cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5114236.v1
title: Computational analysis GeCKO v2 library (human)

description: <b>Table 1 - Non-specific sgRNAs GeCKO v2 (human). </b>This table represents the total of 5,664 sgRNAs within the entire GeCKO v2 library (half-libraries A and B combined) that recognise at least two identical target sites (20 bp protospacer + NGG PAM) within the reference genome. For the analysis, sgRNA target sites were aligned against the human reference genome (GRCh38/hg19 - primary assembly) using BLAT (v36) after optimisation of the algorithm for short length queries (-tileSize=6, -stepSize=3). The resulting alignments were further filtered to only include perfect matches and unique targets (exclusion of hits on alternative assemblies). Analysis was performed using R (v3.2.3) in R studio (v1.0.136) using Ubuntu.<br><b>Table 2 - Flagged genes GeCKO v2 (human).</b> This table represents the total of 775 genes for which more than half the corresponding sgRNAs within the entire human GeCKO v2 library (half-libraries A and B combined) are non-specific, i.e. recognise at least two identical target sites (20 bp protospacer + NGG PAM) within the reference genome. A threshold of &gt;50% non-specific sgRNAs per gene (e.g. 4 out of 6 for protein coding genes; 3 out of 4 for miRNA genes) was set in order to flag a group of sgRNAs. Analysis was performed using R (v3.2.3) in R studio (v1.0.136) using Ubuntu.
DOI: 10.6084/m9.figshare.6633494.v1
title: Integrated analysis of lncRNAs and mRNA expression profiles reveals the potential role of lncRNAs in different bovine lactation stages

description: Long non-coding RNAs (lncRNAs) play a critical role in mammary development and breast cancer biology. Despite their important role in the mammary gland, little is known on the roles of lncRNAs in bovine lactation, particularly regarding the molecular processes underlying it. To characterize the role of lncRNAs in bovine lactation, four samples of Holstein cow mammary gland tissue at peak and late lactation stages were examined after biopsy. We then profiled the transcriptome of mammary gland using RNA sequencing technology. Further, functional lncRNA-mRNA co-expression pairs were constructed to infer the function of lncRNAs using a generalized linear model, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Over 1000 putative lncRNAs were identified, 117 of which were differentially expressed between peak and late lactation stages. Bovine lncRNAs were shorter, with fewer exon numbers, and expressed at significantly lower levels than protein-coding genes. Seventy-two differentially expressed lncRNAs (DE-lncRNAs) were co-expressed with 340 different protein-coding genes. The KEGG pathway analysis showed that target mRNAs for DE-lncRNAs were mainly related to lipid and glucose metabolism, including the peroxisome proliferator-activated receptors (PPAR) and 5' adenosine monophosphate-activated protein kinase (AMPK) signaling pathways. Further bioinformatics and integrative analyses revealed that 12 DE-lncRNAs potentially played important roles in bovine lactation. Our findings provide a valuable resource for future bovine transcriptome studies, facilitate the understanding of bovine lactation biology, and offer functional information for cattle lactation.Keywords: Long non-coding RNA, bovine lactation, mammary gland, co-expression, RNA sequencing
DOI: 10.17632/v2np7vm9pw
title: Data for: The Comoros archipelago: a right-lateral transform boundary between the Somalia and Lwandle plates

description: Structural data (including fault-slip data, extension fractures, dykes, and bedding stratifications) collected in the islands of Mayotte, Anjouan and Mohéli in 2018 and 2019.
DOI: 10.6084/m9.figshare.13681534.v2
title: DepMap 21Q1 Public

description: This dataset contains the results of Avana library CRISPR-Cas9 genome-scale knockout (prefixed with Achilles) as well as mutation, copy number and gene expression data (prefixed with CCLE) for cancer cell lines as part of the Broad Institute’s Cancer Dependency Map project. We have repackaged our fileset to include all quarterly-updating datasets produced by DepMap.<br>The Avana CRISPR-Cas9 genome-scale knockout data has expanded to include 808 cell lines, the RNAseq data includes 1376 cell lines, and the copy number data includes 1740 cell lines. Please see the README files for details regarding data processing pipeline procedures updates.<br>As our screening efforts continue, we will be releasing additional cancer dependency data on a quarterly basis for unrestricted use. For the latest datasets available, further analyses, and to subscribe to our mailing list visit https://depmap.org.<br>Descriptions of the experimental methods and the CERES algorithm are published in http://dx.doi.org/10.1038/ng.3984. Some cell lines were process using copy number data based on the Sanger Institute whole exome sequencing data (COSMIC: http://cancer.sanger.ac.uk.cell_lines, EGA accession number: EGAD00001001039) reprocessed using CCLE pipelines. A detailed description of the pipelines and tool versions for CCLE expression can be found here: https://github.com/broadinstitute/gtex-pipeline/blob/v9/TOPMed_RNAseq_pipeline.md.<br><br>v2: changed dataset name<br>
DOI: 10.6084/m9.figshare.20493417.v2
title: Lycopodium clavatum genome annotation

