cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28672433.v1
title: all_occurrences

description: Data Statement for the Research Article Submitted to <i>Global Ecology and Conservation</i>
DOI: 10.6084/m9.figshare.27605148.v1
title: Mount Isa Inlier SHRIMP Data - Unfiltered

description: This dataset contains unfiltered Sensitive High-Resolution Ion Microprobe (SHRIMP) data collected from zircon samples in the Mount Isa Inlier. This unfiltered version retains all data points, providing a complete record before application of lead loss filtering criteria. For methodological details on filtering criteria and analysis, please refer to the accompanying manuscript.
DOI: 10.6084/m9.figshare.21330924.v3
title: Data and R script: Lean muscle mass, not aggression, mediates a link between dominance rank and testosterone in wild male chimpanzees

description: Data and R script used to prepare a manuscript entitled, "Lean muscle mass, not aggression, mediates a link between dominance rank and testosterone in wild male chimpanzees". Data include behavioral data (e.g., aggression rates, pant-grunts) as well as urinary testosterone and creatinine values for 34 adult male chimpanzees from the Ngogo community of Kibale National Park, Uganda.
DOI: 10.6084/m9.figshare.26771938.v1
title: <b>Fast inference of large-scale air quality using a lightweight ensemble predictor</b>

description: data and codes
DOI: 10.6084/m9.figshare.5122834.v1
title: Supplementary Material for: Arl6ip1 Plays a Role in Proliferation during Zebrafish Retinogenesis

description: <b><i>Objective:</i></b> Arl6ip1 has been reported to play a role in ocular development, but its regulatory function as it relates to proliferation is unclear. Therefore, this study aimed to evaluate how Arl6ip1 may regulate the proliferative behavior of retinal progenitor cells during zebrafish embryogenesis. <b><i>Method:</i></b> Arl6ip1 was specifically knocked down by introducing morpholino nucleic acid oligomers. The DNA content of cells dissociated from morphant eyes was analyzed by fluorescence-activated cell sorting (FACS). Retinal cells in the S- and late G2/M-phase were detected by labeling with BrdU and then immunostaining with anti-BrdU antibody and by immunostaining with phospho-histone H3 antibody, respectively. We also examined the expressions of <i>shh,</i><i>p57kip2,</i> and <i>cyclin D1</i> in retinas of experimental animals. The bidirectional plasmid pGFP:HSE:p57kip2 was used to rescue the defect in cell cycle exit. <b><i>Results:</i></b> FACS analysis showed that the &gt;2C DNA content per cell in the eyes of <i>arl6ip1</i> morphants was 2-fold greater than that of the wild type. Following functional Arl6ip1 knockdown, anti-BrdU- and anti-phospho-histone H3-positive signals were higher and the retinal progenitors kept expressing <i>cyclin D1</i> but not <i>shh</i> or <i>p57kip2,</i> suggesting that eye progenitor cells remained in an early progenitor state and could not exit the cell cycle to progress to differentiation. Interestingly, overexpression of p57kip2, which enables exit from the cell cycle, led to a reduction of anti-BrdU-positive signals in the retinas of <i>arl6ip1</i> morphants. <b><i>Conclusion:</i></b> Arl6ip1 not only affects signals controlling eye development but also plays an important role in the proliferation of retinal progenitor cells.
DOI: 10.6084/m9.figshare.15088722.v1
title: Horizontal gene transfer and evolutionary consequence of gene loss in myriapods

description: Animals have fascinating diversity of life forms. Analyses of the available genome sequence reveals dynamic evolution of gene gain and loss at different lineages in the animal tree of life (e.g. Albalat and Canestro 2016; Sharma et al 2018; Fernandez and Gabaldon 2020; Guijarro-Clarke et al 2020; Jebb et al 2020). Gene gain via another kingdom as well as the evolutionary consequence of gene loss are generally ignored and difficult to interpret. Here we sequenced six new myriapod genomes at key phylogenetic positions of this understudied arthropod lineage (three millipedes and three centipedes). Comparison of myriapod genomes revealed multiple horizontal gene transfer (HGT) of genes shared between centipedes, including <i>glucose/arabinose dehydrogenase</i> that happened at the last common of ancestor of centipedes, while there was no detectable HGT shared between the millipedes. In all millipede lineages, the loss of <i>juvenile hormone O-methyltransferase</i>, a key enzyme in catalysing the last step of sesquiterpenoid hormone methyl farnesoate production in arthropods was revealed. These findings provided the first evidence of shared HGT in the last common ancestor of centipede ancestor, while gene loss event could indeed happen in endocrine system in contrary to the conventional view of stepwise gene gain resulting in diversity of animal physiology for adaptation to environment.
DOI: 10.15468/dl.jskpn7
title: Occurrence Download

description: A dataset containing 1208 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Eucalyptus L'Hér."
 ]
}

