cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28063040.v2
title: Supplementary Material for: Liver X receptors and inflammatory-induced C/EBPb selectively cooperate to control CD38 transcription

description: Introduction. Macrophages abundantly express liver X receptors (LXRs), which are ligand-dependent transcription factors and sensors of several cholesterol metabolites. In response to agonists, LXRs induce the expression of key lipid homeostasis regulators. Crosstalk between LXRs and inflammatory signals exist in a cell type- and gene-specific manner. A common feature in the macrophage response to inflammatory mediators is the induction of CCAAT/enhancer-binding protein beta (C/EBPβ), a master transcriptional regulator and lineage-determining transcription factor in monocytes/macrophages. Methods. Quantitative real-time PCR in control and C/EBPβ-deficient macrophages was used to explore the role of C/EBPβ in the crosstalk between inflammatory mediators and the macrophage response to pharmacological LXR activation. The functional interaction between C/EBPβ and LXRs on selected genomic regions was further characterized by chromatin-immunoprecipitation (ChIP) and gene reporter studies. Results. Whereas inflammatory signals repressed several LXR-regulated genes involved in lipid metabolism, these effects were conserved after deletion of C/EBPβ. In contrast, inflammatory mediators and LXRs synergistically induced the expression of the multifunctional protein CD38 in a C/EBPβ-dependent manner. C/EBPβ and LXRs bound to several regions with enhancer activity upstream and within the mouse Cd38 gene and their functional cooperation in macrophages required intact binding sites for LXR and C/EBPβ. Conclusion. This study reveals positive crosstalk between C/EBPβ and LXRs during the macrophage inflammatory response, which selectively impacts CD38 expression.
DOI: 10.6084/m9.figshare.11520297.v1
title: Training Data - Peptide-Binding Domain-Peptide Interactions

description: Data used to train domain-peptide interactions.<br><b>Data Format</b>Each file describes a specific class of domains. The format for these files are csv files with five columns:<i><br></i><i>Domain UniProt ID,Domain Sequence,Peptidic Sequence,Bound</i><br>Data are de-duplicated (i.e. duplicate interactions are reduced to one) and de-conflicted (i.e. conflicting interactions are removed).<br><br><b>Reference:</b>Cunningham JM, Koytiger G, Sorger PK, AlQuraishi M. "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning."<i> Nature Methods</i> (2020).
DOI: 10.4121/uuid:7100a209-2407-42ea-b6e0-dca5e821fc8d
title: Input data supporting: Atomistic understanding of cation exchange in PbS nanocrystals using simulations with pseudoligands

description: Atomistic understanding of cation exchange in PbS nanocrystals using simulations with pseudoligands, Z. Fan, L-C. Lin, W. Buijs, T.J.H. Vlugt, M.A. van Huis Nature Communications, doi:10.1038/ncomms11503 Sample input files for a MD simulation of 4.7-nm PbS NC in psuedoligands at 550K. Simulations were performed using the LAMMPS code (version 01Nov13). LAMMPS can de downloaded from: http://lammps.sandia.gov
DOI: 10.6084/m9.figshare.23706654.v1
title: <b>Achieving Destination Sustainability</b>

description: We distributed 860 questionnaires and eliminated 114 invalid questionnaires, indi-cating a response rate of 86.74%. Finally, 746 complete, usable responses were included in the data analysis.
DOI: 10.25387/g3.14210594.v3
title: Supplemental Material for Bachvaroff et al., 2021

description: Additional file 1: The <i>C. sapidus</i> genome assembly in fasta format for all sequences over 10kb. Additional file 2: The repeat masked <i>C. sapidus</i> genome in fasta format. Additional file 3: Predicted repeat families for <i>C. sapidus</i>.Additional file 4: The <i>C. sapidus</i> gene predictions in GFF3 format. <br>Table S1: Summary of RNAseq reads, tissue sources and mapping statistics. Table S2: The <i>C. sapidus</i> scaffold size, repeat, gene content, and homologous chromosomes from <i>P. trituberculatus.</i><br>
DOI: 10.6084/m9.figshare.16591889.v1
title: Supplementary Material for: Lack of Oncological Benefit from Bursectomy in Radical Gastrectomy: A Systematic Review

