cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/3128
title: SUPERSEDED - The use of missense variations in functional annotation of the human ARID family of DNA binding proteins

description: ## SUPERSEDED - This dataset has been replaced by the one which can be found at https://doi.org/10.7488/ds/3190 . ## Missense variants are alterations to protein coding sequences that alter the identity of an amino acid at a specific site. They can be deleterious if the site is required for function but are likely to be tolerated at other sites. Consequently, missense variation within a healthy population mirrors the effects of negative selection on protein structure and function. Advances in high-throughput sequencing have dramatically increased the sample size of human variation data, allowing for population-wide interpretations of selective pressures. In this study, we developed a convenient framework for mapping missense variants onto solved or modelled protein structures and applied it to characterize the ARID family of gene regulators. ARID family members are implicated in multiple cancer types, developmental disorders, and immunological diseases but current understanding of their mechanistic roles is incomplete. Combined with phylogenetic and structural analyses, our approach allowed us to identify important sites for protein-protein interactions, histone code recognition, and DNA binding by the ARID proteins. We propose that missense variants can serve as a valuable tool for complementing experimental findings and formulating mechanistic hypotheses.
DOI: 10.7488/ds/3437
title: Optimising the treatment of Bangladeshi adult patients with severe pneumonia and/or ARDS using adaptive version of locally made Bubble CPAP: Feasibility study

description: The dataset comprises 30 adult patients of Bangladesh aged between 18 and 65 years diagnosed with severe pneumonia and hypoxaemia and/or acute respiratory distress syndrome (ARDS) with or without COVID-19 infection. These were obtained from two tertiary level hospitals (1) Dhaka Medical College Hospital, Dhaka and (2) Dhaka Hospital of icddr,b, Dhaka. The dataset includes screening data, inclusion and exclusion form, screening and baseline information, nurses follow-up, follow-up for physicians and conclusion/discharge information. Screening data: This data was obtained from all the patients aged between 18 and 65 years admitted to the ward. Inclusion and Exclusion Form: It was collected according to the enrolment criteria. This data defines the inclusion and exclusion criteria of the screened patients. Screening and Baseline: This data was collected from all the enrolled participants who received bubble CPAP oxygen therapy. A total of 30 participants were enrolled. Nurses Follow-up: This data denotes the scheduled vital records of the enrolled participants. These were obtained by nurses during the start of bCPAP oxygen therapy, one hour later and every four hours from the enrolment time point till the outcome of each participant. Follow-up for physicians: Physicians recorded the vitals every 8 or 12 hours or on demand. Conclusion: This data was obtained during the discharge or outcome of the enrolled participants.
DOI: 10.7488/ds/2789
title: Proteomic analysis of postsynaptic proteins in regions of the human neocortex

description: The postsynaptic proteome of excitatory synapses comprises ~1,000 highly conserved proteins that control the behavioral repertoire and mutations disrupting their function cause &gt;130 brain diseases. Here, we document the composition of postsynaptic proteomes in human neocortical regions and integrate it with genetic, functional and structural magnetic resonance imaging, positron emission tomography imaging, and behavioral data. Neocortical regions show signatures of expression of individual proteins, protein complexes, biochemical and metabolic pathways. The compositional signatures in brain regions involved with language, emotion and memory functions were characterized. Integrating large-scale GWAS with regional proteome data identifies the same cortical region for smoking behavior as found with fMRI data. The neocortical postsynaptic proteome data resource can be used to link genetics to brain imaging and behavior, and to study the role of postsynaptic proteins in localization of brain functions. This dataset replaces https://datashare.is.ed.ac.uk/handle/10283/2811 .
DOI: 10.7488/ds/2986
title: GWAMA summary data for morning plasma cortisol from the Cortisol Network (CORNET) Consortium 2021 (n=25,314)

