul> <li>contains a directory for each U.S. state for inputs and outputs</li> <li><strong>inputs</strong> contain the following: <ul> <li><strong><state-name>_<urban or rural>_<yr>_1km.tif: </strong> Urban and Rural population GeoTIF rasters at a 1km resolution <ul> <li>value per grid cell: number of humans (float)</li> <li>crs: EPSG:102003 - USA_Contiguous_Albers_Equal_Area_Conic - Projected</li> <li>nodata value: -3.40282e+38</li> </ul> </li> <li><strong><state-name>_mask_short_term.tif: </strong> Mask GeoTIF rasters at a 1km resolution that contain values from 0.0 to 1.0 for each 1 km grid cell to help calculate suitability depending on topographic and land use and land cover characteristics <ul> <li>value per grid cell: values from 0.0 to 1.0 (float) that are generated from topographic and land use and land cover characteristics to inform suitability as outlined in the companion publication</li> <li>crs: EPSG:102003 - USA_Contiguous_Albers_Equal_Area_Conic - Projected</li> <li>nodata value: -3.40282e+38</li> </ul> </li> <li><strong><state-name>_<ssp>_popproj.csv: </strong> Population projection CSV files for urban, rural, and total population (number of humans; float) for SSPs 2, 3, and 5 for years 2010-2100</li> <li><strong><state-name>_coordinates.csv: </strong>CSV file containing the coordinates for each 1 km grid cell within the target state. File includes a header with the fields XCoord, YCoord, FID.,Where data types and field descriptions are as follows: (XCoord, float, X coordinate in meters),(YCoord, float, Y coordinate in meters),(FID, int, Unique feature id)</li> <li><strong><state-name>_within_indices.txt: </strong>text file containing a file structured as a Python list (e.g. [0, 1]) that contains the index of each grid cell when flattened from a 2D array to a 1D array for the target state.</li> <li><strong><state-name>_<ssp>_params.csv: </strong>CSV file containing the calibration parameters (alpha_rural, beta_rural, alpha_urban, beta_urban; float) for the `population_gravity` model for each year from 2010-2100 in 10-year time-steps as described in the companion publication</li> </ul> </li> <li><strong>outputs</strong> contain the following: <ul> <li><strong>jones_oneill</strong> directory; these are the comparison datasets used to build Figures 7 and 8 in the companion publication <ul> <li>contains three directories: SSP2, SSP3, and SSP5 that each contain a GeoTIF representing total population (number of humans; float) at 1km resolution for years 2050 and 2100. <ul> <li><strong><state-name>_1km_<ssp>_total_<year>_jones_oneill.tif:</strong> <ul> <li>value per grid cell: number of humans (float)</li> <li>crs: EPSG:102003 - USA_Contiguous_Albers_Equal_Area_Conic - Projected</li> <li>nodata value: -3.40282e+38</li> </ul> </li> </ul> </li> </ul> </li> <li><strong>model</strong> directory; these are the model outputs from `population_gravity` for SSP2, SSP3, and SSP5 that each contain a GeoTIF representing urban, rural, and total population (number of humans; float) at 1km resolution for years 2020-2100 in 10-year time-steps. <ul> <li><strong><state-name>_1km_<ssp>_<urban, rural, or total>_<year>_jones_oneill.tif:</strong> <ul> <li>value per grid cell: number of humans (float)</li> <li>crs: EPSG:102003 - USA_Contiguous_Albers_Equal_Area_Conic - Projected</li> <li>nodata value: -3.40282e+38</li> </ul> </li> </ul> </li> </ul> </li> </ul> <p> </p> <p><strong>zoraghein-oneill_population_gravity_national-ssp-maps.zip</strong></p> <ul> <li>Results of the `population_gravity` model mosaicked to the National scale at a 1km resolution and the comparison Jones and O'Neill research. These are used to generate Figure 6 of the companion paper <ul> <li><strong>National_1km_<ssp>_<urban, rural, or total>_<year>_jones_oneill.tif:</strong> <ul> <li>value per grid cell: number of humans (float)</li> <li>crs: EPSG:102003 - USA_Contiguous_Albers_Equal_Area_Conic - Projected</li> <li>nodata value: -3.40282e+38</li> </ul> </li> <li><strong>National_1km_<ssp>_<urban, rural, or total>_<year>.tif:</strong> <ul> <li>value per grid cell: number of humans (float)</li> <li>crs: EPSG:102003 - USA_Contiguous_Albers_Equal_Area_Conic - Projected</li> <li>nodata value: -3.40282e+38</li> </ul> </li> </ul> </li> </ul> <p> </p>
FIGURE 2 in Supplement to the knowledge of the Tachinus longicornis-group (Coleoptera: Staphylinidae: Tachyporinae) in China
FIGURE 2. Diagnostic features of Tachinus motuoensis Chang, Li & Yin, sp. nov. (A–E. Male. F–G. Female). A, F. Tergite VIII. B. Sternite VII. C, G. Sternite VIII. D–E. Aedeagus, ventral (D) and lateral (E). Scale bars: 0.2 mm.
