cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24346705.v1
title: Leaf morphological database of <i>Quercus aliena</i> and <i>Quercus dentata</i>

description: Leaf morphological data for all samples of <i>Quercus aliena</i> and <i>Quercus dentata</i> data produced by Image J program in TXT format (2328 leaves in total).
DOI: 10.6084/m9.figshare.27095080.v1
title: Flexural strength ceramics data.xlsx

description: The study aimed to evaluate the effect of thermocycling on flexural strength of dental CAD/CAM ceramics of variable thicknesses and structures: An in Vitro Study
DOI: 10.6084/m9.figshare.19721806.v1
title: behavioral data.xlsx

description: 3-year-old children's delay of gratification behavioral data
DOI: 10.6084/m9.figshare.28030838.v1
title: Additional datasets for the effects of nitrogen deposition and biochar application on soil methane uptakes in a subtropical forest

description: We undertook a three-year field trial in a subtropical forest to investigate the impacts of N deposition and biochar application (individually and in combination) on soil methane uptakes. Our objective was to unravel the physicochemical and microbial mechanisms by which biochar mitigates the suppressive effects of nitrogen deposition on soil methane uptakes.
DOI: 10.6084/m9.figshare.14999487.v4
title: Data set repositories

description: 5. Training_TCGA_203samples.txt There are 15 files in this data repository. The descriptions for each file are as follows: 1. tcga_tumor.exp.txt The processed TCGA-CESC RNA-Seq data, which was normalized as fragments per kilobase of transcript per million mapped reads (FPKM) and then log2-transformed. 2.CGCI.tumor.exp.tsv The processed CGCI-HTMCP-CC RNA-Seq data, which was normalized as fragments per kilobase of transcript per million mapped reads (FPKM) and then log2-transformed. 3. GSE72723_GPL6884_data.txt The gene expression data in GSE72723, which was downloaded using R library ‘GEOquery’ and annotated according to GPL6884 platform.<br> 4. GSE72723_GPL10558_data.txt The gene expression data in GSE72723, which was downloaded using R library ‘GEOquery’ and annotated according to GPL10558 platform.<br> This is the training dataset for developing ccHPS model using 70% of TCGA-CESC cohort samples. 6. Test1_TCGA_86samples.txt This is the first validation dataset of ccHPS model using the rest of 30% of TCGA-CESC cohort samples.<br> 7. Test2_CGCI-HTMCP-CC_117samples.txt This is an independent validation dataset using CGCI-HTMCP-CC cohort samples. 8. ccHPS_score_GPL10558.tsv ccHPS score calculated for each sample in GSE72723 with array platform GPL10558. 9. ccHPS_score_GPL6884.tsv ccHPS score calculated for each sample in GSE72723 with array platform GPL6884.<br> 10.ccHPS_score_TCGA.tsv ccHPS score calculated for TCGA samples. 11.ccHPS_score_CGCI-HTMCP-CC.txt ccHPS score calculated for CGCI-HTMCP-CC samples. 12. ccHPS score for cervical cancer cell lines.txt ccHPS score calculated for eight cervical cancer cell lines treated in hypoxic and normoxic conditions. 13.Differential_gene_analysis_rank_between_high_low_risk.txt The different gene analysis result using 'limma' package between high-risk and low-risk samples. 14.ESTIMATEscore.txt The ESTIMATE score for each TCGA-CESC sample. 15. tcga.drug_sensitivity_predicted_allSolidTumor.txt<br> Drug estimated IC50 of each sample. 16.scripts.zip This zip folder includes four R scripts used in data analysis (calculate_CIBERSORT.R, calculate_MCPcounter.R, GSEA analysis.R and ccHPS.R)
DOI: 10.6084/m9.figshare.9423230.v1
title: De novo assembly, structural and functional annotation of the genome of Monilinia fructicola Mfrc123 strain

description: The draft genome assembly of Monilinia fructicola Mfrc123 strain was obtained using a hybrid assembly strategy with both Illumina short reads and PacBio long reads sequencing technologies. Structural genome annotation including gene, mRNA and CDS predictions, repetitive elements coordinates and masked genomic sequences, as well as functional annotation of the predicted proteins are provided.
DOI: 10.6084/m9.figshare.28188848.v1
title: Datasets-Concentrations of VOCs at Tibet Plateau

description: regional air quality and chimate
DOI: 10.6084/m9.figshare.23904300.v1
title: Access restricted data description

