cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5zp3wc1d
title: MassIVE MSV000096655 - Resistance to anti-EGFR targeted therapy in head and neck squamous cell carcinoma
title: Total proteins were extracted in triplicate from cetuximab-sensitive and -resistant SC263 and SCC22b HNSCC cells. The LC system was coupled to a Q-Exactive Plus Orbitrap mass spectrometer (Thermo Fisher Scientific) programmed to acquire in data-dependent mode. A target of 1.7 x103 ions and a maximum injection time of 80 ms were used for MS/MS. The method was set to analyze the top 20 most intense ions from the survey scan and dynamic exclusion was enabled for 20 s. Tandem mass spectra were processed using MaxQuant software version 1.6.7.0. Proteins were identified using the Andromeda search engine and using the Homo sapiens proteome reference database (UniProt, release 20200130, 20366 entries). The parameters chosen for the identification include: digestion enzyme used was trypsin, maximum number of allowed missed cleavages was two. Oxidation of methionine, N-terminal acetylation, and phosphorylation of serine, threonine and tyrosine were set as variable modifications, while carbamidomethylation of cysteine was set as a fixed modification. A maximum number of 5 modifications per peptide was set. The precursor mass tolerance was set to 4.5 ppm and the fragmentation mass tolerance to 20 ppm. The peptide-to-spectrum match (PSM) and protein false discovery rates (FDR) were set at 1%. The match-between-runs and the label-free quantification (LFQ) methods were enabled using default parameters. After data treatment using MaxQuant, statistical analysis was done using Perseus software (version 1.6.7.0). The data matrix was filtered by removing the potential contaminants and decoy reverse sequences. The LFQ intensities were then log2-transformed and missing values were replaced by imputation based on the normal distribution. This resulted in the quantification of the expression of 2,741 unique proteins.
DOI: 10.6084/m9.figshare.c.3602444_d2
title: Additional file 6: of Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms

description: Identified aVMRs with nearest protein coding gene. (XLSX 19 kb)
DOI: 10.15468/dl.3whkm8
title: Occurrence Download

description: A dataset containing 503 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rissoidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 503 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033071-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.35110/19c1b837-a688-49ca-8b6f-22f35911c609
title: Dieppe sémaphore (Seine-Maritime) - MNT - 2014-Auj

description: MNT Dieppe sémaphore sont les Modèles Numériques de Terrain acquis au scanner laser terrestre depuis 2014 sur le front de falaise en dessous du sémaphore de Dieppe. Ces données ont pour objectif de suivre l’évolution de l’érosion des falaises crayeuses.
DOI: 10.6084/m9.figshare.c.3602693_d6
title: Additional file 6: Table S6. of Bioinformatics approach to predict target genes for dysregulated microRNAs in hepatocellular carcinoma: study on a chemically-induced HCC mouse model

description: Most significant functional groups obtained from clusterization process by Genemania, regarding 33 secondary genes, most closely related to liver cancer (FDRâ  â ¤0.05). Excel table presenting the 14 most significant cluster extracted by Genemania after selection of the 33 secondary genes. The table shows the false discovery rate and the gene coverage for each cluster. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3602921_d5
title: Additional file 6: Table S6. of Genetic basis of nitrogen use efficiency and yield stability across environments in winter rapeseed

description: Results of the GWAS for the WOSR populations for each trial × N × trait combination. (XLSX 150 kb)
DOI: 10.6084/m9.figshare.c.3602942_d1
title: Additional file 2: of Development of a prognostic model based on demographic, environmental and lifestyle information for predicting incidences of symptomatic respiratory or gastrointestinal infection in adult office workers

description: Raw data on the relationships between designated risk factors and occurrence of infections. Distribution of weeks with reported exposures to GTI or RTI, and of weeks with reported symptoms of gastrointestinal infection (GTI) or respiratory tract infection (RTI), among subgroups generated according to the answers to the questionnaire. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.c.3602921_d7
title: Additional file 3: Table S3. of Genetic basis of nitrogen use efficiency and yield stability across environments in winter rapeseed

description: Trial designs and crop management strategies. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3602921_d8
title: Additional file 1: Table S1. of Genetic basis of nitrogen use efficiency and yield stability across environments in winter rapeseed

description: Accessions of the WOSR populations. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3602948_d2
title: Additional file 2: of 
                     Drosophila pachea asymmetric lobes are part of a grasping device and stabilize one-sided mating

