cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2626
title: Interleukin-1 receptor antagonist treatment in acute ischaemic stroke does not alter systemic markers of anti-microbial defence

description: Background: Blockade of the cytokine interleukin-1 (IL-1) with IL-1 receptor antagonist (IL-1Ra) is a candidate treatment for stroke entering phase II/III trials, which acts by inhibiting harmful inflammatory responses. Infection is a common complication after stroke that significantly worsens outcome and is related to stroke-induced deficits in systemic immune function thought to be mediated by the sympathetic nervous system. Therefore, immunomodulatory treatments for stroke, such as IL-1Ra, carry a risk of aggravating stroke-associated infection. Our primary objective was to determine if factors associated with antibody-mediated antibacterial defences were further compromised in patients treated with IL-1Ra after stroke. Methods: We assessed plasma concentrations of immunoglobulin isotypes and complement components in stroke patients treated with IL-1Ra or placebo and untreated non-stroke controls using multiplex protein assays. Activation of the sympathetic nervous system (SNS) was determined by measuring noradrenaline, a major SNS mediator. Results: There were significantly lower plasma concentrations of IgM, IgA, IgG1 and IgG4 in stroke-patients compared to non-stroke controls, however there were no differences between stroke patients treated with placebo or IL-1Ra. Concentrations of complement components associated with the classical pathway were increased and those associated with the alternative pathways decreased in stroke patients, neither being affected by treatment with IL-1Ra. Noradrenaline concentrations were increased after stroke in both placebo and IL-1Ra-treated stroke patients compared to non-stroke controls. Conclusion: These data show treatment with IL-1Ra after stroke does not alter circulating immunoglobulin and complement concentrations and is therefore unlikely to further aggravate stroke-associated infection susceptibility through reduced altered availability of these key anti-microbial mediators. Supplementary Figures from the manuscript are also available here.
DOI: 10.7488/ds/2813
title: Molecular Detection of Gram-positive Bacteria in the Human Lung through an Optical Fiber Based Endoscope

description: # Purpose # The relentless rise in antimicrobial resistance is a major societal challenge and requires, as part of its solution, a better understanding of bacterial colonization and infection. To facilitate this, we developed a highly efficient no-wash red optical molecular imaging agent that enables the rapid, selective and specific visualization of Gram-positive bacteria through a bespoke optical fiber based delivery/imaging endoscopic device. # Methods # We rationally designed a no-wash, red, Gram-positive specific molecular imaging agent based on vancomycin and an environmental merocyanine dye. We demonstrated the specificity and utility of the imaging agent in escalating in vitro and ex vivo whole human lung models (n=3), utilizing a bespoke fiber-based delivery and imaging device, coupled to a wide-field, two-color endomicroscopy system. # Results # The imaging agent was specific to Gram-positive bacteria and enabled no-wash imaging of Gram-positive bacteria within the alveolar space of whole ex vivo human lungs within 60s of administration into the field-of-view. # Conclusion # This platform enables the rapid and specific detection of Gram-positive bacteria in the human lung.
DOI: 10.7488/ds/2412
title: Structural, functional and metabolic brain differences between groups with opposite gender identity and sexual orientation. A systematic review on the neuroimaging literature up to 2018
title: Structural, functional and metabolic brain differences between groups with opposite gender identity and sexual orientation. A systematic review and meta-analysis

