cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2425
title: Investigating early cellular and molecular responses to misfolded protein

description: PMDs such as AD, PD, HD and TSE are associated with the accumulation of abnormally folded proteins. However, the mechanisms involving seeding, processing and degradation of these rogue proteins are poorly understood. In this project, the response of primary hippocampal cultures to fibril challenge was investigated on a transcriptome level. This provided insights into molecular mechanisms associated with misfolded protein handling using cultures that either support misfolded protein generation (101LL) or that curtail its production (WT). Initial baseline transcriptome profiles were generated by microarray analysis then a more comprehensive analysis using RNA-sequencing (RNA-seq) for pre and post-fibril challenge transcriptome analysis was carried out.
description: See DataShareInfo.txt
DOI: 10.7488/ds/3038
title: Data on Dinka adjectives and intransitive verbs

description: This dataset consists of transcriptions of a number of forms of intransitive verbs from several dialects of Dinka. The dataset was collected in order to investigate the existence of an adjectival word class in the Dinka language, for the paper “On the nature of adjectives: evidence from Dinka,” to be published in Glossa: a journal of general linguistics.
description: dataset_BorSouth: contains data from the Bor South dialect of Dinka (Bor cluster, 2 speakers); this includes base forms, person/number inflections, and construct states for both adjectival and non-adjectival intransitive verbs; the data in this document formed the basis of the hypotheses on adjectival intransitive verbs in Dinka dataset_HolNgok: contains data from two dialects of Dinka, Hol (Bor cluster, 1 speaker) and Ngok (Padang cluster, 2 speakers) readme: contains metadata about the dataset and information about the files
DOI: 10.7488/ds/2247
title: Proteomic analysis for peripherally accessible biomarkers in Neuronal Ceroid Lipofuscinosis (NCL)

description: iTRAQ and Label free Proteomic data generated from Skeletal muscle of CLN3 and PPT1 murine models of Batten disease.
description: A single word file describing the experimental design, sample collection and processing. A single XL document with 5 tabs: * CLN3 iTRAQ data at 13 months of age * PPT1 Label free data at 1 month of age * PPT1 Label free data at 3 months of age * PPT1 Label free data at 5 months of age * PPT1 Label free data at 7 months of age
DOI: 10.7488/ds/2994
title: CSTR NAM TIMIT Plus

description: CSTR NAM TIMIT Plus (Version 0.8) RELEASE May 2012 The Centre for Speech Technology Research University of Edinburgh Copyright (c) 2012 Junichi Yamagishi jyamagis@inf.ed.ac.uk Overview This CSTR NAM TIMIT Plus corpus includes a parallel whispered speech recorded simultaneously via a non-audible murmur (NAM) microphone which uses urethane-elastomer to create a close contact with the skin and an omni-directional headset-mounted condenser microphone (a DPA 4035). The NAM microphone is a kind of special microphone which can be used as the sensing device of a silent speech interfaces (SSI) system, where alternative signal can be acquired without the user speaking in the normal way. The NAM microphone is a special body-conductive microphone (See Nakajima et al., ICASSP 2003 and Toda et al., ICASSP 2009). It can be used to detect extremely quiet speech (NAM), that even listeners around the speaker can hardly hear. NAM speech tends to be unvoiced, like whispering. The best position to place the NAM microphone is just behind the ear. It can be used to detect various kinds of speech, including whispering and normal speech, conducted through the soft tissue of the head. It is more robust to environmental noise than an ordinary microphone. Compared to other kinds of SSI systems, which may involve electrodes or other sensing devices, a NAM microphone-based SSI system is non-intrusive, cheap and convenient. The corpus comprises 421 sentences, which were selected from newspaper text, 460 sentences, which were selected from the TIMIT texts, and 18 isolated words, which were aimed for an open-source voice command recogniser ``kiku'', uttered by a young female speaker. The 421 newspaper texts were randomly taken from Herald Glasgow, with permission from Herald & Times Group. The TIMIT texts are identical those of the MOCHA-TIMIT corpus: http://www.cstr.ed.ac.uk/research/projects/artic/mocha.html The newspaper recording comprises of two sections: one recorded in clean conditions and the other one in pre-recorded cafeteria noise played over a loudspeaker at 65 dB [A] (resulting in and SNR of approximately 10 dB). The timit and isolated word recordings were conducted only in the noise condition. Both sections of the corpus were recorded in a soundproof hemi-anechoic chamber (noise floor around 25 dB [A]) at 96kHz sampling rate and 24 bit sample depth into a Pro Tools HD system. ACKNOWLEDGEMENTS We are grateful to Dr Tomoki Toda (Nara Institute of Science and Technology) for providing the NAM microphone to us and to Dr Mark Gales and Dr Federico Flego (University of Cambrige) for providing the VTS decoder for this corpus. This corpus was constructed whilst ChenYu Yang was a visitor at the Centre for Speech Technology Research, University of Edinburgh, UK.
DOI: 10.7488/ds/3798
title: Numerical study of the formation and stability of a pair of particles of different sizes in inertial microfluidics

