cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7375856.v1
title: Supplementary Material for: ATP Citrate Lyase and LncRNA NONMMUT010685 Play Crucial Role in Nonalcoholic Fatty Liver Disease Based on Analysis of Microarray Data

description: <b><i>Background/Aims:</i></b> Nonalcoholic fatty liver disease (NAFLD) is the most common cause of liver disease with unclear molecular mechanisms. Our study intended to identify potential long non-coding RNAs (lncRNAs) and genes, and to determine the potential molecular mechanisms of NAFLD pathogenesis. <b><i>Methods:</i></b> The microarrays of GSE24031 and GSE57425 were downloaded from the Gene Expression Omnibus database. GSE24031 included 4 control and 4 model mice and GSE57425 included 3 control and 3 model mice on the basis of GPL1261 platform. Differentially expressed lncRNAs and mRNAs between control and NAFLD liver tissue were calculated. Gene ontology (GO), pathway enrichment analyses, co-expression network and PPI were performed to analyze the biological roles and pathways for the differentially expressed lncRNAs and mRNAs. Non-alcoholic steatohepatitis (NASH) rats were further chosen to investigate the key protein identified based on co-expression network and protein-protein interaction (PPI) network data. <b><i>Results:</i></b> A total of 6 significantly up-regulated and 39 down-regulated lncRNAs, 340 up-regulated and 281 down-regulated mRNAs were identified. LncRNA-mRNA co-expression network were analyzed to show a total of 16 key lncRNAs (node degree &gt; 10) in NAFLD samples compared to control tissues. Three key protein identified on co-expression network and protein-protein interaction (PPI) network data were verified in NASH <i>in vivo</i>. The protein level of ATP-citrate lyase (Acly) was significantly increased while lncNONMMUT010685 and NONMMUT050689 in NAFLD samples, whose regulator gene was x-box binding protein 1 (XBP1) and receptor-interacting protein 1 kinase (RIPK1) respectively, were gradually reduced in NASH. <b><i>Conclusion:</i></b> In summary, we found a set of lncRNAs and mRNAs differentially expressed in the development of NAFLD. LncRNA Ttc39aos1 and Acly, may be crucial biomarkers for NAFLD. LncRNA NONMMUT010685 and NONMMUT050689, the regulator of XBP1 gene and RIPK1 gene respectively, played important roles in the development of NAFLD.
DOI: 10.6084/m9.figshare.24046986.v1
title: ACTION PLAN

description: This document contains one of the partial action plan charts that was designed by student-teachers to develop the pedagogical project during the teaching practicum .
DOI: 10.17632/kdtcs4fk8g
title: GENeSYS-MOD China: Technology, demand, and renewable data

description: This dataset contains renewable potentials, timeseries, technology data, and additional data tables and figures for the article "Decarbonizing China’s Energy System - Modeling the Transformation of the Electricity, Transportation, Heat, and Industrial sectors".
DOI: 10.17632/bx8wb44gp4
title: 3D LiDAR and Photogrammetry Scans of a Stilt House in Tai O Village - 2022 - Case 328954

description: This data includes a point cloud file from a combined photogrammetric and LiDAR scan of a stilt house in Tai O Village. The house is designated "Case 328954" in the research project record. Researchers collected the scan using a single, approximately 10 minute walk-through of the house with the Leica-brand BLK2Go model 3D environment scanner. The scan describes the interior and partial exterior of a stilt house in high detail and color. The scan has been denoised using VRMesh Software to reduce file size. The data provides clear enough rendering of the physical conditions of the house to allow interpretation of the scan into description of the house's construction, contents, and spatial use. The data is available under embargo of one year to protect the personal information of residents of the house, provided for purposes of digital conservation of the building, and for interpretation of the house's physical conditions and interior contents through further research. More detailed information on the dataset, including the date the scan was conducted, the location of the house, and related interview and survey datasets are available upon reviewed request.
DOI: 10.6084/m9.figshare.1613436.v1
title: Gaussian Job Archive for C8H13ClN2O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.17632/z9m5jzcbdb
title: Ishemic stroke and serum uric acid

description: This case-control study was aimed to find any association between serum uric acid (SUA) and ischemic stroke among Bangladeshi population. Data of 169 ischemic stroke cases and 169 controls are saved in this dataset. This dataset containing data on some socio-economic information and some biochemical measurements such as serum uric acid, fasting lipid profile and blood glucose. A significant positive association was found between SUA and ischemic stroke through binary regression after controlling the effect of age, sex, tobacco smoking, diabetes, hypertension, coronary heart disease and dyslipidemia.
DOI: 10.6084/m9.figshare.19582615.v1
title: filtered_feature_bc_matrix.zip