description: Measurements of mating behaviour. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3602948_d3
title: Additional file 1: of 
                     Drosophila pachea asymmetric lobes are part of a grasping device and stabilize one-sided mating

description: Raw measurements of mating behaviour, mating positions and genitalia. (XLSX 62 kb)
DOI: 10.35110/7e8463d2-1643-4522-a571-9832c4795c90
title: Dieppe falaise (Seine-Maritime) - MNT - 2014-Auj

description: MNT Dieppe falaise sont les Modèles Numériques de Terrain acquis au scanner laser terrestre depuis 2014 sur le front de falaise à l'est du sémaphore de Dieppe. Ces données ont pour objectif de suivre l’évolution de l’érosion des falaises crayeuses.
DOI: 10.35110/9e8e66f9-7801-4c30-9486-bdbcd584b577
title: Ailly (Seine-Maritime) - MNT - 2014-Auj

description: MNT Ailly sont les Modèles Numériques de Terrain acquis au scanner laser terrestre depuis 2014 sur le lieu-dit du Petit Ailly à Varengeville sur Mer. Ces données ont pour objectif de suivre l’évolution de l’érosion des falaises crayeuses.
DOI: 10.6084/m9.figshare.c.3603203_d1
title: Additional file 1: of Pollen record of disturbed topsoil as an indirect measurement of the potential risk of the introduction of non-native plants in maritime Antarctica

description: Calculation of the Invasion Index (INV). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3603362_d6
title: Additional file 10: of Physiological and transcriptional analyses of developmental stages along sugarcane leaf

description: This Additional File is an Excel File containing 6 spreadsheets (Additional Tables 4–9) with the results of our gene ontology analysis for each leaf segment. Table S4. Enriched gene ontology terms for genes over-expressed at B0 identified on the contrast B-B0. Table S5. Enriched gene ontology terms for genes over-expressed at B identified on the contrast B-B0. Table S6. Enriched gene ontology terms for genes over-expressed at B identified on the contrast M-B. Table S7. Enriched gene ontology terms for genes over-expressed at M identified on the contrast M-B. Table S8. Enriched gene ontology terms for genes over-expressed at M identified on the contrast T-M. Table S9. Enriched gene ontology terms for genes over-expressed at T identified on the contrast T-M. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3603383_d4
title: Additional file 6: of High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)

description: Recommended PELE-Seq workflow and SNP-calling parameters. An overview of the PELE-Seq analysis pipeline is outlined and optimized variant-calling parameters are provided for various read depths. (XLSX 8 kb)
DOI: 10.35110/48465771-075d-4983-b3a3-58595d79ec16
title: Base de données AIS trafic maritime Caraïbes 2019

description: Base de données PostGre/PostGIS rassemblant les trajectoires calculées à partir des position de l'ensemble des navires détectés par AIS (Automatic identification system) dans la Caraïbe en 2019. Il est produit à partir de données brutes AIS (trame NMEA) couvrant la Caraïbe acquises auprès de la société Exact Earth pour toute l'année 2019,dans le cadre du projet TRAFIC,soutenu par la Fondation de France,et réalisé au sein de l'OHM Littoral-Caraïbe. Les données ont été traitées par Damien Le Guyader (https://www.geo4seas.com/).
DOI: 10.6084/m9.figshare.c.3603362_d7
title: Additional file 6: of Physiological and transcriptional analyses of developmental stages along sugarcane leaf

description: Table with the list of orthologous genes between the five species: Sorghum bicolor (Abbreviation: SBIC), Setaria italica (Abbreviation: SITA), Saccharum sp. SP80–3280 (Abbreviation: SACC), Oryza sativa (Abbreviation: OSAT) and Zea mays (Abbreviation: ZMAY). Groups of orthologous genes were identified by OrthoMCL with an inflation value of 1.5. (BZ2 1258 kb)
DOI: 10.6084/m9.figshare.c.3603383_d6
title: Additional file 8: of High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)

description: Basic PELE-seq SNP-calling scripts. The basic commands used for PELE-Seq analysis are provided as a shell script. (TXT 11 kb)
DOI: 10.6084/m9.figshare.c.3603386_d1
title: Additional file 2 of Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints

description: Code S1. This zip-file contains the MATLAB code used for the simulation example (conversion process) and the application examples (NGF-induced Erk signaling in primary sensory neurons and Raf/MEK/ERK signaling in HeLa cells after release from S-phase arrest) presented in the paper. We provide implementations for the hybrid optimization and simulation-based optimization methods, the models and the optimization. In addition to the implementation, also all data and result files (.mat,.csv) are included. (ZIP 25965 kb)
DOI: 10.6084/m9.figshare.c.3603362_d8
title: Additional file 7: of Physiological and transcriptional analyses of developmental stages along sugarcane leaf