description: <b><i>Background:</i></b> Resection of the omental bursa has been suggested to reduce peritoneal recurrence and facilitate a complete oncological resection during a gastrectomy. The addition of this procedure increases technical complexity and prolongs the procedure. Published data regarding the oncological benefit of this procedure are conflicting. We hypothesized that a bursectomy during a radical gastrectomy does not improve overall survival. <b><i>Methods:</i></b> In accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) reporting guideline, a comprehensive literature search of 3 electronic databases (PubMed, Scopus, and Embase) was conducted to identify the clinical studies that compared bursectomy with no-bursectomy in radical gastrectomy for gastric adenocarcinoma. Qualitative and quantitative data synthesis was performed using RevMan software. A random-/fixed-effect modeling was used depending upon the heterogeneity. Bias and quality assessment tools were applied. The study was registered with the International Prospective Register of Systematic Reviews (PROSPERO) (CRD42019116556). <b><i>Results:</i></b> Of 8 studies assessing the role of bursectomy in gastric adenocarcinoma, 6 (75%) were included – of which 2 (33%) are randomized controlled trials. Of 2,904 patients, 1,273 (%) underwent a bursectomy. There was no statistically significant difference in either overall survival (hazard ratio [HR] = 0.89, 95% CI 0.75–1.06, <i>I</i><sup>2</sup> = 14%) or disease recurrence (HR = 1.01, 95% CI 0.84–1.20, <i>I</i><sup>2</sup> = 22%) in the bursectomy group compared to the no-bursectomy group. <b><i>Conclusion:</i></b> There is no additional oncological benefit of adding bursectomy to radical gastrectomy in all patients with gastric adenocarcinoma.
DOI: 10.15468/dl.empvuu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Holtbyrnia innesi (Fowler, 1934)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((54.1341 -16.2111,54.4917 -16.3924,54.8913 -16.2339,54.9312 -16.1504,54.1138 -16.1504,54.1341 -16.2111))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013467-250525065834625/datasets/export for details.
DOI: 10.6084/m9.figshare.26962567.v2
title: Data and R code for "Aridity modulates the contribution of plant and soil diversity to grassland stability"

description: The data include the value of multile facets of stability and all the variables of each sample site. The R code include all analysis.
DOI: 10.6084/m9.figshare.21904074.v1
title: Anova and KW H3.pdf

description: A-Nova analysis of the sample of students involved in peer- assessment processes at University
DOI: 10.6084/m9.figshare.27913767.v1
title: SEC-MX: An approach to Systematically Study the Interplay Between Protein Assembly States and Phosphorylation

description: Source data underlying main and supplementary figures
DOI: 10.15468/dl.fcv6ss
title: Occurrence Download

description: A dataset containing 243 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Material sample, Material citation, Specimen)",
 "TaxonKey is Arrhenia discorosea (Pilát) Zvyagina, A.V.Alexandrova & Bulyonk."
 ]
}

 The dataset includes 243 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013468-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.11931756.v1
title: GFLOW Iteration script from Predicting defaunation: accurately mapping bushmeat hunting pressure over large areas

description: Bash script to iteratively run GFLOW simulations over a generated resistance map using .txt and .tsv node files stored in input folders. This script runs over multiple cores and iterates through the node files until no nodes have gone unsimulated.
DOI: 10.6084/m9.figshare.25782123.v1
title: Additional data and code for Navigating the Archaeal Frontier: Insights and Projections from Bioinformatic Pipelines

description: The files with KEGG modules and modified manual module architecture, full annotation and synteny tables, as well as custom Python scripts used for the analysis
DOI: 10.6084/m9.figshare.27161472.v1
title: Raw data.xlsx

description: VTE raw data
DOI: 10.6084/m9.figshare.28151783.v1
title: Supplementary BayPass hits

description: <b>Supplementary BayPass hits</b>Supplementary BayPass hits for the paper:<b> </b><b>A century of anthropogenic perturbations impact genomic signatures of the iconic </b><b>migratory Atlantic cod</b> by Cecilia Helmerson, Joël M. Durant, Siv Nam Khang Hoff, Marine Servane Ono Brieuc, Paul Ragnar Berg, Per Erik Jorde, Marius Filomeno Maurstad, Ian Bradbury, Olav Sigurd Kjesbu, Jane Aanestad Godiksen, Nils Chr. Stenseth, Bastiaan Star, Kjetill S. Jakobsen, Sissel Jentoft
DOI: 10.6084/m9.figshare.25126886.v1
title: Application of Multimodal MRI Functional Imaging in the Evaluation of Aathletes' Heart

