cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3611075_d14
title: Additional file 18: Table S5. of Measure transcript integrity using RNA-seq data

description: edgeR detected 665 differentially expressed genes (FDR cutoff = 0.01) in mCRPC samples (without TIN correction). FC = Fold Change; CPM = Count Per Million; FDR = False Discovery Rate. (XLS 97 kb)
DOI: 10.6084/m9.figshare.c.3611111_d8
title: Additional file 11: of De novo assembly and transcriptome characterization of spruce dwarf mistletoe Arceuthobium sichuanense uncovers gene expression profiling associated with plant development

description: Table S8. Differential expression of gene involved in carbohydrate metabolism and energy (XLS 1023Â kb)
DOI: 10.6084/m9.figshare.c.3611075_d13
title: Additional file 19: Table S6. of Measure transcript integrity using RNA-seq data

description: edgeR detected 289 differentially expressed genes (FDR cutoff = 0.01) in mCRPC samples (after TIN correction). FC = Fold Change; CPM = Count Per Million; FDR = False Discovery Rate. (XLS 45 kb)
DOI: 10.6084/m9.figshare.c.3611111_d6
title: Additional file 6: of De novo assembly and transcriptome characterization of spruce dwarf mistletoe Arceuthobium sichuanense uncovers gene expression profiling associated with plant development

description: Table S4. Expression profiles of putative transcription factors in different developmental tissues. (XLS 416Â kb)
DOI: 10.6084/m9.figshare.c.3611075_d11
title: Additional file 14: Table S4. of Measure transcript integrity using RNA-seq data

description: List of 10 low RIN/medTIN mCRPC and 10 higher RIN/medTIN mCRPC samples used for differential expression analysis. “N” = Metastatic bone site, “V1” = Visit 1. Whole datasets are available with accession # GSM1722952. (XLS 97 kb)
DOI: 10.6084/m9.figshare.c.3611075_d10
title: Additional file 3: Table S3. of Measure transcript integrity using RNA-seq data

description: 120 RNA-seq datasets generated from clinical tissues of human metastatic castration resistant prostate cancers (mCRPC). Sample ID, RNA Integrity Numbers (RIN), the median Transcript Integrity Numbers (medTIN), total read pairs, read pairs with mapping quality &gt; 30, and number of genes with at least 10 reads are listed. “B” = Blood, “T” = Metastatic soft tumor tissue, “N” = Metastatic bone site, “V1” = Visit 1, “V2” = Visit 2. (XLS 22 kb)
DOI: 10.6084/m9.figshare.c.3611111_d3
title: Additional file 8: of De novo assembly and transcriptome characterization of spruce dwarf mistletoe Arceuthobium sichuanense uncovers gene expression profiling associated with plant development

description: Table S6. Expression profiles of putative transporters in different developmental tissues. (XLS 2893Â kb)
DOI: 10.6084/m9.figshare.c.3611111_d2
title: Additional file 4 of De novo assembly and transcriptome characterization of spruce dwarf mistletoe Arceuthobium sichuanense uncovers gene expression profiling associated with plant development

description: Table S3. The list of all up/down-regulated DEGs in reproductive compared with vegetative stage. (XLS 5338Â kb)
DOI: 10.6084/m9.figshare.c.3611111_d1
title: Additional file 3: of De novo assembly and transcriptome characterization of spruce dwarf mistletoe Arceuthobium sichuanense uncovers gene expression profiling associated with plant development

description: Table S2. List of tissue-specific genes. (XLS 4063Â kb)
DOI: 10.6084/m9.figshare.c.3611075_d8
title: Additional file 1: Table S1. of Measure transcript integrity using RNA-seq data

description: Twelve RNA-seq datasets generated from human brain Glioblastoma (GBM) cell line2. Accession number, RNA Integrity Numbers (RIN), the median Transcript Integrity Numbers (medTIN), total read pairs, read pairs with mapping qualityâ  &gt;â  30, and number of genes with at least 10 reads are listed. (XLS 7 kb)
DOI: 10.15468/dl.qcqmsq
title: Occurrence Download

description: A dataset containing 4725 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Conidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4725 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033061-241126133413365/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.c.3611075_d6
title: Additional file 2: Table S2. of Measure transcript integrity using RNA-seq data

