cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12859594.v1
title: Magnolin exhibits anti-inflammatory effects on chondrocytes via the NF-κB pathway for attenuating anterior cruciate ligament transection-induced osteoarthritis

description: <b>Purpose:</b> This study aimed to investigate whether magnolin (MGL) possesses the capability of suppressing inflammatory responses that can in turn alleviate osteoarthritis (OA). <b>Methods:</b> We investigated the effects of MGL on the viability of rat chondrocytes at concentrations of 5 to 100 µM, and selected 10 µM for further study. We elucidated the molecular mechanisms and signaling pathways mediating these effects via RNA sequencing, qRT-PCR, immunofluorescent staining, and Western blotting techniques. Following this, we established an anterior cruciate ligament (ACL) transection-induced OA rat model, and injected MGL into the knee articular cavities to verify the <i>in vivo</i> anti-inflammatory effects of MGL. <b>Results:</b> We found that MGL could recover the TNF-α-induced upregulation of IL-1β, COX2, ADAMTS-5, and MMP-1/3/13 at the gene/protein level, as well as the downregulation of cartilaginous ECM synthesis. Gene expression profiles of different groups identified 49 common differentially expressed genes (DEGs), which were mainly enriched in the structural constituents of the ribosome, the extracellular space, and inflammatory response. The NF-κB pathway was highly enriched, and the expression levels of DEGs associated with it (<i>Nfkbia, Ptgs2, Rela, Tnfrsf1a, Tradd, Traf2</i>) under TNF-α stimulation were reversed by MGL. Further studies proved that MGL simultaneously suppressed the cell nucleus translocation of p65 and the phosphorylation of IκBα. Moreover, <i>in vivo</i>, MGL suppressed cartilage matrix degradation, inhibited MMP-13 expression, and promoted cartilage matrix construction by upregulating SOX9 synthesis. <b>Conclusion:</b> MGL demonstrated significant anti-inflammatory bioactivity on chondrocytes by suppressing the activation of NF-κB pathway, which in turn exhibited a significant alleviation of OA.
DOI: 10.6084/m9.figshare.21023485.v1
title: Data for edible insects.xls

description: nutrients, enzymes gut microbiota, metabolites in Clanis bilineata tsingtauica
DOI: 10.6084/m9.figshare.23910111.v1
title: FileS3_surface_mesh_microCT.stl

description: 3D-surface mesh of vascular network imaged by micro-computed tomography. Open access data publication in online repository as supplement to this manuscript.
DOI: 10.6084/m9.figshare.19174367.v1
title: Supplementary Material for: Association between <b><i>Opisthorchis viverrini</i></b> Infection and Glomerular Disease in Thailand

description: <b><i>Introduction:</i></b> <i>Opisthorchis viverrini</i> (OV) is a major cause of infection in Southeast Asia. Previous studies in mouse models have shown that OV infection can contribute to immune-complex glomerulonephritis (GN). However, OV infection in human kidney tissue has never been demonstrated. Herein, we evaluated the association of OV infection with biopsy-proven glomerular disease. <b><i>Methods:</i></b> This study was performed in adult patients who underwent kidney biopsy between July 2016 and February 2017. All kidney tissue samples were processed using the standard techniques for renal pathological diagnoses and immunohistochemistry techniques to detect OV antigen. Pre-implanted donor kidney tissue samples were used as controls. The participants were also assessed for OV infection by serum OV immunoglobulin G antibody (Ab) levels and/or presence of OV eggs in stool. <b><i>Results:</i></b> Forty-three renal tissue samples from glomerular disease patients and 50 from transplant donors were included in the study. Mean age in the GN group was 41.7 ± 15.9 years, estimated glomerular filtration rate (eGFR) was 70.65 ± 36.61 mL/min/1.73 m<sup>2</sup>, and median proteinuria was 3.17 (1.70–4.95) g/day. Lupus nephritis (LN) was the most common diagnosis (32.6%), followed by IgA nephropathy (23.3%), IgM nephropathy (18.6%), and primary membranous nephropathy (MN; 7%). The OV antigen was observed in kidney tissue from patients with IgA nephropathy, LN, primary MN, focal segmental glomerulosclerosis, and IgM nephropathy. By contrast, no OV antigen was detected in tissue samples from the control group. The presence of OV antigens was observed in glomerular endothelial cells, mesangial cells, tubular cells, and peritubular capillaries. The odds ratio of positive serum OV Ab to predict the presence of OV antigen in kidney tissues was 4.47 (<i>p</i> = 0.057), and there was a negative correlation between levels of serum OV Ab and eGFR (<i>r</i> = −0.31, <i>p</i> = 0.04). <b><i>Discussion/Conclusion:</i></b> This is the first study to demonstrate the presence of OV antigen in human kidney tissue, which indicates that OV infection may be associated with biopsy-proven glomerular diseases.
DOI: 10.6084/m9.figshare.3520115.v1
title: Appendix A. Bird species observed and yard-related indices.

