cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27237849.v2
title: Triassic tectonic affinity to Indochina-East Malay for West Sumatra and Paleotethyan implications: Constraints from Late Triassic igneous rocks

description: Zircon in-situ U‒Pb dating, in-situ Lu‒Hf isotopic, whole-rock elemental and Sr‒Nd‒Pb isotopic data for the Sibolga granite batholith and newly identified Late Triassic mafic to felsic igneous rocks (227-211Ma) in the Sibolga-Padang Sidempuan area of WST
DOI: 10.6084/m9.figshare.12612068.v2
title: Source Data and Code for "Determinants of genome-wide distribution and evolution of uORFs in eukaryotes"

description: This dataset contains the Source Data underlying all the data figures, and the custom scripts used to prepare data and perform analyses. See README.md for details.
DOI: 10.6084/m9.figshare.26172811.v1
title: 碳金融是否能够促进清洁能源的发展？——低碳技术创新视角

description: 变量类型变量象征定义因变量清洁能源发展CLE公司清洁能源对一次能源总量的贡献（%）解释变量碳金融咖啡馆（以本币和外币计价的绿色贷款余额）/二氧化碳<sub>2</sub>排放量（%）中介变量低碳技术创新LCTI公司低碳技术发明和实用新型专利数量占专利总数的比例（%）控制变量经济发展水平PGDP的人均国内生产总值（2000年不变价美元）外商直接投资外商直接投资外商直接投资额/国内生产总值 （%）生态足迹英 孚人均公顷数 （gha）城市规模CS系列行政面积（平方公里）/ 总面积（%）产业化水平工业按地区分地区工业增加值占地区GDP比重（%）
DOI: 10.6084/m9.figshare.28440563.v1
title: RNA-Seq in BxPC-3 cells transfected with miR-34a-5p mimics and negative control

description: RNA-Seq in BxPC-3 cells transfected with miR-34a-5p mimics and negative control
DOI: 10.6084/m9.figshare.26179462.v1
title: EST-Biochar-SOC-Iron-Microbes_Open Data_HH.xlsx

description: Data of "Microbially Driven Iron Cycling Facilitates Organic Carbon Accrual in Decadal Biochar-Amended Soil"
DOI: 10.6084/m9.figshare.28598213.v3
title: Raw data

description: The goal was to assess the effectiveness of N-acetyl cysteine (NAC) in protecting the liver from phenytoin-induced hepatotoxicity in rats
DOI: 10.17632/57mwc7kwds
title: Acceptability of minimally invasive autopsy by community members and healthcare workers in Siaya and Kisumu Counties, western Kenya, 2017-2018

description: This data is generated from a formative qualitative study that was carried out in western Kenya in 2017/2018 as part of the Child Health and Mortality Prevention Surveillance (CHAMPS) network. The data consists of transcriptions from qualitative ( FGDs, KIIs and In-depth ) interviews as well as a site-specific codebook. Most of the interviews were conducted in the local language (Dholuo), and later translated into English
DOI: 10.6084/m9.figshare.2065545.v2
title: A Simple Generic Model for Estimating Saturated Vapor Pressure

description: Arguably, the most important of the basic thermodynamic properties of fluids, vapor pressure has been the focus of investigation for over a century. The two main drawbacks of the models currently used for its correlation are that they either exhibit large deviations near critical temperature and triple point or that they have a large number of compound-specific adjusted parameters and hence the inconvenient necessity of having at hand large tabulations of hundreds of model parameters. In this study, by employing the up and coming procedure of genetic programming, a new model, which to a large extent remedies these shortcomings, is proposed. Essentially, having only two compound-specific adjusted parameters and also using two readily available substance parameters of molecular weight and normal boiling point ensure a high level of convenience, yet precision and applicability over a large portion of the vapor–liquid coexistence curve. Concisely, a sizable database comprised of 58,272 data points was gathered for 243 organic and inorganic compounds and elements belonging to a diverse set of chemical families; these were then used in both developing and validating the proposed model and reporting generic and compound/element-specific adjusted parameters. Average absolute relative deviations (AARDs) of 1.47% (for a subset of 40,852 data points) and 1.82% (for a subset of 17,420 data points) for the general model and a slightly modified model applicable to hydrogen-bonded alcohols and phenols, respectively, are a testament to the reliability of the new proposed model.
DOI: 10.6084/m9.figshare.25287325.v1
title: Multicellular ecotypes shape progression of lung adenocarcinoma from ground-glass opacity towards advanced stages

