cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3632798_d8
title: Additional file 9: Table S9. of Transcriptome wide analyses reveal a sustained cellular stress response in the gill tissue of Trematomus bernacchii after acclimation to multiple stressors

description: Homeostatic process: This table provides all differentially expressed genes exceeding the confidence threshold (FDR ≤ 0.05) that are associated with the GO Term homeostatic process (GO:0042592) at 7d, 28d and 56d (n = 4). The table includes the gene sequence name from the reference transcriptome, the BLAST result description, the sequence length, the number of BLAST hits to that gene sequence, the minimum e-value of the BLAST hits, the mean similarity, the # of GO terms associated with that sequence, the list of those GO terms, the Enzyme Codes associated with that sequence, InterproScan results associated with that sequence, the log2 adjusted fold change in expression, the log2 counts per million (CPM) of the reads mapped to that sequence, and the p-value and FDR reflecting the confidence in the displayed differential expression of that gene. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3632798_d9
title: Additional file 5: Table S5. of Transcriptome wide analyses reveal a sustained cellular stress response in the gill tissue of Trematomus bernacchii after acclimation to multiple stressors

description: Cell proliferation: This table provides all differentially expressed genes exceeding the confidence threshold (FDR ≤ 0.05) that are associated with the GO Term cell proliferation (GO:0008283) at 7d, 28d and 56d (n = 4). The table includes the gene sequence name from the reference transcriptome, the BLAST result description, the sequence length, the number of BLAST hits to that gene sequence, the minimum e-value of the BLAST hits, the mean similarity, the # of GO terms associated with that sequence, the list of those GO terms, the Enzyme Codes associated with that sequence, InterproScan results associated with that sequence, the log2 adjusted fold change in expression, the log2 counts per million (CPM) of the reads mapped to that sequence, and the p-value and FDR reflecting the confidence in the displayed differential expression of that gene. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3632801_d8
title: Additional file 12: Table S6. of Germ cell and tumor associated piRNAs in the medaka and Xiphophorus melanoma models

description: Bed file of Xiphophorus piRNA clusters. (BED 1072Â kb)
DOI: 10.6084/m9.figshare.c.3632828_d1
title: Additional file 1: of Nutritional quality and marketing strategies of fast food childrenâ  s combo meals in Guatemala

description: Child-oriented fast food meals in Guatemala. Data on prevalence of child-oriented fast food meals in Guatemala (XLSX 36 kb)
DOI: 10.6084/m9.figshare.c.3632816_d9
title: Additional file 3: Table S3. of Suboptimal culture conditions induce more deviations in gene expression in male than female bovine blastocysts

description: Lists of the genes differentially expressed in all the comparisons (including all the fold-changes), with their corresponding name, fold-change, p-value, and FDR corrected p-value. A positive fold-change indicates that the gene is up-regulated in Group 1 vs. Group 2. Correspondingly, a negative fold-change indicates that the gene is down-regulated in Group 1 vs. Group 2. (XLSX 423 kb)
DOI: 10.6084/m9.figshare.c.3632837_d4
title: Additional file 3: Table S3. of Gene and miRNA expression signature of Lewis lung carcinoma LLC1 cells in extracellular matrix enriched microenvironment

description: List of all KEGG Pathways enriched in differently expressed genes in LLC1 cells under lr-ECM 3D versus 2D cell culture conditions. (XLS 28Â kb)
DOI: 10.6084/m9.figshare.c.3632846_d2
title: Additional file 2: Table S2. of Vector competence of Aedes vexans (Meigen), Culex poicilipes (Theobald) and Cx. quinquefasciatus Say from Senegal for West and East African lineages of Rift Valley fever virus

description: Mosquito tested, number infected, that disseminated and transmitted by species and Rift valley fever strains. (XLS 25 kb)
DOI: 10.6084/m9.figshare.c.3632837_d5
title: Additional file 5: TAble S5. of Gene and miRNA expression signature of Lewis lung carcinoma LLC1 cells in extracellular matrix enriched microenvironment

description: Differentially expressed miRNA (fold change above 2; Pâ
DOI: 10.6084/m9.figshare.c.3632852_d2
title: Additional file 1: Table S1. of Prescription of potentially inappropriate medication in Korean older adults based on 2012 Beers Criteria: a cross-sectional population based study

