cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7390613.v1
title: Stereological and morphological analysis of the effects of aging on spermatogenesis in rat testis

description: Abstract Purpose: To quantify, through stereological and morphometric analysis, spermatogenesis in rats undergoing the natural aging process. Methods: Seventy-two male Wistar rats were divided into 6 equal groups according to age at the time of killing: 3, 6, 9, 12, 18, and 24 months. All the rats were subjected orchiectomy and collection of testicular parenchymal fragments for histological and morphometric analysis. The numerical density of spermatids was calculated using a stereological study, and morphometric analysis was conducted to measure the height of the germinal epithelium and the area of the seminiferous tubules. Results: We found that the 18 and 24 months groups showed a significant reduction in the number of round spermatids. However, the height of the germinal epithelium was not significantly different between the groups. The area of seminiferous tubules was also significantly reduced in the elderly rats compared to that in the young ones. Conclusion: Aging of rats showed a significant reduction in the number of round spermatids and the area of the seminiferous tubules, more pronounced in the rats at 18 and 24 months of life.
DOI: 10.6084/m9.figshare.7390610.v1
title: Chemical characteristics, aerobic stability, and microbiological counts in corn silage re-ensiled with bacterial inoculant

description: Abstract: The objective of this work was to evaluate the effects of re-ensiling and bacterial inoculation on the quality of corn silage. The experiment was carried out in a 2x2 factorial design with or without inoculant (association of Lactobacillus plantarum and Propionibacterium acidipropionici), and with re-ensiling after 36 hours of aerobic exposure or only ensiling of the whole plant of 'BRS 1055' corn. The fermentative quality, nutritional parameters, dry matter losses, aerobic stability, and microbiological counts of silages were evaluated. Re-ensiling caused an increase of pH and in acetic acid and propionic acid concentrations, as well as in the dry matter (DM), crude protein, neutral detergent fiber, and neutral detergent fiber crude protein contents. Conversely, there was a reduction in the nonfiber carbohydrates concentration and in in vitro dry matter digestibility for the re-ensiled material. All changes were explained by the higher-effluent production and DM loss of re-ensiled material that was subjected to two compactions. Microbiology was not altered by the treatments. The use of inoculant altered ash content, but it did not influence other parameters. In contrast, re-ensiling after 36 hours of aerobic exposure caused a reduction in the nutritive value of corn silage and accentuated the DM losses.
DOI: 10.7284/120696
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1504A using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7390541
title: Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny

description: Supplementary data for "Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny."<br>hamstrsearch_model_taxa.sh: Commands used to process translated transcriptomes and predicted proteins from genomes with the HaMStR orthology inference software.<br>HaMStR_v13_modelorganisms_concatenate_orthologs.sh: Script used to create single fasta files for each HaMStR orthogroup from "fa_dir" folders created by HaMStR.<br><br>Phylogenomic_workflow_data_and_script_used.zip:<br>The script orthology_script.sh contains the commands used to go from the output of HaMStR_v13_modelorganisms_concatenate_orthologs.sh to the results in the PhyloTreePruner "pruned" folder. The results of SCaFoS analysis are in /scafos/.<br>18S_rDNA_alignment.phy:Alignment corresponding to Figure S2.<br>Transcriptome_assemblies_and_translations.zip:Newly sequenced transcriptome assemblies generated using Trinity and translations generated using TransDecoder.<br>
DOI: 10.7284/120698
title: Radiometer data collected during research cruise OC1504A using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7390523
title: Vegetation dynamics of Mexican riparian tropical dry forests

description: Data set of: i- measurements of the riparian standing vegetation (abundance, coverage and dbh) and ii- abundance of woody and herbaceous seeds in soil seedbanks along six tributary streams to the Amacuzac River traversing a Mexican tropical dry forest.The study was carried out over a period of two years (2015-2016).
DOI: 10.6084/m9.figshare.7390514
title: Thermohaline-shear instability

description: data used to create figures 1, 2 and 3 for "Thermohaline-shear instability"
DOI: 10.6084/m9.figshare.7390523.v1
title: Vegetation dynamics of Mexican riparian tropical dry forests

