cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19558762.v2
title: Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes (Dataset)

description: Dataset from Diaz-Escandón <em>et a</em>l. Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes. Currrent Biology(2022), https://doi.org/10.1016/j.cub.2022.11.014 <br> <strong>1_Assembly</strong>: All new generated genomes, quality control, and scripts used. <strong>2_Phylogenomics</strong>: All the alignments, trees, and supporting analyses. <strong>3_Annotations</strong>: A set of 115 functional annotated genomes, steps to annotate them and a comparisson step. <strong>4_Comparative_statistics</strong>: A set of R scripts and curated data from annotations, including figure assets, statistics, and tables. <br>
DOI: 10.6084/m9.figshare.22578031.v2
title: A global database for modeling tumor-immune cell communication

description: Our database contained five CSV files. All the deposited data was processed and openly available. The CSV table ‘Experimentally verified TIC communication’ contained detailed information of experimentally verified TIC communications including gene symbols, cell types, interaction types, species, experiments, interaction comments and original reference information. Integrated ligand-receptor interactions were displayed in the CSV table ‘Integrated ligand-receptor interactions’ including gene symbols, functions, sources of LR pairs and evidences. Predicted TIC communications based on bulk RNA-seq were stored in the CSV table ‘Predicted TIC communication based on experimentally verified TICs and bulk RNA-seq’ and the CSV table ‘Predicted TIC communication based on ligand-receptor interactions and bulk RNA-seq’. The former dataset contained the detailed information including gene symbols, cell types, cancer types, interaction strength and p values. However, ligands, receptors, functions, evidences, cancer types, interaction strength and p values were recorded in the latter dataset. The CSV table ‘Predicted TIC communication based on scRNA-seq’ consisted of the detailed information of predicted TIC interactions inferred by five algorithms using 32 scRNA-seq datasets and union of ligand-receptor interactions. This dataset contained ligands, receptors, cell types, prediction methods, evidences, datasets, cancer types and cancer subtypes.
DOI: 10.6084/m9.figshare.28602389.v1
title: Supporting information on the Genome assembly of Diadegma fenestrale (Hymenoptera: Ichneumonidae) and genome integration of its symbiotic virus, DfIV

description: 01. General information of Diadegma fenestrale genome02. Functional annotation (Detox genes)03. Gene Ontology (GO)04. Chromosome synteny (circos)05. Genome data form NCBI_ORFs for orthovenn306. Df_DfIV genome integration summary
DOI: 10.6084/m9.figshare.14910627.v1
title: SDL-PAND model 2.5

description: Model developed in SDL that shows the trend of new cases in Catalonia. The execution can be done using SDLPS at https://sdlps.com or any software that understands SDL.This is part of the project http://pand.sdlps.com.
DOI: 10.6084/m9.figshare.24718602.v2
title: Characterization of atmospheric methane release in the outer Mackenzie River delta from biogenic and thermogenic sources. Point samples data used in Figure 1 and Figure 4.

description: A .pdf file containing geolocated atmospheric CH<sub>4</sub> and CO<sub>2</sub> mixing ratios for the Mackenzie-Beaufort Delta region of the Northwest Territories, Canada. All CH<sub>4</sub> and CO<sub>2</sub> values are in parts per million by volume (ppmv). Discrete point samples of CH<sub>4</sub> and CO<sub>2</sub>mixing ratios were taken by filling 1 L Tedlar bags with ambient air from approximately 1 m above ground level. CH<sub>4</sub> and CO<sub>2</sub>concentrations and δ<sup>13</sup>C-CH<sub>4</sub> were determined using a Picarro G2210i analyser. All point samples were analysed for at least 5 minutes and the values averaged, which increases the Picarro G2210i analyser accuracy to 0.1 ‰ δ<sup>13</sup>C-CH<sub>4</sub>, 0.0001 ppm CH<sub>4</sub> and 0.01 ppm CO<sub>2</sub>. Sample positions were recorded with a Garmin eTrex 10 handheld GPS, which has an accuracy of +/- 3.65 m. Gas mixing ratios were standardized to Ameriflux FB04306 breathing grade air (benchmarked to 0.5 ppb).
DOI: 10.6084/m9.figshare.28787483.v2
title: CRISPR-BEasy raw data