description: The dataset contains the simulation results of heterogeneous-size particle pairs. The simulations were performed using an in-house lattice-Boltzmann-immersed-boundary-finite-element (LB-IB-FE) code. The dataset is reference by the paper Thota et al. (in submission).
DOI: 10.6084/m9.figshare.22709923
title: PLS-SEM Analysis

description: This study aims to determine factors that influence undergraduate students' engagement in online learning. The sample consisted of 609 undergraduate students from four public and private universities in Malaysia. The participation of all students was completely voluntary. Consent was obtained prior to the data collection. An online survey was employed to collect the data. The PLS-SEM was used to analyze the data.
DOI: 10.7488/ds/2431
title: Proteomic profiling of primate synapses during normal healthy ageing

description: Normal mammalian brain ageing is characterised by the selective loss of discrete populations of dendritic spines and synapses, particularly affecting neuroanatomical regions such as the hippocampus. Although previous investigations have quantified this morphologically, the molecular pathways orchestrating preferential synaptic vulnerability remain to be elucidated. Using quantitative proteomics and healthy rhesus macaque and human patient brain regional tissues, we have profiled the temporal expression of the synaptic proteome throughout the adult lifespan in differentially vulnerable brain regions. Comparative profiling of hippocampal (age-vulnerable) and occipital cortex (age-resistant) synapses revealed discrete and dynamic alterations in the synaptic proteome, which appear unequivocally conserved between species. The generation of these unique and important datasets will aid in delineating the molecular mechanisms underpinning primate brain ageing, in addition to deciphering the regulatory biochemical cascades governing neurodegenerative disease pathogenesis.
DOI: 10.7488/ds/2990
title: Anonymised results from the 2020 UoE Research Culture Survey
title: Research Culture Survey

description: Quantitative results of 2020 University of Edinburgh Research Culture Survey, based on Wellcome Trust 2019 Research Culture Survey. Line listing of 1491 responses from research academic, postgraduate research students and research professional staff
description: in associated file data_dictionary.csv
DOI: 10.7488/ds/2293
title: Sex, diet density and feeding centre gene expression

description: # Abstract # ## Background ## Research into energy balance and growth has infrequently considered genetic sex, yet there is sexual dimorphism for growth across the animal kingdom. We test the hypothesis that sexual dimorphism for growth and body weight in birds is potentially dependent on hypothalamic agouti-related peptide (AGRP) expression, since previous research indicates hypothalamic AGRP expression is correlated with growth potential. Because growth has been heavily selected in some chicken lines, food restriction is necessary to improve reproductive performance and welfare, but this increases hunger. Dietary dilution has been proposed to ameliorate this undesirable effect. We aimed to distinguish the effects of gut fullness from nutritional feedback on hypothalamic gene expression and its interaction with sex. ## Methods ## Restricted-fed 12-week-old male and female fast growing chickens were released from restriction and fed ad-libitum or a diet diluted with a non-nutritive bulking agent, ispaghula husk, for 2 days. A control group remained on the quantitative restricted diet. The basal hypothalamus was then dissected and gene expression of hypothalamic satiety peptides were measured using real-time PCR. To confirm observed sex difference effects, the experiment was repeated using only ad-libitum and restricted fed broiler breeders and observations made in an unrelated breed of ad-libitum fed male and female chickens. Linear Mixed Models (Genstat 18) were used for statistical analysis with transformation where appropriate. ## Results ## There were pronounced sex differences in a fast growing chicken strain, AGRP (P&lt;0.001) expression was higher in males. In genetically distinct chickens, males had higher AGRP mRNA (P=0.002) expression than females, suggesting sex difference was not restricted to a fast growing strain. AGRP (P&lt;0.001) expression was significantly decreased in ad-libitum-fed birds but was high and indistinguishable between birds on a quantitative versus qualitative restricted diet. Inversely, anorectic expression was significantly higher in ad-libitum fed birds. ## Conclusion ## Expression of orexigenic peptides in the avian hypothalamus are correlated with sex differences in growth and body weight. The differences in gene expression between sexes provides further evidence of AGRP expression being correlated to growth potential. Results also suggest that gut-fill alone does not reduce orexigenic gene expression.
DOI: 10.7488/ds/2619
title: An eQTL in the cystathionine beta synthase gene is linked to osteoporosis in laying hens