description: Data set of: i- measurements of the riparian standing vegetation (abundance, coverage and dbh) and ii- abundance of woody and herbaceous seeds in soil seedbanks along six tributary streams to the Amacuzac River traversing a Mexican tropical dry forest.The study was carried out over a period of two years (2015-2016).
DOI: 10.7284/120699
title: Radiometer data collected during research cruise OC1504A using a Biospherical QSR-2200 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7390463
title: Numfocus summit talk

description: A set of slides describing the status of the yt project.<br>
DOI: 10.6084/m9.figshare.7390541.v1
title: Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny

description: Supplementary data for "Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny."<br>hamstrsearch_model_taxa.sh: Commands used to process translated transcriptomes and predicted proteins from genomes with the HaMStR orthology inference software.<br>HaMStR_v13_modelorganisms_concatenate_orthologs.sh: Script used to create single fasta files for each HaMStR orthogroup from "fa_dir" folders created by HaMStR.<br><br>Phylogenomic_workflow_data_and_script_used.zip:<br>The script orthology_script.sh contains the commands used to go from the output of HaMStR_v13_modelorganisms_concatenate_orthologs.sh to the results in the PhyloTreePruner "pruned" folder. The results of SCaFoS analysis are in /scafos/.<br>18S_rDNA_alignment.phy:Alignment corresponding to Figure S2.<br>Transcriptome_assemblies_and_translations.zip:Newly sequenced transcriptome assemblies generated using Trinity and translations generated using TransDecoder.<br>
DOI: 10.7284/120700
title: Rain Gauge data collected during research cruise OC1504A using a RM Young 50202 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7390463.v2
title: Numfocus summit talk

description: A set of slides describing the status of the yt project.<br>
DOI: 10.6084/m9.figshare.7390541.v2
title: Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny

description: Supplementary data for "Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny."<br>hamstrsearch_model_taxa.sh: Commands used to process translated transcriptomes and predicted proteins from genomes with the HaMStR orthology inference software.<br>HaMStR_v13_modelorganisms_concatenate_orthologs.sh: Script used to create single fasta files for each HaMStR orthogroup from "fa_dir" folders created by HaMStR.<br><br>Phylogenomic_workflow_data_and_script_used.zip:<br>The script orthology_script.sh contains the commands used to go from the output of HaMStR_v13_modelorganisms_concatenate_orthologs.sh to the results in the PhyloTreePruner "pruned" folder. The results of SCaFoS analysis are in /scafos/.<br>18S_rDNA_alignment.phy:Alignment corresponding to Figure S2.<br>Transcriptome_assemblies_and_translations.zip:Newly sequenced transcriptome assemblies generated using Trinity and translations generated using TransDecoder.<br>
DOI: 10.6084/m9.figshare.7390541.v3
title: Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny

description: Supplementary data for "Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny."<br>hamstrsearch_model_taxa.sh: Commands used to process translated transcriptomes and predicted proteins from genomes with the HaMStR orthology inference software.<br>HaMStR_v13_modelorganisms_concatenate_orthologs.sh: Script used to create single fasta files for each HaMStR orthogroup from "fa_dir" folders created by HaMStR.<br><br>Phylogenomic_workflow_data_and_script_used.zip:<br>The script orthology_script.sh contains the commands used to go from the output of HaMStR_v13_modelorganisms_concatenate_orthologs.sh to the results in the PhyloTreePruner "pruned" folder. The results of SCaFoS analysis are in /scafos/.<br>18S_rDNA_alignment.phy:Alignment corresponding to Figure S2.<br>Transcriptome_assemblies_and_translations.zip:Newly sequenced transcriptome assemblies generated using Trinity and translations generated using TransDecoder.<br>
DOI: 10.6084/m9.figshare.7390463.v1
title: Numfocus summit talk

