cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6834461
title: Supplementary Material for: Potential Role of Gr-1<sup>+</sup> CD8<sup>+</sup> T Lymphocytes as a Source of Interferon-γ and M1/M2 Polarization during the Acute Phase of Murine <b><i>Legionella pneumophila</i></b> Pneumonia

description: In this study, we analyzed interferon (IFN)-γ-producing cells and M1/M2 macrophage polarization in <i>Legionella pneumophila</i> pneumonia following anti-Gr-1 antibody treatment. Anti-Gr-1 treatment induced an M1-to-M2 shift of macrophage subtypes in the lungs and weakly in the peripheral blood, which was associated with increased mortality in legionella-infected mice. CD8<sup>+</sup> T lymphocytes and natural killer cells were the dominant sources of IFN-γ in the acute phase, and anti-Gr-1 treatment reduced the number of IFN-γ-producing CD8<sup>+</sup> T lymphocytes. In the CD3-gated population, most Gr-1-positive cells were CD8<sup>+</sup> T lymphocytes in the lungs and lymph nodes (LNs) of infected mice. Additionally, the number of IFN-γ-producing Gr-1<sup>+</sup> CD8<sup>+</sup> T lymphocytes in the lungs and LNs increased 2 and 4 days after <i>L. pneumophila</i> infection, with anti-Gr-1 treatment attenuating these populations. Antibody staining revealed that Gr-1<sup>+</sup> CD8<sup>+</sup> T lymphocytes were Ly6C-positive cells rather than Ly6G, a phenotype regarded as memory type cells. Furthermore, the adoptive transfer of Gr-1<sup>+</sup> CD8<sup>+</sup> T lymphocytes induced increases in IFN-γ, M1 shifting and reduced bacterial number in the <i>Legionella</i> pneumonia model. These data identified Ly6C<sup>+</sup> CD8<sup>+</sup> T lymphocytes as a source of IFN-γ in innate immunity and partially associated with reduced IFN-γ production, M2 polarization, and high mortality in anti-Gr-1 antibody-treated mice with <i>L. pneumophila</i> pneumonia.
DOI: 10.6084/m9.figshare.6834371
title: Supplementary Material for: Abnormal Expression of Long Noncoding RNAs in Primary Immune Thrombocytopenia: A Microarray Related Study

description: <b><i>Background/Aims:</i></b> Long noncoding RNAs (lncRNAs) are important regulators of biological processes and they contribute to the pathological developments of various diseases, including autoimmune diseases. To gain the further understanding, we estimate the expression of lncRNAs in primary immune thrombocytopenia (ITP). <b><i>Methods:</i></b> In this study, microarray studies were performed to characterize expression profiles of various lncRNAs and mRNAs in blood samples collected from ITP patients. Quantitative real-time PCR (qRT-PCR) was performed to confirm the results, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and gene ontology analysis were used to provide functional annotations, co-expression network construction (CNC) analysis was made to reveal the relations between lncRNAs and their targeted genes. <b><i>Results:</i></b> A total of 1177 and 632 lncRNAs were significantly up-regulated or down-regulated, respectively, in “newly diagnosed ITP” patients versus healthy individuals. In addition, 1182 genes and 737 genes were up-regulated or down-regulated, respectively, in “chronic recurrent ITP” patients versus healthy individuals. In a KEGG analysis, “TNF signaling pathway-Homo sapiens (human)” was a key result. In a gene ontology analysis, “Granulocyte macrophage colony-stimulating factor production (GO: 0032604, ontology: Biological process, P = 1.69577E-05)” and “coreceptor activity (GO: 0015026, ontology: molecular function, P = 4.67594E-06)” were the two most critical results. Data from qRT-PCR and receiver operating characteristic curves further demonstrated that ENST00000440492, ENST00000528366, NR_038920, and ENST00000552576 can efficiently distinguish different stages of ITP, especially NR_038920 and ENST00000528366. In a CNC analysis, four lncRNAs were emphasized, and NR_038920 and ENST00000528366 were both associated with proteins with important roles in autoimmune diseases. <b><i>Conclusions:</i></b> These results suggest that lncRNAs act through targeted genes to mediate their functions and to mediate their functions and affect the pathogenesis of ITP.
DOI: 10.6084/m9.figshare.6834371.v1
title: Supplementary Material for: Abnormal Expression of Long Noncoding RNAs in Primary Immune Thrombocytopenia: A Microarray Related Study