FIGURE 1 in Supplement to the knowledge of the Tachinus longicornis-group (Coleoptera: Staphylinidae: Tachyporinae) in China
FIGURE 1. Habitus of Tachinus motuoensis Chang, Li & Yin, sp. nov., A. Male. B. Female. Scale bars: 1.0 mm.
Supplemental Material to Journal Article "Assessment of a rotor blade extension retrofit as a supplement to the lifetime extension of wind turbines"
<p>This set supplements the figure data to the article "Assessment of a rotor blade extension retrofit as a supplement to the lifetime extension of wind turbines", DOI: .</p>
Data supplement for "Thin-Film Modeling of Resting and Moving Active Droplets"
<p>This dataset contains the data and source files for figures 4-10, 12, and 14-20 in the following publication: </p> <p>S. Trinschek, F. Stegemerten, K. John and U. Thiele</p> <p><em>"Thin-Film Modeling of Resting and Moving Active Droplets"</em></p> <p>published in 2020 in Physical Review E.</p> <p>Please follow the instructions given in 'Readme.txt'.</p>
FIGURE 3 in Description of a new species in the genus Bythotrephes Leydig, 1860 (Crustacea Cladocera: Onychopoda), supplements to selected species, and concluding remarks on the genus
FIGURE 3. Bythotrephes centralasiaticus sp. nov., females, Lake Kadysh (Tyva, Southern Siberia). A, distal part of mandible (a group of broken minute spinules is arrowed). B, anterior mandibular lobe (mandibular process). C, prominences of mandibular process. D, proximal part of tl II and tl III, outer side. E, apical end of pseudognathobase of tl II. F, the same one of tl III. Scale bars: 5µm (C), 10 µm (B, E, F), 25µm (A), 100 µm (D).
FIGURE 5 in Description of a new species in the genus Bythotrephes Leydig, 1860 (Crustacea Cladocera: Onychopoda), supplements to selected species, and concluding remarks on the genus
FIGURE 5. Bythotrephes cederströmii, females of first generation hatched from resting egg, Lake Imandra (Kola Peninsula, Russia) (A-upper, B); B. lilljeborgi, females, Ålsjön (Kragered, Halland, Sweden) (A-lower, C–F). A, distal segments of tl I. B, postabdomen and caudal process. C–F, claws of postabdomen and caudal process.