description: A list of comorbidities corresponding to the ICD-10 diagnostic codes. (CSV 8 kb)
DOI: 10.6084/m9.figshare.c.3632837_d6
title: Additional file 2: Table S2. of Gene and miRNA expression signature of Lewis lung carcinoma LLC1 cells in extracellular matrix enriched microenvironment

description: Differentially expressed genes (fold change above 1.5; Pâ
DOI: 10.6084/m9.figshare.c.3632837_d7
title: Additional file 7: Table S7. of Gene and miRNA expression signature of Lewis lung carcinoma LLC1 cells in extracellular matrix enriched microenvironment

description: List of all KEGG Pathways enriched in differently expressed miRNAs in LLC1 cells grown under lr-ECM 3D versus 2D cell culture conditions. (XLS 32Â kb)
DOI: 10.15468/dl.ebzmgz
title: Occurrence Download

description: A dataset listing the 20 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-68.83228 -32.8667,-68.8331 -32.86666,-68.83325 -32.86723,-68.83352 -32.86827,-68.83376 -32.8692,-68.83384 -32.86949,-68.83397 -32.86998,-68.83409 -32.87046,-68.83441 -32.87166,-68.83468 -32.87266,-68.83496 -32.87371,-68.83536 -32.87511,-68.83567 -32.8763,-68.83597 -32.87746,-68.83627 -32.87859,-68.83656 -32.8797,-68.83627 -32.87973,-68.83614 -32.87974,-68.83509 -32.87982,-68.83376 -32.87992,-68.83236 -32.88002,-68.83097 -32.88013,-68.82956 -32.88023,-68.82816 -32.88034,-68.82728 -32.8804,-68.82644 -32.87706,-68.82639 -32.87686,-68.82632 -32.87676,-68.82621 -32.87662,-68.82611 -32.87652,-68.826 -32.87647,-68.82351 -32.87532,-68.82065 -32.87402,-68.82024 -32.87282,-68.82009 -32.87226,-68.82007 -32.87217,-68.81959 -32.87135,-68.81925 -32.87081,-68.81923 -32.8708,-68.81908 -32.87063,-68.81871 -32.8703,-68.81829 -32.8699,-68.81814 -32.86968,-68.8181 -32.86961,-68.81767 -32.8688,-68.81749 -32.86838,-68.81744 -32.8682,-68.81743 -32.86814,-68.8173 -32.8673,-68.81848 -32.86716,-68.81881 -32.86712,-68.81976 -32.86706,-68.82004 -32.86704,-68.82133 -32.86701,-68.82137 -32.86701,-68.82206 -32.8667,-68.82253 -32.86649,-68.82269 -32.86647,-68.82404 -32.86646,-68.82539 -32.86645,-68.82721 -32.86644,-68.82836 -32.86643,-68.82873 -32.86648,-68.82901 -32.8666,-68.82934 -32.86675,-68.82954 -32.86679,-68.82974 -32.8668,-68.83025 -32.86678,-68.83176 -32.86672,-68.83228 -32.8667))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves"
 ]
}

 The dataset's 20 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033822-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pkgsh2
title: Occurrence Download

description: A dataset containing 181955 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aves",
 "Geometry POLYGON ((-90.46806 17.81083, -89.15111 17.81083, -89.15111 19.2, -90.46806 19.2, -90.46806 17.81083))",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material citation)"
 ]
 }
 }
 ]
}

 The dataset includes 181955 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033824-241126133413365/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.3632918_d1
title: Additional file 1: of Intestinal adaptations to a combination of different diets with and without endurance exercise

description: Spreadsheet of data for brush border membrane assasys. (XLSX 117Â kb)
DOI: 10.6084/m9.figshare.c.3632915_d1
title: Additional file 2: Table S2. of Development of a point-of-care-device for fast detection of periodontal pathogens

description: Primer sequences and product size. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3632918_d2
title: Additional file 3: of Intestinal adaptations to a combination of different diets with and without endurance exercise

description: Spreadsheet of data for rates of glucose uptakes. (XLSX 118Â kb)
DOI: 10.6084/m9.figshare.c.3632915_d2
title: Additional file 3: Table S3. of Development of a point-of-care-device for fast detection of periodontal pathogens

description: Crossing points (CP) corresponding to Fig.Â 5 (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3632918_d3
title: Additional file 4: of Intestinal adaptations to a combination of different diets with and without endurance exercise

