cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2982
title: Supplementary File 1: Key findings from downloaded COVID-19 information for those categorised as high-risk (20 April 2020)

description: Data supporting McClatchey et al "COVID-19 information for people living with asthma: A rapid review of publicly available information" JACI: In practice https://doi.org/10.1016/j.jaip.2021.01.003 . Abstract: In 2020, COVID-19 was declared a pandemic, posing risk to high-risk communities, such as people living with severe asthma. We rapidly reviewed COVID-19 information available online for people with asthma, to assess whether information aligns with risk communication and asthma self-management guidelines. Information from five English-speaking countries and global websites providing COVID-19 information for people with asthma (including those at high-risk of severe disease) were downloaded. Informed by the World Health Organization (WHO) emergency risk communication guideline and the National Institute for Health and Care Excellence asthma guidelines, 102 webpages from 43 unique organisations that provided asthma-related health information were analysed. We found that COVID-19 online information for people with asthma largely followed the WHO emergency risk communication guideline and provided some asthma self-management strategies.
DOI: 10.7488/ds/3186
title: RLT-WP3- D3.5 - Synthetic Load Spectra and Time Series Data

description: "The data set contains non-dimensional load spectra and time series dataset to assist future developers in tidal stream turbine design decisions, datasets available from different test setups have been collected and categorised. Based on the information available from these tests, 21 non-dimensional coefficients are proposed to make these test measurements independent from their turbine designs and flow conditions. The proposed non-dimensional variables take information both from the input measurements as well as internal forces calculated in this analysis based on static equilibrium linear equations, thus common test data, such as thrust and torque, are used to make this easily applicable for future tests. The load spectra and time series have been developed in relation to the tip speed ratio (TSR) of 10 tank tests. These normalised base datasets have successfully been correlated when compared to different datasets from both numerical models and commercial tests. All the non-dimensional coefficients and ratios are presented in both the time domain and the frequency domain for developers to not only consider static load cases but also dynamic loads that impact the fatigue life of the different key components of tidal turbines. The density distribution curves as well as the frequency spectra of these coefficients can be recreated with the produced datasets of this task, which have been stored in the Edinburgh DataShare portal."
DOI: 10.7488/ds/2977
title: Datasets of journal paper "Arduino-Based Myoelectric Control: Towards Longitudinal Study of Prosthesis Use"

description: This dataset comprises the mean absolute value (MAV) to draw Figure 6 and the normalized MAV to draw Figure 7 in paper "Arduino-Based Myoelectric Control: Towards Longitudinal Study of Prosthesis Use".
DOI: 10.7488/ds/3187
title: Developing novel workflows for improved bottom-up, top-down and middle-down mass spectrometry analysis of proteins (Supplementary Data).

description: Supplementary data to support the PhD Thesis of Lavrentis Galanopoulos entitled 'Developing novel workflows for improved bottom-up, top-down and middle-down mass spectrometry analysis of proteins'
DOI: 10.7488/ds/2980
title: SFARI Genes and where to find them; classification modelling to identify genes associated with Autism Spectrum Disorder from RNA-seq data

description: Abstract Motivation: Autism spectrum disorder (ASD) has a strong, yet heterogeneous, genetic component. Among the various methods that are being developed to study it, one that is gaining popularity is the incorporation of transcriptomic data with known mutations associated to the disorder, often using the SFARI Gene list to characterise the latter. Results: SFARI genes were found not to be significantly associated to differential gene expression patterns, nor enriched in co-expression modules with strong module-diagnosis correlation, however, it was confirmed that they do provide useful insights when using network analysis and machine learning models that are able to incorporate information from the whole gene co-expression network. A statistically significant bias related to level of expression was found in the SFARI genes and SFARI scores, which was found to influence transcriptomic results at gene, module and whole-network levels, as well as other ASD gene-scoring systems. This dataset contains all of the data used in our paper cited in this data submission for reproducibility and re-use purposes. The files are described in detail in the source and file structure description section of this entry.
description: These data accompany our paper submission, currently on bioRxiv 10.1101/2021.01.29.428754. The following describes the accompanying files:- All data that is updated by external providers (i.e. not fixed) has the date of download in the filename for version control and reproducibility purposes. FOLDER "NCBI" - contains snapshots of the gene_info and gene2ensembl files from NCBI used in the paper alongside Gene Ontology mappings for human genes. FOLDER "RNASeq" - contains the processed RNA-seq data objects used in this paper in CSV format for re-use by others. FOLDER "SFARI" - contains the snapshots of the SFARIgene rankings for Autism Spectrum Disorder Genes used in this paper. FOLDER "ASDGeneScores" - contains the snapshots from other studies that have calculated association scores between genes and Autism that we have used in this paper. - krishnan_probability_score.xlsx - contains scores from the Krishnan paper cited with this data submission. - sanders_TADA_score.xlsx - contains the scores from the Sanders paper cited with this data submission. - disgenet_21_01_25.csv - contains scores from the DisGenet database cited with this data submission.
DOI: 10.7488/ds/3404
title: Probing the dynamics of turbid colloidal suspensions using Diﬀerential Dynamic Microscopy

