cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/8wrjdknb5k
title: The number of nail fold capillaries and nail fold bleedings reflects the clinical manifestations of systemic sclerosis

description: Participants and imaging methods
Capillaroscopy videos and clinical images were obtained from SSc patients who had given consent between April 2016 and December 2018.The number of SSc patients was 71 and 550 nails were included. All patients were taking oral vasodilators. Capillaroscopy movies were taken with a Toku Capillaro-01 capillaroscope. The capillaroscope itself was fixed on a stand attached to the capillaroscope. After applying a drop of oil to the base of the patient's nail, the patient's finger was placed on the stand with the capillaroscope attached, and the capillaroscope was moved by using a lever on the stand to move the finger.　The video images were saved as MPG files using the supplied software. Fingers with ulcers were not captured.
From the video images, a set of images was extracted using the preview function of the Macintosh. A folder was created for each nail and the cropped images were saved in each folder.
The study was approved by the Ethics Committee of the Graduate School of Medicine of the University of Tokyo (2019093NI). Written informed consent was obtained from all participants.

Overlaying nail images using deep learning
Since NFCs may be unevenly distributed in one nail, NFB and NFC count were evaluated on a nail-by-nail basis to eliminate errors due to the measurement site. On the other hand, images taken by capillaroscopy are at high magnification (300x), and multiple images must be connected to generate a single nail image. In order to count the number of NFCs and NFBs, we first decided to overlay the nail images. In existing reports, characteristic blood vessels were used as a marker for overlapping images. However, in this study, some images were found to have few blood vessels, so we decided to use the nail border as a marker for overlapping images.
The images of 50 nails in 10 cases were annotated by a SSc specialist with supervised data on nail boundaries, NFBs, and NFCs. LabelImg was used for annotation.
We used Tensorflow 1.13.2 and Keras 2.2.4 as a deep learning framework.
First, we trained U-net with images of nails to enable the recognition of nail borders. Second, we draw the nail borders in images using the trained U-net and arranged the images using stitching technique so that the boundary line between the nail and the cuticle was on the arc. Third, we trained yolo-v3, which was the object detection algorithm , using images with NFC and NFB annotations, and detected NFCs and NFBs using the trained yolo-v3.
The system was programmed to detect the NFBs and NFCs specifically. (NFC Count Tool and NFB Count Tool).
For the remaining 61 patients and 500 nails, the NFC and NFB counts were measured using the NFC count tool and the NFB count tool after clipping from the video, and the correlation with the clinical image was examined. We took all remaining nails per patient and averaged them.
DOI: 10.6084/m9.figshare.24907428.v3
title: <b>Correlation of Prolonged Sitting Time and Sitting Posture on Low Back Pain: A Cross-Sectional Study among Medical Students at Universitas Sumatera Utara</b>

description: Background: Low Back Pain (LBP) is the most common musculoskeletal disorder in the world. Medical students, particularly those who use computers for study purposes, are more vulnerable to LBP due to prolonged sitting times and improper sitting posture during lectures. However, prior research showed that the prevalence of LBP among medical students appeared lower when they were enrolled during online pandemic learning. Hence, this research is performed to determine the correlation between the duration of sitting and sitting posture on the incidence of LBP among medical students in Universitas Sumatera Utara, Indonesia. Methods: A cross-sectional study with an analytical descriptive design was conducted in September 2023 among randomly selected 147 medical students at Universitas Sumatera Utara, Indonesia. The inclusion criteria of the research sample are students with BMI&lt; 23 kg/m2 while the exclusion criteria are students who have abnormalities and a history of trauma or spinal fractures. Data was obtained from filling out questionnaires of The Pain and Distress Scale (PAD) and Body Awareness of Postural Habit in Young People (BAPHY). A Chi-square test and logistic regression were used to analyze data with a p-value &lt; 0.05 was regarded as statistically significant. Results: The study's findings revealed that 40.1% of students reported having LBP problems, 72.1% reported sitting for more than seven hours each day, and 33.3% reported having a bad sitting posture. Chi-square analysis revealed a significant correlation between sitting duration and posture on complaints of lower back pain (RR = 1.69, p = 0.041 and RR = 1.69, p = 0.009). At a risk of 2,438 times, sitting posture is the main factor contributing to LBP among medical students at Universitas Sumatera Utara, Indonesia. Conclusions: This research showed a significant correlation between duration and sitting posture on the incidence of low back pain.
DOI: 10.6084/m9.figshare.26745577.v1
title: EGERL