description: The stress hormone cortisol modulates fuel metabolism, cardiovascular homoeostasis, mood, inflammation and cognition. The CORtisol NETwork (CORNET) consortium previously identified a single locus associated with morning plasma cortisol. Identifying additional genetic variants that explain more of the variance in cortisol could provide new insights into cortisol biology and provide statistical power to test the causative role of cortisol in common diseases. The CORNET consortium extended its genome-wide association meta-analysis for morning plasma cortisol from 12,597 to 25,314 subjects and from ~2.2 M to ~7 M SNPs, in 17 population-based cohorts of European ancestries. We confirmed the genetic association with SERPINA6/SERPINA1. This locus contains genes encoding corticosteroid binding globulin (CBG) and α1-antitrypsin. Expression quantitative trait loci (eQTL) analyses undertaken in the STARNET cohort of 600 individuals showed that specific genetic variants within the SERPINA6/SERPINA1 locus influence expression of SERPINA6 rather than SERPINA1 in the liver. Moreover, trans-eQTL analysis demonstrated effects on adipose tissue gene expression, suggesting that variations in CBG levels have an effect on delivery of cortisol to peripheral tissues. Two-sample Mendelian randomisation analyses provided evidence that each genetically-determined standard deviation (SD) increase in morning plasma cortisol was associated with increased odds of chronic ischaemic heart disease (0.32, 95% CI 0.06–0.59) and myocardial infarction (0.21, 95% CI 0.00–0.43) in UK Biobank and similarly in CARDIoGRAMplusC4D. These findings reveal a causative pathway for CBG in determining cortisol action in peripheral tissues and thereby contributing to the aetiology of cardiovascular disease.
DOI: 10.7488/ds/2398
title: SUPERSEDED - A synapse proteome resource for mouse brain regions

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/2399 . ## Data supporting the accepted manuscript Roy et al "Postsynaptic proteome regional signatures define architecture, function and connectivity in mouse brain".
DOI: 10.7488/ds/3099
title: Data for publication "Full spectral fluorescence lifetime Imaging with 0.5 nm spectral and 50 ps temporal resolution"

description: This dataset contains the data underlying the figure 2-5 of the paper "Full spectral fluorescence lifetime imaging with 0.5 nm spectral and 50 ps temporal resolution". The datafiles contain the data for full spectral fluorescence lifetime imaging (FS-FLIM) as follows: Convallaria_Data contains the data for figure 2, the data consists of a FS-FLIM datacube that can be analysed with the code in the file "Code_Full_Specral_FLIM" which requires Matlab (version 2019a or later) to run. BeeWing_Data contains the corresponding data to figure 3 in the form of a FS-FLIM datacube. Lung_Tissue_Slide_Stained_Data and Lung_Tissue_Slide_Unstained_Data contain the data for figure 4, each contain 60 FS-FLIM data cubes formatted for analysis, the folder names correspond to positions on the imaging system sample stage. Fresh_Lung_Tissue_Data contains the data for figure 5 in the form 20 FS-FLIM data cubes the folder names correspond to positions on the imaging system sample stage. The Code_Full_Spectral_FLIM set contains code for the principle analysis of FS-FLIM datacubes along with further code for the extraction of custom regions of interest from the analysed data. The folders contain "readme" files on how to use the code along with extensive comments in the the code itself.
description: Files are organised in 6 Zip files, Convallaria_Data - 1 datafile within folder structure needed for analysis BeeWing_Data - 1 datafile within folder structure needed for analysis Lung_Tissue_Slide_Stained_Data - 60 datafiles within folder structure needed for analysis Lung_Tissue_Slide_Unstained_Data - 50 datafiles within folder structure needed for analysis Fresh_Lung_Tissue_Data - 20 datasets within folder structure needed for analysis Code_Full_Spectral_FLIM - 2 folders for code for prinicple analysis "Analysis_Code" and for region of interest "Region of Interest"
DOI: 10.7488/ds/3055
title: Instances for "A Tractable Multi-Leader Multi-Follower Peak-Load-Pricing Model with Strategic Interaction"

description: Instances of hierarchical Cournot games to show the properties of the algorithm presented in the companion paper. This library contains problem instances for multi-leader, multi-follower games with a special structure that occurs in, e.g., the modelling of the European entry-exit gas market. The instances have different economic and mathematical properties so that other researchers in the field can test and benchmark newly developed methods for this challenging class of problems.
description: The description can be found in the file README.txt.
DOI: 10.7488/ds/2979
title: Impact of the COVID-19 Lockdown on the Electricity System of Great Britain: A Study on Energy Demand, Generation, Pricing and Grid Stability
title: Impact of the COVID-19 Lockdown on the Electricity System of Great Britain
title: Effect of 2020 March Lockdown on the Electricity System

