cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3637670_d4.v1
title: Additional file 2 of Tracing regulatory routes in metabolism using generalised supply-demand analysis

description: PySCeS model descriptor language file for the aspartate model, as required by the IPython notebook provided as Additional file 5 (see instructions within notebook). Software needed for Additional files 1 and 2: PySCeS (see http://pysces.sourceforge.net/docs/userguide.html ). (PSC 2 kb)
DOI: 10.6084/m9.figshare.c.3637670_d6.v1
title: Additional file 1 of Tracing regulatory routes in metabolism using generalised supply-demand analysis

description: PySCeS model descriptor language file for the pyruvate model, as required by the IPython notebook provided as Additional file 5 (see instructions within notebook). (PSC 2 kb)
DOI: 10.17863/cam.82899
title: NMR Data files "Golgi-localised putative S-Adenosyl methionine transporters required for plant cell wall polysaccharide methylation"

description: Raw NMR data of PDSD experiments.
DOI: 10.6084/m9.figshare.c.3637673_d1.v1
title: Additional file 1: Table S1. of Multiplexed automated digital quantification of fusion transcripts: comparative study with fluorescent in-situ hybridization (FISH) technique in acute leukemia patients

description: Raw data. (XLS 67 kb)
DOI: 10.17863/cam.88920
title: Dataset for "Bio-electrocatalytic conversion of food waste to ethylene via succinic acid as the central intermediate”

description: The original data is saved either as Excel (.xls or .xlsx) or Origin files (.ojp or .opju). The data is grouped in folders, corresponding to the particular figures in the manuscript or the supporting information. Please see document "Description Document_ACS Catalysis for more details.
DOI: 10.17863/cam.52027
title: Porosity in Nitride Semiconductors: Supplementary Material

description: This dataset contains supplementary material to Peter Griffin's PhD thesis: "Porosity in Nitride Semiconductors". The data consists of one high resolution image and three videos: - Image1.png shows aligned optical and SEM images, revealing the corellation between the micro and macro structure of a thick porous layer. This data is discussed in section 3.3.4.1 of the thesis. - Video1.avi shows sequential SEM images of the region around a V-pit in a porous GaN DBR, milled by FIB, thus showing how the pore structure changes with depth. This data is discussed in section 4.2.3 of the thesis. - Video2.avi shows serial block-face imaging (SBI) data obtained from sequential FIB-SEM of a porous GaN DBR. This data is discussed in section 4.3.1.1 of the thesis. - Video3.mp4 shows the data shown in Video2, reconstructed to show the pore structure of each layer of a porous GaN DBR. This data is discussed in section 4.3.1.1 of the thesis.
DOI: 10.6084/m9.figshare.c.3637703_d5.v1
title: Additional file 11: Table S6. of Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing

description: Summary of AS contigs obtained in the gene capture and used to build the AS model. (XLS 138 kb)
DOI: 10.6084/m9.figshare.c.3637706_d1.v1
title: Additional file 2: of Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus

description: Table S2. Description: European Nucleotide Archive accession number of each isolate. (XLSX 106 kb)
DOI: 10.6084/m9.figshare.c.3637712_d1.v1
title: Additional file 1: of Inferring microbial interaction network from microbiome data using RMN algorithm

description: The table of OTUs for all the samples at the genus level with OTU assignment before filtering process. (XLS 81 kb)
DOI: 10.6084/m9.figshare.c.3637712_d2.v1
title: Additional file 2: of Inferring microbial interaction network from microbiome data using RMN algorithm

description: The table of OTUs for all the samples at the genus level with OTU assignment after filtering process. (XLS 34 kb)
DOI: 10.17863/cam.82942
title: Research data supporting "Dynamic Diastereomerism on Chiral Surfaces"

description: Molecular dynamics output files of S-alanine and R-alanine desorbing from Cu{531} or Cu{110} (indicated in the filename). Trajectories were calculated with CASTEP V.18.1
DOI: 10.17863/cam.82740
title: Data for 'An Integrated Carbon Nitride-Nickel Photocatalyst for the Amination of Aryl Halides using Sodium Azide'

description: The dataset contains the raw data that supports the findings of the study “An Integrated Carbon Nitride-Nickel Photocatalyst for the Amination of Aryl Halides using Sodium Azide”. Data was collected using the instrumentation described in the Methods section of the study.
DOI: 10.6084/m9.figshare.c.3637787_d2.v1
title: Additional file 4: of Holding it together: rapid evolution and positive selection in the synaptonemal complex of Drosophila

description: Aligned D. melanogaster population sequences from the Drosophila Genetics Reference Panel (DGRP). Sequences were aligned to D. simulans and D. yakuba. Sequences that did not align or were missing data were removed prior to the MK tests. (TXT 929Â kb)
DOI: 10.17863/cam.35439
title: OntoKin ontology, version 1.0.