description: <pre>The source codes that support the paper <b>'</b><b>Synthesizing event semantics for geographical entity representation'</b><br><br>This program provides the implementation of our EGERL as described in our paper.<br><br>DATA: The python file data-process.py can process the event data and use different strategies.Specific details can be found at supplementary instruction.txt<br><br><b>Requirements</b><br>- Python 3.7<br>- Pytorch 1.5.0 & CUDA 10.1<br><br><b>Running commands:</b><br>python -u EGERL.py --dataset ../data --num_iterations 3000 --eval_after 2000 --batch_size 1024 --lr 0.001 --emb_dim 256 --hidden_dim 256 --encoder QGNN --variant D<br><br><br></pre>
DOI: 10.6084/m9.figshare.3405610.v1
title: Regulation of monocyte induced cell migration by the RNA binding protein, FXR1

description: FXR1 belongs to a family of RNA-binding proteins that play critical roles in post-transcriptional regulation of gene expression in immunity, development and cancer. FXR1 is associated with regulation of specific mRNAs in myocytes and macrophages. In quiescent cells (&gt; 24 h of extended serum-starvation, ∼30-48 h or more), a spliced isoform of FXR1, FXR1a, promotes translation of the cytokine TNFα, independent of the effects of RNA levels. Here we examined the role of FXR1 in THP1 human monocytic leukemic cells that were grown in serum, as well as in early (24 h) serum-starvation conditions that demonstrates differences in gene expression mechanisms and is distinct from quiescent (&gt; 24 h extended serum-starvation) cells. Global RNA profiling, conducted to investigate the role of FXR1 on mRNA levels, revealed that FXR1 affects levels of specific mRNAs in serum-grown and in early 24 h serum-starvation conditions. FXR1 decreases levels of several mRNAs, including as previously identified, CDKN1A (p21CIP1 or p21) mRNA in serum-grown cells. Interestingly, we find that FXR1 positively regulates mRNA levels of specific cytokines and chemokines in serum-grown and in early 24 h serum-starvation conditions. These include IL1β and CCL2 that control cell migration. Accordingly, depletion and overexpression of FXR1 decreased and increased levels of CCL2 mRNA. Consistent with the reduced levels of IL1β, CCL2 and other chemokines upon FXR1 depletion, our data reveal that depletion of FXR1 decreases the ability of these cells to induce cell migration of neighboring monocytic cells. These data reveal a new role of FXR1 in controlling induction of monocyte migration.
DOI: 10.17632/38wd6dyvnd
title: Data for: In vitro and in vivo digestibility from bionanocomposite edible films based on native pumpkin flour/plum flour

description: These files provide the transparent date of this article.
DOI: 10.6084/m9.figshare.22567267.v4
title: Supplemetary data of Herrera et al. Vespa velutina

description: Table S1.- Genotypes and sampling data for the 357 individuals analysed in this study and occurrences obtained from genetic studies, GBIF and bibliography.Table S2.- Allelic dropout and null alleles per locus and area, as detected by MICRO-CHECKER. ND denotes no enough data for analysis.R scripts.<br><br>
DOI: 10.6084/m9.figshare.23277392.v2
title: Social Media Corpus: Stigma Identification in Vaccination Discourse (COVID-19)

