cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2784
title: APP NL/F - 1 year rodent EEG and video recordings. Cerebellum reference. Donepezil administration
title: APP_1yr_Cerebellum_Donepezil

description: This dataset relates to the rodent data reported in the manuscript "Circadian and brain state modulation of network hyperexcitability in Alzheimer's disease". (Brown et al., (2018) 27 April 2018, 5 (2) ENEURO.0426-17.2018. DOI: 10.1523/ENEURO.0426-17.2018). These data were previously archived in the interim DataVault, deposited there in June 2018. Please see the Collection page for several other data filesets supporting the same publication: https://datashare.is.ed.ac.uk/handle/10283/3586 . The repository contains EEG data from 12 month old APP NL/F+/+ and age matched C57Bl6J wild-type (WT) control mice. EEG data was acquired for three days. Donepezil at 1.5mg/kg was then administered to the animals (1.5mg/kg) orally daily. Data acquired using Opensource Instruments EEG data acquisition system, and LWDAQ/Neuroarchiver software. The data are saved in .ndf format and can be viewed using Neuroarchiver tool in LWDAQ, available here: http://alignment.hep.brandeis.edu/Software/Download/ Recording electrode coordinates: x: -2.25; y: -2.46 Reference electrode: Cerebellum The repository contains: - This README_APP_1yr_Cerebellum_Donepezil.txt file - "RecordingInfo_1yr_Cerebellum_Donepezil.csv" with variables: - Mouse: The mouse ID - DOB: Date of birth in format dd/mm/yyyy or age of the animal at delivery date - Sex - Genotype - Transmitter: The ID of transmitter. The number after the "." indicates the channel number relating to the data as stored in the .ndf data file - surgery date in format dd/mm/yyyy - first file: name of the first file - last file - last recording date in format dd/mm/yyyy - Drug time: Time at which Donepezil was adminstered daily. If NA, no Donepezil adminstered - Drug days: Days on which Donepezil was administered - Reference: Location of reference electrode - Subfolder: Name of subfolder within "Neuroarchiver data" subfolder that contains the EEG data - Notes: Additional notes - An archive, "APP_1yr_Cerebellum_Donepezil.zip" which contains: - A folder "Neuroarchiver data". This contains subfolders labelled by MouseIDs of recordings contained therein. Each subfolder contains data files saved in .ndf format. The .ndf files are named are named Mxxxxxxxxxx.ndf, where xxxxxxxxxx indicates the Unix time stamp (i.e. number of seconds after 00:00:00 on 1/1/1970) for the start of the file acquisition. The relevant channel number for the specified mouse ID is noted in RecordingInfo_APP1yr_Cerebellum_Donepezil.csv - Transmitter. - A folder "videos", containing subfolders named by date (dd-mm-yyy)_mouseID. Each subfolder contains video data saved in .avi. Data acquired on webcams.
DOI: 10.7488/ds/2774
title: Shilluk_2018_controlled_FloatingQuantity

description: The primary data in this dataset are audio recordings (wav format). They are utterances in the Shilluk language (Nilo-Saharan, South Sudan), recorded from 10 speakers, collected through controlled elicitation. The data were collected in order to investigate the phenomenon of floating quantity in Shilluk, and the analysis of the resulting dataset forms is reported on in the paper "Floating quantity in Shilluk" authored by Remijsen & Ayoker. This paper has been accepted for publication in the journal Language. Apart from the primary data, the dataset includes a segmentation of the vocalic prefix that follows the target word, as described in the above-mentoned paper (in TextGrid objects). In the filenames, the first field holds the speaker code (01-10); the second field specifies the context (utterance-final coded as FIN; utterance-medial as BEN; see Language paper for details); the third field holds the English translation of the target noun (see Language paper for details); the fourth field can be ignored, it is S throughout; the final field holds the repetition number of the realisation, which is almost always 01.
DOI: 10.7488/ds/2791
title: Genome-wide association summary statistics of antidepressant treatment resistance meta-analysis
title: Genome-wide association study of antidepressant treatment resistance in a population-based cohort using health service prescription data and meta-analysis with GENDEP

