cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3635786_d5.v1
title: Additional file 13: of Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks

description: Muscle development network file. Contains motifs that have a conserved association with muscle development-related genes (See â  Methodsâ   regarding motif conservation) in both S. carpocapsae and C. elegans. The first column contains the motif ID, the second column contains the edge weight, and the third and fourth columns contain C. elegans gene IDs in two different formats. (TXT 5Â kb)
DOI: 10.6084/m9.figshare.c.3635786_d6.v1
title: Additional file 5: of Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks

description: S. carpocapsae isoform similarity. S. carpocapsae transcript isoform pairs (where both isoforms have a summed expression &gt; 1 TPM during developmental time course), their isoform similarities (cosine similarities), and the transcript isoform expression (TPM) values of each of the isoforms during development in replicates. Isoforms that had summed expression &lt; 1 TPM were removed from the analysis. (TXT 423Â kb)
DOI: 10.6084/m9.figshare.c.3635786_d7.v1
title: Additional file 7: of Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks

description: Additional Cufflinks gene and isoform annotations for S. carpocapsae . The file was generated by combining Cufflink’s transcript annotations for four developmental stages (embryo, L1, IJ, and adult) with the Augustus-predicted gene annotations (.gtf format). Gene and isoform IDs beginning with “CUFF” were predicted by Cufflinks, whereas ones beginning with “L596_” were predicted by Augustus. The Augustus annotations here match the WormBase gene annotations for S. carpocapsae. (GTF 55690 kb)
DOI: 10.6084/m9.figshare.c.3635786_d8.v1
title: Additional file 3: of Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks

description: 1:1 C. elegans gene identifiers for the 1:1 orthologs conserved across the phylum Nematoda. These represent putative phylogenetic markers though their informative value remains to be tested. (TXT 7Â kb)
DOI: 10.6084/m9.figshare.c.3635786_d9.v1
title: Additional file 10: of Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks

description: S. carpocapsae and C. elegans shared GO term table. Contains all the motif-associated GO (MAG) terms (FDR &lt; 0.05) that are shared between S. carpocapsae and C. elegans. (TXT 188Â kb)
DOI: 10.17863/cam.15567
title: Research data supporting Vortex-ring-induced stratified mixing: mixing model

description: Data associated with the publication "Vortex-ring-induced stratified mixing: mixing model." Includes model implementation and mixing data.
DOI: 10.6084/m9.figshare.c.3635786_d11.v1
title: Additional file 12: of Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks

description: Neurogenesis/axonogenesis network file. Contains motifs that have a conserved association with neurogenesis-related genes (See â  Methodsâ   regarding motif conservation) in both S. carpocapsae and C. elegans. The first column contains the motif ID, the second column contains the edge weight, and the third and fourth columns contain C. elegans gene IDs in two different formats. (TXT 19Â kb)
DOI: 10.6084/m9.figshare.c.3635786_d10.v1
title: Additional file 11: of Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks

description: Embryonic development network file. Contains motifs that have a conserved association with embryonic development-related genes (See â  Methodsâ   regarding motif conservation) in both S. carpocapsae and C. elegans. The first column contains the motif ID, the second column contains the edge weight, and the third and fourth columns contain C. elegans gene IDs in two different formats. (TXT 6Â kb)
DOI: 10.6084/m9.figshare.c.3635786_d13.v1
title: Additional file 8: of Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks

description: MEME motif position weight matrices derived from the final 30 conserved stage-specific gene sets. These motifs were derived from conserved non-coding regions Âą3Â kb of S. carpocapsae orthologs that have conserved stage-specific expression profiles during development between S. carpocapsae and S. feltiae. The motif IDs in the file are numbered from 1 to 30. In parentheses next to each motif number is the developmental stage-specific gene set the motif was derived from (e, f, ef, fi, fa, efi, efa, fia, efia) and its old MEME ID. (TXT 17Â kb)
DOI: 10.6084/m9.figshare.c.3635801_d2.v1
title: Additional file 2 of PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

