cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8357020
title: Trove of Gut Virus Genomes (TGVG)

description: <strong>TGVG_v1.1.genomes.all.fna</strong> Sequences from the Gut Virome Database, the Cenote Human Virome Database, the Metagenomic Gut Virus catalog, and the Gut Phage Database were downloaded and dereplicated at 95% average nucleotide identity (ANI) across 85% alignment fraction (AF) using anicalc.py and aniclust.py from the CheckV (version 0.9.0) package, in line with metagenomic virus sequence community standards. Exemplar sequences from each cluster/singleton from the input sequences were kept and ran through Cenote-Taker 2 (version 2.1.5) to predict virus hallmark genes within each sequence using the ‘virion’ hallmark gene database. Sequences were kept if they 1) encoded direct terminal repeats (signature of complete virus genome), one or more virus hallmark genes, and were over 1.5 kilobases or longer, or 2) encoded 2 or more virus hallmark genes and were over 12 kilobases. Sequences passing this threshold were run through CheckV to remove flanking host (bacterial) sequences and quantify the virus gene/bacteria gene ratio for each contig. Sequences with 3 or fewer virus genes and 3 or more bacterial genes after pruning/were discarded. Finally, sequences passing this threshold were dereplicated again with CheckV scripts at 95% ANI and 85% AF to yield the Trove of Gut Virus Genomes of 110,296 genomes/genome fragments each representing a viral SGB. <strong>TGVG_v1.1_metadata.tsv</strong> For each sequence in the Trove of Gut Virus Genomes CheckV was used to estimate completeness, ipHOP (version 1.1.0) was used to predict bacterial/archael host genus. Bacphlip (version 0.9.3) was run on each of the sequences predicted to be 90% or more complete to predict phage virulence.<br> vConTACT2 (version 0.11.3) was used to cluster viral SGBs from the Trove of Gut Virus Genomes into virus clusters. In addition to viral SGBs with vConTACT2 “Singleton” labels, viral SGBs with vConTACT2 labels “Unassigned”, “Outlier”, “Overlap”, “Clustered/Singleton” were also considered “Singletons” for downstream analysis. Genomad (version 1.5.2) taxonomy module was run on each sequence to obtain taxonomical assignment at the phylum, class, order, and family levels.<br>
DOI: 10.5281/zenodo.8357066
title: MCProj interactive applications

description: MCView applications from the paper: MCProj: metacell projection for interpretable and quantitative use of transcriptional atlases.
DOI: 10.25934/pr00008562
title: Long-term outcomes of renal cell carcinoma patients with stable disease following treatment with Ipilimumab and Nivolumab in randomized controlled trial Checkmate 214

description: There were estimated 79,000 new cases and 13,920 deaths of kidney cancer in the US in 2020, which corresponded to 3.7% of all new cancer cases and 2.3% of cancer-related death. The majority of which were renal cell carcinoma (RCC). Approximately 25% and 30% of the RCC patients presents with regional and distant metastasis at diagnosis. Metastasis means that cancer has spread to a different part of the body than where it started. Even for patients with localized disease, 25-50% patients may eventually develop metastasis. Systemic therapy including molecular inhibitor therapy, immunotherapy or a combination of them are the mainstay of treatment for metastatic RCC. 

Immune checkpoint inhibitors (ICI), a form of immunotherapy for RCC, have the potential to cure patients with metastatic RCC. Combination ICI with Ipilimumab and Nivolumab (Ipi/Nivo) given together followed by maintenance Nivo is one of the approved therapies for metastatic RCC patients. For those experiencing a complete response (CR), induction Ipilimumab (Ipi)/ Nivolumab (Nivo) followed by maintenance Nivo results in overall survival (OS) rates of 97% at 4 years. However, CR rates occur in ~10% of patients. Survival rates plumet in patients with progressive disease (PD) and even stable disease (SD). Despite Nivo maintenance, patients with SD after induction (36%) show significantly reduced 4-year OS rates (55% vs 97%). While by comparison to PD patients (OS rates ~20%), patients with SD derive some benefit from ICI, the full potential of immunotherapy is not realized. We hypothesize that the addition of complementary immune strategies will increase responses and eventually cure rates for patients with SD after induction. This represents an unmet medical need. To unleash the full potential of the immune system, we propose to focus on the patient population that achieved SD after Ipi/Nivo and induce a PR or CR by adding additional immune activating agents to maintenance Nivo. 

