cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5594230.v1
title: Genome-wide Association Study of Piglet Uniformity and Farrowing Interval

description: This "genotype_and_phenotype.zip" file contains the genotypes of 884 individuals (884-individual.map and 884-individual.ped ) and the phenotypic data of piglet university and farrowing interval (phenotype1_Piglet uniformity.xlsx and phenotype2_Farrowing interval.xlsx).
DOI: 10.17632/c2gccnfkgd
title: An explicit model to extract viscoelastic properties of cells from AFM force-indentation curves

description: The data and the codes available here are used in the publication: "An explicit model to extract viscoelastic properties of cells from AFM force-indentation curves"
DOI: 10.17632/gz75x2pzr7
title: German Domestic Air Fares

description: The data set was generated by web scraping and includes the ticket prices on 84 german connections over a period of 6 months. a total of 63,000 prices and connections are included in the data set.
DOI: 10.17632/n57g6p5b9d
title: Replication materials for Falato, Iercosan, Zikes (JFE, Banks as Regulated Traders)

description: This replication package contains code and pseudo-data to replicate the regression
estimates for all the tables in the paper by Falato, Iercosan, Zikes, 2025, Banks as Regulated Traders, JFE, forthcoming
DOI: 10.6084/m9.figshare.22337545.v1
title: Phylogenetic tree of primate MORC2

description: Phylogenetic tree of primate MORC2s from 25 species of primates (newick format). Phylogenetic analyses performed with PhyML (HKY+I+G model) with 1000 bootstrap replicates for statistical supports. Each species is abbreviated by the first three letters of the Genus and the first three letters of the Species (for example homSap, for Homo sapiens).
DOI: 10.6084/m9.figshare.25101452.v1
title: Data and Codes

description: Instruction, Data, and programs
DOI: 10.6084/m9.figshare.5459680.v1
title: The 3D OrbiSIMS – Label-Free Metabolic Imaging with Sub-cellular Lateral Resolution and High Mass Resolving Power

description: We have developed the 3D OrbiSIMS for label-free biomedical imaging. It has an unparalleled simultaneous combination of spatial resolution (under 200 nm for inorganics and under 1.5 µm for biomolecules) and mass resolving power of &gt; 240,000 at <i>m/z</i> 200. This allows the distribution of exogenous and endogenous metabolites to be visualized in 3D with sub-cellular resolution. We image the distribution of neurotransmitters—gamma-aminobutyric acid (GABA), dopamine and serotonin with high spectroscopic confidence in the CA3 and CA1 regions of the hippocampus (murine). GABA is most abundant in the <i>stratum oriens</i>. We identify and map the sub-cellular localisation of 53 glycosphingolipid sulfatide species and demonstrate the ability of tandem mass spectrometry to confirm lipid identity. Single cell metabolomic profiling is demonstrated using rat alveolar macrophage cells incubated with different concentrations of the drug amiodarone. The up-regulation of phospholipid species and cholesterol is correlated with the accumulation of amiodarone.
DOI: 10.17632/2x8z6sw249
title: Crop-country specific AWARE water scarcity factors for 160 crops and global coverage 

description: This work provides water scarcity estimates using the AWARE method, which is a recommended method to assess water scarcity footprints and water consumption in LCA

The worksheets "ctry_crop_AWARE_CF" contains the AWARE CFs specific to the average crop growth patterns (regional and temporal distribution) for 160 crops for each country (details described below).

These CFs can be applied to water consumption of crops grown in these countries, as it provides more specific evaluation than the country average AWARE CFs for agricultural production in Boulay et al. (2018).

This data is e.g. used for the calculation of water scarcity result in Multi-Regional Input-Output (MRIO) assessments of UNEP's IRP Global Resource Outlook (Oberle et al. 2019), the new version of UNEP's SCP-HAT tool (http://scp-hat-beta.fineprint.global/) and by Cabernard et al. 2019 & 2020)
DOI: 10.6084/m9.figshare.21154945.v2
title: DTNUGENT 2022

description: Complete datasets for Nugent et al. 2022. Can switches in disturbance type improve habitat for grassland birds in semi-arid grasslands of south-eastern Australia? Journal: Austral Ecology <br> Data: Birds Vegetation Invertebrates (pitfall and suctioning) Seeds
DOI: 10.6084/m9.figshare.23677407.v1
title: The data for the NEE paper: Structural complexity biases vegetation greenness measures