description: Current research introduces an annotated gold standard dataset based on 2,663 comments from Meta (Facebook). The dataset is manually labelled for stigma, not stigma, and ambiguous sentiment. Each comment is labelled three times (four times in case of dissensus) by independent expert annotators. The overall observed share of agreement reached 68% and Fleiss Kappa agreement rate achieved 0.62 on the annotation task with three labels ("stigma, "not stigma", and "ambiguous" category). Annotation share of agreement between two labels ("stigma, "not stigma") is 89% and Fleiss Kappa is 0.84. The labels are consequently propagated from the annotated Facebook (Meta) to a dataset discussing COVID vaccines with 40,084 comments from Twitter, Reddit, and YouTube corpora. In addition, the corpora are annotated with linguistic features from LIWC (Linguistic Inquiry and Word Count) [1], [2] and additional features: number of characters in the comment string, sentiment score, subjectivity score.
<br>
1. Pennebaker, J. W., Francis, M. E. & Booth, R. J. Linguistic inquiry and word count: Liwc 2001. Mahway: Lawrence<br>
Erlbaum Assoc. 71, 2001 (2001).<br>
2. Tausczik, Y. R. & Pennebaker, J. W. The psychological meaning of words: Liwc and computerised text analysis methods. J. language social psychology 29, 24–54 (2010)<br>
<br>
DOI: 10.6084/m9.figshare.28199684.v1
title: acc_test.zip

description: TEST
DOI: 10.17632/szxs5cy89t
title: (Dataset) Comparative analysis: GDP, GERD, patents registration, scientific publications, number of enterprise entries (Germany, France, and Spain)

description: This dataset presents a linear regression analysis of seven variables to evaluate economic cycles and knowledge spillover. The seven variables are 1) Population, 2) GDP (current US$), 3) GDP annual growth, 4) Gross domestic Expenditure on R&D, 5) Total patent applications, 6) Scientific and technical journal articles, and 7) Number of enterprise entries. The information was collected from the World Bank, WIPO, and OECD, encompassing Germany, France, and Spain, from 2000 to 2018.
DOI: 10.6084/m9.figshare.24911454.v1
title: Precipitation impacts of Amazon deforestation

description: <b>Shared codes and data for “</b><b>Contrasting seasonal precipitation impacts of Amazon Deforestation</b><b>”</b>
DOI: 10.6084/m9.figshare.27889722.v1
title: Supplementary tables from A global biogeographic regionalization for butterflies

description: Supplementary tables.xlsx
DOI: 10.15468/dl.9deb9k
title: Occurrence Download

description: A dataset containing 13176 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hydrocotyle sibthorpioides Lam.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 13176 records from 181 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013167-250525065834625/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.13071824.v1
title: Supplementary Material for: Lipid-Producing Ciliochoroidal Melanoma with Expression of HMG-CoA Reductase

description: Uveal melanoma (UM) is the commonest primary intraocular malignancy in adults. There is limited published data on lipid production in UM. Here, we describe the clinical, histological, immunohistochemical, and molecular findings in a ciliochoroidal melanoma with lipid production and expression of the enzyme HMG-CoA reductase. This case highlights an unusual UM tumour phenotype with a high-risk molecular metastatic profile and discusses tumour lipogenesis and activation of the mevalonate pathway as a potential therapeutic target in managing lipidised ciliochoroidal UM.
DOI: 10.6084/m9.figshare.13501641.v2
title: Hormaphis cornu reference genome and annotation

description: This project contains the <i>Hormaphis cornu</i> reference genome and annotation (GFF) associated with the publication "A novel family of secreted insect proteins linked to plant gall development" by Korgaonkar <i>et al.</i> (2021).<br>Please contact Clair Han at hanc@janelia.hhmi.org with questions. <br>
DOI: 10.6084/m9.figshare.23949225.v1
title: Southern Hemisphere dominates recent decline in global water availability