description: Dataset for the manuscript entitled 'Probing the dynamics of turbid colloidal suspensions using Differential Dynamic Microscopy': Few techniques can reliably measure the dynamics of colloidal suspensions or other soft materials over a wide range of turbidities. Here we systematically investigate the capability of Differential Dynamic Microscopy (DDM) to characterise particle dynamics in turbid colloidal suspensions based on brightfield optical microscopy. We measure the Intermediate Scattering Function (ISF) of polystyrene microspheres suspended in water over a range of concentrations, turbidities, and up to 4 orders of magnitude in time-scales. These DDM results are compared to data obtained from both Dynamic Light Scattering (DLS) and Two-colour Dynamic Light Scattering (TCDLS). The latter allows for suppression of multiple scattering for moderately turbid suspensions. We find that DDM can obtain reliable diffusion coefficients at up to 10 and 1000 times higher particle concentrations than TCDLS and standard DLS, respectively. Additionally, we investigate the roles of the four length-scales relevant when imaging a suspension: the sample thickness $L$, the imaging depth $z$, the imaging depth of field DoF, and the photon mean free path $\ell$. More detailed experiments and analysis reveal the appearance of a short-time process as turbidity is increased, which we associate with multiple scattering events within the imaging depth of field. The long-time process corresponds to the particle dynamics from which particle-size can be estimated in the case of non-interacting particles. Finally, we provide a simple theoretical framework, ms-DDM, for turbid samples, which accounts for multiple scattering.
DOI: 10.7488/ds/2307
title: Kidney vascularisation reviews - summary table

description: Excel sheet containing a summary of reviews discussing vasculogenesis and angiogenesis in the developing kidney. This is a partner file for the article 'Mechanisms of kidney vascularization: what can natural development teach us about vascularizing renal organoids?'
DOI: 10.7488/ds/2715
title: Systematic Review of the Literature on Definitions and Characterisation of MS Lesions
title: Definitions and MR Signal Characterisation of MS Lesions in Conventional Structural MRI

