cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15124/crd42015020614
title: Steroid with local anesthetic injections versus local anesthetic injections for chronic non-cancer pain: a systematic review and meta-analysis

description: Systematic review protocol registration
DOI: 10.15124/crd42015020616
title: Ambulatory treatment of mild or uncomplicated diverticulitis: systematic review and meta-analysis

description: Systematic review protocol registration
DOI: 10.15124/crd42015020618
title: An evidence based review of the treatment of pyogenic spondylodiscitis

description: Systematic review protocol registration
DOI: 10.15124/crd42015020622
title: Age-related macular degeneration and mortality: a systematic review and meta-analysis

description: Systematic review protocol registration
DOI: 10.15124/crd42015024047
title: Extended lymph node resection versus standard resection for pancreatic and peri-ampullary adenocarcinoma [Cochrane Protocol]

description: Systematic review protocol registration
DOI: 10.15124/crd42015024048
title: The use of antibiotics for preventing lower respiratory tract infections in at risk children less than 12 years old [Cochrane Protocol]

description: Systematic review protocol registration
DOI: 10.15124/crd42015024049
title: Paracetamol (acetaminophen) or non-steroidal anti-inflammatory drugs, alone or combined for pain relief in acute otitis media in children [Cochrane Protocol]

description: Systematic review protocol registration
DOI: 10.15124/crd42015024050
title: Factors that influence the provision of intrapartum and postnatal care by skilled birth attendants in low- and middle-income countries: a qualitative evidence synthesis [Cochrane Protocol]

description: Systematic review protocol registration
DOI: 10.15124/crd42015024051
title: Non-drug conservative treatments for acute urinary retention after surgery in adults [Cochrane Protocol]

description: Systematic review protocol registration
DOI: 10.15124/crd42015024052
title: Systemic pharmacological treatments for chronic plaque psoriasis [Cochrane Protocol]

description: Systematic review protocol registration
DOI: 10.15124/crd42015024053
title: Interventions for guttate psoriasis [Cochrane Protocol]

description: Systematic review protocol registration
DOI: 10.15124/crd42015024054
title: Peritoneal dialysis for acute kidney injury [Cochrane Protocol]

description: Systematic review protocol registration
DOI: 10.6084/m9.figshare.28787909
title: Table 2

description: Vehicle Specifications for Simulation.
DOI: 10.15468/dl.yxc7sk
title: Occurrence Download

description: A dataset containing 2993 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriocephalus africanus L."
 ]
}

 The dataset includes 2993 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021584-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/2838045
title: CytoImageNet
DOI: 10.5281/zenodo.5717527
title: Increased Expression of Sorbitol Dehydrogenase in Colorectal Cancer Predicts BetterPrognosis (raw data)

description: COAD/READ/COADREAD_rnaseq_fpkm.txt files contain TCGA RNA-Seq data in FPKM normalisation form for colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD). COAD/READ/COADREAD_rnaseq_tpm.txt files contain TCGA RNA-Seq data in TPM normalisation form for colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD). COAD/READ/COADREAD_clinical_raw.xlsx files contain TCGA clinical data for patients with colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD). COAD/READ/COADREAD_rnaseq_clinical_raw.xlsx files contain corresponding information of TCGA clinical data and RNA-Seq data for patients with colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD). Local_cohort_tumour/adenoma_qPCR_rawdata.xlsx files contain our experimental results of qPCR CT values for SORD and GAPDH (as internal ref), shown as separate values for duplicate wells and average values. Local_cohort_tumour_clinical_rawdata.xlsx contains clinical information and calculated SORD relative expression of our recruited patients.
DOI: 10.5281/zenodo.5717526
title: Increased Expression of Sorbitol Dehydrogenase in Colorectal Cancer Predicts BetterPrognosis (raw data)

description: COAD/READ/COADREAD_rnaseq_fpkm.txt files contain TCGA RNA-Seq data in FPKM normalisation form for colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD). COAD/READ/COADREAD_rnaseq_tpm.txt files contain TCGA RNA-Seq data in TPM normalisation form for colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD). COAD/READ/COADREAD_clinical_raw.xlsx files contain TCGA clinical data for patients with colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD). COAD/READ/COADREAD_rnaseq_clinical_raw.xlsx files contain corresponding information of TCGA clinical data and RNA-Seq data for patients with colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD). Local_cohort_tumour/adenoma_qPCR_rawdata.xlsx files contain our experimental results of qPCR CT values for SORD and GAPDH (as internal ref), shown as separate values for duplicate wells and average values. Local_cohort_tumour_clinical_rawdata.xlsx contains clinical information and calculated SORD relative expression of our recruited patients.
DOI: 10.6084/m9.figshare.17005273.v7
title: BED file for Drosophila telomeric TEs and gene capture

