cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/3059
title: GWAS hair colour
title: GWAS summary statistics for hair colour of unrelated white british

description: Natural hair colour within European populations is a complex genetic trait. Previous work has established that MC1R variants are the principal genetic cause of red hair colour, but with variable penetrance. Here, we have extensively mapped the genes responsible for hair colour in the white, British ancestry, participants in UK Biobank. MC1R only explains 73% of the SNP heritability for red hair in UK Biobank, and in fact most individuals with two MC1R variants have blonde or light brown hair. We identify other genes contributing to red hair, the combined effect of which accounts for ~90% of the SNP heritability. Blonde hair is associated with over 200 genetic variants and we find a continuum from black through dark and light brown to blonde and account for 73% of the SNP heritability of blonde hair. Many of the associated genes are involved in hair growth or texture, emphasising the cellular connections between keratinocytes and melanocytes in the determination of hair colour. These data contain GWAS summary statistics for hair colour of unrelated white British using UK Biobank data: GWAS red hair; GWAS blonde hair; GWAS brown hair.
DOI: 10.7488/ds/3029
title: Human Brain Atlases across the lifespan – Anatomical Segmentations
title: Adult Human Brain Anatomical Atlases

description: Dickie and colleagues generated seven age-specific brain tissue sets/atlases of T1-weighted brain MRI illustrative of the adult lifespan from 25 to 92 years, which are representative of the atrophy and neurovascular health characteristics of normal individuals in seven age-bands: 1) 25-34 years, 2) 35-44 years, 3) 45-54 years, 4) 55-64 years, 5) 71-74 years, 6) 75-78 years, and 7) 91-93 years. These atlases can be downloaded from Edinburgh Datashare at https://doi.org/10.7488/ds/1369. The present dataset contains the anatomical segmentations of the average T1-weighted brain template from each of these sets, with the exception of the cortical segments, obtained using freesurfer 6.0 (https://surfer.nmr.mgh.harvard.edu/). It also contains the scripts used to generate the nifti-1-formatted files of this dataset, written as Linux shell and Matlab scripts.
description: This dataset contains the following files: 1.- Brain_Atlases_Readme_file.pdf (Readme file, PDF format) 2.- Brain_templates_Process_freesurfer_output.m (matlab script, text file) 3.- Run_Freesurfer.sh (shell script, text file) 4.- Subjects_list.csv (CSV, comma delimited) 5.- template_25y.zip (zip file containing 5 nifti-gzip-formatted files of image data) 6.- template_35y.zip (zip file containing 5 nifti-gzip-formatted files of image data) 7.- template_45y.zip (zip file containing 5 nifti-gzip-formatted files of image data) 8.- template_55y.zip (zip file containing 5 nifti-gzip-formatted files of image data) 9.- template_73y.zip (zip file containing 5 nifti-gzip-formatted files of image data) 10.- template_76y.zip (zip file containing 5 nifti-gzip-formatted files of image data) 11.- template_92y.zip (zip file containing 5 nifti-gzip-formatted files of image data)
DOI: 10.7488/ds/3026
title: Data and code for "Bayesian geophysical inversion using invertible neural networks"

description: This dataset contains the data and codes used in manuscript "Bayesian geophysical inversion using invertible neural networks". Details can be found in README.txt.
DOI: 10.7488/ds/3035
title: HemeLB vessel compression simulation data

description: This dataset contains the files to reproduce the HemeLB simulations for the effect of a vessel compression on a downstream bifurcation. In addition, one of the key outputs of the simulations is provided.
DOI: 10.7488/ds/3036
title: Jarvis Salmon QBA
title: Qualitative Behavioural Assessment (QBA) in juvenile farmed Atlantic Salmon (Salmo salar): potential for on-farm welfare assessment