description: Human sexuality is a complex reality, characterised by gender identity and sexual orientation. A widespread approach to study human sexuality is to compare groups with opposite sexual gender identity and sexual orientation such as cisgenders vs transgenders and heterosexuals vs homosexuals. Cisgenderism refers to individuals whose sense of gender identity corresponds to their natal sex, while transgenderism is characterized by an incongruity between biological sex and psychological gender with cross-gender identification. Heterosexuality refers to those who feel an emotional, romantic or sexual attraction towards the opposite sex, while homosexuality is characterized by an emotional, romantic or sexual attraction towards same sex individuals. Neuroimaging studies have found brain differences between these groups of individuals. Nevertheless, their results are conflicting, and limitations such as small samples’ sizes and the considerable overlap between such groups, makes it difficult to draw accurate conclusions. This systematic review and meta-analysis explored structural, functional and metabolic features of the ‘cisgender brain’ compared with the ‘transgender brain’ before hormonal treatment and the ‘heterosexual brain’ compared to the ‘homosexual brain’ from the analysis of the neuroimaging literature. Processing the information that conform this dataset suggests that neuroanatomy, neurophysiology and neurometabolism in transgenders resemble those of their natal sex rather than those of their experienced gender and in homosexuals these resemble those of their same sex heterosexual population rather than their opposite sex heterosexual population. However, the small number of studies that contributed data, their small sample size, the incompleteness of the data, and the heterogeneity of the investigations that were included in this systematic review do not allow drawing general conclusions. This dataset contains all data extracted from the publications included, as well as the search strategy and the results of processing the information extracted from the articles
description: Please see Readme.pdf.
DOI: 10.7488/ds/293
title: Generation Scotland: Donor DNA Databank

description: The Generation Scotland Donor DNA Databank (GS:3D) phenotype was collected from consented blood donors by questionnaire and relates to 4,998 healthy control DNA samples and plasma.
description: Dataset pertaining to the publication “Generation Scotland: Donor DNA Databank; A control DNA resource”. BMC Med Genet 2010 Nov 23;11:166. doi: 10.1186/1471-2350-11-166. URL: http://www.biomedcentral.com/1471-2350/11/166 The data is phenotype information collected from consented donors by questionnaire as described in the research paper and is in an MS Excel table, GS3D phenotype.xls. If you use this dataset, please cite the manuscript in order to acknowledge the contribution of the Generation Scotland: Donor DNA Databank (GS:3D) resource. For information about using GS:3D DNA or plasma samples, or genetic data, please visit http://www.generationscotland.org/ or contact resources@generationscotland.org. All applications to use Generation Scotland resources will be reviewed by the Generation Scotland Access Committee. GS:3D is an NHS Lothian NRS BioResource, governed as a Research Tissue Bank by the GS Access Committee, and has supported over 20 research projects to date. GS:3D was funded by a project grant from the Scottish Executive Health Department, Chief Scientist Office, grant number CZB/4/285. Shona Kerr, on behalf of all co-authors in the corresponding manuscript.
DOI: 10.7488/ds/2545
title: SUPERSEDED - Supplementary Figures: Interleukin-1 receptor antagonist treatment in acute ischaemic stroke does not alter systemic markers of anti-microbial defence

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/2626 ## Supplementary Figures from the manuscript "Interleukin-1 receptor antagonist treatment in acute ischaemic stroke does not alter systemic markers of anti-microbial defence". ## ABSTRACT ## ### Background ### Blockade of the cytokine interleukin-1 (IL-1) with IL-1 receptor antagonist (IL-1Ra) is a candidate treatment for stroke entering phase II/III trials, which acts by inhibiting harmful inflammatory responses. Infection is a common complication after stroke that significantly worsens outcome and is related to stroke-induced deficits in systemic immune function thought to be mediated by the sympathetic nervous system. Therefore, immunomodulatory treatments for stroke, such as IL-1Ra, carry a risk of aggravating stroke-associated infection. Our primary objective was to determine if factors associated with antibody-mediated antibacterial defences were further compromised in patients treated with IL-1Ra after stroke. ### Methods ### We assessed plasma concentrations of immunoglobulin isotypes and complement components in stroke patients treated with IL-1Ra or placebo and untreated non-stroke controls using multiplex protein assays. Activation of the SNS was determined by measuring noradrenaline, a major SNS mediator. ### Results ### There were significantly lower plasma concentrations of IgM, IgA, IgG1 and IgG4 in stroke-patients compared to non-stroke controls, however there were no differences between stroke patients treated with placebo or IL-1Ra. Concentrations of complement components associated with the classical pathway were increased and those associated with the alternative pathways decreased in stroke patients, neither being affected by treatment with IL-1Ra. Noradrenaline concentrations were increased after stroke in both placebo and IL-1Ra-treated stroke patients compared to non-stroke controls. ### Conclusion ### These data show treatment with IL-1Ra after stroke does not alter circulating immunoglobulin and complement concentrations and is therefore unlikely to further aggravate stroke-associated infection susceptibility through reduced availability of these key anti-microbial mediators.
DOI: 10.7488/ds/2987
title: Particle sizing for flowing colloidal suspensions using flow-differential dynamic microscopy

