cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5455000.v1
title: Jump performance - Influence of platinum harmonized textile on neuromuscular, systemic and subjective recovery.xlsx

description: Jump performance data. Counter-movement and Drop Jump data
DOI: 10.6084/m9.figshare.19750627.v3
title: A replication study of the ORBS language-agnostic dynamic analysis

description: A comparative study of existing cross-language dynamic analysis techniques (ORBS) <br> ORBS 10 projects done. Mongo Deap Pyrasite Pyjnius Pysonar2 Affinity Vertx Snappy sbe brotli <br> <br> <br> - How to run ORBS 1. Configuration Configure the ORBS using the five script files located at ./projects/project name&gt;/config/ <br> 2. Running sudo bash ./projects//timeout.sh This script will automatically run the ORBS; stop running ORBS once running for over 24 hours. <br> - Organization ./orbs/ ORBS main code ./projects/ 10 projects and their slicing results. ./OBRS-results-updated.xlsx ORBS running results. ./Repository_List.csv 40001 projects collected from the GitHub.
DOI: 10.6084/m9.figshare.28554056.v1
title: Spatiotemporal distribution and molecular characteristics of porcine diarrhea-associated viruses detected in Chinese pigs.xlsx

description: Recent large-scale outbreaks of diarrhea in pigs in China have been attributed to viral pathogens. The most frequently detected viruses in affected pigs include Porcine Epidemic Diarrhea Virus (PEDV), Porcine Rotavirus (PoRV), Transmissible Gastroenteritis Virus (TGEV), and Porcine Deltacoronavirus (PDCoV). To investigate the primary viral causes of diarrhea, we collected 1,328 fecal samples from 84 pig farms across 20 provinces. PEDV showed the highest positivity rate at 50.90% (684/1,328), with a positive farm rate of 66.67% (54/84). PoRVA had a positive rate of 33.80% (454/1,328) and a positive farm rate of 40.48% (34/84). TGEV and PDCoV exhibited lower positivity rates of 3.10% (41/1,328) and 6.00% (81/1,328), respectively, with positive farm rates of 14.29% (12/84) and 16.67% (14/84). Co-infections, primarily involving PEDV and PoRVA, accounted for 19.05% (253/1,328) of cases. Additionally, an analysis of the spatiotemporal distribution of viruses from 2022 to 2024 was conducted. This study also included phylogenetic and amino acid analyses focusing on PEDV and PoRVA. Among them, PEDV predominantly belongs to GⅡa and GⅡc, while PoRVA predominantly belongs to G4 and G9. We analyzed neutralizing epitopes and functional sites of the PEDV S protein, revealing that the SS2 and SS6 epitopes are relatively conserved, while various mutations were observed in other functional sites. Additionally, significant variability in the VP7 protein of PoRVA was noted among different genotypes, with several conserved amino acid sequences identified, including aa 106-115 (FLTKGWPTGS), aa 159-170 (ILNEWLCNPMDI), and aa 251-259 (KLGPRENVA), primarily located in the loop regions of the VP7 protein. The study investigates the epidemiology and spatiotemporal distribution of viral diarrhea in China from 2022 to 2024, which helps identify high-risk areas and peak periods, thereby providing guidance for epidemic early warning and resource allocation. Additionally, the study conducted a further analysis of the antigenic epitopes of PEDV and PoRVA, providing important information for vaccine design and the formulation of immunization strategies.
DOI: 10.6084/m9.figshare.24912555.v1
title: sub001-010 (continuous EEG data)

description: Continuous EEG recordings for sub 001-010 saved as a zip file.
DOI: 10.6084/m9.figshare.5674423.v1
title: Application of dynamic thermal imaging in a photocarcinogenesis mouse model

description: <b>Introduction:</b> In clinical practice and experimental settings, cutaneous premalignant and malignant lesions are commonly diagnosed by histopathological biopsy. However, this technique is invasive and results in functional or cosmetic defects. Dynamic thermal imaging is a non-invasive technique that quantifies the infra-red (IR) radiation emitted by a subject after the introduction of external thermal stimuli (such as heat or cold). <b>Methods:</b> Forty hairless albino (Crl:SKH1-hr) mice were randomised to the control group or the experimental group. The experimental group was regularly irradiated with artificial ultraviolet. Clinical photographs, immunohistochemical staining and dynamic thermal imaging results of both groups were obtained. <b>Results:</b> As photocarcinogenesis proceeded, faster thermal recovery to basal temperature after heat stimuli was significant on dynamic thermal imaging. With histopathological correlations, it was possible to differentiate normal, premalignant and malignant cutaneous lesions according to thermal imaging results. CD 31 staining analysis showed that increased vasculature was the key change responsible for different thermal imaging results among photocarcinogenesis steps. <b>Conclusions:</b> Dynamic thermal imaging is useful to differentiate normal, premalignant and malignant cutaneous lesions. Increased vasculature is the key change responsible for different thermal imaging results.
DOI: 10.6084/m9.figshare.14769732.v1
title: Genomic annotation of BMA64-1A, SEY6210, BY4742, BY4741, X2180-1A and S288C strains: bed format

