cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5129206.v1
title: Supplementary Material for: Comparison of HER2 Expression in Primary Tumor and Disseminated Tumor Cells in the Bone Marrow of Breast Cancer Patients

description: <b><i>Objective:</i></b> The aim of this study was to measure the human epidermal growth factor receptor 2 (HER2) status of disseminated tumor cells (DTCs) from bone marrow (BM) aspirates and to assess correspondence or discrepancy with the primary tumor. <b><i>Methods:</i></b> DTCs were isolated from the BM of 156 breast cancer patients. Cytokeratin-positive DTCs were further analyzed by the chromogenic in situ hybridization method to detect HER2 gene amplification. <b><i>Results:</i></b> A significant correlation (p = 0.021) was found between the HER2 status of DTCs and the primary tumors. Sixty-one (68.5%) patients had a corresponding status. However, a shift of phenotype between primary tumor and DTCs was found in the remaining patients. <b><i>Conclusion:</i></b> This study showed a significant grade of discordance of the HER2 status between primary tumors and DTCs in the BM of a relevant subgroup of patients. Detection of HER2 amplification on DTCs could therefore help to better stratify patients for a more tailored therapy, since they would benefit from a HER2-targeted therapy.
DOI: 10.17632/zf4jm6tg7y
title: PRISMA for Decoding the Efficacy and Safety Profiles of Antihypertensive Agents by Targeting RAAS: A Systematic Review and Meta-Analysis of Clinical Trials

description: This is PRISMA for Decoding the Efficacy and Safety Profiles of Antihypertensive Agents by Targeting RAAS: A Systematic Review and Meta-Analysis of Clinical Trials
DOI: 10.6084/m9.figshare.22332223.v2
title: HCC01 and HCC03 Stereo-seq Data

description: We profiled two HCC tumor tissues (HCC01 and HCC03) using a new DNA nanoball (DNB)-based spatial transcriptomics technology named Stereo-seq, and segmented the data into 100 * 100 DNB bins (bin 100 resolution, ~50μm diameter). After basic quality control and filtering, we retrieved transcriptomic information from 36,776 and 23,941 bins from HCC01 and HCC03 tumors respectively, with ~4,000 genes and ~14,500 unique molecular identifiers (UMIs) per bin.
DOI: 10.6084/m9.figshare.24523273.v1
title: Supplementary Material for: Non-familial Bilateral Synchronous Renal Cell Carcinoma with Discordant Histology with Eventual Complete Response to Dual Immunotherapy

description: Bilateral synchronous renal cell carcinoma (RCC) is rare, especially in sporadic rather than familial cases. While immunotherapy has improved prognosis, RCC remains a diagnosis with significant morbidity and mortality, particularly pronounced in patients with sarcomatoid RCC (sRCC). We describe a case of a patient with bilateral, synchronous, non-familial RCC, with and without sarcomatoid features and differing genetic markers, who demonstrated a pathologic response after neoadjuvant nivolumab and ipilimumab. The patient then had radical left nephrectomy and partial right nephrectomy followed by adjuvant nivolumab and cabozantinib, after which the patient had no evidence of disease. Our patient’s illustrative case shows the potential therapeutic value of immunotherapy even in sRCC, the disease’s most aggressive clinical subtype.
DOI: 10.6084/m9.figshare.24565030.v1
title: Supplementary Material for: Percutaneous endoscopic sigmoidopexy – still a way to go

description: An abstract is not required.
DOI: 10.6084/m9.figshare.24721608.v1
title: Inclusion of Salicornia ramosissima biomass in diets for juvenile whiteleg shrimp (Penaeus vannamei) induces favourable but transient effects in the immune and oxidative status

description: Inclusion of Salicornia ramosissima biomass in diets for juvenile whiteleg shrimp (Penaeus vannamei) induces favourable but transient effects in the immune and oxidative status
DOI: 10.6084/m9.figshare.28723247.v1
title: DATA - Activity patterns, feeding habits and water consumption in food in Verreaux’s sifakas (<i>Propithecus verreauxi</i>) and red-fronted lemurs (<i>Eulemur rufifrons</i>) during the transition between wet and dry season

