cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26367198.v1
title: Effects of feeding enriched-olive cake on milk quality, metabolic response, and rumen fermentation and microbial composition in mid-lactating Holstein cows

description: The aim of this study was to evaluate the effects of supplementing OC enriched in polyphenols (EOC) to mid-lactating Holstein cows on milk quality, metabolic response, and rumen fermentation and microbiota. Twenty multiparous Holstein dairy cows (10 cows/group) were enrolled for 30 d in two homogeneous groups according to milk yield, days in milking, parity, and body condition score. The control group (CTR) received no supplemented concentrate, whereas the EOC group received concentrate with a 7% inclusion of EOC. Milk and blood samples were collected at 0 d and 30 d of treatment, while rumen fluid samples were collected after 30 d of treatment. Overall, the dietary supplementation of EOC did not affect milk yield and its quality, rumen pH, and rumen VFA. However, milk of EOC cows had lower C10:0, C12:0, C14:0, and C16:0 content, and greater C18:0, C18:1 cis-9, and C18:2 n6 content, compared with CTR cows. Regarding the rumen microbiota composition, EOC diet increased the relative abundance of <i>Bacteroidales_RF16_group</i>, <i>Absconditabacteriales_(SR1)</i>, and <i>Fibrobacteracea</i> in the rumen. On cow’s metabolism, EOC cows showed lower blood haptoglobin and greater ferric reducing antioxidant power (FRAP), cholesterol, and Zn levels compared with CTR cows. The supplementation of EOC led to a milder low-grade inflammatory response of cows and a positive modulation of cholesterol synthesis (probably at both intestinal and hepatic level). Supplementing EOC modulated rumen microbiota and improved the lipid profile of milk. Thereby, OC may be considered a valid feed to be included in the dairy cow’s diet leading to a positive effects on dairy cattle metabolism (less low-grade inflammatory response and oxidative stress) and at the same time giving an added value to the milk with a better profile of the fatty acids. Thanks to its nutritional properties, olive cake is a good alternative to conventional diet when integrated in the diet of dairy cattle, making animal production more sustainable. Diet supplemented with olive cake decreased milk medium-chain FAs C10:0, C12:0, C14:0 and C16:0, and increased long-chain FAs C18:0, C18:1 <i>cis-</i>9 and C18:2 n6 content. At animal level, it positively modulated rumen microbiota and it was able to increase blood cholesterol, Zn, and FRAP, and to decrease blood haptoglobin. Diet supplemented with olive cake clearly led to a milder inflammatory response of cows and improved the lipid profile of milk, being a good alternative to conventional feed.
DOI: 10.17863/cam.54230
title: Research data supporting "Seven principles of toolpath design in conventional metal spinning"

description: The dataset contains data collected during a study conducted by the authors in the Department of Engineering at the University of Cambridge in February-March 2019. The goal of the study was to capture the skill of experienced craftsmen in a metal forming technique known as metal spinning. The dataset is composed of 72 experimental trials performed by 6 different participants. Each participant visited the Department of Engineering for 1 full day of trials. The data collected is made up of: - 1 Word document explaining the sources of data - 1 Excel spreadsheet named “Trials data.xlsx” - 8 folders with data: video recordings, audio recordings, photographs of physical parts, graphics, text files with information about the roller trajectory and workpiece shape, MATLAB scripts.
DOI: 10.6084/m9.figshare.c.3622403_d4
title: MOESM4 of Analyzing the Chinese landscape in anti-diabetic drug research: leading knowledge production institutions and thematic communities

description: Additional file 4. Details of 881 publications in 14 thematic communities. This document provides more detailed information of all articles in 14 thematic communities, it contains: article title, author, organization, geographic region and thematic community.
DOI: 10.17863/cam.78670
title: Open Data for "A one-pot route to tunable sugar-derived sulfonated carbon catalysts for sustainable production of biodiesel by fatty acid esterification" by Rokhum et al. in Renewable Energy