description: - Here is presented the full annotation of genomic sequences used in the differential expression analysis.- These data also appraised annotations of tRNAs, TEs, and lncRNAs.- The annotation of the <i>de novo</i> assembled BMA64-1A strain (NCBI BioProject number PRJNA727478) is also here presented.
DOI: 10.6084/m9.figshare.28296227.v1
title: Source Data - Lysosomal NKG7 Restrains mTORC1 Activity to Promote CD8+ T Cell Durability and Tumor Control.xlsx

description: This source data file contains all of the raw data for a manuscript to be published in Nature Communications with the following title: Lysosomal NKG7 Restrains mTORC1 Activity to Promote CD8+ T Cell Durability and Tumor Control
DOI: 10.6084/m9.figshare.24218775.v1
title: Knee diameter

description: Comparing CFA (complete freund adjuvant) and MIA (monosodium iodoacetate) to induce arthritis
DOI: 10.26181/26344840.v1
title: The impact of plant-derived fire management prescriptions on fire-responsive bird species

description: In fire-prone regions, the occurrence of some faunal species is contingent on the presence of resources that arise through post-fire plant succession. Through planned burning, managers can alter resource availability and aim to provide the conditions required to promote biodiversity. Understanding how species occurrence changes at different spatial and temporal scales after fire is essential to achieve this goal. However, many fire prescriptions are guided primarily by the responses of fire-sensitive plants when setting tolerable fire intervals. This approach assumes that maintaining floristic diversity will satisfy the requirements of fauna. We surveyed bird species in two semi-arid vegetation types across an environmental gradient in south-eastern Australia. We conducted four surveys at each of 253 sites across a 75-year chronosequence of time since fire and used generalized additive mixed models to examine changes in the occurrence of birds in response to time since fire. Model predictions were compared to plant-derived fire prescriptions currently guiding fire management in the region. Time since fire was a significant predictor for 18 of 28 species modeled, in at least one vegetation type, over a gradient of 1.3 degrees of latitude. We detected considerable variation in the responses of some species, both between vegetation types and geographically within a vegetation type. Our evaluation of plant-derived fire prescriptions suggests that the intervals considered acceptable for maintaining floristic diversity may not be sustainable for populations of birds requiring longer unburnt vegetation, with six of the 12 species assessed attaining a mean occurrence probability of 20.3% by the minimum tolerable fire interval, and 57.3% by the maximum tolerable fire interval, in their respective vegetation types. Our findings highlight the potential vulnerability of fire-responsive bird species if fire prescriptions are applied in a manner that fails to account for the slow development of habitat resources needed by some species, and the variation detected within the responses of species. This highlights the need for species-specific data collected at an appropriate spatial scale to inform management plans.
DOI: 10.6084/m9.figshare.22299052.v1
title: Intransitive competition among three dominant ants in coffee farms in Puerto Rico

description: The file named "Data for spatial distribution of ants- Gran Batey" includes the spatial distribution of three dominant ant species (<em>Solenopsis invicta</em>, <em>Wasmannia auropunctata</em>, and <em>Monomorium floricola</em>) in a 30M X 120M plot in the Gran Batey Farm in Utuado, Puerto Rico. Data was taken in January and July from 2019 to 2023. Data represent the proportion of tuna fish baits (out of 5) occupied by ants on coffee plants after 45-60min of the deployment of the tuna fish baits. The fine named "Ten meter transects for Solenopsis<em> </em> and Wasmania" has data on the number of individuals of <em>Selenopsis geminata </em>or <em>Wasmania auropunctata</em> that arrived at 10, 30 and 60 minutes interval to ground baits (tunafish) in 10 meter transects with baits every 40 cm (for a total of 26 baits) per transects.
DOI: 10.6084/m9.figshare.3464237.v1
title: Finite element input mesh & data files