description: CRISPR-dependent base editing (BE) enables the modelling and correction of genetic mutations at single-base resolution. Base editing screens, where point mutations are queried en masse, are powerful tools to systematically draw genotype–phenotype associations and characterize the function of genes and other genomic elements. However, the lack of user-friendly web-based tools for designing base editing screens can hinder broad technology adoption. Here, we introduce CRISPR-BEasy (https://crispr-beasy.cerc-genomic-medicine.ca), a free, automated, web-based server that streamlines the creation of single guide (sg)RNA tiling libraries for base editing screens. Researchers can provide their genes or genomic features of interest, their base editors of choice, and target sequences to act as positive and negative controls. The server designs and annotates sgRNA libraries by integrating custom code with publicly available tools such as crisprVerse and Ensembl’s Variant Effect Predictor. CRISPR-BEasy provides downloadable results, including sgRNA on/off-target scores, predicted mutational outcomes per base editor, and intuitive interactive visualizations for data quality assessment. CRISPR-BEasy also provides a separate tool that assembles sgRNA libraries into oligonucleotides for cloning following the detailed protocol documented in the searchable web-server manual. Together, CRISPR-BEasy ensures the seamless design of cloning-ready sgRNA libraries, seeking to democratize access to base editing screening technologies.
DOI: 10.6084/m9.figshare.28783574.v1
title: Dataset form: Current Status of Diamond Open Access Journals in Peru: An Overview of Open Science Practices

description: Dataset as supplementary material from article "Current Status of Diamond Open Access Journals in Peru: An Overview of Open Science Practices" that analyzes a sample of 223 journals qualified and abstracted in SciELO Peru, Latindex 2.0, DOAJ and MIAR.<br>
DOI: 10.6084/m9.figshare.29086772.v2
title: Non-synthesizable structures

description: The initial screened non-synthesizable structures data used for fine-tuning the large language model.
DOI: 10.6084/m9.figshare.3467768.v1
title: Alignment of PLA2 proteins

description: This is the alignment of venom PLA2 proteins. Used in Figure S4.<br>
DOI: 10.6084/m9.figshare.7491818.v1
title: ARC nonword database, Rastle et al. (2002)

description: Database of 358,534 nonwords<br>reference_to_cite: "Rastle, K., Harrington, J., & Coltheart, M. (2002). 358,534 nonwords: The ARC Nonword Database. Quarterly Journal of Experimental Psychology, 55A, 1339-1362."<br>url_information: "MACS website ( http://rosella.bhs.mq.edu.au/~nwdb/ )"<br>
DOI: 10.17632/77p6rzb73n
title: CSIQ: A Synthesized Dataset of Code Smells, Issues and Quality related Artifacts from Open Source Repositories

description: The dataset contains synthesized code smells, issues, quality, and source code metrics information of 60 versions under 10 different repositories. The dataset is extracted into 3 levels: (1) Class (2) Method (3) Package. The dataset is created upon analyzing 9,420,246 lines of code and 173,237 classes.  The provided dataset contains following folders: code smells, issues, quality attributes, synthesized and four associated Comma Separated Values (CSV) files: repositories.csv, versions.csv, codesmells.csv and attribute − details.csv. The first file (repositories.csv) contains general information (repository name, URL, number of commits, stars, forks, etc.) to understand the size, popularity, and maintainability.   File versions.csv contains general information (version unique ID, number of classes, packages, external classes, external packages, version repository link) to provide an overview of versions and how over time the repository continues to grow. File  attribute-details.csv  contains detailed information  (attribute name,  attribute short form, category, and description) about extracted static analysis metrics and code quality attributes.  The short form is used in the real dataset as a unique identifier to show value for packages, classes, and methods. File codesmells.csv provides the information (Rule, Code Smell, Rule Description) of code smells analyzed from each version.
DOI: 10.17632/b5rtnrdb6b
title: BodyMemoryBehavioral

