Find research datasets worth reusing

opencc-by-4.0Sep 2021View details →

Supplement tables of Facilitating Antiviral Drug Discovery by Genetic and Evolutionary Knowledge

Table S1: 36 human targets for approved antiviral drugs downloaded from Drugbank, Table S2: Supplementary information for Table 2, Table S3: Pockdrug druggability prediction results.

opencc-by-4.0May 2021View details →

Supplemental Material to Journal Article "Probabilistic Approach for the Fatigue Strength Prediction of Polymers"

This set supplements the figure and table data to the article "Probabilistic Approach for the Fatigue Strength Prediction of Polymers", DOI: <a href="https://doi.org/10.2514/1.J060444">https://doi.org/10.2514/1.J060444</a> The Python code to reproduce the results shown in the article is released as v1.0 of the MAMO toolbox for material models DOI: The latest code development can be cloned at <a href="https://github.com/mrosemeier/mamo">https://github.com/mrosemeier/mamo</a>.

opencc-by-4.0Oct 2021View details →

Meso-scale patterns of shallow convection in the trades: supplemental material

Supplemental material to the dissertation: Meso-scale patterns of shallow convection in the trades <ol> <li>ICON_EUREC4A_LES.mov Animation of actual (GOES-16 ABI) and synthetic satellite images for the simulated period. GOES-16 ABI; ICON 624m; ICON 312m (from left to right)  </li> </ol>

opencc-zeroOct 2021View details →

Supplemental material for: Increased large vessel occlusive strokes following the Christchurch 2019 March 15 terror attack

<div class="WordSection1"> Background: The impact of sudden catastrophic events such as terror attacks on stroke is unclear. We investigated the association between the 2019 March 15 Christchurch terror attack and ischaemic stroke admissions and reperfusion therapies. Methods: We used a Bayesian Poisson model to estimate the effect of the terror attack on ischaemic stroke admissions, the numbers of intracranial large vessel occlusion (LVO) and reperfusion therapy, in the week after the attack compared with weekly data from 1st January 2018 until 21st April 2019. These analyses were repeated for the rest of New Zealand with Christchurch data omitted. The probability of the rate observed in the week following the terror attack being higher than the background rate was calculated for each measure, with a probability higher than 99.5% providing strong evidence of an effect. Results: In the week starting on Monday, three days after the terror attack, there was an increase in the number of patients with intracranial LVOs (10, background mean rate=2.4, probability P>99.9%) and those receiving reperfusion therapy (9, mean rate=2.6, P=99.9%), compared with the baseline rates. There was no difference in the total number of ischemic stroke admissions (26, mean rate=27). There was no strong evidence of a change in the numbers of reperfusion therapies or ischaemic stroke admissions in the rest of New Zealand. Conclusion: Sudden catastrophic events such as terror attacks may increase the numbers of patients developing intracranial LVO requiring stroke reperfusion therapies within the affected community. </div>