description: Spreadsheet of data for histology measurements. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.c.3632906_d6
title: Additional file 7: Dataset S1. of Temperature-dependent changes in the host-seeking behaviors of parasitic nematodes

description: Compilation of mean, n, and standard error of the mean (SEM) values for all assays presented in this study. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.c.3632915_d3
title: Additional file 1: Table S1. of Development of a point-of-care-device for fast detection of periodontal pathogens

description: Organisms and cultivation conditions. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3632918_d4
title: Additional file 5: of Intestinal adaptations to a combination of different diets with and without endurance exercise

description: Spreadsheet of data for intestinal wet and dry masses. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3632933_d1
title: Additional file 1: of Smokescreen: a targeted genotyping array for addiction research

description: Smokescreen addiction regions and estimated imputed coverage. This file contains the addiction-related gene regions (chr 1â  22) represented on the Smokescreen array and the estimated imputation-based coverage for each region in European (EUR), Asian (ASN), and African (YRI) populations. (XLSX 338Â kb)
DOI: 10.6084/m9.figshare.c.3632918_d5
title: Additional file 6: of Intestinal adaptations to a combination of different diets with and without endurance exercise

description: Spreadsheet of data for measurements collected at the time of necropsy. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.c.3633011_d3
title: Additional file 4: of Draft genome of the scabies mite

description: Normalized abundance of shared Pfam domains in four mite proteomes. Values represent the number of domains that would be present in a proteome bearing 10,000 Pfam domains. Blue represents minor outliers that are higher than expected and Red represents minor outliers that are lower than expected. There were no major outliers detected. (XLSX 115Â kb)
DOI: 10.6084/m9.figshare.c.3632996_d5
title: Additional file 2: Table S2. of Production of hemolysin BL by Bacillus cereus group isolates of dairy origin is associated with whole-genome phylogenetic clade

description: Virulence-associated genes included in the comparative genomic analysis of Bacillus cereus group isolates. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.c.3633011_d4
title: Additional file 3: of Draft genome of the scabies mite

description: All Pfam hits in the scabies proteome with 1 x 10 â  4 cutoff. This is a redundant list (since some proteins contain multiple domains) that can be used to count the number of specific Pfam domains in the proteome. (XLSX 358Â kb)
DOI: 10.5281/zenodo.14453972
title: Vocabulary Tests LLMs

description: Vocabulary evaluation of LLMs

This repository contains the results for the different vocabulary tests run on LLM tools/models presented in the paper: "The continued usefulness of vocabulary tests for evaluating large language models" currently published  in PLOS ONE: https://doi.org/10.1371/journal.pone.0308259

The name of the files correspond to the vocabulary tests for which results are presented in Tables 3-6 in the paper (note that questions for the TOEFL test are not public).  

In each file, the first column has the question posed to the LLM tool/model, followed by the correct answer. The rest of the columns correspond to the answers of the different LLM tools/models evaluated.  The results and percentages are summarized at the bottom of the file after the last test items.

The models evaluated are:




Model
Link


Llama 2 7b  
https://huggingface.co/meta-llama/Llama-2-7b-chat


Llama 2 13b  
https://huggingface.co/meta-llama/Llama-2-13b-chat


Llama 2 70b
https://huggingface.co/meta-llama/Llama-2-70b-chat


Mistral 7b v0.1
https://huggingface.co/mistralai/Mistral-7B-v0.1


GPT 3.5 turbo 0613
https://platform.openai.com/docs/models/gpt-3-5-turbo


GPT 4 0613  
https://platform.openai.com/docs/models/gpt-4-turbo-and-gpt-4


Bard
 




To cite our work:

@article{10.1371/journal.pone.0308259,
    doi = {10.1371/journal.pone.0308259},
    author = {Martínez, Gonzalo AND Conde, Javier AND Merino-Gómez, Elena AND Bermúdez-Margaretto, Beatriz AND Hernández, José Alberto AND Reviriego, Pedro AND Brysbaert, Marc},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    title = {Establishing vocabulary tests as a benchmark for evaluating large language models},
    year = {2024},
    month = {12},
    volume = {19},
    url = {https://doi.org/10.1371/journal.pone.0308259},
    pages = {1-17},
    number = {12},

}
DOI: 10.5281/zenodo.14453973
title: Vocabulary Tests LLMs

description: Vocabulary evaluation of LLMs

This repository contains the results for the different vocabulary tests run on LLM tools/models presented in the paper: "The continued usefulness of vocabulary tests for evaluating large language models" currently published  in PLOS ONE: https://doi.org/10.1371/journal.pone.0308259

The name of the files correspond to the vocabulary tests for which results are presented in Tables 3-6 in the paper (note that questions for the TOEFL test are not public).  

