cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3636047_d19.v1
title: Additional file 9: Table S1. of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

description: Datasets used for modelling, with results. Data are taken from [16]. Sheet 1: We chose coding regions for which there had been no more than 2-fold differences in either copy number, or mRNA abundances, between 2 different experiments in bloodstream forms. The error in the half-life measurement in bloodstream forms (residual sum of squares) was also less than 0.3. Sim = simulated results; results for model BS-D (columns L & M) were used for the main analyses but those for BS-A and BS-E are also included in columns R-U. Column P has the following categories: “1. High”: mRNA amount is at least 4 times higher than expected; “2. Low”: mRNA amount is at least 4 times less than expected; 3. Normal: mRNA amount is less than 4 times more or less than expected. Column Q is like column P except that the boundary is within 2-fold. Sheet 2: As for sheet 1, but for procyclic forms. In this case mRNAs were taken for which the standard deviation of 3 abundance measurements was less than twice the mean. Sim = simulated results; results for model parameters PC-A (columns L & M) were used for the main analyses but those for PC-B are also included in columns R&S. Sheet 3: Coding regions from sheet 1 for which there was a measured bloodstream-form splicing time of less than 5 min; used for testing all bloodstream-form models except BS-C. Sheet 4: Coding regions from Sheet 4 for which the next gene downstream also had a measured splicing time of less than 5 min; used for testing bloodstream-form model BS-C. (XLSX 1679 kb)
DOI: 10.6084/m9.figshare.c.3636071_d1.v1
title: Additional file 1: of Functional and regulatory profiling of energy metabolism in fission yeast

description: Supplementary tables. Table S1. Colony size ratios from nine genetic screens for respiratory mutants. Table S2. Results of RNA-seq analysis of transcriptomes of cells grown on glycerol versus glucose and selected groups of differentially expressed genes. Table S3. Relative expression data from microarray profiling after shift to respiratory medium and k-means gene clusters. Table S4. List of genes differentially expressed on YES + antimycin A relative to YES. Table S5. List of strains used in this study. (XLSX 1837 kb)
DOI: 10.6084/m9.figshare.c.3636077_d1.v1
title: Additional file 11: Table S3. of Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality

description: List of plasmid SNPs and indels observed in the Shigella strain used here that are different from the GenBank sequence of the Shigella flexneri 2a strain 301 virulence plasmid pCP301 (NC_004851). (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3636077_d4.v1
title: Additional file 5: Table S4. of Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality

description: Table listing tRNA genes and the number of insertions in each. (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3636077_d6.v1
title: Additional file 10: Table S2. of Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality

description: List of chromosomal SNPs and indels observed in the Shigella strain used here that differ from the GenBank sequence NC004741. (TXT 4 kb)
DOI: 10.6084/m9.figshare.c.3636077_d12.v1
title: Additional file 3: Table S1. of Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality

description: Full table of gene characteristics and orthologue relationships used in the analyses. (TXT 411 kb)
DOI: 10.6084/m9.figshare.c.3636080_d1.v1
title: Additional file 6: of Nilotinib (Tasignaâ ˘) in the treatment of early diffuse systemic sclerosis: an open-label, pilot clinical trial

description: List of 106 pathways significantly downregulated in improvers post treatment (false discovery rate (FDR) &lt;5 %). The FDR is provided for each pathway. (XLSX 13 kb)
DOI: 10.17863/cam.100612
title: Research data supporting "The relationship between Mute Swan Cygnus olor population trends in Great Britain and environmental change"

description: .csv file containing the environmental and swan population change used in the regional analyses of Ki et al. 2023, Bird Study. These values were derived from raw values obtained from published sources cited in the main text. Abstract of Ki et al. 2023, Bird Study: Identifying environmental changes that influence the abundance and distribution of wild species is necessary for the development of effective conservation policy and practice (Baillie 2001). Several drivers of change often act simultaneously on a population, and it is sometimes difficult to quantify their relative importance (Green 1995, 2002; Bowler et al. 2018). For example, correlative analyses of temporal variation in population change within a large geographical area may identify drivers different from those identified when the population changes and drivers are analysed at smaller spatial scales.
DOI: 10.17863/cam.58957
title: Dataset supporting 'Quantifying mixing and available potential energy in vertically periodic simulations of stratified flows'

description: A set of Python notebooks to recreate the figures in our new publication. We also provide a Python script for applying the numerical method discussed in the paper.
DOI: 10.6084/m9.figshare.c.3636128_d1.v1
title: Additional file 1: of Insights into the segmental identity of post-oral commissures and pharyngeal nerves in Onychophora based on retrograde fills