description: Multimodal magnetic resonance technology was used to evaluate the cardiac function, myocardial movement, myocardial strain, myocardial microcirculation, myocardial delayed enhancement, myocardial T1 mapping and T2 mapping, myocardial spectroscopy, myocardial oxidation, cardiac cavity and macrovascular blood flow, which provided a certain reference basis for the reserve of normal athletes' cardiac parameters, and provided a normal reference range for subsequent athletes' heart disease.
DOI: 10.6084/m9.figshare.28892273.v1
title: Supplementary Material for: The Prognostic Significance of Ki-67 Expression in Breast Cancers Developing Malignant Effusions

description: Purpose: To investigate the prognostic significance of Ki-67 in breast cancer patients developing malignant effusions.
Methods: In this retrospective study, 76 breast cancer patients developing a malignant effusion were enrolled. The Ki-67 immunohistochemistry (IHC) findings from both initial tissue and paired metastatic effusion samples of these patients were grouped into the following three categories: ≤5, 6-29, and ≥30%. 
Results: Triple negative breast cancer (TNBC) showed higher Ki-67 levels at both initial diagnosis (p&lt;0.001) and malignant effusion samples (p=0.015), compared to the non-TNBC phenotypes at the same tumor evolution phases, respectively. A Ki-67≥30% at initial diagnosis was associated with a shorter overall survival (p=0.031; long-rank test), in addition to an earlier development of a malignant effusion (p&lt;0.001; long-rank test). A Ki-67≤5% at malignant effusion cell block samples was associated with a longer post-effusion survival (p=0.015; long-rank test). Lastly, a Ki-67 index≤5% at the effusion samples showed a significantly lower risk of mortality following the development of malignant effusions (HR: 0.355 (0.150 - 0.842; p=0.019)), after being adjusted for the intrinsic subtype covariate (TNBC vs non-TNBC).
Conclusion: Estimating the Ki-67 IHC expression in malignant effusion cytology samples may have a prognostic significance, when evaluating patients with metastatic breast cancer. However, larger-scale prospective studies would be necessary to provide more evidence on this topic.
DOI: 10.15468/dl.avjrrw
title: Occurrence Download

description: A dataset containing 26975 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Youngia japonica (L.) DC.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 26975 records from 368 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013466-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.13105808.v1
title: Global hybrid simulations of interaction between interplantary rotational discontinuity and bow shock/magnetosphere: Can ion-scale magnetic reconnecion be driven by rotational discontinuity downstream of quasi-parallel shock?

description: Data of 3D global hybrid simulations of interaction between the interplantary rotational discontinuities and the bow shock/magnetosheath system.
DOI: 10.6084/m9.figshare.24115383.v1
title: machine-learning dataset

description: The dataset is used to train machine learning model for the study of passivation effect of small molecules
DOI: 10.6084/m9.figshare.12949244.v1
title: SuppTableS1.docx

description: Two guide RNAs were designed to generate animals carrying indels within the <i>Atg16l1</i> gene
DOI: 10.6084/m9.figshare.23826462.v1
title: <i>fusion </i>target database

description: This file contains all proteins used in the generation of <i>fusion</i>. This file is also a prerequisite to generate fusion organism similarities with https://bitbucket.org/bromberglab/fusion-organism_sim.
DOI: 10.6084/m9.figshare.26394880.v1
title: DDIM image result

description: This is data from an article about "Diffusion Model-Based Generation of Three-dimensional Multiphase Fluid Pore-Scale Images".
DOI: 10.6084/m9.figshare.22691080.v2
title: Untitled Item