description: "An eQTL in the cystathionine beta synthase gene is linked to osteoporosis in laying hens" Dirk-Jan De Koning, Nazaret Dominguez-Gasca, Robert H. Fleming, Andrew Gill, Dominic Kurian, Andrew Law, Heather A. McCormack, David Morrice, Estefania Sanchez-Rodriguez, Alejandro B. Rodriguez-Navarro, Rudolf Preisinger, Matthias Schmutz, Veronica Šmídová, Frances Turner, Peter W. Wilson, Rongyan Zhou, Ian C. Dunn # Paper abstract # ## Background: ## Skeletal damage is a challenge for laying hens, as the physiological adaptations for egg laying make them susceptible to osteoporosis. We have shown that genetic factors explain around 40% of variation in end of lay bone quality and a quantitative trait locus (QTL) of large effect was detected on chromosome 1. ## Results: ## Combining data from the commercial founder white leghorn population and the original F2 mapping population the quantitative trait locus was fine mapped. A number of SNP markers had highly significant associations with tibial breaking strength. The alternative genotypes at the locus had tibial breaking strengths of 200.4 vs 218.1 Newton (p&lt;0.002) and in a subsequent generation the genotype was associated with cortical bone density, and significant effects on the medullary bone. The effects on cortical bone density were confirmed in a further generation where the effect was associated with increased mineralisation maturity of the cortical bone measured by infrared spectrometry and evidence of better collagen cross-linking. The transcriptome of the tibia for each genotype indicated four differentially expressed genes at the locus, one gene, cystathionine beta synthase, having a nine-fold greater expression associated with the allele for low bone quality. The mechanism causing the difference in expression was cis acting and we established that although there was an amino acid difference between alleles, there was no difference in the activity of the enzyme. However plasma homocysteine, the substrate of CBS was greater in the genotype associated with poor bone quality. The effects were associated with increased mineralisation maturity of the cortical bone and evidence of better collagen cross-linking. ## Conclusions: ## We have defined and validated markers predicting bone strength that can be used in selective breeding. At the same time, we have identified a gene that may give us additional routes to manage bone health in layers over and above genetic selection, whilst identifying how genetic variants affect different aspects of bone turnover shows potential for translational medicine.
DOI: 10.7488/ds/2991
title: CARDAMOM Brazil C-cycle analysis (1x1 degree; monthly; 2001-2017)

description: This dataset contains a netCDF file reporting terrestrial C-cycle analysis of Brazil at 1 x 1 degree spatial and monthly temporal resolutions for 2001 to 2017. The analysis uses the CARDAMOM model-data fusion framework to retrieve information on Brazil's terrestrial C-cycle uncertainty uniquely for each location based on location and time specific observations and their uncertainties. The files contains pixel-level estimates of C storage (plant tissues and dead organic matter), C fluxes (photosynthesis, respiration, fire emissions), allocation of C to plant tissues and their residence times. All variables include uncertainty information reporting the 2.5 %, 25 %, 50 %, 75 % and 97.5% quantiles.
description: The dataset contains a single netCDF file ("CARDAMOM_Brazil_1x1_2001_2017_v1.0.nc") which contains pixel-level outputs of the CARDAMOM model-data fusion system. The analysis resolution is 1 x 1 degree and monthly times step for a 17 year period between 2001 and 2017. The file includes estimates of ecosystem carbon stocks, fluxes and key traits. All estimates include uncertainty quantification derived from CARDAMOM at the 2.5 %, 25 %, 50 %, 75 % and 97.5% quantiles.
DOI: 10.7488/ds/2808
title: Gene expression in the cardiovascular system of the domestic sheep (Ovis aries)
title: Gene expression estimates as TPM for seven cardiovascular and one skeletal muscle tissue from sheep

