cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3625730_d1
title: Additional file 5: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

description: Alignment of contigs harboring GA2 T6SS loci with the B. fragilis CL05T00C05 contig bearing the GA2 T6SS locus. (XLSX 16Â kb)
DOI: 10.15468/dl.ygdg7u
title: Occurrence Download

description: A dataset containing 6991 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Macaca mulatta (Zimmermann, 1780)"
 ]
}

 The dataset includes 6991 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033238-241126133413365/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.3625736_d1
title: Additional file 2 of BAMQL: a query language for extracting reads from BAM files

description: This file contains the complete results of the test-suite in a csv format. (XLS 32 kb)
DOI: 10.6084/m9.figshare.c.3625730_d2
title: Additional file 2: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

description: Enumeration of Bacterodales T6SS proteins by genetic architecture and cluster. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3625733_d2
title: Additional file 7: Table S6. of Short chain acyl-CoA dehydrogenase deficiency and short-term high-fat diet perturb mitochondrial energy metabolism and transcriptional control of lipid-handling in liver

description: IPA Pathways. (XLSX 15 kb)
DOI: 10.17863/cam.85571
title: Research data supporting: "Dysregulation of ADAM10 shedding activity in naked mole-rat fibroblasts is due to deficient phosphatidylserine externalisation"

description: There is a Prism file providing the raw data, including statistical analyses, aligning to each of the figures: $$ \ $$ Figure 1.pzfx - CD44 cleavage assay in mouse and naked mole-rat primary skin fibroblasts $$ \ $$ Figure 2.pzfx - Measurement of cellular ADAM10 levels and betacellulin cleavage in mouse and naked mole-rat primary skin fibroblasts $$ \ $$ Figure 3.pzfx - CD44 and betacellulin cleavage assays in mouse and naked mole-rat transformed skin fibroblasts $$ \ $$ Figure 4.pzfx - Plasma membrane phosphatidlylserine quantification in mouse and naked mole-rat primary skin fibroblasts $$ \ $$ Figure 5.pzfx - Analysis of plasma membrane phosphatidlylserine levels and betacellulin cleavage in mouse and naked mole-rat primary skin fibroblasts overexpressing either GFP or the scramblase ANO6 $$ \ $$ Figure 6.pzfx - Analysis of cellular wound closure in naked mole-rat primary skin fibroblasts overexpressing either GFP or the scramblase ANO6, and the impact of inhibiting ADAM10 $$ \ $$ Supplementary Figure 1.pzfx - Concentration response relationship for ionomycin induced CD44 cleavage in mouse and naked mole-rat primary skin fibroblasts $$ \ $$ Supplementary Figure 2.pzfx - Concentration response relationship for ionomycin induced CD44 cleavage in transformed mouse and naked mole-rat skin fibroblasts $$ \ $$ Supplementary Figure 3.pzfx - Levels of cellular ADAM10 levels in mouse and naked mole-rat transformed skin fibroblasts $$ \ $$ Supplementary Figure 4.pzfx - Analysis of plasma membrane phosphatidlylserine levels and betacellulin cleavage in mouse primary skin fibroblasts overexpressing either GFP or the scramblase ANO6, carried out at 32°C $$ \ $$ Supplementary Figure 5.pzfx - Analysis of ANO6 protein levels in mouse and naked mole-rat transformed fibroblasts $$ \ $$ Supplementary Figure 6.pzfx - Analysis of cellular wound closure in mouse primary skin fibroblasts overexpressing either GFP or the scramblase ANO6, and showing the impact of ADAM10 inhibition, carried out at 32°C and 37°C
DOI: 10.6084/m9.figshare.c.3625730_d3
title: Additional file 3: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

description: Identification of putative effector and immunity proteins by comparison to those identified in Zhang et al. [ 21 ]. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.c.3625745_d2
title: Additional file 13: of An efficient algorithm for identifying primary phenotype attractors of a large-scale Boolean network

description: Attractor in the logical T-cell signaling model. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.c.3625733_d3
title: Additional file 6: Table S5. of Short chain acyl-CoA dehydrogenase deficiency and short-term high-fat diet perturb mitochondrial energy metabolism and transcriptional control of lipid-handling in liver