description: Bird species observed and yard-related indices.
DOI: 10.25381/cput.24581064.v1
title: African sustainable microgrid development with solar PV and energy storage

description: This research project developed a microgrid using solar PV to electrify remote communities in the DRC. Given that solar energy is intermittent and is not available during night-time when the electricity demand is usually at its peak, the microgrid was configured with a Battery Energy Storage System (BESS) to ensure an uninterrupted power supply. Also given that the BESS is a high-cost component, the microgrid considered the introduction of a biogas generator, to reduce the BESS architecture which subsequently reduces the cost of the implementation and operation of the system. The microgrid configuration was modeled and simulated using HOMER Pro to determine its techno-economic viability for the electrification of the community compared to the extension of the existing networks.Ethic reference number: 2021FEREC-STD-05
DOI: 10.6084/m9.figshare.12570263.v1
title: HydDB assembly annotation

description: Annotations for catalytic hydrogenase subunits identified with GhostKoala and verified with HydDB in Brothers volcano assemblies. Sheets are arranged as follows:<b>HydDB_annotations: </b>GhostKoala annotations and annotations predicted using the HydDB website. Genes flagged as low confidence are indicated and are not reflected in the final summary.<b>KO_list: </b>KO annotations used to screen for catalytic hydrogenase subunits, and associated HydDB annotations.<br>
DOI: 10.6084/m9.figshare.25592769.v1
title: Spatial variation of marine primary productivity over ridge and trough: A case study in the East China Sea

description: The marine primary productivity in ridge is higher than that in trough. In the ECS, temperature, salinity and dissolved oxygen paly different controlling role in phytoplankton growth from surface to bottom.
DOI: 10.6084/m9.figshare.14428832.v1
title: CLEAN Meds trial Year 2 data

description: Individual participant level data for year 2 of the CLEAN Meds randomized controlled trial. <br>https://clinicaltrials.gov/ct2/show/NCT02744963<br>
DOI: 10.6084/m9.figshare.25195805.v5
title: The SORef Dataset

description: <b>If you are using this dataset, please consider citing as:</b><i>Run Huang and Souti Chattopadhyay. 2024. A Tale of Two Communities: Exploring Academic References on Stack Overflow. In Companion Proceedings of the ACM Web Conference 2024 (WWW '24 Companion), May 13 – 17, 2024, Singapore, Singapore. ACM, New York, NY, USA, 4 pages. https://doi.org/10.1145/3589335.3651464</i><b>Paper:</b>https://doi.org/10.1145/3589335.3651464<br><b>Website:</b>https://github.com/USC-ACE-Lab/sciso-www
DOI: 10.6084/m9.figshare.5853948.v1
title: Computational meshes of the cardiac left ventricle of 50 heart failure subjects

description: Collection of 50 anatomies of the left ventricle of a cohort of subjects selected for cardiac resynchronisation therapy, togheter with their response data.<br>Meshes: provided in VTK format for easier compatibility (original work done with cubic Hermite EX format meshes)<br>Response: excel spreadsheet with the case ID and the class (responder or not responder). <br>"data process.gif" provides an overview of the segmentation and mesh personalization process. Panel A: semi-automatic segmentation by 3D extrapolation (yellow surface and contours) of 2D segmentation contours (red contours and projections) using an open source platform (29). Panel B: mesh template. Panel C: resulting mesh (white surface) overlaid with the segmentation surface colour coded by the distance between them (jet colour map, from 0mm in blue to 1mm in red). <br>
DOI: 10.6084/m9.figshare.19345292.v1
title: Raw data from the studies on cell lines.rar