description: Single-cell RNA sequencing and read processing The cell suspension was loaded into Chromium microfluidic chips with 3’(v3) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v3 reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina Novaseq 6000, according to the manufacturer’s instructions (Illumina). The 10X Genomics CellRanger software pipeline (v 5.0.1) was used to demultiplex cell barcodes and reads were mapped to the hg38 human genome using STAR aligner (v2.7.10a)(Dobin et al., 2013).Filtering, normalization, integration and clustering of scRNA-seq data Seurat (v3.1.0) was used for filtering, selecting variable gene, dataset integration, dimensionality reduction, clustering, cell type annotation, differential expression, and visualization. We applied quality measures on raw gene-cell-barcode matrix for each cell: mitochondrial genes (≤20%, unique molecular identifiers (UMIs), and gene count (ranging from 200 to 6000). We excluded genes with min.cells &lt; 3 and removed mitochondrial as well as ribosomal genes in the subsequent analysis. For the remaining cells and genes, we defined relative expression by centering the gene count through using the ‘ScaleData’ function. In the integration step, function ‘SelectIntegrationFeatures’ was used to select features, which were used to scaled (function ' ScaleData’) and compute the principal component (PCs, function ‘RunPCA’). When identifying integration anchors, one sample from each clinical stage was randomly selected as reference (function ‘FindIntegrationAnchors’, reduction = "rpca"), Then all scRNAseq datasets were integrated using above anchor (function ‘IntegrateData’). Cell clustering, tSNE visualization and UMAP visualization were performed using the FindClusters, RunTSNE and RunUMAP functions, respectively. The annotations of cell identity on each cluster were defined by the expression of known marker genes, including: EPCAM, KRT19, KRT18, CDH1 for epithelial cells; CD3D, CD3E, CD3G for T cells; TRAC, LYZ, MARCO, CD68, FCGR3A for myeloid cells; CD79A for B cells; DCN, THY1, COL1A1, COL1A2 for fibroblasts, PECAM1, FLT1 for endothelial cells; KIT, MS4A2, GATA2 for MAST cells; NKG7, NCAM1, KLRD1 for NK cells.
DOI: 10.6084/m9.figshare.28815548.v1
title: Table S3. Serotype prediction of <i>Salmonella</i> isolates

description: These are the results of serotype prediction for Salmonella isolates, and they were predicted with SeqSero v 1.3.
DOI: 10.6084/m9.figshare.3550515.v1
title: Appendix B. Correlations of sprint speed and critical swimming speed (Ucrit).

description: Correlations of sprint speed and critical swimming speed (Ucrit).
DOI: 10.6084/m9.figshare.3560415.v1
title: Appendix B. Measuring ecosystem variables.

description: Measuring ecosystem variables.
DOI: 10.6084/m9.figshare.4910177.v2
title: II.3 - Agrogenom detection of HGT from statistically supported topological conflict between gene and species trees using Prunier

description: 38,165 Prunier output filesObtained using Prunier 2.0 FastForward with bootstrap support threshold of 0.90 applied to the unicopy subtrees as extracted in item #II.2.
DOI: 10.17632/76s26nrcpv
title: Supplementary materials - STB-VMM: Swin Transformer Based Video Motion Magnification

description: Reference benchmark videos showcased in STB-VMM: Swin Transformer Based Video Motion Magnification. This dataset contains the original benchmarks as well as the results obtained using STB-VMM and learning-based video motion magnification (LB-VMM) [10.48550/arXiv.1804.02684]. These videos serve as a qualitative comparison between both learning based methods' image quality. The dataset is intended to help researchers and practitioners in the field of video motion magnification to evaluate and compare the performance of different methods.

The code for STB-VMM is open source and available at: https://github.com/RLado/STB-VMM
DOI: 10.17632/7z5c8vdsgx
title: Influence of Carbon Dioxide on Micro-cracking in Calcite: An Atomistic Scale Investigation

description: The folder contains datasets generated and analyzed in the research article "Influence of Carbon Dioxide on Micro-cracking in Calcite: An Atomistic Scale Investigation".
DOI: 10.6084/m9.figshare.28219655.v1
title: Demography, common disorders and mortality of Shih Tzu dogs under primary veterinary care in the UK