description: Genotype-by-diet interactions affecting gene expression. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.c.3625736_d2
title: Additional file 1 of BAMQL: a query language for extracting reads from BAM files

description: This directory contains tests written in BAMQL, C, Perl, Python, SAMtools and Sambamba languages. A binary file with the appropriate version is provided for Sambamba. (ZIP 1495 kb)
DOI: 10.6084/m9.figshare.c.3625730_d4
title: Additional file 4: of Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

description: Alignment of the ICE from the Bacteroidales CL02T12 strains against contigs of strains harboring GA1 T6SS loci. (XLSX 48Â kb)
DOI: 10.17863/cam.104057
title: Research data supporting "The ALS/FTD-related C9orf72 hexanucleotide repeat expansion forms RNA condensates through multimolecular G-quadruplexes"

description: Data repository for work contributing to the paper "The ALS/FTD-related C9orf72 hexanucleotide repeat expansion forms RNA condensates through multimolecular G-quadruplexes". Confocal micrographs are presented as raw .TIFF files with corresponding metadata .txt file, which can be opened using text editing software such as Notepad. Confocal micrographs were collected using a Leica SP8 Inverted Confocal microscope (HC PL APO CS2 10x/0.40 DRY | HC PL APO CS2 20x/0.75 DRY objectives). Circular Dichroism spectra were collected using a Quartz High Precision cell (1 mm light path) and analysed in the Jasco J-715 Spectropolarimeter. The RAW data is saved in .xlsx file which can be accessed in Microsoft Excel or any other txt reader. Gel imaging was performed with Typhoon FLA 9500. The images are saved in a .ppt file which can be opened with Microsoft Powerpoint. Flow Cythometry data was aquired using a BD LSRFortessa analyser operated by the FACSDiva software (BD), and the results were analysed using the FlowJo software. The paper is open access and further details for the data acquisition can be found in the Methods section.
DOI: 10.6084/m9.figshare.c.3625745_d9
title: Additional file 2: of An efficient algorithm for identifying primary phenotype attractors of a large-scale Boolean network

description: Attractors for proliferation in the Mitogen-activated protein kinase (MAPK) model. (XLSX 60Â kb)
DOI: 10.6084/m9.figshare.c.3625769_d3
title: Additional file 1: of Expression analysis of the osteoarthritis genetic susceptibility locus mapping to an intron of the MCF2L gene and marked by the polymorphism rs11842874

description: Details of the patients studied in this report for A) qPCR analysis and B) RNA sequencing analysis. (XLSX 22 kb)
DOI: 10.17863/cam.110885
title: Research data supporting "Distance-Independent Efficiency of Triplet Energy Transfer from π-Conjugated Organic Ligands to Lanthanide-Doped Nanoparticles"

description: The provided dataset substantiates ongoing research into the energy transfer mechanisms at play between organic molecules and lanthanide-doped nanoparticles. The dataset is generated through laser spectroscopy techniques, transient absorption spectroscopy mainly, and a combination of FTIR and DFT modelling. Data is formatted in Excel files.
DOI: 10.6084/m9.figshare.c.3625745_d11
title: Additional file 7: of An efficient algorithm for identifying primary phenotype attractors of a large-scale Boolean network

description: Example of how to find the phenotype attractors in HPFP. (XLSX 73Â kb)
DOI: 10.6084/m9.figshare.c.3625733_d9
title: Additional file 5: Table S4. of Short chain acyl-CoA dehydrogenase deficiency and short-term high-fat diet perturb mitochondrial energy metabolism and transcriptional control of lipid-handling in liver

description: Top 25 up- and down-regulated genes. (XLSX 423 kb)
DOI: 10.6084/m9.figshare.c.3625745_d12
title: Additional file 4: of An efficient algorithm for identifying primary phenotype attractors of a large-scale Boolean network

description: Attractors for proliferation in the colitis-associated colon cancer (CACC) model. (XLSX 61Â kb)
DOI: 10.6084/m9.figshare.c.3625745_d13
title: Additional file 6: of An efficient algorithm for identifying primary phenotype attractors of a large-scale Boolean network

description: Attractors for apoptosis in the simplified cancer pathways (SCP) model. (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.c.3625787_d1
title: Additional file 4: of Venom-gland transcriptome and venom proteome of the Malaysian king cobra (Ophiophagus hannah)

