cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2824
title: Degradation of beta-lactams in bacterial growth media

description: The dataset contains growth curves of E. coli RJA002 in various growth media in the presence of beta-lactam antibiotics. These growth curves were used to determine the degradation rate of these antibiotics in a range of experimental conditions. The degradation rate of mecillinam in MOPSgluRDM was also measured using Raman spectroscopy the data for which are also provided.
DOI: 10.7488/ds/1309
title: What is the ‘minimum inhibitory concentration’ (MIC) of pexiganan acting on Escherichia coli? - A cautionary case study

description: We measured the minimum inhibitory concentration (MIC) of the antimicrobial peptide pexiganan acting on Escherichia coli, and report an intrinsic variability in such measurements. These results led to a detailed study of the effect of pexiganan on the growth curve of E. coli, using a plate reader and manual plating (i.e. time-kill curves). The measured growth curves, together with single-cell observations and peptide depletion assays, suggested that addition of a sub-MIC concentration of pexiganan to a population of this bacterium killed a fraction of the cells, reducing peptide activity during the process, while leaving the remaining cells unaffected. This pharmacodynamic hypothesis suggests a considerable inoculum effect, which we quantified. Our results cast doubt on the use of the MIC as 'a measure of the concentration needed for peptide action' and show how 'coarse-grained' studies at the population level give vital information for the correct planning and interpretation of MIC measurements.
description: The .tif files constitute an animation which can be viewed using imagej, which is freely available.
DOI: 10.7488/ds/2473
title: Novel phases in ammonia-water mixtures under pressure

description: While ammonia and water readily form hydrogen-bonded molecular mixtures at ambient conditions, their miscibility under pressure is not well understood, yet crucial e.g. to model the interior of icy planets. We report here on the behaviour of ammonia-water mixtures under extreme pressure conditions, based on first-principles calculations of 15 stoichiometries in the pressure range of 1 atm to 10 Mbar. We show that compression facilitates proton transfer from water to ammonia in all relevant mixtures. This favors ammonia-rich hydrates above 1 Mbar, stabilized by complete de-protonation of water and the formation of the unusual structural motifs O2−·(NH4+)2 and O2−·(N2H7+)2. The hydronitrogen cations persist to the highest pressures studied. We predict a new ammonia-rich 4:1-hydrate at intermediate pressures and find that by 5.5 Mbar, close to the core-mantle boundary of Neptune, all cold ammonia-water mixtures are unstable against decomposition into their constituents.
DOI: 10.7488/ds/2807
title: Mult-Min quantitative method of analysing effects of NaCl and phosphate on bacterial growth

description: Application of the Mult-Min quantiative method to experimental data investigating the effects of combined NaCl and phosphate limitation on growth of the moderately halophilic organim, Halomonas hydrothermalis. This is a method of analysing the effect of multiple extremes on bacterial growth.
DOI: 10.7488/ds/155
title: Carstairs deprivation scores by CATT2, 1981, 1991, 2001

description: Carstairs deprivation scores were used to measure relative deprivation differences between small areas and over time, as the scores are widely used and recognised (Carstairs and Morris 1989; Carstairs and Morris 1991). The Consistent Areas Through Time (CATTs, Exeter, Boyle et al. 2005) were used to provide a consistent geography between the 1981, 1991 and 2001 censuses, for ease of comparison. Specifically the CATT2 small area geography was use, giving 10,058 individual areas with an average population in 2001 of approximately 500 persons. Carstairs deprivation scores were unavailable for the CATT2 geography, therefore were calculated from raw census data. This also enabled a second set of scores to be calculated without the car ownership component (called Adjusted Carstairs hereafter), as car ownership is more of a necessity in rural areas compared with urban areas and can bias deprivation scores (Christie and Fonea 2003). Although unadjusted Carstairs scores have been used for national studies this was considered a useful opportunity to investigate how the car ownership component affected scores in rural areas. The Carstairs score is constructed from four components that have been shown to measure deprivation well (Carstairs and Morris 1989): 1. Overcrowding: the percentage of all persons living in private households with a density of more than one person per room. 2. Male Unemployment: the percentage of economically active males seeking or waiting to start work 3. Low Social Class: the percentage of all persons in private households with an economically active head with head of household in social class IV or V. 4. No Car: the percentage of all persons in private households which do not own a car.
description: Richardson_07_Carstairs_score_construction.pdf - methodology description. Richardson_CarstairsByCATT2_1981_1991_2001v2.xls - data file. GROS_2001_data.xls - data file. Variable_headingsv2.txt - variable names.
DOI: 10.7488/ds/2782
title: Chicxulub data
title: Data from the Chicxulub impact crater