description: A data description for access restricted data stored on the EGA. We provide:A copy of the Data Access Agreement (DAA) that must be agreed and signed by the requesting user, and sent to the Data Access Committee (DAC: https://ega-archive.org/dacs/EGAC00001003048). This DAA is a standard Data Access Agreement provided by the EGA: https://ega-archive.org/files/EU-STANDS4PM_hDAA_v1.0.docxA description of all the data columns in our dataset (https://ega-archive.org/datasets/EGAD00001009890)To access the data on the EGA, fill in the hDAA provided here, and send it to the DAC (https://ega-archive.org/dacs/EGAC00001003048). The DAC meets every two months to discuss and process all data access requests,
DOI: 10.15468/dl.y9hnmc
title: Occurrence Download

description: A dataset containing 2496 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 Podabrus alpinus (Paykull, 1798)"
 ]
}

 The dataset includes 2496 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009667-250426092105405/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.24131640.v1
title: Supplementary Material for: Cytokine, anti-SARS-CoV-2 antibody and neutralizing antibody levels in conventional blood donors who have recovered from COVID-19

description: Background: At the beginning of the pandemic, COVID-19 convalescent plasma (CCP) containing anti-SARS-CoV-2 antibodies was suggested as a source of therapy. In the last three years, many trials have demonstrated the limited usefulness of CCP therapy. This led us to the hypothesis that CCP could contain other elements, along with the desired neutralizing antibodies, which could potentially prevent it from having a therapeutic effect, among them cytokines, chemokines, growth factors, clotting factors, and autoantibodies. Methods: In total, 39 cytokines were analyzed in the plasma of 190 blood donors, and further research focused on the levels of 23 different cytokines in CCP (sCD40L, eotaxin, FGF-2, FLT-3L, Fractalkine, GRO-α, IFNα2, IL-1β, IL-1RA, IL-5, IL-6, IL-8, IL-12, IL-13, IL-15, IL-17E, IP 10, MCP-1, MIP-1b, PDGF-AA, TGFα, TNFα, and TRAIL). Anti-SARS-CoV-2 antibodies and neutralizing antibodies were detected in CCP. Results: We found no significant differences between CCP taken within a maximum of 180 days from the onset of the first COVID-19 symptoms and the controls. We also made a comparison of the cytokine levels between the low neutralizing antibodies (&lt;160) group and the high neutralizing antibodies (≥160) group and found there were no differences between the groups. Our research also showed no correlation either to levels of anti-SARS-CoV-2 IgG Ab or to the levels of neutralizing antibodies. There were also no significant changes in cytokine levels based on the period after the start of COVID-19 symptoms. Conclusions: No elements which could potentially be responsible for preventing CCP from having a therapeutic effect were found.
DOI: 10.6084/m9.figshare.24226003.v1
title: Supplementary Material for: Serial quality of life assessment around screening for familial intracranial aneurysms: a prospective cohort study

description: Introduction: Screening for intracranial aneurysms (IAs) is cost-effective in first-degree relatives of aneurysmal subarachnoid haemorrhage (aSAH) patients, but its psychosocial impact is largely unknown. Patients and methods: A consecutive series of persons aged 20–70 years visiting the University Medical Centre Utrecht for first screening for familial IA was approached between 2017–2020. E-questionnaires were administered at six time points, consisting of the EQ-5D for health-related quality of life (QoL), HADS for emotional functioning and USER-P for social participation. QoL outcomes were compared with the general population, and between participants with a positive and negative screening for IA. Predictors of QoL outcomes were assessed with linear mixed effects models. Results: 105 participants from 75 families were included; in 10 (10%) an IA was found. During the first year after screening we found no negative effect on QoL, except for a temporary decrease in QoL six months after screening in participants with a positive screen (EQ-5D -11.3 [95%CI:-21.7 to -0.8]). Factors associated with worse QoL were psychiatric disease (EQ-5D -10.3 [95%CI:-15.1 to -5.6]), physical complaints affecting mood (EQ-5D -8.1 [95%CI:-11.7 to -4.4]), and a passive coping style (EQ-5D decrease per point increase on the Utrecht Coping List -1.1 [95%CI:-1.5 to -0.6]). Discussion and conclusion: We did not find a lasting negative effect on QoL during the first year after screening for familial IA. Predictors for a worse QoL were psychiatric disease, physical complaints affecting mood, and a passive coping style. This information can be used in counselling about familial IA screening.
DOI: 10.6084/m9.figshare.16438467.v1
title: Data.zip