description: The data for the NEE paper: Structural complexity biases vegetation greenness measures
DOI: 10.6084/m9.figshare.25742892.v1
title: <b>Supplementary Material – </b><b>Montane forest tree species have lower hydraulic efficiency and vulnerability </b><b>than lowland forest species in the Atlantic Forest</b>

description: <b>Table S1 – </b><b>Species incorporated into the statistical analysis from the other three Atlantic Forest areas: Itatiaia National Park (PNI), Macaé de Cima Environmental Protection Area (AMC), Poço das Antas Biological Reserve (RBPA).</b><b>Table S2 – </b><b>Data matrix for PCA of the four analyzed Atlantic Forest areas.</b>
DOI: 10.6084/m9.figshare.28025243.v2
title: aspirin-1000 for class

description: test
DOI: 10.6084/m9.figshare.7121930.v1
title: Additional file 5 of Optimal selection of molecular descriptors for antimicrobial peptides classification: an evolutionary feature weighting approach

description: Predictions of antibacterial activity for APD3_ANTIBACTERIAL. Evaluation of different models with APD3_ANTIBACTERIAL after applying the best compromise solutions and four machine learning algorithms. This file shows the results obtained by each of the best compromise solutions given Îť1 in each fold of the 10-fold cross-validation test. (CSV 34 kb)
DOI: 10.17632/d5b5rx6vmf
title: STTGMA Matching Dataset

description: This data is connected to the Data in Brief article "Trauma Risk Score Matching for Observational Studies in Orthopedic Trauma Dataset and Code"
DOI: 10.6084/m9.figshare.12543587.v3
title: UI logs

description: This is the collection of UI logs used in the evaluation in the research paper: "Candidate routines identification from unsegmented UI logs". The real-life logs are in CSV format and recorded via Action Logger. The synthetic logs are in XES format and generated from colored Petri net models. The models are attached.
DOI: 10.6084/m9.figshare.16846966.v1
title: China Industrial Environmental Database 1998-2015

description: China Industrial Environmental Database (CIED) includes four types of pollutants for China's 31 regions and 39 industrial sectors from 1998 to 2015. Four types of pollutants are: chemical oxygen demand (COD), sulfur dioxide (SO2), ammonia-nitrogen (NH3-N), and nitrogen oxide (NOX).
DOI: 10.6084/m9.figshare.19229190.v1
title: Oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) in lymphoblasts from ALS patients with mutant SOD1 (mutSOD1) and unknown mutation (undSOD1).

description: Oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) parameters in lymphoblasts from ALS patients with mutant SOD1 (mutSOD1) and unknown mutation (undSOD1). Cells were plated at density 160,000 cells/well, as described in Materials and Methods. Mitochondrial Stress Test featuring OCR- and ECAR-associated parameters were assessed with the Seahorse XFe96 Extracellular Flux Analyzer. OCR and ECAR parameters, as well as energy maps showing the metabolic potential of cells. Data were plotted for all cohorts (pool), C1-Female 46 years old, C2- Male 46 years old and C3-Male 26/27 years old. OCR parameters and ECAR evaluated.
DOI: 10.6084/m9.figshare.25590528.v1
title: <b>Higher-order cortical and thalamic pathways shape visual </b><b>processing streams in the mouse cortex</b>

description: Data for Han and Bonin 2024, Current biology https://doi.org/10.1016/j.cub.2024.10.048.Table_HVA_retro: in relation to Figure 1-5. Intracortical pathways projecting to visual cortical areas AL/PM/A.Table_axon_HVA_L5: in relation to Figure 6. L5 Rbp4+ axons from AL/PM to other visual cortical areas.Table_axon_HVA: in relation to Figure S9. Bulk AAV labeled axons from AL/PM to other visual cortical areas.Table_axon_LP: in relation to Figure 7. AAV labeled axons from visual thalamus LP to higher visual cortical areas.For all tables,'idx_animal'= index of the mouse imaged; 'area' = area of FOV; 'area_injection' = area with anterograde or retrograde AAV injection; 'idx_cell' = index of axonal bouton cluster for each FOV; 'idx_cell_unique'= unique numbers of axonal clusters across the dataset; 'layer' = cell body locating in cortical L2/3 or L5 ; 'retro_labeled' = cells is retrograde-labeled or not; 'is_responsive'=cells or boutons pass the selection threshold; 'peak SF' = peak spatial frequency (cpd); 'peak TF' = peak temporal frequency (Hz).<br><br><br><br>
DOI: 10.6084/m9.figshare.25605411.v2
title: Supplemental Data File 6_PKD_6m_vs_WT_6m_Upregulated Genes.xlsx

