cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10311431
title: Table S13 from Multivariable regulation of gene expression plasticity in metazoans

description: An important capacity of genes is the rapid change of expression levels to cope with environment, known as expression responsiveness or plasticity. Elucidating the genomic mechanisms determining expression plasticity is critical for understanding the molecular basis of phenotypic plasticity, fitness and adaptation. In this study, we systematically quantified gene expression plasticity in four metazoan species by integrating changes of expression levels under a large number of genetic and environmental conditions. From this, we demonstrated that expression plasticity measures a distinct feature of gene expression that is orthogonal to other well-studies features including gene expression level and tissue specificity/broadness. Expression plasticity is conserved across species with important physiological implications. The magnitude of expression plasticity is highly correlated with gene function and genes with high plasticity are implicated in disease susceptibility. Genome-wide analysis identified many conserved promoter <i>cis</i>-elements, <i>trans</i>-acting factors (such as CFCF), and gene body histone modifications (H3K36me3, H3K79me2 and H4K20me1) that are significantly associated with expression plasticity. Analysis of expression changes in perturbation experiments further validated a causal role of specific transcription factors and histone modifications. Collectively, this work reveals general properties, physiological implications and multivariable regulation of gene expression plasticity in metazoans, extending the mechanistic understanding of gene regulation.
DOI: 10.6084/m9.figshare.10311431.v1
title: Table S13 from Multivariable regulation of gene expression plasticity in metazoans

description: An important capacity of genes is the rapid change of expression levels to cope with environment, known as expression responsiveness or plasticity. Elucidating the genomic mechanisms determining expression plasticity is critical for understanding the molecular basis of phenotypic plasticity, fitness and adaptation. In this study, we systematically quantified gene expression plasticity in four metazoan species by integrating changes of expression levels under a large number of genetic and environmental conditions. From this, we demonstrated that expression plasticity measures a distinct feature of gene expression that is orthogonal to other well-studies features including gene expression level and tissue specificity/broadness. Expression plasticity is conserved across species with important physiological implications. The magnitude of expression plasticity is highly correlated with gene function and genes with high plasticity are implicated in disease susceptibility. Genome-wide analysis identified many conserved promoter <i>cis</i>-elements, <i>trans</i>-acting factors (such as CFCF), and gene body histone modifications (H3K36me3, H3K79me2 and H4K20me1) that are significantly associated with expression plasticity. Analysis of expression changes in perturbation experiments further validated a causal role of specific transcription factors and histone modifications. Collectively, this work reveals general properties, physiological implications and multivariable regulation of gene expression plasticity in metazoans, extending the mechanistic understanding of gene regulation.
DOI: 10.6084/m9.figshare.21321520.v1
title: Additional file 15 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 15: Table S1. The initial result of the joint prediction using BepiPred-2.0 and ABCPred.
DOI: 10.6084/m9.figshare.21321529.v1
title: Additional file 1 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 1. Information on membrane proteins of Toxoplasma gondii obtained from the UniProt database.
DOI: 10.6084/m9.figshare.21321538.v1
title: Additional file 4 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 4. Initial predicted HLA-I binding epitopes.
DOI: 10.6084/m9.figshare.21321550.v1
title: Additional file 8 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 8. Identified epitopes capable of binding to both HLA-I and mouse MHC-I molecules, and epitopes capable of binding to both HLA-II and mouse MHC-II molecules.
DOI: 10.6084/m9.figshare.21321503
title: Additional file 4 of Accuracy of next-generation sequencing for molecular profiling of small specimen of lung cancer: a prospective pilot study of side-by-side comparison

description: Additional file 4.
DOI: 10.6084/m9.figshare.19219206
title: Additional file 17 of Insights into glucosinolate accumulation and metabolic pathways in Isatis indigotica Fort.