The objective of this study will be to focus on the metastatic RCC patients who achieved SD and PD after Ipi/Nivo and report on the details of the Response Evaluation Criteria in Solid Tumor (RECIST) measurements (exact % increase or decrease in the sum of the longest diameter of metastasis) at baseline and at all follow up time points post treatment along with detailed patient characteristics. This data then can be utilized by other groups to induce objective response (PR or CR) in SD or PD patients by the addition of immune-activating agents to the maintenance Nivo therapy which is the current standard of care.
DOI: 10.5281/zenodo.8357116
title: Determination of the best point of entry of percutaneous insertion of sacroiliac screws depending on patient positioning for surgery: a cadaveric study

description: 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>
DOI: 10.5281/zenodo.8357115
title: Determination of the best point of entry of percutaneous insertion of sacroiliac screws depending on patient positioning for surgery: a cadaveric study

description: 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>
DOI: 10.5281/zenodo.8357129
title: railway accidents

description: railway accidents
DOI: 10.5281/zenodo.8357128
title: railway accidents

description: railway accidents
DOI: 10.5281/zenodo.8357146
title: Transport Starter Data Kit: Bangladesh

description: This Transport Starter Data Kit contains historical annual data (1990–2021) on passenger and freight activity, segregated by mode and fuel. Additionally, historical data on energy intensities, load factors, vehicle stock, population (total, urban, rural, growth), and GDP (total, agriculture, construction, mining, manufacturing, service, energy, growth) are included in the kit, within the 'Data' tab. The historical data can be used as a foundation for transport-energy modelling and/or to identify areas of improvement. This data was verified through consultation with relevant stakeholders before publishing. The definition used for each vehicle mode is found in the 'Definitions' tab, and the description of each data observation status is found in the 'Notes' tab. All data sources are linked where possible.
DOI: 10.5281/zenodo.8357145
title: Transport Starter Data Kit: Bangladesh

description: This Transport Starter Data Kit contains historical annual data (1990–2021) on passenger and freight activity, segregated by mode and fuel. Additionally, historical data on energy intensities, load factors, vehicle stock, population (total, urban, rural, growth), and GDP (total, agriculture, construction, mining, manufacturing, service, energy, growth) are included in the kit, within the 'Data' tab. The historical data can be used as a foundation for transport-energy modelling and/or to identify areas of improvement. This data was verified through consultation with relevant stakeholders before publishing. The definition used for each vehicle mode is found in the 'Definitions' tab, and the description of each data observation status is found in the 'Notes' tab. All data sources are linked where possible.
DOI: 10.5281/zenodo.8357123
title: NAMD Trajectory of a POPC/PSM 70/30 bilayer

description: All-atom bilayer mixture of POPC/PSM 70/30 simulated in an NPT ensemble with NAMD and the CHARMM36 force field from Doktorova et al. 2017 Phys. Chem. Chem. Phys. article (DOI 10.1039/c7cp01921a). The trajectory represents the last 126 ns used for analysis where the area per lipid is equilibrated (the file has 3145 frames output every 40 ps). The bilayer has 200 lipids total (100 lipids per leaflet) and is hydrated with 70 waters/lipid and 140mM NaCl. The simulation was done at 25C (298.15K) and the trajectory is centered on the bilayer midplane.
description: Attached files include the structure (.psf and .pdb), trajectory (.dcd) and a copy of the NAMD input file with simulation parameters.
description: {"references": ["Doktorova M, Harries D, and Khelashvili, G. 2017. Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations. Phys. Chem. Chem. Phys. 19:16806-16818. DOI: 10.1039/C7CP01921A"]}
DOI: 10.5281/zenodo.8357122
title: NAMD Trajectory of a POPC/PSM 70/30 bilayer