description: While inspecting the brain magnetic resonance imaging (MRI) scans from a sample of Multiple Sclerosis (MS) patients, blind to any clinical, cognitive and demographic information, it caught our attention the presence of ovoidal or circular, partially stellate, regions of signal intensities similar to that of the normal brain parenchyma in Fluid Attenuated Inversion Recovery (FLAIR) surrounded by hyperintensities in the periventricular region in a reasonable number of scans, seemingly corresponding in all cases to hypointense regions (i.e. with the same signal level of the cerebrospinal fluid) in T1-weighted. The ovoidal shape of these features, clearly distinctive due to their homogeneously lower signal with respect to their surroundings in the FLAIR sequence prompted us to refer them as FLAIR ‘pseudocavities’. The idea that they could be differentially distinctive and indicative of an underlying process of different aetiology from their surroundings is not implausible. Inversion recovery imaging can potentially discriminate among tissues based on subtle differences in T1 characteristics. Specifically, the FLAIR sequence exploits the fact that many types of pathology have elevated T1 and T2 values resulting from increased free water content compared to background tissue. Higher specific absorption rate due to additional 180 degrees, together with the increased dynamic range, and the additive T1 and T2 contrast, make FLAIR highly susceptible to differentially reflect subtle pathological processes (Bydder & Young, 1985). We, hence, systematically reviewed the literature in the last 10 years (i.e. from March 1999 up to March 2019) to investigate the definitions of MS lesions used up to date and their characterisation, to establish if what we called “FLAIR ‘pseudocavities’” have been described previously. This dataset is conformed by an excel file (Microsoft excel 97-2003 (.xls)) with multiple worksheets which contain all the references found in the two databases explored (i.e. Medline and EMBASE), as well as the data extracted and the results of the analyses. Briefly, from just over a hundred studies that defined MRI lesions in MS, more than half characterised lesions based on the criteria that they were hyperintense on T2-weighted, FLAIR and PD-weighted series, and more than a quarter of the studies characterised lesions based on the criteria that they were hyperintense on T2-weighted, FLAIR and PD-weighted and that they were hypointense on T1-weighted series. The literature review confirmed that what we refer to as FLAIR ‘pseudocavities’ have not yet been acknowledged in the MS literature. Note: The dataset contains a master excel spreadsheet with multiple worksheets. The data from each worksheet in the excel file is also provided as a .csv file
DOI: 10.7488/ds/3215
title: Community Participation Scoping Project, Botanic Gardens Kolkata
title: Regeneration and Ecological Framework Plan, AJC Bose Botanical Gardens, Kolkata

description: A survey of the AJC Botanical Gardens, Kolkata, India. Includes current and historical maps. Studies of specific Ecology and biodiversity agencies.
DOI: 10.7488/ds/2405
title: Proteomics datasets from Shorrock et al (UBA1/GARS-dependent pathways drive sensory-motor connectivity defects in spinal muscular atrophy)

description: Detailed proteomics data files from Shorrock et al., 2018 'UBA1/GARS-dependent pathways drive sensory-motor connectivity defects in spinal muscular atrophy' (Accepted manuscript to be published in Brain).
DOI: 10.7488/ds/2776
title: Motyl AAL, et al. (2020). Pre-symptomatic developmental phenotypes in Spinal Muscular Atrophy
title: Taiwanese mouse model of SMA - E14.5 embryo proteomic dataset, 10-plex TMT mass spectrometry

description: Spinal muscular atrophy (SMA) is a leading genetic cause of infant death, characterised primarily by a loss of lower motor neurons. SMA is caused by mutations in the survival motor neuron 1 (SMN1) gene. New SMN-restoring therapies for SMA have emerged in recent years; however, data from both pre-clinical and clinical studies demonstrate that there is a limited therapeutic time-window for them to be effective. Moreover, it is now clear that peripheral organs and tissues can also be affected by the disease. To better understand the earliest changes occurring during SMA, with implications for defining the optimum time and location of therapy delivery, we undertook a detailed anatomical, histological and molecular analysis of pre-symptomatic, prenatal changes occurring in a mouse model of SMA. We generated 3D-renderings of whole embryos at embryonic day (E)14.5 using micro-computed tomography (µCT). These analyses showed that E14.5 SMA embryos are significantly smaller than littermate controls, indicative of a general developmental delay. Cardiac ventricles were smaller in SMA heart, whilst liver and brain volumes remained unaffected. Morphometric and histological analyses showed no overt structural defects indicative of degenerative pathology in any of the organs examined. We then performed a comparative proteomics' screen of spinal cord, brain, liver, skeletal muscle and heart in SMA and control mice using Tandem Mass Tagging mass spectrometry. This revealed significant molecular perturbations in all organs examined, with the liver showing the greatest magnitude of change. Notably, we found a lack of overlap in affected proteins and molecular pathways between organs, highlighting tissue-specific prenatal molecular phenotypes in SMA. Together, our data demonstrate that considerable changes are already present across numerous tissues and organs at an early, pre-symptomatic stage in SMA mice, suggesting that there is a significant developmental component to SMA pathogenesis.
DOI: 10.7488/ds/2625
title: aNMJ-morph macro