3D-CCD: Supplemental Figures and Video
<p>The cortical collecting duct (CCD) of the mammalian kidney plays a major role in the maintenance of total body electrolyte, acid/base and fluid homeostasis by tubular reabsorption and excretion. The mammalian CCD is heterogeneous, comprised of Na+-absorbing principal cells (PCs) and acid-base transporting intercalated cells (ICs). Perturbations in luminal flow rate alter hydrodynamic forces to which these cells in the cylindrical tubules are exposed. However, most studies of tubular ion transport have been performed in cell monolayers grown on or epithelial sheets affixed to a flat support, since analysis of transepithelial transport in native tubules by in vitro microperfusion requires considerable expertise. Here, we report on the generation and characterization of an in vitro, perfusable 3D kidney CCD model (3D CCD), in which immortalized mouse PC-like mpkCCD cells are seeded within a cylindrical channel embedded within an engineered extracellular matrix and subjected to luminal fluid flow. We find that a tight epithelial barrier composed of differentiated and polarized PCs forms within 1 week. Immunofluorescence microscopy reveals the apical epithelial Na<sup>+</sup> channel ENaC and basolateral Na<sup>+</sup>/K<sup>+</sup>-ATPase. On cessation of luminal flow, benzamil-inhibitable cell doming is observed within these 3D CCDs consistent with the presence of ENaC-mediated Na+ absorption. Our 3D CCD provides a geometrically and microphysiologically relevant platform for studying the development and physiology of renal tubule segments.</p>
Data sets used in the study "To supplement estuaries turbidity theory: An investigation of low turbidity zones in estuaries "
<p>This is the data sets used in the study "To supplement estuaries turbidity theory: An investigation of low turbidity zones in estuaries "</p>
Supplement to "Dynamic model of photovoltaic module temperature as a function of atmospheric conditions"
<p>This dataset contains data from two measurement campaigns in autumn 2018 and summer 2019 that were part of the BMWi project "MetPVNet", and serve as a supplement to the paper "Dynamic model of photovoltaic module temperature as a function of atmospheric conditions", published in the special edition of "Advances in Science and Research", the proceedings of the 19th EMS Annual Meeting: European Conference for Applied Meteorology and Climatology 2019.</p> <p>Data are resampled to one minute, and include:</p> <ol> <li>PV module temperature</li> <li>Ambient temperature</li> <li>Plane-of-array irradiance</li> <li>Windspeed</li> <li>Atmospheric thermal emission</li> </ol> <p>The data were used for the dynamic temperature model, as presented in the paper</p>
Supplemental Data S1
<p>ScanFold output for all genomes. Raw output alongside files used to visualize data on IGV or other genome viewers. Please see README for descriptions of each file. Additional information on using ScanFold and analyzing output files is available in (Andrews et al. 2019). Dataset available as a Zenodo repository at:</p>
Protein Subcellular localization prediction data used in the article entitled "MSclassifier: Median-Supplement model-based Classification tool for automated knowledge discovery"
<p>This repository contains data used to obtain results from a 5-fold cross-validation testing of how MSclassifier and other packages accurately predict protein subcellular localization in the software article entitled "MSclassifier: median-supplement model-based classification tool for automated knowledge discovery." The data used in the software article is derived from data generated in "G. K. Acquaah-Mensah, S. M. Leach, and C. Guda, Predicting the subcellular localization of human proteins using machine learning and exploratory data analysis, Genomics Proteomics Bioinformatics, 4(2):120-133, 2006, <a href="https://doi.org/10.1016/S1672-0229(06)60023-5">https://doi.org/10.1016/S1672-0229(06)60023-5</a>"</p>
Supplemental Materials for "Formation of interstellar complex polycyclic aromatic hydrocarbons: Insights from molecular dynamics simulations of dehydrogenated benzene"