description: Supplemental Data File 6_PKD_6m_vs_WT_6m_Upregulated Genes.xlsx
DOI: 10.6084/m9.figshare.29115149.v2
title: <b>Global Synthesis of Fertilisation-Induced Changes in the Microbial Entombing Effect</b>

description: We conducted a global meta-analysis to evaluate the impact of fertilisation practices on the microbial entombing effect, focusing on microbial necromass C (MNC), microbial biomass C (MBC), and the microbial necromass accumulation coefficient (NAC=MNC/MBC) across 319, 1665, and 199 paired datasets, respectively.
DOI: 10.6084/m9.figshare.8311994.v2
title: Data from: Estimating snakebite incidence from mathematical models: A test in Costa Rica

description: Data used to perform the study. All files must be unzipped in the same folder, and the working directory in the code must be this folder. Maxent file is the java file, which must be located in the dismo folder inside R packages.
DOI: 10.17632/4b4drs7g6d
title: Emerging genetic diversity of Mycoplasma gallisepticum in Mexican House Finches: Evidence of possible independent spillover events

description: In a previous study, we reported for the first time the detection of Mycoplasma gallisepticum (MG) in Mexican house finches (Haemorhous mexicanus). Building on this finding, we explored the genetic diversity of MG, addressing the potential independent spillover events. Samples from 247 wild finches across Mexico revealed MG infection in 72% of choanal swabs and 24% of conjunctival swabs, with no clinical signs observed. Phylogenetic analysis identified two novel MG clades distinct from U.S. house finch-associated and poultry-associated MG strains, suggesting independent evolution within Mexico. Coinfections with diverse haplotypes were common, raising concerns about recombination and shifts in virulence. This research highlights the asymptomatic carrier state of Mexican house finches, their potential as reservoirs, and the ecological implications of pathogen spread and adaptation. These findings underscore the need for enhanced surveillance and further study on MG's dynamics in Mexican avifauna.
DOI: 10.17632/4sjkr76gbf
title: Mechanisms of hematopoietic clonal dominance in VEXAS syndrome

description: Clonal dominance characterizes hematopoiesis during aging and increases susceptibility to blood cancers and common non-malignant disorders. VEXAS syndrome is a recently discovered adult-onset autoinflammatory disease burdened by a high mortality rate and caused by dominant hematopoietic clones bearing somatic mutations in the UBA1 gene. However, pathogenic mechanisms driving clonal dominance are unknown. Moreover, the lack of disease models hampers the development of disease-modifying therapies. Here, we performed immunophenotypic characterization of hematopoiesis and single-cell transcriptomics in a cohort of 9 male patients with VEXAS syndrome, revealing pervasive inflammation across all lineages. Hematopoietic stem/progenitor cells (HSPCs) in patients are skewed toward myelopoiesis and acquire senescence-like programs. Humanized models of VEXAS syndrome, generated by inserting the causative mutation in healthy HSPCs through base editing, recapitulated proteostatic defects, cytologic alterations, and senescence signatures of patients’ cells, as well as disease hematologic and inflammatory hallmarks. Competitive transplants of human UBA1-mutant and wild-type HSPCs showed that while mutant cells are more resilient to the inflammatory milieu, likely through the acquisition of the senescence-like state, wild-type ones are progressively exhausted and overwhelmed by VEXAS clones, overall impairing functional hematopoiesis and leading to bone marrow failure. Our study unveils the mechanism of clonal dominance, provides models for preclinical investigation of therapeutic strategies, and might have implications for clinical management of VEXAS syndrome.
DOI: 10.17632/v9zt547rdb
title: Petrophysical experimental results from 46 samples of South China Sea and micro-CT images series data from two sandstone samples