description: Data from Wigmore et al "Genome-wide association study of antidepressant treatment resistance in a population-based cohort using health service prescription data and meta-analysis with GENDEP". The Pharmacogenomics Journal 20, 329–341 (2020) DOI:10.1038/s41397-019-0067-3 This dataset consists of two sets of GWAS summary statistics: - case-control analysis of treatment resistance phenotype in the Generation Scotland and GENDEP samples (inverse variance weighted meta-analysis). Cases = 358, Controls = 3855. - quantitative stages of resistance phenotype in Generation Scotland. N = 3452.
description: File: TRD_meta.Wigmore2020.txt.gz Description: Meta-analysis of Generation Scotland and GENDEP Columns: - CHR: chromosome - SNP: marker RSID - BP: base-pair position - A1: effect allele - A2: non-effect allele - Freq1: average frequency of A1 - FreqSE: standard error of frequency - logOR: effect of A1 as log Odds Ratio - logOR_SE: standard error of the effect - P: p-value - Direction: direction of effect from each study (order: GENDEP, GenScot) - HetISq, HetChiSq, HetDf, HetPVal: heterogeneity statistics File: TRD_Stages.Wigmore2020.txt.gz Description: Stage of resistance in Generation Scotland Columns: - CHR: chromsome - SNP: marker RSID - BP: base-pair position - A1: effect allele - A2: non-effect allele - Freq: frequency of A1 - beta: effect of A1 - se: standard error of effect - P: p-value
DOI: 10.7488/ds/2434
title: Polymer Simulations of Heteromorphic Chromatin Predict the 3-D Folding of Complex Genomic Loci

description: This dataset contains data corresponding to the figures and supplemental figures of the manuscript "Polymer Simulations of Heteromorphic Chromatin Predict the 3-D Folding of Complex Genomic Loci". Data sets from next generation sequencing experiments (including full raw sequence data) will be deposited separately in the Gene Expression Omnibus. Chromatin folded into 3-D macromolecular structures is often analysed by 3C and FISH techniques, but these frequently provide contradictory results. Chromatin can be modelled as a simple polymer comprised of a connected chain of units. By embedding data for epigenetic marks (H3K27ac), chromatin accessibility (ATAC-seq) and structural anchors (CTCF) we developed a highly predictive heteromorphic polymer (HiP-HoP) model, where the chromatin fibre varied along its length; combined with diffusing protein bridges and loop extrusion this model predicted the 3-D organisation of genomic loci at a population and single cell level. The model was validated at several gene loci, including the complex Pax6 gene, and was able to determine locus conformations across cell types with varying levels of transcriptional activity and explain different mechanisms of enhancer use. Minimal a priori knowledge of epigenetic marks is sufficient to recapitulate complex genomic loci in 3-D and enable predictions of chromatin folding paths.
description: Details of the data are provided in the README text file. Data relating to each figure in the related manuscript are provided in a separate gzipped tar archive, and each of these contains an additional README text files with further details.
DOI: 10.7488/ds/2794
title: Acoustic correlates of plosive voicing in Madurese: supplementary materials

description: This dataset contains supplementary materials to the paper "Acoustic correlates of plosive voicing in Madurese", published in the Journal of the Acoustical Society of America. It contains CSV data files and R code necessary to replicate the analyses reported in the paper, along with a PDF containing plots and post-hoc comparisons.
description: The deposit comprises two tarballs, which can be extracted using tar on Linux, or other decompression software such as 7-zip on Windows. * "madurese_JASA_data.tar.bz2" The out/ directory contain CSV files containing spectral measurements for both the open and closed phases of the CV transition. madurese-raw-2019.csv contains measures for the open phase, and madurese-cl-2019.csv for the closed phase, taken every millisecond; madurese-11bins-2019.csv and madurese-cl11bins-2019.csv are versions with only 11 data points per phase. The scripts/ directory contains R code to reproduce the tables and figures found in the paper. The text/ directory contains a copy of the online appendices, containing the word list, descriptive statistics, estimated marginal means, and plots of acoustic measures by individual. * "madurese_JASA_audio.tar.bz2" The audio files.
DOI: 10.7488/ds/2866
title: Window south side (side short wall) informal settlement fire experiment (Test 6)

description: This dataset presents Test 6 (window south side experiment). Different from Baseline experiment, the window location was changed from front long wall to side short wall, and the other conditions are totally the same with Baseline.
DOI: 10.7488/ds/2620
title: University of Edinburgh Musical Instrument Collections

