cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25624221.v3
title: KMP assembly and gene annotation

description: The total DNA of a blood sample of a male Korean minipig (27 months old) was extracted, and DNA libraries for short, long, and Hi-C reads were constructed and sequenced. Contigs were generated by connecting PacBio subreads (79.78x) using Canu (v1.9), and the high-quality contigs supported by at least 50 subreads were selected for the subsequent procedure. The remaining contigs were polished using GenomicConsensus (v2.3.3). To build a chromosome-level genome assembly, the contigs were scaffolded using short reads, long reads, and multiple reference genomes (Bama, Göttingen, Meishan, Duroc, Landrace, Large white, cow, and goat) by RACA. Subsequently, Hi-C reads were aligned to the scaffolds using the Arima Hi-C mapping pipeline and SALSA2 was run for the Hi-C scaffolding. Lastly, the correction of misassemblies and the gap closing were done with short read data twice using Pilon (v1.22).For gene annotation, RNAs from 26 different tissues (appendix, backfat, bone marrow, brain, colon, forelimb muscle, groin, heart, hindlimb muscle, intestine, kidney, liver, lung, lymph node, nipple, pancreas, phren, pituitary gland, rib, sirloin, spinal cord, spleen, stomach, tenderloin, testis, and thymus) were extracted and sequenced on the Illumina platform. To annotate protein-coding genes, RNA-seq data were mapped to the chromosome-level scaffolds in the KMP assembly using HISAT2 (v2.2.1). Using the RNA-seq and gene annotation data of different species (pig, human, cow, and goat), we predicted the protein-coding genes in the KMP assembly by running GeMoMa (v1.9). For annotating non-coding genes, various types of non-coding RNAs, including rRNA, snRNA, and miRNA, were annotated using the Rfam database and Infernal (v1.1.3). Additionally, tRNA and rRNA were predicted with tRNAscan-SE (v2.0.5) and RNAmmer (v1.2), respectively. The final annotation was generated by merging all predictions using the Perl script (https://github.com/jkimlab/NCMD_study) provided by the previous study.<br>The sequencing read data for genome assembly and annotation can be obtained at NCBI SRA under the project of the PRJNA1104148.
DOI: 10.17632/bnfwf63vcr
title: Colon cancer biofilm composition reveals distinct bacterial species signature

description: Abstract
Human colon hosts a highly organized protective microbial ecosystem in the form of biofilms, increasingly recognized as key contributors to colorectal cancer (CRC) progression through microbial dysbiosis and complex host-microbiota interactions. In India, CRC ranks among the top ten cancers, with an age-standardized incidence rate of approximately 6.3 per 100,000 in males and 3.7 per 100,000 in female highlighting a higher risk in men, late-stage diagnosis, inadequate screening, and treatment limitations, particularly in urban populations. This study aims to explore the microbial composition of colonic biofilms from the Indian cohort of CRC patients from New Delhi, which is witnessing a rise in the incidence of CRC. Colon biopsies were taken from (n = 15) tumors and (n = 15) adjacent nontumor tissues at the Gastrointestinal Department of AIIMS, New Delhi, India. Fluorescence in situ hybridization (FISH) was employed to determine the bacterial population in the biofilm. The workflow included microtomy, deparaffinization, tissue permeabilization, and hybridization with bacterial 16S rDNA probes, and the detected signals were visualized by confocal microscopy. The results showed quite different microbial patterns and tumor-associated biofilms were found to have an increased density of Escherichia coli, Klebsiella pneumoniae, and Bacteroides fragilis, while Fusobacterium nucleatum and polyketide synthase Escherichia coli (pks+) were seen less often. These results confirm the significant dysbiosis and the formation of invasive biofilms in CRC tissues. Understanding the composition of these biofilms may facilitate the development of targeted strategies to restore microbial balance and reduce CRC risk both in the Indian population and globally.
Key points 
• Tumor-associated biofilms show distinct microbial dysbiosis in Indian CRC patients. 
• Enrichment of Escherichia coli, Klebsiella pneumoniae, and Bacteroides fragilis in tumor sites observed.
• Insights into biofilm profiles may aid targeted interventions for CRC risk reduction.
DOI: 10.17632/h5kfd8pr9s
title: Data for: Target quantification and semi-target screening of halogenated carboxylic acids in drinking water using ultra-high performance liquid chromatography-quadrupole orbitrap high-resolution mass spectrometry