description: There is a growing scientific and legislative consensus that fish are sentient, and therefore have the capacity to experience pain and suffering. The assessment of the welfare of farmed fish is challenging due to the aquatic environment and the number of animals housed together. However, with increasing global production and intensification of aquaculture comes greater impetus for developing effective tools which are suitable for the aquatic environment to assess the emotional experience and welfare of farmed fish. This study therefore aimed to investigate the use of Qualitative Behavioural Assessment (QBA), originally developed for terrestrial farmed animals, in farmed salmon and evaluate its potential for use as a welfare monitoring tool. QBA is a ‘whole animal’ approach based on the description and quantification of the expressive qualities of an animal’s dynamic style of behaving, using descriptors such as relaxed, agitated, lethargic, or confident. A list of twenty qualitative descriptors was generated by fish farmers after viewing video-footage showing behaviour expressions representative of the full repertoire of salmon in this context. A separate, non-experienced group of ten observers subsequently watched twenty-five video clips of farmed salmon, and scored the twenty descriptors for each clip using a Visual Analogue Scale (VAS). To assess intra-observer reliability each observer viewed the same twenty-five video clips twice, in two sessions 10 days apart, with the second clip set presented in different order. The observers were unaware that the two sets of video clips were identical. Data were analysed using Principal Component (PC) Analysis (correlation matrix, no rotation), revealing four dimensions that together explained 79% of the variation between video clips, with PC1 (tense/anxious/skittish – calm/mellow/relaxed) explaining the greatest percentage of variation (56%). PC1 was the only dimension to show acceptable inter- and intra-observer reliability, and mean PC1 scores correlated significantly to durations of slow and erratic physical movements measured for the same 25 video clips. Further refinements to the methodology may be necessary, but this study is the first to provide evidence for the potential of Qualitative Behavioural Assessment to serve as a time-efficient welfare assessment tool for juvenile salmon under farmed conditions.
description: The excel file contains 3 sheets. The first two are the two QBA sessions. In each session 25 video Clips were observed by 10 Participants for each term (column Headings). The third sheet is the quantitative behaviour for each of the 25 video clips. There are 6 behaviours recorded - 3 as a duration in seconds, and 3 as a frequency.
DOI: 10.7488/ds/3024
title: Field Induced Modulated State in the Ferromagnet PrPtAl

description: Data supporting the paper: O'Neill, C. D., Abdul-Jabbar, G., Wermeille, D., Bourges, P., Kruger, F., & Huxley, A. D. (Accepted/In press). "A field induced modulated state in the ferromagnet PrPtAl". Physical Review Letters. # ABSTRACT # The theory of quantum order-by-disorder (QOBD) explains the formation of modulated magnetic states at the boundary between ferromagnetism and paramagnetism in zero field. PrPtAl has been argued to provide an archetype for this. Here, we report the phase diagram in magnetic field, applied along both the easy $a$-axis and hard $b$-axis. For field aligned to the $b$-axis, we find that the magnetic transition temperatures are suppressed and at low temperature there is a single modulated fan state, separating an easy $a$-axis ferromagnetic state from a field polarised state. This fan state is well explained with the QOBD theory in the presence of anisotropy and field. Experimental evidence supporting the QOBD explanation is provided by the large increase in the $T^2$ coefficient of the resistivity and direct detection of enhanced magnetic fluctuations with inelastic neutron scattering, across the field range spanned by the fan state. This shows that the QOBD mechanism can explain field induced modulated states that persist to very low temperature.
DOI: 10.7488/ds/3030
title: Spatiotemporal clock patterns in the leaf blade
title: Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf

description: We used luciferase reporter gene imaging to monitor circadian rhythms in leaves of Arabidopsis thaliana plants, achieving resolution close to the cellular level. Leaves grown without environmental cycles for up to 3 wk reproducibly showed spatiotemporal waves of gene expression consistent with intercellular coupling, using several reporter genes. This dataset contains: 1) Experiments performed by Benedicte Wenden: - 35S_LL_120310 - CCA1_LDgrownLLimaged_180310 - CCA1_LL_040210 - CCA1_LL_251109 - CCR2_LL_300610 - TOC1_LL_140710 2) Experiments performed by Sarah Hodge after the publication of Wenden et al., 2012: - 2012-CCA1-Sarah_Hodge-good_quality - 2012-CCA1-Sarah_Hodge-med_quality
description: File descriptions are included in documentation (ReadMe.txt file)
DOI: 10.7488/ds/3034
title: Fill In The World interaction data