 The dataset includes 1208 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009471-250426092105405/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.695084.v1
title: Video footage of fish and shrimp use of mussel spat rope in experimental culverts

description: Video footage of fish and shrimp use of mussel spat rope in experimental culverts. Also contains an indication of the effects of mussel rope on water hydrodynamics in a perspex pipe using dye. Footage captured in June-July 2012.
DOI: 10.6084/m9.figshare.c.3656867_d2.v1
title: MOESM2 of The plant leaf movement analyzer (PALMA): a simple tool for the analysis of periodic cotyledon and leaf movement in Arabidopsis thaliana

description: Additional file 2. Programme files.
DOI: 10.6084/m9.figshare.5126905.v1
title: Supplementary Material for: Stakeholder Analysis in Pharmacogenomics and Genomic Medicine in Greece

description: <b><i>Background:</i></b> The pace of discoveries and advances in genomic research is not reflected in the pace of their translation and incorporation into day-to-day clinical medicine to individualize healthcare decision-making processes. One of the main obstacles is the poor understanding of the policies and the key stakeholders involved in these translation processes. <b><i>Methods:</i></b> We used the computerized version of the <i>PolicyMaker</i> political mapping tool to collect and organize important information about the pharmacogenomics and genomic medicine policy environment, serving as a database for assessments of the policy's content, the major players, their power and policy positions, their interests, and networks and coalitions that interconnect them. <b><i>Results and Conclusions:</i></b> Our findings indicate that the genomic medicine policy environment in Greece seems to be rather positive, as the vast majority of the stakeholders express their medium to high support in the initially set goals of genomic medicine policy environment. The Ministry of Health and public healthcare insurance funds seem to oppose it, most likely due to financial constrains. These findings would contribute in selecting and implementing policy measures that will expedite the adoption of genomics into conventional medical interventions.
DOI: 10.6084/m9.figshare.16735189.v1
title: Interview transcripts

description: Transcripts from 13 interviews conducted with woody perennial polyculture farmers in the US upper Midwest in the summer of 2018. <br><br>See methods section in the paper for details.
DOI: 10.6084/m9.figshare.28502258.v1
title: VO2 and HR Participant Data - 6 Minute Push Test

description: Participant data collected by the VO2 Master Analyzer during the 6MPT. The study related to the collection of this data was approved by the University of Wisconsin – Milwaukee Institutional Review Board (IRB#23.347).
DOI: 10.6084/m9.figshare.19867795.v1
title: VCF_file_experimentally_evolved_Shoepeg_pop_2020_gen3

description: This is the VCF file with SNP markers produced from GBS sequence data from an experimental evolution study with divergent replicated selection. In total we had four subpopulations, two subpopulations were selected for tall plant height, and two subpopulations were selected for short plant height. Each subpopulation has a population size of 5000 plants. After 3 generations of selection, we randomly chooses 96 plants in each subpopulation and genotyped and phenotyped them. This VCF file contains the SNP markers, which were called in a SNP calling pipeline after GBS from those 384 single plants.
DOI: 10.6084/m9.figshare.23514033.v1
title: Supplementary Material for: Learning-Based Longitudinal Prediction Models for Mortality Risk in Very-Low-Birth-Weight Infants: A Nationwide Cohort Study

description: <b><i>Introduction:</i></b> Prediction models assessing the mortality of very-low-birth-weight (VLBW) infants were confined to models using only pre- and perinatal variables. We aimed to construct a prediction model comprising multifactorial clinical events with data obtainable at various time points. <b><i>Methods:</i></b> We included 15,790 (including 2,045 in-hospital deaths) VLBW infants born between 2013 and 2020 who were enrolled in the Korean Neonatal Network, a nationwide registry. In total, 53 prenatal and postnatal variables were sequentially added into the three discrete models stratified by hospital days: (1) within 24 h (TL-1d), (2) from day 2 to day 7 after birth (TL-7d), (3) from day 8 after birth to discharge from the neonatal intensive care unit (TL-dc). Each model predicted the mortality of VLBW infants within the affected period. Multilayer perception (MLP)-based network analysis was used for modeling, and ensemble analysis with traditional machine learning (ML) analysis was additionally applied. The performance of models was compared using the area under the receiver operating characteristic curve (AUROC) values. The Shapley method was applied to reveal the contribution of each variable. <b><i>Results:</i></b> Overall, the in-hospital mortality was 13.0% (1.2% in TL-1d, 4.1% in TL-7d, and 7.7% in TL-dc). Our MLP-based mortality prediction model combined with ML ensemble analysis had AUROC values of 0.932 (TL-1d), 0.973 (TL-7d), and 0.950 (TL-dc), respectively, outperforming traditional ML analysis in each timeline. Birth weight and gestational age were constant and significant risk factors, whereas the impact of the other variables varied. <b><i>Conclusion:</i></b> The findings of the study suggest that our MLP-based models could be applied in predicting in-hospital mortality for high-risk VLBW infants. We highlight that mortality prediction should be customized according to the timing of occurrence.
DOI: 10.6084/m9.figshare.25115357.v3
title: Regional Aridity of Southern California Ecosystems 2022/2023