description: <b><i>Background/Aims:</i></b> Long noncoding RNAs (lncRNAs) are important regulators of biological processes and they contribute to the pathological developments of various diseases, including autoimmune diseases. To gain the further understanding, we estimate the expression of lncRNAs in primary immune thrombocytopenia (ITP). <b><i>Methods:</i></b> In this study, microarray studies were performed to characterize expression profiles of various lncRNAs and mRNAs in blood samples collected from ITP patients. Quantitative real-time PCR (qRT-PCR) was performed to confirm the results, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and gene ontology analysis were used to provide functional annotations, co-expression network construction (CNC) analysis was made to reveal the relations between lncRNAs and their targeted genes. <b><i>Results:</i></b> A total of 1177 and 632 lncRNAs were significantly up-regulated or down-regulated, respectively, in “newly diagnosed ITP” patients versus healthy individuals. In addition, 1182 genes and 737 genes were up-regulated or down-regulated, respectively, in “chronic recurrent ITP” patients versus healthy individuals. In a KEGG analysis, “TNF signaling pathway-Homo sapiens (human)” was a key result. In a gene ontology analysis, “Granulocyte macrophage colony-stimulating factor production (GO: 0032604, ontology: Biological process, P = 1.69577E-05)” and “coreceptor activity (GO: 0015026, ontology: molecular function, P = 4.67594E-06)” were the two most critical results. Data from qRT-PCR and receiver operating characteristic curves further demonstrated that ENST00000440492, ENST00000528366, NR_038920, and ENST00000552576 can efficiently distinguish different stages of ITP, especially NR_038920 and ENST00000528366. In a CNC analysis, four lncRNAs were emphasized, and NR_038920 and ENST00000528366 were both associated with proteins with important roles in autoimmune diseases. <b><i>Conclusions:</i></b> These results suggest that lncRNAs act through targeted genes to mediate their functions and to mediate their functions and affect the pathogenesis of ITP.
DOI: 10.6084/m9.figshare.6834353
title: Two replications of Raymond, Shapiro, and Arnell (1992), The Attentional Blink

description: Dataset of Experiment 1 and Experiment 2 of "Two replications of Raymond, Shapiro, and Arnell (1992), The Attentional Blink".
DOI: 10.6084/m9.figshare.6834353.v1
title: Two replications of Raymond, Shapiro, and Arnell (1992), The Attentional Blink

description: Dataset of Experiment 1 and Experiment 2 of "Two replications of Raymond, Shapiro, and Arnell (1992), The Attentional Blink".
DOI: 10.6084/m9.figshare.6834272
title: Bats data

description: Excel file with capture-recapture data, population counts and newborn counts for the years 1991-2005 for a bats colony (<i>Rhinolophus ferrumequinum</i>) living in the attics of a chapel in Vex (Valais, Switzerland).
DOI: 10.6084/m9.figshare.6834272.v1
title: Bats data

description: Excel file with capture-recapture data, population counts and newborn counts for the years 1991-2005 for a bats colony (<i>Rhinolophus ferrumequinum</i>) living in the attics of a chapel in Vex (Valais, Switzerland).
DOI: 10.6084/m9.figshare.6834254
title: Przepiora_rawdata_new

description: Przepiora_raw_data
DOI: 10.6084/m9.figshare.6834248
title: SupplementaryCode2_map_external_proteins_to_protein_haplotypes.pl

description: Exact mapping of the full-length UniProt and RefSeq sequences to full-length protein haplotypes, minus any trailing stop codon, was performed using a simple Perl script
DOI: 10.6084/m9.figshare.6834254.v1
title: Przepiora_rawdata_new

description: Przepiora_raw_data
DOI: 10.6084/m9.figshare.6834107
title: DBLP results

description: DBLP rule-driven methodology results<br>
DOI: 10.6084/m9.figshare.6834191
title: SupplementaryData2-all_protein_haplotypes_GRCh37.fa.gz

description: Fasta protein sequences of all protein haplotypes in 1000 Genomes
DOI: 10.6084/m9.figshare.6834107.v1
title: DBLP results

description: DBLP rule-driven methodology results<br>
DOI: 10.6084/m9.figshare.6834086
title: Supplementary Material for: Association Between Hypoxia-Inducible Factor-2α (HIF-2α) Expression and Colorectal Cancer and Its Prognostic Role: a Systematic Analysis