description: Data needed for the analysis and figure preparation for manuscript "Paralog Knockout Profiling Reveals DUSP4/6 as a Digenic Dependence in MAPK-Pathway Driven Cancers".
DOI: 10.6084/m9.figshare.20137649.v2
title: Salt marsh radiocarbon and loss on Ignition data

description: Measurements of radiocarbon and organic matter from core subsamples (Supplementary_Data.xlsx). Radiocarbon data and calibration results are presented in the Radiocarbon data tab and source data used for deriving carbon % are presented on the Subsample carbon data tab. Core locations and other site information are presented in Table_1.docx
DOI: 10.6084/m9.figshare.9913085.v1
title: Incremental validity of dispositional mindfulness over and above the Big Five

description: Data set of on the incremental validity of dispositional mindfulness over and abov the Big Five in accounting for mental health.
DOI: 10.6084/m9.figshare.28792241.v1
title: Data of Comparison of the Effects of Transcranial Direct Current Stimulation Combined with Different Rehabilitation Interventions on Motor Function in People Suffering from Stroke-related Symptoms: A Systematic Review and Network Meta-Analysis

description: Contains the data and code used in the article
DOI: 10.6084/m9.figshare.6859784.v1
title: Supplementary Material for: Restating the Case for a Sharp Population Decline in <b><i>Lemur catta</i></b>

description: As with many other species in the primate order, ring-tailed lemurs <i>(Lemur catta)</i> are threatened with extinction. Our articles documented declines in wild ring-tailed lemur populations and noted that fewer than 2,500 wild ring-tailed lemurs are known to persist in 32 [Gould and Sauther: <i>Primate Conservation</i> 2016; 30: 89–101] and 34 [LaFleur et al.: <i>Folia Primatologica</i> 2017; 87: 320–330] sites. A criticism of our articles [Murphy et al.: <i>International Journal of Primatology</i> 2017; 38: 623–628] suggested that we have inadequately sampled ring-tailed lemur populations and habitats, and misused the literature. We disagree, and provide both a detailed rebuttal and responses to specific critique points herein. Moreover, we restate our case outlining a dramatic decline of ring-tailed lemurs resulting from anthropogenic pressures (deforestation, severe habitat fragmentation, extraction for the pet and bushmeat trades). We pose several thought-provoking questions as to when is the appropriate time for researchers to “sound the alarm” about a species’ decline, and remain committed to understanding the drivers of unsustainable exploitation of this emblematic lemur, and preventing their extinction in the wild.
DOI: 10.6084/m9.figshare.16385280.v3
title: Data for draft genome sequence of the earthworm Eudrilus eugeniae

description: The dataset contains promoter information of <i>Eudrilus eugeniae</i> genome. Also it contains the software code and data used to create the earthworm genome resource web application at https://sudhakar-sivasubramaniam-labs.shinyapps.io/eudrilus_genome/
DOI: 10.6084/m9.figshare.27853776.v1
title: Supplementary Material for: ERNICA Evidence Based Guideline on Surgical Aspects of Necrotizing Enterocolitis in Premature Neonates

description: Background 
Necrotizing enterocolitis (NEC) is a severe intestinal condition primarily affecting preterm neonates. It has ahigh mortality rate, particularly in infants with a birth weight of below 1500 grams or for those requiring surgical intervention. The European Reference Network for Inherited and Congenital Anomalies (ERNICA) has developed a clinical practice guideline to aid clinical decision-making pertaining to the surgical treatment and management of NEC in preterm neonates. 
Summary 
This guideline was developed in accordance with the Guidelines 2.0 checklist and GRADE methodology. A multidisciplinary group of Europe’s top experts collaborated with patient representatives to develop this guideline. After selecting critical points in care for which recommendations are required, a systematic review of the literature and critical appraisal of the evidence was performed. The Evidence to Decision framework was used as a guide to structure the consensus meetings and draft the recommendations. The panel developed seven recommendations and three good-practice statements on the following topics: indications for surgery, peritoneal drainage, surgical technique, management of extensive NEC, enteral feeding and neurodevelopmental outcomes in premature neonates with NEC. The certainty of evidence was graded as (very) low for most recommendations. However, the panel weighed up the benefits and harms in light of all relevant arguments and expert opinion. 
Key Messages
This guideline provides recommendations on caring for premature neonates with NEC. These recommendations can assist clinicians in their care decisions and can inform families on treatment options and relevant considerations. This guideline will be revised every five years to ensure it remains up to date.
DOI: 10.6084/m9.figshare.21781544.v1
title: Patient and public involvement in hearing research: opportunities, impact and reflections with case studies from the Manchester Centre for Audiology and Deafness