description: Additional file 17: Table S7. Raw data of Ka/Ks ratio calculation results. The ratio was coloured to show the variation tendency. Source genes are from I. indigotica, and query genes from other Brassicaceae species. Eight processes were divided according to the gene functions in glucosinolate metabolic pathways. For subgroup division, CYP79 and CYP83 are thought to be key enzymes in GSL biosynthesis. GGP, SUR and UGT74B are shared with both aliphatic and indole GSL biosynthesis processes, named “common genes”. Different members of GST and ST5 are linked to different GSL formation, and were grouped together. Atypical myrosinases include BGLU28, BGLU30, PEN2 and PYK10, contrast to typical myrosinase TGGs. For side-chain modification, FMO, AOP and GSL-OH take their parts in aliphatic GSL modification, while CYP81F and IGMT modify indole ring in the nature.
DOI: 10.6084/m9.figshare.12408674.v2
title: Atmospheric factors controlling stable isotope variations in modern precipitation of the tropical region of Bangladesh

description: The study investigates the factors that control the isotopic composition of tropical precipitation in Bangladesh. Daily and monthly rainfall samples were collected from three stations from 2013 to 2015: (1) northern and moderately high altitude: Sylhet, (2) middle part of the country (close to Tropic of Cancer): Savar, and (3) southern coastal region: Barisal. To escape from the post-evaporation effect, proper care was adopted. This is supported by the fact that the local meteoric water lines (LMWLs) derived for the daily precipitations of all stations mostly follow the global meteoric water line (GMWL). The results exhibit a clear seasonal and spatial variation in both <i>δ</i><sup>18</sup>O and <i>δ</i><sup>2</sup>H of precipitation. <sup>18</sup>O is more depleted in samples collected during rainy (monsoon) seasons, while <sup>18</sup>O enrichment is associated to winter and summer (pre-monsoon) seasons. During rainy season, intra-seasonal variability of δ<sup>18</sup>O rainfall is clearly seen and remarkable depletion of <sup>18</sup>O is observed during the period of intense convective activity over the Bay of Bengal. This feature indicates that isotope variability in Bangladesh is controlled by large-scale convective activity rather than local rainfall amount.
DOI: 10.6084/m9.figshare.21321503.v1
title: Additional file 4 of Accuracy of next-generation sequencing for molecular profiling of small specimen of lung cancer: a prospective pilot study of side-by-side comparison

description: Additional file 4.
DOI: 10.6084/m9.figshare.21321523.v1
title: Additional file 16 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 16: Table S2 Antigenicity, allergenicity, toxicity, transmembrane localization, signal peptide and hydrophilicity profiling of selected peptides.
DOI: 10.6084/m9.figshare.21321505.v1
title: Additional file 10 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 10. Worldwide population coverage of HLA alleles by the vaccine.
DOI: 10.6084/m9.figshare.21321553
title: Additional file 9 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 9. Binding capacity of selected T cell epitopes.
DOI: 10.5281/zenodo.10679449
title: Analyse de la Valeur - nouvelle voie

description: Présentation d'un cas classique d'Analyse de la Valeur - nouvelle voie ?
DOI: 10.5281/zenodo.10679450
title: Analyse de la Valeur - nouvelle voie

description: Présentation d'un cas classique d'Analyse de la Valeur - nouvelle voie ?
DOI: 10.6084/m9.figshare.21321526.v1
title: Additional file 17 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 17: Table S3 Alignment of experimentally verified epitopes and selected sequences in the vaccine construct.
DOI: 10.6084/m9.figshare.21321523
title: Additional file 16 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 16: Table S2 Antigenicity, allergenicity, toxicity, transmembrane localization, signal peptide and hydrophilicity profiling of selected peptides.
DOI: 10.6084/m9.figshare.21321532.v1
title: Additional file 2 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 2. Amino acid sequences of the proteins presented in Additional file 1.
DOI: 10.6084/m9.figshare.21321544
title: Additional file 6 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 6. Initial predicted mouse MHC-I binding epitopes.
DOI: 10.6084/m9.figshare.21321526
title: Additional file 17 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 17: Table S3 Alignment of experimentally verified epitopes and selected sequences in the vaccine construct.
DOI: 10.6084/m9.figshare.21321529
title: Additional file 1 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 1. Information on membrane proteins of Toxoplasma gondii obtained from the UniProt database.
DOI: 10.6084/m9.figshare.25212497
title: Data sets for 'Factors affecting senior managers’ decisions when implementing Management Information Systems (MIS) in UK manufacturing organisations'