description: Twenty RNA-seq datasets generated from human peripheral blood mononuclear cell (PBMC)1. Accession number, RNA Integrity Numbers (RIN), and the median Transcript Integrity Numbers (medTIN), total reads, total reads with mapping quality &gt;30, and number of gene with at least 10 reads are listed. The PBMC samples were stored at room temperature for 0 h, 12 h, 24 h, 48 h and 84 h. Each time point contains 4 individuals (replicates). (XLS 9 kb)
DOI: 10.6084/m9.figshare.c.3611075_d7
title: Additional file 21: Table S7. of Measure transcript integrity using RNA-seq data

description: edgeR detected top 1000 differentially expressed genes (FDR cutoff = 0.01) in GBM samples without TIN correction. FC = Fold Change; CPM = Count Per Million; FDR = False Discovery Rate. (XLS 143 kb)
DOI: 10.6084/m9.figshare.c.3606812_d3
title: Additional file 2: Table S4. of Target identification in Fusobacterium nucleatum by subtractive genomics approach and enrichment analysis of host-pathogen protein-protein interactions

description: Non-human homologous proteins present in F. nucleatum. Table S5. Metabolic pathways of non-human homologous proteins according to KEGG. Table S6. Pathogen-specific metabolic pathways of screened proteins in F. nucleatum. Table S7. Subcellular localization of druggable proteins. (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.c.3606812_d1
title: Additional file 3: Table S8. of Target identification in Fusobacterium nucleatum by subtractive genomics approach and enrichment analysis of host-pathogen protein-protein interactions

description: Homology based HP-PPIs predicted from HPIDB. Table S9. Pathway enrichment analysis of host genes from DAVID functional annotation tool. Table S10. Gene ontology report of host genes. Table S11. Disease enrichment analysis of host genes participated in HP-PPIs. Table S12. Total functional annotation cluster analysis of host genes. (XLSX 99Â kb)
DOI: 10.6084/m9.figshare.c.3606812_d2
title: Additional file 1: Table S1. of Target identification in Fusobacterium nucleatum by subtractive genomics approach and enrichment analysis of host-pathogen protein-protein interactions

description: List of essential genes in F. nucleatum from DEG. Table S2. virulence factors list from VFDB search and literature. Table S3. List of resistance causing proteins from ARG-ANNOT tool. (XLSX 66Â kb)
DOI: 10.6084/m9.figshare.c.3606767_d5
title: Additional file 5: of 
                     De novo transcriptome sequencing and gene expression analysis reveal potential mechanisms of seed abortion in dove tree (Davidia involucrata Baill.)

description: DEGs between normal and abortive seeds. (XLS 1148 kb)
DOI: 10.6084/m9.figshare.c.3606767_d3
title: Additional file 1: of 
                     De novo transcriptome sequencing and gene expression analysis reveal potential mechanisms of seed abortion in dove tree (Davidia involucrata Baill.)

description: Sequences of all assembled unigenes. (FA 48010 kb)
DOI: 10.6084/m9.figshare.c.3606767_d4
title: Additional file 2 of 
                     De novo transcriptome sequencing and gene expression analysis reveal potential mechanisms of seed abortion in dove tree (Davidia involucrata Baill.)

description: All annotated unigenes. (XLS 29890 kb)
DOI: 10.6084/m9.figshare.c.3606719_d5
title: MOESM4 of Suppression of RAF/MEK or PI3K synergizes cytotoxicity of receptor tyrosine kinase inhibitors in glioma tumor-initiating cells

description: Additional file 4. Antibody list in RPPA analysis.
DOI: 10.6084/m9.figshare.c.3606719_d4
title: MOESM5 of Suppression of RAF/MEK or PI3K synergizes cytotoxicity of receptor tyrosine kinase inhibitors in glioma tumor-initiating cells

description: Additional file 5. Data of RPPA analysis.
DOI: 10.6084/m9.figshare.c.3606719_d2
title: MOESM3 of Suppression of RAF/MEK or PI3K synergizes cytotoxicity of receptor tyrosine kinase inhibitors in glioma tumor-initiating cells

description: Additional file 3. Gene expression of GSC11, GSC2 and GSC20.
DOI: 10.5063/f1xk8d14
title: OS-Prey (Omnibus study of prey) V2

description: The diet composition of a predator is a direct reflection of its role in a food web, resulting from interactions with prey species. Raptors (including hawks, eagles, owls, and falcons) are ubiquitous predators with diverse diets. We present a database of over 2000 raptor diets, representing 130 raptor species from across the world. The database comprises published records of raptor diets from pellets, prey remains, direct or photographic observations, prey DNA, and raptor gut contents. For each diet, we present the amounts and proportions of consumed prey as well as metadata such as location, habitat, and season.
DOI: 10.5066/p9utmb64
title: Estimating the presence of paved surface parking lots in the conterminous U.S. from land use coefficients for 1974, 1982, 1992, 2002, and 2012