description: This zip file includes all the raw data supporting the findings in the article "Single-cell RNA sequencing reveals hub genes of myocardial infarction-associated endothelial cells" submitted to <i><b>All Life</b></i>.
DOI: 10.6084/m9.figshare.15043236.v1
title: Esquema espacial de análisis Subcuencas y Regiones Shapefiles

description: Delimitación de las Unidades Hidrográficas del Perú por Subcuencas, y Regiones de Análisis (AAA)
DOI: 10.6084/m9.figshare.25305109.v2
title: Sequence alignments for Bullatosporium taxicola - FUSE - Bullatosporium taxicola, a new genus and species in Mytilinidiaceae (Pleosporomycetidae,Dothideomycetes) from western Norway; doi: 10.3114/fuse.2024.14.13

description: The new genus and species Bullatosporium taxicola are described from dead wood of Taxus baccata in western Norway. Despite some morphological resemblance with Hysteriaceae, including low ascomata with a thick carbonized peridium and mainly five-septate ascospores, multigene analysis of the five molecular markers SSU, ITS, LSU, TEF1-α and RPB2 revealed an affinity to Mytilinidiaceae. The new species formed a strongly supported sister clade to the remaining strains of Mytilinidiaceae. Dichotomous keys to genera of Mytilinidiaceae and to hysterioid species with phragmospores in Fennoscandia are provided to aid identification.
DOI: 10.6084/m9.figshare.14378519.v3
title: KC_WES_Proband

description: Whole exome sequencing reveal
DOI: 10.6084/m9.figshare.21779819.v1
title: Climatic conditions and Acacia tortilis tree growth in two range edges

description: This data was used to investigate the climatic drivers for stem growth of acacia trees in two world range edges (Israel and South Africa) four files: 1. dendrometer data from Israeli study site 2. dendrometer data from SA study site 3. combined climatic conditions of both sites 4. lagged effect of the climatic conditions on tree growth
DOI: 10.6084/m9.figshare.25560645.v1
title: ARMViz enables seamless genomics analysis and visualization of antimicrobial resistance

description: Data supporting the manuscript "ARMViz enables seamless genomics analysis and visualization of antimicrobial resistance"
DOI: 10.6084/m9.figshare.7381865.v1
title: Lesion effect on motor recovery

description: The study was approved by the Ethics Review Board of the Loewenstein Hospital. All patients signed an informed consent prior to recruitment for the study. Normalized lesion data were used for voxel-based lesion-symptom mapping (VLSM) analyses, performed separately for patients with left and right hemisphere damages. Function of the hemiparetic upper limb was examined using the Fugl-Meyer test and the Box and Blocks test.
DOI: 10.6084/m9.figshare.13204925.v1
title: R0196-DLC_output

description: deeplabcut output and processed 3D reconstructions of data for rat 0196."_direct" zip files contain .csv's from the direct view and .mat files with cropping regions"_right/left" zip files contain .csv's from the mirror view and .mat files with cropping regions"_processed" files contain 3D reconstructions and reach analyses
DOI: 10.6084/m9.figshare.27890997.v1
title: Voigts et al.: Spatial reasoning via recurrent neural dynamics in mouse retrosplenial cortex

description: Ephys data for Jakob Voigts, Ingmar Kanitscheider, Nicholas J. Miller, Enrique H.S. Toloza, Jonathan P. Newman, Ila R. Fiete, Mark T. Harnett: Spatial reasoning via recurrent neural dynamics in mouse retrosplenial cortex (https://www.biorxiv.org/content/10.1101/2022.04.12.488024v1)<br>
DOI: 10.6084/m9.figshare.25486387.v1
title: Emal_final_gene_models.gff3

description: We assembled a chromosome-scale genome of malabar grouper (Epinephelus malabaricus) and conducted a transcriptomic analysis of nine larval developmental stages.
DOI: 10.6084/m9.figshare.4312046.v1
title: Iddawela et al: Integrative analysis of copy number and gene expression using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study

description: Copy number data from the paper Iddawela et al: Integrative analysis of copy number and gene expression using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study
DOI: 10.6084/m9.figshare.7488854.v2
title: Parker, Calkin, Seldin et al, Nature, 2019: Raw HMDP lipidomics data

description: .WIFF files<br>mapping files in .xls formatprotocol outline in .doc format<br>
DOI: 10.15468/dl.keep5n
title: Occurrence Download

description: A dataset containing 406 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Leucophora obtusa (Zetterstedt, 1837)"
 ]
}