description: These are the filtered_feature_bc_matrix files generated from cellranger for zebrafish testis scRNA-seq data (10X Genomics). More information can be found in our published paper:"Qian P, Kang J, Liu D and Xie G (2022) Single Cell Transcriptome Sequencing of Zebrafish Testis Revealed Novel Spermatogenesis Marker Genes and Stronger Leydig-Germ Cell Paracrine Interactions. <em>Front. Genet.</em> 13:851719. doi: 10.3389/fgene.2022.851719".
DOI: 10.15131/shef.data.9934055.v5
title: Data for paper "MRI-based anatomical characterisation of lower-limb muscles in older women"

description: Please cite "Montefiori E, Kalkman BM, Henson WH, Paggiosi MA, McCloskey EV, Mazzà C (2020) MRI-based anatomical characterisation of lower-limb muscles in older women. PLoS ONE 15(12): e0242973. https://doi.org/10.1371/journal.pone.0242973"<br>This Figshare contains:1. Supplementary material.docx, including supplementary information associated with the paper "MRI-based anatomical characterisation of lower-limb muscles in older women";2. Segmentations for the eleven subjects in the study labelled as MC17, MC18, MC19, MC20, MC22, MC24, MC25, MC26, MC27, MC28, MC29 (corresponding to Subject 1 to 11, respectively, see additional material for details):a. bone and soft tissue (skin) segmentations as stl files;b. muscle segmentations as stl files;3. Muscle centrelines as vtk files.
DOI: 10.6084/m9.figshare.1019859_d3
title: cBOTv7_sbsv2_allreps_log.gct

description: cBOTv7_sbsv2_allreps_log.gct is the raw normalized and logged read counts for the first group of cancer cell lines undergoing pooled shRNA screening.
DOI: 10.6084/m9.figshare.12594149.v1
title: Supplementary Material for: Histologic and Clinical Effects of Different Topical Corticosteroids for Eosinophilic Esophagitis: Lessons from an Updated Meta-Analysis of Placebo-Controlled Randomized Trials

description: <b><i>Background:</i></b> Topical corticosteroids (TS) have become standard therapy for eosinophilic esophagitis (EoE). However, a variety of drug formulations have been used for which results of histological and clinical responses may be different. We aimed at determining the short-term histologic efficacy of TS for EoE based on randomized placebo-controlled trials and to review clinical response. <b><i>Methods:</i></b> We searched MEDLINE, ISI Web of Science, and clinicaltrials.gov for randomized controlled trials (RCTs) on TS versus placebo for active EoE published until June 2019. Treatment effects were calculated as risk ratios (RRs) comparing histologic remission between groups. <b><i>Results:</i></b> Nine RCTs (6 budesonide and 3 fluticasone) involving a total of 483 participants were included. A substantial overall effect of TS on acute histologic remission (RR 12.5, 95% confidence interval 6.0–25.9) was found despite varying definitions of histologic response. Indirect comparisons between drug and formulation types showed a trend for a better histologic efficacy of budesonide (RR 13.5 vs. 10.4 fluticasone) and for the orodispersible tablet (RR 46.2 vs. 11.5 suspension, and 10.4 nebulized formula/spray), but only based on small patient numbers. Scores used for clinical response assessment were different between studies, and short-term clinical results were less impressive: significant differences favoring TS were found in 4/9 RCTs (4/6 budesonide, 0/3 fluticasone). <b><i>Conclusions:</i></b> TS are effective for short-term induction of histological remission in EoE with less impressive clinical response rates. The mode of drug delivery to the esophagus may be a relevant factor for the degree of histologic remission. Further trials should use uniform assessment criteria and long-term patient-centered outcomes.
DOI: 10.15468/dl.6ga2au
title: Occurrence Download

description: A dataset containing 9505390 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tracheophyta",
 "Geometry POLYGON((-124.48 32.53, -124.48 42.01, -114.13 42.01, -114.13 32.53, -124.48 32.53))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2020"
 ]
}