description: OntoKin is an ontology developed for representing chemical kinetic reaction mechanisms. The ontology is represented in OWL format.
DOI: 10.6084/m9.figshare.c.3637787_d3.v1
title: Additional file 3: of Holding it together: rapid evolution and positive selection in the synaptonemal complex of Drosophila

description: Aligned D. melanogaster population sequences from the Drosophila Population Genomics Project (DPGP). Sequences were aligned to D. simulans and D. yakuba. Sequences that did not align or were missing data were removed prior to the MK tests. (TXT 676Â kb)
DOI: 10.6084/m9.figshare.c.3637787_d4.v1
title: Additional file 2: of Holding it together: rapid evolution and positive selection in the synaptonemal complex of Drosophila

description: Aligned sequences of Drosophila SC genes. Text file containing the aligned sequences of each SC gene from the respective Drosophila species. Alignments were performed by MAFFT, MUSCLE, and PRANK. (TXT 1116Â kb)
DOI: 10.17863/cam.59634
title: Research data supporting ''structural effects of C3 oxygenated fuels on soot formation in ethylene coflow diffusion flames''

description: Chemical mechanisms used in structural effects of C3 oxygenated fuels on soot formation in ethylene coflow diffusion flames. The zipped folder contains three sub-folders with chemical mechanisms of dimethoxymethane (DMM), dimethyl carbonate (DMC), isopropanol (IPA). Within each of the sub-folders, there are three txt files with the chemical mechanism file, thermo file and transport file in CHEMKIN format. The txt files can be readily used without alterations in the kinetics software to run plug flow reactor simulations. The details of the simulation conditions can be found in the manuscript.
DOI: 10.17863/cam.38245
title: Dataset for the paper "Temporal Trends without Seasonal Effects on Gestational Diabetes Incidence Relate to Reductions in Indices of Insulin Secretion: The Cambridge Baby Growth Study" [Dataset]

description: Dataset used for the paper " Temporal Trends without Seasonal Effects on Gestational Diabetes Incidence Relate to Reductions in Indices of Insulin Secretion: The Cambridge Baby Growth Study" published as a preprint in BioRXiv (https://doi.org/10.1101/556886) and containing data from the Cambridge Baby Growth Study. Uncompressed Microsoft 2013 (.xlsx) file (1,084 rows including header; 23 columns including one for a dummy identifier) containing data relevant to the publication collected as part of the Cambridge Baby Growth Study (data collection 2001-2018). All the study participants were recruited from pregnancy clinics at the Rosie Maternity Hospital, Cambridge (2001-2009) around week 15 of pregnancy. A research 75 g oral glucose tolerance test (after an overnight fast) was performed on each of these participants around week 28 of pregnancy. Gestational diabetes was characterised according to International Association of Diabetes in Pregnancy Study Groups criteria. Insulin and c-peptide concentrations were measured using enzyme-linked immunosorbent assays and glucose by a standard laboratory technique. HOMA modelling was performed using the online HOMA calculator (https://www.dtu.ox.ac.uk/homacalculator/). The index of multiple deprivation was estimated from residential post codes. Missing data are presented by the term “missing”. For further information about the study please contact Dr. Clive Petry (address below; email: cjp1002@cam.ac.uk). For further general information about the Cambridge Baby Growth Study please contact Dr. Carlo Acerini (Department of Paediatrics, Box 116, Addenbrooke's Hospital, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, U.K.; email: cla22@cam.ac.uk).
DOI: 10.6084/m9.figshare.c.3637844_d4.v1
title: Additional file 1: of Phase I clinical trial of autologous NK cell therapy using novel expansion method in patients with advanced digestive cancer

description: Table S1. Summary of NK cell expansion from 31 cancer patients (supplementary information of reference #25).
DOI: 10.6084/m9.figshare.c.3637844_d5.v1
title: Additional file 4: of Phase I clinical trial of autologous NK cell therapy using novel expansion method in patients with advanced digestive cancer