description: Open Data for the full paper entitled "A one-pot route to tunable sugar-derived sulfonated carbon catalysts for sustainable production of biodiesel by fatty acid esterification" published by S.L. Rokhum et al. in Renewable Energy, 2022, 184, 908-919. In this work, synthetic data report the synthesis and regeneration/reuse of a glucose-derived sulfonated carbon catalyst for biodiesel synthesis. The following supporting data are deposited: Solid-state magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy data. Spectra were measured for 4 fresh catalyst samples (HTC3, HTC9, HTC10, HTC11) and also for D-(+)-glucose (from Fisher scientific, 99.99% purity). Separately, data were also obtained for fresh, used (5 times) catalyst HTC3 and its regenerated (re-sulfonated) derivative HTC3-R (see main manuscript for synthetic protocols). All NMR spectroscopic data were obtained using a Bruker AVANCE 400 MHz instrument equipped with a 9.4 T magnet and a 4 mm double resonance probe. Data are presented for 1H and 1H–13C cross-polarization (CP) experiments. These were performed using 10 kHz MAS, and applying 100 kHz 1H broadband SPINAL64, 4 ms CP contact time (using 75 kHz ramped 1H and 65 kHz square 13C contact pulses). A 2 s recycle delay was employed. Chemical shifts were referenced externally using the methyl signal of trimethylsilylpropanoic acid at 0.0 ppm (1H) and the methylene signal of glycine at 43.1 ppm (13C). Experiments were conducted using Bruker TopSpin 2.1 and the raw output can be processed and viewed using Bruker TopSpin, Mestrelab MNova or similar software.
DOI: 10.17863/cam.74391
title: Crystallographic diffraction data for structure of vaccinia virus protein E2

description: Crystallographic diffraction data used to solve the structure of vaccina virus strain Western Reserve protein E2 as deposited with the PDB ID 7PHY. For more information, see the README.txt file.
DOI: 10.6084/m9.figshare.c.3622454_d4
title: Additional file 6: Table S6. of Improving sensitivity of linear regression-based cell type-specific differential expression deconvolution with per-gene vs. global significance threshold

description: Functional enrichment analysis of LRCDE significant differentially expressed genes in kidney transplant dataset. “Category” – General functional category; “ID” - unique identifier of the functional category; “Name” – Category name; “Source” – Database reference; “p-value” - non-adjusted p-value; “q-value FDR B&H” – FDR-adjusted p-value; “Hit Count in Query List/Genome” – Number of differential genes/genes in the whole genome annotated with a functional category, respectively; “Hit in Query List” – Names of differentially expressed genes annotated with a functional category. (XLSX 246 kb)
DOI: 10.6084/m9.figshare.c.3622454_d5
title: Additional file 2: Table S2. of Improving sensitivity of linear regression-based cell type-specific differential expression deconvolution with per-gene vs. global significance threshold

description: An example of LRCDE and csSAM analysis results of simulated data with 18 samples per group. Target condition number (kappa) – 100, target mean squared error – 1.5, target cell proportion SD – 0.1. Range of the effect sizes introduced in the first 500 genes – 0.001 to 1.0. “site” – Probe ID; “Gene” – Gene label; “base” – estimated non-negative control group cell type-specific expression level; “case” - estimated non-negative case group cell type-specific expression level; “diff.est” – estimated cell type-specific differential expression between case and base; “mse.control” – Observed mean squared error of the control group regression; “mse.case” – Observed mean squared error of the case group regression; “cell” – Cell type name; “cell.sd” – Cell type-specific standard deviation of cell proportions across samples; “kappa.1/2” – Observed condition number of squared cell proportions matrix for the case/control group, respectively; “t.crit” – Critical t-value against which observed t-statistic is compared; “t.stat” – Observed t-statistic; “p.val.t” – Unadjusted p-value for t-statistic; “se1/2”– Standard error of the control/case group cell type-specific expression (regression coefficient) estimate, respectively; “se.p” – Welch’s combined standard error calculated for t-statistic; “t.power” – Observed power calculated from t-statistic and critical t-value; “FDR” – False discovery rate as reported by csSAM. (XLSX 136 kb)
DOI: 10.6084/m9.figshare.c.3622454_d6
title: Additional file 4: Table S4. of Improving sensitivity of linear regression-based cell type-specific differential expression deconvolution with per-gene vs. global significance threshold

