cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28665107.v1
title: Major element and volatile compositions for 2022 Hunga pyroclasts and standards

description: Supplementary Tables 1–6 for accepted manuscript in <i>Nature Geoscience</i>: Low sulfur emissions from 2022 Hunga eruption due to seawater-magma interactions. The files include (1) Supplementary Table 1: Major, minor, and volatile elements in melt inclusions and microlite-poor matrix glass as well as the associated minerals determined by EMPA; (2) Supplementary Table 2: SiO<sub>2</sub> and sulfur (S) in microlite-poor matrix glass from the whole eruptive sequence determined by EMPA; (3) Supplementary Table 3: Total H<sub>2</sub>O (H<sub>2</sub>O<sub>t</sub>) in matrix glass determined by FTIR microspectroscopy; (4) Supplementary Table 4: Total H<sub>2</sub>O (H<sub>2</sub>O<sub>t</sub>) in melt inclusions determined by FTIR microspectroscopy; (5) Supplementary Table 5: Water in melt inclusions and matrix glass determined by Raman microspectroscopy; and (6) Supplementary Table 6: Data for glass calibration standards used to quantify H<sub>2</sub>O concentrations by Raman microspectroscopy.
DOI: 10.6084/m9.figshare.24791094.v2
title: 404,627 SNPs for 1,973 sorghum landraces in VCF and numeric format.

description: 404,627 SNPs for a collection of 1,973 sorghum landraces for manuscript "Climate resilience conserved in global germplasm repositories"Sequences provided in VCF and numeric format, reformatted from: Jesse R. Lasky <i>et al., </i>Genome-environment associations in sorghum landraces predict adaptive traits. <i>Sci. Adv. </i><b>1</b>, e1400218(2015).DOI:10.1126/sciadv.1400218Kinship matrix calculated using GAPIT with the Zhang method.HapMap files from original publication can be found on Digital Dryad: https://datadryad.org/stash/dataset/doi:10.5061/dryad.jc3ht
DOI: 10.6084/m9.figshare.22270969.v1
title: Dataset for long term Covid-19 mental health research.sav

description: This dataset is linked to a longitudinal study that captures the mental illness and mental well-being of university students over a one year period of the Covid-19 pandemic, capturing data at four time points.
DOI: 10.5281/zenodo.15315424
title: A single-cell RNA-seq dataset of synovial fluid from rheumatoid arthritis treated with TNF-α/JAK inhibitor

description: Although multiple single-cell RNA sequencing (scRNA-seq) based studies have explored rheumatoid arthritis (RA), most have focused on synovial tissue, limiting the ability to perform paired pre- and post-treatment comparisons and to elucidate dynamic changes. Moreover, the single-cell impact of TNF-α and JAK inhibitors on RA remains poorly understood, hindering effects toward precision medicine for RA. Here, we present a comprehensive scRNA-seq analysis of synovial fluid samples of RA patients treated with tofacitinib or adalimumab, both pre- and post-treatment. Following stringent quality control, we analyzed 106,506 high-quality cells, providing an in-depth characterization of cell composition, molecular signaling pathways, and functional properties. This rich dataset offers a valuable resource to address diverse research questions, from uncovering the mechanisms of action of TNF-α and JAK inhibitors, to identifying novel therapeutic targets for RA, and advancing our understanding of the pathogenesis of inflammatory diseases.
DOI: 10.5281/zenodo.15315425
title: A single-cell RNA-seq dataset of synovial fluid from rheumatoid arthritis treated with TNF-α/JAK inhibitor

description: Although multiple single-cell RNA sequencing (scRNA-seq) based studies have explored rheumatoid arthritis (RA), most have focused on synovial tissue, limiting the ability to perform paired pre- and post-treatment comparisons and to elucidate dynamic changes. Moreover, the single-cell impact of TNF-α and JAK inhibitors on RA remains poorly understood, hindering effects toward precision medicine for RA. Here, we present a comprehensive scRNA-seq analysis of synovial fluid samples of RA patients treated with tofacitinib or adalimumab, both pre- and post-treatment. Following stringent quality control, we analyzed 106,506 high-quality cells, providing an in-depth characterization of cell composition, molecular signaling pathways, and functional properties. This rich dataset offers a valuable resource to address diverse research questions, from uncovering the mechanisms of action of TNF-α and JAK inhibitors, to identifying novel therapeutic targets for RA, and advancing our understanding of the pathogenesis of inflammatory diseases.
DOI: 10.6084/m9.figshare.21424347.v2
title: Six Supplemental Data Files (referenced in manuscript)