description: A set of slides describing the status of the yt project.<br>
DOI: 10.7284/120701
title: Speedlog data collected during research cruise OC1504A using a Furuno DS-50 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7390385
title: Marasas et al. 1984 “Toxigenic <i>Fusarium</i> Species: Identity and Mycotoxicology” revisited

description: This study was conducted to determine the species identity and mycotoxin potential of 158 <i>Fusarium</i> strains originally archived in the South African Medical Research Council’s Mycotoxigenic Fungal Collection (MRC) that were reported to comprise 17 morphologically distinct species in the classic 1984 compilation by Marasas et al., <i>Toxigenic Fusarium Species: Identity and Mycotoxicology</i>. Maximum likelihood and maximum parsimony molecular phylogenetic analyses of single and multilocus DNA sequence data indicated that the strains represented 46 genealogically exclusive phylogenetically distinct species distributed among eight species complexes. Moreover, the phylogenetic data revealed that 80/158 strains were received under a name that is not accepted today (ex <i>F. moniliforme</i>) or classified under a different species name. In addition, gas chromatography–mass spectrometry (GC-MS) and/or high-performance liquid chromatography–mass spectrometry (HPLC-MS)-based mycotoxin analyses were conducted to determine which toxins the strains could produce in liquid and/or solid cultures. All of the trichothecene toxin–producing fusaria were nested within the <i>F. sambucinum</i> (FSAMSC) or <i>F. incarnatum-equiseti</i> (FIESC) species complexes. Consistent with this finding, GC-MS analyses detected trichothecenes in agmatine-containing broth or rice culture extracts of all 13 FSAMSC and 10/12 FIESC species tested. Species in six and seven of the eight species complexes were able to produce moniliformin and beauvericin, respectively, whereas B-type fumonisins were only detected in extracts of cracked maize kernel cultures of three species in the <i>F. fujikuroi</i> (FFSC) species complex.
DOI: 10.7284/120702
title: Water Temperature data collected during research cruise OC1504A using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7390385.v1
title: Marasas et al. 1984 “Toxigenic <i>Fusarium</i> Species: Identity and Mycotoxicology” revisited

description: This study was conducted to determine the species identity and mycotoxin potential of 158 <i>Fusarium</i> strains originally archived in the South African Medical Research Council’s Mycotoxigenic Fungal Collection (MRC) that were reported to comprise 17 morphologically distinct species in the classic 1984 compilation by Marasas et al., <i>Toxigenic Fusarium Species: Identity and Mycotoxicology</i>. Maximum likelihood and maximum parsimony molecular phylogenetic analyses of single and multilocus DNA sequence data indicated that the strains represented 46 genealogically exclusive phylogenetically distinct species distributed among eight species complexes. Moreover, the phylogenetic data revealed that 80/158 strains were received under a name that is not accepted today (ex <i>F. moniliforme</i>) or classified under a different species name. In addition, gas chromatography–mass spectrometry (GC-MS) and/or high-performance liquid chromatography–mass spectrometry (HPLC-MS)-based mycotoxin analyses were conducted to determine which toxins the strains could produce in liquid and/or solid cultures. All of the trichothecene toxin–producing fusaria were nested within the <i>F. sambucinum</i> (FSAMSC) or <i>F. incarnatum-equiseti</i> (FIESC) species complexes. Consistent with this finding, GC-MS analyses detected trichothecenes in agmatine-containing broth or rice culture extracts of all 13 FSAMSC and 10/12 FIESC species tested. Species in six and seven of the eight species complexes were able to produce moniliformin and beauvericin, respectively, whereas B-type fumonisins were only detected in extracts of cracked maize kernel cultures of three species in the <i>F. fujikuroi</i> (FFSC) species complex.
DOI: 10.7284/123997
title: Timeserver data collected during research cruise OC1504A using a Microsemi SyncServer S350 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120703
title: Transmissometer data collected during research cruise OC1504A using a WET Labs C-Star instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7390280
title: Fast Video of Capillary formation in a very simple Plate-Water-Plate system