 The dataset includes 9505390 records from 452 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009375-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/7y4gbwk44k
title: Bacterial community assembly between soybean rhizosphere and endosphere

description: This dataset consists of the processing of the microbial 16S rDNA sequencing data of our study, and this dataset includes the processed OTU table, the RStudio code used for visualization, and the resulting tables and images. The analysis of this dataset provides supplementary evidence for the two-step selection model that is a widely accepted explanation of the mechanism of root-associated microbial community construction. With this dataset, we provide a reference for others to learn the process of analyzing microbial 16S rDNA data.
DOI: 10.17632/g4nzmtdpwr
title: Dataset DNA Methylation

description: Infinium MethylationEPIC BeadChip from Illumina The description is in the file
DOI: 10.17632/tzvtpjzknk
title: A finite-temperature Hartree–Fock code for shell-model Hamiltonians

description: This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract The codes HFgradZ.py and HFgradT.py find axially symmetric minima of a Hartree–Fock energy functional for a Hamiltonian supplied in a shell model basis. The functional to be minimized is the Hartree–Fock energy for zero-temperature properties or the Hartree–Fock grand potential for finite-temperature properties (thermal energy, entropy). The minimization may be subjected to additional constraints besides axial symmetry and nucleon numbers. A single-particle operator can be used to constrain t... Title of program: HFgradZ.py, HFgradT.py Catalogue Id: AFAX_v1_0 Nature of problem Find Hartree-Fock minima of shell-model Hamiltonians Versions of this program held in the CPC repository in Mendeley Data AFAX_v1_0; HFgradZ.py, HFgradT.py; 10.1016/j.cpc.2016.06.023
DOI: 10.6084/m9.figshare.14286856.v1
title: MY BUSINESS AND I: ENTREPRENEUR PERSONALITY TRAITS AND CAPITAL STRUCTURE CHOICE

description: ABSTRACT Purpose: This research seeks to identify how entrepreneurs’ personality traits can influence the capital structure of micro and small private businesses in Brazil, which are important for the economic growth and the subsistence of their owners. Originality/value: The study of the behavioral dimension of business decisions can help financial agents to better understand client behavior, including the adoption of mechanisms that identify possible risky or inefficient decisions made by managers based on their personality traits. It can also assist the government and institutions supporting micro and small private businesses in developing strategies to reduce the mortality of such companies. Design/methodology/approach: The proposed model involves 19 expected relationships that evaluate the relationships between the optimism, risk tolerance, sense of control (external and internal), attitude towards debt, and entrepreneur gender constructs. The sample includes 625 micro and small entrepreneurs in the state of Rio Grande do Sul, Brazil. Confirmatory factor analysis and structural equation modeling were performed. Findings: Results showed that attitude towards debt and gender were the most significant constructs and had a direct influence on the capital structure, while optimism and internal locus of control exerted a negative indirect influence, while risk tolerance had a positive indirect effect. Female managers demonstrated higher optimism and internal locus of control than male managers, but they had a worse attitude towards debt.
DOI: 10.6084/m9.figshare.24277285.v1
title: Supplementary 3. Target Proteins Associated with viral respiratory diseases

description: Target Proteins Associated with viral respiratory disease
DOI: 10.6084/m9.figshare.24419710.v1
title: AT & SA dataset

description: The dataset of manuscript
DOI: 10.6084/m9.figshare.12613811.v1
title: In vitro recordings_oxytocin

description: In vitro recordings in auditory cortical slices from naive virgins. Extracellular stimulation was locally applied during whole-cell current clamp recordings - spike probability for each stimulation was measured before/during/after oxytocin wash. Control group = ACSF (repetitive stimulation in the absence of oxytocin).<br>Raw data (.abf) associated with Extended Data Fig. 9 from Schiavo et al. (2020). <br>Accompanying excel sheet lists relevant file names and protocols.
DOI: 10.6084/m9.figshare.13102958.v1
title: Fluorescence microscopy B cell data set