description: This compressed folder contains the patient-specific FE models that consists of the all necessary input files to run the simulations of the in-silico oncoplasic breast surgery, as well as the corresponding finite element meshes.<br>All files can be opened using a conventional text editor, while the finite element meshes can be viewed using Gmsh (http://gmsh.info/).<br><br>
DOI: 10.17028/rd.lboro.12601556.v1
title: Supplementary information files for article: A method to assess the feasibility of implementing distributed Localised Manufacturing strategies in the food sector

description: Large-scale globalised food manufacturing systems have generated competitive advantages through economies of scale. However, these systems often show low environmental sustainability and resilience due to factors such as reliance on global food supply-chain actors and high emissions associated to transportation and storage. This article proposes increasing the sustainability of food production through a transition towards a ‘Distributed Localised Manufacturing’ (DLM) strategy. A novel assessment method is presented to evaluate the feasibility of DLM for different food products using nine distinctive metrics and a decision-support model to identify the most appropriate DLM system model for a specific scenario. An industrial case study is used to demonstrate the application of the novel assessment method. The results show that the DLM assessment method can accurately identify products that can benefit from the DLM strategy and potentially provide environmental and social benefits. In addition, the DLM assessment method demonstrated the ability to categorise key assessment criteria and support the selection of the most appropriate system model for a specific application. Finally, the method also provides guidelines to help to identify benefits, drivers and potential challenges that should be considered in future DLM implementations. In summary, this research presents a practical and powerful assessment method to support the implementation of a DLM strategy in the food-manufacturing sector in order to increase the long-term sustainability of food systems
DOI: 10.6084/m9.figshare.2058930.v1
title: Masking experiment Data for "A cross modal performance-based measure of sensory stimuli intricacy"

description: This archive contains matlab data files for the results of 12 test subjects. Each of the test subjects participated in the masking experiment described in our paper: "A cross modal performance-based measure of sensory stimuli intricacy".In each test subject the data structure contains the following variables:"FirstLetter" is the list of masked letters which the test subjects were asked to identify "answer" is the letter the subject indicated that they saw."distractorindex" is the index of the Brodatz image used to mask the letter in the experiment.<br>
DOI: 10.6084/m9.figshare.25650441.v1
title: <b>Analysis of nearly 3,000 archaeal genomes from terrestrial geothermal springs sheds light on </b><b>interconnected biogeochemical processes</b><b> </b>

description: This dataset contains supplementary data for the analyses presented in:Yan-Ling Qi<sup>*</sup>, Ya-Ting Chen<sup>*</sup>, Yuan-Guo Xie, Yu-Xian Li, Yang-Zhi Rao, Meng-Meng Li, Qi-Jun Xie, Xing-Ru Cao, Lei Chen, Yan-Ni Qu, Zhen-Xuan Yuan, Zhi-Chao Xiao, Lu Lu, Jian-Yu Jiao, Wen-Sheng Shu, Wen-Jun Li<sup>†</sup>, Brian P. Hedlund<sup>†</sup>, Zheng-Shuang Hua<sup>†</sup>. Analysis of nearly 3,000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes (under review)<b>Dataset contents:</b><b>Archaea.treefile</b>:<b> </b>Archaeal phylogenomic tree of 53 concatenated conserved archaeal marker genes in newick format.<b>Hydrogenase.treefile</b>: The phylogenetic tree of hydrogenase in newick format.<b>Microbial networks.pdf</b>: Figures of co-occurrence networks between Archaea and Bacteria based on <i>rpS3</i> protein sequences in 48 thermoacidic (a) and 31 thermoalkaline (b) springs.<b><i>rpS3 </i></b><b>database</b><b>.fasta</b>: The curated database of <i>rpS3</i> protein sequences in fasta format.
DOI: 10.6084/m9.figshare.25670445.v2
title: Shear capacity of reinforced UHPC beams

description: Shear capacity of reinforced UHPC beams
DOI: 10.6084/m9.figshare.27085657.v3
title: 4D Cellular Morphology Atlas Construction Simultaneously Reveals Shape-adhesion Patterns During Embryogenesis