description: Dataset for "Particle sizing for flowing colloidal suspensions using flow-differential dynamic microscopy". Particle size is a key variable in understanding the behaviour of the particulate products that underpin much of our modern lives. Typically obtained from suspensions at rest, measuring the particle size under flowing conditions would enable advances for in-line testing during manufacture and high-throughput testing during development. However, samples are often turbid, multiply scattering light and preventing the direct use of common sizing techniques. Differential dynamic microscopy (DDM) is a powerful technique for analysing video microscopy of such samples, measuring diffusion and hence particle size without the need to resolve individual particles while free of substantial user input. However, when applying DDM to a flowing sample, diffusive dynamics are rapidly dominated by flow effects, preventing particle sizing. Here, we develop ``flow-DDM'', a novel analysis scheme that combines optimised imaging conditions, a drift-velocity correction and modelling of the impact of flow. Flow-DDM allows a decoupling of flow from diffusive motion that facilitates successful particle size measurements at flow speeds an order of magnitude higher than for DDM. We demonstrate the generality of the technique by applying flow-DDM to two separate microscopy methods and flow geometries.
DOI: 10.7488/ds/2728
title: A Celebration of Scottish Health Cohort Studies: Participants' attitudes towards data research

description: BACKGROUND. The UK hosts many of the world’s longest running prospective longitudinal birth cohort studies. These projects make repeated observations of their participants and use this data to explore health outcomes and mortality. An alternative method for data collection is record linkage; the linking together of electronic health and administrative records. Applied nationally, this could provide unrivalled opportunities to follow a large number of people in perpetuity. However, public attitudes to the use of data and samples in research are currently unclear. Here we report on an event at which we collected attitudes towards recent opportunities and controversies within health data science. METHODS. The event was attended by ~250 individuals (cohort members and their guests), who had been invited through the offices of their participating cohort studies. Attendees heard talks describing key research results and participated in 15 multiple-choice questions using interactive voting pads. RESULTS. Our participants showed a high level of trust in researchers and doctors, but less trust in commercial companies. They supported the idea of researchers using information from both neonatal blood spots (Guthrie spots) and from health records. Participants said they would be willing to wear devices like a “fit-bit” and to undergo a brain scan that might predict later mental illness. However, they were less willing to change an aspect of their lifestyle or take a new drug for research purposes. They were very keen to encourage others to take part in research; whether that be offering the opportunity to pregnant mothers or indeed extending invitations to their own children and grandchildren CONCLUSIONS. Our participants were broadly supportive of research access to data and samples, albeit less supportive when commercial interests are involved. Public engagement events that facilitate two-way interactions can influence and support future research and public engagement efforts. Ethical permission for this work was granted by The Psychology Research Ethics Committee (PREC) at the University of Edinburgh (Ref No: 327-1718/3). No identifying data were collected from participating individuals. Videos are publicly available on the CCACE YouTube Channel: https://www.youtube.com/channel/UCaemWVOehYht6pylL9zq4nw
DOI: 10.7488/ds/2812
title: Exploratory use of fluorescent SmartProbes for the rapid detection of microbial isolates causing corneal ulcer