description: Fluorescence microscopy data set of B cells with corresponding ground truth. The images were captured with an Zeiss AxioSscan.Z1.<br>Sample Preparation:Naive murine B cells from C57Bl/6 mice were isolated from the spleen by negative selection. The cells<br>were activated with lipopolysaccharide (LPS, 10 <i>µ</i>g/ml) for 72 h in RPMI1640 medium supplemented with<br>fetal calf serum (FCS)(10%), L-glutamine (2 mM), Pyruvate (1 mM), Penicillin (50 U/ml), Streptomycin<br>(50 <i>µ</i>g/ml) and ?-Mercaptoethanol (50 <i>µ</i>M). Teflon-coated microscope slides with 8 wells each were<br>coated with aBCR (10 <i>µ</i>g/ml rat anti BCR monoclonal) [1] or αCD19 (rat anti CD19<br>monoclonal) [3]. 2x10^4 B cells were seeded on the slides and incubated for 45min in a<br>humidified incubator (5% CO2 atmosphere in RPMI1640 supplemented as described above but without<br>FCS). On the control sample, B cells were treated with Cytochalasin D [2], a mycotoxin<br>that inhibits actin polymerization. Cell were fixated in phosphate buffered saline (PBS) containing 4%<br>para-formaldehyde which also stops cell spreading. Fixed cells were washed and permeabilized in PBS with<br>0.1% Triton X-100. Phalloidin-Rhodamin (Molecular Probes) specifically stained the F-actin intracellularly<br>and DAPI (Roth) stains DNA in the nuclei. Slides were mounted in MOWIOL(Roth) [4].<br>References:[1] Cambier, J. C., Heusser, C. H., and Julius, M. H. (1986). Abortive activation of B lymphocytes by<br>monoclonal anti-immunoglobulin antibodies. Journal of immunology (Baltimore, Md. : 1950) 136,<br>3140–6<br>[2] Cooper, J. A. (1987). Effects of cytochalasin and phalloidin on actin. The Journal of Cell Biology 105,<br>1473–1478. doi:10.1083/jcb.105.4.1473<br>[3] Krop, I., Shaffer, A. L., Fearon, D. T., and Schlissel, M. S. (1996). The signaling activity of murine CD19<br>is regulated during cell development. Journal of immunology (Baltimore, Md. : 1950) 157, 48–56<br>[4] Wiesmann, V., Reimer, D., Franz, D., Hüttmayer, H., Mielenz, D., and Wittenberg, T. (2015). Automated<br>high-throughput analysis of B cell spreading on immobilized antibodies with whole slide imaging.<br>Current Directions in Biomedical Engineering 1, 224–227. doi:10.1515/cdbme-2015-0056<br>
DOI: 10.6084/m9.figshare.23742060.v2
title: Bird ringing data, traits plus EURING codes

description: Dataset accompanying the paper <strong>Co-migration fidelity at a stopover site increases over time in African-European migratory landbirds</strong>. The dataset<strong> </strong>includes individual catch data (Sheet1), EURING codes (Sheet2) and traits (Sheet3) of 31 most abundant non-resident species landing on the stopover area of Ponza over a period of 15 years (2007 to 2021), during which the procedures were fully standardized. <br>
DOI: 10.6084/m9.figshare.28829693.v2
title: Table S4, PlasmidFinder summary

description: Table S4, PlasmidFinder summaryIdentification of plasmid replicon types was conducted using the Staramr pipeline (v0.11.0) [12], incorporating PlasmidFinder (database version 14.11.2024).
DOI: 10.6084/m9.figshare.18480857.v1
title: Intertidal species abundance near Tor Bay Provincial Park, Nova Scotia, Canada

description: This file shows data on the abundance (individuals per 25 cm x 25 cm plot) and percent cover of macroalgae and invertebrates found in wave-exposed habitats and wave-sheltered habitats at the rocky mid-intertidal zone near Tor Bay Provincial Park (Nova Scotia, Canada) on 25-26 October 2007.
DOI: 10.6084/m9.figshare.25450414.v1
title: Supplementary Material for: Neuropsychiatric profiles and cerebral amyloid burden in adults without dementia

description: Introduction: We comprehensively evaluated how self- and informant-reported neuropsychiatric symptoms (NPS) differentially associated with cerebral amyloid-beta (Aβ) PET levels in older adults without dementia.
Methods: 221 participants (48% female, age=73.4y±8.4, CDR=0 [n=184] or 0.5 [n=37]) underwent an Aβ-PET scan (Florbetapir or PIB), comprehensive neuropsychological testing, and self-reported (Geriatric Depression Scale- 30 item), and informant-reported interview (Neuropsychiatric Inventory Questionnaire) of NPS. Cerebral Aβ burden was quantified using Centiloids (CL). NPI-Q and GDS-30 queried presence of NPS within 4 subdomains and 6 subscales, respectively. Regression models examined the relationship between NPS and Aβ-PET CL.
Results: Both higher self- and informant-reported NPS were associated with higher Aβ burden. Among specific NPI-Q subdomains, informant-reported changes in depression, anxiety, and irritability were all associated with higher Aβ-PET. Similarly, self-reported (GDS-30) subscales of depression, apathy, anxiety, and cognitive concern associated with higher Aβ-PET. When simultaneously entered, only self-reported cognitive concern associated with Aβ-PET in the GDS-30 model, while both informant-reported anxiety and depression associated with Aβ-PET in the NPI-Q model. Clinical status moderated the association between self-reported NPS and Aβ-PET, such that the positive relationship between self-perceived NPS and Aβ burden strengthened with increasing functional difficulties.
Conclusions: In a cohort of older adults without dementia, both self- and informant-reported measures of global NPS, particularly patient-reported cognitive concerns and informant-reported anxiety and depression, corresponded with cerebral Aβ burden. NPS may appear early in the prodromal disease state and relate to initial AD proteinopathy burden, a relationship further exaggerated in those with greater clinical severity.
DOI: 10.6084/m9.figshare.6571304.v1
title: Supplementary Material for: RA190, a Proteasome Subunit ADRM1 Inhibitor, Suppresses Intrahepatic Cholangiocarcinoma by Inducing NF-KB-Mediated Cell Apoptosis

