cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27636237.v1
title: Supplementary Material for: Exploring the spatial distribution of interstitial cells in kidney tissue

description: Introduction: Interstitial cells are crucial to the development of kidney structure and function, although the mechanism underlying their role in it remains unclear to date. Our previous study identified cell clusters in human fetal kidney tissue, and we further analyzed the interstitial cell cluster within this context. 
Methods: We extracted the barcoded cDNA from tissue samples and prepared spatial transcriptome libraries. Sequencing data was quality-checked, normalized, and clusters were identified using Seurat. Single-cell and spatial data were integrated using MIA and cell types were deconvoluted. DEGs in interstitial cells were identified and functionally annotated using DAVID. CellPhoneDB was used to predict ligand-receptor interactions between cell types.
Results: The results of the present study revealed that this cluster of interstitial cells appeared to be scattered in the junction between the cortical and medullary regions. The subsequent KEGG pathway analysis revealed that the differentially expressed genes (DEGs) in this cluster of interstitial cells were involved in the WNT signaling pathway. The Gene Ontology (GO) analysis revealed that these DEGs were involved in multiple pathways associated with kidney development, with six of the genes (NKD2, TCF21, WNT5A, WNT4, MDK, and SFRP1) associated with kidney development exhibiting significant upregulation. Accordingly, it was inferred that these interstitial cells might be involved in regulating epithelial cell differentiation, ureteral bud development, and morphogenesis. The subsequent cell-cell communication analysis revealed that the cellular crosstalk was primarily regulated mainly by ligand-receptor pairs. Additionally, 17 genes reported to be associated with kidney disease were focused on, and these genes were found to be predominantly expressed in a single cell type. 
Conclusion: In summary, the present study revealed the characteristics of a previously identified cluster of interstitial cells in the kidney tissue, thereby providing fresh insights into the process of kidney development.
DOI: 10.6084/m9.figshare.14943204.v1
title: Data sets for: Elastoplasticity Mediates Dynamical Heterogeneity Below the Mode Coupling Temperature

description: Data sets comprising:<br><br>(a) FigData (Figure data):<br>.npz files<br>(https://numpy.org/doc/stable/reference/generated/numpy.savez.html)<br>containing pandas data structures<br>(https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.Series.html,<br>https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.html,<br>https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.concat.html)<br>(effectively, N-dimensional arrays with labelled axes)<br>containing the data plotted in the paper,<br>named according to the figure to which the data corresponds<br>(e.g. S1a_inset contains the data for the inset to subfigure a of figure 1 of<br>the Supplementary Material).<br>As well as having the data in .npz files,<br>versions of the data are stored in .pkl pandas data frames<br>(read with "import pandas as pd; pd.read_pickle('path-to-bla.npz')")<br>as well as .csv (comma-separated values) files (a text format).<br>Note: Bootstrapped data will not be identical to that from the paper,<br>due to the use of an unset seed when generating the figures for the paper.<br><br>(b) FigGenData (Figure-generation data)<br>Data sets used in the actual generation of the figures,<br>as seen in the figure-generation code (FigGen.py file)<br>at https://physics.paperswithcode.com/paper/elastoplasticity-mediates-dynamical<br>To read the metadata of file bla.npz,<br>which includes the name of the code used to generate it, use:<br>import numpy as np<br>np.load('path-to-bla.npz',allow_pickle=True)['metadata'].flat[0]<br>
DOI: 10.6084/m9.figshare.25593252.v1
title: Stratman & Hoebel 2024 J.E.B.