description: Regional climatic data collected from various weather stations throughout southern California. De Martonne Aridity index was calculated utilizing total precipitation/(mean annual temperature +10).
DOI: 10.6084/m9.figshare.5123854.v1
title: Supplementary Material for: Genomic Sequence and Analysis of EhV-99B1, a New Coccolithovirus from the Norwegian Fjords

description: Coccolithoviruses are giant dsDNA viruses that infect <i>Emiliania huxleyi</i>, the most ubiquitous marine microalga. Here, we present the genome of the latest coccolithovirus strain to be sequenced, EhV-99B1, and compare it with two other coccolithovirus genomes (EhV-86 and EhV-163). EhV-99B1 shares a pairwise nucleotide identity of 98% with EhV-163 (the two strains were isolated from the same Norwegian fjord but in different years), and just 96.5% with EhV-86 (isolated in the same spring as EhV-99B1 but in the English Channel). We confirmed and extended the list of relevant genomic differences between these EhVs from the Norwegian fjord and EhVs from the English Channel, namely the removal/insertions of: a phosphate permease, an endonuclease, a transposase, and two specific tRNAs. As a whole, this study provided new clues and insights into the diversity and mechanisms driving the evolution of these large oceanic viruses, in particular those processes involving selfish genetic elements.
DOI: 10.6084/m9.figshare.28782383.v1
title: Supplementary Material for: Intratumoral Holmium-166 Microsphere Injection in Patients with Unresectable Pancreatic Ductal Adenocarcinoma: a Single-Center, Single-Arm, Open-Label Feasibility and Safety Study

description: Introduction
Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis and lacks local treatment options. This study aimed to assess the feasibility and safety of the first-in-human intraoperative ultrasound-guided intratumoral injection of radioactive holmium-166 microsphere in patients with PDAC.
Methods
Patients with proven PDAC eligible for open surgical resection were included. If resection was abandoned during exploration, study intervention was performed. Feasibility was defined by injection success and on/off-target radiation. Safety was based on adverse event (AE) monitoring for 12 weeks categorized by severity grade and study attribution.
Results
Three of the thirteen included patients received study intervention. Injection was successful in all three patients. Mean tumor doses of 5.0, 17.0 and 39.0 Gy and maximum tumor doses of 25.0, 41.0 and 256.0 Gy were achieved. Off-target radiation was found once in the lungs and once in the colon with a mean dose &lt;1.0 Gy. There were no AEs with high study attribution, 16, 14 and 19 AEs with low study attribution, including 3, 2 and 4 AEs with grade ≥3. Holmium-166 microspheres appeared hyperdense on CT.
Conclusion
Intratumoral injection of holmium-166 microspheres in patients with unresectable PDAC seems feasible and safe. Research into minimally invasive image-guided application is advised.
DOI: 10.6084/m9.figshare.28785353.v1
title: Table 2.1

description: Top countries in the world by Corruption Perception Index
DOI: 10.6084/m9.figshare.8550914.v1
title: Non-typhoidal Salmonella bloodstream infections: surveillance in DR Congo 2007-2017

description: This dataset contains the data on non-typhoidal Salmonella bloodstream infections collected during a blood culture surveillance project in the Democratic Republic of the Congo from 2007-2017. <br>The report "Increase in non-typhoidal <i>Salmonella </i>bloodstream infections in the Democratic Republic of the Congo (2015-2017): emergence of O5-negative <i>Salmonella</i> Typhimurium and alarming rates of resistance" was based on the data available in this dataset.
DOI: 10.6084/m9.figshare.12593225.v1
title: Supplementary Material for: The Prospective Studies of Atherosclerosis (Proof-ATHERO) Consortium: Design and Rationale