description: Raw data of some typical samples of drinking water.
DOI: 10.17632/tk77frmwg8
title: Bearing Rotating System Dynamic Model for Fault Detection

description: This is a dynamic model coded in Simulink, that generates synthetic time history responses of a rotating system with bearings, which may be subjected to faults generated randomly with specified severity. The generated datasets can then be used as training data for fault detection algorithms and monitoring techniques.
DOI: 10.17632/z755vh3m5h
title: Metal Oxides

description: metal oxides, nanoparticles, micro crystals
DOI: 10.6084/m9.figshare.12756020.v1
title: The association of smoking status with SARS-CoV-2 infection, hospitalisation and mortality from COVID-19: A living rapid evidence review and Bayesian meta-analyses (version 6) - Data

description: Data extraction from identified articles reporting on SARS-CoV-2 infection, COVID-19 hospitalisation, severity or mortality.
DOI: 10.6084/m9.figshare.13030241.v4
title: Data with meta-data

description: The purpose of this observational experiment is to observe and record the living habits and characteristics of different bird species in a specific environmental field. After changing several locations and conducting non-continuous observations, I chose York University, which has abundant bird species with active behaviors, to conduct observational experiments. According to the consistency of the morning bird activity time, I chose to observe after 11 am. A specific observation point was selected on the platform between Vari Hall and grassland. Because this kind of observation field is more conducive to observe more birds. The total observation duration was around an hour. During this period, all the different birds observed, along with their real-time activities and durations had been recorded in as much detail as possible in the wild dataset. After reorganizing the notes, the species, numbers and related activities of the birds that appeared during the observation period are shown in the following table. Also, there is meta-data presented together with the table.<br>
DOI: 10.6084/m9.figshare.3561174.v1
title: Appendix A. Detailed information about the trait database and the phylogeny.

description: Detailed information about the trait database and the phylogeny.
DOI: 10.6084/m9.figshare.9637259.v1
title: Additional file 2: of Evaluating the quality of the 1000 genomes project data

description: Statistics for the experimental sequencing. (XLSX 21 kb)
DOI: 10.17632/v5sgn4hfy3
title: Data for: The determinants of sovereign bond liquidity during WWI
DOI: 10.17632/ws7wgmwfcj
title: FEA Dataset of Prequalified and Proposed End-Plate Connections for Beam-to-Column Joints and Two-Story Moment Frames
DOI: 10.6084/m9.figshare.1591908.v1
title: Supplementary Table 1: The list of the 43 complete genomes of Staphylococcus aureus used for the fineStructure analysis.

description: Supplementary Table 1: The list of the 43 complete genomes of<em> Staphylococcus aureus</em> used for the fineStructure analysis.
DOI: 10.6084/m9.figshare.8156525.v3
title: Flotation and Sedimentation Experiments

description: Data collected from a DAF treatment. The effluent used comes from a bus washing system. The parameters analysed were colour, turbidity, COD, electric condutivity and pH. Flotation values were achieved by using two different coagulants: PAC and Aquafloc/LS
DOI: 10.6084/m9.figshare.8309714.v1
title: ECCITE-seq protein and mRNA counts

description: Protein data were acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3596101, file GSM3596101_CTCL-ADT-count.csv.gz.<br><code>velocyto</code> processing: velocyto run (bam directory)/(BAM file).bam (transcriptome directory)/genes/genes.gtf<br><br>
DOI: 10.6084/m9.figshare.9926636.v1
title: TEM pictures

description: Tem pictures in raw .tiff
DOI: 10.17632/pdz4cys2r7
title: Synchronized VRP Test Instance for Food Bank Operations

description: We generated random data to test a synchronized vehicle routing problem models for effective and equitable food allocation in food banks.
DOI: 10.6084/m9.figshare.19780558.v1
title: Table 1. Genome sequence context for JMJD1C SNPs associated with bovine congestive heart failure (BCHF)