description: Patient and public involvement (PPI) in research improves relevance to end users and improves processes including recruitment participants. PPI in our research has gone from being non-existent to ubiquitous over a few years. We provide critical reflections on the benefits and challenges of PPI. Case studies are reported according to a modified GRIP2 framework; the aims, methodology, impact of PPI and critical reflections on each case and our experiences with PPI in general. We report five UK projects that included PPI from teenagers, families, people living with dementia, autistic people, and people from South Asian and d/Deaf communities. Our experience has progressed from understanding the rationale to grappling methodologies and integrating PPI in our research. PPI took place at all stages of research, although commonly involved input to design including recruitment and development of study materials. Methodologies varied between projects, including PPI co-investigators, advisory panels and online surveys. On-going challenges include addressing social exclusion from research for people that lack digital access following increasing on-line PPI and involvement from underserved communities. PPI was initially motivated by funders; however the benefits have driven widespread PPI, ensuring our research is relevant to people living with hearing loss.
DOI: 10.6084/m9.figshare.25469971.v1
title: Supplementary material for Chapter 2

description: This dataset contains the metadata for the species molecular phylogeny used for the macroevolutionary study in the second chapter of my thesis. More specifically, it provides information on how the species in my morphological dataset were associated with the phylogeny from Thornhill et al. (2019).
DOI: 10.6084/m9.figshare.25661784.v1
title: Dharmawan et al. (2024) Vegetation dynamics. LAND

description: The Dynamics of Vegetation Structure-Composition and Carbon Stock Potency at Peatland Ecosystem of Old Secondary Forest in Riau and South Sumatra Provinces (Research Article). LAND
DOI: 10.6084/m9.figshare.1408718.v1
title: oct -data

description: oct -data
DOI: 10.6084/m9.figshare.12479090.v1
title: Suppl Table 1.xlsx

description: Signals that were both polymorphic and had statistical significance in the replication sample.
DOI: 10.6084/m9.figshare.3184534.v2
title: Metadata and Data for https://doi.org/10.1002/lol2.10026

description: <b>Citation:</b>Hogle SL, Bundy RM, Blanton JM, Allen EE, Barbeau KA. Copiotrophic marine bacteria are associated with strong iron-binding ligand production during phytoplankton blooms. Limnol Oceanogr Lett. 2016 Oct 7. http://dx.doi.org/10.1002/lol2.10026<br><b>Description:<br></b>This project investigated the production of different classes of iron-binding ligands, iron concentrations, macronutrient concentrations, and phytoplankton and bacterioplankton assemblage composition in iron amended microcosm incubations conducted in oligotrophic waters collected off the Southern California Bight.
DOI: 10.6084/m9.figshare.7102301.v1
title: Frequency of ocular diseases among recipients of disability benefits in the metropolitan region of Recife, Brazil

description: ABSTRACT Purpose: To identify the frequency of ocular diseases among recipients of disability benefits in the metropolitan region of Recife, Brazil. Methods: A review was performed of 217,221 cases of disability benefits granted between 2010 and 2015 by the executive managerial department of the Brazilian National Institute of Social Security (Instituto Nacional do Seguro Social [INSS]) in Recife, which encompasses 14 municipalities of the metropolitan region, including the capital. The frequencies of the identified cases of ocular morbidity were then determined according to their group in the International Classification of Diseases, 10th Revision (ICD-10), their cause, the age, sex, and income of the recipient, and the type and duration of the benefit. Results: Of all disability benefits granted, 5,324 (2.5%) were due to ocular disease, the majority (91.1%) consisting of sick pay. Most of the beneficiaries (64.6%) were males, were 20 to 59 years of age, and 61.2% earned the minimum wage or less. The principal ocular diseases for which sick pay benefits were granted were cataract (24.5%), conjunctivitis (21.1%), and pterygium (8.8%). Blindness and low vision were the principal ocular diseases in cases of accident indemnity and disability retirement. Conclusions: The results highlight the magnitude of the problem of ocular diseases to the social security system, with serious economic and social losses, and emphasize the need for measures aimed at their prevention. Moreover, integration between the national departments of health and social security needs to be improved.
DOI: 10.6084/m9.figshare.21976526.v1
title: Chia genome assembly and annotation

