cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2286
title: Global sensitivity and uncertainty analysis of an atmospheric chemistry transport model: the FRAME model (version 9.15.0) as a case study

description: Atmospheric chemistry transport models (ACTMs) are widely used to underpin policy decisions associated with the impact of potential changes in emissions on future pollutant concentrations and deposition. It is therefore essential to have a quantitative understanding of the uncertainty in model output arising from uncertainties in the input pollutant emissions. ACTMs incorporate complex and non-linear descriptions of chemical and physical processes which means that interactions and non-linearities in input–output relationships may not be revealed through the local one-at-a-time sensitivity analysis typically used. The aim of this work is to demonstrate a global sensitivity and uncertainty analysis approach for an ACTM, using as an example the FRAME model, which is extensively employed in the UK to generate source-receptor matrices for the UK Integrated Assessment Model and to estimate critical load exceedances. An optimised Latin hypercube sampling design was used to construct model runs within ± 40 % variation range for the UK emissions of SO2, NOx and NH3, from which regression coefficients for each input-output combination and each model grid (&gt;10,000 across the UK) were calculated. Surface concentrations of SO2, NOx and NH3 (and of deposition of S and N) were found to be predominantly sensitive to the emissions of the respective pollutant, while sensitivities of secondary species such as HNO3 and particulate SO42-, NO3- and NH4+ to pollutant emissions were more complex and geographically variable. The uncertainties in model output variables were propagated from the uncertainty ranges reported by the UK National Atmospheric Emissions Inventory for the emissions of SO2, NOx and NH3 (± 4 %, ± 10 % and ± 20 % respectively). The uncertainties in the surface concentrations of NH3 and NOx and the depositions of NHx and NOy were dominated by the uncertainties in emissions of NH3, and NOx respectively, whilst concentrations of SO2 and deposition of SOy were affected by the uncertainties in both SO2 and NH3 emissions. Likewise, the relative uncertainties in the modelled surface concentrations of each of the secondary pollutant variables (NH4+, NO3-, SO42- and HNO3) were due to uncertainties in at least two input variables. In all cases the spatial distribution of relative uncertainty was found to be geographically heterogeneous. The global methods used here can be applied to conduct sensitivity and uncertainty analyses of other ACTMs. The dataset contains FRAME model outputs and calculated regression coefficients (RCs), standardised regression coefficients (SRCs), and uncertainty ranges.
DOI: 10.7488/ds/2629
title: Fan cells in layer 2 of lateral entorhinal cortex are critical for episodic-like memory

description: Episodic memory requires different types of information to be bound together to generate representations of experiences. The lateral entorhinal cortex (LEC) and hippocampus are required for episodic-like memory in rodents. The LEC is critical for integrating spatial and contextual information about objects. Further, LEC neurons encode objects in the environment, the locations where objects were previously experienced, and generate representations of time during the encoding and retrieval of episodes. However, it remains unclear how specific populations of cells within the LEC contribute to the integration of episodic memory components. Layer 2 (L2) of LEC manifests early pathology in Alzheimer’s Disease (AD) and related animal models. Projections to the hippocampus from L2 of LEC arise from fan cells in a superficial sub-layer (L2a) that are immunoreactive for reelin and project to the dentate gyrus. Here, we establish an approach for selectively targeting fan cells using Sim1:Cre mice. Whereas complete lesions of the LEC were previously found to abolish associative recognition memory, we report that after selective suppression of synaptic output from fan cells mice can discriminate novel object-context configurations but are impaired in recognition of novel object-place-context associations. Our experiments suggest that memory functions are segregated between distinct LEC networks.
description: Supplemental Data: raw data for object recognition behaviour
DOI: 10.7488/ds/2472
title: Environmental & Load Data: 1:15 Scale Tidal Turbine subject to a variety of Regular Wave Conditions

description: The data described in this article was obtained from experimental tank testing of a 1:15 scale tidal stream turbine subject to a range of regular wave conditions in the presence of a fixed mean current velocity. Waves are generated both following and opposing the current direction, and wave frequencies and amplitudes are systematically varied. Turbine load data, along with corresponding surface elevations and velocity measurements are provided.
description: Please read "Data_Description.pdf"
DOI: 10.7488/ds/2444
title: Data accompanying 'A growing bacterial colony in two dimensions as an active nematic'