description: This zip file is the datasets of petrophysical experimental results from 46 sandstone samples of South China Sea, and micro-CT images series data from two sandstone samples. There are four files, include: 'measured data from core samples.xlsx', 'WZ-01.rar', 'WZ-01-continue.rar' and 'WC-04.rar'. WZ-01 means the Sample NO. WZ-01. WC-04 means the Sample No. WC-04. 'WZ-01.rar' and 'WZ-01-continue.rar' form a complete file. The file 'measured data from core samples.xlsx' include: petrophysical experimental results from 46 sandstone samples of three Basins in South China Sea, such as location, sampling depth, porosity, permeability, formation factor and pore-throat radius and so on. Three files 'WZ-01.rar' with 'WZ-01-continue.rar' and 'WC-04.rar' are micro-CT scanning images series data: Resolution: 0.95 micron/pixel. Pore-solid segmentation: black represents pore area, and white represents solid grain. The data is continuous slices in *.bmp format. Please also refer to "A fractal electrical conduction model of porous media: Insight into Archie’s law" under review in JGR Solid Earth 2020. Contact: chenxj@cug.edu.cn Xiaojun Chen
DOI: 10.6084/m9.figshare.6226646.v1
title: sequence data for Kobresia and Blysmus

description: 2b-RAD sequence data for <i>Kobresia tibetica</i> and<i> Blysmus sinocompressus</i>
DOI: 10.6084/m9.figshare.9876386.v4
title: Canadian Candy Sales

description: Data from StatsCan.Candy = sales in dollars.
DOI: 10.17632/vbrxhnrvf2
title: Materials Learning Algorithms (MALA): Scalable machine learning for electronic structure calculations in large-scale atomistic simulations

description: We present the Materials Learning Algorithms (MALA) package, a scalable machine learning framework designed to accelerate density functional theory (DFT) calculations suitable for large-scale atomistic simulations. Using local descriptors of the atomic environment, MALA models efficiently predict key electronic observables, including local density of states, electronic density, density of states, and total energy. The package integrates data sampling, model training and scalable inference into a unified library, while ensuring compatibility with standard DFT and molecular dynamics codes. We demonstrate MALA's capabilities with examples including boron clusters, aluminum across its solid-liquid phase boundary, and predicting the electronic structure of a stacking fault in a large beryllium slab. Scaling analyses reveal MALA's computational efficiency and identify bottlenecks for future optimization. With its ability to model electronic structures at scales far beyond standard DFT, MALA is well suited for modeling complex material systems, making it a versatile tool for advanced materials research.
DOI: 10.25442/hku.28157336.v1
title: Supporting data for "A Precise shRNA Backbone for siRNA Target Screening and Quantitative microRNA Biology"

description: Over the past two decades, short hairpin RNA (shRNA) has emerged as a powerful tool for loss-of-function studies, enabling researchers to effectively silence gene expression and investigate gene function. Current shRNA backbones, however, were designed without consideration for small RNA homogeneity, resulting in imprecise processing by endogenous microRNA biogenesis machinery. This inherent limitation leads to the production of unintended small RNAs, which can be loaded onto Argonaute (AGO) proteins and yield functional small RNAs, introducing unintended gene regulation beyond the intended gene knockdown and restricting broader applications.To address this limitation, we engineered a novel shRNA backbone, named shRNAoneV4, which allows for precise processing and significantly reduces the production of unintended guides. shRNAoneV4 demonstrates enhanced small RNA homogeneity of the intended guide while expressing a library of guides with varying thermostability at both ends, making it a robust tool for precise small RNA expression in RNA interference (RNAi) screening.Furthermore, we propose that shRNA screening could replace siRNA screening, as both strategies leverage the endogenous RNAi pathway. As a proof-of-concept experiment, we applied shRNAoneV4 in an siRNA target tiling screen, utilizing a library of shRNAoneV4 targeting tiling sites on TTR transcripts. We identified two regions on TTR transcripts that contained efficient shRNA target sites, suggesting that these regions are more effective for RNAi. The efficiencies of these shRNA target sites were validated with siRNAs, underscoring the feasibility of replacing the labour-intensive siRNA screening approach with a simpler pooled shRNA screening method.Additionally, we demonstrated the utility of shRNAoneV4 in studying microRNA functions. By mimicking endogenous microRNAs with the shRNAoneV4 library, we successfully identified microRNAs that regulate sorafenib resistance in hepatocellular carcinoma (HCC). This highlights the potential of exploiting shRNAoneV4 to investigate microRNA functions in various biological contexts—an endeavour that was hindered by previous shRNA backbones due to noise introduced by imprecisely processed small RNAs. Moreover, libraries encoding microRNA variants revealed microRNAs that rely on non-seed regions for target recognition, facilitating studies on the principles governing non-seed contributions to defining target sites.In conclusion, we present a new gold standard shRNA backbone to the research community worldwide, opening a reliable approach for RNAi screening. Our findings demonstrate the feasibility of employing this RNAi screening strategy for the large-scale identification of microRNA functions, thereby accelerating the research community’s understanding of microRNAs’ roles in various biological processes.
DOI: 10.6084/m9.figshare.21394737.v1
title: Source data