opencc-by-nc-sa-3.0Oct 2021View details →

The State of the Urban Forest in New York City - Supplemental Datasets

Summary: The files available here contain summary data for the urban forest of New York City, associated with the report, The State of the Urban Forest in New York City, developed by The Nature Conservancy and released in 2021. Methods and data used in development of these files are described in Appendix 1 of the report. and additional details and supplemental code are available at <a href="https://github.com/tnc-ny-science/NYC_StateOfUrbanForest_Docs">https://github.com/tnc-ny-science/NYC_StateOfUrbanForest_Docs</a>. If you do not find what you are looking for here, you may contact Michael Treglia at michael.treglia@tnc.org.   Terms of Use © The Nature Conservancy. This material is provided as-is, without warranty under a Creative Commons Attribution-NonCommercial-ShareAlike License as set forth in our Conservation Gateway Terms of Use (available at: <a href="http://conservationgateway.org/Pages/Terms-of-Use.aspx">http://conservationgateway.org/Pages/Terms-of-Use.aspx</a>) If using these data, please cite the both the report and the data, based on the following recommended citations. Recommended citation for the report: Treglia, M.L., Acosta-Morel, M., Crabtree, D., Galbo, K., Lin-Moges, T., Van Slooten, A., Maxwell, E.N. 2021. The State of the Urban Forest in New York City. The Nature Conservancy. doi: 10.5281/zenodo.5532876 Recommended citation for the data is: Treglia, M.L., Acosta-Morel, M., Crabtree, D., Galbo, K., Lin-Moges, T., Van Slooten, A., Maxwell, E.N. 2021. The State of the Urban Forest in New York City - Supplemental Datasets. The Nature Conservancy. doi: 10.5281/zenodo.5210261   Contents canopy_jurisdiction_landuse_borough.zip - Zipped folder with comma separated values (.csv) file of land and canopy area summaries by approximated general ownership type, land use categories, and natural/developed breakdown, with Data Dictionary files in .docx and .html formats. canopy_streettree_summaries.zip - Zipped folder containing GeoPackage, Esri File Geodatabase, and comma separated values (.csv) files with canopy and street tree summary data at the scales of Neighborhood Tabulation Area, Community District, City Council District, and Borough, with Data Dictionary files in .docx and .html formats. equity_data.zip - Zipped folder containing GeoPackage, Esri File Geodatabase, and comma separated values (.csv) files with data used for equity analyses at the scale of Neighborhood Tabulation Area, with Data Dictionary files in .docx and .html formats. naturalareas_canopy_jurisdiction_borough.zip - Zipped folder with comma separated values (.csv) file of summaries of natural area canopy data by approximated general ownership type and by borough, with Data Dictionary files in .docx and .html formats.   *Note for the contents of equity_data.zip: For data in this .zip folder, the column named "relativecanopychange_percent" represents relative canopy change from 2010 to 2017 as proportions, not percentages. To convert these numbers to percentages, values can be multiplied by 100. The data are accurately depicted in the report, and column names are otherwise accurate in this repository.

opencc-zeroOct 2021View details →

Dietary nitrate supplementation prevents radiotherapy-induced xerostomia

Management of salivary gland hypofunction caused by irradiation (IR) therapy for head and neck cancer remains lack of effective treatments. Salivary glands, especially the parotid gland, actively uptake dietary nitrate and secrete it into saliva. Here, we investigated the effect of dietary nitrate on the prevention and treatment of IR-induced parotid gland hypofunction in miniature pigs, and elucidated the underlying mechanism in human parotid gland cells (hPGCs). We found that nitrate administration prevented IR-induced parotid gland damage in a dose-dependent manner, by maintaining the function of irradiated parotid gland tissue. Mechanically, Nitrate could increase sialin expression, a nitrate transporter expressed in the parotid gland, making the nitrate-sialin feedback loop that facilitates nitrate influx into cells for maintaining cell proliferation and inhibiting apoptosis. Nitrate enhanced cell proliferation via the epidermal growth factor receptor (EGFR)–protein kinase B (AKT)–mitogen-activated protein kinase (MAPK) signaling pathway in irradiated parotid gland tissue. Collectively, nitrate effectively prevented IR-induced xerostomia via the EGFR–AKT–MAPK signaling pathway. Dietary nitrate supplementation may provide a novel, safe, and effective way to resolve IR-induce xerostomia.

opencc-zeroOct 2022View details →

Data From: Long-term winter food supplementation shows no significant impact on reproductive performance in Mountain Chickadees in the Sierra Nevada Mountains

Supplemental feeding of wild animal populations is popular across many areas of the world and has long been considered beneficial, especially to avian taxa. Over four billion dollars are spent by hobby bird feeders in the United States each year alone. However, there is mixed evidence whether wildlife feeding is beneficial, including when it is implemented as a conservation management tool, a targeted experimental design, or an avocation. Much of the current evidence suggests that providing supplemental food is advantageous to the reproductive output and general survival of focal taxa. However, many of these studies are limited in scope and duration, leaving possible negative impacts unaddressed. This is particularly true regarding passive backyard feeding, which describes the majority of supplemental feeding, including the immense effort of millions of public enthusiasts. Here we show that winter supplemental feeding prior to reproduction had no significant impact on a range of reproductive parameters in a resident, montane passerine species, the Mountain Chickadee (Poecile gambeli). This population resides in an intact natural environment with no exposure to supplemental food beyond our experimental treatments, and individual birds were tracked across six years using radio frequency identification technology. Our results add to the growing evidence that supplemental feeding alone, isolated from the effects of urban environments, may have little to no impact on the population dynamics of some avian taxa.

opencc-by-4.0Jan 2022View details →

Host phylogeny and elevation predict infection by avian haemosporidians in a diverse New Guinean bird community (R script for analyses, figures, and supplemental figures )

This script performs the glmm analysis of the elevation and infection prevalence data as well as the script required to generate the figures in the article.

opencc-by-4.0Oct 2022View details →

Supplemental data for "Applications and Limitations of Portable Density Meter Measurements Of Na-Ca-Mg-K-Cl-SO4 Brines"

Geochemistry, brine density measurements, environmental observations and geochemical modeling of the Bonneville Salt Flats and surrounding area.