description: Lycopodium clavatum genome annotation files:cds,pep and gff
DOI: 10.6084/m9.figshare.28051286.v1
title: Supplementary Material for: Glucosamine use reduces the risk of first-ever optic neuritis: A nationwide 16-year longitudinal analysis

description: Introduction: Evidence of neuroprotective effects of glucosamine on Asian optic neuritis (ON) patients remains sparse. We aimed to examine the longitudinal association between glucosamine use and the incidence of first-ever ON to identify the factors contributing to reducing ON risk in older Asian populations. 

Methods: This nationwide cohort study from 2000 to 2015 evaluated 24,155 individuals. The International Classification of Diseases-9-Clinical Modification code 377 determined newly diagnosed ON. Outcomes include the annual trend of first-ever ON incidence, crude/adjusted hazard ratios (HRs) of incident ON stratified by sociodemographic characteristics and comorbidities.

Results: Glucosamine exposure has been significantly associated with reduced ON incidence (Log-rank p &lt; 0.001) since the fifth year of clinical surveillance. The overall adjusted HR of ON among glucosamine users was 0.718 (CI = 0.524–0.901, p = 0.001), and in the glucosamine-exposed group, disease onset was approximately 129 days later than in non-users (6.83 ± 4.27 vs. 6.47 ± 4.01 years to ON, p &lt; 0.001). Moreover, glucosamine was associated with reduced ON risk in patients without diabetes mellitus, hypertension, tobacco use and chronic heart failure. While administering glucosamine, the risk was reduced by more than half among individuals aged between 45 and 64 years (aHR = 0.433, CI = 0.316–0.544, p &lt; 0.001) and patients from medical centers (aHR = 0.453, CI = 0.330–0.568, p &lt; 0.001).

Conclusion: Taiwanese glucosamine users have a decreased risk of developing ON. Our work provides a theoretical basis for expanding glucosamine indications in regions with minimal prevalence of ON.
DOI: 10.17632/v52nk44mm3
title: dataset-EMGSH-hypothermia

description: experimental data including the effects of sevoflurane, pentobarbital, and hypothermia
DOI: 10.17632/7tpypv754y
title: Flow Behavior and Processing Map of Newly Developed ECO-AlMag8 Alloy During Hot Compression: Raw Data

description: This data set contains the raw data of the hot compression test, EBSD and optical microstructure of samples used in the paper submitted to the Results in Engineering under the title of "Flow Behavior and Processing Map of Newly Developed ECO-AlMag8 Alloy During Hot Compression".
DOI: 10.6084/m9.figshare.19728139.v1
title: Research data - Garcia, Delattre, Berton, Divrechy and Rao. Comparison of Landing Kinematics and Kinetics Between Experienced and Novice Volleyball Players during Block and Spike Jumps

description: qtm files containing kinematics and kinetics data for 30 participants. Each participant performed 8 trials of block jump-landing and spike jump-landing.
DOI: 10.6084/m9.figshare.22688434.v1
title: GWAS summary data of hypothalamus in ABCD

description: GWAS summary data of hypothalamus in ABCD
DOI: 10.6084/m9.figshare.28713194.v2
title: Bonn Roof Material + Satellite Imagery Dataset