description: These are the accompany data and codes files for the Science paper “Southern Hemisphere dominates recent decline in global water availability".Those files have been compiled by Congcong Li and Yongqiang Zhang from the Chinese Academy of Sciences.Last updated on 12th August 2023.The data files comprise the following:1. Annual Data: This includes three sets of annual data covering the period 2001-2020: Simple model output averaging (SMA), Bayesian model averaging (BMA), and machine learning (ML).2. Global Land Area: It provides land area (km2) for each grid cell spanning from +90 degrees to -60 degrees, corresponding to areas with available water availability (WA) data.3. Aridity Index (AI): The AI represents the ratio of mean annual precipitation to potential evapotranspiration, with a higher value indicating a wetter climate.4. Trend Data: This section presents trends in WA derived from SMA, BMA, ML, and their ensemble mean. Additionally, trends in leaf area index obtained from MOD15A2 are included.5. WA-SOI Correlation: The correlation between water availability (WA) and the Southern Oscillation Index (SOI).6. Precipitation Contribution Ratio: This file offers the contribution ratio of precipitation as determined by SMA.7. Spreadsheets: Includes data for Figure 1A and Figures 2D and 2E.<br>The MATLAB (R2021a) code files consist of:Fig1A.m: Code for Figure 1A.Fig1C.m: Code for Figure 1C.Fig2B_2C.m: Code for Figures 2B and 2C.Fig2D_2E.m: Code for Figures 2D and 2E.Fig3B.m: Code for Figure 3B.Fig3C.m: Code for Figure 3C.Should you have any further questions, please feel free to inquire Professor Yongqiang Zhang (yongqiang.zhang2014@gmail.com) and Ms Congcong Li (licongcong0825@163.com).
DOI: 10.6084/m9.figshare.6205235.v1
title: Dataset_S1.xlsx

description: Dataset S1 for Getz et al., Parallel Evolution of Key Genomic Features and Cellular Bioenergetics Across the Marine Radiation of a Bacterial Phylum, bioRxiv 307454; doi: https://doi.org/10.1101/307454.
DOI: 10.17632/59cs8gj76c
title: Untargeted metabolomics data from the analysis of craft and industrial beers, and craft beer brewing samples

description: This dataset contains metabolomics data from analyzing craft beers, industrial beers, and brewing samples of an in-production wheat ale craft beer. Data was acquired via an Agilent LC-MS system, obtained both in positive and negative ionization modes. Raw data from the instrument was converted to the mzXML format via ProteoWizard MSConvert.
DOI: 10.17632/nxz24s6t5y
title: Data for: Mathematics Achievement and Orientation: A Systematic Review and Meta-Analysis of Education Technology

description: Data and R Code for Mathematics Achievement and Orientation: A Systematic Review and Meta-Analysis of Education Technology
DOI: 10.25452/figshare.plus.22781714.v1
title: Genome Analyses of 1,154 budding yeasts

description: Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,090 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation. 
<br>
This item includes the raw data for multiple analyses conducted on the genomic data. Each folder contains a readme.txt file that details the analysis and file formats. The analyses included in this folder are
<br>

 <strong>annotations_pep_interproscan.zip</strong>: InterPro - InterProScan was run on every genome annotation. The raw results are reported for all 1,154 yeasts. 
 <strong>y1000p_codetta_output.tar.gz</strong>: Codetta analysis - Codetta was run on every genome to determine the likely genetic code. 
 <strong>y1000p_orthofinder.tar.gz</strong>: Orthfinder Results - Orthofinder was run on all genome annotations to create orthogroups 
  <strong>y1000p_tRNA_scan.tar.gz</strong>: tRNAscan Results - tRNAscan was run on each genome assembly to determine the copy number, location and state of tRNAs within the genomes
 <strong>y1000plus_annotations_pep_kegg.tar.gz: </strong>KEGG Annotations - KEGG orthology was assigned to each genome annotation. 
 <strong>y1000p_repeatmsker_analysis.tar.gz: </strong>Repeatmasker analysis - Repeatmasker was run on all genome assemblies. A masked version of each genome is included in this folder
 <strong>Y1000p_BUCO_fulltable.tar.gz: </strong>BUSCO analysis - BUSCO was run on all genome assemblies. The "full table" results are reported for each genome
DOI: 10.6084/m9.figshare.28388330.v1
title: Texture and Noise Dual Adaptation for Infrared Image Super-Resolution