description: Parking lots may be a significant source of pollution. Oil, sediments, and heavy metals may accumulate on their surface, then be flushed into rivers, streams, and lakes via rainfall. At present no dataset provides a mapping or estimation of parking lot area or locations nationwide. This product consists of a time series of five national 60-meter raster datasets which estimate the proportion of each pixel represented by parking lots, based on land-use coefficients. The rasters span the conterminous United States, for the years 1974, 1982, 1992, 2002, and 2012. The dataset was derived by calculating coefficients for 18 land-use types (Commercial, Industrial, Residential, Recreation, and so on) from the 2012 U.S. Geological Survey NAWQA Wall-to-wall Anthropogenic land-use Trends (NWALT) product. The coefficients were calculated by comparing NWALT land-uses to 1-meter rasters representing detailed paved surface parking lot polygons available from six cities: Bloomington, IN; Chattanooga, TN; Denver, CO; Hartford, CT; Raleigh, NC; and St. Paul, MN. The land-use classification overlying the largest amount of parking lot land areas was Commercial land (20.1% of land area), followed by Industrial land (19.6%), and Major Transportation (7.4%). The results were cross-validated against ground-truth data withheld from the calculations. The coefficients derived from the year 2012 data were then applied to the prior four years to create a time series. The rasters provide a way to estimate percent parking lot area by watershed or other area of interest, over the last four decades.
DOI: 10.5281/zenodo.10977925
title: Supporting data and code for High Concentrations of Nanoparticles from Isoprene Nitrates Predicted in Convective Outflow Over the Amazon

description: The Archive includes the CloudChem model code, which is used to simulate gas-phase chemical reactions and gas interactions with clouds. Additionally, it includes the simulated gas and particle concentration dataset used to produce figures for the paper "High Concentrations of Low Volatility Isoprene Nitrates Predicted in Convective Outflow Over the Amazon". For more information about the simulation setup and the results, please refer to the paper.
DOI: 10.5281/zenodo.12507119
title: Ma_et al_2024
DOI: 10.5523/bris.2t3lur8am5chu2ovswdb92qs5d
title: Ballell et al Ecological drivers of jaw morphological evolution in lepidosaurs

description: Supplementary Data for Ballell, A. et al. Ecological drivers of jaw morphological evolution in lepidosaurs. Proceedings of the Royal Society B.
DOI: 10.6084/m9.figshare.27187344.v1
title: Platelet-rich plasma as a potential therapy of cystocele: A systematic review and meta-analysis

description: Background: Platelet-rich plasma (PRP) therapy, is known for its regenerative properties. PRP may be able to help with cystocele cases. This review aims to explore how it might be applied to urogynecological cases, particularly those involving cystocele. Methods: The present systematic review adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guideline 2020, Meta-Analysis of Observational Studies in Epidemiology (MOOSE) guideline. The present systematic review was registered with PROSPERO with the registered number CRD42023414366. PubMed, Science Direct, Epistemonikos, COCHRANE, Google Scholar, and ProQuest were among the databases we searched. "(PRP OR Platelet-Rich Plasma) AND (Cystocele OR Anterior Pelvic Organ Prolapse)" from January 2007 to December 2022. Based on the PICO framework (Population = Patients with Cystocele; Intervention = Reconstruction with platelet-rich plasma injection; Compare = Reconstruction only; Outcome: Recurrency of Cystocele), four investigators (AMS, PMA, EAU, RSD, and AH) independently assessed eligibility by titles and abstracts. Using the Joanna Briggs Institute Critical Appraisal tool, each author evaluated full-text articles based on the kind of articles they had received. When consensus could not be obtained, disagreements were settled by involving the supervisors (EF, EMK, and BS). Results: A total of 8,924 studies were identified. After removing duplicates and applying eligibility criteria, two articles were included, encompassing 65 patients. In two studies, PRP injections were found and administered post-anterior colporrhaphy at the pubovesical fascia. According to these two trials, women who had anterior colporrhaphy and PRP injections required fewer reoperations. Conclusion: PRP has the potential to be a good alternative treatment to prevent cystocele recurrence. However, it cannot be generalized to large populations due to the small number of findings. Further studies with large samples examining the efficacy and safety of the therapy are needed to prove it.<br>
DOI: 10.6084/m9.figshare.c.3602330_d4
title: Additional file 4 of QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics

description: Spreadsheet file with the results summary file as downloaded from LINCS, for the HDAC signature used to validate the software. (CSV 4259.84 kb)
DOI: 10.5066/p98012he
title: Annual California Sea Otter Census-2018 Spring Census Summary

description: The spring 2018 mainland sea otter count began on April 26, and was completed by May 24, 2018. Overall viewing conditions this year were good and rounded off to the same conditions experienced during the 2017 spring census (View Score 2.4, where 0=poor, 1=fair, 2=good, 3=very good, and 4=excellent). The surface canopies of kelp (Macrocystis sp.) were considered by most participants to be above normal for this time of year in most areas of the mainland range, and considerably above what was encountered during the 2017 spring census. Sea otters along the mainland coast were surveyed from Pillar Point in San Mateo County in the north to Rincon Point in the south at the Santa Barbara/Ventura County line. A separate ground-based survey of the sea otter population at San Nicolas Island was completed earlier in the spring (April 13-15) under fair to good survey viewing conditions (View Score = 1.5). Surface kelp canopies at San Nicolas Island were estimated to be near the seasonal normal. These data support the following U.S. Geological Survey Data Series: Hatfield, B.B., Yee, J.L., Kenner, M.C., Tomoleoni, J.A., and Tinker, M.T., 2018, California sea otter (Enhydra lutris nereis) census results, spring 2018: U.S. Geological Survey Data Series 1097, 10 p., https://doi.org/10.3133/ds1097.
DOI: 10.5281/zenodo.10407320
title: Towards metadata for machine learning - Crosswalk tables

description: Crosswalks for Machine Learning models and datasets used for training

Here we present a collection of crosswalks for ML models (in TSV and XLSX formats) and datasets used for training (in TSV and XLSX formats). These crosswalks were created during an NFDI4DataScience hackathon organized by the Semantic Technologies team (SemTec) at ZB MED Information Centre for Life Sciences (ZB MED) with the aim of provindg a starting point for a common proposal towards a metadata schema for ML models based on schema.org.

Files



2023.11.23 Metadata for ML - ML dataset Union.tsv: Crosswalks for datasets in TSV format

2023.11.23 Metadata for ML - ML dataset Union.xlsx: Crosswalks for datasets in XLSX format

2023.11.23 Metadata for ML - ML model union.tsv: Crosswalks for ML models in TSV format

2023.11.23 Metadata for ML - ML model union.xlsx: Crosswalks for ML models in XLSX format
DOI: 10.5281/zenodo.12702466
title: Fracture intensity dataset for the paper entitled "Pre-existing off-fault damage can impede coseismic on-fault slip"

description: The locations of observation outcrops and pre-existing tectonic fracture intensity for the article: Wu, C. H., Cui, P., Klinger, Y., Tan, X. B.,Yi, S. J., & Li, Y. S. (2024). Pre‐existing off‐fault damage can impede coseismic on‐fault slip. Geophysical Research Letters,51, e2024GL111198. https://doi.org/10.1029/2024GL111198
DOI: 10.5281/zenodo.13148844
title: IFS CAT EDR Ensemble Data

description: This dataset contains ECMWF IFS ensemble forecast data of CAT-EDR index (https://www.ecmwf.int/en/newsletter/168/meteorology/forecasting-clear-air-turbulence) analyzed in Gisinger, Bramberger, Dörnbrack, and Bechtold (2024, GRL).
DOI: 10.6084/m9.figshare.25990594.v1
title: Influence of Atmospheric Slant Path on Geostationary Hyperspectral Infrared Sounder Radiance Simulations

description: The main code is in the 'code' file, where each '*.py' file is named with the name of the corresponding image. 'Data' file used in code data. The 'figure' file contains the image generated by the code
DOI: 10.14284/699
title: The intersect of the Exclusive Economic Zones and IHO sea areas, version 5
DOI: 10.15468/dl.jyvpk2
title: Occurrence Download

description: A dataset containing 5886 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Klebsiella pneumoniae (Schroeter, 1886) Trevisan, 1887"
 ]
}