description: *_lessfilt_genBrowser.bed: no filter on divergence; no filter on contig length; filter on telomeric hit length (&gt;=longest*0.5)<br>*_filt_genBrowser.bed: filter on divergence (&lt;= 0.3); filter with contig length (&gt;=50kb); filter with the longest hit
DOI: 10.5281/zenodo.5508710
title: wln510/Data_for_SWCs: Data for SWCs (for revision manuscript).

description: This is the data for revision manuscript.
DOI: 10.5281/zenodo.5508389
title: wln510/Data_for_SWCs: Data for SWCs (for revision manuscript).

description: This is the data for revision manuscript.
DOI: 10.6084/m9.figshare.12851093
title: Reversible cross-tolerance to platelet-activating factor signaling by bacterial toxins

description: Bacterial toxins signaling through Toll-like receptors (TLRs) are implicated in the pathogenesis of many inflammatory diseases. Among the toxins, lipopolysaccharide (LPS) exerts its action via TLR-4 while lipoteichoic acid (LTA) and bacterial lipoproteins such as Braun lipoprotein (BLP) or its synthetic analogue Pam3CSK4 act through TLR-2. Part of the TLR mediated pathogenicity is believed to stem from endogenously biosynthesized platelet-activating factor (PAF)- a potent inflammatory phospholipid acting through PAF-receptor (PAF-R). However, the role of PAF in inflammatory diseases like endotoxemia is controversial. In order to test the direct contribution of PAF in TLR-mediated pathogenicity, we intraperitoneally injected PAF to Wistar albino mice in the presence or absence of bacterial toxins. Intraperitoneal injection of PAF (5 μg/mouse) causes sudden death of mice, that can be delayed by simultaneously or pre-treating the animals with high doses of bacterial toxins- a phenomenon known as endotoxin cross-tolerance. The bacterial toxins- induced tolerance to PAF can be reversed by increasing the concentration of PAF suggesting the reversibility of cross-tolerance. We did similar experiments using human platelets that express both canonical PAF-R and TLRs. Although bacterial toxins did not induce human platelet aggregation, they inhibited PAF-induced platelet aggregation in a reversible manner. Using rabbit platelets that are ultrasensitive to PAF, we found bacterial toxins (LPS and LTA) and Pam3CSK4 causing rabbit platelet aggregation via PAF-R dependent way. The physical interaction of PAF-R and bacterial toxins is also demonstrated in a human epidermal cell line having stable PAF-R expression. Thus, we suggest the possibility of direct physical interaction of bacterial toxins with PAF-R leading to cross-tolerance.
DOI: 10.6084/m9.figshare.12851093.v1
title: Reversible cross-tolerance to platelet-activating factor signaling by bacterial toxins

description: Bacterial toxins signaling through Toll-like receptors (TLRs) are implicated in the pathogenesis of many inflammatory diseases. Among the toxins, lipopolysaccharide (LPS) exerts its action via TLR-4 while lipoteichoic acid (LTA) and bacterial lipoproteins such as Braun lipoprotein (BLP) or its synthetic analogue Pam3CSK4 act through TLR-2. Part of the TLR mediated pathogenicity is believed to stem from endogenously biosynthesized platelet-activating factor (PAF)- a potent inflammatory phospholipid acting through PAF-receptor (PAF-R). However, the role of PAF in inflammatory diseases like endotoxemia is controversial. In order to test the direct contribution of PAF in TLR-mediated pathogenicity, we intraperitoneally injected PAF to Wistar albino mice in the presence or absence of bacterial toxins. Intraperitoneal injection of PAF (5 μg/mouse) causes sudden death of mice, that can be delayed by simultaneously or pre-treating the animals with high doses of bacterial toxins- a phenomenon known as endotoxin cross-tolerance. The bacterial toxins- induced tolerance to PAF can be reversed by increasing the concentration of PAF suggesting the reversibility of cross-tolerance. We did similar experiments using human platelets that express both canonical PAF-R and TLRs. Although bacterial toxins did not induce human platelet aggregation, they inhibited PAF-induced platelet aggregation in a reversible manner. Using rabbit platelets that are ultrasensitive to PAF, we found bacterial toxins (LPS and LTA) and Pam3CSK4 causing rabbit platelet aggregation via PAF-R dependent way. The physical interaction of PAF-R and bacterial toxins is also demonstrated in a human epidermal cell line having stable PAF-R expression. Thus, we suggest the possibility of direct physical interaction of bacterial toxins with PAF-R leading to cross-tolerance.
DOI: 10.6084/m9.figshare.17040607
title: Code to run the three-process model from Scaffolding layered control architectures through constraint closure: insights into brain evolution and development