description: Background Shih Tzus are a popular dog breed in the UK although there is relatively little reported informationon their health. This study aimed to characterise the demography, common disorders and mortality of Shih Tzusunder primary veterinary care during 2016 in the UK using de-identified clinical records from the VetCompass™Programme.Results The study population of 336,865 dogs under veterinary care during 2016 included 11,082 Shih Tzus (3.3%).The median age was 4.1 years (IQR: 2.1–7.1, range: 0.3–20.4) and mean adult bodyweight was 7.9 kg (SD: 1.9 kg).Annual proportional births increased from 2.2% of all dog births in 2005 to 3.8% in 2013, dropping to 3.3% by 2016.From a random subset of 2,423 Shih Tzus that had information extracted on disorders diagnosed during 2016,the most prevalent fine-level precision disorders were periodontal disease (n = 229, prevalence 9.5%, 95% CI: 8.4–10.7),anal sac impaction (180, 7.4%, 95% CI: 6.5–8.5) and ear disorders (134, 5.5%, 95% CI: 4.7–6.5). The most prevalentgrouped-level precision disorders were cutaneous (n = 402, prevalence: 16.6%, 95% CI: 15.2–18.1), dental (322, 13.3%,95% CI: 12.0–14.7), and ophthalmological (289, 11.9%, 95% CI: 10.7–13.3). Males were more likely than females to bediagnosed with skin disorders (P = 0.007) and musculoskeletal disorders (P = 0.010) while females were more likelythan males to be diagnosed with hernias (P = 0.005). The median age of death was 12.7 years (IQR 8.7–14.3, range2.0–19.9) and did not differ statistically between males and females. The most common grouped causes of deathwere enteropathy (7.9%, 95% CI: 3.9–15.4), heart disease (7.9%, 95% CI: 3.9–15.4) and poor quality of life (7.9%, 95% CI:3.9–15.4).Conclusions Periodontal disease, anal sac impaction and ear disorders were identified as common health issues.Shih Tzus had higher prevalence of anal sac impaction, umbilical hernias and eye problems than reported previouslyin dogs overall, suggesting potential predispositions. Shih Tzus appear to be relatively long-lived compared to previousreports of lifespan in dogs overall. The results can inform veterinarians and owners on priority disorders for monitoringto protect welfare. Oral hygiene was highlighted as a healthcare priority.
DOI: 10.6084/m9.figshare.28667669.v1
title: Data supporting "Learning Pairwise Interaction for Extrapolative and Interpretable Machine Learning Interatomic Potentials with Physics-informed Neural Network"

description: <b>Data supporting "Learning Pairwise Interaction for Extrapolative and Interpretable Machine Learning Interatomic Potentials with Physics-informed Neural Network"</b><br>This archive contains training data used for models in the manuscript, which are created from the authors or modified/subsampled from public datasets. All molecular geometries are saved as extended xyz (extxyz) format.<b>Dataset file description</b><b>Ethanol</b>`ethanol/ethanol_dissociation.xyz`: The geometries for calculating PES of ethanol dissociation.`ethanol/ethanol_optimized.xyz`: The optimized geometry used for computing pairwise interaction energies and intrinsic bond strength index (IBSI).<b>Extrapolation data</b>The files listed in `extrapolation_data` are the dataset for <b>Figure 2</b> of the manuscript, which are splitted to train and test dataset as described in the manuscript.<b>S</b><sub><strong>N</strong></sub><b>2 reaction</b><br>`sn2_reaction/sn2_reaction_I_Br.xyz`: The subset of publicly available S<sub>N</sub>2 reaction of methyl halide[1], only containing I and Br as halogen species.`sn2_reaction/sn2_I_Br_subsampled.xyz`: Normal mode sampled (NMS) images & AIMD trajectory of the reaction CH<sub>3</sub>I + Br<sup>-</sup> &lt;=&gt; CH<sub>3</sub>Br + I<sup>-</sup>.`sn2_reaction/sn2_I_Br_noTS.xyz`: NMS-only dataset for the same reaction.<b>Liquid water</b>Classical MD trajectory of liquid water. The original dataset is created from the authors of [2]. We subsampled the dataset with 500 geometries.<br>`water/water_0.5k_train.xyz`: 450 geometries for training the model`water/water_0.5k_val.xyz`: 50 geometries for validation steps.<b>References</b>[1] Unke, O. T.; Meuwly, M. PhysNet: A neural network for predict-ing energies, forces, dipole moments, and partial charges. Journal of chemical theory and computation 2019, 15 (6), 3678-3693[2] Fu, X.; Wu, Z.; Wang, W.; Xie, T.; Keten, S.; Gomez-Bombarelli, R.; Jaakkola, T. Forces are not Enough: Benchmark and Critical Evaluation for Machine Learning Force Fields with Molecular Simulations. 2023; https://arxiv.org/abs/2210.07237.<br>
DOI: 10.6084/m9.figshare.29144462.v1
title: Foclóir Tráchtais v1.7