description: This dataset includes gene expression estimates, from RNA-Seq, for seven cardiovascular and one skeletal muscle tissue from the sheep gene expression atlas dataset (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006997). The raw RNA-seq data are deposited in the European Nucleotide Archive (ENA) under study accession number PRJEB19199 (http://www.ebi.ac.uk/ena/data/view/PRJEB19199). For each tissue a set of expression estimates (averaged across biological replicates from where possible n=6 adult sheep), as transcripts per million (TPM), were obtained using the transcript quantification tool Kallisto v0.43.0. It was necessary to normalise these estimates to account for the two different library types (ribo-depleted total RNA (left ventricle) and poly-A selected mRNA (all other tissues).
DOI: 10.7488/ds/188
title: RNA composition metrics

description: Mutating RNA virus genomes to alter codon pair (CP) frequencies and reduce translation efficiency has been advocated as a method to generate safe, attenuated virus vaccines. However, selection for disfavoured CPs leads to unintended increases in CpG and UpA dinucleotide frequencies that also attenuate replication. We designed and phenotypically characterised mutants of the picornavirus, echovirus 7, in which these parameters were independently varied to determine which most influenced virus replication. CpG and UpA dinucleotide frequencies primarily influenced virus replication ability while no fitness differences were observed between mutants with different CP usage where dinucleotide frequencies were kept constant. Contrastingly, translation efficiency was unaffected by either CP usage or dinucleotide frequencies. This mechanistic insight is critical for future rational design of live virus vaccines and their safety evaluation; attenuation is mediated through enhanced innate immune responses to viruses with elevated CpG/UpA dinucleotide frequencies rather the viruses themselves being intrinsically defective.
description: 1) Supplementary File 1: Nucleotide sequences of mutants used in the study Supplementary File 1.doc 2) Composition and codon usage metrics for human mRNA Human mRNA composition.xls 3) Composition and codon usage metrics for A. thaliana mRNA A.thaliana Composition table.xls 4) Composition and codon usage metrics for C. elegans mRNA C.elegans_Composition table.xls 5) Composition and codon usage metrics for E. coli mRNA E.coli_Composition table.xls 6) Codon pair usage tables for human, A. thaliana, C. elegans and E. coli. CPS tables.xls
DOI: 10.7488/ds/2917
title: 2020_Thesis_SupplementaryData_s1569052_Tissue-resident immune cells in health and disease: their heterogeneity and associated gene signatures

description: The dataset includes supplementary figures and tables in support of the University of Edinburgh thesis titled "Tissue-resident immune cells in health and disease: their heterogeneity and associated gene signatures".
DOI: 10.7488/ds/1444
title: Datasets of genes expressed in the mouse nervous system

description: Data supporting paper Summers K et al (In Submission).
description: Please see readme.txt.
DOI: 10.7488/ds/2993
title: CARDAMOM Kenyan C-cycle analysis (0.25 degree, monthly, 2014-2017): Forest and savannah specific

description: This dataset contains two netCDF file reporting terrestrial C-cycle analysis of Kenya at 0.25 x 0.25 degree spatial and monthly temporal resolutions for 2014 to 2017. One analysis specifically focused on forested land of Kenya, the other analysis focused on savannah land. The analysis uses the CARDAMOM model-data fusion framework to retrieve information on Kenya's terrestrial C-cycle uncertainty uniquely for each location based on location and time specific observations and their uncertainties. The files contains pixel-level estimates of C storage (plant tissues and dead organic matter), C fluxes (photosynthesis, respiration, fire emissions), allocation of C to plant tissues and their residence times. All variables include uncertainty information reporting the 2.5 %, 25 %, 50 %, 75 % and 97.5% quantiles.
description: This dataset contains two netCDF file reporting terrestrial C-cycle analysis of Kenya at 0.25 x 0.25 degree spatial and monthly temporal resolutions for 2014 to 2017. One analysis specifically focused on forested land of Kenya, the other analysis focused on savannah land. The analysis uses the CARDAMOM model-data fusion framework to retrieve information on Kenya's terrestrial C-cycle uncertainty uniquely for each location based on location and time specific observations and their uncertainties. The files contains pixel-level estimates of C storage (plant tissues and dead organic matter), C fluxes (photosynthesis, respiration, fire emissions), allocation of C to plant tissues and their residence times. All variables include uncertainty information reporting the 2.5 %, 25 %, 50 %, 75 % and 97.5% quantiles.
DOI: 10.7488/ds/2333
title: SUPERSEDED - Synaptic and non synaptic proteome in ageing murine cortical isolates