description: How a single bacterium becomes a colony of many thousand cells is important in biomedicine and food safety. Much is known about the molecular and genetic bases of this process, but less about the underlying physical mechanisms. Here we study the growth of single-layer micro-colonies of rod-shaped Escherichia coli bacteria confined to just under the surface of soft agarose by a glass slide. Analysing this system as a liquid crystal, we find that growth-induced activity fragments the colony into microdomains of well-defined size, whilst the associated flow orients it tangentially at the boundary. Topological defect pairs with charges ± 1/2 are produced at a constant rate, with the +1/2 defects being propelled to the periphery. Theoretical modelling suggests that these phenomena have different physical origins from similar observations in other extensile active nematics, and a growing bacterial colony belongs to a new universality class, with features reminiscent of the expanding universe.
DOI: 10.7488/ds/2113
title: SUPERSEDED - Summary GWAS data for morning plasma cortisol from the Cortisol Network (CORNET) Consortium 2014 (n=12,597)
title: Genome Wide Association Identifies Common Variants at the SERPINA6/SERPINA1 Locus Influencing Plasma Cortisol and Corticosteroid Binding Globulin

description: ## This Item has been replaced by the one which can be found at https://doi.org/10.7488/ds/2986 . ## Variation in plasma levels of cortisol, an essential hormone in the stress response, is associated in population-based studies with cardio-metabolic, inflammatory and neuro-cognitive traits and diseases. Heritability of plasma cortisol is estimated at 30–60% but no common genetic contribution has been identified. The CORtisol NETwork (CORNET) consortium undertook genome wide association meta-analysis for plasma cortisol in 12,597 Caucasian participants, replicated in 2,795 participants. The results indicate that &lt;1% of variance in plasma cortisol is accounted for by genetic variation in a single region of chromosome 14. This locus spans SERPINA6, encoding corticosteroid binding globulin (CBG, the major cortisol-binding protein in plasma), and SERPINA1, encoding α1-antitrypsin (which inhibits cleavage of the reactive centre loop that releases cortisol from CBG). Three partially independent signals were identified within the region, represented by common SNPs; detailed biochemical investigation in a nested sub-cohort showed all these SNPs were associated with variation in total cortisol binding activity in plasma, but some variants influenced total CBG concentrations while the top hit (rs12589136) influenced the immunoreactivity of the reactive centre loop of CBG. Exome chip and 1000 Genomes imputation analysis of this locus in the CROATIA-Korcula cohort identified missense mutations in SERPINA6 and SERPINA1 that did not account for the effects of common variants. These findings reveal a novel common genetic source of variation in binding of cortisol by CBG, and reinforce the key role of CBG in determining plasma cortisol levels. In turn this genetic variation may contribute to cortisol-associated degenerative diseases.
description: gwama_1_fixed.out: Morning plasma cortisol GWAS meta-analysis (n=12,597) README_CORNET.pdf
DOI: 10.7488/ds/2291
title: Dataset concerning the manuscript "Rare variants implicate ENPP6 as a regulator of reduced visceral adiposity"

description: The Orkney Complex Disease Study (ORCADES) is a family-based population cohort with DNA, biological samples, and a wide range of clinical data from ~2,000 adult volunteers from the Orkney Islands. Genotype data is also available, derived using genome-wide arrays. The dataset provided here consists of genome-wide association study (GWAS) summary statistics for the log-transformed trait of the ratio of android and gynoid fat percentage in ORCADES. Android and Gynoid fat percentages were obtained by dual-energy x-ray analysis of a subset of the ORCADES participants.
DOI: 10.7488/ds/2378
title: Long range electronic phase separation in CaFe3O5

description: Data are to accompany 'Long range electronic phase separation in CaFe3O5', by K. H. Hong et al, Nature Communications (2018). Details of data files; (1) D2 instrument powder X-ray diffraction - cif file and data file for 300 K structure refinement. (2) Electrical properties measurements - data files for resistance and magnetoresistance vs temperature measurements. (3) Magnetisation measurements - data files for magnetisation vs temperature measurements and magnetisation vs field at specified temperatures. (4) Powder neutron diffraction - cif files, magnetic cif files and data files for structure refinements at indicated temperatures. (5) Powder synchrotron X-ray diffraction - cif files and data files for structure refinements at indicated temperatures.
DOI: 10.7488/ds/2046
title: Imaging Drug Uptake by Bioorthogonal Stimulated Raman Scattering Microscopy

description: Stimulated Raman scattering (SRS) microscopy in tandem with bioorthogonal Raman labelling strategies is set to revolutionise the direct visualisation of intracellular drug uptake. Rational evaluation of a series of Raman-active labels has allowed the identification of highly active labels which have minimal perturbation on the biological efficay of the parent drug. Drug uptake has been correlated with markers of cellular composition and cell cycle status, and mapped across intracellular structures using dual-colour and multi-modal imaging. The minimal photoxicity and low photobleaching associated with SRS microscopy has enabled real time imaging in live cells. These studies demonstrate the potential for SRS microscopy in the drug development process.
DOI: 10.7488/ds/2249
title: Effects of nanoparticle heating on the structure of a concentrated aqueous salt solution