Supplemental Fig.S5

Supplemental Fig. S5 Different anatomy of the RV and LV. (A) Schematic diagram of the anatomy of the RV and LV. (B) HE staining of the heart on P7. Noted that the RV has two layers and two types of fibers (clockwise spiral fibers and longitudinal fibers), whereas the LV has three layers and three types of fibers (clockwise spiral fibers, anti-clockwise spiral fibers, and longitudinal fibers).

Supplemental Fig.S4

Supplemental Fig. S4 Immune response associated GO and KEGG terms enriched by volume overload (VO). (A) Top 10 immune response associated GO terms enriched in RV comparison. (B) Top 10 immune response associated KEGG terms enriched in RV comparison. (C) Top 10 immune response associated GO terms enriched in LV comparison. (E) Top 10 immune response associated KEGG terms enriched in LV comparison.

Supplemental Fig.S3

Supplemental Fig. S3 Biological process (BP) and Cellular component (CC)  terms of GO analysis shared by the LV and RV under the condition of VO. (A) Biological process (BP) terms of the GO analysis shared by the LV and RV under VO conditions. (B) Cellular component (CC) terms of the GO analysis shared by the LV and RV under VO conditions.

Supplemental Fig.S2

Supplemental Fig. S2 Biological process (BP) and Cellular component (CC)  terms of GO analysis shared by the LV and RV under the condition of VO. (A) Biological process (BP) terms of GO analysis shared by LV and RV. (B) Cellular component (CC) terms of GO analysis shared by LV and RV.

Video supplement for Ho et al. (2022: GMD)

Video Supplement for the publication

opencc-zeroNov 2022View details →

Supplemental data for: Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities

Microbiomes are intricately intertwined with human health, geochemical cycles, and food production. While many microbiomes of interest are highly complex and experimentally intractable, cheese rind microbiomes have proven powerful model systems for the study of microbial interactions. To provide a more comprehensive view of the genomic potential and temporal dynamics of cheese rind communities, we combine longitudinal, multi-platform metagenomics of three ripening washed-rind cheeses with whole genome sequencing of community isolates. Sequencing-based approaches revealed a highly reproducible microbial succession in each cheese, co-existence of closely related Psychrobacter species, and enabled the prediction of plasmid and phage diversity and their host associations. Combined with culture-based approaches, we established a genomic catalog and a paired 16-member in vitro washed rind cheese system. The combination of multi-platform metagenomic time-series data and an in vitro model provides a rich resource for further investigation of cheese rind microbiomes both computationally and experimentally.

Lipid metabolism, fatty acid composition and meat quality in broilers supplemented with increasing levels of defrosted black soldier fly larvae

Dataset for the experiment to evaluate the effects of increasing levels of whole black soldier fly larvae (BSFL) in broiler diets on lipid metabolism, fatty acid composition, and meat quality of birds. Chicks received the whole BSFL at 10%, 20%, or 30% of the feed intake of control chickens that received no BSFL but only age-specific diets. <a href="https://doi.org/10.3920/JIFF2022.0125">https://doi.org/10.3920/JIFF2022.0125</a>

opencc-zeroDec 2022View details →

Supplemental information and Data for: Colloidal physics modeling reveals how per-ribosome productivity increases with growth rate in E. coli

Faster growing cells must synthesize proteins more quickly. Increased ribosome abundance only partly accounts for increases in total protein synthesis rates. The productivity of individual ribosomes must increase too, almost doubling by an unknown mechanism. Prior models point to diffusive transport as a limiting factor but surface a paradox: faster growing cells are more crowded, yet crowding slows diffusion. We suspected physical crowding, transport, and stoichiometry, considered together, might reveal a more nuanced explanation. To investigate, we built a first-principles physics-based model of E. coli cytoplasm in which Brownian motion and diffusion arise directly from physical interactions between individual molecules of finite size, density, and physiological abundance. Using our microscopically-detailed model, we predict that physical transport of individual ternary complexes accounts for ~80% of translation elongation latency. We also find that volumetric crowding increases at faster growth even as cytoplasmic mass density remains relatively constant. Despite slowed diffusion, we predict that improved proximity between ternary complexes and ribosomes wins out, illustrating a simple physics-based mechanism for how individual elongating ribosomes become more productive. We speculate how crowding imposes a physical limit on growth rate and undergirds cellular behavior more broadly. Unfitted colloidal-scale modeling offers systems biology a complementary "physics engine" for exploring how cellular-scale behaviors arise from physical transport and reactions among individual molecules.