description: Data details all raw data points and uncut gels for the main and supplementary figures in the paper
DOI: 10.6084/m9.figshare.23580024.v2
title: Dataset on the Chemical Modification of Ascorbic Acid (AA) to L-ascorbyl-6-palmitate (AP): A Novel Approach For Improved Antioxidant Therapy in Traumatic Brain Injury (TBI)

description: The data support the findings of the research entitled, Chemical Modification of Ascorbic Acid (AA) to L-ascorbyl-6-palmitate (AP): A Novel Approach For Improved Antioxidant Therapy in Traumatic Brain Injury.AA was chemically modified into L-ascorbyl-6-palmitate (AP), a lipophilic derivative, and its impact on oxidative stress biomarkers in TBI-induced rats was investigated.TBI was induced in rats using a weight drop injury (WDI) model. Experimental groups were the AA-receiving group, AP-receiving group, traumatized non-treated (TNT), and non-traumatized non-treated (NTNT) control groups. The activities of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx), as well as the levels of malondialdehyde (MDA), were evaluated in serum and brain tissue samples using Cayman’s assay kits according to the manufacturer’s instructions. The Means were computed from five replicates (n = 5) for each parameter. A statistical test, ANOVA was used to determine noteworthy differences between the means. Dunnett’s post hoc test was used to compare treatment groups with control group.In the current study, we utilized DMSO as the vehicle for L-ascorbyl-6-palmitate. We tried various solvents such as water, normal saline, and alcohol, and none of these completely dissolved L-ascorbyl-6-palmitate. We then tried various concentrations of DMSO and only 100% DMSO completely dissolved L-ascorbyl-6-palmitate. Thus, as DMSO itself possesses antioxidant properties, we decided to include the DMSO-treated group to compare and contrast its effects with those of L-ascorbyl-6-palmitate. In the current study, the administration of DMSO alone decreased oxidative stress by decreasing MDA levels, and augmented SOD, CAT, and GPx activities. However, it has less effect when compared to the L-ascorbyl-6-palmitate-treated group. Therefore the second dataset contains the full data including those from the DMSO group. Since this is a novel approach to the TBI experiment, researchers who are interested in furthering the work are welcome to try different solvents and concentrations. Due to limited resources, we were able to analyze MDA levels, SOD, CAT, and GPx activities. Therefore, subsequent work using L-ascorbyl-6-palmitate can include functional and cognitive analysis, as well as histology and immunohistochemistry assays to completely attribute the antioxidative effects of L-ascorbyl-6-palmitate in the TBI.
DOI: 10.17632/c3c9xbspzp
title: GUIMesh: A tool to import STEP geometries into Geant4 via GDML

description: Detailed radiation analysis of instruments flown in space is critical to ensure mission safety, often requiring the use of state-of-the-art particle transport simulation tools. Geant4 is one of the most powerful toolkits to simulate the interaction and the passage of particles through matter, but it is not prepared to receive Standard for The Exchange of Product data (STEP) files, the most versatile Computer-Aided Design (CAD) format, as input, requiring previous conversion to other CAD formats. This may lead to loss of detail and under or overestimation of the quantities under study, especially when the instruments have complex shapes, and/or a large number of volumes. Though several solutions have been proposed to import complex geometries from STEP files into Geant4, so far, only commercial options are available. In this paper we present a new tool, GUIMesh, that embeds FreeCAD libraries, an open-source CAD editor, to tessellate volumes, and convert them to Geometry Description Markup Language (GDML), a Geant4 readable format, in a straightforward way. Several degrees of freedom are given to the user regarding mesh precision and choice of material. Different geometries were tested for material definition, geometry and navigation errors, and the method used was successfully validated.