description: All-atom bilayer mixture of POPC/PSM 70/30 simulated in an NPT ensemble with NAMD and the CHARMM36 force field from Doktorova et al. 2017 Phys. Chem. Chem. Phys. article (DOI 10.1039/c7cp01921a). The trajectory represents the last 126 ns used for analysis where the area per lipid is equilibrated (the file has 3145 frames output every 40 ps). The bilayer has 200 lipids total (100 lipids per leaflet) and is hydrated with 70 waters/lipid and 140mM NaCl. The simulation was done at 25C (298.15K) and the trajectory is centered on the bilayer midplane.
description: Attached files include the structure (.psf and .pdb), trajectory (.dcd) and a copy of the NAMD input file with simulation parameters.
description: {"references": ["Doktorova M, Harries D, and Khelashvili, G. 2017. Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations. Phys. Chem. Chem. Phys. 19:16806-16818. DOI: 10.1039/C7CP01921A"]}
DOI: 10.6084/m9.figshare.22257139
title: Impaired resilience to climate change in Chornobyl barn swallows

description: 1. Global warming and degradation of natural habitats are the two main factors causing ecophysiological stress on individuals and risk for biodiversity. Hyperthermia is a common response to stress in homeothermic animals, in particular to heat, pathogens and environmental contamination. 2. Resilience of biological systems to global warming may be deteriorated in polluted habitats. Here we investigated how body temperature of a wild bird, the barn swallow (Hirundo rustica), responded to global warming while simultaneously exposed to radioactive contamination from Chernobyl accident. 3. Our results showed that both rising air temperatures and environmental radioactive contamination increased internal body temperature of individuals. Importantly, global warming and radioactive contamination both lead to hyperthermia, which in turn is associated with reduced fecundity thus posing a risk to population growth rates. 4. Our results suggest that local habitat contamination can hamper resilience of wild animals to rising temperatures, and that contamination directly and indirectly impairs animal performance. The cumulative and interactive negative effects of multiple stressors, such as those emerging from increasing habitat degradation and climate change, will likely accelerate biodiversity losses globally.
DOI: 10.5281/zenodo.8357178
title: Contamination gx reports for TH

description: .
DOI: 10.5281/zenodo.8357177
title: Contamination gx reports for TH

description: .
DOI: 10.6084/m9.figshare.24158637
title: Cluster_59_linelist

description: Widespread human-to-human transmission of the severe acute respiratory syndrome coronavirus two (SARS-CoV-2) stems from a strong affinity for the cellular receptor angiotensin converting enzyme two (ACE2). We investigate the relationship between a patient’s nasopharyngeal <i>ACE2</i> transcription and secondary transmission within a series of concurrent hospital associated SARS-CoV-2 outbreaks in British Columbia, Canada.<i>Methods</i>: Epidemiological case data from the outbreak investigations was merged with public health laboratory records and viral lineage calls, from whole genome sequencing, to reconstruct the concurrent outbreaks using infection tracing transmission network analysis. <i>ACE2</i> transcription and RNA viral load were measured by quantitative real-time polymerase chain reaction. The transmission network was resolved to calculate the number of potential secondary cases. Bivariate and multivariable analyses using Poisson and Negative Binomial regression models was performed to estimate the association between <i>ACE2</i> transcription the number of SARS-CoV-2 secondary cases.<br><br>Data Dictionary:<br><b>Unit_of_Transmission:</b> Hospital Unit where a infection prevention and control epidemiologist identified a possible transmission event.<br><b>Unit_Acquisition:</b> Hospital Unit where a infection prevention and control epidemiologist identified a possible acquisition event.<br><b>Collection Date (yyyy-mm-dd, UTC):</b> date at which a nasopharyngeal specimen was collected from a symptomatic case for SARS-CoV-2 molecular diagnostic testing using qRT-PCR.<br><b>log_GE: </b> Logarithmic base ten genome-equivalents per millilitre of SARS-CoV-2 detected by envelope gene target using qRT-PCR.<br><b>Fold.Change.ace3: </b> Relative gene expression data of <i>ACE2</i> expression (full-length/ transmembrane transcript variant).<br><b>Linearge: </b>SARS-CoV-2 viral lineage as classified by the PANGOLIN tool (Version 1.15.1), viral genome alignments are available on GISAID. <br>
DOI: 10.6084/m9.figshare.3761562.v2712
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.5281/zenodo.6564970
title: SCI-3000: A Novel Dataset for the Task of Figure, Table and Caption Extraction from Scientific PDFs