description: <b><i>Background/Aims:</i></b> Although some studies showed that HIF-2α expression was correlated with an unfavorable prognosis in colorectal cancer (CRC), the prognostic results remain conflicting in CRC. The present study was performed to evaluate the association between HIF-2α expression and the clinicopathological features of this disease and to examine the potential prognostic role of HIF-2α expression in CRC. <b><i>Methods:</i></b> Pooled odds ratios (ORs) or hazard ratios (HRs) were calculated from available publications, The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) datasets. Trial sequential analysis (TSA) was used to estimate the required sample information. <b><i>Results:</i></b> HIF-2α protein expression was more frequent in CRC than in normal colonic tissues (OR = 150.49, <i>P</i> &lt; 0.001), higher in male than female CRC patients (OR = 1.47, <i>P</i> = 0.008), and lower in high-grade than low-grade CRC (OR = 0.49, <i>P</i> = 0.029). TSA verified the reliability of the above results. HIF-2α expression was not linked to the prognosis of CRC in overall survival (OS), disease-specific survival (DSS), metastasis-free survival, and relapse-free survival, and no significant correlation was found between HIF-2α alteration and OS or disease-free survival (DFS) of CRC. Expression of both HIF-2α and vascular endothelial growth factor (VEGFA, VEGFB, or VEGFC) was associated with a poor metastasis-free survival of CRC (HR = 6.95, HR = 113.51, and HR = 8.11, respectively). No association was observed between HIF-2α expression and DFS in other cancers, but HIF-2α expression was correlated with a worse DFS of CRC (HR = 1.23, <i>P</i> = 0.037). Moreover, HIF-2α expression was linked to a good survival benefit in some cancers (B-cell lymphoma and lung adenocarcinoma: OS, multiple myeloma: DSS, breast cancer: distant metastasis-free survival, liposarcoma: distant recurrence-free survival) (all HRs &lt; 1, <i>Ps</i> &lt; 0.05). <b><i>Conclusions:</i></b> HIF-2α expression may be associated with the carcinogenesis of CRC, which is higher in males than in females, negatively linked to tumor differentiation, and correlated with a worse DFS of CRC. Additional prospective studies are needed.
DOI: 10.6084/m9.figshare.6834077
title: Supplementary Material for: Na<sup>+</sup>-Leak Channel, Non-Selective (NALCN) Regulates Myometrial Excitability and Facilitates Successful Parturition

description: <b><i>Background/Aims:</i></b> Uterine contractility is controlled by electrical signals generated by myometrial smooth muscle cells. Because aberrant electrical signaling may cause inefficient uterine contractions and poor reproductive outcomes, there is great interest in defining the ion channels that regulate uterine excitability. In human myometrium, the Na<sup>+</sup> leak channel, non-selective (NALCN) contributes to a gadolinium-sensitive, Na<sup>+</sup>-dependent leak current. The aim of this study was to determine the role of NALCN in regulating uterine excitability and examine its involvement in parturition. <b><i>Methods:</i></b> Wildtype C57BL/6J mice underwent timed-mating and NALCN uterine expression was measured at several time points across pregnancy including pregnancy days 7, 10, 14, 18 and 19. Sharp electrode current clamp was used to measure uterine excitability at these same time points. To determine NALCN’s contribution to myometrial excitability and pregnancy outcomes, we created smooth-muscle-specific NALCN knockout mice by crossing NALCN<i>fx/fx</i> mice with myosin heavy chain Cre (MHC<i>CreeGFP</i>) mice. Parturition outcomes were assessed by observation via surveillance video recording cre control, flox control, smNALCN<sup>+/-</sup>, and smNALCN<sup>-/-</sup> mice. Myometrial excitability was compared between pregnancy day 19 flox controls and smNALCN<sup>-/-</sup> mice. <b><i>Results:</i></b> We found that in the mouse uterus, NALCN protein levels were high early in pregnancy, decreased in mid and late pregnancy, and then increased in labor and postpartum. Sharp electrode current clamp recordings of mouse longitudinal myometrial samples from pregnancy days 7, 10, 14, 18, and 19 revealed day-dependent increases in burst duration and interval and decreases in spike density. NALCN smooth muscle knockout mice had reduced myometrial excitability exemplified by shortened action potential bursts, and an increased rate of abnormal labor, including prolonged and dysfunctional labor. <b><i>Conclusions:</i></b> Together, our findings demonstrate that the Na<sup>+</sup> conducting channel NALCN contributes to the myometrial action potential waveform and is important for successful labor outcomes.
DOI: 10.6084/m9.figshare.6834083
title: SupplementaryData1.tar.gz