description: Synthetic sequences. Synthetic sequences with USF-IRF1 binding sites. (FASTA 55 kb)
DOI: 10.6084/m9.figshare.c.3635801_d1.v1
title: Additional file 1 of PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

description: PC-TraFF analysis with different distance constrains. Significant pairs found by PC-TraFF using different distance constrains in the sequences of human RefSeq genes. (XLS 13 kb)
DOI: 10.6084/m9.figshare.c.3635801_d3.v1
title: Additional file 7 of PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

description: Breast cancer analysis in the context of miRNA genes. PC-TraFF significant pairs identified in the promoter sequences of breast cancer-associated miRNA genes. (XLS 13 kb)
DOI: 10.6084/m9.figshare.c.3635801_d4.v1
title: Additional file 5 of PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

description: Genome-wide analysis in the context of miRNA genes. PC-TraFF significant pairs identified in the genome-wide promoter sequences of miRNA genes. (XLS 3 kb)
DOI: 10.6084/m9.figshare.c.3635801_d5.v1
title: Additional file 3 of PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

description: Genome-wide analysis in the context of RefSeq genes. PC-TraFF significant pairs identified in the genome-wide promoter sequences of RefSeq genes. (XLS 4 kb)
DOI: 10.17863/cam.34266
title: Digital Preservation Maturity Model, Risks, Trusted Digital Repository Certification and Workflow Crosswalk

description: A crosswalk that describes selected digital preservation maturity models, risk management models, Trusted Digital Repository (TDR) certifications and digital preservation workflow models. This crosswalk can be used as the basis for determining a holistic approach to digital preservation policy, strategy, planning and certification, as well as requirements development.
DOI: 10.6084/m9.figshare.c.3635801_d6.v1
title: Additional file 6 of PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

description: Breast cancer analysis in the context of RefSeq genes. PC-TraFF significant pairs identified in the promoter sequences of breast cancer-associated RefSeq genes. (XLS 12 kb)
DOI: 10.6084/m9.figshare.c.3635849_d1.v1
title: Additional file 5: of The phylogeny of brown lacewings (Neuroptera: Hemerobiidae) reveals multiple reductions in wing venation

description: Nexus file with instructions for Mr. Bayes. (ZIP 18.1 kb)
DOI: 10.6084/m9.figshare.c.3635852_d4.v1
title: MOESM1 of Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants

description: Additional file 1: BIOM-File S1. Final operational taxonomic unit (OTU) table in BIOM format, format specification 1.0.0. Contained are clustered OTUs with specific OTU IDs, their supporting 16S rRNA gene sequence counts per sample, and as metadata taxonomic classification per OTU, descriptive labels per sample.
DOI: 10.6084/m9.figshare.c.3635861_d2.v1
title: Additional file 2: Table S2. of Reserve-related activities and MRI metrics in multiple sclerosis patients and healthy controls: an observational study

description: Results of non-parametric tests comparing strenuous change groups in relapsing-remitting patients. (XLS 13 kb)
DOI: 10.6084/m9.figshare.c.3635861_d1.v1
title: Additional file 1: Table S1. of Reserve-related activities and MRI metrics in multiple sclerosis patients and healthy controls: an observational study

description: Descriptive statistics of MRI measures. (XLS 10 kb)
DOI: 10.17863/cam.81748
title: Data supporting "Operational speed strategy opportunities for autonomous trucking on highways"