description: # Purpose # To explore the use of optical SmartProbes for the rapid evaluation of corneal scrapes from patients with suspected microbial keratitis, as a clinical alternative to Gram stain. # Design # Experimental study with evaluation of a diagnostic technology. # Subjects # Corneal scrapes from 267 patients presenting with suspected microbial keratitis at a referral cornea clinic within a specialist tertiary care hospital in South India were evaluated. # Methods # Corneal scrapes were flooded with SmartProbe (BAC One (all microbe, n = 107) or BAC Two (specific to gram-negative bacteria, n = 160)) and evaluated by fluorescence microscopy (without the need for sample washing or further processing). The microscopist was masked to the clinical result when scoring the SmartProbe sample. # Main Outcome Measures # Score the SmartProbe labelled sample as bacteria/fungi/none (BAC One) or gram-negative bacteria/none (BAC Two) and compare to Gram stain and culture reports, determining the sensitivity, specificity, positive and negative predictive values and accuracy. # Results # Compared to Gram stain, BAC One demonstrated sensitivity and specificity of 80.0 and 87.5 percent respectively, positive and negative predictive values of 93.8 and 65.1 percent and an accuracy score of 82.2. BAC Two demonstrated sensitivity and specificity of 93.3 and 84.8 percent respectively, a negative predictive value of 99.2 percent and an accuracy of 85.6 percent. Twenty percent of fungal samples were recorded as positive for BAC Two, leading to a positive predictive value of 38.9, however, when morphology and positive fluorescent signal were considered together, the positive predictive value increased to 88.8. When the corresponding culture results were compared to the direct microscopy (Gram stain) result, the sensitivity and specificity were 73.4 and 70.7 percent respectively, the positive and negative predictive values were 86.5 and 51.0 percent, and there was an overall accuracy of 72.6. # Conclusions # Fluorescent SmartProbes offer a comparative method to direct microscopy (Gram stain) for delineating gram-positive or gram-negative bacteria or fungi within corneal scrapes. We demonstrate equivalent or higher scores for sensitivity, specificity, positive and negative predictive values and accuracy than culture to Gram stain. Our approach has scope for point-of-care clinical application to aid in the diagnosis of microbial keratitis.
DOI: 10.7488/ds/1395
title: Serial AFP measurement in confirmed HCC cases
title: AFP values for patients diagnosed in the ‘HCC case series’

description: This dataset was used in the work to define a Bayesian analysis of serial AFP fluctuations in patients with hepatocellular carcinoma (HCC) in order to improve HCC detection. It consists of all 66 patients whom had AFP values taken prior to diagnosis of HCC and were in a defined HCC screening program at the time of HCC diagnosis. Data has been approved for deposition in publicly available repository by local ethics committee.
description: Column descriptions HCC case reference, Anonymised reference for HCC case Sex, Male =1, Female =0 Age at HCC diagnosis, Patient age on date of HCC diagnosis AFP, AFP value (kU/l) Time relative, Days difference between sample date and HCC diagnosis (negative values were serum samples taken prior to date of HCC diagnosis) post Rx sample, x denotes serum samples taken after application of HCC specific therapy aetiology, aetiology of liver disease treatment, Received HCC specific treatment =y, no HCC specific treatment received =n, prior to census Treatment type, Mode(s) of specific HCC therapy applied prior to census
DOI: 10.7488/ds/2773
title: Frugal filtering optical lenses for point-of-care diagnostics

description: Abstract: Infectious diseases are the leading cause of morbidity and mortality in low and middle income countries (LMICs). Rapid diagnosis of infections in LMICs presents many challenges especially in rural areas where access to health care, including diagnostics is poor. Microscopy is one of the most commonly used platforms to diagnose bacterial infections on clinical samples. Fluorescence microscopy has high sensitivity and specificity but to date is mostly performed within a laboratory setting due to the high-cost, low portability and highly specialist nature of equipment. Point-of-care diagnostics could offer a solution to the challenge of infection diagnosis in LMICs. In this paper we present frugal, easy to manufacture, doped polydimethylsiloxane filtering optical lenses that can be integrated into smartphone microscopes for immediate detection of fluorescently labelled bacteria. This provides a breakthrough technology platform for point-of-care diagnostics.
DOI: 10.7488/ds/1397
title: Serial serum AFP results for HCC free patients in HCC surveillance cohort
title: AFP values for patients in the ‘AFP screening cohort’