 The dataset includes 5886 records from 87 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010042-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/pb8rmn
title: Amphibians of Ecuador/Anfibios de Ecuador

description: Ecuador ocupa el cuarto lugar en el mundo con la mayor diversidad de anfibios (600 especies, 276 endémicas), después de Brasil, Colombia y Perú. Sin embargo, entre estos países megadiversos, Ecuador es el más diverso si se considera su número de especies por unidad de superficie (0.002 especies por kilómetro cuadrado ). Es decir, Ecuador alberga en su territorio 3 veces más especies por kilómetro cuadrado que Colombia y 21 veces más que Brasil.
Esta inmensa diversidad numérica va de la mano de la diversidad genómica, proteómica, morfológica, ecológica, etológica, de formas de vida, de belleza estética, de usos biomédicos potenciales, de conocimientos ancestrales, de valores económicos, e innumerables otras razones, las cuales por si solas o en conjunto justifican por demás que esta riqueza anfibia sea considerada un patrimonio natural de la humanidad y por ende su investigación y conservación sean prioritarias. No cabe duda que el Buen Vivir depende de lo que las generaciones actuales y futuras hagan por este grupo de animales que enfrentan una crisis global de extinción, pues los anfibios son un termómetro y las primeras víctimas de nuestra dañina huella ecológica.
Los esfuerzos globales y locales por ayudar a los anfibios son por ahora casi insignificantes y distan de lograr sus objetivos. Las disminuciones y extinciones catastróficas de anfibios en la región andina de Ecuador, las cuales se reportan de mediados de los años ochenta (Coloma & Lombeida, 1992), son ejemplo de un fenómeno que no se pudo predecir ni ha sido solucionado. Actualmente, no menos del 28 % (188 especies) de anfibios ecuatorianos están en categorías de riesgo de extinción, y de entre ellos 13 especies ya están posiblemente extintas (ver Lista Roja en http://www.anfibiosecuador.ec/index.php?lr,10). Por otra parte, los datos son insuficientes para establecer el estatus de conservación de 152 especies.
La complejidad de entender la extinción anfibia al igual que lo problemático de detener la marcha de este desastre requiere de acciones proactivas de enorme magnitud. Nuevas amenazas a la diversidad (cambio climático global, patógenos emergentes) se suman a las ya conocidas como destrucción de hábitat, contaminación, especies introducidas, y otras. Por tanto, es substancial que la investigación académica y prácticas conservacionistas se fortalezcan y renueven acorde a las nuevas amenazas. En tal sentido, es esencial el desarrollo de nuevas tecnologías y el uso vanguardista de aquellas disponibles. Por ejemplo, es necesario el desarrollo de métodos de preservación criogénica de células germinales de anfibios, el desarrollo de tecnologías para la cría de anfibios ex situ, etc. Por su parte, la bioinformática permite ahora disponer de información veraz y actualizada —con la participación de la comunidad (ciencia ciudadana)—, como una herramienta útil para tomar decisiones y ejecutar acciones rápidas y apropiadas.
DOI: 10.15485/2324642
title: Model output from simulations of manganese-carbon interactions in temperate forest soil profiles

description: This archive contains model output, code, and scripts for simulations of coupled manganese-carbon cycling in temperate forest soil profiles. These model results were generated as part of a study investigating how manganese availability influences soil organic carbon stocks and demonstrating a new model framework for coupling carbon and manganese cycling. The simulations were in support of a manuscript: "Modeling interactive effects of manganese bioavailability, nitrogen deposition, and warming on soil carbon storage." The study addresses the research questions: How does Mn bioavailability, as driven by subsurface mineral properties, pH, and redox status, affect temperate forest soil organic carbon and litter carbon stocks?How is the relationship between Mn bioavailability and carbon cycling affected by changes in temperature and nitrogen deposition?"Model simulations were conducted in a reactive transport modeling framework using PFLOTRAN coupled to python. Multiple model simulations testing different Mn-bearing mineral solubilities, hydrological patterns, nitrogen deposition rates, and temperatures are included. Soil properties, including total and exchangeable Mn concentrations, are based on values reported for the Susquehanna Shale Hills Critical Zone Observatory (SSHCZO), a temperate forested watershed in central Pennsylvania, U.S.A where Mn cycling through vegetation has been documented.File formats include netCDF (.nc), python script (.py), shell script (.sh), plain text PFLOTRAN input file (.in), and plain text PFLOTRAN database file (.dat), and gzipped tar archive (tar.gz).
DOI: 10.17632/ccw5mvg69r.1
title: OPG Dataset for Kennedy Classification of Partially Edentulous Arches

description: This dataset contains orthopantomography (OPG) dental x-ray images along with annotations for three dental issues namely, broken root, periodontally compromised tooth, and Kennedy classification of partially edentulous arches. 
This prepared data has been utilized in the code file, also provided here, to train several models using different object detection architectures, hyperparameters, and training techniques. See the 'READ ME.txt' for further details.
DOI: 10.24432/c5kg68
title: Yeast