opencc-by-4.0Dec 2022View details →

Supplemental Information in Support of "Moment tensor event identification for collapses"

Supplemental Information in support of manuscript "Moment tensor event identification for collapses". File 00_Collapse_MT_Table.csv is a summary of moment tensor solutions for all of the collapses in this manuscript. A Jupyter notebook (file 00_Collapse_MT_Table.ipynb) is provided which loads the information from the provided table and creates an example plot of one of the full moment tensor solutions and plots all the solutions on a global map. The notebook creates two PNG images mt.png and map.png which are also provided. Directories (e.g., 1980-06-12_Southern_Nevada) contain figures showing waveform fits for the collapses. For each event, the waveforms to the left show displacement data (black) and synthetics (red - used in inversion, blue - predicted only) for the vertical, radial, and transverse components.  Detailed information about the event and the moment tensor solution are provided on the right-hand side of the last figure.

opencc-zeroDec 2022View details →

Data from: Lipidome modulation by dietary omega-3 polyunsaturated fatty acid supplementation or selective soluble epoxide hydrolase inhibition suppresses rough LPS-accelerated glomerulonephritis in lupus-prone mice

Lipopolysaccharide (LPS)-accelerated autoimmune glomerulonephritis (GN) in lupus-prone NZBWF1 mice is a preclinical model that is potentially applicable for investigating lipidome-modulating interventions. LPS can be expressed as one of two chemotypes: smooth LPS (S-LPS) and rough LPS (R-LPS) which is devoid of O-antigen polysaccharide sidechain. Since these chemotypes differentially affect TLR4-mediated immune cell responses, these differences may influence GN induction. Therefore, we initially compared the effects of subchronic i.p. injection for 5 wk with 1) Salmonella S-LPS, 2) Salmonella R-LPS, or 3) saline vehicle (VEH) (Study 1) in female NZBWF1 mice. R-LPS induced robust elevations in blood urea nitrogen, proteinuria, and hematuria that were not evident in VEH- or S-LPS-treated mice. Histopathologic examination of R-LPS-treated mice one week after final injection further revealed more robust hypertrophy, hyperplasia, thickened membranes, lymphocytic accumulation containing B and T cells, and glomerular IgG deposition consistent with GN but not in VEH- or S-LPS-treated groups. R-LPS but not S-LPS induced spleen enlargement with lymphoid hyperplasia as well as modest inflammatory cell recruitment in the liver. We next employed our optimized R-LPS model to discern the impact of two lipidome-modulating interventions, omega-3 polyunsaturated fatty acid (PUFA) supplementation and soluble epoxide hydrolase (sEH) inhibition, on GN (Study 2). Specifically, the effects of consuming the omega-3 PUFA docosahexaenoic acid (DHA) (10 g/kg diet) and/or the sEH inhibitor TPPU (22.5 mg/kg diet) on R-LPS triggering were compared. Resultant blood fatty acid profiles and epoxy fatty acid concentrations reflected the anticipated DHA- and TPPU-mediated lipidome changes. The relative rank order of R-LPS-induced GN severity among groups fed experimental diets based on proteinuria, hematuria, histopathologic scoring, and glomerular IgG deposition was: VEH/CON < R-LPS/DHA ≈ R-LPS/TPPU <<< R-LPS/ TPPU+DHA ≈ R-LPS/CON. These interventions had modest to negligible effects on R-LPS-induced splenomegaly, plasma antibody responses, liver inflammation, and inflammation-associated kidney gene expression. Collectively, our results show for the first time that absence of O-antigenic polysaccharide in R-LPS is critical to accelerated GN in lupus-prone mice. Furthermore, intervention by lipidome modulation through DHA feeding or sEH inhibition suppressed R-LPS-induced GN; however, these ameliorative effects were greatly diminished upon combining the treatments.