description: Supplemental Data corresponding to manuscript submitted to Journal of Evolutionary Biology in 2024.
DOI: 10.6084/m9.figshare.22274623.v1
title: Supplementary Material for: Subcutaneous adipose tissue is associated with acute kidney injury after abdominal trauma based on the generalized propensity score approach: A retrospective cohort study

description: Introduction: Obesity is associated with an increased risk of acute kidney injury (AKI) after trauma. However, the associations between different adipose tissue depots and AKI remain unknown. Our study aims to quantify the effect of abdominal adiposity on AKI in trauma patients. Methods: We performed a retrospective cohort study of abdominal trauma patients who were admitted into our hospital from January 2010 to March 2020. Abdominal VAT (visceral adipose tissue) and SAT (subcutaneous adipose tissue) were measured at the level of the third lumbar vertebra using computed tomography. Causal modeling based on the generalized propensity score was used to quantify the effects of BMI (body mass index), VAT and SAT on AKI. Results: Among 324 abdominal trauma patients, 67 (20.68%) patients developed AKI. Patients with AKI had higher BMI (22.46 kg/m2 vs. 22.04 kg/m2, P = 0.014), higher SAT areas (89.06 cm2 vs. 83.39 cm2, P = 0.151) and VAT areas (140.02 cm2 vs. 91.48 cm2, P = 0.001) than those without AKI. By using causal modeling, we found that the risk of developing AKI increased by 8.3% (P = 0.001) and 4.8% (P = 0.022) with one unit increase in BMI (per 1 kg/m2), and ten units increase in SAT (per 10 cm2), respectively. However, VAT did not show a significant association with AKI (P = 0.327). Conclusion: SAT, but not VAT, increased the risk of AKI among abdominal trauma patients. Measurement of SAT might help to identify patients at higher risk of AKI.
DOI: 10.6084/m9.figshare.4970558.v1
title: Million Dollar List full data 2000-2012 used for PLOS ONE paper

description: Million Dollar List full data 2000-2012 used for PLOS ONE paper
DOI: 10.6084/m9.figshare.1381876.v4
title: Table S2 Epidemiologic parameters for EVD and Marburg by Study

description: Epidemiologic parameters for EVD and Marburg by Study
DOI: 10.6084/m9.figshare.17122094.v1
title: Training images

description: Training images
DOI: 10.6084/m9.figshare.27137880.v1
title: <b>Table 2 Environmental and Technological Factors Affecting Agricultural Yield </b>

description: <b>Table 2 Environmental and Technological Factors Affecting Agricultural Yield (different plots in the south of Kyrgyzstan, 2023)</b>. To identify optimal areas for cherry cultivation and refine agrotechnical practices, we analyzed the effects of local conditions and geography on yield.Table 2 presents the relationship between environmental factors (altitude, temperature, precipitation), cultivation methods, irrigation, and technologies addressing yield challenges.
DOI: 10.6084/m9.figshare.24631164.v2
title: Partitioning of root, litter and microbial respiration by plant input manipulation in forests.<sub>2</sub>.xlsx

description: Partitioning of root, litter and microbial respiration by plant input manipulation in forests.
DOI: 10.4225/49/58b61096a4fca
title: UniFun

description: UniFun variants
DOI: 10.6084/m9.figshare.14502267.v1
title: Dataset health consciousness

description: Dataset for validtion analysis of health consciousness.<br>
DOI: 10.6084/m9.figshare.729253.v1
title: Bargh et al. (2001), Study 1 Replication Attempt

description: This is the data set from the replication attempt of Study 1 (achievment priming expt) from: Bargh, J. A., Lee-Chai, A., Barndollar, K., Gollwitzer, P. M., & Trötschel, R. (2001). The automated will: Nonconscious activation and pursuit of behavioral goals. Journal of personality and social psychology, 81(6), 1014.
DOI: 10.6084/m9.figshare.19114913.v1
title: Supplementary Material for: Metastatic Meningioma of the Neck: A Case Report and Systematic Review