description: In seasonal habitats, animals may have difficulties accessing enough food and water year-round because environmental factors change massively. In the dry forests of Madagascar, lemurs adapt their behavior and diet to cope with resource scarcity, but their water requirements remain poorly understood. This study compared the activity patterns, feeding habits, and water consumption in food of Verreaux’s sifakas (<i>Propithecus verreauxi</i>) and red-fronted lemurs (<i>Eulemur rufifrons</i>) in Kirindy Forest during the transition from the wet to the dry season. We hypothesized that both species would reduce their activity levels to conserve energy and water, adapt their diets to resource availability, and consume foods with higher water content. From March to May 2024, we recorded behavior and food preferences of 6 lemur groups and collected food item samples to analyze their water content. We found that <i>E. rufifrons</i> rested more and fed less than sifakas, but both species rested less when humidity was higher. Sifakas preferred leaves, while red-fronted lemurs fed more on fruits. The two species consumed food with a similar water content that was unaffected by seasonal transitions, and their diets remained consistent despite seasonal climatic variations. By exploring these behavioral adaptations, this research provides insight into how these lemur species cope with seasonal resource dynamics.
DOI: 10.4121/17878508.v1
title: Data underlying the research of Distributed assembly flexible job shop scheduling problem with flexible assembly

description: According to the numbers of product and processing factory, 35 sets of data are formed, which conform to the distributed assembly flexible job shop scheduling problem with flexible assembly. Among them, the number of processing factory ranges from 2 to 8, and the number of product ranges from 2 to 6, 6 to 10, 10 to 14, 14 to 18, 18 to 22, 22 to 26 and 26 to 30. In addition, the data in each sheet represents a scale. The basic unit of measurement for all data is "1".
DOI: 10.17632/5thy2mcwn7
title: Data for Alcohol use and burden for 195 countries and territories, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016

description: Data underlying figures and relative risk curves within the article. Provides readers the mean value and uncertainty intervals for prevalence of current drinking, drinks per day by location, relative risks by outcome and dose, along with results for the weighted all-cause relative risk curve used to justify TMREL within the study. Based off sources mentioned in Appendix I. From Abstract in linked paper: Background Alcohol use is a leading risk factor for death and disability, but its overall association with health remains complex given the possible protective effects of moderate alcohol consumption on some conditions. With our comprehensive approach to health accounting within the Global Burden of Diseases, Injuries, and Risk Factors Study 2016, we generated improved estimates of alcohol use and alcohol-attributable deaths and disability-adjusted life-years (DALYs) for 195 locations from 1990 to 2016, for both sexes and for 5-year age groups between the ages of 15 years and 95 years and older. Methods Using 694 data sources of individual and population-level alcohol consumption, along with 592 prospective and retrospective studies on the risk of alcohol use, we produced estimates of the prevalence of current drinking, abstention, the distribution of alcohol consumption among current drinkers in standard drinks daily (defined as 10 g of pure ethyl alcohol), and alcohol-attributable deaths and DALYs. We made several methodological improvements compared with previous estimates: first, we adjusted alcohol sales estimates to take into account tourist and unrecorded consumption; second, we did a new meta-analysis of relative risks for 23 health outcomes associated with alcohol use; and third, we developed a new method to quantify the level of alcohol consumption that minimises the overall risk to individual health
DOI: 10.6084/m9.figshare.1038764.v1
title: Mills, Goddings et al. 2014 Developmental Mismatch Original Figures and Tables

description: The original figures and tables for our project: The Developmental Mismatch in Structural Brain Maturation during Adolescence. CC BY-NC-SA
DOI: 10.6084/m9.figshare.28925930.v1
title: Pretrained Bootstrapped-Random Forest Tree (B-RFT) models for predicting gravimetric and volumetric hydrogen storage capacity in MOFs

description: This repository provides two pre‑trained machine‑learning models for rapid prediction of hydrogen storage capacities in metal–organic frameworks (MOFs). Both models were trained on 80% (78,956) of the curated global MOF dataset using bootstrap‑random forest techniques and are deployable in MATLAB.<b>Included Files:</b><code>UG_net_80_rand.mat</code>Predicts usable gravimetric capacity (wt. %)<code>UV_net_80_rand.mat</code>Predicts usable volumetric capacity (g H₂ L⁻¹)<b>Required Input Variables:</b>Single crystal density (g/cm³)Gravimetric surface area (m²/g)Volumetric surface area (m²/cm³)Void fractionPore volume (cm³/g)Large cavity diameter (Å)Pore limiting diameter (Å)Usage Example:% Load the pretrained modelUG= load('UG_net_80_rand.mat'); UV= load('UV_net_80_rand.mat');% Input variablesinp_val = [Single crystal density, Gravimetric surface area, Volumetric surface area, Void fraction, Pore volume, Large cavity diameter, Pore limiting diameter]% PredictionUG_pre=predict(UG.BaggedEnsemble,inp_val);UV_pre=predict(UV.BaggedEnsemble,inp_val);
DOI: 10.17632/tsfxgsp3z6
title: Plant disease dataset

