cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.a5jzmm
title: Occurrence Download

description: A dataset containing 4352 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 Vespa crabro Linnaeus"
 ]
}

 The dataset includes 4352 records from 109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009355-250426092105405/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.14442206.v1
title: OX_heart_cDNA_representative.fa.gz

description: OX_heart representative cDNA sequences
DOI: 10.6084/m9.figshare.14832813.v1
title: Multi-omic and survival datasets used for "DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data"

description: We obtained the 32 cancer multi-omic datasets from NCBI using TCGA portal (https://tcgadata.nci.nih.gov/tcga/). We used the package TCGA-Assembler (versions 2.0.5) and wrote custom scripts to download RNA-Seq (UNC IlluminaHiSeq RNASeqV2), miRNA Sequencing (BCGSC IlluminaHiSeq, Level 3), and DNA methylation (JHU-USC HumanMethylation450) data from the TCGA website on November 4-14th, 2017. We also obtained the survival information from the portal: https://portal.gdc.cancer.gov/. We used the same preprocessing steps as detailed in our previous study. We first downloaded RNA-Seq, miRNA-Seq and methylation data using the functions DownloadRNASeqData, DownloadmiRNASeqData, and DownloadMethylationData from TCGAAssembler, respectively. Then, we processed the data with the functions ProcessRNASeqData, ProcessmiRNASeqData, and ProcessMethylation450Data. In addition, we processed the methylation data with the function CalculateSingleValueMethylationData. Finally, for each omic data type, we created a gene-by-sample data matrix in the Tabular Separated Value (TSV) format using a custom script. <br>
DOI: 10.17632/nrrmpnkwzy
title: Data for: Field development optimization using a cooperative micro-particle swarm optimization with variable tuning schemes

description: Here PUNQ-S3 reservoir model data in Eclipse 100 data file format.
DOI: 10.6084/m9.figshare.18133754.v1
title: Supplementary Material for: Clinical Utility of KidneyIntelX in Early Stages of Diabetic Kidney Disease in the CANVAS Trial

description: <b><i>Introduction:</i></b> KidneyIntelX is a composite risk score, incorporating biomarkers and clinical variables for predicting progression of diabetic kidney disease (DKD). The utility of this score in the context of sodium glucose co-transporter 2 inhibitors and how changes in the risk score associate with future kidney outcomes are unknown. <b><i>Methods:</i></b> We measured soluble tumor necrosis factor receptor (TNFR)-1, soluble TNFR-2, and kidney injury molecule 1 on banked samples from CANagliflozin cardioVascular Assessment Study (CANVAS) trial participants with baseline DKD (estimated glomerular filtration rate [eGFR] 30–59 mL/min/1.73 m<sup>2</sup> or urine albumin-to-creatinine ratio [UACR] ≥30 mg/g) and generated KidneyIntelX risk scores at baseline and years 1, 3, and 6. We assessed the association of baseline and changes in KidneyIntelX with subsequent DKD progression (composite outcome of an eGFR decline of ≥5 mL/min/year [using the 6-week eGFR as the baseline in the canagliflozin group], ≥40% sustained decline in the eGFR, or kidney failure). <b><i>Results:</i></b> We included 1,325 CANVAS participants with concurrent DKD and available baseline plasma samples (mean eGFR 65 mL/min/1.73 m<sup>2</sup> and median UACR 56 mg/g). During a mean follow-up of 5.6 years, 131 participants (9.9%) experienced the composite kidney outcome. Using risk cutoffs from prior validation studies, KidneyIntelX stratified patients to low- (42%), intermediate- (44%), and high-risk (15%) strata with cumulative incidence for the outcome of 3%, 11%, and 26% (risk ratio 8.4; 95% confidence interval [CI]: 5.0, 14.2) for the high-risk versus low-risk groups. The differences in eGFR slopes for canagliflozin versus placebo were 0.66, 1.52, and 2.16 mL/min/1.73 m<sup>2</sup> in low, intermediate, and high KidneyIntelX risk strata, respectively. KidneyIntelX risk scores declined by 5.4% (95% CI: −6.9, −3.9) in the canagliflozin arm at year 1 versus an increase of 6.3% (95% CI: 3.8, 8.7) in the placebo arm (<i>p</i> &lt; 0.001). Changes in the KidneyIntelX score at year 1 were associated with future risk of the composite outcome (odds ratio per 10 unit decrease 0.80; 95% CI: 0.77, 0.83; <i>p</i> &lt; 0.001) after accounting for the treatment arm, without evidence of effect modification by the baseline KidneyIntelX risk stratum or by the treatment arm. <b><i>Conclusions:</i></b> KidneyIntelX successfully risk-stratified a large multinational external cohort for progression of DKD, and greater numerical differences in the eGFR slope for canagliflozin versus placebo were observed in those with higher baseline KidneyIntelX scores. Canagliflozin treatment reduced KidneyIntelX risk scores over time and changes in the KidneyIntelX score from baseline to 1 year associated with future risk of DKD progression, independent of the baseline risk score and treatment arm.
DOI: 10.6084/m9.figshare.28437020.v2
title: Piecewise SEM - Alpha & beta diversity models