description: Table S2. Change in NK population in PBL.
DOI: 10.17863/cam.104101
title: Data relating to "Practical, high-speed Gaussian coherent state continuous variable quantum key distribution with real-time parameter monitoring, optimised slicing, and post-processed key distillation"

description: Data used in compilation of paper "Practical, high-speed Gaussian coherent state continuous variable quantum key distribution with real-time parameter monitoring, optimised slicing, and post-processed key distillation"
DOI: 10.17863/cam.101517
title: Research data supporting "Structural Color from Cellulose Nanocrystals or Chitin Nanocrystals: Self-Assembly, Optics and Applications"

description: see summary provided as pdf. Figure041 - transmission spectra from integrating sphere and UV-vis; reflection spectra from integrating sphere and double-ended probe. Figure044 - angle-resolved optical spectroscopy spectra for specular, scattering and tilt modes. Figure046 - POM for reflection (R) and transmission (T) from the same region of interest (ROI 4). Figure047 - POM for bright field (BF) and dark field (DF) at the same region of interest (ROI 3). Figure048 - POM at various magnifications (5x, 10x, 20x) at the same region of interest (ROI 2). Figure049 - POM and spectra in various imaging modes (unpolarised UP, parallel polarisers PP, crossed polarisers XP, circular polarisation LP and RP) at the same region of interest (ROI 2). Figure050 - POM in bright field (BF) in various imaging modes (reflection R or transmission T, or both RT) and polarization (unpolarized UP, parallel PP or crossed polarizers XP)
DOI: 10.6084/m9.figshare.c.3637907_d2.v1
title: MOESM2 of AQP5-1364A/C polymorphism and the AQP5 expression influence sepsis survival and immune cell migration: a prospective laboratory and patient study

description: Additional file 2. Raw data from the figures are available as an excel file.
DOI: 10.6084/m9.figshare.c.3637925_d2.v1
title: MOESM2 of Elucidation of the roles of adhE1 and adhE2 in the primary metabolism of Clostridium acetobutylicum by combining in-frame gene deletion and a quantitative system-scale approach

description: Additional file 2. Dataset S1. Transcriptomic data of the total open reading frames (ORFs).
DOI: 10.17863/cam.85777
title: Data supporting 'Selection of vehicle size and extent of multi-drop deliveries for autonomous goods vehicles: An assessment of potential for change'

description: Folder contains all sets of VRP analyses described in the article. Analyses include full datasets, radial and random data subsets for 'Customer Deliveries' and 'Intermediate Distribution' case studies. Each folder consists of the following files: DistMatrix.txt: This is a matrix of distances between each destination in the analysis in kilometres FVOT.txt: This a small table listing the different values of FVOT (Freight Value of Time) LocDemand.txt: This is a table listing the reference numbers of the destinations in the dataset, the quantity of cargo required to be delivered to each destination and the coordinates of the destination. To preserve commercial confidentiality, coordinates have been removed for the uploaded datasets. In the 'Intermediate Distribution' cases, cargo loads are created in multiples of 12 cages with dummy location numbers used to differentiate between each multiple of 12 cages. VehParams.txt: This is a table of vehicle parameters including hourly driver and vehicle cost (in £/hr), mass capacity of the vehicle (in tonnes), volume capacity (in units of cargo, e.g. crates for LGVs and cages for rigid/tractor-trailer), mass per unit volume, fuel consumption when the vehicle is empty and full respectively. LWFMVRP.py: This is the Python program which runs the optimization analysis using Gurobi commercial solver. Output.xlsx: This is the excel output of the analysis and includes a summary as well as output matrices for the best solution discovered by the analysis.
DOI: 10.6084/m9.figshare.c.3637943_d1.v1
title: Additional file 2: of Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida

description: List of the coding sequences (CDSs) being in the core genomes of the 43 aeromonad strains studied. (XLSX 98 kb)
DOI: 10.6084/m9.figshare.c.3637943_d3.v1
title: Additional file 4: of Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida

description: List of the coding sequences (CDSs) being in the core genomes of the 8 A. salmonicida strains studied. (XLSX 110 kb)
DOI: 10.6084/m9.figshare.c.3637970_d3.v1
title: Additional file 6: of Identification of four functionally important microRNA families with contrasting differential expression profiles between drought-tolerant and susceptible rice leaf at vegetative stage