description: This zip file contains the data used to validate Haplosaurus. It contains a directory for each test gene in which there is the original GTF file and its Tabix index, the original FASTA file, a log file describing each applied test case and two directories: "hap" which contains a FASTA and GFF file per generated haplotype and "vcf" which contains a Tabix indexed VCF file per test case.<br>
DOI: 10.6084/m9.figshare.6834065
title: DBLP RML rules

description: DBLP RML rules<br>
DOI: 10.6084/m9.figshare.6834062
title: Development of the Social Participation Restrictions Questionnaire (SPaRQ) through consultation with adults with hearing loss, researchers, and clinicians: a content evaluation study

description: <b>Objective:</b> This research aimed to evaluate the content of the Social Participation Restrictions Questionnaire (SPaRQ) in terms of its relevance, clarity, comprehensiveness, acceptability to adults with hearing loss, and responsiveness. <b>Design:</b> Cognitive interviews and a subject matter expert survey were conducted. The interview data were analysed using thematic analysis and a taxonomy of questionnaire clarity problems. Descriptive statistics were calculated for the survey data. <b>Study sample:</b> Fourteen adults with hearing loss participated in the cognitive interviews. Twenty clinicians and academics completed the subject matter expert survey. <b>Results:</b> The majority of the SPaRQ content was found to be relevant, clear, comprehensive, and acceptable. However, an important clarity problem was identified: many adults with hearing loss struggled to switch from answering positively worded items (e.g. “I can attend social gatherings”) to answering negatively-worded items (e.g. “I feel isolated”). Several subject matter experts found responsiveness difficult to assess. The SPaRQ was amended where necessary. <b>Conclusion:</b> Few hearing-specific questionnaires have undergone content evaluation. This study highlights the value of content evaluation as a means of identifying important flaws and improving the quality of a measure. The next stage of this research is a psychometric evaluation of the measure.
DOI: 10.6084/m9.figshare.6834065.v1
title: DBLP RML rules

description: DBLP RML rules<br>
DOI: 10.6084/m9.figshare.6834050
title: DBpedia RML rules

description: DBpedia RML rules 20180703<br>
DOI: 10.6084/m9.figshare.6834062.v1
title: Development of the Social Participation Restrictions Questionnaire (SPaRQ) through consultation with adults with hearing loss, researchers, and clinicians: a content evaluation study

description: <b>Objective:</b> This research aimed to evaluate the content of the Social Participation Restrictions Questionnaire (SPaRQ) in terms of its relevance, clarity, comprehensiveness, acceptability to adults with hearing loss, and responsiveness. <b>Design:</b> Cognitive interviews and a subject matter expert survey were conducted. The interview data were analysed using thematic analysis and a taxonomy of questionnaire clarity problems. Descriptive statistics were calculated for the survey data. <b>Study sample:</b> Fourteen adults with hearing loss participated in the cognitive interviews. Twenty clinicians and academics completed the subject matter expert survey. <b>Results:</b> The majority of the SPaRQ content was found to be relevant, clear, comprehensive, and acceptable. However, an important clarity problem was identified: many adults with hearing loss struggled to switch from answering positively worded items (e.g. “I can attend social gatherings”) to answering negatively-worded items (e.g. “I feel isolated”). Several subject matter experts found responsiveness difficult to assess. The SPaRQ was amended where necessary. <b>Conclusion:</b> Few hearing-specific questionnaires have undergone content evaluation. This study highlights the value of content evaluation as a means of identifying important flaws and improving the quality of a measure. The next stage of this research is a psychometric evaluation of the measure.
DOI: 10.6084/m9.figshare.6834008
title: Supplementary_Code_1-Figure2.tar.gz

description: R code and data used to generate Figure 2
DOI: 10.6084/m9.figshare.6834050.v1
title: DBpedia RML rules

description: DBpedia RML rules 20180703<br>
DOI: 10.6084/m9.figshare.6834005
title: DBpedia results

description: DBpedia results of our rule-driven methodology<br>
DOI: 10.6084/m9.figshare.6834005.v1
title: DBpedia results

description: DBpedia results of our rule-driven methodology<br>
DOI: 10.6084/m9.figshare.6834008.v1
title: Supplementary_Code_1-Figure2.tar.gz