description: Data on the microbiology of the Chicxulub crater (Mexico) and associated geochemical data.
description: Data analysis during the International Ocean Discovery Program and International Continental Scientific Drilling Program (IODP/ICDP) Expedition 364 drilled into the Chicxulub crater peak ring
DOI: 10.7488/ds/2575
title: Data associated with publication "Detectability of biosignatures in a low-biomass simulation of martian sediments"

description: Data associated with Stevens et al. "Detectability of biosignatures in a low-biomass simulation of martian sediments" (In submission).
description: See "MarsMudrockData ReadMe.txt"
DOI: 10.7488/ds/3475
title: Collected cookie dialogs and dark patterns

description: Dataset of collected cookie dialogs, cookies, and dark patterns. Includes screenshots of the identified dialogs as well as automatically extracted text and the CSS selector used to locate the dialog. Similarly a list of dark patterns identified on those sites are listed. Dataset is associated with an undergraduate thesis the pdf of which is also included. The data was collected on three separate sets of websites drawn from the Tranco list of popular websites. Data for the smaller sets was human-verified. The 10k set is automatic only.
description: See the README.md file
DOI: 10.7488/ds/2303
title: Y-Mars Analogue Characterisation

description: This dataset contains a range of analytical characterisations of the Y-Mars analogue, which is intended to simulate a mudstone found in Gale Crater, Mars.
description: 1 Grain size calculations 2 Commercial GCMS data 3 Quantitative XRD calculations 4 Collection of Raman spectra (in .txt format) and detected peaks 5 Collection of VIS-NIR spectra (in .txt format) and background calculations 6 XRD comparison of analogue material to MSL data 7 XRF Major Element Concentrations
DOI: 10.7488/ds/99
title: StORe online questionnaire

description: Project wiki: http://jiscstore.jot.com/WikiHome
description: This is an anonymised file containing the responses to the StORe online questionnaire
DOI: 10.7488/ds/1489
title: Research data management training survey, 2016

description: The aim of this survey was to collect feedback about existing training programmes in research data management for researchers at the University of Edinburgh, as well as respondents’ preferred methods for training, and their requirements for new courses. The survey was circulated via e-mail to research staff and postgraduate students across three colleges of the University of Edinburgh: the College of Arts, Humanities and Social Sciences; the College of Science and Engineering; and the College of Medicine and Veterinary Medicine. The survey was conducted on-line using the Bristol Online Survey tool, March through July 2016. 191 responses were received.
DOI: 10.7488/ds/3050
title: Company-Director graphs for UK publicly traded companies between January and July 2020

description: This dataset accompanies the paper "THE DIRECTOR DAISY CHAIN: EMPIRICAL EVIDENCE OF THE INTERCONNECTIVITY OF UK DIRECTORS OF PUBLICLY TRADED COMPANIES". It contains graphs representing the interconnections of UK publicly traded companies and their directors via directorships of executive and non-executive types. There are two graphs consisting of 1) all companies, and 2) companies that are not members of the Association of Investment Companies.
description: This dataset consists of two plain text files AllCompanies.txt and NonAicCompanies.txt. Each contains a representation of the company-director-directorship graph for all companies and the subset of companies that are not AIC members, respectively. The graph structure is represented in plain text format, with the details of the companies, directors and directorships explained in the header section of each file.
DOI: 10.7488/ds/196
title: Parallel simplex benchmarking results

description: Data used to generate results in "Parallelizing the dual revised simplex method" http://www.maths.ed.ac.uk/hall/HuHa13/, a copy of which is attached.
DOI: 10.7488/ds/3191
title: GWAS summary statistics pertaining to the publication "Genetic regulation of post-translational modification of two distinct proteins"