description: <b><i>Background:</i></b> Although meningiomas are the most common central nervous system neoplasms, extracranial metastases are exceedingly rare. There are even fewer reports of metastatic meningiomas to the neck. <b><i>Methods:</i></b> We described a patient with multiply recurrent orbital meningioma with metastasis to the neck found incidentally during neck exploration for composite resection and free tissue reconstruction. We performed a systematic review for all records pertaining to metastatic meningiomas to the cervical regions. <b><i>Results:</i></b> We found 9 previous reports of cervical metastatic meningiomas. Almost all cases underwent extensive local resection. There was no evidence of an association between the histological grade of the tumor and risk of metastasis to the neck. Cervical lymph node dissemination is more common in patients presenting after previous primary tumor resection. <b><i>Conclusions:</i></b> In the context of a neck mass, our findings suggest that metastatic meningioma should be included in the differential diagnosis, especially in patients with previous resections.
DOI: 10.6084/m9.figshare.8090852.v1
title: Wilson et al 2019_DBA data.xlsx

description: Data associated with the paper "Estimates for energy expenditure in free-living animals using acceleration proxies; a reappraisal", accepted for publication in the Journal of Animal Ecology in 2019.
DOI: 10.6084/m9.figshare.7452392.v1
title: Metabolic syndrome in bipolar disorder: prevalence, demographics and clinical correlates in individuals with bipolar I, bipolar II, and healthy controls

description: Abstract Background: The metabolic syndrome is a growing global public health problem and highly prevalent in patiens with bipolar disorder. There are a few studies about relationship between metabolic syndrome and bipolar disorder subtypes. Objective: The aim of this study was to investigate the prevalence of metabolic syndrome (MS) and its individual components in subjects with bipolar I (BD I) and bipolar II (BD II) disorder compared with non-psychiatric controls, and to determine the variables affecting MS. Methods: A total of 210 individuals (mean age 42.5 ± 11.87, 58.1% female) of whom 70 had BD I, 70 BD II, and 70 controls, were included in this study. MS was diagnosed according to the National Cholesterol Education Program Adult Treatment Panel III (NCEP ATP III), the adapted ATP III (ATP III-A) and the International Diabetes Federation (IDF) criteria. Results: Participants with BD I had a significantly higher prevalence of MS when compared to individuals BD II and non-psychiatric controls according to the NCEP-ATP III, ATP III-A, and IDF criteria (ps &lt; 0.01). In individuals with MS, increased waist circumference was the most common abnormality. Logistic regression analysis revealed that the presence of physical illness, age and number of cigarettes smoked significantly predicted the presence of MS. Discussion: This study showed that MS was more prevalent among BD I individuals compared to BD II and controls, and highlighted the importance of regular screening for MS in individuals with BD.
DOI: 10.6084/m9.figshare.5437420.v1
title: mtCOI reference data for species ID of Bemisia tabaci

description: mtCOI reference data set for Bemisia tabaci whitefly updated from GenBank on 22 May 2017.
DOI: 10.6084/m9.figshare.7091900.v1
title: Supplemental Data File 1 from Expression of a novel surfactant protein gene is associated with sites of extrapulmonary respiration in a lungless salamander

description: Spreadsheet with all of the sequence data used in the study.
DOI: 10.6084/m9.figshare.25458127.v1
title: DATABASE.xlsx

description: Database of the questionnaires applied to employees of the Peruvian retail sector.
DOI: 10.6084/m9.figshare.3510444.v1
title: Appendix E. Distributions of six trait metrics for leaf nitrogen produced by four community assembly simulation models.

description: Distributions of six trait metrics for leaf nitrogen produced by four community assembly simulation models.
DOI: 10.6084/m9.figshare.28151372.v1
title: Gridded dataset of daily U component of 10-m wind speed forecast from the ECMWF 50-member ensemble forecast

description: This dataset contains gridded spatial fields of daily 10-meter wind speed U-component (m/s) ensemble forecasts with a 48-hour lead time. The forecast data are from the European Centre for Medium-Range Weather Forecasts' (ECMWF) 50-member ensemble, and the time range of forecast days is 10 years from 2007-01-03 to 2017-01-02. The forecast is on a 0.5° × 0.5° grid, covering the region from -10° E to 30° E and from 30° N to 70° N, resulting in 81 × 81 grid points roughly covering Europe.
DOI: 10.6084/m9.figshare.24438649.v1
title: Data for ccAF version 2