description: The Dataset contains records for 5198 objects in the University of Edinburgh’s Musical Instrument Collection. The collection ranks among the world's most important collections of musical heritage. All the main types or musical sound-making device are represented, and are presented to the public at St Cecilia’s Hall Concert Room and Music Museum where c.500 instruments are on display. The c.6000 objects in the collection constitute a rich research resource of both breadth and depth, and include many historically typical models of musical instrument spanning over 500 years, together with prized rare and unique items. The data is accompanied by a readme.txt file that contains further contextualisation of the data. For more information please see www.ed.ac.uk/is/crc or email is-crc@ed.ac.uk
DOI: 10.7488/ds/2487
title: 1D NMR of Scotch Whisky - Standard Sample Set

description: NMR spectra for Scotch Whisky samples. Spectra acquired as per the method previously published by Kew et al (Magn Reson Chem. 2017 Sep;55(9):785-796. doi: 10.1002/mrc.4621). Briefly, 500 μL of Scotch Whisky was added to a 5 mm NMR tube with a D2O buffer (100 μL) containing DSS-d6 and sodium acetate/acetic acid buffer at final concentrations of 1 mM and 25 mM, respectively. Spectra acquired on a Bruker 600 MHz NMR spectrometer with Avance III HD console and TCI cryoprobe. The sample set here comprise the Scotch Whisky Research Institute's Standard Sample Set of Scotch Whisky from 2010, 2012, and 2014, representing the vast majority of Scotch produced and sold. The samples have been anonymised, but sample information is provided in a CSV file. The sample naming scheme is SYY-XXXX, where YY is the year the sample was received, and XXXX is a unique 4-digit ID within that year. Each sample has four associated 1D NMR spectra - experiment number (expno) 10 is a simple water presaturation (zgpr) experiment used to locate the water resonance frequency, expno 11 is a non-refocused reverse INEPT showing the 13C satellites of ethanol, used for ethanol frequency determination, expno 12 is a 1D 13C NMR spectrum showing the carbon chemical shifts of ethanol, and finally expno 13 is a 1D 1H NMR spectrum showing the full spectrum of Scotch Whisky with ethanol and water signals suppressed. DSS (0 ppm, 1 mM) is used for internal reference and calibration. See previous related dataset - https://datashare.is.ed.ac.uk/handle/10283/2733 - and the previously mentioned publication for full technical parameters and example 2D NMR spectra.
description: Raw data in Bruker format are provided in Standard_Sample_Sets_2010_2012_2014.zip. The data are provided in the original Bruker raw data formats - fid, processed (pdata 1), and aligned processed (pdata 1002). Additionally, the processed and aligned spectra, uniformly binned to 0.001 ppm, are provided tabulated as a CSV file with sample information Aligned-Data-0.001bin.csv. The sample information itself is also provided in SampleInformation.csv.
DOI: 10.7488/ds/2502
title: Comparison of DNA methylation profiles from Generation Scotland blood samples stored on Whatman FTA cards and in EDTA tubes: EWAS summary statistics

description: This dataset contains summary statistics for the epigenome-wide association studies (EWASs) performed to ascertain the feasibility of profiling DNA methylation using dried blood spot (DBS) DNA from Generation Scotland participants' blood samples that were stored on Whatman FTA cards and the comparability of these DBS methylation profiles with those obtained from paired blood samples stored in EDTA tubes. Paired DBS and EDTA tube blood samples were profiled using the Illumina 450K methylation array and EWASs for age and smoking performed to assess (i) whether loci previously found to be associated with these traits were identified in the DBS samples and (ii) whether the method of storing the blood sample (EDTA tube or Whatman FTA card) moderated the relationship between these traits and DNA methylation. The data is described fully in the associated pre-print, which is available on bioRxiv (https://doi.org/10.1101/546606).
description: The dataset comprises seven .csv files. Each file contains the results from one EWAS in a dataframe with probes represented in rows and columns representing the estimated coefficient (coef), the standard error of the coefficient (SE), the p-value (P_VAL), the mean M-value (mean), the standard deviation of the M-values (SD) and the number of samples included in the analysis (N). The files are named as follows: 1. "storage_time_DBS_EWAS_summary_stats.csv": EWAS of storage time carried out using blood samples stored on Whatman FTA cards; 2. "age_EDTA_EWAS_summary_stats.csv": EWAS of age carried out using blood samples stored in EDTA tubes; 3. "age_DBS_EWAS_summary_stats.csv": EWAS of age carried out using blood samples stored on Whatman FTA cards; 4. "smoking_EDTA_EWAS_summary_stats.csv": EWAS of current vs. never smokers carried out using blood samples stored in EDTA tubes; 5. "smoking_DBS_EWAS_summary_stats.csv": EWAS of current vs. never smokers carried out using blood samples stored on Whatman FTA cards; 6. "age_storage_method_interaction_EWAS_summary_stats.csv": EWAS of the interaction between age and storage method (EDTA tube vs. Whatman FTA card) carried out using paired blood samples; 7. "smoking_storage_method_interaction_EWAS_summary_stats.csv": EWAS of the interaction between smoking status (current or never) and storage method (EDTA tube vs. Whatman FTA card) carried out using paired blood samples.
DOI: 10.7488/ds/2795
title: GapFire