description: We put two micro glass slides (75 mm x 25 mm x 1.2 mm) together and dipped in a coloured (KMnO4) water solution. The liquid rises in the gap (determined by the plates' roughness and flatness) between the two plates. Once completely filled, the plates were taken out and placed vertically (as shown in the video). This system was then allowed to evaporate from all the four open sides.We see the formation of a dominant capillary even in such a simple system. In soils, the formation of a dominant capillary is augmented by several particles. The configuration we used can be considered as a model to understand the formation of films in (wet) soils undergoing evaporation.<br>
DOI: 10.6084/m9.figshare.7390280.v1
title: Fast Video of Capillary formation in a very simple Plate-Water-Plate system

description: We put two micro glass slides (75 mm x 25 mm x 1.2 mm) together and dipped in a coloured (KMnO4) water solution. The liquid rises in the gap (determined by the plates' roughness and flatness) between the two plates. Once completely filled, the plates were taken out and placed vertically (as shown in the video). This system was then allowed to evaporate from all the four open sides.We see the formation of a dominant capillary even in such a simple system. In soils, the formation of a dominant capillary is augmented by several particles. The configuration we used can be considered as a model to understand the formation of films in (wet) soils undergoing evaporation.<br>
DOI: 10.7284/120704
title: TSG (Thermosalinograph) data collected during research cruise OC1504A using a Sea-Bird SBE-45 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7390235
title: PA14 NR-Lib IA Sensitivity Screen

description: The PA14 non-redundant transposon mutant library was screened for a knockout that eliminated or reduced production of the inhibitory agent that reduces growth in Pseudomonas strains carrying pMPPla107.
DOI: 10.6084/m9.figshare.7390235.v1
title: PA14 NR-Lib IA Sensitivity Screen

description: The PA14 non-redundant transposon mutant library was screened for a knockout that eliminated or reduced production of the inhibitory agent that reduces growth in Pseudomonas strains carrying pMPPla107.
DOI: 10.6084/m9.figshare.7390226
title: Promoter haplotypes of the corticotropin-releasing hormone encoding gene modulate the physiological stress response <i>in vitro</i> and <i>in vivo</i>

description: The corticotropin-releasing hormone (CRH) is a neuropeptide mediating stress responses. CRH exerts effects via the hypothalamus pituitary adrenal axis as well as immediate effects on the sympathetic-adrenal-medullary system. Genetic variants of the <i>CRH</i> promoter were previously found to be associated with altered <i>CRH</i> promoter activity and physiological reactions. Functional characterization of three <i>CRH</i> promoter haplotypes have been performed <i>in vitro</i> using a reporter gene assay under different stimulation conditions. Furthermore, 232 healthy subjects were genotyped and the influence of <i>CRH</i> haplotypes on basal parameters such as post-awakening cortisol and blood pressure as well as on stress reactivity measured after socially evaluated cold pressor test (SeCPT) was investigated. <i>In vitro, CRH</i> haplotype 2 showed the highest promoter activity under baseline conditions and after forskolin stimulation compared with other haplotypes. Forskolin treatment resulted in a two fold increase of haplotype 2 promoter activity compared with the baseline condition. Cell line-dependent promoter activation was found after hydrocortisone treatment. <i>In vivo</i>, <i>CRH</i> haplotype 2 carriers showed significant higher baseline blood pressure (<i>p</i> = .002) and blood pressure after SeCPT (<i>p</i> CRH promoter variants on physiological stress response parameters.
DOI: 10.7284/120720
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1505A using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7390229.v1
title: Transcriptomic study of the mechanism of anoikis resistance in head and neck squamous carcinoma