description: This data is used to validate a cell cycle classifier. It is a processed version of data from this published work: https://www.nature.com/articles/s41467-020-17186-5
DOI: 10.6084/m9.figshare.12885425.v1
title: BASE and Primary Experiments' PM25 and NO2

description: Surface hourly PM25 and NO2 for the primary and base modeling experiments.
DOI: 10.6084/m9.figshare.1399185.v6
title: GlobWave multimission corrected Significant Wave Height for January, 2002

description: The complete GlobWave dataset is found at: ftp://ftp.ifremer.fr/ifremer/cersat/products/swath/altimeters/waves/data/ For access please consult: globwave.ifremer.fr/products/globwave-satellite-data
DOI: 10.6084/m9.figshare.9730628.v1
title: Benchmarking microbial growth rate predictions from metagenomes

description: This repository hosts supplemental metagenome-assembled genomes (MAGs) and co-assemblies for the manuscript: <br><br>"<b>Benchmarking microbial growth rate predictions from metagenomes</b>” by Andrew M. Long, Shengwei Hou, J. Cesar Ignacio-Espinoza, and Jed A. Fuhrman (https://doi.org/10.1038/s41396-020-00773-1). You can also find our non-peer reviewed manuscript here: https://www.biorxiv.org/content/10.1101/786939v1 <br><b>File description: </b><br><b>1. MAGs</b>: MAGs.zip<b>2. co-assemblies</b>: assembly.fasta.gz<br><br>
DOI: 10.6084/m9.figshare.9777299.v1
title: Differential expressed LncRNAs, protein-coding genes, and miRNAs

description: Differential expressed lncRNAs, protein-coding genes, and miRNAs for patients before and after CD19-CAR-T therapy
DOI: 10.6084/m9.figshare.28429103.v1
title: GSEM-DPC GWAS

description: GSEM-DPC GWAS SumStats
DOI: 10.6084/m9.figshare.5110768.v1
title: Picea abies chorology

description: Distribution map of Norway spruce (<i>Picea abies</i>)<br><br>These maps were produced by combining numerous and heterogeneous data collected from atlas monographs providing complete species distribution maps, from national to regional atlases, occurrence geodatabases and scientific literature.<br>The maps were created using ESRI shapefiles (*.shp, *.shx, *.dbf, *.prj files) archived in the ZIP file. Species range is mapped with polygon features (name suffix “plg”), which define continuous areas of occupancy of the species, and with point features (name suffix “pnt”), which identify more fragmented and isolated populations. If synanthropic occurrences are reported outside the species natural range, additional point and/or polygon shapefiles are also present (suffix “syn”).<br>All polygon borders delimiting the range are generalized across the mainland and sea boundaries, and not clipped to a specific coastline. This offers the possibility to mask sea areas, or to clip and extract the terrestrial range parts using GIS data layers of the users’ choice. <br><br>Please cite as:<br>Caudullo, G., Welk, E., San-Miguel-Ayanz, J., 2017. Chorological maps for the main European woody species. Data in Brief 12, 662-666. DOI: doi.org/10.1016/j.dib.2017.05.007 <br><br>Additional information and used references are on 'supplementary materials' document:<br>https://doi.org/10.6084/m9.figshare.5091901<br><br>Chorological maps are part of the "European Atlas of Forest Tree Species" project:<br>https://w3id.org/mtv/FISE-Comm/v01
DOI: 10.6084/m9.figshare.28359971.v1
title: NETWORKS KSTAR v1

description: KSTAR Networks (NetworKIN based) with the new pregenerated background activity lists released in v1.0 of KSTAR
DOI: 10.6084/m9.figshare.3188830.v2
title: Mole-rat FEA