description: This dataset consists of annotated high-resolution aerial imagery of roof materials in Bonn, Germany, in the Ultralytics YOLO instance segmentation dataset format. Aerial imagery was sourced from OpenAerialMap, specifically from the Maxar Open Data Program. Roof material labels and building outlines were sourced from OpenStreetMap. Images and labels are split into training, validation, and test sets, meant for future machine learning models to be trained upon, for both building segmentation and roof type classification.The dataset is intended for applications such as informing studies on thermal efficiency, roof durability, heritage conservation, or socioeconomic analyses. There are six roof material types: roof tiles, tar paper, metal, concrete, gravel, and glass.Note: The data is in a .zip due to file upload limits. Please find a more detailed dataset description in the README.md<br><br>
DOI: 10.17632/vxdrzs4bk3
title: NiGaCa Experimental Data

description: This dataset contains raw experimental data acquired from H₂ temperature-programmed reduction (H₂-TPR), CO₂ temperature-programmed desorption (CO₂-TPD), X-ray diffraction (XRD), and transmission electron microscopy (TEM) analyses. The dataset includes mass spectrometry data presented as mass-to-charge ratio (m/z) versus time and
micro-gas chromatography (micro-GC) outputs given as peak area versus time or temperature. These data support the characterization and evaluation of catalytic materials.
DOI: 10.6084/m9.figshare.13751023.v1
title: Rat 7M Videos Subject 1 - Day 1

description: All videos for Subject 1, Day 1 of Rat 7M.<br><br>The video naming scheme is s{subject_id}-d{recording_day}-camera{camera_id}-{starting_frame_idx}.mp4.<br><br>Subject ID, recording day, and camera ID match videos to the data in the motion capture and camera calibration parameter .mat files.<br><br>Videos are provided in 3500 frame chunks, with the index of the starting frame in each file denoted by the {starting_frame_idx} portion of the filename.<br><br>Using the 'frames' field in the 'cameras' struct inside 'mocap.mat', the corresponding video file and frame index can be calculated by used frame_idx // 3500 to get the {starting_frame_idx} and frame_idx % 3500 to get the frame in that file. <br>
DOI: 10.6084/m9.figshare.28892783.v1
title: Dataset for "<b>Data to Physics in Minutes: An Agentic Large Language Model Solves a Competitive Adsorption Puzzle</b>"

description: Scientific modeling often requires navigating a trade-off between physical interpretability and empirical accuracy—a task that can take weeks of iteration, especially in systems with partial observability, structural complexity, and experimental errors. Here, we show how a state-of-the-art agentic reasoning-and-coding large language model, OpenAI o3, autonomously solved a modeling challenge in surface chemistry that puzzled us for months: quantifying the competitive adsorption of carboxylic acids on metal–organic layers. With experimental data and a concise problem formulation, o3 rapidly formulated a physically grounded adsorption model, derived the mathematical equations, implemented the corresponding codes to fit the experimental data, revised its assumptions, and ultimately derived a competitive adsorption model with three parameters that matched experimental data across more than a dozen of tested molecules. The resulting model—simple, mechanistically transparent, and quantitatively robust—incorporates both classical Langmuir competition and structural constraints such as site accessibility. Beyond addressing this particular challenge, our findings highlight a transformative shift in scientific methodology: from manual trial-and-error approaches to AI-driven hypothesis generation and model refinement. This represents a new paradigm in research, wherein language models surpass the traditional roles of machine learning in data analysis and computational support, actively participating in scientific reasoning and hypothesis development. Here is the experimental dataset in this work.
DOI: 10.6084/m9.figshare.28934993.v3
title: 2019-2022 10-m maize and soybean maps over the United States