In each file, the first column has the question posed to the LLM tool/model, followed by the correct answer. The rest of the columns correspond to the answers of the different LLM tools/models evaluated.  The results and percentages are summarized at the bottom of the file after the last test items.

The models evaluated are:




Model
Link


Llama 2 7b  
https://huggingface.co/meta-llama/Llama-2-7b-chat


Llama 2 13b  
https://huggingface.co/meta-llama/Llama-2-13b-chat


Llama 2 70b
https://huggingface.co/meta-llama/Llama-2-70b-chat


Mistral 7b v0.1
https://huggingface.co/mistralai/Mistral-7B-v0.1


GPT 3.5 turbo 0613
https://platform.openai.com/docs/models/gpt-3-5-turbo


GPT 4 0613  
https://platform.openai.com/docs/models/gpt-4-turbo-and-gpt-4


Bard
 




To cite our work:

@article{10.1371/journal.pone.0308259,
    doi = {10.1371/journal.pone.0308259},
    author = {Martínez, Gonzalo AND Conde, Javier AND Merino-Gómez, Elena AND Bermúdez-Margaretto, Beatriz AND Hernández, José Alberto AND Reviriego, Pedro AND Brysbaert, Marc},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    title = {Establishing vocabulary tests as a benchmark for evaluating large language models},
    year = {2024},
    month = {12},
    volume = {19},
    url = {https://doi.org/10.1371/journal.pone.0308259},
    pages = {1-17},
    number = {12},

}
DOI: 10.6084/m9.figshare.c.3633008_d6
title: MOESM1 of Levels of DNA methylation and transcript accumulation in leaves of transgenic maize varieties

description: Additional file 1. Output results of NormFinder algorithm used for determining the best endogenous normalizer genes. Leunig (LUG) and Membrane protein PB1A10.07c (MEP) showed the best combination of two normalizer genes with a stability value of 0.025.
DOI: 10.6084/m9.figshare.c.3633011_d5
title: Additional file 1: of Draft genome of the scabies mite

description: BSUCO analysis metrics for Scabies and other acari genomes and gene sets. (XLSX 6Â kb)
DOI: 10.6084/m9.figshare.c.3633011_d6
title: Additional file 6: of Draft genome of the scabies mite

description: Locations and putative identities of scabies homologs for vaccine candidates listed in [ 110 ]. (XLSX 5Â kb)
DOI: 10.6084/m9.figshare.c.3633047_d1
title: Additional file 4: of Transcriptomes of post-mitotic neurons identify the usage of alternative pathways during adult and embryonic neuronal differentiation

description: List of genes expressed in the nervous system obtained from ZebrafishMine (http://www.zebrafishmine.org/begin.do) and Panther Classification system [ 27 ]. (XLSX 146Â kb)
DOI: 10.6084/m9.figshare.c.3633047_d2
title: Additional file 6: of Transcriptomes of post-mitotic neurons identify the usage of alternative pathways during adult and embryonic neuronal differentiation

description: DESeq2 results showing a comparison between labeled mRNA from adult brain and labeled mRNA from embryos with padjâ
DOI: 10.5281/zenodo.14453224
title: Bayesian phylogeographical analyses of the world's language families

description: Contained in this repository are in- and output files for phylogeographical analyses of the world’s language families using BayesTraits. Tree topologies come from Glottolog and branch lengths are adapted from ASJP LDN measures. Full detail is provided in the file Pipeline.pdf at https://github.com/Sokiwi/SpreadRates. Here scripts are furthermore provided for replicating the analyses and parsing the output.
DOI: 10.5281/zenodo.14453223
title: Bayesian phylogeographical analyses of the world's language families

description: Contained in this repository are in- and output files for phylogeographical analyses of the world’s language families using BayesTraits. Tree topologies come from Glottolog and branch lengths are adapted from ASJP LDN measures. Full detail is provided in the file Pipeline.pdf at https://github.com/Sokiwi/SpreadRates. Here scripts are furthermore provided for replicating the analyses and parsing the output.
DOI: 10.6084/m9.figshare.c.3633080_d4
title: Additional file 4: Table S2. of Tartaric acid pathways in Vitis vinifera L. (cv. Ugni blanc): a comparative study of two vintages with contrasted climatic conditions