description: Atherosclerosis – the pathophysiological mechanism shared by most cardiovascular diseases – can be directly or indirectly assessed by a variety of clinical tests including measurement of carotid intima-media thickness, carotid plaque, ­ankle-brachial index, pulse wave velocity, and coronary ­artery calcium. The Prospective Studies of Atherosclerosis ­(Proof-ATHERO) consortium (https://clinicalepi.i-med.ac.at/research/proof-athero/) collates de-identified individual-participant data of studies with information on atherosclerosis measures, risk factors for cardiovascular disease, and incidence of cardiovascular diseases. It currently comprises 74 studies that involve 106,846 participants from 25 countries and over 40 cities. In summary, 21 studies recruited participants from the general population (<i>n</i> = 67,784), 16 from high-risk populations (<i>n</i> = 22,677), and 37 as part of clinical trials (<i>n</i> = 16,385). Baseline years of contributing studies range from April 1980 to July 2014; the latest follow-up was until June 2019. Mean age at baseline was 59 years (standard deviation: 10) and 50% were female. Over a total of 830,619 person-years of follow-up, 17,270 incident cardiovascular events (including coronary heart disease and stroke) and 13,270 deaths were recorded, corresponding to cumulative incidences of 2.1% and 1.6% per annum, respectively. The consortium is coordinated by the Clinical Epidemiology Team at the Medical University of Innsbruck, Austria. Contributing studies undergo a detailed data cleaning and harmonisation procedure before being incorporated in the Proof-ATHERO central database. Statistical analyses are being conducted according to pre-defined analysis plans and use established methods for individual-participant data meta-analysis. Capitalising on its large sample size, the multi-institutional collaborative Proof-ATHERO consortium aims to better characterise, understand, and predict the development of atherosclerosis and its clinical consequences.
DOI: 10.6084/m9.figshare.27013139.v1
title: Longitudinal Analysis of Tear Cytokine Ratios in Association with Dry Eye Signs and Symptoms in the Dry Eye Assessment and Management (DREAM) Study

description: To extend cross-sectional data on cytokine ratios (CRs) in dry eye disease (DED) signs by investigating longitudinal change in pro- to anti-inflammatory CRs and associations with change in DED signs and symptoms. Secondary analysis of fifty-four subjects [mean age 57.3 (SD 13.2) years, 85.2% female; 68.5% white] with ≥ 4 uL pooled tear volumes at months 0, 6, and 12. Pro-inflammatory (IL-1b, IL-6, IL-8, IL-17A, IFN-g, and TNF-a) to anti-inflammatory (IL-6, IL-10) cytokine ratios (CR) were calculated. DED signs (corneal and conjunctival staining scores, tear break-up time, Schirmer test, Meibomian gland plugging, tear osmolarity, composite sign severity score) and symptoms [Ocular Surface Disease Index (OSDI)] were measured. Changes over time in DED signs, symptoms, and CRs were evaluated using longitudinal models. Correlations between changes in CR and changes in DED signs and symptoms were evaluated using Spearman correlation coefficients (rho). DED signs which improved over time (<i>p</i> &lt; 0.001) included corneal and conjunctival staining score, tear break-up time, tear osmolarity, and composite sign severity score. Using IL-10 as anti-inflammatory, changes in corneal and conjunctival staining and composite severity score significantly correlated with changes in pro- to anti-inflammatory CRs from month 0 to 6 (|rho|: 0.29-0.45, <i>p</i>: 0.003-0.04) but not between month 0 to 12 (|rho|: 0.01 to 0.24, all <i>p</i> &gt; 0.08). DED symptoms decreased across one year (<i>p</i> &lt; = 0.001) for all OSDI measures; these changes did not correlate with changes in CRs (|rho|: 0.00 to 0.29, all <i>p</i> &gt; 0.04). Improvement in some DED signs across one year correlated weakly with decreases in pro- to anti-inflammatory CRs, in alignment with the understanding of DED as inflammatory. CRs may provide greater insight than absolute tear cytokine concentrations as possible DED biomarkers. Additional studies that provide standardized clinical information and tear collection and analysis are needed to validate CRs in DED.
DOI: 10.6084/m9.figshare.14601417.v1
title: Martin et al (2021) Journal of Insect Conservation.xlsx

description: Raw data that was analysed in Martin et al. (2021) "The potential for parasite spill-back from commercial bumblebee colonies: a neglected threat to wild bees?" published in the Journal of Insect Conservation.<br>This spreadsheet presents parasite data from the bumblebee colonies placed in the everbearer strawberry crop.
DOI: 10.6084/m9.figshare.28738010.v1
title: image-shenyang(2).7z

description: Shenyang Image
DOI: 10.15468/dl.vp7jye
title: Occurrence Download

description: A dataset containing 1891 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 Phosphuga atrata (Linnaeus, 1758)"
 ]
}