description: This Additional File is an Excel File containing 3 spreadsheets (Additional Tables 1–3) with the results of our differential expression analysis contrasting two leaf segments. Table S1. Differentially expressed genes between the contrast B-B0. Table S2. Differentially expressed genes between the contrast M-B. Table S3. Differentially expressed genes between the contrast T-M. (XLSX 150 kb)
DOI: 10.6084/m9.figshare.c.3603383_d7
title: Additional file 3: of High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)

description: SNP-calling results from E. coli spike-in libraries using the PELE-Seq, ORP, and Standard DNA-Seq methods. The performance of the PELE-Seq, ORP, and standard DNA-Seq methods at detecting rare alleles at various read depths. SNP results for spike-in libraries 1â  4 are reported, as well as read depths and other metrics for the libraries. Various allele frequency and quality score cutoffs were tested to optimize rare variant identification with the method, and the SNP-calling results are reported here. Recommended workflow and SNP-calling parameters are reported here and in Additional file 6. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.c.3603389_d1
title: Additional file 1: of HERMIONE: a randomized Phase 2 trial of MM-302 plus trastuzumab versus chemotherapy of physician’s choice plus trastuzumab in patients with previously treated, anthracycline-naïve, HER2-positive, locally advanced/metastatic breast cancer

description: HERMIONE IRB Data. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3603362_d9
title: Additional file 4: of Physiological and transcriptional analyses of developmental stages along sugarcane leaf

description: Sugarcane Trinity contigs were mapped to KEGG pathway using the single-directional best hit approach available in the KEGG Automatic Annotation Service ( http://www.genome.jp/tools/kaas/ ). This is a table with the results of such mapping. The table has three columns, 1. The name of the sugarcane transcript/contig, 2. The identifier for the KEGG pathway, and 3. The name of the pathway. (BZ2 76 kb)
DOI: 10.6084/m9.figshare.c.3603392_d1
title: Additional file 7: of Transcriptomic network analyses of leaf dehydration responses identify highly connected ABA and ethylene signaling hubs in three grapevine species differing in drought tolerance

description: kME values of all transcripts in each of the gene modules determined by WGCNA. (XLSX 15417Â kb)
DOI: 10.6084/m9.figshare.c.3603836_d9
title: Additional file 7: Table S7. of Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum

description: Differentially expressed sRNA under nutrient-rich and starvation conditions (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.c.3603881_d2
title: Additional file 9: of Genome-wide mapping of Hif-1Îą binding sites in zebrafish

description: A table of differentially regulated genes containing a ChIP peaks in their TSS. A table showing the position of ChIP peaks relative the differentially expressed genes from the vhl Vs WT microarray data found using GREAT version 2.02. Fold change, Unigene ID and presence of a HRE are indicated. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3603890_d1
title: Additional file 6: of Insights into the innate immunome of actiniarians using a comparative genomic approach

description: Alignment of NACHT domains from metazoan species. (FASTA 36Â kb)
DOI: 10.15468/dl.n7vkg4
title: Occurrence Download

description: A dataset containing 90 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anatomidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 90 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033072-241126133413365/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.3603881_d4
title: Additional file 2: of Genome-wide mapping of Hif-1Îą binding sites in zebrafish

description: The unfiltered list of differentially regulated genes for vhl vs wild-type. The unfiltered list of genes which were differentially regulated with a fold change â Ľ 2 in vhl mutants versus wild-type at 4dpf. Contains; Probe ID, Log 2 Fold Change, AveExpr: Average Expression across all arrays and Channels, t: moderated t statistic, p-value, add.j.p-value: p-value adjusted for multiple testing, B: B statistic, the log of the odds that the probe is differentially expressed, Unigene Description, Unigene ID and Gene Symbol. (XLSX 6344 kb)
DOI: 10.6084/m9.figshare.c.3603881_d5
title: Additional file 7: of Genome-wide mapping of Hif-1Îą binding sites in zebrafish

description: Wild-type ChIP sequencing peaks filtered for presence of a HRE. Filtering performed using MACS. (BED 2 kb)
DOI: 10.6084/m9.figshare.c.3603890_d4
title: Additional file 4: of Insights into the innate immunome of actiniarians using a comparative genomic approach