description: Scenario on the evolution of the arthropod brain. Animation, swf file. Anterior is up. The compound brain of arthropods (sensu Richter et al. [5]) most likely evolved by a fusion of initially separate proto-, deuto- and tritocerebral ganglia. Note that the tripartite brain of arthropods alternatively might have evolved several times independently, as some groups, including branchiopod crustaceans, show a bipartite brain (e.g. [29]).
DOI: 10.6084/m9.figshare.c.3636128_d2.v1
title: Additional file 2: of Insights into the segmental identity of post-oral commissures and pharyngeal nerves in Onychophora based on retrograde fills

description: Scenario on the evolution of the onychophoran brain. Animation, swf file. Anterior is up. The composite brain of onychophorans (sensu Richter et al. [5]) most likely evolved by anteriorly moving somata, which give rise to the deutocerebrum.
DOI: 10.6084/m9.figshare.c.3636131_d2.v1
title: Additional file 2: of The genetic basis of discrete and quantitative colour variation in the polymorphic lizard, Ctenophorus decresii

description: Analysis of expected and observed allele frequencies under proposed models of inheritance. (XLSX 65Â kb)
DOI: 10.6084/m9.figshare.c.3636167_d2.v1
title: Additional file 1: of T-REx: Transcriptome analysis webserver for RNA-seq Expression data

description: Archive file containing all T-REx output files. (R 38 kb)
DOI: 10.6084/m9.figshare.c.3636167_d3.v1
title: Additional file 6: of T-REx: Transcriptome analysis webserver for RNA-seq Expression data

description: T-REx R functions. (ZIP 179 kb)
DOI: 10.15468/dl.gyauax
title: Occurrence Download

description: A dataset containing 197058 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Myiozetetes similis (Spix, 1825)"
 ]
}

 The dataset includes 197058 records from 97 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037885-241126133413365/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.3636197_d1.v1
title: Additional file 1: of 
                     phoP, SPI1, SPI2 and aroA mutants of Salmonella Enteritidis induce a different immune response in chickens

description: List of primers used in real-time PCR. Primers used for the quantification of chicken gene expression by real time PCR are listed in this file.
DOI: 10.6084/m9.figshare.c.3636206_d1.v1
title: Additional file 1: Appendix 1. of Geographical distribution of typhoid risk factors in low and middle income countries

description: Overdispersion. Appendix 2. Full specification of regression outputs. Appendix 3. TRF index (type 5) by sub-national boundary. Appendix 4. Final TRF index values by sub-national boundary. Appendix 5. TRF index in Bangladesh. (ZIP 1995Â kb)
DOI: 10.6084/m9.figshare.c.3636266_d1.v1
title: Additional file 6: of An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH

description: GlnA sequences used for the phylogenetic tree depicted in Fig.Â 5. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3636266_d3.v1
title: Additional file 7: of An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH

description: MCE-related proteins encoded by the genomes of BMG5.1, Dg1 and Dg2. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.c.3636266_d7.v1
title: Additional file 2: of An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH

description: Secondary metabolite production encoded on genomes of Frankia Cluster II strains. (XLSX 12 kb)
DOI: 10.17863/cam.106099
title: Research data supporting "In-situ electrochemically regenerated ultrathin active SERS sensors"

description: This dataset contains the data of all main and supplementary information figures of the manuscript. The data are in txt files, tab separated, and with columns labelled. All further information is contained in the captions of the manuscript. The data are organized in folders for each figure, with files named according to the figure number and panel.
DOI: 10.15468/dl.ghyusm
title: Occurrence Download

description: A dataset containing 1183 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Okenia hypogaea Schltdl. & Cham."
 ]
}

 The dataset includes 1183 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037897-241126133413365/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.3636278_d1.v1
title: Additional file 3: of Forging a link between mentoring and collaboration: a new training model for implementation science

description: Collaboration[year][activity].net: Pajek.net file for collaboration network for each year and activity. (ZIP 24 kb)
DOI: 10.6084/m9.figshare.c.3636278_d2.v1
title: Additional file 5: of Forging a link between mentoring and collaboration: a new training model for implementation science

description: Attributes[year].csv: comma-separated file of IRI member attributes for each year. (ZIP 1 kb)
DOI: 10.6084/m9.figshare.c.3636278_d3.v1
title: Additional file 2: of Forging a link between mentoring and collaboration: a new training model for implementation science

description: Contact[year].net: Pajek.net file for contact network for each year. (ZIP 11 kb)
DOI: 10.6084/m9.figshare.c.3636278_d5.v1
title: Additional file 4: of Forging a link between mentoring and collaboration: a new training model for implementation science

description: Mentor[year].net: Pejak.net file for mentor networks for each year. (ZIP 5 kb)
DOI: 10.5519/qd.tq1wpivs
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (297 records)
DOI: 10.17863/cam.104448
title: Research data supporting 'Metal to insulator transition for conducting polymers in plasmonic nanogaps'