description: This dataset contains server logs with user interaction data from user studies with the "Fill In The World" language learning game. "Fill In The World" is available at http://fitw.azurewebsites.net/
description: Every JSON file consists of a single array of server event messages. Every message has 4 fields: a username (who created the event, it could be a user, but it could also be part of the application), a timestamp (with the current server time), text (the message content itself), and verboseOnly (a boolean flag to help filter out messages that are less important). The usernames and world names have been anonymised to preserve privacy, and the server data wiped after user studies, so the IDs in this data set do not refer to any existing values,
DOI: 10.7488/ds/3039
title: Systematic review of signal post-processing methods in blood-brain barrier dysfunction assessments via dynamic-contrast enhanced magnetic resonance imaging

description: DCE-MRI enables quantification of vascular permeability, but current acquisition and processing protocols may be sub-optimal. While the literature has started to recognise this is indeed a problem, decisions concerning the application of post-processing or the lack thereof is still being driven by intuition or experience in high permeability scenarios and not necessarily by facts, potentially compromising the quality of subsequent analyses. In this systematic revision of the literature, we seek to identify MRI issues affecting BBB assessments via DCE-MRI, identify post-processing techniques typically considered to cope with them, and determine whether researchers thoroughly evaluate their effect prior to their application. This dataset contains the results of such a systematic search and data extraction. ## Funders ## This work was supported by the following: - the MRC Doctoral Training Programme in Precision Medicine (JB - Award Reference No. 2096671); - the UK Dementia Research Institute which receives its funding from DRI Ltd, funded by the UK MRC, Alzheimer's Society and Alzheimer's Research UK; - the Fondation Leducq Network for the Study of Perivascular Spaces in Small Vessel Disease (16 CVD 05); - the Stroke Association 'Small Vessel Disease-Spotlight on Symptoms (SVD-SOS)' (SAPG 19\100068); - the Row Fogo Charitable Trust Centre for Research into Aging and the Brain (MVH) (BRO-D.FID3668413); - a British Heart Foundation Chair award (RMT) (CH/12/4/29762); - the European Union Horizon 2020, PHC03-15, project No666881, 'SVDs@Target'.
DOI: 10.7488/ds/3027
title: SUPERSEDED - Whose behaviour? Ca2+ imaging in medial prefrontal cortex during social dominance interactions in a Tube-Test

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/3415 # This data set is a supplement for the article entitled "Whose behaviour? Ca2+ imaging in medial prefrontal cortex during social dominance interactions in a Tube-Test" that is submitted for in PNAS, Saxena et al 2021. Using this data one can reproduce the figures and the analysis done in the above-mentioned article and figures.
DOI: 10.7488/ds/3044
title: Competitive environments affect aggression of dairy cows (Bos taurus)

description: We examined aggressive interactions between dairy cows in a range of competitive environments associated with different resources (pasture, milking line, cubicles and feed-face) and determined their relationship with production parameters.
DOI: 10.7488/ds/3033
title: Ammonium fluoride's analogy to ice: possibilities and limitations

description: Ammonium fluoride, NH4F, is often seen as an analogue to ice, with several of its solid phases closely resembling known ice phases. While its ionic and hydrogen-ordered nature puts topological constraints on the ice-like network structures it can form, it is not clear what consequences these constraints have for NH4F compound formation and evolution. Here, we explore computationally the reach and eventual limits of the ice analogy for ammonium fluoride. By combining data mining of known and hypothetical ice networks with crystal structure prediction and density functional calculations we explore the high-pressure phase diagram of NH4F and host-guest compounds of its hydrides. Pure NH4F departs from ice-like behaviour above 80 GPa with the emergence of close-packed ionic structures. The predicted stability of NH4F hydrides shows that NH4F can act as host to small guest species, albeit in a topologically severely constraint configuration space. Finally, we explore the binary NH3-HF chemical space, where we find candidate structures for several unsolved polyfluoride phases, among them the chemical analogue to H2O2 dihydrate.
DOI: 10.7488/ds/3046
title: Sex-stratified linear mixed models: Clinical binary traits (Item 1/3)