description: PAML results using the Yang and Nielsen [33] method. PAML results for complete sequences only of TLR, MyD88, NF-ÎşB, TMD-containing NLRs, Novel Gene 1, Novel Gene 2 and Novel Gene 3. (XLSX 46Â kb)
DOI: 10.35110/0aebb489-44d8-4164-8d03-6fa32615cb48
title: Jeu de données Drone de la Landes de l'Hermitage (Natura2000) - Vallée du Canut

description: Suivi temporel de la landes de l'Hermitage (vallée du Canut) par drone et capteurs multisources (RGB,Multispectral). Suivi réalisé dans le cadre du projet MITI LANDMAN et OSUR Interdisciplinaire Blanc "Intéractions sol / plantes / atmosphère dans les Landes bretonnes".
DOI: 10.35110/83bf7877-e3fe-4dc9-8e32-61e26f9268ee
title: Jeu de données Drone de la Tourbières de Landemarais

description: Suivi temporel de la Tourbières de Landemarais par drone et capteurs multisources (RGB,Multispectral,thermique). Suivi réalisé dans le cadre de la Zone Atelier Armorique par la Plateforme D2T au printemps et fin d'été / automne. Contribution au suivi dans le cadre du SNO Tourbières.
DOI: 10.6084/m9.figshare.c.3604451_d2
title: Additional file 2: of Introduction of digital speech recognition in a specialised outpatient department: a case study

description: Raw dataset to calculate “time to letter finalised”. Parameter “time to letter finalised” for each letter that has been sent in 2015 (in days; numeric) and respective month when letter was created (1–12; string). (CSV 16 kb)
DOI: 10.6084/m9.figshare.c.3604631_d2
title: Additional file 2: of GeneSCF: a real-time based functional enrichment tool with support for multiple organisms

description: The list of organisms supported by GeneSCF for Gene ontology functional database. (XLS 9 kb)
DOI: 10.6084/m9.figshare.c.3604646_d1
title: MOESM2 of Characterization of sugarcane (Saccharum spp.) leaf senescence: implications for biofuel production

description: Additional file 2. Analysis of variance (ANOVA) of the (A) SPAD index, (B) macronutrients, (C) micronutrients, and (D) neutral monosaccharides. The significant data were highlighted in red.
DOI: 10.6084/m9.figshare.c.3604640_d2
title: MOESM3 of Knowledge, attitudes and perceptions of occupational hazards and safety practices in Nigerian healthcare workers

description: Additional file 3. Summation of composite knowledge, attitude and perception ratings.
DOI: 10.6084/m9.figshare.c.3604628_d3
title: Additional file 2: Table S1. of Coevolution of female and male genital components to avoid genital size mismatches in sexually dimorphic spiders

description: Phylogenetic correlation results from PDAP for all pairs of parameters. Abbreviations: FTPL: Female Tibia-Patella Length. FCL: Female Carapace Length.sq_RA: square-root Reproductive Area. sq_EA: square-root Epigynal Area. DBO: distance between copulatory openings. open_W: copulatory opening Width. duct_L: reproductive duct Length. cube_SV: cube-root Spermatheca Volume. MBL: Male Body Length. MTPL: Male Tibia-Patella Length. MCW: Male Carapace Width. MCL: Male Carapace Length. ECL: Embolic Conductor Length. cube_BV: cube-root pedipal Bulb Volume. cube_PV: cube-root pedipalp Volume. EW: Embolus Width. cube_EV: cube-root embolus Volume. SSD_BL: FBL/MBL. SSD_TPL: FTPL/MTPL. SSD_CW: FCW/MCW. SSD_CL: FCL/MCL. SGD_SB: Spermatheca volume/Pedipalp Bulb volume. SGD_SP: Spermatheca volume/Pedipalp volume. SGD_EB: Epigynal area/Pedipalp Bulb volume. SGD_EP: Epigynal area/Pedipalp volume. SGD_RB: Reproductive Area/Pedipalp Bulb volume. SGD_RP: Reproductive Area/Pedipalp volume. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.c.3604631_d3
title: Additional file 11: of GeneSCF: a real-time based functional enrichment tool with support for multiple organisms

description: Enrichment analysis results for list-B genes from GeneSCF and DAVID 6.7 using KEGG as a reference database. (XLS 112 kb)
DOI: 10.6084/m9.figshare.c.3604631_d4
title: Additional file 10: of GeneSCF: a real-time based functional enrichment tool with support for multiple organisms

description: Enrichment analysis results for list-A genes from GeneSCF, DAVID and Gorilla using Gene Ontology, Biological Process (GO_BP) as a reference database. (XLS 1589 kb)
DOI: 10.6084/m9.figshare.c.3604649_d2
title: Additional file 2: Figure S1. of Decreased neuroinflammation correlates to higher vagus nerve activity fluctuations in near-term ovine fetuses: a case for the afferent cholinergic anti-inflammatory pathway?