description: GapFire is a model developed as part of a pilot REDD+ project in conjunction with the Mpingo Conservation & Development Initiative. It has been designed to predict changes in above ground biomass of miombo woodlands in response to observations of early and late fire frequency. The model is an intrinsic part of an established VCS methodology for C storage: VM0029 "Methodology for Avoided Forest Degradation through Fire Management”.
description: VM0029-Methodology-for-Avoided-Degradation-through-Fire-Management-v1.0.pdf provides details to operate the code and the files.
DOI: 10.7488/ds/2827
title: SUPERSEDED - Interaction between Nearly Hard Colloidal Spheres at an Oil-Water Interface

description: ## This dataset has been replaced by the one which can be found at https://doi.org/10.7488/ds/2848 . ## We show that the interaction potential between sterically stabilised, nearly hard-sphere (PMMA-PLMA) colloids at a water-oil interface has a negligible unscreened-dipole contribution, suggesting that models previously developed for charged particles at liquid interfaces are not necessarily applicable to sterically stabilised particles. Interparticle potentials, U(r), are extracted from radial distribution functions (g(r), measured by fluorescence microscopy) via Ornstein-Zernike (OZ) inversion and via a reverse Monte Carlo scheme. The results are then validated by particle tracking in a blinking optical trap. Using a Bayesian model comparison, we find that our PMMA-PLMA data is better described by screened monopole only rather than a functional form having a screened monopole plus an unscreened dipole term. We postulate that the long range repulsion we observe arises mainly through interactions between neutral holes on a charged interface i.e. the charge of the liquid interface cannot, in general, be ignored. In agreement with this interpretation, we find that the interaction can be tuned by varying salt concentration in the aqueous phase. Inspired by recent theoretical work on point charges at dielectric interfaces, which we explain is relevant here, we show that a screened 1/r^2 term can also be used to fit our data. Finally, we present measurements for PMMA-PHSA particles at a water-oil interface. These suggest that, for PMMA-PHSA particles, there is an additional contribution to the interaction potential. This is in line with our optical-tweezer measurements for PMMA-PHSA colloids in bulk oil, which indicate that they are slightly charged.
DOI: 10.7488/ds/2838
title: Protein genome-wide associations from the paper 'Linking protein to phenotype with Mendelian Randomization detects 38 proteins with causal roles in human diseases and traits'.

description: Data in support of the manuscript "Linking protein to phenotype with Mendelian Randomization detects 38 proteins with causal roles in human diseases and traits".
description: Two tarballs, one per cohort (ORCADES / CROATIA-Vis), each containing 249 tab-separated results files, and other associated metadata files. Bzip2 compression used throughout.
DOI: 10.7488/ds/2739
title: Royal Mile Mercat Cross and Adam Smith Statue

description: A Scan of a section of the Royal Mile including the Mercat Cross and statue of Adam Smith, 7 Scan locations, captured with a BLK 360, registered using Autodesk Recap Pro, exported to .e57 file format.
DOI: 10.7488/ds/2735
title: Edinburgh Scrapyard

description: A Scan of a scrapyard in Edinburgh and surrounding houses, 10 Scan locations, captured with a BLK 360, registered using Autodesk Recap Pro, exported to .e57 file format.
DOI: 10.7488/ds/2737
title: Feshie River Bed

description: A Scan of a river bed (Feshie), 8 Scan locations, captured with a BLK 360, registered using Autodesk Recap Pro, exported to .e57 file format. https://en.wikipedia.org/wiki/River_Feshie
DOI: 10.7488/ds/2852
title: The emergence of systematic argument distinctions in artificial sign languages (dataset)