description: Sex-stratified GWAS can help shed light on sexual differences in genetic architecture. In Bernabeu et al (2021) we fit sex-stratified linear mixed models (using DISSECT) across a total of 530 phenotypes to assess the effects of sex on genetic effect estimates, and compared estimates between males and females in a search for genetic variants that presented significant differences in association to the traits considered. Here, the summary statistics of said efforts, pertaining to clinical binary traits, are included (note: does not include UK Biobank cancer traits – these are found in DataShare item pertaining to non-clinical binary traits). Each file contains the results for a single clinical binary trait, as stated in the file name, using its corresponding UK Biobank trait code. Trait descriptions, including their respective UK Biobank codes, are stated in the “trait_description.tsv” file. For each trait (each .gz file), GWAS summary statistics obtained for over 4 million genetic variants across the genome (both autosomal, and X chromosome, MAF 10% filtered) and circa 450K individuals, as well as the results of the t-test comparing genetic effect estimates between the sexes, are included.
description: This DataShare deposit is one of three. This deposit includes datasets for traits of binary - clinical nature. Each file represents a trait, as stated in the file title. A table is also included which matches each trait code with a description. Each trait's file contains the following fields: SNP, alternative allele, genetic effect estimates for males and females, standard errors of said estimates, genetic effect estimates and corresponding SEs normalized by sex-specific phenotypic standard deviation for each sex, p-value of genetic effects, t-statistic comparing male to female genetic effects, and p-value corresponding to said t-statistic.
DOI: 10.7488/ds/2974
title: multimodal TRIPOD

description: The data contain multimodal features extracted for the TRIPOD dataset and used in the AAAI 2021 paper "Movie Summarization via Sparse Graph Construction". The data contain 122 pickle files, each one corresponding to a movie from the dataset and include sentence-level textual features from the movie screenplays and visual and audio features for the frames/segments of the corresponding videos. All different features/modalities are aligned and given by scene (we consider a scene as manually indicated in the screenplays).
DOI: 10.7488/ds/3047
title: Sex-stratified linear mixed models: Non-clinical binary traits (Item 2/3)

description: Sex-stratified GWAS can help shed light on sexual differences in genetic architecture. In Bernabeu et al (2021) we fit sex-stratified linear mixed models (using DISSECT) across a total of 530 phenotypes to assess the effects of sex on genetic effect estimates, and compared estimates between males and females in a search for genetic variants that presented significant differences in association to the traits considered. Here, the summary statistics of said efforts, pertaining to non-clinical binary traits, are included (note: includes UK Biobank cancer traits). Each file contains the results for a single non-clinical binary trait, as stated in the file name, using its corresponding UK Biobank trait code. Trait descriptions, including their respective UK Biobank codes, are stated in the “trait_description.tsv” file. For each trait (each .gz file), GWAS summary statistics obtained for over 4 million genetic variants across the genome (both autosomal, and X chromosome, MAF 10% filtered) and circa 450K individuals, as well as the results of the t-test comparing genetic effect estimates between the sexes, are included.
description: This DataShare deposit is one of three. This deposit includes datasets for traits of binary - clinical nature. Each file represents a trait, as stated in the file title. A table is also included which matches each trait code with a description. Each trait's file contains the following fields: SNP, alternative allele, genetic effect estimates for males and females, standard errors of said estimates, genetic effect estimates and corresponding SEs normalized by sex-specific phenotypic standard deviation for each sex, p-value of genetic effects, t-statistic comparing male to female genetic effects, and p-value corresponding to said t-statistic.
DOI: 10.7488/ds/3137
title: Supporting material for "Orbital forcing strongly influences seasonal temperature trends during the last millennium"