description: C-Fos in fetal sheep brain. A. Western blot establishing the specificity of this antibody in near-term fetal sheep brainstem, cerebellum and cortex. B. Western blot: raw data of the image shown in Fig. S1A. C. c-Fos immunohistochemistry (IHC) in near-term fetal sheep and guinea pig brainstems. Top left: positive control staining. The cervical vagus nerve trunks were stimulated bilaterally (the stimulation was applied proximal to the bilateral cervical vagatomy to ensure strictly afferent signaling). Note diffuse c-Fos signal with high levels of background stain. Top right: negative control staining. Similar procedure was performed as in afferent stimulation, except the stimulation was performed distal of the vagatomy site ensuring strictly efferent signaling. Bottom left: example of a UCO group fetal sheep staining. Bottom right: Here we demonstrate the IHC approach regarding secondary antibody and visualization techniques; as primary antibody we used MBP (details in Methods). (ZIP 85110 kb)
DOI: 10.15468/dl.vv8n9e
title: Occurrence Download

description: A dataset containing 303 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Margaritidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 303 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033073-241126133413365/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.3604628_d5
title: Additional file 3: Matrix S1. of Coevolution of female and male genital components to avoid genital size mismatches in sexually dimorphic spiders

description: A nexus file containing raw data, phylogenetic trees, and PDAP analyses. (TXT 81 kb)
DOI: 10.6084/m9.figshare.c.3604631_d5
title: Additional file 7: of GeneSCF: a real-time based functional enrichment tool with support for multiple organisms

description: Pathway enrichment results from GeneSCF for p53 bound genes at 12Â h (Case study 2) predicted by GeneSCF using KEGG as a reference database. (XLS 55 kb)
DOI: 10.6084/m9.figshare.c.3604646_d3
title: MOESM3 of Characterization of sugarcane (Saccharum spp.) leaf senescence: implications for biofuel production

description: Additional file 3. Correlation matrix between macronutrients, micronutrients, SPAD index, and neutral monosaccharides into in-leaf senescence gradient. (A) base, (B) middle, and (C) tip portions of the leaf blade. Significant correlation data (Pearson’s correlation matrix) were highlighted in red (p value ≤0.05).
DOI: 10.6084/m9.figshare.c.3604631_d6
title: Additional file 9: of GeneSCF: a real-time based functional enrichment tool with support for multiple organisms

description: Functional enrichment results from GeneSCF for p53 bound genes at 12Â h (Case study 2) predicted by GeneSCF using Gene ontology, Molecular Function (GO_MF) as a reference database. (XLS 97 kb)
DOI: 10.6084/m9.figshare.c.3604631_d7
title: Additional file 5: of GeneSCF: a real-time based functional enrichment tool with support for multiple organisms

description: Pathway enrichment results from GeneSCF for CLL associated differentially expressed genes (Case study 1) predicted using KEGG as reference database. (XLS 230 kb)
DOI: 10.6084/m9.figshare.c.3604856_d1
title: Additional file 1: of Still mesoendemic onchocerciasis in two Cameroonian community-directed treatment with ivermectin projects despite more than 15 years of mass treatment

description: Datasets of Bafia and Yabassi health districts supporting this study. (XLSX 114 kb)
DOI: 10.6084/m9.figshare.c.3604853_d6
title: Additional file 8: of Genomic consequences of selection and genome-wide association mapping in soybean

description: The descriptive summary of GWAS for 9 agronomic traits in soybean. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.c.3605006_d1
title: Additional file 2: of The relevance of cortical lesions in patients with multiple sclerosis

description: Detailed analyses of attentional, mnestic and executive functions (z-scores). (XLS 29Â kb)
DOI: 10.6084/m9.figshare.c.3605105_d1
title: Additional file 1: of Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda)

description: Putative primer pairs for the class I and class II SSRs in the coding regions of Norway spruce (Picea abies ) and Loblolly pine ( Pinus taeda ). (XLSX 4157 kb)