description: The MIDOG++ dataset represents an extension of the data set used in the MIDOG 2021 and 2022 challenges. We provide region of interest images from 503 histological specimens of seven different tumor types with variable morphology: breast carcinoma, lung carcinoma, lymphosarcoma, neuroendocrine tumor, cutaneous mast cell tumor, cutaneous melanoma, and (sub)cutaneous soft tissue sarcoma. The human and canine samples were processed and stained at different human and veterinary pathology laboratories with standard H&E dye and digitized with different digital whole slide image scanners. We provide labels for 11,937 mitotic figures that have been differentiated against 14,351 imposter cells in a blinded consensus by two pathologists and a final decision by a third pathologist for disagreed labels.
DOI: 10.6084/m9.figshare.25219880.v1
title: Datasets: COVID anomaly in the correlation analysis of S&P 500 market states

description: Analyzing market states of the S&P 500 components on a time horizon January 3, 2006 to August 10, 2023, we found the appearance of a new market state not previously seen and we shall discuss its possible implications as an isolated state or as a beginning of a new general market condition. We study this in terms of the Pearson correlation matrix and relative correlation with respect to the S&P 500 index. In both cases the anomaly shows strongly.(Authors: M. Mijaíl Martínez-Ramos, Manan Vyas, Parisa Majari, Thomas H. Seligman)arXiv:2308.14830<br>
DOI: 10.6084/m9.figshare.26190458.v1
title: <b>Revealing antagonistic interactions in the adverse effects of polystyrene and </b><b>polymethylmethacrylate </b><b>microplastics in bumble bees</b>

description: The three data sets are the row data corresponding to the three experiments. The codes used for the statistical analyses are reported in the Word file named "Codes". The ReadMe file contains all the information reported in the row data.
DOI: 10.6084/m9.figshare.29203418.v1
title: CIHS2025

description: <i>Intellectual humility, a virtue associated with open-mindedness and acknowledgment of one’s intellectual limitations, has gained attention in psychological research. This study examined the psychometric properties of the Comprehensive Intellectual Humility Scale (CIHS) with Indonesia sample using both Classical Test Theory and Item Response Theory approaches. A total of 418 Indonesian adults completed the CIHS. Analysis was done using Confirmatory Factor Analysis and the Rasch Rating Scale Model. The CFA results supported a four-factor structure with acceptable fit indices and reliability across all dimensions. Rasch analysis demonstrated that the scale fulfilled the assumptions of unidimensionality, had strong item and person reliability, and met fit criteria for most items. Wright map analysis showed that item difficulty was generally aligned with participant ability, though some items were too easily endorsed. These findings affirm the CIHS’s internal consistency, construct validity, and cultural applicability in Indonesia</i>
DOI: 10.6084/m9.figshare.21799604.v3
title: Data of Evelien Van Hoeymissen for manuscript "Gain-of-function variants in the ion channel gene TRPM3 underlie a spectrum of neurodevelopmental disorders"

description: Raw data for figures generated by Evelien Van Hoeymissen Data of Prof Tibor Rohacs included
DOI: 10.6084/m9.figshare.14938068.v1
title: Data set - Enhanced bedside mortality prediction combining point-of-care lactate and the quick Sequential Organ Failure Assessment score (qSOFA) in patients hospitalized with suspected infection in southeast Asia.

description: This is a part of prospective observational (non-interventional) study of community-acquired sepsis and severe sepsis in Sunpasithiprasong Hospital, Ubon Ratchathani province, northeast Thailand (NCT02217592; Ubon-sepsis cohort) and a multinational multicentre cross-sectional study for causes and outcomes of sepsis in Southeast Asia (NCT02157259; SEAICRN cohort). The study shows that A rapid, bedside assessment using a score combining qSOFA and lactate can identify patients at risk of sepsis-related mortality and may be useful for early prognostication in resource-limited settings.<br>The data comprises of 4,980 patients enrolled in the Ubon-sepsis cohort, Thailand and 792 patients enrolled in the SEAICRN cohort. There are three files, the data of Ubon-sepsis cohort, the data of SEAICRN cohort and the data descriptions.<br>
DOI: 10.6084/m9.figshare.21215147.v1
title: Malesian genus origins

description: Dataset of Malesian plant genus origins. Either Sunda or Sahul origin.
DOI: 10.6084/m9.figshare.21731150.v2
title: LAMMPS test input files