description: This dataset is published in relation to the preprint titled "Impact of the COVID-19 Lockdown on the Electricity System of Great Britain: A Study on Energy Demand, Generation, Pricing and Grid Stability" which is accepted to the Energies journal. The aim of this study was to assess the effect of the March 2020 lockdown on the electricity system and market. This dataset contains all data used for the analyses and plots presented in the paper which uses Britain as a case study. The dataset primarily contains data from March 2020. However, it additionally has March 2019 data in some subfolders where it was used for comparison in the paper. This dataset is separated into 4 categories following the structure of the paper: (1) Demand, (2) Generation, (3) Forecast and Grid Stability, and (4) Pricing. Please see the README file for more information about the contents, resolution and structure of this dataset. To access any additional data, the Electricity Data Pipeline code presented in our paper can be employed.
description: Please see the Summary_of_Dataset.pdf for more information.
DOI: 10.7488/ds/3056
title: Mechanical Adaptation of Brachiopod Shells Via Hydration-Induced Structural Changes

description: This dataset accompanies the paper "Mechanical Adaptation of Brachiopod Shells Via Hydration-Induced Structural Changes", where using ptychographic X-ray tomography, electron microscopy and spectroscopy, we describe the hierarchical structure and composition of the shell of the brachiopod Discinisca tenuis as a function of hydration. We show that absorption of water by these shells results in structural changes at the micron- nano- and molecular scales, resulting in the material switching from hard and stiff when dry to malleable when hydrated within minutes. The deposited dataset includes the reconstructed X-ray ptychography tomograms of shells that were dry, exposed to 70 % relative humidity and 100 % relative humidity and the original electron microscopy images (SEM, STEM) that are presented in the paper.
DOI: 10.7488/ds/2399
title: A synapse proteome resource for mouse brain regions

description: Data supporting the paper Roy, M.; Sorokina, O.; McLean, C.; Tapia-González, S.; DeFelipe, J.; Armstrong, J.D.; Grant, S.G.N. Regional Diversity in the Postsynaptic Proteome of the Mouse Brain. Proteomes 2018, 6, 31. https://doi.org/10.3390/proteomes6030031
DOI: 10.7488/ds/3192
title: Breeding strategies for integrating new and orphan crops in production systems

description: 25/11/2021 Author: Jon Bancic Contact: jon.bancic@gmail.com Dataset consists of R scripts and datasets used for the analysis in Chapter 2, 3, 4 of my thesis. Each research chapter has its own directory and contains: • code folder: includes R and other scripts necessary to perform most of the analysis • data folder: includes raw and QC cleaned data • supplementary folder: includes high quality figures and\or tables that were not included in the thesis (particularly Chapter2) Should further clarification be needed, please, do not hesitate to contact me on the above email.
DOI: 10.7488/ds/3440
title: Raw data for the paper "A comprehensive model of surface abrasion based on the discrete element method"

description: This dataset includes the raw data shown in the paper "A comprehensive model of surface abrasion based on the discrete element method" by R.Capozza and K. Hanley. The article describes a new model for abrasion. It simulates the evolution of a surface abraded by a rigid object and describes both the abrasion due to scratching and normal/oblique impact. A group of particles models the surface, characterised by the hardness. When the pressure overcomes a threshold, particles are displaced to account for the change in surface profile. In the case of impact, the abraded volume grows with the velocity and reaches a maximum between 0 and 90◦. In the case of scratching, the dependence of the abraded volume on the normal load is linear in a limited range of loads (Archard’s law) and transitions to a non-linear behaviour with the increase of load. Energy dissipation is naturally included in the model without additional parameters. This conceptually simple approach can easily be extended to model a variety of industrial applications and predict wear patterns under varying scenarios.
DOI: 10.7488/ds/3277
title: Cawthorn Lab: Data for sex differences manuscript