description: A dataset for plant disease analysis
DOI: 10.6084/m9.figshare.12999101.v1
title: Small scale environmental variation modulates plant defence syndromes of understorey plants in deciduous forests of Europe

description: quantitative data on understorey plant traits that allocate to the overall physical and chemical resistance and tolerance to herbivores. Environmental data.
DOI: 10.6084/m9.figshare.14369891.v1
title: Rock the Boat SLR - Selection

description: Article selection for SLR on ICT Competency on Educators
DOI: 10.6084/m9.figshare.15038850.v1
title: VTMaxHerp: a data set of Voluntary Thermal Maximum temperatures of amphibians and reptiles from two Brazilian hotspots

description: Herein we provide a dataset of 312 individual voluntary thermal maximum (VT<sub>Max</sub>) values, the maximum temperature tolerated by individuals before actively moving to a colder place, for 53 species of amphibians and reptiles of the Atlantic Forest and Cerrado savannas of southeastern South America
DOI: 10.6084/m9.figshare.20055539.v3
title: Supplementary files: Global prevalence and potential influencing factors of COVID-19 vaccination hesitancy: a meta-analysis

description: Supplementary files: Global prevalence and potential influencing factors of COVID-19 vaccination hesitancy: a meta-analysis
DOI: 10.6084/m9.figshare.21378201.v1
title: Supplementary Material for: Modeling Low Muscle Mass Screening in Hemodialysis Patients

description: <b><i>Introduction:</i></b> Computed tomography (CT) can accurately measure muscle mass, which is necessary for diagnosing sarcopenia, even in dialysis patients. However, CT-based screening for such patients is challenging, especially considering the availability of equipment within dialysis facilities. We therefore aimed to develop a bedside prediction model for low muscle mass, defined by the psoas muscle mass index (PMI) from CT measurement. <b><i>Methods:</i></b> Hemodialysis patients (<i>n</i> = 619) who had undergone abdominal CT screening were divided into the development (<i>n</i> = 441) and validation (<i>n</i> = 178) groups. PMI was manually measured using abdominal CT images to diagnose low muscle mass by two independent investigators. The development group’s data were used to create a logistic regression model using 42 items extracted from clinical information as predictive variables; variables were selected using the stepwise method. External validity was examined using the validation group’s data, and the area under the curve (AUC), sensitivity, and specificity were calculated. <b><i>Results:</i></b> Of all subjects, 226 (37%) were diagnosed with low muscle mass using PMI. A predictive model for low muscle mass was calculated using ten variables: each grip strength, sex, height, dry weight, primary cause of end-stage renal disease, diastolic blood pressure at start of session, pre-dialysis potassium and albumin level, and dialysis water removal in a session. The development group’s adjusted AUC, sensitivity, and specificity were 0.81, 60%, and 87%, respectively. The validation group’s adjusted AUC, sensitivity, and specificity were 0.73, 64%, and 82%, respectively. <b><i>Discussion/Conclusion:</i></b> Our results facilitate skeletal muscle screening in hemodialysis patients, assisting in sarcopenia prophylaxis and intervention decisions.
DOI: 10.6084/m9.figshare.26965903.v2
title: <b>3D multimodal dental dataset based on CBCT and oral scan.​</b>

description: We collected CBCT and oral scan data from 300 patients aged 19-28 years and invited three doctors to aid in the creation of a multi-modal dental dataset. After thorough data screening and desensitization, we obtained 289 paired dental medical images. We believe that publicly releasing this dataset will provide researchers with valuable new resources to further advance the safeguarding of oral health globally.
DOI: 10.6084/m9.figshare.28916231.v1
title: Supplementary Table12 Gene List Solanum pennellii・Solanum arcanum Enrichment analysis.csv