 The dataset includes 406 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009500-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.7093718.v1
title: The isotopic evolution of the Kohistan Ladakh arc from subduction initiation to continent arc collision

description: Data and Concordia plots of data samples.
DOI: 10.6084/m9.figshare.13078931.v1
title: Ovaries reduced, PC2 RNAi

description: Ovaries from a 15 day old Tribolium beetle, injected with dsRNAi to PC2 at the pupal stage. Stained for nuclei and actin. <br>
DOI: 10.6084/m9.figshare.24517093.v1
title: Supplementary Material for: Characterizing Adverse Events of Biologic Treatment of T2 Disease: A Disproportionality Analysis of the FDA Adverse Event Reporting System

description: Introduction: Over the last 3 years, the FDA has approved dupilumab, omalizumab, and mepolizumab for the treatment of CRSwNP; however, adverse events of these biologics have not been described in post-marketing surveillance trials. By utilizing the FDA’s Adverse Event Reporting System (FAERS), this study describes and compares biologic-associated adverse events in T2 disease. Methods: This case-non-case study assessed disproportionate reporting rates using Reporting Odds Ratios (ROR). RORs and p-values for biologic-associated AEs were categorized and compared among dupilumab, omalizumab, and mepolizumab. This analysis included AEs associated with all treatment indications. Relative AE rates and outcomes were calculated. Results: There were a total of 112,560, 24,428, and 18,741 unique AE reports associated with dupilumab, omalizumab, and mepolizumab, respectively. Omalizumab had the strongest association with anaphylaxis (ROR = 20.80, 95% CI 18.58, 23.29). Dupilumab had large relative proportions and positive signals in the ophthalmologic category (7.76%, ROR = 6.20, 95% CI 6.06, 6.35), such as with blurry vision (ROR = 3.80, CI 3.52, 4.12) and visual impairment (ROR = 1.98, CI 1.80, 2.19). Dupilumab was the only biologic associated with injection-site reactions (7.98%, ROR = 8.17, 95% CI 7.98, 8.37). Discussion/Conclusion: This is the first large-scale comparative analysis of the AE profiles of dupilumab, omalizumab, and mepolizumab. Our data suggest possible relations between dupilumab and ophthalmologic and injection-site AEs. Omalizumab was the only biologic with a positive anaphylaxis signal. This FAERS investigation suggests important AE differences among these biologics.
DOI: 10.6084/m9.figshare.28049831.v1
title: Cotton Flower Detection Dataset

description: This contains the portion of the cotton flower dataset with bounding box annotations. It is organized in YOLO format. That is, the label format is:class, center_x, center_y, width, heightThis dataset has training, testing, and validation splits. The data in the test and validation splits are from different years than the training data. They also contain some images taken with a UAV, which is a modality not present in the training dataset at all.
DOI: 10.6084/m9.figshare.24057120.v2
title: The atmospheric inorganic nitrogen deposition fluxes in China

description: The atmospheric IN deposition fluxes database consists of three files. The ‘data file’ provides yearly data on the dry, wet and total IN deposition fluxes. Specifically, dry deposition is the sum of two forms, gaseous and particulate, including NO<sub>2</sub>，HNO<sub>3</sub>，NH<sub>3</sub>，NO<sub>3</sub><sup>-</sup>，NH<sub>4</sub><sup>+</sup>.Wet deposition is the sum of both NO<sub>3</sub><sup>-</sup>-N and NH<sub>4</sub><sup>+</sup>-N. The ‘readme file’ describes the ‘data file’ and the units of all variables included. The ‘source file’ includes the full references used in the database, which comprise satellite data and precipitation data.
DOI: 10.6084/m9.figshare.17032157.v1
title: transcripome analysis.xlsx

description: Transcriptome analysis of human glial cells.
DOI: 10.6084/m9.figshare.25457977.v1
title: Supplementary Material for: First In Vivo Experiment with PulmValve Endobronchial Valve: Feasibility, Efficiency, and Safety