description: *an updated version of this item can be found at https://doi.org/10.7488/ds/3758* Source data for figures included in our manuscript about age-dependent sex differences in the metabolic effects of caloric restriction (version date 12 January 2022). The abstract is as follows: "Caloric restriction (CR) is a nutritional intervention that reduces the risk of age-related diseases in numerous species, including humans. CR’s metabolic effects, including decreased fat mass and improved insulin sensitivity, play an important role in its broader health benefits; however, many aspects of the CR response remain poorly understood. In particular, sex differences in metabolic function are increasingly well recognised, yet the extent and basis of sex differences in CR’s health benefits have been largely ignored. Herein, we addressed this gap in knowledge. In young (3-month-old) male mice, 30% CR decreased fat mass and fasting blood glucose and improved glucose tolerance and insulin sensitivity; however, in young female mice these effects were blunted or absent. Indirect calorimetry revealed that females’ resistance to fat and weight loss is not explained by decreased energy expenditure, while positron emission tomography-computed tomography (PET/CT) with 18F-fluorodeoxyglucose (18F-FDG) showed that altered peripheral glucose uptake does not account for the sex differences in glucose tolerance. Instead, the latter is associated with altered hepatic function, with CR decreasing gluconeogenesis and altering liver ceramide content in males but not in females. To determine if oestrogen contributes to these sex differences, we next investigated the metabolic effects of CR initiated in aged mice (18-months old), when females are anoestrus. Strikingly, in these aged mice CR decreased fat mass and improved glucose homeostasis to a similar extent in both sexes. Finally, we found that CR-induced fat loss in humans is also sex- and age-dependent, with younger females resisting fat loss compared to younger males. Collectively, these studies identify age-dependent sex differences in the metabolic effects of CR and highlight adipose tissue, the liver and oestrogen as key determinants of CR’s metabolic benefits. This has important implications for understanding the interplay between diet and health, and for maximising the benefits of CR in humans."
DOI: 10.7488/ds/2080
title: Segmentation of the 4DL Connectome 1: Data analysis

description: Connectomic analysis of the nervous system aims to discover and establish principles that underpin normal and abnormal neural connectivity and function. In Hirst et al (2013) we performed image analysis of motor unit connectivity in the fourth deep lumbrical muscle (4DL) of mice, using transgenic expression of fluorescent protein in motor neurones as a morphological reporter. We developed a method that accelerated segmentation of confocal image projections of 4DL motor units, by applying high resolution (63×, 1.4 NA objective) imaging or deconvolution only where either proved necessary, in order to resolve axon crossings that produced ambiguities in the correct assignment of axon terminals to identified motor units imaged at lower optical resolution (40×, 1.3 NA). This dataset contains files with the major analyses done for the paper, in particular global_analysis.pzf – generated in Graphpad Prism. The remainder of the data relating to this study can be found grouped together in the "Connectomic analysis of the mouse fourth deep lumbrical muscle connectome" DataShare Collection at http://datashare.is.ed.ac.uk/handle/10283/2657.
DOI: 10.7488/ds/3216
title: Systematic map dataset of the most recent evidence on ruminant production-limiting disease prevalence and associated mortality in Ethiopia

description: A stable copy of the systematic map dataset of the most recent evidence on ruminant production-limiting disease prevalence and associated mortality in Ethiopia in the form of an excel file is provided here to ensure long term storage of the dataset. This systematic map dataset can be accessed through the livestockdata.org website via a Tableau visualization which has extensive filtering and searching capabilities. As new references are added, the dashboard will be updated and act as a living systematic map of the ruminant disease evidence in Ethiopia. Updates will happen at least twice a year using a machine learning methodology applied by informatics experts. The development of the dataset was funded by the Bill & Melinda Gates Foundation (Grant no: R83537) through the work of SEBI-Livestock.
description: The dataset in Excel format presented here contain the following sheets: META-DATA: Contains a description of the data in each column of the spreadsheets. STUDY_DETAILS: Contains all the study level information, each row represents a study. STUDY_RESULTS: Contains all the study results, one or more rows per study detailing results reported in the study e.g. species, disease, diagnostic test, prevelance/mortality rates. BIBLIOGRAPHY: Contains all the bibliograhic information about the study e.g. reference, journal. LABEL_VALUE: Contains the non numerical data in a long format of LABEL and Value for easy filtering of data. Data entries with multiple entries e.g. experimental factor are split into seperate rows.
DOI: 10.7488/ds/2230
title: The Edinburgh Computed tomography and genetic diagnostic criteria for lobar intracerebral haemorrhage associated with cerebral amyloid angiopathy: model development, internal validation and diagnostic test accuracy study
title: Lothian IntraCerebral Haemorrhage, Pathology, Imaging and Neurological Outcome [LINCHPIN] study - CT and pathology data