description: These files are the 6 supplemental data files referenced in our Ecography paper entitled "Completeness analylsis for over 3000 United States bee species identifies persistent data gaps". Funding provided for this project was provided across several NSF grants, listed below and in the associated README.md document.
DOI: 10.6084/m9.figshare.26727340.v1
title: Data and code used for Blattner et al.: Urbanization-associated range expansion genetically homogenizes a butterfly species

description: SNP genotype data sets used for the different analyses presented in the Blattner et al. study on genetic homogenization in <i>Pieris mannii</i> butterflies, plus a sample descriptor file used for PCA. Each of these four files is accompanied by a separate metadata file describing the data content, and specifying what code section of the original code compilation was used for the corresponding analysis. The original code compilation is also included in this file package. The two largest data files are gzipped and need to be unzipped to be analyzed. The SNP data are derived from raw sequence data available from the NCBI sequence read archive (BioProject accession: PRJNA1083579; https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1083579).
DOI: 10.6084/m9.figshare.12827615.v1
title: tms_gene_data_rv1

description: The data for the TMS gene analysis accompanying the paper "Mouse Aging Cell Atlas Analysis Reveals Global and Cell Type Specific Aging Signatures", eLife, 2021.
DOI: 10.6084/m9.figshare.28422647.v1
title: Anexos de la Propuesta Hacia una Gestión del Conocimiento Dinámica y Eficaz en el PAE

description: Anexos
DOI: 10.6084/m9.figshare.16641532.v2
title: Seurat_object_whole_NMR_Thymus_Lymphnode_sortedTHY_pt1

description: This item comprises <br>each 4 ADT- and RNA-libraries for thoracic thymus: two for 3 year-old Naked mole-rats (THY1, THY2), two for 11 year-old Naked mole-rats (THY3, THY4);<br>each 4 ADT- and RNA-libraries for cervical thymus: two for 3 year-old Naked mole-rats (TLN1, TLN2), two for 11 year-old Naked mole-rats (TLN3, TLN4);<br>each 2 ADT- and RNA-libraries for lymph nodes of two 3 year-old Naked mole-rats (BLN1, BLN2);<br>each 1 ADT- and RNA-library for sorted thoracic thymus of two pooled 3 year-old Naked mole-rats (CD34).<br>Part 1 of a split file 7-zip archive.
DOI: 10.6084/m9.figshare.19687923.v2
title: 2018 and 2020 non-Geonews Video.xlsx

description: Performance of 2018 and 2020 non-Geonews Video on YouTube
DOI: 10.6084/m9.figshare.28233854.v2
title: Model files, simulation process, setting and data

description: Model dimensional scale effects study on molecular dynamics simulation of bituminous materials
DOI: 10.6084/m9.figshare.12401618.v1
title: ClipKIT: a multiple sequence alignment-trimming algorithm for phylogenomic inference

description: Highly divergent sites in multiple sequence alignments, which stem from erroneous inference of homology and saturation of substitutions, are thought to negatively impact phylogenetic inference. Trimming methods aim to remove these sites prior to phylogenetic inference, but recent analysis suggests that doing so can worsen inference. We introduce ClipKIT, a trimming method that instead aims to retain phylogenetically-informative sites; phylogenetic inference using ClipKIT-trimmed alignments is accurate, robust, and time-saving.
DOI: 10.6084/m9.figshare.20496564.v1
title: Supplementary Material for: Ablation Surgeries for Treatment-Resistant Depression: A Meta-Analysis and Systematic Review of Reported Case Series

description: <b><i>Background and Objectives:</i></b> Ablative lesion procedures remain as the last option in treatment of refractory depression. Contemporary ablative psychosurgeries involve producing lesions in the anterior limb of the internal capsule (bilateral anterior capsulotomy – BAC), the supragenual anterior cingulate gyrus and cingulum (bilateral anterior cingulotomy – BACING), and subgenual anterior cingulate gyrus and subcortical orbitofrontal white matter (bilateral subcaudate tractotomy – BST). A combination of BACING and BST is known as limbic leukotomy (bilateral limbic leukotomy – BLL). All procedures claim some success, but cohorts are small, depression assessment instruments differ, and inclusion and outcome criteria and follow-up duration vary. In some cohorts, more than one type of surgery was performed in several patients, further confounding interpreting the available data. Current evidence is equivocal on which surgical target works best. <b><i>Method and Aim:</i></b> This systematic review and meta-analysis using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) standard on published cohorts was conducted to review and identify which is the best standalone ablative procedure for treatment-resistant depression (TRD) based on response rate (event rate) and adverse-effect profile using the Comprehensive Meta-Analysis software. <b><i>Results and Conclusion:</i></b> As a standalone neurosurgical procedure, we found that BAC appears to be the most effective and safest of all the ablative targets for TRD. A major limitation of this conclusion is the paucity of published case series where sample sizes are small and all are open label.
DOI: 10.6084/m9.figshare.28730975.v1
title: <i>Speaking in Tongues: Bilingual Theatre Text Creation as Inclusive Actor Training</i>