description: Piecewise structural equation modeling (pSEM) using different alpha and beta diversity metrics to assess soil respiration, beta-glucosidase activity, and soil microbial biomass C.
DOI: 10.6084/m9.figshare.5127466.v1
title: Supplementary Material for: Treatment of Organic Livestock with Medicinal Plants: A Systematic Review of European Ethnoveterinary Research

description: <b><i>Background:</i></b> The EC Regulation for Organic Farming states that organic livestock should be treated preferably with phytotherapeutic products. In spite of the high importance of organic livestock in Europe, primarily ruminants, today almost no phytotherapeutic product is registered for livestock. Also, information regarding veterinary phytotherapy is rare. The aim of this paper is to find approaches to cope with health problems of organic ruminants in Europe on the basis of findings from the European ethnoveterinary medicine (EuEVM). <b><i>Methods:</i></b> A systematic review of ethno-biomedicinal papers was conducted with the aid of the Scopus database, and 75 papers, from European countries were analyzed regarding ethnoveterinary information. <b><i>Results:</i></b> A total of 590 plant species referring to 102 different plant families are reported to be used for animal treatment, with <i>Asteraceae</i>, <i>Fabaceae</i> and <i>Lamiaceae</i> being the most important families. The traditional use of some plant species (e.g. mallow, chamomile, wormwood) corresponds with findings from recent scientific literature. The large number of less studied plant species, such as white lupin as an antiparasitic herb, and <i>Helleborus</i> spp. as potential immunostimulatory agent, opens an interesting field for future research. <b><i>Conclusions:</i></b> In general, EuEVM provides interesting treatment approaches for gastrointestinal and dermatological disorders as well as parasitosis. Findings regarding disorders of female genital or respiratory tract are less consistent. Nevertheless, EuEVM offers a solid basis for stimulating research in veterinary phytotherapy in Europe with a perspective to solve animal health problems in organic or even nonorganic ruminant production.
DOI: 10.6084/m9.figshare.9638867.v1
title: Gene expression counts matrix

description: Compressed .txt file of RNA-seq counts object created using the 6.gene_abundance_estimation.sh script and the phenotype file that can be found in the git repository https://git.exeter.ac.uk/jffpviana/ClozapineZebrafish.gitDetails of data analysis can also be found on the git repository.
DOI: 10.15468/dl.wwkpq3
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Valeriana jatamansi Jones)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "Country is India",
 "Geometry POLYGON ((60.85388 15.95789, 105.0447 15.95789, 105.0447 39.31873, 60.85388 39.31873, 60.85388 15.95789))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1980"
 ]
}

 The dataset includes 11 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009354-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/8kfc6ssnkm
title: water_consumption_of_two_sites

description: Daily water Consumption of two sites in 2016 to 2017
DOI: 10.6084/m9.figshare.14554989.v1
title: Supplementary Material for: Molecular identification and cellular localisation of a corticotropin-releasing hormone type neuropeptide in an echinoderm

description: Medicine
DOI: 10.6084/m9.figshare.7890176.v1
title: gVCF_HG01351

description: 1000 Genomes gVCF mapped to hs37d5 for HG01351. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.24923943.v1
title: Supplementary Material for: X-linked lymphoproliferative syndrome: a spectrum of clinical and immunological profile and novel pathogenic variants from Chandigarh, India