description: For evaluation, we created three specialized datasets: M3FD5, M3FD15, and M3FD20, from the M3FD dataset, each with different sample sizes and scene compositions.
DOI: 10.6084/m9.figshare.28883756.v2
title: README

description: This project presents a computer vision-based method for the screening of Parkinson’s disease. We specifically focus on detecting bradykinesia, a core motor symptom, by analyzing finger tapping performance. Using simultaneous bilateral finger tapping, we extract motion features from video recordings and assess the presence of motor slowing patterns associated with Parkinson’s disease. The provided Jupyter Notebook includes the full pipeline: video processing, feature extraction, and classification. This work aims to support early and accessible screening of Parkinson's disease through non-invasive, vision-based assessment techniques.
DOI: 10.6084/m9.figshare.29190698.v1
title: Book1.xlsx

description: This is a list of test data with placeholder values.
DOI: 10.17632/7rptdf44zt
title: Metagenomics sequencing shows microbiome differences in brain abscess samples

description: The data reported here are the sequence information and microbiome characteristics of three culture-negative brain abscess samples. The processed sequences were used for Operational Taxonomic Units (OTU) analysis and sequences that possessed more than 97% similarity were grouped into the same OTUs.
DOI: 10.17632/7szms6xrdb
title: Dataset of COVID-19 Cases and Vaccinations at Local and National Levels in Indonesia

description: The dataset includes daily records of COVID-19 cases in Bandung City, West Java, and Indonesia and vaccination data in Indonesia. The daily records of the COVID-19 cases dataset consist of confirmed cases, confirmed active cases, confirmed recovered cases, confirmed deaths cases, suspect cases, monitored suspect cases, discarded suspect cases, close contact cases, discarded close contact cases, increase in confirmed cases, increase in confirmed active cases, increase in confirmed recovered cases, increase in confirmed death cases, increase in suspect cases, increase in monitored suspect cases, increase in discarded suspect cases, increase in close contact cases, and increase in discarded close contact cases.
DOI: 10.17632/kd232wy5ph
title: Publications on the Monetary Policy Transmission research

description: All 202 publications on the topic of the Monetary Policy Transmission on Scopus for bibliometric analysis!
DOI: 10.25452/figshare.plus.22802147.v2
title: Genomes and Annotations of 1,154 budding yeasts

description:   
<strong>Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,090 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation</strong>. 
<br>
This item contains the genomes and annotations for the 1,154 budding yeasts that were sequenced or re-annotated in this project. 
<br>

 <strong>y1000p_cds_files.tar.gz</strong> - Fasta files of the nucleotide sequences for the gene annotations in the format assembly_fullID.final.cds
 <strong>y1000p_gff3_files.tar.gz</strong> - GFF3 files of the gene annotations in the format assembly_fullID.final.gff3
 <strong>y1000p_gtf_files.tar.gz</strong> - GTF files of the gene annotations in the format assembly_fullID.final.gtf
 <strong>y1000p_pep_files.tar.gz</strong> - Fasta files of the amino acid sequences for the gene annotations in the format assembly_fullID.final.pep
 <strong>y1000p_genome_files.zip</strong> - Fasta files of the assembled genome sequences in the format assembly_fullID.fas.gz
DOI: 10.6084/m9.figshare.19658676.v1
title: Figure 5 - example calcium timetrace

description: w; ; Mef2-GAL4 klar /UAS-GCaMP6s midgut shows calcium pulses viewed on the dorsal side of the anterior midgut. <br> <br> TIFF file shows max intensity projection over the same timecourse, with timesteps of 10s, 10s, 70s, 10s,10s, 70s, etc between frames