cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14798432.v1
title: Platelets enhance CD4+ central memory T cell responses via platelet factor 4-dependent mitochondrial biogenesis and cell proliferation

description: Platelets regulate multiple aspects of CD4<sup>+</sup> T cell immunity, and may exert distinct regulations among different T cell subsets. Our aim was to investigate how platelets regulate CD4<sup>+</sup> central memory T cell (Tcm) responses. αCD3/αCD28-stimulated human CD4<sup>+</sup> Tcm cells were cultured without or with platelets or platelet-derived mediators. Polyclonal stimulation induced cell proliferation and Th1 and Treg cell activation of Tcm cells. Platelet factor 4/PF4 neutralization abolished platelet-enhanced Tcm effector responses, whilst TGFβ neutralization only partially inhibited platelet-enhanced Treg cell activation. PF4 supplementation mimicked the effects of platelet co-cultures, while PF4 receptor CXCR3 blockade and CXCR3 knockdown with siRNAs inhibited or abolished PF4-enhanced Th1 and Treg cell responses. Platelet co-cultures or PF4-treatment increased Tcm cell proliferation, whilst CXCR3 blockade counteracted. PF4-enhanced Tcm proliferation and effector cell responses were associated with mitochondrial biogenesis. Overexpression of mitochondrial transcription factor A (TFAM) mimicked PF4 effects, and PF4 treatment attenuated Akt phosphorylation of activated Tcm cells, leading to mitochondrial biogenesis. Impacts of platelets and PF4 on Tcm proliferation were further confirmed by that CXCR3 knockdown/blockade counteracted PF4-enhanced Tcm cell proliferation. In conclusion, platelets enhance Th1 and Treg cell responses of CD4<sup>+</sup> Tcm cells, via PF4-dependent mitochondrial biogenesis and cell proliferation of Tcm cells.
DOI: 10.6084/m9.figshare.13225538
title: Additional file 2 of Prenatal diagnosis of Duchenne muscular dystrophy revealed a novel mosaic mutation in Dystrophin gene: a case report

description: Additional file 2.
DOI: 10.6084/m9.figshare.6933944.v1
title: Additional file 3: of Insights into the cotton anther development through association analysis of transcriptomic and small RNA sequencing

description: Table S2. Differentially expressed genes KEGG enriched TOP10. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.6933947.v1
title: Additional file 4: of Insights into the cotton anther development through association analysis of transcriptomic and small RNA sequencing

description: Table S3. Metabolism and signaling pathway gene expression levels. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6933959
title: Additional file 8: of Insights into the cotton anther development through association analysis of transcriptomic and small RNA sequencing

description: Table S6. Target gene prediction for differentially expressed miRNAs, which between SCP and MRP, and KEGG enrichment of target genes. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6933776
title: Additional file 5: of Dealing with the adaptive immune system during de novo evolution of genes from intergenic sequences

description: Full Table with numbers of transcripts per tissue for all populations and classes. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.13225535
title: Additional file 1 of Prenatal diagnosis of Duchenne muscular dystrophy revealed a novel mosaic mutation in Dystrophin gene: a case report

description: Additional file 1.
DOI: 10.6084/m9.figshare.13225535.v1
title: Additional file 1 of Prenatal diagnosis of Duchenne muscular dystrophy revealed a novel mosaic mutation in Dystrophin gene: a case report

description: Additional file 1.
DOI: 10.6084/m9.figshare.6933935.v1
title: Additional file 14: of Insights into the cotton anther development through association analysis of transcriptomic and small RNA sequencing

description: Table S8. Primers list in real-time qRT-PCR. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.22662435
title: Additional file 1 of Current status and influencing factors of spiritual needs of patients with advanced cancer: a cross-sectional study

description: Additional file 1. Raw Data-Spiritual Needs of Patients with Advanced Cancer.
DOI: 10.6084/m9.figshare.22662441.v1
title: Additional file 2 of Optimizing yeast for high-level production of kaempferol and quercetin

description: Additional file 2: Feeding profile for glucose limited fed-batch fermentation of kaempferol and quercetin.
DOI: 10.6084/m9.figshare.6933953
title: Additional file 6: of Insights into the cotton anther development through association analysis of transcriptomic and small RNA sequencing

description: Table S4. Differential genes expression. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.13225712
title: Additional file 1 of Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms

description: Additional file 1. Table S1: Whole-genome sequencing data of NA12878 based on four sequencing platforms. Table S2: Number and length statistics of all 50 CNV sets. Table S3: Regional distribution of all 50 CNV sets across the genome. Table S4: List of the complete CNV benchmark of NA12878. Table S5: CNV detection tools using whole-genome sequencing data.
DOI: 10.6084/m9.figshare.6933953.v1
title: Additional file 6: of Insights into the cotton anther development through association analysis of transcriptomic and small RNA sequencing