description:   
<strong>Background:</strong>  The power and resolution of genome-wide association studies (GWAS) may be enhanced with increased DNA marker density and reduced ascertainment bias of whole genome sequence (WGS) technology compared to that of bead-based microarrays.  However, validation of WGS marker associations may be challenging since preexisting assays for these variants will not always be available.  Here, our aim was to provide preliminary molecular, genetic, and statistical information for JMJD1C variants associated with bovine congestive heart failure (BCHF) for the purpose of assay development.
<strong>Methods: </strong> A WGS data set with greater than 10-fold genome coverage per animal was generated from 102 BCHF matched case-control pairs.  Paired nominal data from 11 million single nucleotide polymorphisms (SNPs), filtered for frequency and quality, were analyzed with McNemar’s test and sorted genome-wide by false discovery rate (FDR).
<strong>Results:</strong>   A 45 kb region spanning introns 2 and 3 of JMJD1C on chromosome 28 was identified as being significantly associated with BCHF with a FDR q-value less than 0.05.  This association was in addition to those in ARRDC3 and NFIA previously reported (Heaton et al. F1000Research 2022, 11:385).  Nine linked SNPs in JMJD1C comprised exactly two haplotypes with an average minor allele frequency (MAF) of 0.005 and 0.132 in the cases and controls, respectively.  Two copies of the major SNP alleles were associated with disease development, while one or two copies of the minor SNP alleles were not.   There were 25 informative pairs for each of the nine linked SNPs, and the “protective” allele was absent from all 25 diseased animals in these informative pairs (McNemar’s b/c = 0/25, OR = 0, mid p-value = 3.0 x 10E-8, FDR = 9.8 x 10E-3).
 <strong>Conclusion:</strong> These preliminary results indicate that selection for the protective JMJD1C  alleles may be useful in reducing BCHF in severely affected herds, however genotype assay development will be needed for further validation.   The marker details are publicly available for use without restriction (https://doi.org/10.6084/m9.figshare.19780558.v1).
DOI: 10.6084/m9.figshare.24328828.v1
title: Forward Modeling Dataset, protocol files, and forward modeling code (ResIPy)

description: The files are final forward model simulations for four geophysical array configurations.Protocol files for each of the geophysical array and the forward model code (ResIPy) is included.
DOI: 10.6084/m9.figshare.24592401.v1
title: Supplementary Material for: The association between antiplatelet therapy and changes in intraplaque hemorrhage in patients with mild to moderate symptomatic carotid stenosis: a longitudinal MRI study

description: Introduction: Carotid atherosclerotic intraplaque hemorrhage (IPH) predicts stroke. Patients with a history of stroke are treated with antiplatelet agents to prevent secondary cardiovascular events. A positive association between previous antiplatelet use and IPH was reported in a cross-sectional analysis. We investigated changes in IPH over two years in patients who recently started versus those with continued antiplatelet use.
Methods: In the Plaque at Risk (PARISK) study, symptomatic patients with &lt;70% ipsilateral carotid stenosis underwent carotid plaque MRI at baseline and after two years to determine IPH presence and volume. Participants were categorized into new users (starting antiplatelet therapy following the index event) and continued users (previous use of antiplatelet therapy before the index event). The association between previous antiplatelet therapy and the presence of IPH at baseline MRI was investigated using multivariable logistic regression analysis. IPH volume change over a period of two years, defined as the difference in volume between follow-up and baseline, was investigated in each group with a Wilcoxon signed-rank test. The IPH volume change was categorized as progression, regression, or no change. Using multivariable logistic regression, we investigated the association between new antiplatelet use and 1) newly developed ipsilateral or contralateral IPH and 2) IPH volume progression.
Results: A total of 108 patients underwent carotid MRI at baseline and follow-up. At baseline, previous antiplatelet therapy was associated with any IPH (OR=5.6, 95% CI: 1.3–23.1; p=0.02). Ipsilateral IPH volume did not change significantly during the two years in patients who continued receiving antiplatelet agents (86.4 mm3 [18.2-235.9] vs. 59.3 mm3 [11.4-260.3]; p=0.6) nor in the new antiplatelet users (n=31) (61.5 mm3 [0.0-166.9] vs. 27.7 mm3 [9.5-106.4]; p=0.4). Similar results of a nonsignificant change in contralateral IPH volume during those two years were observed in both groups (p&gt;0.05). No significant associations were found between new antiplatelet use and newly developed IPH at two years (odds ratio (OR)=1.0, 95% CI:0.1-7.4) or the progression of IPH (ipsilateral: OR=2.4, 95% CI:0.3-19.1; contralateral: OR=0.3, 95% CI:0.01-8.5).
Conclusion: Although the baseline association between IPH and previous antiplatelet therapy was confirmed in this larger cohort, the new onset of antiplatelet therapy after TIA/stroke was not associated with newly developed IPH or progression of IPH volume over the subsequent two years.
DOI: 10.6084/m9.figshare.8091329.v1
title: Diseases.csv