description: Sequence comparision of Malaysian Ophiophagus hannah (MOh; current study) with Balinese species (BOh; Vonk et al. [ 20 ]) and other reported O. hannah toxins deposited in public database. First column indicates the sources of the sequence used in the comparison. Second column indicates the protein family and ID of the current study and NCBI deposited public database (Abbrev.: 3FTx, three-finger toxin; SVMP, snake venom metalloproteinase; PLA2, phospholipase A2; CRISP, cysteine-rich secretory protein; KUN, Kunitz-type proteinase inhibitor; LAAO, L-amino acid oxidase; CVF, Cobra venom factor; IGF, insulin-like growth factor; NP, natriuretic peptide; SVSP, snake venom serine protease; PDE, phosphodiesterase; NGF, nerve growth factor; AChE, acetylcholinesterase; PLB, phospholipase-B; DPP IV, dipeptidylpeptidase IV; CTL, C-type lectin; VEGF, vascular endothelial growth factor). Third column shows the accession number of NCBI and SwissProt database on the first row and (where present) the number of the line in which the peptide match is found in the protein in the subsequent rows. Forth column shows the comparison of MOh with BOh (Vonk et al. [20]) and other reported O. hannah toxins using the sequences retrieved from MOh transcriptome (current study) and NCBI database. Fifth column shows the coverage of the MOh sequences as compared to the aligned sequences. Underline indicates signal peptide sequences; green indicates peptide matches; red indicates the amino acids diverse from the aligned sequences; purple indicated sequences neither matched to O. hannah species nor BOh toxins. *Sequence comparision were based on the annotated protein ID in Addtional file 2; two filters were made for the selections: 1) every protein ID annotated to O. hannah species; 2) proteins of other snake species which are also reported in Vonk et al. [20], i.e., neurotoxin-like protein 1, belonged to [Causus rhombeatus] species but reported in BOh species. (XLSX 31 kb)
DOI: 10.17863/cam.23196
title: Data for "No task specialisation among Damaraland mole-rat helpers"

description: Behavioural data of captive Damaraland mole-rats followed longitudinally across development. Data takes the form of all occurrence scan sampling conducted at 4-minute sampling intervals (within an overall observation period of 12 hours); each row represents a single observation at one of the sampling intervals.
DOI: 10.17863/cam.17349
title: Data supporting 'Testing linear marginal stability in stratified shear layers'

description: The Diablo input files required to re-run the simulations outlined in the journal article, and the numerical data required to recreate figures 1, 3 and 4 in the paper.
DOI: 10.17863/cam.35449
title: Research data supporting "Quantifying cultural ecosystem services: disentangling the effects of management from landscape features"

description: This dataset contains the points collected as part of a participatory GIS survey investigating the cultural values of Thetford Forest. Data were collected using the online spraycan tool 'Map-Me' (http://map-me.org/). Participants were asked to mark maps with the areas that they valued for four cultural ecosystem services. Further details of the method are available in Tew et al. "Quantifying cultural ecosystem services: disentangling the effects of management from landscape features". People and Nature (accepted).
DOI: 10.17863/cam.84829
title: Research data supporting "A novel transposable element-mediated mechanism causes antiviral resistance in Drosophila through truncating the Veneno protein"

description: This deposit contains the raw data and scripts to reproduce statistics and figures in Brosh et al 2022 "A novel transposable element-mediated mechanism causes antiviral resistance in Drosophila through truncating the Veneno protein" Proceedings of the National Academy of Sciences. For each figure panel in the manuscript there is a seperate folder, numbered according to the figures in the manuscript. Within the folder there is a csv file containing the raw data and an R script. The R script will read the data, plot the figure in the manuscript, and reproduce the statistical analysis reported in the text. A detailed description of how the data are generated is provided in the manuscript.
DOI: 10.17863/cam.66055
title: Research data supporting "The role of oxygenated species in the growth of graphene, fullerenes and carbonaceous particles"

description: Ensemble of simulated molecules at 2.5 ms and 5.0 ms of simulation time for all conditions studied in the parameter space
DOI: 10.17863/cam.15230
title: Research data supporting "Whose ideas are most fixating, your own or other people’s? The effect of idea agency on subsequent design behaviour".