description: Post-translational modifications diversify protein functions and dynamically coordinate their signalling networks, influencing most aspects of cell physiology. Nevertheless, their genetic regulation or influence on complex traits is not fully understood. Here, we compare for the first time the genetic regulation of the same PTM of two proteins - glycosylation of transferrin and immunoglobulin G (IgG). By performing genome-wide association analysis of transferrin glycosylation, we identified 10 significantly associated loci, 9 of which were novel. Comparing these with IgG glycosylation-associated genes, we note protein-specific associations with genes encoding glycosylation enzymes (transferrin - MGAT5, ST3GAL4, B3GAT1; IgG - MGAT3, ST6GAL1), as well as shared associations (FUT6, FUT8). Colocalisation analyses of the latter suggest that different causal variants in the FUT genes regulate fucosylation of the two proteins. Glycosylation of these proteins is thus genetically regulated by both shared and protein specific mechanisms.
description: Please see readme.txt for details.
DOI: 10.7488/ds/3426
title: Dataset for the paper "Mitigation of Rotor Thrust Fluctuations through Passive Pitch"
title: Simulations for the paper "Mitigation of Rotor Thrust Fluctuations through Passive Pitch"

description: The RKE-SM simulations described in the paper "Mitigation of Rotor Thrust Fluctuations through Passive Pitch" are included in this dataset. The paper is available at https://www.research.ed.ac.uk/en/publications/mitigation-of-rotor-thrust-fluctuations-through-passive-pitch , DOI: 10.1016/j.jfluidstructs.2022.103599 . More information about the simulations can be found in "Simulation Information.docx" file.
DOI: 10.7488/ds/3125
title: Dataset - Experimental Data of a Hexagonal Floating Structure under Waves

description: Floating structures have a wide range of application and shapes. This experimental investigations observes a hexagonal floating structure under wave conditions for three different draft configurations. Regular waves as well as a range of white noise tests were conducted to quantify the response amplitude operator (RAO). Further irregular waves focused on the survivability of the floating structure. The presented dataset includes wave gauge data as well as 6 degree of freedom motion measurement to quantify the response only restricted by a soft mooring system. Additional analysis include the measurement of the mass properties of the individual configuration, natural frequency of the mooring system as well as the comparison between requested and measured wave heights. This allow to use the provided dataset as a validation experiment. This research was carried out at the FloWave Ocean Energy Research Facility of the Institute for Energy Systems, University of Edinburgh.
DOI: 10.7488/ds/3477
title: Molecular dynamics investigation of clustering in aqueous glycine solutions

description: This dataset provides molecular dynamics simulations input files required to reproduce the simulation results reported in the following paper: “Molecular dynamics investigation of clustering in aqueous glycine solutions”. URL: TBC ### Abstract: Recent experiments with undersaturated aqueous glycine solutions have repeatedly exhibited the presence of giant liquid-like clusters, or nanodroplets, around 100 nm in diameter. These droplets reappear even after careful efforts at their removal and purification of the glycine solution. The composition of these clusters is not clear, although it has been suggested they are mainly composed of glycine, a small and very soluble amino acid. To gain insight into this phenomenon, we study the aggregation of glycine in aqueous solutions at concentrations below the experimental solubility limit using large-scale molecular dynamics simulations at ambient conditions. Three protonation states of glycine (neutral=GLY, anion=GLA, cation=GLC) are simulated using molecular force fields based on the 1.14*CM1A partial charge scheme, which incorporates the OPLS all atom force field, and TIP3P water. When initiated from dispersed states, we find giant clusters do not form in our simulations unless salt impurities are present. Moreover, if simulations are initiated from giant cluster states, we find they tend to dissolve in the absence of salt impurities. Therefore, the simulation results provide little support for the possibility that the giant clusters seen in experiments are composed purely of glycine (and water). Considering that strenuous efforts are made in experiments to remove impurities such as salt, we propose that the giant clusters observed might instead result from the aggregation of reaction products of aqueous glycine, such as diketopiperazine or other oligoglycines which may be difficult to separate from glycine using conventional methods, or their co-aggregation with glycine. Detailed work is needed to explore this possibility. ### In this paper we reported molecular dynamics simulation results for 6 samples. Simulations were performed using the LAMMPS software package (See https://www.lammps.org/). Each directory in the dataset correspond to one simulated sample. The directory name has information on the concentration of each simulated molecular species, and whether the simulation was initiated from dispersed or pre-clustered state. Each directory contains the following three essential files: lammps.input (LAMMPS input script), forcefield.dat (input forcefield file), and data.dat (initial atom positions, bonds, and angles). To run these simulations on Linux, it is sufficient to use the command "/PATH-TO-LAMMPS/lammps &lt; lammps.input".
DOI: 10.7488/ds/3068
title: Proteomic analysis to identify the pathways and processes affected by altered levels of Sideroflexin3 (SFXN3) in the synapse.
title: SFXN3 KO proteomics