description: Download the c++ script and build it from the command line using e.g., ‘g++ -o model WilsonPrescott2021.cpp’. Then run the model using e.g., ‘./model log.txt’ to save a summary of the results into the file log.txt for inspection.
DOI: 10.6084/m9.figshare.17040607.v1
title: Code to run the three-process model from Scaffolding layered control architectures through constraint closure: insights into brain evolution and development

description: Download the c++ script and build it from the command line using e.g., ‘g++ -o model WilsonPrescott2021.cpp’. Then run the model using e.g., ‘./model log.txt’ to save a summary of the results into the file log.txt for inspection.
DOI: 10.5281/zenodo.5653587
title: EvidenceGRADEr dataset

description: <strong>What is EvidenceGrader?</strong> Assessment of the quality of medical evidence is a critical step in the systematic review of clinical evidence.<br> We aim to develop and evaluate a machine-learning system to enable automation of this step. The system should provide<br> an overall quality rating for each outcome as well as finer-grained justification for different quality criteria according to<br> the GRADE formalisation framework. Our goal is to work towards evaluating the quality of bodies of evidence (BoE)<br> for a specific clinical question, rather than assessing the quality of individual primary studies. <strong>The dataset</strong> We have built a dataset of 13,459 instances built from quality-related information available in Cochrane Database of Systematic Reviews. To obtain the full dataset, a request needs to be made first through: https://community.cochrane.org/form/cochrane-library-data-request, upon which we can share all dataset files. The file <em>fold_ids.json</em> available here contains only the identifiers of summary-of-findings tables from which we extracted the data instances. One instance corresponds to one outcome per summary-of-finding table (there can be more than one outcome). The entire collection is split into 10 folds.
DOI: 10.5281/zenodo.5653586
title: EvidenceGRADEr dataset

description: <strong>What is EvidenceGrader?</strong> Assessment of the quality of medical evidence is a critical step in the systematic review of clinical evidence.<br> We aim to develop and evaluate a machine-learning system to enable automation of this step. The system should provide<br> an overall quality rating for each outcome as well as finer-grained justification for different quality criteria according to<br> the GRADE formalisation framework. Our goal is to work towards evaluating the quality of bodies of evidence (BoE)<br> for a specific clinical question, rather than assessing the quality of individual primary studies. <strong>The dataset</strong> We have built a dataset of 13,459 instances built from quality-related information available in Cochrane Database of Systematic Reviews. To obtain the full dataset, a request needs to be made first through: https://community.cochrane.org/form/cochrane-library-data-request, upon which we can share all dataset files. The file <em>fold_ids.json</em> available here contains only the identifiers of summary-of-findings tables from which we extracted the data instances. One instance corresponds to one outcome per summary-of-finding table (there can be more than one outcome). The entire collection is split into 10 folds.
DOI: 10.6084/m9.figshare.17059673
title: E_gene_delimitation_supplementary

description: Input and output files for the TBEV E gene delemitation analysis.<br>ABGD, PTP and GMYC output statistics.<br>BEAST v1.10.4 .xml file
DOI: 10.6084/m9.figshare.17059673.v1
title: E_gene_delimitation_supplementary

description: Input and output files for the TBEV E gene delemitation analysis.<br>ABGD, PTP and GMYC output statistics.<br>BEAST v1.10.4 .xml file
DOI: 10.5281/zenodo.5717631
title: Transcriptomic Analysis of Streptococcus agalactiae Periprosthetic Joint Infection