description: Novel miRNA analysis. (A) Novel miRNA candidates identified to be conserved in at least two libraries, (B) Novel miRNA candidates with miRNA*, (C) Predicted and validated targets (with GO annotation) of the 26 novel miRNA candidates. (XLSX 74 kb)
DOI: 10.6084/m9.figshare.c.3637970_d4.v1
title: Additional file 5: of Identification of four functionally important microRNA families with contrasting differential expression profiles between drought-tolerant and susceptible rice leaf at vegetative stage

description: The Solexa sequencing expression profile of known Oryza sativa mature miRNAs deposited in miRBase 21. Tables show mature miRNA names, mature miRNA sequences and the counts of expression level of (A) conserved and (B) non-conserved miRNA families from 12 small RNA libraries. (XLSX 68 kb)
DOI: 10.17863/cam.44367
title: Data to support: Sensitization of knee-innervating sensory neurons by tumor necrosis factor-α activated fibroblast-like synoviocytes: an in vitro, co-culture model of inflammatory pain.

description: Prism files containing all the raw data that support the 4 figures in the main manuscript and the supplementary data. This includes, the raw Ca2+-imaging and electrophysiology records for example traces, densitometry raw data for electrophoresis image and analysis and full overview of all statistical analysis present.
DOI: 10.17863/cam.50419
title: Downloads of research data EMP STATUS BY SECTOR for England and Wales COUNTIES 1851-1911 supporting “WP 26: Supplement to BBCE User Guide: Website definitions, downloads, Atlas of Entrepreneurship, and linkage to I-CeM”

description: BBCE data for entrepreneurs by sector for counties. The downloads include the total number of the economically active population from the BBCE broken down by sector, sex, for employers, own-account proprietors, and workers. All data are weighted for 1861 archival loss (E&W) and census non-response bias in 1891-1911.
DOI: 10.17863/cam.65723
title: Data supporting ROOTS publication "Behavioral measures of impulsivity and compulsivity in adolescents with non-suicidal self-injury"

description: Included in file "Lutz ROOTS data description"
DOI: 10.6084/m9.figshare.c.3638072_d1.v1
title: Additional file 1: Table S1. of Comparative M-protein analysis of Streptococcus pyogenes from pharyngitis and skin infections in New Zealand: Implications for vaccine development

description: Group A streptococcal isolates and emm types included in this study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3638078_d6.v1
title: Additional file 4: Table S2. of Karyotype differentiation in 19 species of river loach fishes (Nemacheilidae, Teleostei): extensive variability associated with rDNA and heterochromatin distribution and its phylogenetic and ecological interpretation

description: GenBank accession numbers of cyt b, IRBP and RAG1 sequences of nemacheilids and one botiid species (B. lohachata). (XLSX 17 kb)
DOI: 10.17863/cam.37731
title: Research data supporting "Software Prefetching for Indirect Memory Accesses: A Microarchitectural Perspective"

description: Source code and benchmarks to implement indirect memory access prefetching in LLVM, including new experiments for the TOCS journal paper, using Collective Knowledge.
DOI: 10.17863/cam.90534
title: Agda code accompanying the paper "Locally Nameless Sets"

description: The zip archive locns-agda.zip contains code for Agda (version 2.6.2.2) that was used to develop the theory of locally nameless sets and to check some of the proofs in the paper Andrew M. Pitts. 2023. Locally Nameless Sets. Proc. ACM Program. Lang. 7, POPL, Article 17 (January 2023), 27 pages. https://doi.org/10.1145/3571210 The root is the file Everything.agda (for browsable code start at html/Everything.html). The code mainly targets proofs that involve equational reasoning combined with the use of atoms and indices that are sufficiently fresh (via cofinite quantification). Some of these proofs involve a lot of nested case analysis on elements of sets with decidable equality (atoms and indices); some of the equational axioms are unfamiliar-looking and combinatorially complicated; and it is easy to forget to check necessary freshness conditions are satisfied when doing informal proofs. For all these reasons the use of an interactive theorem prover to produce machine-checked proofs was essential to gain assurance that the results in the paper are correct. The Agda code is stand-alone: some standard definitions (that might otherwise be called from the Agda Standard Library) are collected in the file Prelude.agda. The last part of the development requires function extensionality, which we postulate in the file FunExt.agda.
DOI: 10.6084/m9.figshare.c.3638171_d2.v1
title: Additional file 2: of Genome-wide predictors of NF-κB recruitment and transcriptional activity