description: High-resolution crop maps over large spatial extents are fundamental to many agricultural applications; however, generating high-quality crop maps consistently across space and time remains a challenge. In this study, we improved a workflow for operational crop mapping and developed the first openly available, annual, 10-m spatial resolution maize and soybean maps over the Contiguous United States (CONUS) from 2019 to 2022. We obtained all available Sentinel-2 surface reflectance data between May and October for every year, applied quality assurance, corrected the bidirectional reflectance distribution function (BRDF) effects, and generated 10-day analysis ready data (ARD) composites. We then derived multi-temporal metrics from the 10-day ARD as training features for the national-scale wall-to-wall mapping. We implemented a stratified, two-stage cluster sampling, and then conducted annual field surveys and collected ground data. Utilizing the training data with Sentinel-2 multi-temporal metrics, we trained random forest models generalized for annual maize and soybean classification separately. Validated using field data from the two-stage cluster sample, our annual maps achieved consistent overall accuracies (OA) greater than 95% with standard errors of less than 1%. User’s accuracies (UAs) and producer’s accuracies (PAs) for maize were higher than 91% and 84% across the years, and UAs and PAs for soybean were greater than 88% and 82%, respectively. To illustrate the substantial improvement of the 10-m map over existing datasets, e.g., the 30-m Cropland Data Layer (CDL), we aggregated the 10-m maps to 30-m spatial resolution and quantified the amount of 30-m mixed pixels that can be reduced at field, regional, and national levels. The counties with the most maize and soybean production in Iowa, Illinois and Nebraska had the lowest reduction in mixed pixels, ranging from 1% to 10%, whereas southern counties had a higher reduction in mixed pixels. Overall, the median percentages of mixed maize and soybean pixels across all counties were 14% and 16%, respectively, illustrating the substantial benefits of 10-m maps over 30-m maps. With more Sentinel-2-like data available from continuous observations and incoming satellite missions, we anticipate that 10-m crop maps will greatly benefit long-term monitoring for agricultural practices from the field to global scales.
DOI: 10.6084/m9.figshare.7148651.v1
title: Dataset Dairy Heat Stress Gunn et al. 2018 PLOS ONE part 1

description: This dataset includes raw downscaled climate projections (1950-2100) for multiple locations across the U.S. with estimations of temperature humidity index, heat stress frequency, dry matter intake and milk production loss with or without heat abatement. This is the first set of data
DOI: 10.17632/tsp5gfd559
title: Generated assembly line balancing precedence graphs from automotive OEM

description: This dataset contains information on twelve precedence graphs describing assembly tasks. These were generated based on actual observations at a large automotive company based in the United States. Data was collected from three different assembly lines to generate different versions of precedence graphs with order strengths of 20, 40, 60, and 80, respectively. To create this data, the current allocation of tasks to workstation has been used considering that each task may only have predecessors at the same or preceding stations. Each csv file presented here contains the information for a single precedence graph. The pdf provides a visual representation of all precedence graphs created.
DOI: 10.6084/m9.figshare.19658229.v1
title: intact mass measurement raw data

description: Intact protein mass measurement data
DOI: 10.6084/m9.figshare.16940365.v2
title: The problem of Reference Rot in Spatial Metadata Catalogues

description: This dataset contains the results of the reference rot analysis performed over the catalogues registered in the INSPIRE Discovery Services of EU and EFTA countries.
DOI: 10.6084/m9.figshare.17435054.v1
title: NYTimes_Novels_WordEmbeddings

description: Word embedding model of ca 400 contemporary novels reviewed in the New York Times.
DOI: 10.6084/m9.figshare.17074856.v1
title: Supplementary Material for: BRAF V600E Mutation in Triple-Negative Breast Cancer: A Case Report and Literature Review

description: <b><i>Background:</i></b> The B-Raf proto-oncogene (BRAF<sup>V600E</sup>) gene mutation has been identified in a variety of malignancies, but no evidence of the efficacy of vemurafenib treatment in BRAF<sup>V600E</sup> mutant breast cancer (BC) has been reported. <b><i>Case Presentation:</i></b> We reported a 60-year-old woman with confirmed triple-negative BC with BRAF<sup>V600E</sup> mutation. Progression-free survival (PFS) for first-line chemotherapy was 7 months. The patient received vemurafenib and albumin-bound paclitaxel as second-line therapy, exhibiting regression of some pulmonary metastatic lesions with concomitant progression of other lesions, and achieved 4.4 months of PFS. Genetic testing of the progressed pulmonary lesion revealed the BRAF<sup>V600E</sup> mutation, and acquired new mutations and AR amplification. The patient ultimately died of multiple organ failure and achieved 12 months of overall survival. <b><i>Conclusions:</i></b> The BRAF<sup>V600E</sup> mutation may be a potential prognostic factor and therapeutic target for BC.
DOI: 10.6084/m9.figshare.21103774.v1
title: Fresh and Aged Beef Electronic Nose Data

description: The characteristics of fresh beef from Brazil, Canada, and Horqin and aged beef stored for two years were collected using an electronic nose.
DOI: 10.6084/m9.figshare.29149106.v3
title: Dataset

description: this study investigates four decades of sedimentary and morphological changes in the Yangtze Estuary using an integrated framework. Drawing on grain size analysis, grain trend analysis, bathymetric data, and sediment budget calculations (e.g., sediment diversion ratio), we characterize temporal shifts in sediment transport and depocenter dynamics.
DOI: 10.17632/bwckvktwdh
title: Data for: Income and Factor Substitution: An Investigation on the Solow Growth Model under the Constant Elasticity of Substitution

description: This document includes dataset and codes used in the paper "Income and Factor Substitution: An Investigation on the Solow Growth Model under the Constant Elasticity of Substitution". 