description: <b><i>Background/Aims:</i></b> Effective drug treatment for intrahepatic cholangiocarcinoma (ICC) is currently lacking. Therefore, there is an urgent need for new targets and new drugs that can prolong patient survival. Recently targeting the ubiquitin proteasome pathway has become an attractive anti-cancer strategy. In this study, we aimed to evaluate the therapeutic effect of and identify the potential mechanisms involved in targeting the proteasome subunit ADRM1 for ICC. <b><i>Methods:</i></b> The expression of ADRM1 and its prognostic value in ICC was analyzed using GEO and TCGA datasets, tumor tissues, and tumor tissue arrays. The effects of RA190 on the proliferation and survival of both established ICC cell lines and primary ICC cells were examined <i>in vitro</i>. Annexin V/propidium iodide staining, western blotting and immunohistochemical staining were performed. The <i>in vivo</i> anti-tumor effect of RA190 on ICC was validated in subcutaneous xenograft and patient-derived xenograft (PDX) models. <b><i>Results:</i></b> ADRM1 levels were significantly higher in ICC tissues than in normal bile duct tissues. ICC patients with high ADRM1 levels had worse overall survival (hazard ratio [HR] = 2.383, 95% confidence interval [CI] =1.357 to 4.188) and recurrence-free survival (HR = 1.710, 95% CI =1.045 to 2.796). ADRM1 knockdown significantly inhibited ICC growth <i>in vitro</i> and <i>in vivo</i>. The specific inhibitor RA190 targeting ADRM1 suppressed proliferation and reduced cell vitality of ICC cell lines and primary ICC cells significantly <i>in vitro</i>. Furthermore, RA190 significantly inhibited the proteasome by inactivating ADRM1, and the consequent accumulation of ADRM1 substrates decreased the activating levels of NF-κB to aggravate cell apoptosis. The therapeutic benefits of RA190 treatment were further demonstrated in both subcutaneous implantation and PDX models. <b><i>Conclusions:</i></b> Our findings indicate that up-regulated ADRM1 was involved in ICC progression and suggest the potential clinical application of ADRM1 inhibitors (e.g., RA190 and KDT-11) for ICC treatment.
DOI: 10.6084/m9.figshare.1185480.v1
title: BIOL 2050 Ecology Lab 2 Grassland Dataset 2

description: Measuring various grassland qualities.
DOI: 10.6084/m9.figshare.28248427.v1
title: Detection of carob flour in cocoa powder by direct analysis in real time-mass spectrometry (DART-MS)

description: Cocoa is a high value product and therefore a potential target for economic adulteration with less expensive ingredients. Carob flour is less expensive than cocoa powder and is frequently cited as a potential cocoa substitute. While carob has legitimate uses as a cocoa replacement, these characteristics also make it a potential adulterant of cocoa powder. Direct analysis in real time mass spectrometry (DART-MS) is an ambient ionization MS technique that can be used to rapidly interrogate samples. Samples of cocoa powders, carob flours, and mixtures of the two were extracted with buffer and interrogated by DART-MS. The mass spectra were used to develop models to distinguish between cocoa powder and cocoa powder adulterated with carob. A principal component-linear discriminant analysis (PCA-LDA) model was used to discriminate between cocoa powder and cocoa powder amended with 15% carob flour. The accuracy using internal validation was 100%. Using an external validation dataset, the accuracy, precision, and recall were 96.0%, 94.8%, and 97.3%, respectively. These results demonstrate that DART-MS can be used to discriminate between cocoa powder and cocoa powder adulterated with 15% carob.
DOI: 10.6084/m9.figshare.25927315.v1
title: Read me

description: Read me file
DOI: 10.6084/m9.figshare.28755566.v1
title: Dataset

description: Custom R code script related to analysis of paired extracts available (RADDi)TAMRA fluorescence output files are available.<br>
DOI: 10.6084/m9.figshare.3808539.v1
title: Measures of malaria burden after long-lasting insecticidal net distribution and indoor residual spraying at three sites in Uganda: A prospective observational study

description: Databases used for all analyses in support of the published manuscript<br>