description: Is foclóir ríomheolaíochta é an Foclóir Tráchtas curtha le chéile ag Seathrún (Jeffrey) Sardina dá thráchtas PhD. Cruthaíodh é chun téarmaí ríomheolaíochta nach raibh ar fáil i bhfoclóirí eile a chur ar fáil.
DOI: 10.15468/dl.48v5sq
title: Occurrence Download

description: A dataset containing 5210 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Pilosella aurantiaca (L.) F.W.Schultz & Sch.Bip.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 5210 records from 189 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013157-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c54x54v8p
title: MassIVE MSV000098888 - Label free proteomic analysis of human pancreatic beta cells at four stages of development
title: We have developed a comprehensive multi-omics platform to investigate the underlying changes that lead to the formation of healthy pancreatic beta-cells. To achieve this, human induced pluripotent stem cells (hiPSCs) were induced in vitro to undergo pancreatic differentiation stages through a careful combination of growth factors, small molecules, and optimized culture conditions. We utilized a panel of specific antibody markers analyzed via immunofluorescence, imaging, and flow cytometry to evaluate differentiation efficiency and characterize the resultant pancreatic cell populations. Our global proteomic analysis was conducted at four key stages: iPSCs, definitive endoderm (DE), pancreatic progenitors (PP), and mature beta-cells, with four biological replicates processed in triplicates. Each replicate consisted of fresh frozen pellets containing 1x10^6 cells. This proteomic analysis complements our global RNA-seq findings in healthy developing beta-cells. The LFQ proteomic examinations were performed using a Q-Exactive Plus Orbitrap quadrupole mass spectrometer (Thermo) following established protocols (Scifo et al., J Proteomics 2015; Srinivasan et al., 2025). Overall, we quantified 5,046 human proteins, with over 4,600 proteins quantified at each developmental stage. After filtering for differentially abundant proteins (DEPs), we identified 212 DEPs between DE and iPSCs, 454 between PP and DE stages, and 406 between mature beta-cells and the PP stage. Principal component analysis (PCA) revealed a substantial separation among the stages analyzed, while the abundance plot of non-normalized intensities indicated a high degree of concordance across the proteomic samples. Additionally, global Gene Ontology (GO) analysis highlighted the inclusion of all cellular components, biological processes, and molecular functions, underscoring the technical accuracy achieved in these measurements.
DOI: 10.15468/dl.ka58xr
title: Occurrence Download

description: A dataset containing 2918011 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "DatasetKey is EOD – eBird Observation Dataset",
 "PublishingCountry is China"
 ]
}

 The dataset includes 2918011 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017159-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15100485
title: An updated Bioconductor workflow for correlation profiling subcellular proteomics

description: Files for users of the workflow "An updated Bioconductor workflow for correlation profiling subcellular proteomics". Files include the Proteome Discoverer (v3.1) processing and consensus workflows used to process the use case raw MS files. For raw data please refer to PRIDE (dataset identifier PXD055123).

Also provided are the files required for users to run the workflow on the use-case data. This includes the PSM and protein-level output .txt files corresponding the the Proteome Discoverer identification search, the mrk.csv file containing subcellular markers and the bandleres.rda and tagm_mcmc_params.rda files for users to load the bandleres and mcmc_model objects.  

The Appendix is provided as a pdf file. The Appendix contains information about 1) the identification search of the use-case data with Proteome Discoverer, 2) alternative data import methods, 3) how to adapt the workflow to MaxQuant output data, and 4) an example DIA correlation profiling workflow using data output from DIA-NN. The input files required to run the example DIA workflow are also provided here (diann_report.tsv and 220813_Universal_Protein_Contaminants_HaoGroup_modified.fasta).