description: It is recommended that users of the aNMJ-morph macro are familiar with the original NMJ-morph workflow in a practical setting; please refer to the following publication for background details: "NMJ-morph reveals principal components of synaptic morphology influencing structure-function relationships at the neuromuscular junction" (Jones RA et al, Open Biology, 2016, doi.org/10.1098/rsob.160240). # Contents # 1. aNMJ-morph macro; 2. aNMJ-morph tutorial video; 3. Reference images (20 sample NMJ images for use with aNMJ-morph) ; 4. Reference spreadsheet (data generated from aNMJ-morph analysis of the 20 sample NMJ images).
DOI: 10.7488/ds/2417
title: Region-specific depletion of synaptic mitochondria in the brains of patients with Alzheimer's disease - TEM data

description: Of all of the neuropathological changes observed in Alzheimer's disease (AD), the loss of synapses correlates most strongly with cognitive decline. The precise mechanisms of synapse degeneration in AD remain unclear, although strong evidence indicates that pathological forms of both amyloid beta and tau contribute to synaptic dysfunction and loss. Synaptic mitochondria play a potentially important role in synapse degeneration in AD. Many studies in model systems indicate that amyloid beta and tau both impair mitochondrial function and impair transport of mitochondria to synapses. To date, much less is known about whether synaptic mitochondria are affected in human AD brain. Here we used transmission electron microscopy (TEM) to examine synapses and synaptic mitochondria in two cortical regions (BA41/42 and BA46) from 8 AD and 9 control cases. In this study, we observed 3000 synapses and find region-specific differences in synaptic mitochondria in AD cases compared to controls. In BA41/42, we observe a four-fold reduction in the proportion of presynaptic terminals that contain multiple mitochondria profiles in AD. We also observe ultrastructural changes including abnormal mitochondrial morphology, the presence of multivesicular bodies in synapses, and reduced synapse apposition length near plaques in AD. Together, our data show region-specific changes in synaptic mitochondria in AD and support the idea that the transport of mitochondria to presynaptic terminals may be impaired in AD. This dataset includes all of the raw transmission electron micrographs used in the analysis.
DOI: 10.7488/ds/2855
title: Grid cells are modulated by local head direction

description: In vivo tetrode recordings from the medial entorhinal cortex of mice during open field exploration. This data set contains recordings from grid cells, conjunctive cells and other spatial cells. Please look at Gerlei_et_at_2020_where_to_find_data_and_code.xlsx to find which files to download to replicate specific figures. If you only need the data from the sorted clusters, (firing times, position...) download SORTED_CLUSTERS.zip
description: Histology data - Images of brain slices with tetrode locations (see methods in paper for details of histology protocol).
DOI: 10.7488/ds/2552
title: SUPERSEDED - 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 http://hdl.handle.net/10283/3354 ## Full datasets for all figures in 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.
description: Files are included in ".pzf" format (GraphPad Prism) and, to provide accessibility for users who do not have GraphPad Prism, copies of all data are also provided in Excel format ".xlsx".
DOI: 10.7488/ds/2570
title: SUPERSEDED - 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 ## 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/2352
title: Role of accelerated ageing in limb muscle wasting of patients with Chronic Obstructive Pulmonary Disease (COPD)

description: Skeletal muscle wasting is an independent predictor of health-related quality of life, and survival in COPD, but the complexity of the molecular mechanisms associated with this process have not been fully elucidated. We aimed to determine whether an impaired ability to repair DNA damage contributes to muscle wasting and the accelerated ageing phenotype in patients with COPD. These data support the publication: Role of accelerated ageing in limb muscle wasting of patients with Chronic Obstructive Pulmonary Disease (COPD). Ramzi Lakhdar, Dagmara McGuinness, Ellen M Drost, Paul G Shiels,Ricardo Bastos, William MacNee and Roberto A Rabinovich. International Journal of COPD 2018 (Accepted manuscript). We observed a decrease in γH2AX expression in COPDL, which occurred in association with a tendency to increase in CDKN2A/p16ink4a and a significant decrease in SIRT1 and SIRT6 protein levels. Cellular damage and muscle inflammatory markers were also increased in COPDL. These data are in keeping with an accelerated ageing phenotype as a result of impaired DNA repair and dysregulation of cellular homeostasis in the muscle of COPD patients with a low FFMI. These data indicate cellular degeneration via stress-induced premature senescence and associated inflammatory responses abetted by the senescence-associated secretory phenotype and reflected an increased expression of markers of oxidative stress and inflammation.