description: This page contains data sets underlying the thesis by Nahid Izadpanah Mehrkish called 'Factors affecting senior managers’ decisions when implementing Management Information Systems (MIS) in UK manufacturing organisations'. Materials include:A survey output with 400 board level senior managersInterview transcripts of 12 board level senior managersA survey output with 96 board level senior managers
DOI: 10.6084/m9.figshare.12408674.v1
title: Atmospheric factors controlling stable isotope variations in modern precipitation of the tropical region of Bangladesh<sup>*</sup>

description: The study investigates the factors that control the isotopic composition of tropical precipitation in Bangladesh. Daily and monthly rainfall samples were collected from three stations from 2013 to 2015: (1) northern and moderately high altitude: Sylhet, (2) middle part of the country (close to Tropic of Cancer): Savar, and (3) southern coastal region: Barisal. To escape from the post-evaporation effect, proper care was adopted. This is supported by the fact that the local meteoric water lines (LMWLs) derived for the daily precipitations of all stations mostly follow the global meteoric water line (GMWL). The results exhibit a clear seasonal and spatial variation in both <i>δ</i><sup>18</sup>O and <i>δ</i><sup>2</sup>H of precipitation. <sup>18</sup>O is more depleted in samples collected during rainy (monsoon) seasons, while <sup>18</sup>O enrichment is associated to winter and summer (pre-monsoon) seasons. During rainy season, intra-seasonal variability of δ<sup>18</sup>O rainfall is clearly seen and remarkable depletion of <sup>18</sup>O is observed during the period of intense convective activity over the Bay of Bengal. This feature indicates that isotope variability in Bangladesh is controlled by large-scale convective activity rather than local rainfall amount.
DOI: 10.6084/m9.figshare.21321532
title: Additional file 2 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 2. Amino acid sequences of the proteins presented in Additional file 1.
DOI: 10.6084/m9.figshare.21321544.v1
title: Additional file 6 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 6. Initial predicted mouse MHC-I binding epitopes.
DOI: 10.6084/m9.figshare.21321550
title: Additional file 8 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 8. Identified epitopes capable of binding to both HLA-I and mouse MHC-I molecules, and epitopes capable of binding to both HLA-II and mouse MHC-II molecules.
DOI: 10.6084/m9.figshare.21321535
title: Additional file 3 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 3. Linear B cell epitopes predicted by the ABCPred server.
DOI: 10.6084/m9.figshare.21321538
title: Additional file 4 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 4. Initial predicted HLA-I binding epitopes.
DOI: 10.6084/m9.figshare.21321553.v1
title: Additional file 9 of Epitope vaccine design for Toxoplasma gondii based on a genome-wide database of membrane proteins

description: Additional file 9. Binding capacity of selected T cell epitopes.
DOI: 10.5281/zenodo.10679386
title: 2020 Masbate surface rupture drone data

description: The drone dataset comprises orthomosaic photos and digital elevation models generated from multiple flight missions utilizing a DJI Phantom 4 Pro. These missions were specifically carried out along the surface rupture of the 2020 Masbate earthquake to aid mapping efforts across flat terrains. The drone photos were processed using Agisoft Metashape.
DOI: 10.5281/zenodo.10679475
title: ЛИНГВОСТИЛИСТИЧЕСКИЕ   ОСОБЕННОСТИ  СЛОЖНЫХ ПРЕДЛОЖЕНИЙ С ПАРЕНТЕЗНЫМ ВСТАВНЫМ  КОМПОНЕНТОМ КАК ЛИНГВОСТИЛЕМ В РЕЧИ
DOI: 10.5281/zenodo.10679476
title: ЛИНГВОСТИЛИСТИЧЕСКИЕ   ОСОБЕННОСТИ  СЛОЖНЫХ ПРЕДЛОЖЕНИЙ С ПАРЕНТЕЗНЫМ ВСТАВНЫМ  КОМПОНЕНТОМ КАК ЛИНГВОСТИЛЕМ В РЕЧИ
DOI: 10.6084/m9.figshare.15178526
title: Additional file 1 of Multi-omics network characterization reveals novel microRNA biomarkers and mechanisms for diagnosis and subtyping of kidney transplant rejection

description: Additional file 1. CORE genes identified in this study.
DOI: 10.6084/m9.figshare.15178532
title: Additional file 3 of Multi-omics network characterization reveals novel microRNA biomarkers and mechanisms for diagnosis and subtyping of kidney transplant rejection

description: Additional file 3. Significantly enriched BP terms by identified miRNA biomarkers.
DOI: 10.25403/upresearchdata.25174799
title: Experimental results of compressive sensing on wireless multimedia sensor networks.