description: Files for finite element analysis of two mole-rat species: Bathyergus suillis and Fukomys mechowi. Included in this dataset are: 3D reconstructions of the skull (made in Avizo); FE model files and project files for use in VOX-FE; resulting displacement files also from VOX-FE.
DOI: 10.6084/m9.figshare.5128972.v1
title: Supplementary Material for: Long-Term Evaluation of Colestilan in Chronic Kidney Disease Stage 5 Dialysis Patients with Hyperphosphataemia

description: <b><i>Background:</i></b> This study investigated in a North American patient population the longer-term treatment effects of the phosphate binder, colestilan, in patients with CKD Stage 5D and hyperphosphataemia. <b><i>Methods:</i></b> One hundred and sixteen CKD Stage 5D patients with hyperphosphataemia were entered into a multi-centre, open-label study where they received flexible dose colestilan (6-15 g/day) to maintain serum phosphorus levels between 3.5 and 5.5 mg/dl. The primary endpoint was safety, assessed by treatment-emergent adverse events. Efficacy was assessed by changes in serum phosphorus, mineral metabolism, lipids, HbA1c, uric acid and bone markers. <b><i>Results:</i></b> Serum phosphorus was significantly reduced by 1.18 mg/dl (p &lt; 0.001), from 6.99 mg/dl at baseline to 5.80 mg/dl at week 52. LDL-cholesterol was also significantly reduced as well as uric acid. Significant change was observed only for one bone marker - PINP. Most adverse events were of mild or moderate intensity. Nausea (22.4%), vomiting (21.6%), and diarrhoea (19.8%) were most commonly reported. <b><i>Conclusions:</i></b> Long-term flexible dosing with colestilan reduces serum phosphorus and demonstrates an acceptable safety and tolerability profile.
DOI: 10.6084/m9.figshare.11309669.v1
title: SAC 2020 KLP micro-influencer dataset

description: This dataset contains Five Factor Model and Basic Human Values scores computed from text. This dataset also contains Gold Stardard defined for micro-influencers. Gold Standard labels are in each "y" subfolder inside "scores". For ease of use there is one folder called "allinone" where all data from all topics are stored in a single csv file. Each folder contains data obtained searching the hashtag used as folder name on Twitter. Data were retrieved from September 2018 to March 2019.<br>"candidates" folder contains the list of Twitter users considered in the analysis, they had from 1k to 100k followers at the time of the analysis and they were posting tweets with the folder name hashtag at the time we performed the experiment.<br><br>"followers" contains as many file as users in candidates folder, each file contains the associated candidate followers the time we performed the experiment. <br><br>"tweets" contains as many file as users in candidates folder, each file contains the associated candidate tweets (whole history) the time we performed the experiment. Due to privacy concerns just tweet ids are stored. You need to query Twitter to retrieve the associated text.<br>"scores" contains both scores compute by us using our algorithms and micro-influencer labels coming from our gold standard (in subfolder "y").<br>For further details look at the paper "Mining Micro-Influencers from Social Media Posts" in KLP SAC2020 proceedings, or open an issue in the GitHub repository.<br>
DOI: 10.6084/m9.figshare.24981705.v1
title: Supplementary Material for: Serum angiopoietin-2 levels predict the development of hepatocellular carcinoma following hepatitis C virus eradication using direct-acting antiviral agents