description: To what extent can bilingual theatre text creation serve as a pedagogical strategy to enhance inclusivity, cultural agency, and performative competence in student actor training within a multilingual South African context?<i>Pinocchio 'n Pantomini</i> is a bilingual musical pantomime that reimagines Carlo Collodi’s classic tale within a South African sociocultural setting. The production was collaboratively devised with undergraduate students and performed in both Afrikaans and English. Set in the fictional town of Fussili, the narrative follows Pinocchio’s journey toward becoming a “real boy,” framed by moral choices and community interaction. Key characters include Kroke-é Kriek, a sardonic narrator-conscience, and Miss Riri Co-a, a flamboyant drag fairy guardian.In addition to scripted dialogue, the production featured original lyrics composed specifically for the performance. These songs—such as <i>“Dreams Collide”</i>, <i>“Strings”</i>, and <i>“Pleasure Island”</i>—functioned not only as narrative devices but also as expressive training tools, enabling students to explore characterisation, rhythm, and bilingual lyricism through embodied performance.
DOI: 10.6084/m9.figshare.5122657.v1
title: Supplementary Material for: Focal Adhesion Kinase Regulates Neuronal Growth, Synaptic Plasticity and Hippocampus-Dependent Spatial Learning and Memory

description: The focal adhesion kinase (FAK) is a non-receptor tyrosine kinase abundantly expressed in the mammalian brain and highly enriched in neuronal growth cones. Inhibitory and facilitatory activities of FAK on neuronal growth have been reported and its role in neuritic outgrowth remains controversial. Unlike other tyrosine kinases, such as the neurotrophin receptors regulating neuronal growth and plasticity, the relevance of FAK for learning and memory in vivo has not been clearly defined yet. A comprehensive study aimed at determining the role of FAK in neuronal growth, neurotransmitter release and synaptic plasticity in hippocampal neurons and in hippocampus-dependent learning and memory was therefore undertaken using the mouse model. Gain- and loss-of-function experiments indicated that FAK is a critical regulator of hippocampal cell morphology. FAK mediated neurotrophin-induced neuritic outgrowth and FAK inhibition affected both miniature excitatory postsynaptic potentials and activity-dependent hippocampal long-term potentiation prompting us to explore the possible role of FAK in spatial learning and memory in vivo. Our data indicate that FAK has a growth-promoting effect, is importantly involved in the regulation of the synaptic function and mediates in vivo hippocampus-dependent spatial learning and memory.
DOI: 10.26188/5da555f8c2b02
title: EPiC database - Natural rubber

description: This material is part of the free Environmental Performance in Construction (EPiC) Database. The EPiC Database contains embodied environmental flow coefficients for 250+ construction materials using a comprehensive hybrid life cycle inventory approach.<br><br>Rubber is a highly elastic polymer (elastomer) that can be obtained naturally, or produced synthetically using oil-based production methods. It has a high tensile strength, resistance to fatigue and tearing, abrasion resistance and a high resilience/ability to return to its original shape and size. In addition to this, it has good insulative qualities and adheres well to itself and other materials.<br><br>Natural rubber is harvested in the form of latex from the sap of rubber trees, which is refined and converted into rubber. Variations in quality can be observed in natural rubber, due to the geographical area, weather and soil conditions.<br><br>In comparison with natural rubber, synthetic rubber is generally tolerant to a broader range of temperatures, is resistant to oil and grease, and ages well against weathering. Natural rubber is favoured for its high performance and low cost, which is not directly tied to the price of petroleum.
DOI: 10.6084/m9.figshare.28856366.v1
title: Prediction models

description: Nothing
DOI: 10.15468/dl.vwugk8
title: Occurrence Download

description: A dataset containing 5142 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Megachile willughbiella (Kirby, 1802)"
 ]
}