description: <b>3D Shape Training: </b>Ground truth (GT) for training membrane recognition (TUNETr)<b>3D Shape Evaluation: </b>GT for evaluation and comparison of segmentation<b>2D Time-lapse Evaluation: </b>GT for time-lapse embryos (cell morphology map)<b>Nuclei Generative Training: </b>GT for training m2nGAN (pseudo nuclei image generation) with real stained fluorescence images<b>Nuclei Generative Evaluation: </b>GT for evaluating m2nGAN (pseudo nuclei image generation) with real stained fluorescence images<b>Shape-adhesion E-cadherin</b>: Dataset for discovering shape-adhesion patterns<b>CTransformer (mainly TUNETr) Code Link</b>: https://github.com/chiellini/CTransformer<b>m2nGAN Code Link:</b> https://github.com/chiellini/m2nGAN<b>Image Processing Python Script Link:</b> https://github.com/chiellini/CImageProcessor<b>Visualization Python Script Link: </b>https://github.com/chiellini/GUIData
DOI: 10.6084/m9.figshare.28721963.v1
title: algal_reef_biod_proj_plt_div.csv

description: Citizen science is a valuable approach for large-scale ecological research. Community-based citizen science, in particular, can help local residents better understand their surrounding environment while providing high-resolution data for scientific studies. In this study, we collaborated with residents near the Guanxin Algal Reef Ecosystem Wildlife Refuge in Taiwan to conduct a coastal habitat survey. Due to a national referendum in 2021, this location received media attention; however, the public and even local residents — still lack a full understanding of the area’s environment. Thus, we developed a simple, standardized survey method and trained residents to carry out the survey. Even after the scientists’ team concluded the project, the local residents continued to conduct surveys using the same method. To verify the reliability of data collected with and without scientists' supervision, we compared the datasets using coefficients of variation. The results showed no significant differences between the two datasets, indicating that the data collected independently by residents were reliable and consistent. We then combined the two datasets to analyze coastal habitat ecology regarding organism abundance, species richness, and biodiversity (Shannon index). Our findings revealed that the pebble habitat had the highest Shannon index, while the sand habitat had the lowest abundance, richness, and Shannon index values. The mid-tide zone showed the highest abundance of organisms, and summer and autumn had the highest abundance, richness, and Shannon index values. We predicted species richness and Shannon index across different habitats, tidal zones, and seasons using a species accumulation curve function with twice the sample size. Most results aligned with the original findings, although the sand habitat's predicted richness and Shannon index exceeded that of the algal reef habitat. Our research provides objective, citizen science-based insights to deepen understanding of this region, which has been a focal point of debate in Taiwan.
DOI: 10.6084/m9.figshare.13397987.v1
title: Expression of 97 surface markers and RNA (transcriptome wide) in 13165 cells from a healthy young bone marrow donor

description: Seurat v3 object<b><br></b><b>ASSAYS</b>:AB: Antibody expression dataRNA: mRNA expression dataBOTH: Concatenated mRNA and antbody expression matrices<br><b>DIMENSIONALITY REDUCTION</b>MOFA: Multi-OMICS factor analysis to integrate AB and RNA data. MOFA served as input for clustering and further dimensionality reduction.MOFAUMAP: UMAP performed on MOFA dimensions. Display used in the manuscript.<br>MOFATSNE: UMAP performed on MOFA dimensions.
DOI: 10.6084/m9.figshare.14618217.v1
title: The skull of Sanajeh indicus, a Cretaceous snake with an upper temporal bar, and the origin of ophidian wide-gaped feeding

description: <b>Supplementary File S1. </b>File containing the combined molecular and morphological dataset (Sanajeh_Total_evidence_matrix-Phylip_Format; Sanajeh_Total_evidence_matrix TNT_Format). <br> <b>Supplementary File S2. </b>List of DNA partitions (Sanajeh_Total_evidence-characters_set_RAxML_format).<br>
DOI: 10.6084/m9.figshare.26213747.v1
title: Data Repository-Raw Data

description: An increasing number of studies have confirmed the role of intestinal microbiota in early life maturation including maturation of intestinal immune function. The interaction of the TLR4 with colonizing bacteria in intestinal development is incompletely understood. Thisstudy investigates the mechanism (s) by which TLR4 interacts with metabolites (postbiotics) of the colonizing bacterium, <i>Bifidobacteria Longum </i>subsp. <i>Infantis (B. Infantis) </i>to determine its effect on intestinal development. By using a fetal human small intestinal cell line, authenticatedby human fetal intestinal organoids, we found that TLR4-mediated postbiotics induced immature enterocyte proliferation and filamentous actin (F-actin) maturation both at the mRNA and protein levels. Oral feeding of wild-type (WT) and TLR4 gene knockout (TLR4 <sup>-/-</sup>) neonatal mice of<i>B.Infantis</i> postbiotics increased proliferation of mRNA levels in wild-type mice but not in TLR4<sup> -/-</sup> mice, both in the ileum and colon. Postbioticscan also change tight junction distribution in WT neonatal mouse colon but not in TLR4 <sup>-/- </sup>mice. Our data suggest a novel regulation of intestinal development by a synergistic role of the innate immune receptor TLR4 and early life colonizing bacteria, such as <i>B. Infantis,</i> in both the fetal human and immature mouse intestine. This study should provide new insights into the mechanisms of intestinal maturation as well as opportunities to target novel approaches to NEC prevention and treatment.
DOI: 10.6084/m9.figshare.26362324.v3
title: Magnetic Anomaly Data of Auckland Volcanic Field