description: This Database belongs to “A Database for Using Machine Learning and Data Mining Techniques for Coronary Artery Disease diagnosis” research paper. This database includes 15 tables. We chose to index papers related to CAD detection using machine learning and data mining approaches that are published between 1992 and 2018. These criteria result in 126 papers in which 490 authors contributed to these papers. These papers studied 68 different datasets with almost more than 360 distinct features collected in 18 countries from Asia, Europe, and America. In these papers, 140 different machine learning or data mining techniques were applied to diagnose CAD. To use csv file, open it in excel or import it in your database.
DOI: 10.6084/m9.figshare.1617512.v4
title: Chinese herbal medicine treatment improves the overall survival rate of individuals with hypertension among type 2 diabetes patients and modulates in vitro smooth muscle cell contractility

description: Type 2 diabetes (T2D) is a chronic, multifactorial, and metabolic disorder accounting for 90% diabetes cases worldwide. Among them, almost half of T2D have hypertension, which is responsible for cardiovascular disease, morbidity, and mortality in these patients. The Chinese herbal medicine (CHM) prescription patterns of hypertension individuals among T2D patients have yet to be characterized. This study, therefore, aimed to determine their prescription patterns and evaluate the CHM effect. A cohort of one million randomly sampled cases from the National Health Insurance Research Database (NHIRD) was used to investigate the overall survival rate of CHM users, and prescription patterns. After matching CHM and non-CHM users for age, gender and date of diagnosis of hypertension, 980 subjects for each group were selected. The CHM users were characterized with slightly longer duration time from diabetes to hypertension, and more cases for hyperlipidaemia. The cumulative survival probabilities were higher in CHM users than in non-CHM users. Among these top 12 herbs, Liu-Wei-Di-Huang-Wan, Jia-Wei-Xiao-Yao-San, Dan-Shen, and Ge-Gen were the most common herbs and inhibited in vitro smooth muscle cell contractility. Our study also provides a CHM comprehensive list that may be useful in future investigation of the safety and efficacy for individuals with hypertension among type 2 diabetes patients.
DOI: 10.6084/m9.figshare.23584862.v1
title: Surgical Correction of Metatarsal Angular Deviation in a Thoroughbred Filly Using Wedge Metatarsal Ostectomy: a case report

description: Abstract This study describes a corrective procedure for a metatarsal angular malformation using wedge ostectomy in a 41-day-old Thoroughbred filly. A 41.6 °angular malformation of the metatarsus was corrected with wedge ostectomy of the left hindlimb in association with a type II external fixator and methyl methacrylate resin. The animal was subjected to the surgical procedure under general anesthesia. The filly was placed in dorsal recumbency with the left hind limb free for manipulation. A bone saw was used for the wedge ostectomy, while the bars for external fixation were placed using a drill. A Kirschner pin and acrylic resin were then applied. Radiographic images obtained immediately after surgery confirmed a total malformation reduction of 32.6 (from 41.6° to 9°). With medication and a Robert Jones bandage, intensive postoperative care was instituted to ensure that the animal adapted properly to the linear external fixator without overloading the pins and connection bars. No postoperative complications were observed. On the day after surgery, the filly was standing and walking with no signs of pain. After 180 days, total osseous calcification was achieved, and the implants were removed during the second surgery. The filly demonstrated adequate locomotion, performed all the movements, and ran without any difficulty in the paddock. The remaining discrete angular deviations were partially corrected using hoof trimming.
DOI: 10.6084/m9.figshare.24649641.v1
title: Leaf productivity Summer season

description: Dataset contains leaf productivity, shoot density and leaf width data from the Thalassia Experimental Network
DOI: 10.17605/osf.io/zqpt5
title: Fire-smart Bioenergy nexus

description: here we present the data and code for the following paper Integrating fire-smart fuels management with bioenergy benefits remote and Indigenous communities in Canada
DOI: 10.17632/67d4schwp9
title: Data for: Temporal and spatial variability of traffic-related PM2.5 sources: Comparison of exhaust and non-exhaust emissions

description: PMF input files and results
DOI: 10.17632/7mk8w57ypc
title: Replication Folder. Global Drivers of Inflation: The Role of Supply Chain Disruptions and Commodity Price Shocks

description: The current folder contains all replication files for the following paper:

Diaz E.M., Cunado J., Perez de Gracia F. (2024) Global Drivers of Inflation: The Role of Supply Chain Disruptions and Commodity Price Shocks. Economic Modelling, forthcoming