Finally, the .Rmd file containing the code used to generate the final F1000 publication is provided, along with a .pdf file of the publication
DOI: 10.15468/dl.bwdxt8
title: Occurrence Download

description: A dataset containing 2795 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is one of (Honduras, Guatemala, Nicaragua, El Salvador, Belize, Costa Rica, Mexico)",
 "TaxonKey is Liquidambar styraciflua L."
 ]
}

 The dataset includes 2795 records from 116 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017174-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xetmep
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is da86174a-a605-43a4-a5e8-53d484152cd3",
 "TaxonKey is Adansonia digitata L."
 ]
}

 The dataset includes 56 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017177-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/2n3hhd
title: U.S. Government Tweet Ids

description: &lt;p&gt;This dataset contains the tweet ids of 9,673,959 tweets for approximately 3400 U.S. government accounts. These are accounts that are associated with federal government agencies, not individuals. They were collected between January 20, 2017 and July 20, 2018 from the GET statuses/user_timeline method of the Twitter API using &lt;a href="https://gwu-libraries.github.io/sfm-ui/"&gt;Social Feed Manager&lt;/a&gt;.&lt;/p&gt;

&lt;p&gt;There is a README.txt file containing additional documentation on how this dataset was collected. There is also an accounts.csv file listing the Twitter accounts that were collected.&lt;/p&gt;

&lt;p&gt;Note that accounts have been added and deleted during the collection period. This may contain tweets from accounts that were erroneously collected (e.g., accounts of government officials or accounts that were previously government accounts but since taken over by non-government users).&lt;/p&gt;

&lt;p&gt;The GET statuses/lookup method supports retrieving the complete tweet for a tweet id (known as hydrating). Tools such as &lt;a href="https://github.com/DocNow/twarc"&gt;Twarc&lt;/a&gt; or &lt;a href="https://github.com/DocNow/hydrator"&gt;Hydrator&lt;/a&gt; can be used to hydrate tweets.&lt;/p&gt;

&lt;p&gt;Per Twitter’s Developer Policy, tweet ids may be publicly shared for academic purposes; tweets may not.&lt;/p&gt;

&lt;p&gt;We intend to update this dataset periodically.&lt;/p&gt;

&lt;p&gt;Questions about this dataset can be sent to sfm@gwu.edu. George Washington University researchers should contact us for access to the tweets.&lt;/p&gt;
DOI: 10.7910/dvn/f2feh1
title: Malawi (2009): HIV/AIDS TRaC Survey among Evidence-based Targeted HIV Prevention (EBT Prev) Target Populations in Malawi. Round One.

description: BACKGROUND & RESEARCH OBJECTIVES. More than 20 years into the HIV/AIDS epidemic, Malawi faces numerous prevention challenges similar to those in other East and Southern African nations. A high HIV prevalence of 12% points to very high incidence among most at-risk groups and, increasingly, to substantial levels of transmission in the general population. In March 2009, PSI/Malawi initiated a five-year Evidence Based Targeted HIV Prevention (EBT Prev) project designed to reduce the incidence of HIV
in Malawi, by targeting prevention efforts at populations and settings with high risk behaviors. The purpose of the TRaC survey among these target populations is the identification and monitoring of key behavioral determinants in the target populations that are related to condom use and partner reduction including concurrency. DESCRIPTION OF INTERVENTION. The program will target the following high risk groups fishermen/women, plantation/estate workers and vendors. The program will deliver integrated, behavior change communications activities which includes interpersonal communications, peer education, targeted outreach communications, and mass media activities to promote condoms and partner reduction among the target groups. METHODOLOGY. Study sites were identified through the PLACE methodology, in partnership with key stakeholders, notably the Ministry of Health, HIV/AIDS Unit, and approved by USAID. The following sites were chosen: Lilongwe (Urban), Zomba rural (markets), Mwanza border, Thyolo and Mulanje (plantation area) and Mangochi district (lakeshore). Each site is presumed to be representative of local HIV/AIDS related attitudes and practices for the associated target group on a national scale. In mid-2010, PSI/Malawi conducted a cross-sectional, venue-based baseline survey designed to monitor trends in condom use and concurrent partnerships. Randomly selected vendors, plantation workers, and fisher men and women were sampled from the venues within the areas mentioned above. The participants were sexually active, aged 20-49 years, and provided consent. A total of 3,075 people were interviewed including: 1,034 vendors, 1,023 plantation workers, and 1,018 fishermen and women. Logistic regression was used to assess association between health behaviors and determinants. Socio-demographic characteristics were controlled for in the analyses.
DOI: 10.7910/dvn/lgt5o6
title: An optical lattice with sound

description: Data files for paper arXiv:2104.13922
DOI: 10.7910/dvn/x06tqk
title: DM GAIT 2019 1

description: ANTHROPOMETRY & GAIT