description: Introduction: X-linked lymphoproliferative syndrome (XLP) is a rare primary immune deficiency. Two types of XLP have been described: XLP-1 and XLP-2.
Methods: We found 7 patients with XLP (3 had XLP-1 and 4 had XLP-2) after reviewing the data from Pediatric Immunodeficiency Clinic from 1997-2021.
Results: Mean age at diagnosis was 3.8 years and mean delay in diagnosis was 2.6 years. Five patients had recurrent episodes of infections. Four patients developed at least one episode of hemophagocytic lymphohistiocytosis (HLH) (2 with XLP-1 and 2 with XLP-2). Of these, 2 had recurrent HLH (both with XLP-2). Epstein-Barr virus (EBV) infection was detected in 2 (1 with XLP-1 and 1 with XLP-2). Both these patients had HLH. One child with XLP-2 had inflammatory bowel disease. Hypogammaglobulinemia was seen in 3 (2 with XLP-1 and 1 with XLP-2). Genetic analysis showed previously reported variants in 5, while 2 had novel variants (one in exon 7 of XIAP gene [c.1370dup p. Asn457Lysfs Ter16] and other had splice site variant in intron 1 of SH2D1A gene [c.138-2_138-1insG]). Episodes of HLH were managed with intravenous immunoglobulin (IVIg), methylprednisolone, oral prednisolone, cyclosporine and rituximab. Inflammatory bowel disease was managed using oral prednisolone and azathioprine. One patient underwent haploidentical hematopoietic stem cell transplantation (HSCT). One child with XLP-2 and WAS died because of fulminant pneumonia. 
Discussion/Conclusions: XLP should be considered as a strong possibility in any patient with features of HLH, repeated infections with hypogammaglobulinemia, persistent EBV infection and early onset IBD.
DOI: 10.6084/m9.figshare.19248449.v1
title: Supplementary Material for: Refractive surgery for older children and adults with accommodative esotropia: a systematic review

description: Introduction: Accommodative esotropia (AET) is characterized by an esodeviation of the eyes due to uncorrected hyperopia, deficient fusional divergence, or high accommodative convergence. Decreasing hyperopia would reduce accommodative convergence and strabismus. We sought to review the existing evidence regarding the outcomes of refractive surgery in patients with AET. Methods: A four-database search (Pubmed, ISI Web of Science, Cochrane, and Scopus) was performed from inception to March 2021 using the MeSH terms: ("Refractive Surgical Procedures" OR "Keratomileusis, Laser In Situ" OR "Photorefractive Keratectomy" OR "Lens Implantation, Intraocular") AND ("Esotropia" OR "Accommodative Esotropia" OR "Refractive Esotropia” OR "Accommodative Strabismus"). No meta-analysis was performed due to studies’ heterogeneity. Results: Twenty-eight studies including 22 case series enrolling 378 patients and 6 case reports enrolling 8 patients were selected among 185 original abstracts. In the case series, a total of 378 patients (726 eyes) were recruited with an age range of 8-52 years. All studies reported mean follow-up periods of at least 12 months. Photorefractive keratectomy was performed in 7 studies, laser-assisted in situ keratomileusis in 9 studies, laser-assisted sub-epithelial keratectomy was reported in 1 study and 3 studies implanted IOL lenses, including iris-fixated and collamer. Considering the adult patients with a preoperative corrected esodeviation ≤10PD (n=129), all but five (3.9%) presented orthophoria or ≤10PD after refractive surgery. All children but 4 (4.5%) ended up with an esodeviation ≤10PD after surgery with those exceptions being in the range of 11 to 15PD. Six case reports were included in this review, comprising a total of 8 patients (16 eyes) with an age range of 7 to 34 years and a follow-up range of 4 to 48 months.Six case reports were included in this review, comprising a total of 8 patients (16 eyes) with an age range of 7 to 34 years and a follow-up range of 4 to 48 months. Discussion/Conclusion: Evidence produced so far points out that refractive surgery may be an alternative for spectacle correction for adults with accommodative esotropia ≤10PD. There is not enough evidence to recommend its use for patients under 18 years. The safety and predictability of these procedures for this purpose remains unclear as the selection criteria used for these patients are much different than the usual indications and there are no studies with long-term follow-up.
DOI: 10.6084/m9.figshare.28589762.v1
title: <b>Linking morpho-taxonomy to ecosystem functions: trait-based estimation of biomass and potential carbon budget in omnivore nematodes</b>