description: Microsoft Excel spreadsheet containing data values for figures in paper including: - Cumulative fuel consumption v time for sample reference 3. (Data acquired from fleet operator referred to in paper, simulated fuel consumption calculated using methodology described in paper) - Instantaneous (rolling 5-second average) fuel consumption v time for sample reference 3. (Data acquired from fleet operator referred to in paper, simulated fuel consumption calculated using methodology described in paper) - Summary of fuel consumption validation modelling. (Data acquired from fleet operator referred to in paper, simulated fuel consumption calculated using methodology described in paper) - Sample highway drive-cycles (sourced from EPA, see reference in paper, and from fleet operator referred to in paper) - Breakdown of fuel consumption rates (l/100km) by energy component for Tractor-trailer loaded to 50% cargo mass capacity (calculated using methodology described in paper) - Combined driver and fuel cost £/100km under Drive cycle 1 conditions. (calculated using methodology described in paper) - Combined cost v target speed for tractor-trailer, half load, Drive Cycle 1 (calculated using methodology described in paper) - Combined cost for tractor trailer, half filled by mass, medium Vc, drive cycle 1 (calculated using methodology described in paper) - Net savings (£/km) for human driver and AV resulting from reducing target speed from 90km/h to 80km/h and 70km/h. Vehicles loaded 50% to capacity by mass. (calculated using methodology described in paper) - Savings in £/100km and % by scenario and speed strategy for HD and AV. (calculated using methodology described in paper) - Allocation of case study distance travelled by road speed limit (sourced from fleet operator referred to in paper and calculated using methodology described in paper) - Cargo value of time required to maintain baseline speed strategy £/tonne/hr (calculated using methodology described in paper) - Distribution of in-use fleet time across the day (sourced from fleet operator referred to in paper) - Slow speed strategy outcomes replicated for US context. Tractor trailer, load to 50% cargo capacity by mass. Drive cycle 1. No allowance for cargo value of time (calculated using methodology described in paper)
DOI: 10.17863/cam.26302
title: Data for 'Pyrolysis of wood pellet in the presence of oxygen carriers in a fluidised bed coupled with a DBD reactor for tar quantification'

description: This work was supported by EP/L022427/1. The data include time-based mole fractions of gaseous products, XRD results, plasma signals and etc.
DOI: 10.6084/m9.figshare.c.3636005_d4.v1
title: Additional file 2: Table S2. of Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimerâ  s disease

description: Technical replication of six 450Â K CpGs using the targeted Sequenom EpiTYPER assays. (XLSX 40 kb)
DOI: 10.17863/cam.89030
title: Gaussian Approximation Potential for Tungsten

description: Potential and original training data. The GAP code to is used to work with this potential, see https://libatoms.github.io/GAP/
DOI: 10.6084/m9.figshare.c.3636005_d5.v1
title: Additional file 6: Table S3. of Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimerâ  s disease

description: CpGs in significant DMRs with annotation. (XLSX 689 kb)
DOI: 10.6084/m9.figshare.c.3636005_d9.v1
title: Additional file 9: Table S5. of Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimerâ  s disease

description: Enrichment results for brain histone mark datasets. (XLSX 10 kb)
DOI: 10.17863/cam.85818
title: Research data supporting "Structurally Colored Radiative Cooling Cellulosic Films"

description: Electronic supporting Information is available from the publisher (Advanced Science). The data is provided within a structured set of folders compressed in zip, each correlating to a specific figure in the article. Spreadsheets are provided as ‘.xlsx’ or '.txt'; images as ‘.bmp’, ‘.jpeg’, ‘.tiff’ or ‘.png’. The data include photograph and the results of polarized optical microscopy, UV-VIS spectroscopy, FTIR spectroscopy, goniometer measurement, field test, and SEM. The methods part of the published paper has the detailed description of how the data were generated, collected, and processed.
DOI: 10.6084/m9.figshare.c.3636005_d10.v1
title: Additional file 10: Table S6. of Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimerâ  s disease

description: DMRs occurring within 250Â kb of a GWAS SNP associated with AD. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.c.3636005_d11.v1
title: Additional file 8: Table S4. of Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimerâ  s disease

description: Top GO enrichments for genes associated with DMRs. (XLSX 51 kb)
DOI: 10.17863/cam.112500
title: Research data supporting: "Solar Fuel Synthesis using a Semi-artificial Colloidal Z-Scheme"