description: Compressed Sensing (CS) was presented as a means to achieve overcome the challenges faced by Wireless Multimedia Sensor Networks. A sensing matrix is crucial to the compressed sensing framework. The sensing matrix can maintain the fidelity of a compressed signal, diminish the sampling rate obligation and improve the strength and performance of the recovery algorithm. A great number of measurement matrices have been proposed to either offer reduced computational complexity or good recovery performance, but only some have managed to accomplish both, and even fewer have been proven in a compelling manner. Experiments were conducted to evaluate the fidelity and energy efficiency of different compressive sensing matrices for applications on Wireless Multimedia Sensor Networks.
DOI: 10.25403/upresearchdata.25174799.v1
title: Experimental results of compressive sensing on wireless multimedia sensor networks.

description: Compressed Sensing (CS) was presented as a means to achieve overcome the challenges faced by Wireless Multimedia Sensor Networks. A sensing matrix is crucial to the compressed sensing framework. The sensing matrix can maintain the fidelity of a compressed signal, diminish the sampling rate obligation and improve the strength and performance of the recovery algorithm. A great number of measurement matrices have been proposed to either offer reduced computational complexity or good recovery performance, but only some have managed to accomplish both, and even fewer have been proven in a compelling manner. Experiments were conducted to evaluate the fidelity and energy efficiency of different compressive sensing matrices for applications on Wireless Multimedia Sensor Networks.
DOI: 10.5281/zenodo.10679479
title: Artefact for ``Addressing Combinatorial Experiments and Scarcity of Subjects by Provably Orthogonal and Crossover Experimental Designs''
DOI: 10.5281/zenodo.10679480
title: Artefact for ``Addressing Combinatorial Experiments and Scarcity of Subjects by Provably Orthogonal and Crossover Experimental Designs''
DOI: 10.6084/m9.figshare.12408824.v1
title: The association between metabolic syndrome and benign prostatic hyperplasia: a systematic review and meta-analysis

description: We performed this meta-analysis to assess the association between metabolic syndrome (MetS) and benign prostatic hyperplasia (BPH). We conducted extensive searches on the PubMed, Science and Cochrane Library to identify all articles. Outcomes including annual prostate growth rate, prostate volume (PV), International Prostate Symptom Score (IPSS), IPSS sub-scores (voiding and storage), prostate- specific antigen (PSA), maximum urine flow rate (Qmax), post-void residual urine volume (PVR) and quality of life (QoL) were assessed. 21 studies with 15,317 patients were included. Patients with MetS had higher annual prostate growth rate [weighted mean difference (WMD) = 0.79; <i>p</i> &lt; .001], larger PV (WMD = 2.62; <i>p</i> &lt; .001), lower Qmax (WMD = −0.48; <i>p</i> = .001) and more PVR (WMD = 8.28; <i>p</i> &lt; .001). However, no significant differences were found between two groups in IPSS (WMD = 0.20; <i>p</i> = .37), IPSS-voiding (WMD = −0.05; <i>p</i> = .78), IPSS-storage (WMD = −0.22; <i>p</i> = .26), PSA (WMD = 0.04; <i>p</i> = .43), and QoL (WMD = −0.01; <i>p</i> = .70). The study suggested that MetS may be one of the risk factors for the clinical progress of BPH. However, further study is warranted to support these results.
DOI: 10.6084/m9.figshare.7155674
title: Additional file 1: of Profiling the B/T cell receptor repertoire of lymphocyte derived cell lines