description: This dataset is the aeromagnetic anomaly data of the Auckland Volcanic Field (AVF), covering most of the field except for the Boggust Park volcano. The data were initially published by Eccles et al. (2005), Cassidy et al. (1999), and Rout et al. (1993). The aeromagnetic data has been de-spiked but not micro-levelled due to the absence of tying lines. <b>Diurnal magnetic variations have been removed from all data except Craig Miller's southern AVF aeromagnetic data (CA_Miller_1996_AVF_SouthPart.csv) due to instrumental errors</b>. Please consult Eccles (2003), Miller (1996), and Rout (1991) for more details. X-Y positions are given in NZMG and NZTM coordinate systems, while flight Z is relative to the ground and sea surfaces.
DOI: 10.6084/m9.figshare.12782924.v1
title: Data, Improvement of exclusive breastfeeding in preterm infants.xlsx

description: Intervention study with control group and intervention group. Data on exclusive breastfeeding, gestational age groups, postmenstrual age at establishment of exclusive breastfeeding and use of six clinical practices.
DOI: 10.6084/m9.figshare.19173986.v1
title: Supplementary Material for: First-in-human effects of PPT1 inhibition using the oral treatment with GNS561/ Ezurpimtrostat in patients with primary and secondary liver cancers

description: Introduction - GNS561/Ezurpimtrostat is a first-in-class, orally bioavailable, small molecule that blocks cancer cell proliferation by inhibiting late-stage autophagy and dose-dependent build-up of enlarged lysosomes by interacting with the palmitoyl-protein thioesterase 1 (PPT1). Methods - This phase I, open-label, dose-escalation trial (3+3 design) explored two GNS561 dosing schedules: one single oral intake three times a week (Q3W) and twice daily (BID) continuous oral administration in patients with advanced hepatocellular carcinoma, cholangiocarcinoma, and pancreatic adenocarcinoma or colorectal adenocarcinomas with liver metastasis. The primary objective was to determine GNS561 recommended phase II dose (RP2D) and schedule. Secondary objectives included evaluation of the safety/tolerability, pharmacokinetics, pharmacodynamics, and antitumor activity of GNS561. Results - Dose escalation ranged from 50-400mg Q3W to 200-300mg BID. Among 26 evaluable patients for safety, 20 were evaluable for efficacy and no dose-limiting toxicity was observed. Adverse events (AEs) included gastrointestinal grade 1-2 events, primarily nausea and vomiting occurred in 13 (50%) and 14 (54%) patients respectively, and diarrhea in 11 (42%) patients. Seven (7) grade 3 adverse events were reported (diarrhea, decreased appetite, fatigue, ALT and AST increased). Q3W administration was associated with limited exposure and the BID schedule was preferred. At 200 mg BID GNS561, plasma and liver concentrations were comparable to active doses in animal models. Liver trough concentrations were much higher than in plasma a median time of 28 days of administration with a mean liver to plasma ratio of 9559 (Min 149-Max 25759), which is in accordance with rat preclinical data observed after repeated administration. PPT1 expression in cancer tissues in the liver was reduced upon GNS561 exposure. There was no complete or partial response. Five patients experienced tumor stable diseases (25%), including one minor response (-23%). Conclusion - Based on a favourable safety profile, exposure, and preliminary signal of activity, oral GNS561 RP2D was set at 200mg BID. Studies to evaluate the antitumor activity of GNS561 in HCC and iCCA are to follow. NCT 03316222
DOI: 10.6084/m9.figshare.28710602.v1
title: Pisa_monthly_precipitation_dataset.csv

description: Monthly precipitation amount observed in Pisa (Tuscany, Italy) from May 1707 to December 2024
DOI: 10.6084/m9.figshare.21067618.v1
title: 实验数据处理-ACY-20210326.xlsx

description: Detailed experimental data.