<p>Supplemental Materials for the article entiled "Formation of interstellar complex polycyclic aromatic hydrocarbons: Insights from molecular dynamics simulations of dehydrogenated benzene" authored by M. Hanine et al. at Laboratory for Relativistic Astrophysics, Department of Physics, Guangxi University, 530004 Nanning, China.</p> <p>email: zw@gxu.edu.cn (Zhao Wang)</p> <p>SuppMater1.zip :</p> <p>Atomistic configurations of the formed PAH molecules (in 4.0 ns) at all studied temperatures are available in .xyz format. These .xyz files contain the atomic coordinates of the formed molecules by giving the total number of atoms that will be read on the first line; the comment text on the second; and the atomic number and three atomic Cartesian coordinates in the following lines. The name of the .xyz file consists of four parts separated by ``\_'' including the source molecule type, the temperature, the formation environment (with NP or in gas phase), and the molecular ID (among multiple molecules formed in a simulation). For instance, ``C6H2\_300K\_gas\_2.xyz'' stands for the 2nd molecule formed from C6H at 300K in the gas phase. Please read the 'readme.txt' file before using the data.</p> <p> </p> <p>SuppMater2.pdf:</p> <p>A data file that contains the DFT-calculated optimized structures and their atomic coordinates.</p> <p> </p> <p>SuppMater3.mp4:</p> <p>An animation demonstrating the formation process of PAHs on a carbon NP.</p>
A Unified Translation of Linear Temporal Logic to ω-Automata: Supplemental Material for the Experimental Evaluation
<p>This dataset contains the evaluated tools and the data on which the experimental evaluation section of the article "A Unified Translation of Linear Temporal Logic to ω-Automata" by Javier Esparza, Jan Křetínský, and Salomon Sickert is based on. Further, we include instructions on how to recreate the results.</p>
Supplemental tables from: Antifibrogenic activities of CYP11A1-derived vitamin D3-hydroxyderivatives are dependent on RORγ
<p>Previous studies showed that non-calcemic 20(OH)D3, a product of CYP11A1 action on vitamin D3, has antifibrotic activity in human dermal fibroblasts and in a bleomycin mouse model of scleroderma. In this study we tested the role of RORγ, which is expressed in skin, in the action of CYP11A1-derived secosteroids using murine fibroblasts isolated from the skin of wild type (RORg<sup>+/+</sup>), knock out (RORg<sup>-/-</sup>) and heterozygote (RORg<sup>+/-</sup>) mice<span>. CYP11A1-derived </span>20(OH)D3, 20,23(OH)<sub>2</sub>D3, 1,20(OH)<sub>2</sub>D3, and 1,20,23(OH)<sub>3</sub>D3 inhibited proliferation of RORγ<sup>+/+</sup> fibroblasts in a dose-dependent manner with a similar potency to 1,25(OH)<sub>2</sub>D3. Surprisingly, this effect was reversed in RORγ<sup>+/-</sup> and RORγ<sup>-/-</sup> fibroblasts with the most pronounced stimulatory effect seen in RORγ<sup>-/-</sup> fibroblasts. All of the analogs tested inhibited TGF-β1-induced collagen synthesis in RORγ<sup>+/+</sup> fibroblasts and the expression of other fibrosis-related genes. This effect was curtailed or reversed in ROR<span>γ</span><sup>-/-</sup> fibroblasts. These results show that the antiproliferative and antifibrotic activities of the vitamin D hydroxy-derivatives are dependent on a functional RORγ. The dramatic changes in the transcriptomes of fibroblasts of RORg<sup>-/-</sup> versus wild type mice following treatment with 20(OH)D3 or 1,20(OH)<sub>2</sub>D3 provide a molecular basis to explain, at least in part, the observed phenotypic differences</p>
Supplemental Materials: Identification of proteins associated with the early restoration of insulin sensitivity after biliopancreatic diversion
<p><b>ABSTRACT</b></p> <p><b>CONTEXT:</b> Insulin resistance (IR) is a risk factor for type 2 diabetes, diabetic kidney disease, cardiovascular disease and non-alcoholic steatohepatitis. Biliopancreatic diversion (BPD) is the most effective form of bariatric surgery for improving insulin sensitivity.</p> <p><b>OBJECTIVE:</b> To identify plasma proteins correlating with the early restoration of insulin sensitivity after BPD.</p> <p><b>DESIGN: </b>Prospective single centre study including twenty insulin resistant men with morbid obesity scheduled for BPD. Patient characteristics and blood samples were repeatedly collected from baseline up to four weeks post-surgery. IR was assessed by HOMA-IR, Matsuda Index and by studying metabolic profiles during meal tolerance tests. Unbiased proteomic analysis was performed to identify plasma proteins altered by BPD. Detailed plasma profiles were made on a selected set of proteins by targeted multiple reaction monitoring mass spectrometry (MRM/MS). Changes in plasma proteome were evaluated in relation to metabolic and inflammatory changes.</p> <p><b>RESULTS</b>: BPD resulted in improved insulin sensitivity and reduced body weight. Proteomic analysis identified 29 proteins changed following BPD. Changes in plasma levels of afamin, apolipoprotein A-IV (ApoA4) and apolipoprotein A-II (ApoA2) correlated significantly with changes in IR.</p> <p><b>CONCLUSION:</b> Circulating levels of afamin, ApoA4 and ApoA2 were associated with and may contribute to the rapid improvement in insulin sensitivity after BPD.</p>