description: An example of LRCDE and csSAM analysis results of simulated data with target MSE of 0.5 per regression. Sample size – 14, target condition number (kappa) – 100, target mean squared error – 2.5, target cell proportion SD – 0.06. Range of the effect sizes introduced in the first 500 genes – 0.001 to 1.0. Column names legend as in Additional file 1. (XLSX 138 kb)
DOI: 10.6084/m9.figshare.c.3622469_d2
title: Additional file 4 of Netter: re-ranking gene network inference predictions using structural network properties

description: Add 4 Performance tests individual results.xlsx. Additional file 4 is an xlsx file containing the detailed results of all performance tests. (XLSX 295 KB)
DOI: 10.6084/m9.figshare.c.3622475_d2
title: Additional file 8: Table S1. of MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing

description: Human Samples used in this study. (XLS 8Â kb)
DOI: 10.6084/m9.figshare.c.3622478_d1
title: Additional file 3: Table S1. of Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome

description: Feature Importance Scores for genus-level supervised learning. The feature importance score is the percentage increase in error rate when the given feature is permuted while other values remain constant. As there are only two categories, the increased error rate is equal for both categories. (XLSX 42Â kb)
DOI: 10.6084/m9.figshare.c.3622508_d3
title: Additional file 5: of Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease

description: Genbank files (.gb) of the 14 plasmids submitted to AddGene. (ZIP 41 kb)
DOI: 10.6084/m9.figshare.c.3622493_d7
title: Additional file 11: Table S6. of Transcriptomic profiling of host-parasite interactions in the microsporidian Trachipleistophora hominis

description: Testing for enrichment of differentially expressed genes in KEGG pathways. Fischerâ  s exact test with Benjamini and Hochberg correction [121] for the enrichment of genes identified as significantly differentially expressed in KEGG pathways in the RK-13 cell line. (XLSX 70Â kb)
DOI: 10.6084/m9.figshare.c.3622493_d8
title: Additional file 2: Table S1. of Transcriptomic profiling of host-parasite interactions in the microsporidian Trachipleistophora hominis

description: Expression levels of T. hominis transcripts. These include novel transcripts identified in this study (Locus tag labelled as â  NAâ  ). Genes annotated in the T. hominis genome but not detected during this study are also included for reference. In some cases multiple locus tags map to a single transcript, as discussed in the main text. (XLSX 486Â kb)
DOI: 10.6084/m9.figshare.c.3622520_d2
title: Additional file 2: of Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans

description: Supplementary tables. (XLSX 1030Â kb)
DOI: 10.6084/m9.figshare.c.3622508_d5
title: Additional file 3: of Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease

description: Primers and probes used in this study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3622493_d10
title: Additional file 3: Table S2. of Transcriptomic profiling of host-parasite interactions in the microsporidian Trachipleistophora hominis

description: Predicted T. hominis intron junctions. The genomic location and sequencing depth of all intron junctions identified in the T. hominis genome by TopHat (see Methods). (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3622568_d2
title: MOESM2 of A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly

description: Additional File 2: Table S1. Targets of Nb-105k microarray probes in Transcriptomes v.3 and v.5.
DOI: 10.5281/zenodo.14443556
title: Banco de dados SINASC SC cardiopatias 2011-2019
DOI: 10.5281/zenodo.14443557
title: Banco de dados SINASC SC cardiopatias 2011-2019
DOI: 10.6084/m9.figshare.c.3622589_d1
title: Additional file 1 of Integrative modeling of multi-omics data to identify cancer drivers and infer patient-specific gene activity

description: An example of the defined membership functions and general fuzzy rules in FCL (Fuzzy Control Language) format. (FCL 8.15 kb)
DOI: 10.6084/m9.figshare.c.3622589_d2
title: Additional file 2 of Integrative modeling of multi-omics data to identify cancer drivers and infer patient-specific gene activity

description: GoF and LoF gene scores for those genes that are mutated in more than 1 % of the samples. (CSV 37.9 kb)
DOI: 10.17863/cam.80852
title: Basal melt rates derived from radar measurements at Sermeq Kujalleq (Store Glacier) in Greenland