description: Compilation of proteomic data concerning the four proteins of interest. (ZIP 824 kb)
DOI: 10.6084/m9.figshare.c.3633104_d1
title: Additional file 2: of Estimating cumulative pathway effects on risk for age-related macular degeneration using mixed linear models

description: Pathway Gene Lists. This Excel file contains lists of all genes contained within each pathway assessedâ  one column per pathway. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.c.3633101_d4
title: MOESM6 of What are the effects of agricultural management on soil organic carbon in boreo-temperate systems?

description: Additional file 6. Articles Unobtainable as Full Texts.
DOI: 10.6084/m9.figshare.c.3633101_d5
title: MOESM7 of What are the effects of agricultural management on soil organic carbon in boreo-temperate systems?

description: Additional file 7. Systematic Map Database.
DOI: 10.6084/m9.figshare.c.3633101_d6
title: MOESM5 of What are the effects of agricultural management on soil organic carbon in boreo-temperate systems?

description: Additional file 5. Database of Reviews and Meta-analyses.
DOI: 10.6084/m9.figshare.c.3633128_d8
title: Additional file 2 of Addressing inaccuracies in BLOSUM computation improves homology search performance

description: List of best performing matrix/gap parameter combinations. (CSV 47.6 kb)
DOI: 10.6084/m9.figshare.c.3633152_d1
title: Additional file 1: of Assessment of subchondral bone marrow lesions in knee osteoarthritis by MRI: a comparison of fluid sensitive and contrast enhanced sequences

description: Supplementary imaging protocol, method description and figures. (ZIP 5644 kb)
DOI: 10.15468/dl.4f879g
title: Occurrence Download

description: A dataset containing 1281 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-74.07462 4.76578,-74.07421 4.76694,-74.07881 4.77462,-74.08388 4.78398,-74.08707 4.79066,-74.09029 4.79721,-74.09163 4.79872,-74.09457 4.80108,-74.09875 4.79961,-74.10019 4.7958,-74.09786 4.78909,-74.08947 4.77633,-74.07798 4.76009,-74.07462 4.76578))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1281 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033830-241126133413365/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.3633218_d3
title: Additional file 3 of Case-oriented pathways analysis in pancreatic adenocarcinoma using data from a sleeping beauty transposon mutagenesis screen

description: CIS and pathways association table. (TXT 3.87 kb)
DOI: 10.5063/f11c1vbr
title: Lake Borgne, Louisiana, Summer 2021, 2023, 2024, Spring 2022 benthic community data

description: Sediment cores for benthic community analysis were collected in Lake Borgne in Louisiana during the summer of 2021, spring 2022, summer 2023, and summer 2024. Samples for summer 2021 only contained sites for a Before-After Control-Impact (BACI) study for dredge sites in the area. Spring 2022 sampling added sample sites throughout the lake, and only sampled these additional sites. Summer 2023 and summer 2024 sampling covered the original BACI sites and the added spring 2022 sites. The sampling of summer 2024 also included YSI measured environmental variables. The identifications of benthic organisms across the sampling periods were used for temporal comparisons. Biomass data was collected from samples. Biomass was split between an ecologically relevant species, Rangia cuneata, and all other species found in the sample. These data files contain the benthic community identifications, calculated biomass of samples, any collected environmental data, and coordinates for sample site locations.
DOI: 10.6084/m9.figshare.c.3633284_d1
title: Additional file 1: of Impact of kinetic isotope effects in isotopic studies of metabolic systems

description: R scripts used to construct the models, perform the simulations and generate the figures. (TAR 137 kb)
DOI: 10.6084/m9.figshare.c.3633278_d3
title: Additional file 6: Figure S5. of 
                     Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

description: Percentage of the variation in MIC values explained by each mutated codon in candidate genes. Bars in red represent significant independent associations with increased MIC (pâ
DOI: 10.15468/dl.qp8fyq
title: Occurrence Download

description: A dataset containing 53179 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "Geometry POLYGON ((-90.46806 17.81083, -89.15111 17.81083, -89.15111 19.2, -90.46806 19.2, -90.46806 17.81083))",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material citation)"
 ]
 }
 }
 ]
}

 The dataset includes 53179 records from 143 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033831-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.