description: Data used for analysis is related submission to PLOS ONE. Ethical approval given for deposition in publicly available repository by local ethics committee. Individual patients each have a series of AFP results (serum) taken over time. Reference in days is given with respect to the most recent sample. Relevant clinical details are provided.
description: Column descriptions ID, Number taken from original cohort of 1547 patients Consecutive no., Number of patient following data clean up – removal of non screening patients and duplicates Sampleno, Number of AFP sample in chronically order (oldest first) resultAFP. AFP value (kU/l) logresultAFP, AFP value (log10 kU/l) Daysfromlastscreening, Days difference between sample date and last sample date Sexcat, Male =1; Female =0 agein2009, Patient age on at first sample in 2009 Aetgroup, 0= alcoholic liver disease, 1=Hepatitis C virus, 2=Non-alcoholic liver disease, 3=Hepatitis B Virus, 4=Primary biliary cholangitis, 5= hereditary haemochromatosis, 6=autoimmune hepatitis, 7=other (includes cryptogenic cirrhosis, primary sclerosing cholangitis, drug related hepatitis, granulomatous liver disease, eosinophilic hepatitis, a1 antitrypsin, veno-occlusive disease, Wilson’s disease)
DOI: 10.7488/ds/2719
title: Pavlidis et al_Nat Comms_Data source

description: Data in support of publication: Cervical epithelial damage promotes Ureaplasma parvum ascending infection, intrauterine inflammation and preterm birth induction in mice.
DOI: 10.7488/ds/2585
title: Generation Scotland Survey Monkey data

description: Generation Scotland (GS) conducted a recontact survey on ~7,000 participants who could be contacted by email. The survey used Survey Monkey Inc. to understand GS participant opinions on health research. A total of 2,316 participants responded. This dataset include the summary level data and anonymised individual level data.
DOI: 10.7488/ds/2277
title: Generation Scotland SFHS Data Dictionary

description: The GS:SFHS Data Dictionary is a set of information describing the contents, format, and structure of the phenotype data collected during recruitment (2006-2011) to the Generation Scotland Scottish Family Health Study (GS:SFHS), or derived subsequently from study data collected during recruitment. This dataset replaces the one at https://datashare.is.ed.ac.uk/handle/10283/2724
DOI: 10.7488/ds/2799
title: VEP predictions for ClinVar and gnomAD variants

description: Variant effect predictions and DMS data for ClinVar and gnomAD variants in BRCA1, P53, CALM1, PTEN, HRAS and TPK1.
DOI: 10.7488/ds/3757
title: EDEM Simulation Deck: Concrete Cylinder Example for Edinburgh Beam Bond Model
title: Bonded Particle Assembly for Concrete Cylinder Simulations

description: Particle assembly used in DEM simulations of a concrete cylinder under uniaxial compression. The simulation deck is for use with EDEM (versions 2019 +).
DOI: 10.7488/ds/2299
title: SUPERSEDED - Dutch English Lombard Speech Native and Non-Native (DELNN)

description: ## SUPERSEDED - This dataset has been replaced by the one which can be found at https://doi.org/10.5281/zenodo.4267819 ## The DELNN (Dutch English Lombard speech Native and Non-Native) corpus consists of 30 native Dutch speakers reading sentences in a quiet environment and in a noisy environment, to elicit Lombard speech. The Dutch speakers had two sessions, one for English sentences (non-native speech) and one for Dutch sentences (native speech). An additional nine native American-English speakers were run and completed the English condition.
DOI: 10.7488/ds/2926
title: Unconventional magnetism in the high pressure ‘all transition metal’ double perovskite Mn2NiReO6

description: Standard crystallography files (cif format and data in gss format) for refinements of the title material at different temperatures as indicated by the filenames. Also some plotted results data in opj format.
DOI: 10.7488/ds/3762
title: HeadOn feasibility study

description: This is the dataset generated from the HeadOn clinical feasibility study which examined the usability and acceptability of a digital health intervention for concussion. The study took place between November 2021 to April 2022 and recruited 50 participants presenting with a concussion to the emergency department in Edinburgh, United Kingdom. The data covers the participants demographic, clinical findings, imaging and clinical outcomes.
description: The data covers study participants demographics, clinical and imaging findings and a number of clinical outcomes. The data parameters are within labelled columns. Four outcome measures are included within the following range of columns: Glasgow Outcome Scale Extended: column AM; Mobile App Usability Questionnaire: columns AN - BD; Rivermead Post-concussion Questionnaire: columns BQ - CF; Patient Health Questionnaire 9: columns CG - CP
DOI: 10.7488/ds/1456
title: Dataset pertaining to the publication "Increased Level of Linkage Disequilibrium in Rural Compared with Urban Communities"

description: See Readme.txt.