description: Data contains basal melt rates derived from autonomous phase-sensitive radio echo-sounding (ApRES) at site S30 on Sermeq Kujalleq (Store Glacier) in Greenland. The data covers the period 3 August - 4 December 2014 and are provided in daily mean values as described by Young et al. (2022).
DOI: 10.6084/m9.figshare.c.3622637_d1
title: Additional file 2: of Fab glycosylation of immunoglobulin G does not associate with improvement of rheumatoid arthritis during pregnancy

description: Data used for analysis. Contains the relative abundances of the observed glycans and the calculated glycosylation traits for the RA patients and healthy controls used in the current study. (XLSX 120Â kb)
DOI: 10.6084/m9.figshare.c.3622634_d2
title: MOESM2 of Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion

description: Additional file 2.
DOI: 10.17863/cam.13813
title: Cambridge Bridge Inspection Dataset

description: A labelled dataset for the scope of visual bridge inspection is not publically available. We have composed a new dataset for evaluating the performance of different detection methods on this dataset.
DOI: 10.5281/zenodo.13132236
title: Enhancing dairy processing with machine learning and domain knowledge: A combined analysis of offline and time series data - Accompanying material

description: The data complement the article "Enhancing dairy processing with machine learning and domain knowledge: A combined analysis of offline and time series data" published by Jox et al. (2024) in the Journal of Food Engineering (https://doi.org/10.1016/j.jfoodeng.2024.112423). The work was supported by the IGF Project of the FEI within the program for promoting the Industrial Collective Research (IGF) of the Federal Ministry of Economic Affairs and Climate Action (BMWK), based on a resolution of the German Parliament [01IF22840N].

The provided data includes tables of all features and describes the data sources.
DOI: 10.5281/zenodo.13149573
title: Enhancing dairy processing with machine learning and domain knowledge: A combined analysis of offline and time series data - Accompanying material

description: The data complement the article "Enhancing dairy processing with machine learning and domain knowledge: A combined analysis of offline and time series data" published by Jox et al. (2024) in the Journal of Food Engineering (https://doi.org/10.1016/j.jfoodeng.2024.112423). The work was supported by the IGF Project of the FEI within the program for promoting the Industrial Collective Research (IGF) of the Federal Ministry of Economic Affairs and Climate Action (BMWK), based on a resolution of the German Parliament [01IF22840N].

The provided data includes tables of all features and describes the data sources.
DOI: 10.17863/cam.100127
title: COL4A1/A2 transcriptomic

description: Bulk RNAseq analysis of hiPSC-derived MC for COL4A1/A2 SVD-related mutations and isogenic control lines.
DOI: 10.17863/cam.88917
title: Research data supporting "Quantitative monitoring and modelling of retrodialysis drug delivery in a brain phantom"

description: The data was generated as part of the EPSRC IRC in Targeted Delivery for Hard-to-Treat Cancers . In this work we present a platform which can be used to investigate and optimise the performance of microdialysis probes in the context of drug delivery. Our detailed experimental rig and the software supplied with our work is aimed at facilitating the transition of this delivery technique to clinical trials. Above all, our work is a significant contribution to the field as we can rapidly image and measure drug concentration far from the probe and discuss the size and shape of the drug plume. The images are taken with the following setup: a collimated light source (CX0202-WHIIC, Edmund Optics) shines parallel beams through the brain phantom. A telecentric objective lens (TitanTL 0.184X, Edmund Optics) is mounted on a digital camera (Basler Ace acA1920-150um, 2/3" 10-bit monochromatic sensor). A pass-band filter (FB500-40, Thorlabs) centred around 500 nm, with a bandwidth of 40 nm is mounted at the back of the lens. Images are recorded at 1 frame per minute with a fixed exposure time for each series (in the range 9 ms to 11 ms). Images are processed using Python environment and open-source packages. The microdialysis probe used in this study is the 70 MD Bolt Catheter, from Mdialysis. The brain phantom is an agarose gel 0.6% in Dulbecco's phosphate-buffered saline. The model drug solution is methylene blue 0.2 mg/mL in DPBS.
DOI: 10.17863/cam.65676
title: Research data supporting "Non-Planar Geometrical Effects on the Magnetoelectrical Signal in a Three-Dimensional Nanomagnetic Circuit"