description: Normal epithelial cells rapidly undergo apoptosis as soon as they lose contact with the extracellular matrix (ECM), which is termed as anoikis. However, cancer cells tend to develop a resistance mechanism to anoikis. This acquired ability is termed as anoikis resistance. Cancer cells, with anoikis resistance, can spread to distant tissues or organs via the peripheral circulatory system and cause cancer metastasis. Thus, inhibition of anoikis resistance blocks the metastatic ability of cancer cells. Anoikis-resistant CAL27 (CAL27AR) cells were induced from CAL27 cells using the suspension culture approach. Transcriptome analysis was performed using RNA-Seq to study the differentially expressed genes (DEGs) between the CAL27AR cells and the parental CAL27 cells. Gene function annotation and Gene Ontology (GO) enrichment analysis were performed using DAVID database. Signaling pathways involved in DEGs were analyzed using Gene Set Enrichment Analysis (GSEA) software. Analysis results were confirmed by reverse transcription PCR (RT-PCR), Western blotting, and gene correlation analysis based on the TCGA database. The figure in here is some full-length uncropped blots about our study.
DOI: 10.7284/120707
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise OC1505A using a Sea-Bird SBE-911+ instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7388756
title: GmHapMap Frequency

description: Frequency of varinats in GmHapMap
DOI: 10.6084/m9.figshare.7388777
title: Père David deer gut microbiome

description: <b>Père David deer gut microbiome changes across captive and translocated populations: implications for conservation</b>
DOI: 10.6084/m9.figshare.7390226.v3
title: Promoter haplotypes of the corticotropin-releasing hormone encoding gene modulate the physiological stress response <i>in vitro</i> and <i>in vivo</i>

description: The corticotropin-releasing hormone (CRH) is a neuropeptide mediating stress responses. CRH exerts effects via the hypothalamus pituitary adrenal axis as well as immediate effects on the sympathetic-adrenal-medullary system. Genetic variants of the <i>CRH</i> promoter were previously found to be associated with altered <i>CRH</i> promoter activity and physiological reactions. Functional characterization of three <i>CRH</i> promoter haplotypes have been performed <i>in vitro</i> using a reporter gene assay under different stimulation conditions. Furthermore, 232 healthy subjects were genotyped and the influence of <i>CRH</i> haplotypes on basal parameters such as post-awakening cortisol and blood pressure as well as on stress reactivity measured after socially evaluated cold pressor test (SeCPT) was investigated. <i>In vitro, CRH</i> haplotype 2 showed the highest promoter activity under baseline conditions and after forskolin stimulation compared with other haplotypes. Forskolin treatment resulted in a two fold increase of haplotype 2 promoter activity compared with the baseline condition. Cell line-dependent promoter activation was found after hydrocortisone treatment. <i>In vivo</i>, <i>CRH</i> haplotype 2 carriers showed significant higher baseline blood pressure (<i>p</i> = .002) and blood pressure after SeCPT (<i>p</i> CRH promoter variants on physiological stress response parameters.
DOI: 10.7284/120709
title: Fluorometer data collected during research cruise OC1505A using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7390226.v2
title: Promoter haplotypes of the corticotropin-releasing hormone encoding gene modulate the physiological stress response <i>in vitro</i> and <i>in vivo</i>

description: The corticotropin-releasing hormone (CRH) is a neuropeptide mediating stress responses. CRH exerts effects via the hypothalamus pituitary adrenal axis as well as immediate effects on the sympathetic-adrenal-medullary system. Genetic variants of the <i>CRH</i> promoter were previously found to be associated with altered <i>CRH</i> promoter activity and physiological reactions. Functional characterization of three <i>CRH</i> promoter haplotypes have been performed <i>in vitro</i> using a reporter gene assay under different stimulation conditions. Furthermore, 232 healthy subjects were genotyped and the influence of <i>CRH</i> haplotypes on basal parameters such as post-awakening cortisol and blood pressure as well as on stress reactivity measured after socially evaluated cold pressor test (SeCPT) was investigated. <i>In vitro, CRH</i> haplotype 2 showed the highest promoter activity under baseline conditions and after forskolin stimulation compared with other haplotypes. Forskolin treatment resulted in a two fold increase of haplotype 2 promoter activity compared with the baseline condition. Cell line-dependent promoter activation was found after hydrocortisone treatment. <i>In vivo</i>, <i>CRH</i> haplotype 2 carriers showed significant higher baseline blood pressure (<i>p</i> = .002) and blood pressure after SeCPT (<i>p</i> CRH promoter variants on physiological stress response parameters.