description: Proteomic data from TMT based analysis of synapses biochemically isolated from Sfxn3-KO mice (http://www.mousephenotype.org/data/genes/MGI:2137679). See attached word/.txt description for further information. Briefly - Synapses are a primary pathological target in neurodegenerative diseases. Identifying therapeutic targets at the synapse could delay progression of numerous conditions. The mitochondrial protein SFXN3 is a neuronally-enriched protein expressed in synaptic terminals and regulated by key synaptic proteins, including alpha-synuclein (previously reported in Amorim et al., 2017 [PMID:28049726] and Graham et al., 2017 [PMID: 29078798]). Applying high-resolution proteomics to synapses biochemically isolated from Sfxn3-KO mice (http://www.mousephenotype.org/data/genes/MGI:2137679), we sought to identify what the molecular consequences of altered SFXN3 expression are in vivo. Analysis of the data contained within this submission suggest that Sfxn3 regulates proteins and pathways associated with neurodegeneration and cell death (including CSP alpha and caspase-3), as well as cascades altered in other neurological conditions (including Parkinson’s disease and Alzheimer’s disease).
description: Attached are two documents describing the rational, methodology employed and confirming ethical approval are in place (1 x word and 1 x .txt). The data set comprises an xl file with multiple tabs: Tab 1 - Molecular tag identification numbers. Tab 2- Raw proteomic data Tab 3 - Filtered by number of unique peptides Tab 4 - Filtered by fold change Tab 5 - Molecules involved in Iron Homeostasis - derived from Ingenuity Pathway Analysis Tab 6 - Molecules involved in Iron Synthesis - derived from Ingenuity Pathway Analysis
DOI: 10.7488/ds/3070
title: PSD95 Lifetime Synaptome Atlas of the mouse brain.
title: List of mouse brain regions and subregions

description: Where memories are stored in the brain and how the capacity to learn and remember changes with age are poorly understood. Synapse proteins are necessary for all behaviour and their lifetime may instruct us on how memories are stored in synapses and how diseases cause cognitive and behavioural impairments. We have developed methods to visualise and quantify the lifetime of proteins in individual synapses across the mouse brain and lifespan. We mapped the lifetime of PSD95, a postsynaptic protein required for writing and maintenance of memories, in individual synapses across the brain of young, mature and old mice. Synapses with diverse protein lifetimes form a special architecture in dendrites, circuits and brain regions that changes across the lifespan. The spatiotemporal distribution of synapses with different memory durations may explain normal and pathological features of memory.
DOI: 10.7488/ds/3072
title: A Populations Genetics Analysis of the United Kingdom's Non-Pedigree Cats
title: Domestic cat genotypes

description: This study investigated the population genetics of 1290 UK cats.
description: PLINK genotype files: UK_Feline_1290.bed UK_Feline_1290.bim UK_Feline_1290.fam
DOI: 10.7488/ds/2996
title: Whole genome sequencing SNP data of honey bee drones

description: Genotype data from processing of whole genome sequence data for 689 honey bee drones representing samples from 14 countries and 7 subspecies.
description: "VCF files at various stages of processing: raw.vcf.gz (raw) raw.QC.vcf.gz (QC filtered) raw.QC.imputed.vcf.gz (QC filtered &gt; imputed) raw.QC.imputed.LD.vcf.gz (QC filtered &gt; imputed &gt; LD filtered) ancestral.QC.imputed.vcf.gz (QC filtered &gt; imputed &gt; ancestral allele set) ancestral.QC.imputed.LD.vcf.gz (QC filtered &gt; imputed &gt; ancestral allele set &gt; LD filtered) Genetic map generated for use with RFMIX: ancestral.QC.imputed.vcf.genmap (genetic map for ancestral.QC.imputed.vcf.gz) Complete genetic maps generated from Liu's et al.'s crossover data: geneticMaps.tar.gz (archive of genetic maps generated after NCBI LiftOver of Liu et al.'s crossover data from Amel_4.5 to Amel_HAv3.1, fields are [1] Linkage group accession number, [2] physical position (bp), [3] genetic position (cM), [4] rate of recombination, [5] chromosome number) Sample metadata: metadata.csv (sample metadata indicating colony (FID) sample ID, ENA accessions, country of sample origin, type)"
DOI: 10.7488/ds/3779
title: More than ADEQUATE: doubling the sensitivity of 13CH–13CH correlations in double-quantum NMR experiments
title: NMR spectra acquired by the improved ADEQUATE method