description: Table S4. Differential genes expression. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.13225660
title: Additional file 2 of A comprehensive investigation of metagenome assembly by linked-read sequencing

description: Additional file 2: Table S4. Annotations of assemblies for the subsampled linked-reads from human gut microbiome.
DOI: 10.6084/m9.figshare.13225660.v1
title: Additional file 2 of A comprehensive investigation of metagenome assembly by linked-read sequencing

description: Additional file 2: Table S4. Annotations of assemblies for the subsampled linked-reads from human gut microbiome.
DOI: 10.6084/m9.figshare.13219295
title: Additional file 1 of Improving antitumor efficacy via combinatorial regimens of oncolytic virotherapy

description: Additional file 1: Table 1. Summary of current ongoing combination therapy trials of OVs on ClinicalTrial.gov.
DOI: 10.6084/m9.figshare.13225663.v1
title: Additional file 3 of A comprehensive investigation of metagenome assembly by linked-read sequencing

description: Additional file 3: Table S7 A summary of 65,535 microbes in human microbiome project covered by 10x linked-reads from human gut microbiome. Table S8. A summary of 1,285 microbes in human microbiome project covered by 10x linked-reads of human gut microbiome with genomic coverage&gt;90% and sequencing depth &gt; 20X.
DOI: 10.5281/zenodo.10524829
title: CEX Project - Dataset and Gold Standard

description: The files represent the new version of Cioffi, A. (2022) Data for Testing and Evaluating References Extraction and Parsing Tools (1.0) https://doi.org/10.5281/zenodo.6182066. The 56 files of Cioffi, 2022 were corrected and additional 56 PDFs were manually annotated and aligned to the project guidelines. The TEI files of the whole dataset (112 documents) can be found under GoldStandard_TEI zip folder, while the PDFs are in GoldStandard_PDF folder.GoldStandard.txt contains the list of the bibliographic references of each article. When an entry is marked as "Restricted", it means the correspondent PDF is not in Open Access format, thus it is not shared in the present publication and cannot be found in the GoldStandard_PDF folder, the other Open Access papers are shared in it.

The code can be found at Pagnotta, O. (2024). olgagolgan/CEX-Project: CEX Project Code (software). Zenodo. https://doi.org/10.5281/zenodo.10638757.

The output dataset of Anystyle, GROBID and OUTCITE can be found here  Pagnotta, O. (2024). CEX Project - Output Dataset (Anystyle, GROBID, OUTCITE) (Version 1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10524898.

The annotated training dataset for GROBID can be found here Pagnotta, O. (2024). CEX Project - GROBID annotation aligned Gold Standard (Version 1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10529646.

The trained GROBID citation models can be found here Pagnotta, O. (2024). CEX Project - trained GROBID citation models. Zenodo. https://doi.org/10.5281/zenodo.10529709.

Some results can be found here Pagnotta, O. (2023). Investigating the performance of GROBID and OUTCITE (Version v1). Zenodo. https://doi.org/10.5281/zenodo.10036455.

The final service can be found here Pagnotta, O. and Paolini, L. (2024). opencitations/cec: alpha version (service). Zenodo. https://doi.org/10.5281/zenodo.10635630.

The work is part of my Thesis research for the Digital Humanities and Digital Knowledge Master's Course at University of Bologna.
DOI: 10.6084/m9.figshare.13219295.v1
title: Additional file 1 of Improving antitumor efficacy via combinatorial regimens of oncolytic virotherapy

description: Additional file 1: Table 1. Summary of current ongoing combination therapy trials of OVs on ClinicalTrial.gov.
DOI: 10.6084/m9.figshare.13219427
title: Additional file 2 of De novo assembly and analysis of the transcriptome of the Dermacentor marginatus genes differentially expressed after blood-feeding and long-term starvation

description: Additional file 2: Table S2. Overview of sequencing quality control.
DOI: 10.6084/m9.figshare.13225663
title: Additional file 3 of A comprehensive investigation of metagenome assembly by linked-read sequencing

description: Additional file 3: Table S7 A summary of 65,535 microbes in human microbiome project covered by 10x linked-reads from human gut microbiome. Table S8. A summary of 1,285 microbes in human microbiome project covered by 10x linked-reads of human gut microbiome with genomic coverage&gt;90% and sequencing depth &gt; 20X.
DOI: 10.25402/fsg.14798544.v1
title: Supplementary Table 2. Computational drug repositioning for ischemic stroke: Neuroprotective drug discovery

description: Supplementary Table 2
DOI: 10.6084/m9.figshare.7982387.v1
title: Quantitative proteomics reveals the mechanisms of hydrogen-conferred protection against hyperoxia-induced injury in type II alveolar epithelial cells