description: This dataset contains 5 folders: ----------------------- Folder 1: "001_Fabrication stream file" The file "G3_w50_w500_gr011_theta025.str" is a text file containing the exposure instructions imported into the electron microscope to perform the exposure. The first column of this file represents exposure time, the second gives the x position of the beam in pixel units and the third column gives the y position of the beam in pixel units. ----------------------- Folder 2: "002_Micromagnetic(magnumfe)" This folder contains: 1) One .pvd file which represents the geometry of the 3D bridge 2) Ten .vtu files, which are visualisation of the magnetisation profiles in Paraview of 3D nanonbridge for field applied from 0 -90 degree simulated from Magnum.fe ----------------------- Folder 3: "003_SEM Characterisation" This folder contains 2 SEM micrographs of the structure studied with at two different angles as described in the Supporting Information. ----------------------- Folder 4: "004_Magneto transport data" This folder contains the ten .txt files which are the the full dataset of magneto-transport measurements results for field applied from 0-90 degree. ----------------------- Folder 6: "005_Macrospin and FEM results" This folder contains: 1) One .stl file which is the 3D model used in the FEM simulation 2) '001_data_macrospin.mat' which is the resultant magnetisation calculated from the macrospin model described in the supporting information for field applied 0-90 degree at 5 degree interval. 3) '002_data_FEM.mat' contains the resultant AMR, MMR, AHE and OHE calculated using the FEM model.
DOI: 10.17863/cam.7350
title: Research data supporting The austenite-ferrite transformation in enhanced-niobium, low-carbon steel

description: Microstructural and other images associated with the publication
DOI: 10.17863/cam.51342
title: Research data supporting "How does the human visual system compare the speeds of spatially separated objects?"

description: The titles of the excel files indicate the experiments they correspond to in the PLOS ONE paper they accompany. Within each file, there are separate pages corresponding to individual participants and a final page giving averages. There are separate tables on each page for discrimination thresholds and for response times (which are given in milliseconds).
DOI: 10.6084/m9.figshare.c.3622724_d1
title: MOESM1 of Palaeolithic diet decreases fasting plasma leptin concentrations more than a diabetes diet in patients with type 2 diabetes: a randomised cross-over trial

description: Additional file 1. Supporting data set. Data set supporting our results on hormones (adipokines, glucagon and incretins), post hoc analysis and previously published outcomes (worksheet ‘Data set’). Each row numbered 1-13 in first column ‘Person-ID’ corresponds to data from one participant. Each column heading contains a variable name stating what individual mean has been measured, in what unit and whether on the Paleolithic diet, diabetes diet or if it is the difference between the two diets (DeltaPd, value during Paleolithic diet minus value during diabetes diet). The variable names and their description are listed below.
DOI: 10.15468/dl.zmu5dw
title: Occurrence Download

description: A dataset containing 176 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "Month is January",
 "TaxonKey is Lacerta agilis Linnaeus, 1758"
 ]
}

 The dataset includes 176 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033213-241126133413365/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.3622733_d1
title: Additional file 6 of Propagation of errors in citation networks: a study involving the entire citation network of a widely cited paper published in, and later retracted from, the journal Nature

description: Bibliographic references. BibTE X file with all bibliographic references to expand the labels that occur in the two dot files and in the graphs with named nodes. (BIB 695 kb)
DOI: 10.17863/cam.66696
title: Supporting data for "High-yield parallel fabrication of quantum-dot monolayer single-electron devices displaying Coulomb staircase, contacted by graphene"

description: The data used in the accompanying paper are included here. Please see readme file for more details
DOI: 10.6084/m9.figshare.c.3622733_d3
title: Additional file 3 of Propagation of errors in citation networks: a study involving the entire citation network of a widely cited paper published in, and later retracted from, the journal Nature

description: Specification of the 2015 citation network. dot file [33] that contains a complete specification of the 2015 citation network. As above. (TXT 80.4 kb)
DOI: 10.6084/m9.figshare.c.3622739_d1
title: Additional file 3: of Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines

description: Defense related genes differentially expressed in early stages of seed development. Column â  Sâ   reports the stages of development in which the gene is differentially expressed. Genes down-regulated in 3mlpa mutant are indicated by negative values of log 2 ratio. Adjusted P-values are only reported for the stages in which the gene is differentially expressed. (XLSX 60Â kb)