description: Abstract: Insolation changes caused by the axial precession induce millennial trends in last millennium temperature, varying with season and latitude. A characteristic seasonal trend pattern can be detected in both insolation and modeled surface temperature response. In the extratropical Northern Hemisphere, the maximum insolation trend occurs around April/May, while the minimum trend occurs between July and September. The temperature trend lags behind insolation trend by around a month. Hence orbital forcing potentially affects long‐term trends in proxy data, which are often sensitive to a distinct seasonal window. We find that tree‐ring reconstructions based on early growing season dominated records show different millennial trends from those for late summer dominated proxies. The differential response is similar to that seen in pseudo proxy reconstructions when considering proxy seasonality. This suggests that orbital forcing has influenced long‐term trends in climate proxies. It is therefore vital to use seasonally homogeneous data for reconstructing multicentennial variability.
description: insolation.zip: analysis of millennial insolation trends at the top of the atmosphere, induced by orbital forcing (variation of obliquity, precession and eccentricity). Readme file included in insolation.zip. models.zip: analysis of millennial surface temperature trends, including 7 all forced CMIP5 models (datasets not included) and single forcing experiments from the CESM-LME. Readme file included in models.zip reconstructions.zip: analysis of seasonal trends in last Millennium temperature reconstructions from tree-rings. Readme file included in reconstructions.zip
DOI: 10.7488/ds/3136
title: HadCM3 model data used in the article "Seasonal long-term trends during the last Millennium strongly influenced by orbital forcing" by Lucie Luecke, Andrew Schurer, Rob Wilson and Gabriele Hegerl

description: HadCM3 model simulation including orbital forcing only from 12/850 to 11/1850. The dataset is divided into atmosphere monthly mean and ocean monthly mean files. All files are in netcdf format. Abstract: Orbital forcing has played a minor role on global annual temperature variation during the last Millennium. Prior to industrialisation, volcanism has been the largest contributor to naturally forced large-scale variability. While orbital forcing is strongest on time-scales of Millions of years, the axial precession causes changes in seasonal insolation at millennial timescales. Here we investigate the effects of orbital forcing on long-term temperature trends in model simulations and proxy reconstructions of the Last Millennium. We show that in contrast to any other forcings, orbital forcing induces a strong seasonal signal in modelled surface temperatures, lagging behind the forcing by one to two months. We find that seasonal proxy reconstructions can reproduce a similar trend pattern as found in climate models and that they roughly agree on the magnitude of the Millennial trend. Our work emphasises the importance of using seasonally homogeneous data for reconstructing low frequency data.
DOI: 10.7488/ds/3048
title: Sex-stratified linear mixed models: Non-binary traits (Item 3/3)

description: Sex-stratified GWAS can help shed light on sexual differences in genetic architecture. In Bernabeu et al (2021) we fit sex-stratified linear mixed models (using DISSECT) across a total of 530 phenotypes to assess the effects of sex on genetic effect estimates, and compared estimates between males and females in a search for genetic variants that presented significant differences in association to the traits considered. Here, the summary statistics of said efforts, pertaining to non-binary traits, are included. Each file contains the results for a single non-binary trait, as stated in the file name, using its corresponding UK Biobank trait code. Trait descriptions, including their respective UK Biobank codes, are stated in the “trait_description.tsv” file. For each trait (each .gz file), GWAS summary statistics obtained for over 9 million genetic variants across the genome (both autosomal, and X chromosome) and circa 450K individuals, as well as the results of the t-test comparing genetic effect estimates between the sexes, are included.
description: This DataShare deposit is one of three. This deposit includes datasets for traits of binary - clinical nature. Each file represents a trait, as stated in the file title. A table is also included which matches each trait code with a description. Each trait's file contains the following fields: SNP, alternative allele, genetic effect estimates for males and females, standard errors of said estimates, genetic effect estimates and corresponding SEs normalized by sex-specific phenotypic standard deviation for each sex, p-value of genetic effects, t-statistic comparing male to female genetic effects, and p-value corresponding to said t-statistic.
DOI: 10.7488/ds/2872
title: Vertical window informal settlement fire experiment (Test 12)

description: This dataset presents Test 12. Different from Baseline experiment, the window height has been increased, and the other conditions are totally the same with Baseline.