Cite the paper if you make use of these codes. Data sources are cited in the paper; if utilized, please cite accordingly.
DOI: 10.17632/pxjmjyfdh2
title: The RHMCD-20 datasets for Depression and Mental Health Data Analysis with Machine Learning

description: the RHMCD-20 dataset, we took care to include information from a wide range of sources, including teenagers from Bangladesh, college students, housewives, professionals from
businesses and corporations, and other people.This is survey data for Depression and Mental Health Data Analysis.
Survey questions : 
Age: Represents the age of the participants.
Gender: Indicates the gender of the participants.
Occupation: Represents the participant's occupations.
Days_Indoors :Indicates the number of days the participant has not been out of the house
Growing_Stress: Indicates the participant's stress is increasing day by day (Yes/No).
Quarantine_Frustration: Frustrations in the first two weeks of quarantine (Yes/Maybe/No).
Changes_Habits: Represents major changes in eating habits and sleeping (Yes/Maybe/No).
Mental_Health_History : A precedent of mental disorders in the previous generation (Yes/No).
Weight_Change :Highlights changes in body weight during quarantine (Yes/Maybe/No)
Mood_Swings: Represents extreme mood changes (Low/Medium/High).
Coping_Struggles: The inability to cope with daily problems or stress (Yes/Maybe/No).
Work_Interest :Represents whether the participant is losing interest in working (Yes/No).
Social_Weakness :Conveys feeling mentally weak when interacting with others (Yes/No).
DOI: 10.6084/m9.figshare.12214364.v2
title: Source data for paper entitled "Low-frequency ultrasound-mediated cytokine transfection enhances T cell recruitment at local and distant tumor sites"

description: This is the source data that was used to generate the Figures and Supplementary Figures in the PNAS paper entitled "Low-frequency ultrasound-mediated cytokine transfection enhances T cell recruitment at local and distant tumor sites".
DOI: 10.6084/m9.figshare.28307192.v1
title: GPMAG

description: To investigate genomic and functional insights of grapevine phyllosphere microbiome, GPMAGs were generated with 103 HiFi datasets acquired from 103 grapevine leaf accessions.
DOI: 10.6084/m9.figshare.5577340.v1
title: Kirstie Whitaker - Better Science through Better Data 2017 keynote scribe images

description: Scribe images for Kirstie Whitaker's Better Science through Better Data 2017 keynote talk.
DOI: 10.17632/rr4cv2ngr9
title: Data for: An evaluation of kinetic models for the simulation of Claus reaction furnaces in sulfur recovery units under different feed conditions.

description: Performance of reduced reaction kinetics for the prediction of effluent gas from Claus reaction furnace. Comparison with predictions from detailed reaction mechanism and with plant data.
DOI: 10.4121/14317574.v1
title: Raw data "E-perceptions and business 'mating': The Communication Effects of the Relative Width of Males' Faces in Business Portraits"

description: This is the raw data that belongs to the manuscript 'E-perceptions and Business 'Mating': The Communication Effects of the Relative Width of Males' Faces in Business Portraits', as published by Eveline van Zeeland and Jörg Henseler (2021) in Frontiers in Psychology.
DOI: 10.6084/m9.figshare.20430963.v5
title: metadata and silva classifier

description: metadata and silva classifier
DOI: 10.6084/m9.figshare.21587451.v2
title: Data for "Plant C:N ratio predicts community composition changes under N addition in an alpine meadow"

description: Plant functional traits play important roles in determining plant responses to environmental change and further shaping community composition, but the role of plant stoichiometry remains poorly understood in regulating community responses to continually increased nitrogen (N) deposition. Here, we used a five-year manipulative experiment with six N addition rates (N<sub>rate</sub>) to explore how the N response of different plant functional groups links to aboveground plant carbon-to-N ratio in an alpine meadow. We found that functional groups with higher C:N tended to grow better and have greater abundance over increasing N<sub>rate</sub>, yet those with lower C:N were at risk of loss, subsequently mitigating the N-caused decline in community-level plant C:N. This was mainly due to that functional groups with higher C:N not only possessed higher N use efficiency but also had greater competitiveness for aboveground light due to higher plant height. Our results show that the N responses of different herbaceous plants can be well explained by plant C:N. Thus, we suggest the prediction of plant community composition changes under N deposition would be greatly improved by considering this easily measured stoichiometric trait. Here we share our dataset related to our manuscript.
DOI: 10.6084/m9.figshare.4040124.v1
title: HDFS Logs

description: HDFS logs used in SOSP'2009