description: Introduction: Our previous studies showed that serum angiopoietin-2 (Ang-2) and C-X-C motif chemokine ligand 10 (CXCL10) levels predicted improvement in liver fibrosis following sustained virological response (SVR) of hepatitis C virus (HCV) obtained with administration of with direct-acting antiviral agents (DAAs). These levels were evaluated retrospectively as predictive indicators of hepatocellular carcinoma (HCC) development following SVR.
Methods: We enrolled individuals from a historical cohort of 89 chronic HCV patients without history of HCC at baseline and with SVR following DAA therapy and had baseline serum levels of Mac-2 binding protein glycosylation isomer ≥ 2.0 C.O.I.
Results: Multivariate analyses revealed that only the Ang-2 level at 24 weeks following the end of treatment (EOT24W) was significantly related to HCC development (hazard ratio 2.27; P = 0.003). This result was reproduced in individuals without history of HCC and with advanced liver fibrosis (M2BPGi level ≥ 3.3 C.O.I. at baseline). Time-dependent receiver operating characteristic curve analyses for the future risk of developing HCC within 5 years of follow-up (5y-HCC) showed the best cut-off Ang-2 level at the EOT24W was 2,780 pg/mL, and significantly stratified the cumulative incidence of HCC (≥ 2,780 vs. &lt; 2,780 pg/mL, 5y-HCC: 45.5 vs. 8.2%, P &lt; 0.001).
Conclusions: At the EOT24W, serum Ang-2 level predicts the likelihood of developing HCC following SVR to DAA therapy.
DOI: 10.6084/m9.figshare.9808526.v1
title: HRD score and HRD score components matrix for array data

description: This file contains the array-derived HRD scores and HRD score components (HRD-LOH, LST and NtAI) for the array-derived data.
DOI: 10.6084/m9.figshare.17012756.v1
title: Supplementary Material for: Secular Trends in the Incidence, Prevalence, and Medications for Epilepsy from 2007 to 2015 in Taiwan: A Nationwide Population-Based Study

description: <b><i>Background:</i></b> Patients with epilepsy have a higher mortality rate than the general population. Up-to-date estimates of epilepsy incidence, prevalence, and medication use are critical to assist policymaking. <b><i>Methods:</i></b> Using the National Taiwan Insurance Research Database, the standardized incidence and prevalence of epilepsy were estimated in each calendar year from 2007 to 2015. We used the incident cases of epilepsy to analyze the change in prescribing patterns from 2007 to 2015. Joinpoint regression was used to estimate secular trends. <b><i>Results:</i></b> From 2007 to 2015, the age- and sex-standardized incidence decreased from 0.72 (95% confidence interval [CI] 0.70–0.73) to 0.54 (95% CI 0.53–0.55) per 1,000 person-years, giving an annual percentage change (APC) of −2.73 (<i>p</i> &lt; 0.05). Among patients younger than 20 years, the incidence did not change significantly. The age- and sex-standardized prevalence decreased from 6.94 (95% CI 6.90–6.98) to 6.86 (95% CI, 6.82–6.89) per 1,000 people, giving an APC of −0.31 (<i>p</i> &lt; 0.05). However, the prevalence increased in the 35- to 49- and 50- to 64-year age-groups. The most common first-line anticonvulsant was phenytoin in 2007 and valproate in 2015. The use of levetiracetam, clobazam, and valproate increased during the study period, with APCs of 25.48% (95% CI 19.97–31.24), 6.41 (3.09–9.85), and 2.83 (1.51–4.16), respectively. The use of carbamazepine, phenytoin, and topiramate decreased; the APCs were −23.86% (95% CI −25.25 to −22.44), −6.61 (−8.40 to −4.79), and −4.29% (−7.87 to −0.57), respectively. <b><i>Conclusions:</i></b> The overall prevalence and incidence of epilepsy decreased slightly from 2007 to 2015. The prescribed first-line anticonvulsant also changed over time.
DOI: 10.6084/m9.figshare.25425199.v1
title: Electro-acupuncture alleviates myocardial ischemia reperfusion injury by inhibiting hypothalamic paraventricular nucleus neurons projecting to the rostral ventrolateral medulla

description: Accumulating evidence suggests that electroacupuncture (EA) has obevious therapeutic effects and unique advantages in alleviating myocardial ischemia-reperfusion injury (MIRI), while the underlying neuromolecular mechanisms of EA intervention for MIRI have not been fully elucidated. The aim of the study is to investigate the role of the neural pathway of hypothalamic paraventricular nucleus (PVN) neurons projecting to the rostral ventrolateral medulla (RVLM) in the alleviation of MIRI rats by EA preconditioning.