description: <b>Purpose/Aim:</b> Exposure to hyperoxia leads to lung injury both <i>in vivo</i> and <i>in vitro</i>, molecular hydrogen has been reported to protect against hyperoxia-induced lung injury; however, the underlying molecular mechanisms remain largely unknown. The objective of this study was to characterize differentially regulated proteins and biological processes in hydrogen-treated hyperoxic primary type II alveolar epithelial cells (AECIIs) to elucidate the protective mechanism of hydrogen using quantitative proteomics. <b>Materials and Methods:</b> AECIIs were divided into three groups that were cultured for 24 h in three different conditions: control (21% oxygen), hyperoxia (95% oxygen), and hyperoxia + hydrogen. Morphologic examination, flow cytometric analysis, cell viability assessment and analysis of the expression of apoptosis-associated proteins Bax and Bcl-2 as well as AECI markers (AQP5, T1α) and an AECII marker (SP-C) were performed for each group. The TMT labeling quantitative proteome technique was used to detect changes in the protein expression profile, and bioinformatics analysis was performed. <b>Results:</b> Hydrogen plays a protective role in hyperoxia-induced damage in AECIIs, as evidenced by reduced apoptosis, increased viability and survival, improved morphology, and enhanced transdifferentiation of AECIIs into AECIs. A total of 5782 proteins were identified in our study, of which 162 were significantly altered in abundance after hyperoxia exposure, and 97 were significantly altered in abundance in response to hydrogen treatment. The Gene Ontology and KEGG enrichment analyses identified a large number of proteins and biological processes that may responsible for the protective effect of hydrogen, including VEGFA, PDGFB, IGFBP3, EDN1, NADPH oxidase, the coagulation cascade, etc. <b>Conclusions:</b> Molecular hydrogen protects AECIIs from hyperoxic injury by complex mechanisms involving a variety of proteins and biological processes, such as VEGFA, PDGFB, IGFBP3, EDN1, NADPH oxidase and the coagulation cascade. These findings suggest novel pathways that need to be investigated as possible therapeutic targets for hyperoxia-induced lung injury.
DOI: 10.6084/m9.figshare.13225538.v1
title: Additional file 2 of Prenatal diagnosis of Duchenne muscular dystrophy revealed a novel mosaic mutation in Dystrophin gene: a case report

description: Additional file 2.
DOI: 10.6084/m9.figshare.14798334
title: Early Paleozoic tectono–magmatic evolution in the South Altun orogenic belt, northwest China: Insights from zircon U–Pb geochronology, Hf isotope and geochemistry of the granitoids

description: Precise timing of granitoids and constraints of their magma sources are critical to understanding the subduction–collision tectonic evolution of the Altun orogenic belt (AOB), a vital part of the Qinghai-Tibet plateau in northwestern China. We provide in-situ zircon U–Pb age, Hf isotopic composition and whole-rock geochemistry of the Yusupualeke granitic pluton in the South Altun orogenic belt (SAOB), an integral unit of the AOB, to determine the tectono-magmatic evolution of the SAOB at early Palaeozoic. The Yusupualeke granitic pluton comprises the medium-coarse grained porphyritic monzogranite and medium-fine grained granodiorite. The monzogranite sample yielded a weighted mean <sup>206</sup>Pb/<sup>238</sup>U age of 476.8 ± 3.6 Ma (MSWD = 0.59), while the granodiorite yielded a weighted mean <sup>206</sup>Pb/<sup>238</sup>U age of 453.2 ± 4.7 Ma (MSWD = 0.013). Zircon U–Pb ages suggest that the subduction–collision process of the SAOB remained from the middle stage of the early Palaeozoic to the end. Both of the studied granitoids belong to metaluminous to weakly peraluminous series and show typical I-type granite characteristics with depletions in Ba, Nb, Sr, P, and Ti, and enrichments in light rare earth elements (LREEs), Rb, Th, K, and slightly negative Eu anomalies. Based on the geochronological data and regional geological background, we believe that the porphyritic monzogranites were formed during the northward subduction process of the South Altun ocean (SAO), while the granodiorites were formed during the tectonic regime transition stage. Besides, combing the previous research achievements with our newly obtained data, we put forward a new division and geodynamic model of the early Palaeozoic tectono-magmatic evolution for the South Altun orogenic belt.
DOI: 10.6084/m9.figshare.13219439.v1
title: Additional file 6 of De novo assembly and analysis of the transcriptome of the Dermacentor marginatus genes differentially expressed after blood-feeding and long-term starvation