description: Zip folder containing all research data supporting the findings of this study. The ‘manuscript’ folder contains data and images for manuscript Figure 1–6: schematics, TEM images, XPS spectra, XRD, photocatalysis, UV–vis spectra, 1H NMR spectra, CA, CV, QCM, PEIS, TPC, and IMVS (as PNG, XLSX, tif files). The ‘SI’ folder contains data and images for Supporting Information Figure S1–S26: Tauc plots, Mott–Schottky plots, SEM images, TEM images, EDX mapping, XRD patterns, UV–vis spectra, 1H NMR spectra, ATR-FTIR spectrum, photoreactor information, lamp setup, photograph of electrodes (as EPS, PDF, JPG, PNG, XLSX files). Date of data collection: Aug 2023 - Aug 2024 Geographic location of data collection: Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW More details can be found in the readme.txt file.
DOI: 10.6084/m9.figshare.c.3636011_d1.v1
title: Additional file 1: of Two-headed mutants of the lamprey, a basal vertebrate

description: The sample list with summary of malformations. (XLS 27 kb)
DOI: 10.17863/cam.89629
title: Report presented to Jisc for article processing charges for RCUK funded papers managed by the University of Cambridge, 1 April 2021 - 31 March 2022

description: This Excel spreadsheet records the open access article processing charges (APCs) charged to The Research Council's UK (RCUK) block grant held by Cambridge University Library, via the Office of Scholarly Communication, between 1 April 2021 - 31 March 2022
DOI: 10.6084/m9.figshare.c.3636026_d1.v1
title: Additional file 5: of Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars

description: Annotation, transcript abundance values, and ANOVA results of all genes on the NimbleGen Whole-Genome microarray measured in five grape cultivars. Red highlighted rows identify the possibility of cross-hybridization of probes with other genes from Cramer et al. [41]. Cultivar and treatment abbreviations for experimental replicates: Cabernet Sauvignon (CS), Merlot (ME), Pinot Noir (PN), Chardonnay (CD), and Semillon (SM) grown under well-watered (W) and water deficit (D) conditions, nâ  =â  5. The probe.cross.hybridization column refers to the number of probes for that transcript that have the potential to cross-hybridize with other probes. Other column headings refer to a combination of cultivar name, treatment, and replicate number. (XLS 33741Â kb)
DOI: 10.6084/m9.figshare.c.3636026_d4.v1
title: Additional file 6: of Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars

description: Annotation, read counts, transcript normalized log2 counts per million (CPM) values, and edgeR statistical results of all genes with unique counts assigned from Illumina RNAseq, with ‘.count’ and ‘.log2CPM’ suffixes respectively. Cultivar and treatment abbreviations for experimental replicates: Cabernet Sauvignon (CS), Merlot (ME), Pinot Noir (PN), Chardonnay (CD), and Semillon (SM) grown under well-watered (W) and water deficit (D) conditions, n = 3. Other column headings refer to a combination of cultivar name, treatment, and replicate number. (XLS 25195 kb)
DOI: 10.6084/m9.figshare.c.3636026_d6.v1
title: Additional file 4: of Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars

description: ANOVA results for the quantifiable (1211) proteins (log2 NSAF) in five grape cultivars, with p-value (p) and adjusted p-value (adjp) prefixing each effect. Cultivar and treatment abbreviations for experimental replicates: Cabernet Sauvignon (CS), Merlot (ME), Pinot Noir (PN), Chardonnay (CD), and Semillon (SM) grown under well-watered (W) and water deficit (D) conditions, nâ  =â  3. Other column headings refer to a combination of cultivar name, treatment, and replicate number. (XLS 1032Â kb)
DOI: 10.6084/m9.figshare.c.3636026_d7.v1
title: Additional file 8: of Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars

description: BinGO results for overrepresented GO biological process functional categories for all quantifiable proteins (1211). The proteins are identified by their UniProtKB accession name. (XLS 303Â kb)
DOI: 10.6084/m9.figshare.c.3636026_d8.v1
title: Additional file 7: of Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars

description: Mean relative abundance values, M/Z, and results from the ANOVA for all primary and secondary metabolomic details for all metabolites (67) analyzed by GC-MS and (42) analyzed by LC-MS in five grape cultivars. Cultivar and treatment abbreviations for experimental replicates: Cabernet Sauvignon (CS), Merlot (ME), Pinot Noir (PN), Chardonnay (CD), and Semillon (SM) grown under well-watered (W) and water deficit (D) conditions, nâ  =â  6. (XLS 76Â kb)
DOI: 10.6084/m9.figshare.c.3636026_d10.v1
title: Additional file 9: of Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars

description: Correlations of protein and transcript abundance. Protein data are log2 NSAF values, n = 3, RNAseq data are log2 normalized counts per million (CPM), n = 3, and microarray data are log2 RMA values, n = 5. Relationships of proteins with either RNAseq (CPM) or microarray (RMA) are indicated. (XLS 370 kb)
DOI: 10.6084/m9.figshare.c.3636026_d9.v1
title: Additional file 3: of Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars

description: Annotation, protein spectral counts, Normalized Spectral Abundance Factor (NSAF) values and log2 transformed NSAF values for each replicate and protein identified, with ‘.count’, ‘.NSAF’, and ‘.NSAF.log2’ suffixes, respectively. Mass weight (Mr) and amino acid (AA) length are approximated values. Cultivar and treatment abbreviations for experimental replicates: Cabernet Sauvignon (CS), Merlot (ME), Pinot Noir (PN), Chardonnay (CD), and Semillon (SM) grown under well-watered (W) and water deficit (D) conditions, n = 3. Other column headings refer to a combination of cultivar name, treatment, and replicate number. For example, CDD2, is Chardonnay, water deficit and replicate 2. (XLS 4096 kb)
DOI: 10.17863/cam.50385
title: Data supporting "Femtosecond Transient Absorption Microscopy of Singlet Exciton Motion in Side-Chain Engineered Perylene-Diimide Thin Films"

description: The dataset contains all data in the main text of the paper and is laid out in a folder structure: - Figure 2: absorption spectra and XRD patterns for measured PDI films - Figure 3: Transient absorption microscopy data organised according to PDI sample. File name mentions the relevant step size and panel. kinetics refers to panel a of main text figure 3, sigma denotes time-dependent standard deviation, GaussMSD is the mean-square displacement curve - Figure 4: relevant data to generate Box-plots for statistical evaluation. PDI1-4_lifetimes contains the retrieved fast lifetime components from the transient dynamics. PDIX_linear_diffusion_values collect the diffusion constants for the different time regimes for a given PDI sample
DOI: 10.6084/m9.figshare.c.3636047_d18.v1
title: Additional file 1: of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Script for model BS-A (R 2Â kb)
DOI: 10.6084/m9.figshare.c.3636047_d20.v1
title: Additional file 19: Table S5. of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Ribosome density calculations and comparisons. Sheet 1. Ribosome densities in procyclic forms. The average number of ribosomes per ORF was calculated as follows. First, we needed to correct the ribosome profiling results for the gene copy number in the genome assembly, since during the initial alignments, the reads had been spread out among all orthologues. Orthologue counts were taken from TritrypDB. Unexpected numbers were checked against our previous read alignment data [20], and in some cases manually. Read results for some gene families (such as amino acid transporters) are unreliable because related genes show different regulation. The orthologue counts used are in column D. All RPM were multiplied by the orthologue count (column H). Numbers of mRNAs per cell [16] were previously calculated assuming a total of 19,000 non-VSG mRNAs in bloodstream forms, and 43,000 non-EP-procyclin mRNAs/cell in procyclics [17]. There are about 275000 ribosomes per procyclic parasite and 125000 per bloodstream form [17]. The ribosome densities are calculated using these numbers. In practice, the densities are likely to be lower. About 5 % of ribosomes are likely to be on ORFs that were excluded from the analysis (Procyclin, VSG, ESAGs, and from repetitive elements). Approximately 70 % of all ribosomal RNA is in polysomes, 20 % is in monosomes and the rest is in subunits (our unpublished results); we do not know what proportion of the ribosomes in the monosomal fraction is engaged in translation. Sheet 2. Ribosome densities in bloodstream forms. Sheet 3. Ribosome densities and half-lives in procyclic forms, using only the “reliable” values that were chosen for modelling. Sheet 4. Ribosome densities and half-lives in bloodstream forms, using only the “reliable” values that were chosen for modelling. (XLSX 2688 kb)