description: Supplemental data from the study entitled "Transcriptomic Analysis of <em>Streptococcus agalactiae </em>Periprosthetic Joint Infection"
DOI: 10.5281/zenodo.5717630
title: Transcriptomic Analysis of Streptococcus agalactiae Periprosthetic Joint Infection

description: Supplemental data from the study entitled "Transcriptomic Analysis of <em>Streptococcus agalactiae </em>Periprosthetic Joint Infection"
DOI: 10.6084/m9.figshare.13147324.v12
title: QMOF Database

description: This repository hosts the Quantum MOF (QMOF) database as described in: https://doi.org/10.1016/j.matt.2021.02.015.<br>IMPORTANT NOTE: Please check out the QMOF GitHub repository for a description of the files hosted here, supplemental scripts, and other related information:https://github.com/arosen93/QMOF. Additional tabulated and raw data can be accessed via the GitHub page!<br>This work was supported in part by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences through the Nanoporous Materials Genome Center under Award Number DE-FG02-17ER16362.
DOI: 10.5517/ccdc.csd.cc256vz7
title: CCDC 2002599: Experimental Crystal Structure Determination

description: Related Article: Xinyi Wan, Shan Wang, Chengjun Wu, Jianbo Gan, Cunde Wang|2021|Org.Lett.|23|8799|doi:10.1021/acs.orglett.1c03301
DOI: 10.5517/ccdc.csd.cc26pf5j
title: CCDC 2046377: Experimental Crystal Structure Determination

description: Related Article: Xinyi Wan, Shan Wang, Chengjun Wu, Jianbo Gan, Cunde Wang|2021|Org.Lett.|23|8799|doi:10.1021/acs.orglett.1c03301
DOI: 10.25403/upresearchdata.13669963
title: Cardiopulmonary effects of three different ventilation treatments in healthy anaesthetised dogs

description: Arterial and central venous blood gas results at the start (0 minutes) and end (20 minutes) of each ventilation treatment (CPAP, PCV+PEEP and Spontaneous breathing)Physiological variables and spirometry measures at 5-minute intervals from start to end for each ventilation treatment.
DOI: 10.25403/upresearchdata.13669963.v1
title: Cardiopulmonary effects of three different ventilation treatments in healthy anaesthetised dogs

description: Arterial and central venous blood gas results at the start (0 minutes) and end (20 minutes) of each ventilation treatment (CPAP, PCV+PEEP and Spontaneous breathing)Physiological variables and spirometry measures at 5-minute intervals from start to end for each ventilation treatment.
DOI: 10.25403/upresearchdata.13705936
title: Reference intervals for haematology, clinical chemistry and acute phase reactants in free-ranging African elephants (Loxodonta africana)

description: The dataset was used to generate reference intervals for haematology, clinical chemistry and acute phase reactants for the free ranging African elephant (Loxodonta africana). Samples were obtained of animals from the Kruger National Park, both sexes and all ages were used. <br>The 3rd table data set contains data of the injured elephants, to evaluate acute phase reactants within this species. <br>
DOI: 10.25403/upresearchdata.13705936.v1
title: Reference intervals for haematology, clinical chemistry and acute phase reactants in free-ranging African elephants (Loxodonta africana)

description: The dataset was used to generate reference intervals for haematology, clinical chemistry and acute phase reactants for the free ranging African elephant (Loxodonta africana). Samples were obtained of animals from the Kruger National Park, both sexes and all ages were used. <br>The 3rd table data set contains data of the injured elephants, to evaluate acute phase reactants within this species. <br>
DOI: 10.25403/upresearchdata.13725952
title: Reticulocyte count and indices in dogs naturally and experimentally infected with Babesia rossi

description: This data contains results from three groups:1. Haematological variables and reticulocyte indices from experimentally Babesia rossi-infected dogs over 6 days.2. Haematological variables and reticulocyte indices from naturally Babesia rossi-infected dogs upon presentation. Two study cohorts are documented.3. Haematological variables and reticulocyte indices from a control group.
DOI: 10.15151/esrf-es-536310535
title: Structural Biology BAG - Portugal

description: The Portuguese MX BAG includes 13 PIs from three different institutions. Our research interests include soluble and membrane proteins of biomedical interest from humans or pathogenic organisms, many of which can be drug targets. Focus is also given to structural enzymology, aimed at the elucidation of reaction mechanisms, active sites, and inhibition tolerance in proteins with potential biotechnology applications. In several cases, complementary structural biology approaches are being used, combining MX with SAXS and, more recently, CryoEM.
DOI: 10.15151/esrf-es-541412206
title: Proteins and protein/DNA/RNA complexes involved in biosynthesis, protein folding and degradation, splicing, cancer, host pathogen interacti
DOI: 10.15151/esrf-es-542560924
title: Structural investigation of membrane and water soluble proteins