description: The video data stored in this repository are from a lab-based experiment in which hearing English speaking participants were asked to communicate with a partner using only gesture. Participants took part in pairs, and were organised in transmission chains of 5 generations, such that each generation comprised a pair of participants.
description: The video data are organised by chain, generation and participant. E.g. to find data for participant SP23, you would navigate to the folder for that chain (c3), for that generation (1) and that participant (SP23). Each participant folder contains 16 videos, for each trial in the experiment. Each trial contains gestures for 2 events. All participants included here gave consent for their video data to be shared publicly. One participant (SP29) did not and so their data is not included in this dataset. A snapshot copy of the analysis files has been added; the latest version of the analysis data, and the linked manuscript reporting the study can be found at https://osf.io/hp5md/.
DOI: 10.7488/ds/2849
title: XP-EHH and XP-CLR scores across water buffalo and cattle breeds

description: This dataset consists of XP-EHH and XP-CLR scores calculated using the hapbin (https://github.com/evotools/hapbin) and xpclr (https://github.com/hardingnj/xpclr) software with default parameters across 79 water buffalo and 294 cattle whole genome sequences. The breeds being compared and the chromosome number are indicated in each file name. The water buffalo positions are with respect to the UOA_WB_1 genome assembly and the cattle with respect to ARS-UCD1.2. This dataset replaces an earlier version (https://doi.org/10.7488/ds/2721).
description: Information about the file/directory structure.
DOI: 10.7488/ds/2491
title: ISST Deca-Alanine
title: Infinite Switch Simulated Tempering trajectory

description: This dataset contains a deca-alanine trajectory analysed in paper "Local and Global Perspectives on Diffusion Maps in the Analysis of Molecular Systems" by Trstanova et.al. 2019. The trajectory was obtained using an implementation of the Infinite Switch Simulated Tempering method (Martinsson et. al 2018) within the MIST library with GROMACS.
description: See GROMACS file format http://manual.gromacs.org/documentation/2016/user-guide/file-formats.html The ISST weights are in isst.out.
DOI: 10.7488/ds/2785
title: APP NL/F - 1 year rodent EEG and video recordings. Cortex reference
title: APP_1yr_Cortex

description: This dataset relates to the rodent data reported in the manuscript "Circadian and brain state modulation of network hyperexcitability in Alzheimer's disease". (Brown et al., (2018) 27 April 2018, 5 (2) ENEURO.0426-17.2018. DOI: 10.1523/ENEURO.0426-17.2018). These data were previously archived in the interim DataVault, deposited in June 2018. Please see the Collection page for several other data filesets supporting the same publication: https://datashare.is.ed.ac.uk/handle/10283/3586 . The repository contains EEG data from 12 month old APP NL/F+/+ and age matched C57Bl6J wild-type (WT) control mice. Data acquired using Opensource Instruments EEG data acquisition system, and LWDAQ/Neuroarchiver software. The data are saved in .ndf format and can be viewed using Neuroarchiver tool in LWDAQ, available here: http://alignment.hep.brandeis.edu/Software/Download/ Recording electrode coordinates: x: -2.25; y: -2.46 Reference electrode: x: +2.25; y: -2.46 The repository contains: - This README_APP_1yr_Cortex.txt file - "RecordingInfo_APP_1yr_Cortex.csv" with variables: - Mouse: The mouse ID - DOB: Date of birth in format dd/mm/yyyy or age of the animal in weeks for animals with unspecified DOB - Sex - Genotype - Transmitter: The ID of transmitter. The number after the "." indicates the channel number relating to the data as stored in the .ndf data file - surgery date in format dd/mm/yyyy - first file: name of the first file - last file - last recording date in format dd/mm/yyyy - Reference: Location of reference electrode - Subfolder: Name of subfolder within "Neuroarchiver data" subfolder that contains the EEG data - An archive, "APP_1yr_Cortex.zip" which contains: - A folder "Neuroarchiver data". This contains subfolders labelled by start_date of recordings contained therein. Each subfolder contains data files saved in .ndf format. The .ndf files are named are named Mxxxxxxxxxx.ndf, where xxxxxxxxxx indicates the Unix time stamp (i.e. number of seconds after 00:00:00 on 1/1/1970) for the start of the file acquisition. The relevant channel number for the specified mouse ID is noted in RecordingInfo_APP_1yr_Cortex.csv - Transmitter. - A folder "videos", containing subfolders named by date (dd-mm-yyy)_mouseID. Each subfolder contains video data saved in .avi. Data acquired on webcams.