description: Omnivore nematodes within the order Dorylaimida are among the largest free-living soil-dwelling nematodes, suggesting a significant role in soil biomass and carbon cycling. However, their contribution to these soil processes remains underexplored. Estimating biomass based on nematode morphological traits provides a practical and reliable approach for assessing their contribution in carbon dynamics. This study provides estimated individual biomass and the daily carbon budget of dorylaimids, utilizing a database of taxon-specific body-size measurements sourced from publicly available literature. We calculated biomass and potential carbon budgets for 618 reported populations worldwide, encompassing 464 species, 127 genera, 47 subfamilies, and 19 families. Biomass estimates, using body diameter as a single predictor, based on two recently developed formulae and two adjusted formulae developed in this study were compared against Andrássy's original formula which is using both body length and body diameter as predictors. Adjusted formulae fitted in this study provided a better fit than recently published formulae. Overall, we found an estimated average individual omnivore nematode biomass (fresh weight) of 3.33 µg for females and 3.55 µg for males, and the corresponding daily carbon budgets of 0.03903 µg and 0.04163 µg for females and males, respectively. The considerable variability in biomass data across the taxonomic ranks, highlight the need for robust taxonomic resolution for ecological studies. This study offers a comprehensive dataset and improved formulae for estimating biomass and potential carbon budget in omnivore nematodes, enhancing our understanding of their functional roles in carbon dynamics and other ecosystem processes.
DOI: 10.6084/m9.figshare.13653272.v1
title: Source Data 5

description: <b>Source Data 5. </b>Lineage-dependent essentiality of 17 lineages and common essentiality computed using ADaM for six theta
DOI: 10.6084/m9.figshare.20038367.v1
title: Adaptability and stability of corn inbred lines regarding resistance to gray leaf spot and northern leaf blight

description: Abstract The objectives of this study were to identify resistant and susceptible corn inbred lines based on their stability and adaptability for resistance to disease symptoms of gray leaf spot and northern leaf blight, suggest resistant inbred lines aimed at producing synthetics, and identify the sowing dates with higher occurrence of diseases to use these dates for identification of genetic resistance. We evaluated 41 corn inbred lines in randomized block designs with three replications and 11 sowing dates. Evaluations were performed 30 days after silking. Stability and adaptability analyses were performed by the regression method. The highest severities of disease occurred in sowing from June to September. On average, all the inbred lines were classified as resistant; however, considering adaptability and stability, five inbred lines were found suitable to produce dent synthetics resistant to both diseases. For flint synthetics resistant to both diseases, inbred lines IVF1-7, IVF1-10, 2F, 9F, and 10F are most suitable.
DOI: 10.6084/m9.figshare.21909075.v1
title: E-cadherin is a biomarker for ferroptosis sensitivity in diffuse gastric cancer

description: raw data and raw blots
DOI: 10.6084/m9.figshare.9696779.v1
title: Maximizing the efficiency of residents operating room scheduling: a case study at a teaching hospital

description: Abstract Paper aims To find efficient operation room scheduling for residents considering several resources constraints and ensuring a minimum number of surgeries for approval in the training program. Originality We find no research in current literature addressing operation room resource allocation for residents training in order to meet legislation approval criteria. Research method The number of procedures to be performed by each resident was defined by Brazilian legislation and by the rules obtained from interviews with the chief professor of a vascular hospital. To solve the allocation of doctors to surgeries planning problem, also addressed in literature as Master Surgical Schedule (MSS), we propose a mathematical programming approach. Main findings The mathematical model showed that some of the current rules of resource availability bring about infeasible planning when trying to achieve the legislation quantitative rules for the residents training. Implications for theory and practice The model allowed the decision maker to plan and schedule vascular surgeries in a better and faster way, through an automated system, instead of allocating residents to surgeries manually, which takes many hours per month. Furthermore, changing the input data in the proposed model can allow other hospitals or specialists to get efficient results in less time.
DOI: 10.6084/m9.figshare.12515364.v1
title: Rezzoagli_etal_2020_rawdata.xlsx

description: This item contains all the raw data of the paper by Rezzoagli et al. Combining antibiotics with antivirulence compounds can have synergistic effects and reverse selection for antibiotic resistance in <i>Pseudomonas aeruginosa. PLOS Biology</i><b></b>
DOI: 10.6084/m9.figshare.5120479.v1
title: Supplementary Material for: Prevalence of Obesity and Abdominal Obesity in Swedish Primary Care and Occupational Health Clinics