description: The portfolio of this BAG includes structural investigation of membrane proteins as well as soluble proteins relevant to various scientific fields. These range from basic science to application-related projects with impact on biotechnology (optogenetics, biocatalysts) and medicine (understanding and combating bacterial and viral pathogens).
DOI: 10.15151/esrf-es-569732859
title: Measuring the alignment and breakdown of worm-like micelles at ultra-high shear rates

description: Worm-like micelle solutions will be measured in a high-shear capillary rheometer to better understand the microstructural alignment, breakdown, and shear thinning rheology. Our capillary rheometer, previously developed for neutron scattering [1], was modified to expand the accessible shear rates up to 10^7 s-1 when using high-flux X-ray sources. A non-monotonic change in micelle alignment [1] is hypothesized to occur from breakage of the micelles into shorter lengths at high shear rates. The USAXS 2D detector will enable measurement of both the micelle lengths (100-10000 nm) and orientation distribution of micelle radii (10 nm) as a function of shear rate and concentration. To our knowledge, such measurements are only possible at ID02 USAXS. If desirable, we are eager to share knowledge and rheometer design with others at the ESRF, further improving the rheometer for future users aiming to measure the rheology and nanostructure of complex fluids at high shear rates.
DOI: 10.15151/esrf-es-569044652
title: Formation and development of induced mechanical strains in the presence of residual strains: A in-situ X-ray indentation on avian eggshells

description: The eggshell evolved with the paradox of being strong enough to preserve the embryo from mechanical stresses but brittle enough to allow the chick to hatch. The shell is a biomineralized tissue composed of distinct calcitic layers incorporated with organic molecules at both structural (intercrystalline) and atomic (intracrystalline) scales. These inclusions and microarchitectural arrangements of the crystalline layers result in the combination of high Young’s modulus and direction-dependent fracture toughness in the bioceramics. On the other hand, impurities come with consequence, the formation of interfaces with mismatches that can evolve and integrate internal forces within materials. The presence of these internal forces, which are the sources of residual strains/stresses, has been reported. However, to this day , how these residual strains/stresses modulate the mechanical performance and functionality of the eggshell remains unclear.
DOI: 10.15151/esrf-es-569045821
title: Decomposing the anisotropy of the magnetic susceptibility signal of Oman serpentinites by texture analysis
DOI: 10.6084/m9.figshare.16640209.v4
title: Supplementary data to publication "Untargeted metabolomics reveals metabolic stress alleviation by prepartum exercise in transition dairy cows"

description: Prepartum exercise has been proposed as an optimal strategy for peripartum management to improve the health of dairy cows. However, the mechanism by which prepartum exercise impacts metabolism has not been described in detail. Therefore, the objective of this study was to investigate metabolic changes in transition dairy cows with and without prepartum exercise. Twenty-four Holstein transition multiparous dairy cows were assigned to an exercise (n = 12) or control (n = 12) group, and plasma was collected at –21, –7, 0, +7, and +30 d relative to calving. The cows in the exercise group walked with the assistance of the researchers for a targeted 45 min at 3.25 km/h, 2 times/d. Plasma non-esterified fatty acid (NEFA), β-hydroxybutyric acid (BHBA), glucose, and triglyceride levels were measured, and metabolic profiles were analyzed using ultra-high-performance liquid chromatography time-of-flight mass spectrometry. Compared with those of the control group, the concentrations of NEFA at –7 d, glucose at 0 d, and BHBA at +7 d relative to calving were markedly decreased in the exercised group. Untargeted metabolomics and pathway analyses showed differences in the levels of key metabolites and their upstream metabolites between exercise and control cows, including gentisic acid, kynurenine, Trp, homovanillic acid, dopamine, cis-9-palmitoleic acid, and palmitic acid. Correlation and fold change analyses indicated that prepartum exercise may decrease homovanillic acid and cis-9-palmitoleic acid levels and increase tryptophan and gentisic acid levels to alleviate the metabolic stress of dairy cows during the transition period.