We use two data files: 

1-) data_cross is for the cross sectional analysis
2-) data_panel is for the panel data analysis.
DOI: 10.17632/chnsdxfg7y
title: Dataset_FEVOR

description: For the performance evaluation on the cluttered data, we propose to present a dataset of 10 texture-less objects acquired by a lightweight handy 3D RGBD camera (Intel Realsense D435). The presence of partial reference models, shiny objects, and cluttered scenes with varying distances and rotations are the challenges found in the proposed dataset for recognition techniques. We also provide code of our proposed technique FEVOR. If you have any query please contact me. Email: piyushjoshi3839@gmail.com
DOI: 10.17632/n2dckzzrw7
title: “Annual tuberculosis screening in patients on biologics has questionable value”

description: Supplementary Material
DOI: 10.6084/m9.figshare.13643252.v2
title: MedSeg Liver segments dataset

description: In total 50 cases segmented with liver segments 1-8.Free to use and download. <br>Check out our 5 segment model at www.medseg.ai<br>All cases obtained Decathlon's dataset, see details and reference here: https://arxiv.org/abs/1902.09063<br><br>Segmentations done by MedSeg<br>#Update 2/4/21: 40 new cases added, case 1 replaced with new case
DOI: 10.6084/m9.figshare.21632141.v1
title: rostral MMC

description: scRNA-seq data and cell subclusters of MMC
DOI: 10.6084/m9.figshare.22396054.v1
title: synthetic_alerts

description: Synthetic alerts.
DOI: 10.6084/m9.figshare.24805488.v1
title: Bible Genres of Amharic, English, and Tigrigna

description: Nine Genres of a Bible in three translations: Tigrigna, Amharic and English.
DOI: 10.6084/m9.figshare.26409307.v1
title: Cleaned CosMx dataset used by most analyses in "Single cell spatial transcriptomic profiling of childhood-onset lupus nephritis reveals complex interactions between kidney stroma and infiltrating immune cells." A failed slide has been removed.

description: Cleaned dataset used in analyses from the manuscript "Single cell spatial transcriptomic profiling of childhood-onset lupus nephritis reveals complex interactions between kidney stroma and infiltrating immune cells". Called by code hosted at https://github.com/Nanostring-Biostats/childhood-onset-lupus-nephritis-analyses
DOI: 10.6084/m9.figshare.3564399.v1
title: Appendix A. Results of principal component analysis (PCA) with soil chemistry after conditioning as dependent variables and conditioning species as samples.

description: Results of principal component analysis (PCA) with soil chemistry after conditioning as dependent variables and conditioning species as samples.
DOI: 10.15468/dl.xj6qbm
title: Occurrence Download

description: A dataset containing 307 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Kalanchoe pinnata",
 "Country is Brazil",
 "HasCoordinate is true"
 ]
}

 The dataset includes 307 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025876-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29951885
title: Sykes - Chapter 1 - Appendix S4

description: <b>Appendix S4. </b>Table of isolate names, taxonomy, and sequence data for cultures isolated in this study
DOI: 10.6084/m9.figshare.29951885.v1
title: Sykes - Chapter 1 - Appendix S4

description: <b>Appendix S4. </b>Table of isolate names, taxonomy, and sequence data for cultures isolated in this study
DOI: 10.15468/dl.bkvzqv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Kalanchoe pinnata",
 "Country is Burundi",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025877-250811113504898/datasets/export for details.
DOI: 10.15468/dl.nv8ett
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schinus molle",
 "Country is Angola",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025796-250811113504898/datasets/export for details.
DOI: 10.15468/dl.qwb62n
title: Occurrence Download

description: A dataset containing 356 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Platyarthridae",
 "Year 2017-2019",
 "Continent is Europe",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Machine Observation, Human Observation, Occurrence evidence, Observation)"
 ]
}

 The dataset includes 356 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049869-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.