description: This dataset contains bounding boxes of figures, tables, captions in 34,791 pages extracted from 3000 open-access scientific publications from the fields of medicine, chemistry, physics, computer science, and technology. The underlying publications are also included in PDF form. For more details, refer to the README file.
description: V1.2 Adds a training/test split for models trained on SCI-3000
DOI: 10.5281/zenodo.6564971
title: SCI-3000: A Novel Dataset for the Task of Figure, Table and Caption Extraction from Scientific PDFs

description: This dataset contains bounding boxes of figures, tables, captions in 34,791 pages extracted from 3000 open-access scientific publications from the fields of medicine, chemistry, physics, computer science, and technology. The underlying publications are also included in PDF form. For more details, refer to the README file.
DOI: 10.5281/zenodo.8165783
title: SCI-3000: A Novel Dataset for the Task of Figure, Table and Caption Extraction from Scientific PDFs

description: This dataset contains bounding boxes of figures, tables, captions in 34,791 pages extracted from 3000 open-access scientific publications from the fields of medicine, chemistry, physics, computer science, and technology. The underlying publications are also included in PDF form. For more details, refer to the README file.
description: V1.1 Adds clarification on rasterization techniques (important for reproducibility)
DOI: 10.5281/zenodo.8357124
title: SCI-3000: A Novel Dataset for the Task of Figure, Table and Caption Extraction from Scientific PDFs

description: This dataset contains bounding boxes of figures, tables, captions in 34,791 pages extracted from 3000 open-access scientific publications from the fields of medicine, chemistry, physics, computer science, and technology. The underlying publications are also included in PDF form. For more details, refer to the README file.
description: V1.2 Adds a training/test split for models trained on SCI-3000
DOI: 10.57909/maxar/ge01_msi_l1b.001
title: GeoEye-1 Level 1B Multispectral 4-Band Satellite Imagery
DOI: 10.57909/maxar/ge01_msi_l2a.001
title: GeoEye-1 Level 2A Multispectral 4-Band Satellite Imagery
DOI: 10.57909/maxar/ge01_pan_l1b.001
title: GeoEye-1 Level 1B Panchromatic Satellite Imagery
DOI: 10.57909/maxar/ge01_pan_l2a.001
title: GeoEye-1 Level 2A Panchromatic Satellite Imagery
DOI: 10.57909/maxar/ge01_msi_3d.001
title: GeoEye-1 Level 3D Multispectral 4-Band Satellite Imagery
DOI: 10.57909/maxar/ge01_pan_3d.001
title: GeoEye-1 Level 3D Panchromatic Satellite Imagery
DOI: 10.21227/8n9n-gq97
title: counting-station-1471

description:  The dataset offers a comprehensive view of traffic conditions observed at a specific counting station, presumably located on a major roadway. It encapsulates various metrics, including the total number of vehicles, categorizations into light and heavy vehicles, and corresponding speed metrics across multiple lanes. Each entry in the dataset represents hourly observations, detailing the traffic flow and speed dynamics. Furthermore, with columns dedicated to average and 85th percentile speeds, the dataset provides insights into typical speed behavior as well as potential speed outliers. The information captured in this dataset is instrumental for urban planners, transportation researchers, and policymakers to analyze traffic patterns, study congestion periods, and formulate strategies for efficient traffic management. Given its focus on both volume and speed metrics, this dataset can also serve as a foundation for predictive modeling endeavors aiming to forecast future traffic conditions.
DOI: 10.6084/m9.figshare.24153333.v1
title: The Dataset for the paper submission entitled as "Practitioner Views on Setting up Analytics for Software Startups: A Guide Based on Gray Literature"