description: Our bodies provide a necessary scaffold for memories of past events. Yet, we are just beginning to understand how fundamental feelings of one’s own body during the encoding of realistic events shape memory accuracy and phenomenology. Here, participants formed memories for immersive, lifelike events by watching pre-recorded 3D videos that involved a first-person view of a mannequin’s body through head mounted displays. We manipulated feelings of body ownership over the mannequin using a perceptual full-body illusion. Participants saw an object touch the mannequin and simultaneously felt touches on the corresponding location of their real body, which created an illusory sense of ownership over the mannequin. As a control condition, we disrupted the illusion by delivering seen and felt touches in an alternating pattern in half of the videos. Participants completed cued recall questions pertaining to event details and subjective ratings (i.e. degree of reliving, emotional intensity, vividness, and belief in memory accuracy) for each video immediately following encoding and one week later. Repeated-measures ANOVAs show that sensing the mannequin’s body as one’s own during encoding enhanced cued recall accuracy at both testing points, reliving at immediate testing, and emotional intensity, vividness, and belief in memory accuracy at delayed retrieval, compared to the disembodied control condition. These findings suggest that a basic sense of bodily selfhood provides a crucial foundation for the accurate and vivid reliving of the personal past. Acronyms: Sync = synchronous condition Async = asynchronous condition Ill = illusion Con = control CR = cued recall Imm = immediate Del = delayed Cent = central details Periph = peripheral details EI = emotional intensity Reliv = reliving Viv = vividness Bel = belief in memory accuracy
DOI: 10.17632/mh94mxn3nh
title: DataSet for PCOS 

description: This datasets provides the results of an untargeted metabolomic survey was conducted on the metabolites in the FF of 35 patients with PCOS and 37 age-matched individuals as control.
DOI: 10.17632/rsbn88vszz
title: experimetal data of static and dynamic data

description: experimetal data of static and dynamic data
DOI: 10.17632/sd47rzc4nz
title: User-Centered Design of Smart Home Voice System for Chinese Older Adult

description: This data set corresponds to the paper entitled "User-Centered Design of Smart Home Voice System for Chinese Older Adult". The dataset includes the original interview data, questionnaire questions, questionnaire raw data, smart voice assistant tones, and APP source code.
DOI: 10.6084/m9.figshare.12888563.v2
title: Bremen Sample Stations and customer nodes

description: Bremen Sample customer nodes
DOI: 10.6084/m9.figshare.17064409.v2
title: Neural and behavioural effects of typicality, denotation and composition in an adjective–noun combination task

description: Formal semantics states that the meanings of phrases are composed from the meanings of constituent parts and syntax. Little is known about how composition is neurally implemented. We studied ERP and behavioural responses to determiner-adjective-noun phrases. We assessed the effects of typicality and denotation, using intersective (typical: “A green turtle”, atypical: “An orange turtle”) or subsective adjectives (typical: “A slow turtle”, atypical: “A fast turtle”). After each phrase, participants responded to two questions (e.g., for “A fast turtle”: “Is it a common turtle?”; “Is it a fast animal?”). We contrasted these 4 semantic conditions, requiring composition, to 2 nonsemantic conditions, where the adjective was replaced with a pseudoword or a nonword. This contrast revealed a larger P600, if participants performed the task without instructions and feedback (experiment 1), or a larger sustained negativity, if they were nudged to pay attention to meaning by instructions and feedback (experiment 2). Typicality or denotation had an impact only on behavioural responses. We discuss implications for theories of language processing and compositional semantics.
DOI: 10.6084/m9.figshare.29145308.v1
title: DNABERT-H-2M