description: This excel file contains: i) the numerical data resulting from the scoring of the videos recorded during each experimental session, ii) the participants’ comments collected through the ‘think aloud’ method, and iii) the participants’ responses to the post-experimental questions. The videos and the audio-recordings are not available for ethical reasons. The file includes several spreadsheets, whose naming corresponds to the various set of results reported in the publication (Whose ideas are most fixating, your own or other people’s? Sunk cost effects and psychological ownership in design ideation). In each spreadsheet, the column headings are self-explanatory, provided you also have the corresponding publication given above as a reference. The data was collected from January to May 2017 from 40 engineering students at the University of Cambridge, UK. Participants were tested individually and received £10 for your participation. They were initially told that the study aimed at investigating how people played computer games. The real aim of the study was revealed to the participants at the end of each experimental session, during the debriefing phase. Demographic data was collected from the participants and are reported in the first spreadsheet of the file. The study was approved by the local Ethical Committee and the participants signed a Consent Form before starting with the experiment.
DOI: 10.17863/cam.78088
title: Research data supporting "Single photon multiclock lock-in detection by picosecond time stamping"

description: This folder contains research data of every figure in the paper. This includes histograms of the lock-in frequencies as well as time tracks of the optical signal locked-in to the laser repetition rate, the laser modulation and the sweep of a delay stage. Finally, we record time-resolved coherent anti-Stokes Raman scattering to determine the vibrational lifetime of molecules in a plasmonic nanocavity.
DOI: 10.6084/m9.figshare.c.3625802_d6
title: MOESM2 of Profiling and bioinformatics analyses reveal differential circular RNA expression in radioresistant esophageal cancer cells

description: Additional file 2: Table S2. circRNA expression profiling data.
DOI: 10.6084/m9.figshare.c.3625814_d3
title: Additional file 1: Table S1. of A missense mutation in solute carrier family 12, member 1 (SLC12A1) causes hydrallantois in Japanese Black cattle

description: Primer information for Y chromosome and GAPDH. Table S2.The shared haplotype of hydrallantois in the affected fetuses. Positions are based on the UMD3.1 assembly of the bovine genome. Table S3.Detailed features of CNVs in the critical region of hydrallantois in 1481 Japanese Black cattle. Positions are based on the UMD3.1 assembly of the bovine genome. CNVs were detected from 1481 Japanese Black cattle [17] using the Illumina BovineHD BeadChip Array [15]. 1 loss type of CNV is the deleted type; gain type of CNV is the duplicated type. 2 Haplotypes of 1481 animals were determined by Beagle software. Table S4.Genes within the critical region of hydrallantois in Japanese Black cattle. Positions are based on the UMD3.1 assembly of the bovine genome. Table S5.Primer information for g.62111230G &gt; A and g.62382825G &gt; A. Positions are based on the UMD3.1 assembly of the bovine genome. Table S6.Transcript and protein ID of bovine SLC12A1. Table S7.Genotypes of two variants validated using Sanger sequencing. 1 Phenotype was diagnosed by veterinarians following the standard guidelines and textbooks (for diagnosis criteria, see [1]). 2 Haplotypes were genotyped by GGP_SuperLDv2-0 26 K BeadChip and determined by Beagle software. 3 N = Non-risk-haplotype; Risk = risk-haplotype. Table S8.Primer information for exon of SLC12A1. Positions are based on the UMD3.1 assembly of the bovine genome. Table S9.Bartter syndrome-associated genes and their positions on the UMD3.1 assembly of the bovine genome. Positions are based on the UMD3.1 assembly of the bovine genome. 1 Bartter syndrome type 4B is caused by simultaneous mutations in both the CLCNKA and CLCNKB genes. 2 CLCNKB is not identified or mapped on the UMD3.1 assembly of the bovine genome. 3 Gitelman syndrome is formerly considered a subset of the Bartter syndrome. (XLSX 50 kb)
DOI: 10.13145/bacdive109610.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive109610.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0101313.10fu
title: SH0101313.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive109611.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive109611.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive109612.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive109612.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0101314.10fu
title: SH0101314.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive109613.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive109613.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0101315.10fu
title: SH0101315.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive109614.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive109614.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.