description: This data set contains the experiment and simulation data for the manuscript. This includes DF spectra, SERS spectra and simulations. All files are given in .txt, .csv, .npz and .h5py. Abstract for related manuscript: Conjugated polymers are promising material candidates for many future applications in flexible displays, organic circuits, and sensors. Their performance is strongly affected by their structural conformation including both electrical and optical anisotropy. Particularly for thin layers or close to crucial interfaces, there are few methods to track their organization and functional behaviors. Here we present a platform based on plasmonic nanogaps that can assess the chemical structure and orientation of conjugated polymers down to sub-10 nm thickness using light. We focus on a representative conjugated polymer, poly(3,4-ethylenedioxythiophene) (PEDOT), of varying thickness (2-20 nm) while it undergoes redox in situ. This allows dynamic switching of the plasmonic gap spacer through a metal-insulator transition. Both dark-field (DF) and surface-enhanced Raman scattering (SERS) spectra track the optical anisotropy and orientation of polymer chains close to a metallic interface. Moreover, we demonstrate how this influences both optical and redox switching for nanothick PEDOT devices.
DOI: 10.17863/cam.8829
title: Research data supporting “Development of structural colour in leaf beetles”

description: Original or unprocessed data is provided in support of the article “Development of structural colour in leaf beetles”. The article was accepted for publication in 2017 in the journal "Scientific Reports". Electronic supporting Information is available from the publisher. The data is structured into eight folders, each correlating to a specific data type presented in the published article. Folder 1: Photographs of the beetles at different stages of life. Folder 2: the data sets used to reconstruct the 3D volumes shown in Figure 2 (Synchrotron microtomography) in the manuscript. Folder 3: the complete set of TEM (Transmission Electron Microscopy) images available. The folder is further subdivided by beetle’s stage of life. Folder 4: optical microscope images before processing. The scale bar is included for reference. Folder 5 is relative to the Figure 5 in the manuscript: it is divided into two folders. The first one contains the Python code used to generate the simulated spectra. This file also includes the input files (i.e. the layer thickness as measured from the TEM sections). The second main folder includes the MATLAB files used to generate Fig.5 (that is, the experimental spectra collected by optical microspectroscopy and the simulated signal). In folder “Supporting”, one can find the two supporting video and the MATLAB code used to generate the supplementary images and the relative input files.
DOI: 10.6084/m9.figshare.c.3636335_d3.v1
title: Additional file 11: of Identification of candidate genes involved in Witches’ broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil

description: P-values of single and multiple QTLs and haplotype combinations associated with witches’ broom disease. The first tab contains the single QTL with their different parental haplotype combinations. The different columns contain the total number of trees with each haplotype and the results of the Chi-squared test for resistance and susceptibility. The last column contains the percentage of resistant trees with the particular haplotype combination. The second and third tab contain the same info but for combinations of two and three QTL, respectively. The combinations marked in grey belong to the top five of lowest P-values and indicate the highest associations between the QTL and WBD resistance/susceptibility. (XLS 81 kb)
DOI: 10.6084/m9.figshare.c.3636335_d2.v1
title: Additional file 16: of Identification of candidate genes involved in Witches’ broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil

description: Differential gene expression analysis of candidate genes. (XLS 300 kb)
DOI: 10.6084/m9.figshare.c.3636335_d4.v1
title: Additional file 13: of Identification of candidate genes involved in Witches’ broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil

description: Genes identified in all of the QTL regions associated with witches’ broom disease resistance. The annotation of the genes was based on the Matina 1–6 v1.1. genome. The genes indicated in red are genes that are most likely involved in disease resistance. Genes indicated in yellow contain a SNP marker that had the highest association with the disease in each QTL. Genes indicated in orange were identified as differentially expressed by Teixeira et al. [77]. The homologues in Arabidopsis thaliana (if known) were used, together with the GO Slim terms to identify the cellular components, the molecular components and the biological functions of the genes within the QTL regions. (XLS 155 kb)
DOI: 10.6084/m9.figshare.c.3636335_d7.v1
title: Additional file 1: of Identification of candidate genes involved in Witches’ broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil

description: Layout of the field experiment. Individual trees were planted in 2002 in a 3 × 3 m grid. Every fifth row in the field contained 5–19 trees (depending on the length of the rows) of the variety ‘Comum’, which is susceptible to WBD and serves as a natural and permanent inoculum source. Shade was provided using the traditional ‘cabruca’ system in which the trees are grown amongst the Atlantic Forest's native canopies. (XLS 97 kb)
DOI: 10.6084/m9.figshare.c.3636335_d12.v1
title: Additional file 8: of Identification of candidate genes involved in Witches’ broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil

description: Phenotypic data of witches’ broom disease in MP01. (XLS 184 kb)
DOI: 10.15468/dl.ugrhma
title: Occurrence Download

description: A dataset containing 19891 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Nyctidromus albicollis (J.F.Gmelin, 1789)"
 ]
}