description: LAMMPS input files
DOI: 10.6084/m9.figshare.12317123.v1
title: Salerno et al Progenesis exported protein list.xlsx

description: To assess the hierarchical importance of multipotent differentiation compared with trophic/immunoregulatory functions of MSCs, we have undertaken a detailed analysis of how these properties change with in vitro ageing of the cells. Using in vitro differentiation and repair models and integrating transcriptomics and proteomics data, we show that the multipotent differentiation capacity of MSCs falls with increasing passage, whereas trophic repair and immunoregulatory potency are maintained. In total four cell lines were profiled using LC-MSon a QExactive HF quadrupole-Orbitrap mass spectrometer coupled to a Dionex Ultimate 3000 RSLC nano-liquid chromatograph. Cell lines were isolated from four individuals. Secretome was collected from each cell line at passage 1, 5, 10 and 15 for a total of 16 samples.
DOI: 10.6084/m9.figshare.14785983.v1
title: Supplemental Table 1 Final.xlsx

description: Proteomic analysis data spreadsheets of conditioned culture media proteome from neutrophil elastase vs control treated RAW264.7 macrophage cultures.
DOI: 10.6084/m9.figshare.28270886.v1
title: Cat - bodyweights 2014-23

description: Calculation of standard bodyweights for dogs, cats, rabbits, and guinea pigsStuart D. Becker, Dan G. O’Neill, Siân-Marie Frosini, Laura E. Stapleton, David M. Hughes, Dave C. BrodbeltPlos One (2025) doi: 10.1371/journal.pone.0318734This item is the data set used to calculate standard bodyweights adjusted for juvenile growth in cats. Please see linked paper for methodology.
DOI: 10.6084/m9.figshare.1263451.v1
title: cytb_BI_consensus_tree

description: Bayesian Inference bootstrap consensus tree (mrbayes) for cytb mtDNA locus as in Harris et al. (2015) Deep genetic differentiation within Janetaescincus spp. from the Seychelles Islands. Herpetological Journal
DOI: 10.6084/m9.figshare.23300756.v1
title: Supplementary Material for: Acute kidney injury after multiple cycles of cisplatin chemotherapy: A nomogram for risk assessment

description: Abstract Background: Acute kidney injury (AKI) caused by cisplatin is common and has a higher incidence of multiple use, resulting in a poor short- and long-term prognosis for patients. There is currently no good pre-medication AKI risk assessment tool. The aim of this study is to establish an AKI risk assessment nomogram for patients with multiple cisplatin applications. Methods: This study was a retrospective analysis of patients who were treated with non-first-time cisplatin chemotherapy regimen in Changzhou second people's Hospital affiliated to Nanjing Medical University from January 2016 to January 2022. All data of the development group were used to screen the impact factors of AKI via univariate and multivariate analyses. A nomogram was developed based on these impact factors and verified with verification group. The area under the curve (AUC) of receiver-operating characteristic (ROC) curve, calibration curves, and decision curve analyses (DCAs) were used to evaluate the nomogram. Results: Among the 256 patients enrolled in 450 cycles of chemotherapy, 282 were in the development cohort (97 AKI), and 168 were in the validation cohort (61 AKI). Multivariate logistic regression revealed that age, hypertension, diabetes, sCysC, uKim1 and a single dose of cisplatin were independently associated with AKI. The results showed that our model yielded satisfied diagnostic performance with an AUC value of 0.887 and 0.906 using the development group and on verification group. The calibration plots and DCA showed the superior clinical applicability of the nomogram. These results were verified in the validation cohort. Conclusion: A nomogram combining functional (sCysC) and tubular (uKim1) injury biomarkers with conventional clinical factors might assess the risk of AKI after multiple cycles of cisplatin chemotherapy.
DOI: 10.4121/20895367.v1
title: Business-to-Business data sharing via data marketplace meta-platforms: Exploring governance mechanisms to enhance data sovereignty

description: This file contains parts of the research data collected during a master thesis project in partial fulfillment of the Management of Technology program at the faculty of Technology, Policy and Management of the Delft University of Technology from February-September 2022. Included in the file: <br> 1. Thesis project one-pager 2. Interview protocol 3. Slides with visuals used during interviews 4. Informed Consent form 5. Eleven anonymised summaries of the expert interviews