 The dataset includes 5142 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009577-250426092105405/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.22643872.v1
title: Data funding projects - Spanish public universities

description: This is the dataset used to study the funding projects from Spanish universities.
DOI: 10.6084/m9.figshare.26361787.v1
title: 血清 meatibolites

description: 宿主来源<i>植物乳杆菌</i>通过改善肠道微生物群落和水解酶介导的嘌呤核苷降解来缓解高尿酸血症
DOI: 10.6084/m9.figshare.9912815.v1
title: Supplementary Material for: Are Conditioned Open Placebos Feasible as an Adjunctive Treatment to Opioids? Results from a Single-Group Dose-Extender Pilot Study with Acute Pain Patients

description: Medicine
DOI: 10.6084/m9.figshare.23452988.v1
title: Supplementary Material for: Serum IGFBP7 deriving from spleen and lung could be used for early recognition of cardiac surgery-associated acute kidney injury

description: Introduction: The utility of arithmetic product of urinary tissue metalloproteinase inhibitor 2 (TIMP2) and insulin-like growth factor-binding protein 7 (IGFBP7) concentrations has been widely accepted on early diagnosis of acute kidney injury (AKI). However, which organ is the main source of those two factors and how the concentration of IGFBP7 and TIMP2 changed in serum during AKI still remain to be defined. Methods: In mice, gene transcription and protein levels of IGFBP7/TIMP2 in the heart, liver, spleen, lung, and kidney were measured in both ischaemia-reperfusion injury (IRI)- and cisplatin-induced AKI models. Serum IGFBP7 and TIMP2 levels were measured and compared in patients before cardiac surgery, and at inclusion (0 h), 2 h, 6 h and 12 h after Intensive Care Unit (ICU) admission, and compared with serum creatinine, blood urea nitrogen (BUN), estimated glomerular filtration rate (eGFR) and serum uric acid (UA). Results: In mouse IRI-AKI model, compared with the sham group, the expression levels of IGFBP7 and TIMP2 did not change in the kidney, but significantly upregulated in the spleen and lung. Compared with patients who did not develop AKI, the concentration of serum IGFBP7 at as early as 2 h after ICU admission (s[IGFBP7]-2 h) was significantly higher in patients who developed AKI. The relationships between s[IGFBP7]-2 h in AKI patients and log2(SCr), log2(BUN), log2(eGFR), and log2(UA) were statistically significant. The diagnostic performance of s[IGFBP7]-2 h measured by the macro-averaged area under the receiver operating characteristic curve (AUC) was 0.948 ([95% CI], 0.853 to 1.000; P&lt;0.001). Discussion/Conclusion: The spleen and lung might be the main source of serum IGFBP7 and TIMP2 during AKI. The serum IGFBP7 value demonstrated good predictive accuracy for AKI following cardiac surgery within 2 h after ICU admission.
DOI: 10.6084/m9.figshare.12769655.v1
title: ibidi8_perTrial_v2_wt1_2019Jul01

description: Image dataset for smFISH.<br>
DOI: 10.6084/m9.figshare.22728485.v1
title: OFICIAL Trabalho Dissertaçaõ.dta

description: <em>Organizations must recognize and act on the factors that affect their performance, which requires the inclusion of people in improving their processes. Kaizen, a continuous improvement principle, encourages employees to use their knowledge to create better solutions. This knowledge, referred to as tacit, is strategic to be shared, through socialization, or articulated as explicit knowledge through externalization. The Kaizen of a department of a multinational metallurgical industry in the south of Santa Catarina, Brazil, has historically had an involvement rate lower than 50% established as a goal. Thus, the work proposed to analyze the effects of the socialization-externalization interface and to list the barriers that connect the understanding of these points to the current rate of involvement in continuous improvement. As a methodology, the literature review was followed by the application of a questionnaire, which served as a scale for an exploratory factor analysis to determine the validity of the model for the objectives outlined. Factorial verification confirmed the lack of application of meritocratic means, Ba context and management involvement. Furthermore, 3 organizational factors and 3 individual barriers to knowledge sharing were retained in the factorial model. In conclusion, it was shown that the current level of employee involvement in Kaizen contrasts significantly with the effects of the socialization-externalization interface and the barriers to knowledge sharing, which can guide the organization in reviewing strategies to encourage participation in Kaizen.</em> <em><strong>Palavras-chave:</strong></em><em> Knowledge Management, Knowledge Sharing, Tacit Knowledge, Continuous Improvement, Kaizen, Exploratory Factor Analysis.</em>
DOI: 10.6084/m9.figshare.21646685.v1
title: Supplementary Material for: The Olfactomedin-4-Defined Human Neutrophil Subsets Differ in Proteomic Profile in Healthy Individuals and Patients with Septic Shock