description: # Background: # Spontaneous intracerebral haemorrhage (ICH) is usually diagnosed by computed tomography (CT). Case series have described CT features of lobar ICH accompanied by cerebral amyloid angiopathy (CAA) on pathological examination. Whether CT features are diagnostic of CAA-associated lobar ICH is unclear. # Methods: # We identified adults with first-ever ICH diagnosed by CT in a prospective, population-based inception cohort study, who died and underwent research post-mortem. Two radiologists rated CT imaging appearances using a standardised proforma, blinded to clinical, genetic and histopathological features. We used blood or cerebellar tissue to determine apolipoprotein E (APOE) genotype. A neuropathologist rated brain tissue for small vessel diseases – including CAA, identified by beta-amyloid immunohistochemistry, rated using a standardised scale – masked to clinical, radiographic and genetic features. The primary outcome was CAA-associated lobar ICH (left cerebral hemisphere summed parenchymal CAA score ≥5). # Findings: # Among 110 adults (median age 83 years [IQR 76-87], 49 [45%] male), ICH was lobar in 62 (56%), deep in 41 (37%) and infratentorial in seven (6%). Among 62 lobar ICH, 36 (58%) were CAA-associated and they were independently associated with subarachnoid haemorrhage (32/36 [89%] versus 11/26 [42%]; p=0·01), ICH with finger-like projections (14/36 [39%] versus 0/26 [0%]; p=0·04) and APOE ε4+ (18/36 [50%] versus 2/26 [8%]; p=0·002). Diagnostic criteria for CAA-associated lobar ICH using these three variables had excellent discrimination (c-statistic 0.92, 95%CI 0.86-0.98), confirmed by internal validation. The rule-out criteria neither subarachnoid haemorrhage nor APOE ε4+ had 100% sensitivity (95%CI 88-100%). The rule-in criteria subarachnoid haemorrhage and either APOE ε4+ or finger-like projections had 96% specificity (95%CI 78-100%). # Interpretation: # Diagnostic criteria based on CT and APOE genotype show excellent discrimination for CAA-associated lobar ICH. These ‘rule-in’ and ‘rule-out’ criteria may might inform prognostic and therapeutic decisions that depend on identifying CAA-associated lobar ICH.
DOI: 10.7488/ds/3214
title: Neocortex saves energy by reducing coding precision during food scarcity

description: Information processing is energetically expensive. In the mammalian brain, it is unclear how information coding and energy use are regulated during food scarcity. Using whole-cell recordings and two-photon imaging in layer 2/3 mouse visual cortex, we found that food restriction reduced AMPA receptor conductance, reducing synaptic ATP use by 29%. Neuronal excitability was nonetheless preserved by a compensatory increase in input resistance and a depolarized resting potential. Consequently, neurons spiked at similar rates as controls but spent less ATP on underlying excitatory currents. This energy-saving strategy had a cost because it amplified the variability of visually-evoked subthreshold responses, leading to a 32% broadening of orientation tuning and impaired fine visual discrimination. This reduction in coding precision was associated with reduced levels of the fat mass-regulated hormone leptin and was restored by exogenous leptin supplementation. Our findings reveal that metabolic state dynamically regulates the energy spent on coding precision in neocortex.
description: This dataset contains 4 archives (ATP imaging, Electrophysiology, Calcium Imaging, Figure Data Points) containing data included in the published manuscript. Each archive contains README.txt files describing the data included. All raw data are available on request from the lead author (n.rochefort@ed.ac.uk).