description: R code and data used to generate Figure 2
DOI: 10.6084/m9.figshare.6834002
title: Effects of high-intensity interval training and moderate-intensity continuous training on body adiposity and cardiorespiratory fitness in adolescents with central obesity

description: Data from the article submitted to Plos One.
DOI: 10.6084/m9.figshare.6834002.v1
title: Effects of high-intensity interval training and moderate-intensity continuous training on body adiposity and cardiorespiratory fitness in adolescents with central obesity

description: Data from the article submitted to Plos One.
DOI: 10.6084/m9.figshare.6833936
title: Supplementary Material for: NS3 Variability in Hepatitis C Virus Genotype 1A Isolates from Liver Tissue and Serum Samples of Treatment-Naïve Patients with Chronic Hepatitis C

description: <b><i>Background:</i></b> Hepatitis C virus (HCV) NS3 resistance-associated substitutions (RASs) reduce HCV susceptibility to protease inhibitors. Little is known about NS3 RASs in viral isolates from the liver of chronic hepatitis C (CHC) patients infected with HCV genotype-1a (G1a). <b><i>Aim:</i></b> The objective of this work was to study NS3 variability in isolates from the serum and liver of HCV-G1a-infected patients naïve to direct-acting antivirals (DAAs). <b><i>Methods:</i></b> NS3 variability of HCV-G1a isolates from the serum and liver of 11 naïve CHC patients, and from sera of an additional 20 naïve CHC patients, was investigated by next-generation sequencing. <b><i>Results:</i></b> At a cutoff of 1%, NS3 RASs were detected in all the samples examined. At a cutoff of 15%, they were found in 54.5% (6/11) and 27.3% (3/11) of the paired liver and serum samples, respectively, and in 22.5% (7/31) of the overall serum samples examined. Twenty-six out of thirty-one (84%) patients showed NS3 variants with multiple RASs. Phylogenetic analysis showed that NS3 sequences clustered within 2 clades, with 10/31 (32.2%) patients infected by clade I, 15/31 (48.8%) by clade II, and 6/31 (19.3%) by both clades. <b><i>Conclusions:</i></b> Though the number of patients examined was limited, NS3 variants with RASs appear to be major components of both intrahepatic and circulating viral quasispecies populations in DAA-naïve patients.
DOI: 10.6084/m9.figshare.6833927
title: Supplementary Material for: HCC Immune Surveillance and Antiviral Therapy of Hepatitis C Virus Infection

description: <b><i>Objective:</i></b> HCV clearance by current antiviral therapies improves clinical outcomes but falls short in eliminating the risk for hepatocellular carcinoma (HCC) emergence. As the HCC immune surveillance establishment is vital for the control of neoplastic development and growth, we investigated its correlation with on-/post-treatment HCC emergence, and further analyzed the influence of viral eradication on this setup in patients with HCV-related liver cirrhosis. <b><i>Design:</i></b> PBMC isolated at baseline and longitudinally during therapy were analyzed for tumor-associated antigen (TAA)-specific CD8+ T cell responses against glypican-3 overlapping peptides in vitro using high-definition flow cytometry. Multianalyte profiling of fifty soluble inflammatory mediators (SIM) in the plasma was also performed using Luminex-based multiplex technology. <b><i>Results:</i></b> Cirrhosis patients were characterized by an altered profile of distinct SIMs at baseline. At this time point, immune-surveilling T cells targeting specific HCC-associated antigens were readily detectable in HCV-free cirrhosis patients whilst being rather weak in such patients who further developed HCC upon virus eradication. Therapy-induced cure of HCV infection analogously reduced the strength of the prevailing HCC immune surveillance machinery, particularly by CD8+ T cells in cirrhosis patients. These results were further validated by T cell reactivities to six immuno-dominant HCC-associated HLA-A2-restricted epi­topes. Further, we demonstrated that this phenomenon was likely orchestrated by alterations in SIMs – with evidence of IL-12 being a major culprit. <b><i>Conclusion:</i></b> Given the relationship between the baseline HCC-specific immune surveilling T cell responses and therapy-associated HCC emergence, and the impact of HCV clearance on its strength and magnitude, we recommend a continued HCC screening in cirrhotic HCV patients despite HCV resolution.
DOI: 10.6084/m9.figshare.6833888
title: Measurement_Data.xlsx

description: Full Dataset "Biomechanical evaluation of hybrid double plate osteosynthesis using a locking plate and an inverted third tubular plate for the treatment of proximal humeral fractures"