description: Introduction: Endoscopic Lung Volume Reduction (ELVR) with endobronchial valves has been widely recognized for treating hyperinflation in advanced COPD and emphysema patients. The main challenges include the technical complexity of upper lobe implantation and the number of endobronchial valves required. These issues might be addressed by placing larger-diameter valves in the lobar bronchus. This study evaluated the feasibility, efficiency, and safety of the new valve PulmValve (model PV-13) in porcine models.
Methods: Six PV-13 valves were bronchoscopically implanted into the caudal lobe bronchus of six healthy pigs. The procedure time, valve deployment, and removability were recorded. Follow-up examinations included blood tests, chest CT scans, and bronchoscopy at 30 minutes, 14 days, 28 days, and 84 days post-procedure, with necropsy and pathological evaluations after the final follow-up examination.
Results: The successful in vivo deployment and removal of PV-13 valves was established, with a median procedure time of 6.5 minutes. The distal lung volume reduction was evident at 30 minutes post-operation and was persistently monitored on day 84. No migration or malfunction of any PV-13 valves was detected, but a mild angle deviation was found in three cases. Coughing was observed in four pigs within the first seven days, and localized granulation tissue was observed in all pigs. No cases of pneumothorax, diffuse pneumonia, or hemoptysis were detected.
Conclusions: In this study, we report the successful implantation and removal of a new valve PulmValve in a short operation time. Complete lobar atelectasis was induced without device migration, malfunction, or severe complications. Further studies are warranted to evaluate the long-term, sustained effects, and potential benefits in human patients.
DOI: 10.6084/m9.figshare.28751330.v1
title: Supplemental material.docx

description: Supplemental material
DOI: 10.6084/m9.figshare.23264525.v1
title: <strong>Persian form of the paranoia scale</strong>

description: this is the SPSS file which consists of items and responses.
DOI: 10.6084/m9.figshare.25615434.v1
title: Annotation of Alosa sapidissima genome

description: Annotation of Alosa sapidissima genome using KEGG and Interproscan databases
DOI: 10.6084/m9.figshare.4039821.v1
title: 16_S10_L001_R1_001_run1.fastq.gz

description: This is the raw sequence file (R1 direction) of a paired-end Illumina MiSeq sequencing run.
DOI: 10.6084/m9.figshare.809554.v2
title: Peaks of Twitter Activity

description: This dataset contains the information concerning the peaks of Twitter activity detected during the season and their corresponding broadcasted scene. The process of peaks detection and labelling is described in details at: https://medium.com/next-media-society/60319348c61a.
DOI: 10.6084/m9.figshare.22582027.v1
title: Raw data for Yang et al., 2023 TJFE

description: Raw data for the study of drought effects on invertebrates in streams by Qiao Yang et al., 2023, Journal of Freshwater Ecology
DOI: 10.6084/m9.figshare.24288679.v1
title: Supplementary Material for: Targeting cartilage miR-195/497 cluster for osteoarthritis treatment regulates the circadian clock

description: Introduction: Osteoarthritis (OA) is the most prevalent and debilitating joint disease without an effective therapeutic option. Multiple risk factors for OA have been identified, including abnormal chondrocyte miRNA secretion and circadian rhythms disruption, both of which have been found to cause progressive damage and loss of articular cartilage. Environmental disruption of circadian rhythms in mice predisposes animals to cartilage injury and OA. Methods: The role of miR-195/497 cluster during OA progression was verified by mouse OA model with intraarticular injection of Agomir and Antagomir. We performed micro-CT analysis, Osteoarthritis Research Society International scores, and histological analysis in mouse knee joints. RNA sequencing was performed on the mouse cartilage cell line to explore the molecular mechanism of the miR-195/497 cluster and proteins in signaling pathway were evaluated using western blot. Senescence associated phenotypes were detected by western blot, senescence β-galactosidase Staining, and immunofluorescence. Results: This study demonstrated that miR-195/497-5p expression is disrupted in OA with senescent chondrocytes. In addition, miR-195/497-5p influenced the circadian rhythm of mice chondrocytes by modulating the expression of the Per2 protein, resulting in the gradual degradation of articular cartilage. We found that the miR-195/497 cluster targets DUSP3 expression. The deletion of the miR-195/497 cluster increased the level of DUSP3 expression and decreased the levels of phosphorylated ERK 1/2 and CREB. Per2 transcription is up-regulated by stimulating CREB and ERK1/2 phosphorylation. Conclusion: Our findings identify a regulatory mechanism connecting chondrocyte miR-195/497-5p to cartilage maintenance and repair and imply that circadian rhythm disturbances affected by miR-195/497-5p are risk factors for age-related joint diseases such as OA