description: <pre>DNABERT-H-2M is a DNA language model based on DNABERT-S (1) and trained using Hierarchical Multi-label Contrastive Learning from Use All The Labels [2].<br><br>[1] https://github.com/MAGICS-LAB/DNABERT_S<br>[2] (https://arxiv.org/abs/2204.13207)<br></pre>
DOI: 10.6084/m9.figshare.13551362.v1
title: Dryas Spectra from Bison Gulch and Twelve Mile Summit

description: Reflectance data from dry leaves of Dryas ajanensis, Dryas alaskensis, and their hybrids. Data from two locations: Bison Gulch and Twelve Mile Summit. See tm_pops.csv and bg_pops.csv for metadata.
DOI: 10.6084/m9.figshare.15180192.v1
title: MedSeg Inferior Vena Cava Dataset

description: In total 20 cases with the inferior vena cava segmented from confluence of iliac veins to upper level with the right atrium.<br>All cases obtained Decathlon's dataset, see details and reference here: https://arxiv.org/abs/1902.09063<br><br>Segmentations done by MedSeg
DOI: 10.6084/m9.figshare.26927707.v6
title: A dataset mapping the temperate savanna in Northeastern China (2022)

description: Temperate savanna shares a wide geographical distribution. It plays a crucial role in supporting a substantial portion of rangelands and livestock, thereby contributing significantly to human livelihoods.We develop a new temperate savanna identification method for mapping the temperate savanna in Northeastern China within a minimum identifiable area of 5000 m<sup>2</sup> by integrating Unmanned Aerial Vehicle(UAV) imagery with high-resolution satellite imagery of Sentinel-1 and Sentinel-2 by using Random Forest regression and Classification and Regression Tree algorithms. The training and validation datasetswere collected from UAV imagery.The proposed method achieved with the overall accuracy of 0.82 for savanna identification.Temperate savanna in Northeastern China covering a total area of 170,000 km<sup>2</sup>.This map enhances our understanding of the spatial extent and area of temperate savanna. The derived method provides a new insight to explore the extent of regional and global savannain the future.The code and generated maps are publicly accessible. To make the method to reproduce and exploit and to promote its usage, we have provided users with the python code used to produce temperate savanna map. The generated maps of fractional woody vegetation cover, fractional herbaceous vegetation cover and temperate savanna in Northeastern China are stored in TIFF format, including the fractional woody and herbaceous vegetation cover map of 20 m with the file name of FWVC20m.tif and FHVC20m.tif, and the temperate savanna map at 70.7 m (70.7 m ×70.7 m equivalent to unit area scale of 5000 m<sup>2</sup>) with the file name of tsavanna71m.tif. In temperate savanna map, we recorded temperate savanna as “1”. All image data can be viewed by geographic information system software, such as ArcGIS.The UAV imagery dataset consists of 75 TIFF files that are publicly accessible through Figshare (https://doi.org/10.6084/m9.figshare.27651468.v1).
DOI: 10.6084/m9.figshare.28878359.v1
title: AP_3_(-)3.itmx3D OrbiSIMS Metabolic Profiling of E. coli Reveals Effects of FMT- Derived Faecal Filtrate and Phage-Azithromycin on Amino Acids and Lipid Pathways.

description: Antimicrobial resistance (AMR) represents a pressing global health threat, necessitating innovative alternatives to traditional antibiotics. Among these, bacteriophage therapy and faecal microbiota transplantation (FMT)-based interventions have emerged as promising strategies. However, the metabolic responses of multidrug-resistant (MDR) pathogens to these therapies remain poorly understood. In this study, we applied advanced 3D Orbitrap Secondary Ion Mass Spectrometry (3D OrbiSIMS) metabolomics, offering ultra-high mass resolution (&gt;240,000) and sub-2 ppm mass accuracy, to profile metabolic alterations in pathogenic Escherichia coli strains, Enteroaggregative (EAEC) and Enteroinvasive (EIEC), following treatment with lytic phage vB_EcoM_SVMS_56, phage–azithromycin combination therapy, and sterile faecal filtrates from healthy FMT donors (n = 4; mean age 33.75 ± 2.38 years).
DOI: 10.6084/m9.figshare.6743207.v8
title: GBIF for CREST database