description: Bruker format NMR data as per provided List of spectra
description: Published paper + Supporting information + Bruker format NMR data as per provided List of spectra
DOI: 10.7488/ds/2995
title: Continuation part of CMIP5/PMIP3 HadCM3 past1000 simulation

description: Numerical climate output from the HadCM3 climate model simulation runs for the NERC funded Euroclim500 project: Causes of change in European mean and extreme climate over the past 500 years. These data were produced by Andrew Schurer, Mike Mineter and Simon Tett using the HadCM3 climate model on the HECTOR supercomputer at the University of Edinburgh. They have been published as part of a larger collection at CEDA - but are here in CMOR format. On CEDA, this simulation is labelled experiment ALL, ensemble 1. The first part of this simulation 850-1849 is the PMIP3/CMIP5 past1000 run. The part archived here (1850-2000) is the historical continuation part. The format is identical to that on the PMIP/CMIP database. The simulations form the historical continuation from the CMIP5/PMIP3 HadCM3 past1000 simulation and start from the past1000 experiment in 01/1850. The data is all at monthly resolution and is contained in one compressed folder which is subdivided into atmosphere, ocean, land, sea ice and land ice variables, following the CMIP5 convention.
DOI: 10.7488/ds/3777
title: Data from paper: Synaptic resilience is associated with maintained cognition during ageing

description: It remains unclear why age increases risk of Alzheimer’s disease and why some people experience age-related cognitive decline in the absence of dementia. Here we test the hypothesis that resilience to molecular changes in synapses contribute to healthy cognitive ageing. We examined post-mortem brain from people in mid-life (n=15), healthy ageing with either maintained cognition (n=9) or lifetime cognitive decline (n=8), and Alzheimer’s disease (n=13). Synapses were examined with high resolution imaging, proteomics, and RNA sequencing. Stem cell-derived neurons were challenged with Alzheimer’s brain homogenate. Synaptic pathology increased, and expression of genes involved in synaptic signalling decreased between mid-life, healthy ageing and Alzheimer’s. In contrast, brain tissue and neurons from people with maintained cognition during ageing exhibited decreases in synaptic signalling genes compared to people with cognitive decline. Efficient synaptic networks without pathological protein accumulation may contribute to maintained cognition during ageing. This dataset includes all analysed spreadsheets and statistical analysis macros from the study for further use. ## Image data ## For raw images associated with the study, which are stored in Edinburgh DataVault, please contact the authors for download links. ## Associated publications ## * King, D., Holt, K., Toombs, J., He, X., Dando, O., Okely, J., Rose, J., Gunn, C., Correia, A., Montero, C., Tulloch, J., Lamont, D., Taylor, A., Harris, S., Redmond, P., Cox, S. R., Henstridge, C., Deary, I. J., Smith, C., & Spires-Jones, T. (2022). Synaptic resilience is associated with maintained cognition during ageing. Alzheimer's & Dementia: The Journal of the Alzheimer's Association. https://doi.org/10.1002/alz.12894 * Declan King, Kris Holt, Jamie Toombs, Xin He, Owen Dando, J. A. Okely, Jamie Rose, Ciaran Gunn, Adele Correia, Carmen Montero, Jane Tulloch, Douglas Lamont, Adele M Taylor, Sarah E Harris, Paul Redmond, Simon R Cox, Christopher M Henstridge, Ian J Deary, Colin Smith, Tara L Spires-Jones. medRxiv 2022.05.04.22274679; doi: https://doi.org/10.1101/2022.05.04.22274679 This article is a preprint and has not been peer-reviewed [what does this mean?]. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.
DOI: 10.21227/b24r-z076
title: Horticulture recomendation system

description: Horticulture recomendation system