description: The specific granule glycoprotein olfactomedin-4 (Olfm4) marks a subset (1–70%) of human neutrophils and the Olfm4-high (Olfm4-H) proportion has been found to correlate with septic shock severity. The aim of this study was to decipher proteomic differences between the subsets in healthy individuals, hypothesizing that Olfm4-H neutrophils have a proteomic profile distinct from that of Olfm4 low (Olfm4-L) neutrophils. We then extended the investigation to septic shock. A novel protocol for the preparation of fixed, antibody-stained, and sorted neutrophils for LC-MS/MS was developed. In healthy individuals, 39 proteins showed increased abundance in Olfm4-H, including the small GTPases Rab3d and Rab11a. In Olfm4-L, 52 proteins including neutrophil defensin alpha 4, CXCR1, Rab3a, and S100-A7 were more abundant. The data suggest differences in important neutrophil proteins that might impact immunological processes. However, in vitro experiments revealed no apparent difference in the ability to control bacteria nor produce oxygen radicals. In subsets isolated from patients with septic shock, 24 proteins including cytochrome b-245 chaperone 1 had significantly higher abundance in Olfm4-H and 30 in Olfm4-L, including Fc receptor proteins. There was no correlation between Olfm4-H proportion and septic shock severity, but plasma Olfm4 concentration was elevated in septic shock. Thus, the Olfm4-H and Olfm4-L neutrophils have different proteomic profiles, but there was no evident functional significance of the differences in septic shock.
DOI: 10.6084/m9.figshare.3860289.v1
title: Supplementary Material for: A Multi-Institutional Feasibility Study on the Use of Automated Screening Systems for Quality Control Rescreening of Cervical Cytology

description: <b><i>Objective:</i></b> To evaluate the efficacy of the automated screening system FocalPoint for cervical cytology quality control (QC) rescreening. False-negative rates (FNRs) were evaluated by a multi-institutional retrospective study. <b><i>Study Design:</i></b> Cervical cytology slides that had already been reported as negative for intraepithelial lesion or malignancy (NILM) were chosen arbitrarily for FocalPoint rescreening. Slides stratified into the highest 15% probability of being abnormal were rescreened by a cytotechnologist. The slides that were abnormal were reevaluated by a cytopathologist to be false negatives. <b><i>Results:</i></b> Rescreening of 12,000 slides, i.e. 9,000 conventional slides and 3,000 liquid-based cytology (LBC) slides, was performed; 9,826 (7,393 conventional and 2,433 LBC) were satisfactory for FocalPoint (2,174 were determined unsatisfactory) and those within the highest 15% of probability (1,496, i.e. 1,123 conventional and 373 LBC) were rescreened. As a result, 117 (96 conventional and 21 LBC) were determined as abnormal (other than NILM) and the FNR was 1.19%. Among these 117 slides, 40 (35 conventional and 5 LBC) were determined as high-grade squamous intraepithelial lesion and greater (HSIL+). <b><i>Conclusion:</i></b> Of 117 (1.19%) abnormal slides detected, 40 (0.41%) were determined to be HSIL+. This result suggests that FocalPoint is effective for QC rescreening of cervical cytology.
DOI: 10.6084/m9.figshare.27146685.v2
title: Sargassum eBOMB Model Default Interpolant Data and Source Code

description: NetCDF data required to run the default eBOMB Sargassum model and associated source code.<br>These data are collected for the year 2018 in the north Atlantic.<br>The main repository for the associated code is: https://github.com/70Gage70/Sargassum.jl
DOI: 10.6084/m9.figshare.7190474.v2
title: Supplementary Information from Vertebral morphometrics and lung structure in non-avian dinosaurs.

description: A .zip file containing landmark data, classifier variables and the R code necessary to replicate the main findings of the paper.
DOI: 10.6084/m9.figshare.11870976.v3
title: Supplementary Materials

description: Supplementary Table 1. 2233 genes with variance importance in projection score &gt; 1.5.Supplementary Table 2. Enrichment analysis of transcription factors based on T peripheral helper cells signature genes.Supplementary Table 3-5. Enrichment analysis of Gene Ontology Biological Process (3), Molecular Function (4) and Cellular Component (5) based on T peripheral helper cells signature genes.
DOI: 10.6084/m9.figshare.19246224.v2
title: Data-AuNStoAuNP

description: Identification of Plasmon-driven Nanoparticle-coalescence-dominated Growth of Gold Nanoplates through Nanopore Sensing;<br>Dataset