description: Currently, domesticated species available on the market have been developed through the breeding of wild relatives. We collected gene expression data of domesticated species of rice, tomato, and soybean, along with their presumed ancestral species, and conducted a meta-analysis to investigate differentially expressed genes during domestication. In wild relatives, the expression of gene groups involved in osmotic, drought, and wound stress tolerance was upregulated. In contrast, in domesticated species, upregulated ex-pression was observed in gene groups related to auxin and those involved in the efflux of heavy metals and harmful substances. By identifying these genes with differential ex-pression levels, we can gain insights into how domestication has influenced changes in crop traits. In particular, breeding strategies that make use of wild relatives with high genetic diversity are attracting attention as an important approach for addressing climate change and ensuring a sustainable food supply. The findings obtained in this study are expected to contribute to the realization of rapid breeding and the development of new varieties capable of growing in harsh natural environments. To address this issue, a new cultivation method called "De novo domestication" has been proposed, which combines the genetic diversity of currently unused wild relatives and wild relatives with genome editing technologies that enable rapid breeding.
DOI: 10.6084/m9.figshare.3458918.v1
title: Supplementary Material for: A Novel Phytase Derived from an Acidic Peat-Soil Microbiome Showing High Stability under Acidic Plus Pepsin Conditions

description: Four novel phytases of the histidine acid phosphatase family were identified in two publicly available metagenomic datasets of an acidic peat-soil microbiome in northeastern Bavaria, Germany. These enzymes have low similarity to all the reported phytases. They were overexpressed in <i>Escherichia coli</i> and purified. Catalytic efficacy in simulated gastric fluid was measured and compared among the four candidates. The phytase named rPhyPt4 was selected for its high activity. It is the first phytase identified from unculturable Acidobacteria. The phytase showed a longer half-life than all the gastric-stable phytases that have been reported to date, suggesting a strong resistance to low pH and pepsin. A wide pH profile was observed between pH 1.5 and 5.0. At the optimum pH (2.5) the activity was 2,790 μmol/min/mg at the physiological temperature of 37°C and 3,989 μmol/min/mg at the optimum temperature of 60°C. Due to the competent activity level as well as the high gastric stability, the phytase could be a potential candidate for practical use in livestock and poultry feeding
DOI: 10.17632/kd3n5k784m
title: Collective ERK/Akt dynamics in epithelia

description: Experimental single-cell time series of ERK and Akt activity from fluorescent time lapse microscopy, and R/Python scripts required to reproduce the figures from the accompanying publication: Gagliardi et al. "Collective ERK/Akt activity waves orchestrate epithelial homeostasis by driving apoptosis-induced survival". Pre-print available from here: https://doi.org/10.1101/2020.06.11.145573
DOI: 10.6084/m9.figshare.14879700.v2
title: Menard_et_al_Afforestation_Quebec

description: This table contains the dataset of afforestation and reforestation on unproductive territories in Quebec (open woodlands, poorly regenerated burns and abandoned farmlands).
DOI: 10.6084/m9.figshare.20105186.v1
title: CarvingDetc Dataset

description: CarvingDetc dataset is a novel Balinese carving dataset for Balinese carving sub-motif detection.
DOI: 10.6084/m9.figshare.22348565.v2
title: Feature Screening with Conditional Rank Utility for Big-Data Classification

description: Feature screening is a commonly used strategy to eliminate irrelevant features in high-dimensional classification. When one encounters big datasets with both high dimensionality and huge sample size, the conventional screening methods become computationally costly or even infeasible. In this article, we introduce a novel screening utility, Conditional Rank Utility (CRU), and propose a distributed feature screening procedure for the big-data classification. The proposed CRU effectively quantifies the significance of a numerical feature on the categorical response. Since CRU is constructed based on the ratio of the mean conditional rank to the mean unconditional rank of a feature, it is robust against model misspecification and the presence of outliers. Structurally, CRU can be expressed as a simple function of a few component parameters, each of which can be distributively estimated using a natural unbiased estimator from the data segments. Under mild conditions, we show that the distributed estimator of CRU is fully efficient in terms of the probability convergence bound and the mean squared error rate; the corresponding distributed screening procedure enjoys the sure screening and ranking properties. The promising performances of the CRU-based screening are supported by extensive numerical examples. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.28854899.v1
title: Relative paleointensity data of IODP Site U1505

description: The RPI data of IDOP Site U1505 in depth and time domain.
DOI: 10.17632/yphm77tg24
title: Dataset - chemokines, cytokines, and biomarkers in the saliva of children with Sjögren’s syndrome