description: Additional file 6: Table S6. Unigenes used in molecular function, cellular component and biological process anaylisis by GO annotation.
DOI: 10.6084/m9.figshare.14798432
title: Platelets enhance CD4+ central memory T cell responses via platelet factor 4-dependent mitochondrial biogenesis and cell proliferation

description: Platelets regulate multiple aspects of CD4<sup>+</sup> T cell immunity, and may exert distinct regulations among different T cell subsets. Our aim was to investigate how platelets regulate CD4<sup>+</sup> central memory T cell (Tcm) responses. αCD3/αCD28-stimulated human CD4<sup>+</sup> Tcm cells were cultured without or with platelets or platelet-derived mediators. Polyclonal stimulation induced cell proliferation and Th1 and Treg cell activation of Tcm cells. Platelet factor 4/PF4 neutralization abolished platelet-enhanced Tcm effector responses, whilst TGFβ neutralization only partially inhibited platelet-enhanced Treg cell activation. PF4 supplementation mimicked the effects of platelet co-cultures, while PF4 receptor CXCR3 blockade and CXCR3 knockdown with siRNAs inhibited or abolished PF4-enhanced Th1 and Treg cell responses. Platelet co-cultures or PF4-treatment increased Tcm cell proliferation, whilst CXCR3 blockade counteracted. PF4-enhanced Tcm proliferation and effector cell responses were associated with mitochondrial biogenesis. Overexpression of mitochondrial transcription factor A (TFAM) mimicked PF4 effects, and PF4 treatment attenuated Akt phosphorylation of activated Tcm cells, leading to mitochondrial biogenesis. Impacts of platelets and PF4 on Tcm proliferation were further confirmed by that CXCR3 knockdown/blockade counteracted PF4-enhanced Tcm cell proliferation. In conclusion, platelets enhance Th1 and Treg cell responses of CD4<sup>+</sup> Tcm cells, via PF4-dependent mitochondrial biogenesis and cell proliferation of Tcm cells.
DOI: 10.6084/m9.figshare.7466168.v1
title: Additional file 9: of Transcriptome profile in bursa of Fabricius reveals potential mode for stress-influenced immune function in chicken stress model

description: Table S7. Protein-protein interaction network for all SDEGs. Sheet 1 showed the interactions with a confidence scoreâ &gt;â 0.7, sheet 2 showed the log2FoldChange values of genes in sheet1, sheet 3 showed the KEGG analysis result of the genes in the 19 modules. (XLSX 29 kb)
DOI: 10.25402/fsg.14798451.v1
title: Supplementary Table 3. Computational drug repositioning for ischemic stroke: Neuroprotective drug discovery

description: Supplementary Table 3<br>
DOI: 10.6084/m9.figshare.13219304.v1
title: Additional file 2 of Clinical and mutational profiles of adult medulloblastoma groups

description: Additional file 2. Supplementary Tables S1–S6
DOI: 10.15468/dl.5g6t8c
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oxalis gracilipes Schltr."
 ]
}

 The dataset includes 11 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066660-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rvmzek
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Palaquium clarkeanum King & Gamble"
 ]
}

 The dataset includes 19 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066661-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m6993f
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Osteospermum pyrifolium Norl."
 ]
}

 The dataset includes 23 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066662-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jwfar8
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oreocharis cordatula (Craib) Pellegr."
 ]
}

 The dataset includes 28 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066664-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jgpgqy
title: Occurrence Download

description: A dataset containing 5997 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Patrinia scabiosifolia Fisch. ex Trevir."
 ]
}

 The dataset includes 5997 records from 142 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066663-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m26p2q
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oxalis gracilis Jacq."
 ]
}

 The dataset includes 82 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066665-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vfr4d9
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Palaquium cochleariifolium P.Royen"
 ]
}

 The dataset includes 46 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066666-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.85e3z3
title: Occurrence Download

description: A dataset containing 159 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Osteospermum rigidum Aiton"
 ]
}

 The dataset includes 159 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066667-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ny5gwa
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oreocharis cotinifolia (W.T.Wang) Mich.Möller & A.Weber"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066668-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x9x84w
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oxalis grammopetala Sond."
 ]
}

 The dataset includes 29 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066669-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gshmh2
title: Occurrence Download

description: A dataset containing 309 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters is less than or equal to 9919.0",
 "Geometry POLYGON((-166.26531 -57.47005,-32.19183 -57.47005,-32.19183 71.16802,-166.26531 71.16802,-166.26531 -57.47005))",
 "TaxonKey is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 309 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066670-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e9pq74
title: Occurrence Download

description: A dataset containing 516 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Patrinia scabra Bunge"
 ]
}

 The dataset includes 516 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066671-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3fgu5e
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Palaquium confertum H.J.Lam"
 ]
}

 The dataset includes 14 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066672-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.