description: This dataset has been used to synthesize the results of the video data on analytics in startups
DOI: 10.34740/kaggle/ds/3754307
title: learn view the watch media
DOI: 10.5281/zenodo.8357266
title: Patterns of Alluviation in Mixed Bedrock-Alluvial Channels

description: <strong>morph2d</strong> Filename: morph2D.f90<br> 2-Dimensional Morphodynamic Model<br> Written by Jongseok Cho and Peter A. Nelson<br> Department of Civil and Environmental Engineering<br> Colorado State University, Fort Collins, Colorado<br> <br> Filename: P1505.mat<br> Results from the simulation of bar formation in a straight flume.<br> <br> Filename: BRtopo.txt<br> Randomly abraded bedrock topography is used to simulate the mixed bedrock-alluvial channels.<br> <br> Filename: XYZ.mat<br> The x- and y-coordinates and bedrock elevation are used in the simulations of mixed bedrock-alluvial channels.<br> <br> Filename: 2-Ax.mat, 2-Bx.mat, and 2-Dx.mat<br> Time evolution of alluvial thickness and the fraction of exposed bedrock surface for the simulations starting from the bare bedrock bed channel.<br> <br> Filename: 2-A.mat and 2-B.mat<br> Time evolution of alluvial thickness and the fraction of exposed bedrock surface for the simulations starting from the alluvial bed channel.<br> <br> Filename: 2-B2-z.mat<br> Time evolution of alluvial thickness and the fraction of exposed bedrock surface for the simulations starting from the alluvial bed channel with different sediment layer thickness.<br> <br> Filename: 2-B2-k.mat<br> Time evolution of total, bed surface, sediment transport, and bedform roughnesses for the simulations starting from the alluvial bed channel with different sediment layer thickness.<br> <br> Filename: 2-B2-x.mat<br> Time evolution of alluvial thickness and the fraction of exposed bedrock surface for the simulations starting from the alluvial bed channel without the effects of bedform and sediment transport roughnesses and shear stress correction for bedload transport.
DOI: 10.18112/openneuro.ds003020.v2.0.3
title: An fMRI dataset during a passive natural language listening task
DOI: 10.25422/azu.data.23820741.v1
title: Post-processed Weather Research and Forecasting model and Community Earth System Model datasets to understand extreme Texas drought and flood years

description: This collection of data includes post-processed Weather Research and Forecasting model (WRF) outputs to understand the extreme Texas drought and flood years. Specific statistical analysis methods used include: Probability of Detection (POD), False Alarm Rate (FAR), Relative Operating Characteristics (ROC), Probability distribution of daily precipitation frequency and pattern correlation maps. Data format includes: Matlab and NetCDF. This data collection is part of research material for a Journal of Geophysical Research - Atmosphere manuscript. Refer to Statistical analysis templates for the Weather Research and Forecasting model and Community Earth System Model for the associated code files. <br> <em>For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu</em> <br>
DOI: 10.25422/azu.data.23820741
title: Post-processed Weather Research and Forecasting model and Community Earth System Model datasets to understand extreme Texas drought and flood years

description: This collection of data includes post-processed Weather Research and Forecasting model (WRF) outputs to understand the extreme Texas drought and flood years. Specific statistical analysis methods used include: Probability of Detection (POD), False Alarm Rate (FAR), Relative Operating Characteristics (ROC), Probability distribution of daily precipitation frequency and pattern correlation maps. Data format includes: Matlab and NetCDF. This data collection is part of research material for a Journal of Geophysical Research - Atmosphere manuscript. Refer to Statistical analysis templates for the Weather Research and Forecasting model and Community Earth System Model for the associated code files. <br> <em>For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu</em> <br>
DOI: 10.6084/m9.figshare.24158691
title: Hussan_2023_PDBs.zip

description: PDB files for septin protein structure prediction and nucleotide binding generated by AlphaFold or <i>in silico</i> docking, respectively.
DOI: 10.6084/m9.figshare.24158691.v1
title: Hussan_2023_PDBs.zip

description: PDB files for septin protein structure prediction and nucleotide binding generated by AlphaFold or <i>in silico</i> docking, respectively.
DOI: 10.5519/qd.fqy9sby5
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (230 records)