 The dataset includes 1891 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009472-250426092105405/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.9896246.v1
title: HLPa3_2.fq.gz

description: The sequence of bacteria in 0-10 cm plantation soil in Hulunbuir Sandy Land
DOI: 10.25381/cput.24324049.v1
title: IMPACT OF MALL DESIGN ON CUSTOMER EXPERIENCE: THE CASE OF KHAYELITSHA MALL

description: Ethics Reference Number:FBMSREC049<br><br>Dataset for the Masters of Business Administration in Project Management Research Topic: IMPACT OF MALL DESIGN ON CUSTOMER EXPERIENCE: THE CASE OF KHAYELITSHA MALL
DOI: 10.6084/m9.figshare.28475837.v1
title: Supplementary Data CAL 3

description: To isolate endophytic fungi from Centella asiatica and evaluate its biological potential.
DOI: 10.6084/m9.figshare.5720023.v1
title: Survival outcome among patients with Ewing’s sarcoma of bones and joints: a population-based cohort study

description: ABSTRACT BACKGROUND: The aim here was to elucidate the current survival condition of patients diagnosed with Ewing’s sarcoma of the bones and joints and determine independent risk factors associated with the prognosis. DESIGN AND SETTING: Retrospective cohort study based on the Surveillance, Epidemiology and End Results (SEER) database in the United States. METHODS: We identified 397 patients who were diagnosed with Ewing’s sarcoma of the bones and joints between January 2004 and December 2013. The multivariate Cox proportional hazards model was used to determine factors associated with the risk of death by adjusting for various factors. RESULTS: The one, two and five-year disease-specific survival rates were 89.08%, 78.08% and 62.47%, respectively. The factors related to death were age (≥ 18 years versus &lt; 18 years; hazard ratio, HR = 1.77; 95% confidence interval, CI: 1.38-2.31); tumor site (extremity versus spine and pelvis; HR = 2.03; 95% CI: 1.31-2.62); tumor size (&gt; 10 cm versus ≤ 10 cm; HR = 1.78; 95% CI: 1.34-2.56); and type of treatment (surgery alone versus radiotherapy with surgery; HR = 0.51; 95% CI: 0.38-0.89; or radiotherapy alone versus radiotherapy with surgery; HR = 1.61; 95% CI: 1.10-2.39; or no treatment versus radiotherapy with surgery; HR = 1.86; 95% CI: 1.23, 2.58). CONCLUSIONS: Patients with Ewing’s sarcoma showed poor survival in situations of age ≥ 18 years, tumor size &gt; 10 cm, receiving radiotherapy alone and receiving no treatment. Patients undergoing surgery alone had better survival.
DOI: 10.6084/m9.figshare.22611520.v1
title: Additional file 11 of Trends and influence factors in the prevalence, intervention, and control of metabolic syndrome among US adults, 1999–2018

description: Additional file 11. sTable 10 Change in distribution of characteristics among elevated blood glucose from 1999 to 2018.
DOI: 10.6084/m9.figshare.897972.v1
title: Crossmark Processing slides

description: Slide set from 2013 member meeting for technical presentation of Crossmark deposit handling.
DOI: 10.6084/m9.figshare.12382610.v1
title: TV2 Regionerne News Corpus

description: A corpus of about 50000 news articles in Danish, with full metadata, published on TV2 Regionerne between 2010 and 2020. Stored as multiple JSON files, one per article.<br>Licensed CC-BY. You must reference this Figshare entry if you use this data:<br>Leon Derczynski and Claus Ladefoged, "TV2 Regionerne News Corpus" (2020). doi:10.6084/m9.figshare.12382610 <br><br>See articles/README.md, articles/LICENSE.md and articles/DATASTATEMENT.md.<br>
DOI: 10.6084/m9.figshare.20153648.v1
title: IHC staining

description: IHC staining of DHA
DOI: 10.6084/m9.figshare.6856262.v4
title: Average Monthly Precipitation for Boulder, CO (.csv)

description: These data are used in the Earth Analytics Bootcamp Day 4 Lesson on Pandas Dataframes. These data were originally downloaded from the National Oceanic and Atmospheric Administration (NOAA).