description: INTRODUCTION Sjögren’s syndrome can occur in children. While the concentrations of chemokines, cytokines, and biomarkers (CCBMs) are reported in the saliva of adults with Sjögren’s syndrome, this data is not known in the saliva of children with Sjögren’s syndrome. We hypothesized that CCBMs associated with lymphocyte and mononuclear cell functions were present in the saliva of children with Sjögren’s syndrome. This dataset is associated with 2 studies recently published by Gomez Hernandez et al. A distinguishing profile of chemokines, cytokines, and biomarkers in the saliva of children with Sjögren’s syndrome. Rheumatology (accepted January 17, 2021) and Hikkaduwa Withanage et al. Dataset - chemokines, cytokines, and biomarkers in the saliva of children with Sjögren’s syndrome. Data in Brief (submitted January 17, 2021). METHODS Saliva was collected from 11 children diagnosed with Sjögren’s syndrome and 16 normal healthy children. The presence and concentrations of 105 CCBMs (pg/ml) were determined using multiplex fluorescent microparticle-based immunoassays. CCBM concentrations were interpolated from their MFI values using five parameter logistic curves created from the standard concentrations and their respective MFI readings using xPonent v3.1 software (Luminex, Austin, TX) or using Milliplex Analyst v5.1 software (EMD Millipore, Billerica, MA). Occasionally, there were CCBM concentrations below the standard curve. These concentrations were extrapolated from their MFI values using curves created from zero concentration to the lowest standard concentration and their respective MFI readings. For example, CCL27 concentrations in saliva were below the standard curve. After extrapolation, the mean (standard error of the mean), minimum - maximum values were 4.6 (0.8), 1.7-9.7 pg/ml for children with Sjögrens syndrome and 2.6 (0.3), 0.6-5.8 pg/ml for normal healthy children. There were also CCBM concentrations above the standard curve. These concentrations were extrapolated from their MFI values using curves extended beyond the highest concentration and their respective MFI readings. For example, B2M concentrations in saliva were above the standard curve. After extrapolation, the mean (standard error of the mean), minimum - maximum values were 122,671.6 (14,485.0), 98,850.0-266,527.2 pg/ml for children with Sjögrens syndrome and 98,060.6 (6,038.4), 9,110.0-111,270.0 pg/ml for normal healthy children. RESULTS 43/105 of CCBMs were significantly different between these 2 groups and 71/105 CCBMs were not. The 43 CCBMs were associated with leukocyte chemotaxis, migration, proliferation, and regulation of T-cell activation. CONCLUSION This dataset is among the first to report the concentrations of CCMBs in the saliva of children with Sjögren’s syndrome. It will assist others in their work to understand the etiopathogenesis of Sjögren’s syndrome in children, and assist in the identification of early markers of disease in children.
DOI: 10.6084/m9.figshare.13564265.v1
title: A First-Generation Pediatric Cancer Dependency Map

description: These files accompany the publication "A First-Generation Pediatric Cancer Dependency Map" by Dharia et al (2021). <br>Specifically, the annotation of cancer cell lines as "pediatric solid or brain tumors" by the above manuscript was used to subset data from the DepMap 20Q1 release (https://figshare.com/articles/dataset/DepMap_20Q1_Public/11791698) for ease of access to these data.
DOI: 10.6084/m9.figshare.14113118.v1
title: Dataset for urban logistics stakeholders interview

description: The additional file to the paper "Stakeholders’ Analysis of Environmental Sustainability in Urban Logistics: A Case Study of Tricity, Poland" published in <i>Energies </i>journal
DOI: 10.6084/m9.figshare.27603876.v2
title: A comprehensive dataset on microbiome dynamics in rheumatoid arthritis from a large-scale cohort study

description: Alterations in intestinal microbiota have been identified as a key risk factor in rheumatoid arthritis (RA). In this study, we present a multidimensional gut microbiota profile from a large cohort of RA patients, stratified by disease stage and treatment regimens, and compared to healthy controls. Our dataset comprises gut microbiota profiles from 2,238 individuals, including 1,034 RA patients and 1,204 healthy controls. This dataset is enriched with detailed clinical metadata, including patient profiles, treatment histories, and environmental factors, providing a comprehensive "disease exposome" for RA. By integrating 16S rRNA gene sequencing with demographic, clinical, and environmental data, we offer a valuable resource to explore the complex relationships between gut microbiota and RA progression. This large-scale dataset is expected to be a foundation for collaborative research, advancing our understanding of the microbiome's systemic effects in RA and other autoimmune diseases, and potentially guiding new therapeutic approaches.