description: Figure S1. Expression of CD19/CD20, CD79A/B and RAG1/RAG2 in blood cancer cell lines. X axis: 164 blood cancer cell lines grouped base on the disease types (rectangle color bar below the X axis), each dot in X axis represent one cell line, and the Y axis, expression level (log2 value) of indicated genes. Figure S2. Clonal fraction (filtered by &gt;30 reads) of B-ALL, multiple myeloma, diffuse large B cell lymphoma, Burkitt lymphoma, B cell lymphoma (unspecified) and mantle cell lymphoma base on IGH or IGHK/L. Blue color indicates the clonotype fraction of the most dominant clone, Red color indicate the clonotype fraction of second dominant clone, Yellow color indicate the third dominant clone, while any smaller subclones were aggregated and labelled in grey. Figure S3. Clonal fraction (filtered by &gt;30 reads) of T-ALL and anaplastic large cell lymphoma base on TRCA or TRCB. Blue color indicates the clonotype fraction of dominant clone, red color inidicate the clonotype fraction of second dominant clone, while gray color indicate the third dominant clone. Figure S4. Heatmap showing the usage of IGK/L V genes (A), IGK/L J genes (B), and constant region (C) in 462 samples of EBV transformed normal B lymphocytes. Figure S5. The phylogenetic tree inferred based on the rearrangement of the CDR3 region of IGH, IGK and IGL of EBV transformed B lymphocyte samples ERR188025, ERR188358 and ERR188212. These three cell lines have much higher number of rearrangement types than the other B lymphocyte lines. Clonal Fraction (upper panel) and the read counts (lower panel) of the dominant clone of 462 samples of EBV transformed normal B lymphocytes. (ZIP 1290 kb)
DOI: 10.6084/m9.figshare.15178529
title: Additional file 2 of Multi-omics network characterization reveals novel microRNA biomarkers and mechanisms for diagnosis and subtyping of kidney transplant rejection

description: Additional file 2. The constructed KTR-specific miR-PPIN.
DOI: 10.6084/m9.figshare.19745056.v1
title: Additional file 1 of N6-methyladenosine-modified TRAF1 promotes sunitinib resistance by regulating apoptosis and angiogenesis in a METTL14-dependent manner in renal cell carcinoma

description: Additional file 1: Table S2. Sequences of shRNA&siRNA against specific target in this study. Fig. S1 A Colony formation assay of sunitinib-resistant cell lines and control cell lines with DMSO in 12-well dish for 3 weeks (n = 3). Fig. S2 A TRAF1 pathways in KEGG. B Proteins involed in angiogenesis signaling were mediated by TRAF1 in OS-RC-2 cells. Fig. S3 A and B ChIP assays were used to assess the degree of H3K4me3 within the regions 1-3 of the TRAF1 promoter in 78S and 78R cells.
DOI: 10.6084/m9.figshare.7165976.v1
title: Comparison of stroke- and bleed-related healthcare resource utilization and costs among patients with newly diagnosed non-valvular atrial fibrillation and newly treated with dabigatran, rivaroxaban, or warfarin

description: <b>Background</b>: This is one of the first head-to-head real-world evidence studies comparing stroke-related and bleed-related healthcare and resource utilization (HCRU) and costs among non-valvular atrial fibrillation (NVAF) patients initiating oral anticoagulants. <b>Methods</b>: Adult NVAF patients newly diagnosed and treated with dabigatran, rivaroxaban, or warfarin between 10/01/2010 and 12/31/2014 were identified using MarketScan Commercial and Medicare Supplemental databases. Per-patient-per-month stroke and bleed-related HCRU and costs were reported. <b>Results</b>: Dabigatran patients were matched 1:1 to 26,592 rivaroxaban and 33,024 warfarin patients (mean age=68 years). Compared to rivaroxaban, dabigatran patients had lower bleed-related inpatient and outpatient HCRU (0.004 vs. 0.005; 0.099 vs. 0.145) and significantly lower adjusted bleed-related costs ($116 vs. $172), all <i>p</i> &lt;0.05. Compared to warfarin, dabigatran patients had significantly lower stroke-related outpatient visits (0.034 vs. 0.048, <i>p</i>&lt;0.001) and higher bleed-related outpatient visits (0.101 vs. 0.091, <i>p</i>=0.045). Multivariate adjusted bleed-related costs were significantly lower for dabigatran patients than warfarin patients ($94 vs. $138, <i>p</i>&lt;0.001). <b>Conclusions</b>: The results suggest that dabigatran patients had lower bleed-related HCRU and costs than rivaroxaban patients, and lower outpatient stroke-related HCRU, higher bleed-related outpatient HCRU, and lower bleed-related costs than warfarin patients. It provides valuable stroke-related and bleed-related HCRU and costs information among commercially insured and Medicare patients.