description: ## SUPERSEDED - this dataset has been replaced by the one which can be found at https://doi.org/10.7488/ds/3181 . ## Label free proteomic analysis of "synaptic" and "non-synaptic" mitochondrial subpopulations isolated from murine cortex throughout the process of "normal healthy" ageing. These are sub populations of mitochondria as isolated and defined by Lai JC, Walsh JM, Dennis SC, Clark JB. Synaptic and non-synaptic mitochondria from rat brain: isolation and characterization. J Neurochem. 1977;28(3):625-31. Files attached are: 1. Methodology. 2. Synaptic; or 3. non-synaptic; mitochondrial time course data output from Progenesis software.
description: File 1_ Methodological Information_Ageing mouse mitochondrial subpopulation profiling.pdf FIle 2_Mouse synaptic mitochondria ageing timecourse_raw for upload.xlsx File 3_Mouse non-synaptic mitochondria ageing timecourse_raw for upload.xlsx
DOI: 10.7488/ds/2949
title: Epilepsy-related mortality during the COVID-19 pandemic: a nationwide study of routine Scottish data

description: Methods: This was a national, population-based, cross-sectional study of routinely-collected mortality and demographic data pertaining to March–August of 2020 (COVID-19 pandemic) compared to the corresponding periods in 2015–2019. ICD-10-coded causes of death of deceased people of any age were obtained from a national mortality registry of death certificates. The G40–41 ICD-10 codes for epilepsy were used to define epilepsy-related deaths, with or without a U07·1–07·2 ICD-10 code for COVID-19 listed as an additional cause. Deaths unrelated to epilepsy were defined as all remaining Scottish deaths without G40–41 ICD-10 codes listed as a cause. We assessed the number of epilepsy-related deaths in 2020 compared to mean year-to-year variation observed in 2015–2019 (overall, men, women). We assessed proportionate mortality and odds ratios (OR) for deaths with COVID-19 listed as the underlying cause in people with epilepsy-related deaths compared to in deaths unrelated to epilepsy, reporting 95% confidence intervals (95% CIs). Sheet 1 contains a key to the remaining dataset.
DOI: 10.7488/ds/2992
title: Polygenic risk scores and GWAS summary statistics for an analysis of the contribution of common risk variants to multiple sclerosis in Orkney and Shetland

description: Orkney and Shetland, the population isolates which make up the Northern Isles of Scotland, are of particular interest to multiple sclerosis (MS) research. While MS prevalence is high in Scotland, Orkney has the highest global prevalence, higher than more northerly Shetland. Many hypotheses for the excess of MS cases in Orkney have been investigated, including vitamin D deficiency and homozygosity: neither was found to cause the high prevalence of MS. It is possible that this excess prevalence may be explained through unique genetics. We used polygenic risk scores (PRS) to look at the contribution of common risk variants to MS. Analyses were conducted using ORCADES (97/2118 cases/controls), VIKING (15/2000 cases/controls) and Generation Scotland (30/8708 cases/controls) datasets. However, no evidence of a difference in MS associated common variant frequencies was found between the three control populations, aside from HLA-DRB1*1501 tag SNP rs9271069. This SNP had a significantly higher risk allele frequency in Orkney (0.23, p-value = 8 x 10-13) and Shetland (0.21, p-value = 2.3 x 10-6) than mainland Scotland (0.17). This difference in frequency is estimated to account for 6 (95% CI 3, 8) out of 150 observed excess cases per 100,000 individuals in Shetland and 9 (95% CI 8, 11) of the observed 257 excess cases per 100,000 individuals in Orkney, compared with mainland Scotland. Common variants therefore appear to account for little of the excess burden of MS in the Northern Isles of Scotland.
DOI: 10.7488/ds/2237
title: Biochemical data associated with the paper "Structural basis of DNA end processing by Tdp1"

description: These data support the results reported in our paper "Structural basis for DNA 3'-end processing by human Tyrosyl-DNA phosphodiesterase 1” Fiona J. Flett, Emilija Ruksenaite, Lee Armstrong, Shipra Bharati, Elizabeth R. Morris, Roberta Carloni, C. Logan Mackay, Heidrun lnterthal and Julia M. Richardson, published in Nature Communications 2017. The data are organised according to the Figure in the paper to which they refer, as indicated by the individual file names.
description: Data are arranged in folders according to the figures in the paper to which they relate.