 The dataset includes 19891 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037896-241126133413365/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.3636335_d16.v1
title: Additional file 3: of Identification of candidate genes involved in Witches’ broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil

description: Primer and probe sequences for candidate gene expression analysis. (XLS 35 kb)
DOI: 10.6084/m9.figshare.c.3636341_d1.v1
title: Additional file 1: of Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence

description: Node support values and divergence time estimates for all phylogenetic analyses. Node numbers correspond to those on Fig.Â 1, 2, 3, and Additional file 2, 3, 4, 6, 7. Bold indicates an unsupported node. Asterix indicates the node is not represented in that topology. (XLSX 38 kb)
DOI: 10.17863/cam.54489
title: Antarctic Grounding Line Location from Sentinel-1A/B double-difference interferometry, 2019, supporting "Antarctic ice-shelf advance driven by anomalous atmospheric and sea-ice circulation".

description: This dataset contains ESRI shapefiles of Larsen C Ice Shelf’s grounding line location (GLL), 2019, as constrained from double-difference interferometric synthetic aperture radar (SAR) techniques applied to ESA Sentinel-1a/b SAR imagery. Multiple GLLs are provided and correspond to the position of the grounding line as imaged from consecutive Sentinel-1a/b 6-day repeat-pass interferometric image pairs acquired during austral winter and early springtime (June, July, August, and September) of 2019. Further methods are outlined in the associated manuscript, and detailed information on the metadata associated with each shapefile is provided in the README.txt file. How to Cite If using these products, please cite the following: Christie, F.D.W, Benham T.J., Batchelor, C.L., Rack, W., Montelli, W. and Dowdeswell, J.A. (2022a). Antarctic ice-shelf advance driven by anomalous atmospheric and sea-ice circulation, Nature Geoscience, doi:10.1038/s41561-022-00938-x Christie, F.D.W, Benham T.J., Batchelor, C.L., Rack, W., Montelli, W. and Dowdeswell, J.A. (2022c). Antarctic Grounding Line Location from Sentinel-1A/B double-difference interferometry, 2019, supporting ‘Antarctic ice-shelf advance driven by anomalous atmospheric and sea-ice circulation’. Cambridge Apollo (2022); https://doi.org/10.17863/CAM.54489
DOI: 10.6084/m9.figshare.c.3636341_d6.v1
title: Additional file 12: of Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence

description: List of sequence length and loci coverage for samples in the mitochondrial dataset. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.c.3636341_d7.v1
title: Additional file 5: of Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence

description: Divergence matrix for the cytochrome b locus for selected Callicebus species. Bold indicates distance valuesâ
DOI: 10.6084/m9.figshare.c.3636341_d5.v1
title: Additional file 9: of Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence

description: List of the 22 loci used in this study and primer information. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3636341_d8.v1
title: Additional file 13: of Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence

description: List of sequence characteristics per locus including length, variation, sample coverage and dataset. Site information and sample coverage represent Callicebus taxa only. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.c.3636341_d11.v1
title: Additional file 10: of Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence

description: List of the GenBank accession numbers for all sequences. In bold are the sequences newly generated for this study. (XLSX 58 kb)
DOI: 10.17863/cam.52591
title: Data for Simultaneous investigation of the liquid transport and swelling performance during tablet disintegration

description: Raw data. The files contained in this folder are .mat files for the terahertz data and .csv files for the mercury porosimetry data. The subfolders are: Mercury porosimetry data; Terahertz time-domain spectroscopy data in the folder (THz-TDS); Terahertz pulsed imaging data in the folder (TPI). See the readme.txt file for detailed information about this dataset.
DOI: 10.17863/cam.44399
title: Research data supporting “Methodological diversity and theoretical integration: research in design fixation as an example of fixation in research design?”

description: This data supports an article titled “Methodological diversity and theoretical integration: research in design fixation as an example of fixation in research design?”. There is one explanatory document and two Comma-Separated Values (CSV) files. All files are related to the production of a citation map which is presented in the research article. The citation map is for publications related to design fixation. Those publications (texts) are cited in the accepted manuscript which can be found by following the repository link in the ‘Relationships’ section below (unfortunately those citations were removed from the published article during typesetting). Texts relevant to design fixation are represented as nodes. Edges (links) between nodes represent citations from one text to another. This work was partly supported by the UK’s Engineering and Physical Sciences Research Council (EP/K008196/1).