description: Chia genome assembly and annotation
DOI: 10.6084/m9.figshare.19779709.v1
title: Input_PyRate

description: Input data to run PyRate analyses
DOI: 10.48420/18776093.v1
title: Avoidance of Single Gamma Source in Simulation

description: Simulation results from a Jackal UGV commanded to navigate over a point gamma radiation source. The UGV and gamma source were in an open simulated environment, therefore able to take any diversion the path planner generated.<br>The robot has three possible states of knowledge of the radiation field: no information, known knowledge, or unknown knowledge. These three states are labelled as "no_avoidance", "known" and "unknown" respectively.<br>In the no avoidance scenario, the robot is not made aware of any radiation information. In the known environment, the robot is driven manually around the environment to build up a map of the radiation field, before being asked to perform navigation tasks. In the unknown case, the robot has no prior knowledge, but can react to new radiation information as it completes a navigation task.<br>By adjusting the upper thresholds of cost associated with radiation risk, the robot is more or less cautious (there is lower or higher cost associated with navigating through regions of increased radiation dose rate).<br>When the robot is aware of the radiation field, its accummulated dose is reduced, at the expense of greater time required to complete the task. Reduction in dose is readily an order of magnitude compared to the no_avoidance case.<br>Data is in comma separated format, with header. Header format is: time (s), x (m), y(m), z (m), value (arb units). Value represents radiation intensity.<br>
DOI: 10.6084/m9.figshare.20301120.v1
title: Supplementary Material for: Sulfatase-2 from cancer associated fibroblasts – an environmental target for hepatocellular carcinoma?

description: Introduction: Heparin sulfate proteoglycans in the liver tumour microenvironment (TME) are key regulators of cell signaling, modulated by Sulfatase-2 (SULF2). SULF2 overexpression occurs in hepatocellular carcinoma (HCC). Our aims were to define the nature and impact of SULF2 in the HCC TME. Methods: In liver biopsies from 60 patients with HCC, expression and localisation of SULF2 was analysed associated with clinical parameters and outcome. Functional and mechanistic impacts were assessed with immunohistochemistry (IHC), in silico using The Cancer Genome Atlas (TGCA), in primary isolated cancer activated fibroblasts, in monocultures, in 3D spheroids and in an independent cohort of 20 patients referred for sorafenib. IHC targets included αSMA, glypican-3, β-catenin, RelA-P-ser536, CD4, CD8, CD66b, CD45, CD68 and CD163. SULF2 impact of peripheral blood mononuclear cells was assessed by migration assays, with characterization of immune cells phenotype using fluorescent activated cell sorting. Results: We report that while SULF2 was expressed in tumour cells in 15% (9/60) of cases, associated with advanced tumour stage and type-2-diabetes, SULF2 was more commonly expressed in cancer associated fibroblasts (CAFs)(52%) and independently associated with shorter survival (7.2 versus 29.2 months, p=0.003). Stromal SULF2 modulated glypican-3/β-catenin signalling in-vitro, although in vivo associations suggested additional mechanisms underlying the CAF-SULF2 impact on prognosis. Stromal SULF2 was released by CAFS isolated from human HCC. It was induced by TGFβ1, promoted HCC proliferation and sorafenib resistance, with CAF-SULF2 linked to TGFβ1 and immune exhaustion in TGCA HCC patients. Autocrine activation of PDGFRβ/STAT3 signalling was evident in stromal cells, with release of the potent monocyte/macrophage chemoattractant CCL2 in vitro. In Human PBMCs, SULF2 preferentially induced migration of macrophage precursors (monocytes), inducing a phenotypic chance consistent with immune exhaustion. In human HCC tissues, CAF-SULF2 was associated with increased macrophage recruitment, with tumouroid studies showing stromal-derived SULF2 induced paracrine activation of the IKKβ/NF-κB pathway, tumour cell proliferation, invasion and sorafenib resistance. Conclusion: SULF2 derived from CAFs modulates glypican-3/β-catenin signalling, but also the HCC immune TME, associated with tumour progression and therapy resistance via activation of the TAK1/IKKβ/NF-κB pathway. It is an attractive target for combination therapies for patients with HCC.