description: NF-κB Target Genes (Gene Name, RefSeq Id, Ensembl Id), log 2 Fold Change (TNF stimulated vs unstimulated), Differential Expression Significance Call (TRUE/FALSE) and NF-κB Peak Detected after TNF Stimulation (TRUE/FALSE) (Data). (CSV 24 kb)
DOI: 10.17863/cam.83169
title: D. simulans s49 and D. sechellia NF100 genomes

description: This dataset is associated with the following article: "Trans-Regulatory Changes Underpin the Evolution of the Drosophila Immune Response". This dataset includes the variant calling files and accordingly generated genomes of D. simulans Sz49 and D. sechellia DenisNF100. dsim49_24.vcf and dsecNF100_20.vcf are the corresponding variant calling files to Sz49 and DenisNF100. dsim49.fasta and dsecNF100.fasta are the corresponding genomes generated for Sz49 and DenisNF100 using the respective variant calling files. We used publicly available data to produce reference genomes for the Drosophila lines. Whole genome sequencing data for D. simulans Sz49 was obtained from NCBI Sequence Read Archive, under BioProject PRJNA318623 (BioSample: SAMN05157406). Whole genome sequencing data for D. sechellia DenisNF100 was obtained from NCBI Sequence Read Archive, under BioProject PRJNA395473 (BioSample: SAMN07407394). Genomic sequencing reads of Sz49 and DenisNF100 were mapped to D. simulans reference genome(FlyBase Dsim r2.01) and the D. sechellia reference genome (FlyBase Dsec r1.3) respectively using the default parameters of the BWA-MEM algorithm in the BWA package. Duplicated read pairs were removed using Markduplicates in the Picard toolkit (http://broadinstitute.github.io/picard/). Subsequently, variants were called against the reference genome using the GATK (v4.1.4.1) HaplotypeCaller toolkit. Single nucleotide polymorphisms (SNPs) and indels were separated for Base Quality Score Recalibrations (BQSR). Each round of BQSR (GATK toolkit) was performed using hard-filtered variants from the previous round as “true set”. For SNPs, the hard-filtering criteria were set with QualByDepth &lt; 2.0, StrandOddRatio&gt;3.0, FisherStrand &gt; 60.0, RMSMappingQuality&lt;40.0, MappingQualityRankSumTest &lt; -12.5 and ReadPosRankSumTest &lt; -8.0. For indels, the hard-filtering criteria were set with QualByDepth &lt; 2.0, FisherStrand &gt; 200.0, ReadPosRankSumTest &lt; -20.0. BQSR were performed until the number of output variants plateaued or oscillated around a constant number. The finalised sets of variants after BQSR were then used to modify the reference genomes and generate Sz49 and DenisNF100 genomes with GATK FastaAlternateReferenceMaker toolkit.
DOI: 10.17863/cam.12959
title: Data supporting NSPN publication "Compulsivity and impulsivity are linked to distinct developmental trajectories of fronto-striatal myelination"

description: See file: data-description.txt
DOI: 10.6084/m9.figshare.c.3638243_d1.v1
title: Additional file 2: of Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination

description: Transcriptional and translational profiles of chloroplast-encoded genes. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.c.3638243_d3.v1
title: Additional file 14: of Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination

description: Transcriptional and translational profiles of carbohydrate metabolic enzymes. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.c.3638243_d5.v1
title: Additional file 17: of Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination

description: Transcriptional and translational profiles of redox proteins. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3638243_d7.v1
title: Additional file 18: of Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination

description: Transcriptional and translational profiles of respiratory system proteins. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.c.3638243_d8.v1
title: Additional file 19: of Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination

description: Pathway activities calculated based on metabolome data. (XLSX 24 kb)
DOI: 10.17863/cam.60610
title: Research data supporting "Octopaminergic neurons have multiple targets in Drosophila larval mushroom body calyx and can modulate behavioral odor discrimination"

description: The supporting data include microscopy images, quantitative analyses of images, and statistical analyses, for each figure presented in the linked paper. See the Readme.pdf file for a detailed description of the contents of each folder and for a list of file formats.
DOI: 10.6084/m9.figshare.c.3638312_d2.v1
title: Additional file 3: Table S1. of Optimizing sgRNA structure to improve CRISPR-Cas9 knockout efficiency

description: sgRNA sequences. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3638312_d3.v1
title: Additional file 2: of Optimizing sgRNA structure to improve CRISPR-Cas9 knockout efficiency

description: Dataset S1. Deep sequencing raw data of CCR5 target site modification of Fig.Â 2b. (XLSX 236 kb)