description: This database contains all the presence records of plants, beetles, chironomids, foraminifera and diatoms contained in the GBIF database in October 2020.<br>The coordinates of the presence records have been homogenised on a 0.25x0.25° grid, and corresponding bioclimatic values from the Worldclim2.0 database have been added.<br>These data are formatted and ready to use by the CREST software. Additional python scripts have been added to group plant species into pollen types.<br><b>To download the latest version of the database, please follow this link: https://figshare.com/articles/GBIF_for_CREST_database/6743207</b><b><br></b>Please cite all the appropriate datasets from the following list:GBIF.org, 2020. Lycopodiopsida occurrence data downloaded on September 24th, 2020. doi: 10.15468/dl.ydhyhzGBIF.org, 2020. Anthocerotopsida occurrence data downloaded on September 24th, 2020. doi: 10.15468/dl.t9zenfGBIF.org, 2020. Liliopsida occurrence data downloaded on September 24th, 2020. doi: 10.15468/dl.axv3ydGBIF.org, 2020. Diatoms occurrence data downloaded on September 24th, 2020. doi: 10.15468/dl.vfr257GBIF.org, 2020. Cycadopsidae occurrence data downloaded on September 24th, 2020. doi: 10.15468/dl.sfjzxuGBIF.org, 2020. Foraminifera occurrence data downloaded on September 24th, 2020. doi: 10.15468/dl.692yg6GBIF.org, 2020. Magnoliopsida occurrence data downloaded on September 24th, 2020. doi: 10.15468/dl.ra49dtGBIF.org, 2020. Pinopsidae occurrence data downloaded on September 24th, 2020. doi: 10.15468/dl.x2r7paGBIF.org, 2020. Rodentia occurrence data downloaded on September 24th, 2020. doi: 10.15468/dl.fscw6qGBIF.org, 2020. Gingkoopsidae occurrence data downloaded on September 24th, 2020. doi: 10.15468/dl.da9wz8GBIF.org, 2020. Polypodiopsida occurrence data downloaded on September 24th, 2020. doi: 10.15468/dl.87tbp6GBIF.org, 2020. Beetles occurrence data downloaded on September 24th, 2020. doi: 10.15468/dl.nteruyGBIF.org, 2020. Chironomids occurrence data downloaded on September 24th, 2020. doi: 10.15468/dl.jv3wshGBIF.org, 2020. Gnetopsidae occurrence data downloaded on September 24th, 2020. doi: 10.15468/dl.h2kjnc<br><br>
DOI: 10.6084/m9.figshare.7707605.v2
title: Global High-Resolution Soil-Water Balance

description: The Global High-Resolution Soil-Water Balance dataset provides hydrological raster data describing actual evapotranspiration and soil water deficit with resolution of 30 arc seconds.
DOI: 10.6084/m9.figshare.14356418.v1
title: Reference draft genome of Heliopora coerulea

description: To examine phylogenetic relationships within the genus <i>Heliopora</i>, we applied Multiplexed ISSR Genotyping by sequencing (MIG-seq) method for &gt;1,000 colonies across the Indo-West Pacific. For discriminating <i>Heliopora</i> genome sequences from symbiont or other genomic DNA, MiSeq [v3–600] was used to sequence 16 G bp of <i>Heliopora</i> genomic DNA extracted from symbiont-free larvae of <i>Heliopora coerulea</i> collected in Japan, which was used in the study Richards et al. (2018). Genome stats: sum=465489301, n=291784, ave=1595.32, largest=357742 (N50=2436, n=46691)
DOI: 10.6084/m9.figshare.28029101.v1
title: Questionnaire Bamako, Mali

description: Questionnaire of farmers, fishers, and sand miners around Bamako, Mali
DOI: 10.6084/m9.figshare.28321805.v2
title: Situational Awareness Dataset for Instruct-Tuning (SAD-Instruct)