Movement rules determine nomadic species' responses to resource supplementation and degradation
<p>1. In environments that vary unpredictably, many animals are nomadic, moving in an irregular pattern that differs from year to year. Exploring the mechanisms of nomadic movement is needed to understand how animals survive in highly variable environments, and to predict behavioral and population responses to environmental change. 2. We developed a network model to identify plausible mechanisms of nomadic animal movement by comparing the performance of multiple movement rules along a continuum from nomadism to residency. Using simulations and analytical results, we explored how different types of habitat modifications (that augment or decrease resource availability) might affect the abundance and movement rates of animals following each of these rules. 3. Movement rules for which departure from patches depended on either resource availability or competition performed almost equally well and better than residency or uninformed movement under most conditions, even though animals using each rule moved at substantially different rates. Habitat modifications that stabilized resources, either by resource supplementation or degradation, eroded the benefits of informed nomadic movements, particularly for movements based on resource availability alone. 4. These results suggest that simple movement rules can explain nomadic animal movements and determine species' responses to environmental change. In particular, landscape stabilization and supplementation might be useful strategies for promoting populations of resident animals, but would be less beneficial for managing highly mobile species, many of which are threatened by habitat disruption and changes in climate. </p>
Supplemental material for: Growth curves for children with X-linked hypophosphatemia"
<p><span><i>Context: </i>We characterized linear growth in infants and children with X-linked hypophosphatemia (XLH).</span></p> <p><span><i>Objective</i>: Provide linear growth curves for children with XLH from birth to early adolescence.</span></p> <p><span><i>Design</i>: Data from four prior studies of XLH were pooled to construct growth curves. UX023-CL002 was an observational, retrospective chart review. Pre-treatment data were collected from three interventional trials: two phase 2 trials (UX023‑CL201, UX023‑CL205) and a phase 3 trial (UX023-CL301). </span></p> <p><span><i>Setting</i>: Medical centers with expertise in treating XLH. </span></p> <p><span><i>Patients</i>: Children with XLH, 1-14 years of age.</span></p> <p><span><i>Intervention</i>: None.</span></p> <p><span><i>Main Outcome Measure</i>: Height-for-age linear growth curves including values for the 5<sup>th</sup>, 10<sup>th</sup>, 25<sup>th</sup>, 50<sup>th</sup>, 75<sup>th</sup>, 90<sup>th</sup>, and 95<sup>th</sup> percentiles for children with XLH compared to population norms. </span></p> <p><i>Results</i>: 228 patients (132 girls, 96 boys) with 2,381 height measurements were included. Nearly all subjects (>99%) reported prior management with supplementation therapy. Compared to the CDC growth curves, boys at age 0.25, 0.50, 0.75, 1.0, and 2.0 years-old had median height percentiles of 46%, 37%, 26%, 18%, and 5%, respectively; for girls the median height percentiles were 52%, 37%, 25%, 18%, and 7%, respectively. Annual growth in children with XLH fell below that of healthy children near 1 year of age and progressively declined during early childhood, with all median height percentiles <8% between 2 and 12 years old.</p> <p><i>Conclusion</i>: Children with XLH show decreased height gain by 1 year of age and remain below population norms thereafter. These data will help evaluate therapeutic interventions on linear growth for pediatric XLH.<a name="IDX"></a></p>
ScienceDex guides
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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.