description: <i>Background: </i>The objective of this study was to describe the prevalence of obesity and abdominal obesity in the Swedish primary and occupational health care setting. <i>Patients and Methods: </i>Weight, height, and waist circumference (WC) were measured in 1,583 consecutive patients, aged between 18–65 years (46.4 ± 12.7 years), in 39 primary care and occupational health practices in Sweden, in 2006. The National Cholesterol Education Program (NCEP) WC reference values were used to define abdominal obesity (102 and 88 cm for men and women, respectively). <i>Results: </i>The distribution across obesity categories differed significantly between men and women with close to 70 and 55% of men and women, respectively, having a body mass index (BMI) ≧ 25. More men than women were overweight (BMI 25–29.9; 45.1 vs. 31.1%) and obese (BMI 30–34.9; 19.8 vs. 12.9%), but less men than women were morbidly obese (4.0 vs. 8.9%; BMI ≧ 35). Increasing prevalence with age was seen until age 60 for both overweight and obesity. More women than men were abdominally obese (42.5 vs. 32.7%; p &lt; 0.001). Only 48 and 64% of the abdominally obese women and men, respectively, had a BMI ≧ 30. <i>Conclusion: </i>Compared to national Swedish data, the prevalence of overweight and obesity was higher in primary and occupational health care settings. Both morbid obesity and abdominal obesity were highly prevalent and more common in women, implying that awareness of sex differences may be important or that recommended cut-offs are not comparable across sex. Furthermore, a large fraction of the abdominally obese had a BMI &lt; 30. Both BMI and WC may therefore be important to determine routinely and incorporate into treatment guidelines, in order not to miss patients at risk of obesity-related morbidity.
DOI: 10.17632/6kx55f599p
title: Data for: Generation of an Immortalized Human Choroid Endothelial Cell Line (iCEC-1) Using an Endothelial Cell Specific Promoter

description: RNA-Seq results from iCEC1 cell line.
DOI: 10.17632/yytvxk6kdr
title: Temperament differences in boys and girls from 3 to 5 years old

description: The present study tried to determine if there are differences between temperament´dimensions of boys and girls between three to five years old. The sample includes 406 participants: 221 boys and 185 girls, from 9 pre-schools districts (Arequipa-Peru). The study was descriptive and correlational, trying to find the relationship between dimensions of temperament in boys and girls. The Buss and Plomin scale of temperament: emotionality, activity and sociability (shyness) (EAS), and a demographic card built by the researchers were used. Significant differences were found in favor of girls in the dimensions of sociability and activity. On the other hand, there are no significant differences in relation to the different ages of the participants.
DOI: 10.6084/m9.figshare.13133270.v2
title: Prokka annotation for the genomes of Streptomyces sp. G11C, CHD11 and Vc74B-19

description: Prokka annotation for the genomes of Streptomyces sp. G11C, CHD11 and Vc74B-19, as described in referenced article<br>
DOI: 10.6084/m9.figshare.23613534.v1
title: <strong>Polycystic Ovarian Syndrome Physiologic Pathways Implicated Through Clustering of Genetic Loci.</strong> Maria I. Stamou*, Kirk T. Smith*, Hyunkyung Kim*, Ravikumar Balasubramanian, Kathryn J. Gray, Miriam Udler.

description: Tables S1-S8 for manuscript entitled " <strong>Polycystic Ovarian Syndrome Physiologic Pathways Implicated Through Clustering of Genetic Loci.".</strong> <br>
DOI: 10.6084/m9.figshare.28436138.v1
title: R Script and Data for Propagules, disturbance lower invasibility - revision

description: We manipulated soil disturbance and propagule pressure in three habitat types (aspen forest, shrub vegetation, prairie grassland) and examined their impact on the germination success of three pairs of phylogenetically similar native and non-native plant species (<i>Bromus ciliatus</i>/<i>B</i>. <i>inermis</i>, <i>Elymus trachycaulus</i>/<i>Agropyron cristatum</i>, <i>Poa secunda</i>/<i>P</i>. <i>pratensis</i>) for three months after seed addition.
DOI: 10.6084/m9.figshare.3830082.v1
title: Car Analysis in Parking Lot 2016

description: Meta DataColour - description of paint job of the vehiclesCar Company - description of who made the vehicles<br>At designated school parking lot at York University <br>
DOI: 10.6084/m9.figshare.9963533.v1
title: pheno and genetype data20191010

description: phenotypic, genetype and <em>supplementary table</em>