description: Situational Awareness Database (SAD) is a dataset for dynamic task guidance. It contains situationally-aware instructions for performing a wide range of everyday tasks or completing scenarios in 3D environments. The dataset provides step-by-step instructions for these scenarios which are grounded in the context of the situation. This context is defined through a scenario-specific scene graph that captures the objects, their attributes, and their relations in the environment. The dataset is designed to enable research in the areas of grounded language learning, instruction following, and situated dialogue.
DOI: 10.6084/m9.figshare.28943708.v1
title: Terahertz Time-Domain Spectroscopy of Substituted Gadolinium Gallium Garnet

description: Raw data for journal article "Terahertz Time-Domain Spectroscopy of Substituted Gadolinium Gallium Garnet".Figure 1-6 are included.
DOI: 10.6084/m9.figshare.6895682.v1
title: Microsatellite dataset on Sinanodonta woodiana

description: Microsatellite marker dataset of Sinanodonta woodiana from Europe and China in GenAlEx format
DOI: 10.6084/m9.figshare.930480.v2
title: TCA cycle-html

description: TCA cycle
DOI: 10.17632/h5j8yrksch
title: Association between psoriasis and risk of dementia: a systematic review and meta-analysis - Supplemental Material
DOI: 10.6084/m9.figshare.28543970.v1
title: UAVImagesofBurrows

description: This dataset is UAV images of marmot burrows at the Rocky Mountain Research Laboratory in Colorado, U.S.A
DOI: 10.17632/3mhxk62y3c
title: Autoimmune blistering disorders and cardiovascular risks

description: Supplementary material
DOI: 10.17632/j9j4mdm9yr
title: A multiplex single-cell RNA-Seq pharmacotranscriptomics pipeline for drug discovery

description: We developed a single-cell transcriptomics pipeline for high-throughput pharmacotranscriptomic screening. We explored the transcriptional landscape of three HGSOC models (JHOS2, a representative cell line; PDC2 and PDC3, two patient-derived samples) after treating their cells for 24 hours with 45 drugs representing 13 distinct classes of mechanism of action. Our work establishes a new precision oncology framework for the study of molecular mechanisms activated by a broad array of drug responses in cancer. 
.
├── 3D UMAPs/ → Interactive 3D UMAPs of cells treated with the 45 drugs used for multiplexed scRNA-seq. Related to Figure 4. 
 Coordinates: x = UMAP 1; y = UMAP 2; z = UMAP 3.
 Legend: green = PDC1; blue = PDC2; red = JHOS2.
│ ├── DMSO_3D_UMAP_Dini.et.al.html → 3D UMAP of untreated cells.
│ └── drug_3D_UMAP_Dini.et.al.html → 3D UMAP of cells treated with (drug).
├── QC_plots/ → Diagnostic plots. Related to Figures 2–4. 
│ ├── model_QC_violin_plot_2023.pdf → Violin plots of the QC metrics used to filter the data.
│ ├── model_col_HTO or model_row_HTO before and after filt → Heatmaps of the row or column HTO expression in each cell.
│ └── model_counts_histogram_2023.pdf → Histogram of the distribution of the total counts per cell after filtering for high-quality cells.
├── scRNAseq/ → scRNA-seq data. Related to Figures 2–4. 
│ ├── AllData_subsampled_DGE_edgeR.csv.gz → Differential gene expression analyses results between treated and untreated cells via pseudobulk of aggregate subsamples, for each of the three models. Related to Figure 3. 
│ └── All_vs_all_RNAclusters_DEG_signif.txt → Differential gene expression analysis results (p.adj &lt; 0.05) of FindAllMarkers for the Leiden/RNA clusters. 
├── PDCs.transcript.counts.tsv → Bulk RNA-seq count data for PDCs 1–3 processed by Kallisto. Related to Figure S6.
└── PDCs.transcript.TPM.tsv → Bulk RNA-seq TPM data for PDCs 1–3 processed by Kallisto. Related to Figure S6.