description: These files contain original simulation data for Figures 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, and 13. (Figures 1 and 10 contain images.) They are all plain text files, each with two columns in xy format. The filenames refer to subfigures and are appended with the same labels used in the legends.
description: The full file listing and figure captions are given in the accompanying readme.txt file.
DOI: 10.7488/ds/2443
title: Native MS Analysis of Encapsulated Ferritins from Rhodospirillum rubrum, Haliangium ochraceum and Pyrococcus furiosus

description: Intact mass spectrometry (LC-MS) and native mass spectrometry analysis of 3 homologs of the encapsulated ferritin enzyme. This data is used in the study: 'Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea'. N.B. Datasets archived as .raw files (Waters data file extension; can be viewed using MassLynx).
DOI: 10.7488/ds/2971
title: Ergonomic assessment of the Dix-Hallpike’s test

description: Abstract Objectives: Numerous tasks carried out in the otolaryngology clinic increase the chances of developing injury among practitioners. To mitigate this, we aim to observe the risk of musculoskeletal injury in practitioners when carrying out common procedures. We observe the performance of the Dix-Hallpike manoeuvre, deducing whether technique has an impact on the likelihood of developing injury. Design: Participants were asked to perform the Dix-Hallpike manoeuvre as they normally would in clinic, on departmental colleagues. Data that was collected included chosen preference of position when carrying out manoeuvre, level of seniority of practitioner and risk of musculoskeletal injury to practitioner. Setting: Simulated outpatient department; St John’s Hospital, Edinburgh. Participants: Otolaryngology consultants and trainees with clinic commitments, having regularly performed the Dix-Hallpike manoeuvre. Main outcome measures: Risk of musculoskeletal injury was measured using the validated Rapid Upper Limb Assessment (RULA) tool. Results: 3 consultants and 7 trainees were included in this study performing on average 4 Dix-Hallpike’s during the study period – totalling 40 attempts. The median RULA score was 4 for the sitting position, compared to 6 for standing (p&lt;0.0001). There was similar statistical significance when consultants and trainees were evaluated separately. Conclusions: A doctor’s wellness is of great importance to facilitate long-term job satisfaction and productivity. It is important to improve conditions for the practitioner in the otology clinic, and one factor is procedural technique. Further work is needed to raise ergonomic awareness amongst otolaryngology surgeons.
description: BadBacks.sav Dataset file to be opened using SPSS. BadBacks.csv Dataset file in .csv format to increase accesibility. Ergonomic assessment of Dix Hallpike test.rtf README file on method used to analyse data sets.
DOI: 10.7488/ds/2238
title: Flow over a swift shaped wing and delta wing (RSOS, Muir et al., 2017, Fig. 4, 5, 6, 7 and 8)

description: Matlab files with data of Fig. 4, 5, 6, 7 and 8 in RSOS, Muir et al., 2017. The files named "Set_n_Re" contain the X,Y,u and v of every image. The files named "Set_n_Re_data" contain the results of applying the Q-criterion and the Gamma2 criterion to the previous files. These files contain variables Q, Gamma, hi, ho. Where Q is the Q-criterion, Gamma is the Gamma2 criterion, hi is the velocity field component in the X direction and ho is the velocity field component in the Y direction, after the convection velocity subtraction performed in the Gamma2 criterion.
DOI: 10.7488/ds/2120
title: Data from "Language learners privilege structured meaning over surface frequency"

description: Although it is widely agreed that learning the syntax of natural languages involves acquiring structure-dependent rules, recent work on acquisition has nevertheless attempted to characterize the outcome of learning primarily in terms of statistical generalizations about surface distributional information. In this paper we investigate whether surface statistical knowledge or structural knowledge of English is used to infer properties of a novel language under conditions of impoverished input. We expose learners to artificial-language patterns that are equally consistent with two possible underlying grammars—one more similar to English in terms of the linear ordering of words, the other more similar on abstract structural grounds. We show that learners’ grammatical inferences overwhelmingly favor structural similarity over preservation of superficial order. Importantly, the relevant shared structure can be characterized in terms of a universal preference for isomorphism in the mapping from meanings to utterances. Whereas previous empirical support for this universal has been based entirely on data from cross-linguistic language samples, our results suggest it may reflect a deep property of the human cognitive system—a property that, together with other structure-sensitive principles, constrains the acquisition of linguistic knowledge.
DOI: 10.7488/ds/2440
title: Imaging for a Forward Scanning Automotive Synthetic Aperture Radar

description: Data supporting the publication: Gishkori, S, Daniel, L, Gashinova, M & Mulgrew, B 2018, 'Imaging for a Forward Scanning Automotive Synthetic Aperture Radar' IEEE Transactions on Aerospace and Electronic Systems. DOI: 10.1109/TAES.2018.2871436. In this paper, we propose a forward scanning synthetic aperture radar methodology for a forward-looking automotive (low-terahertz) radar which combines scene scanning with synthetic aperture processing, resulting in enhanced angular resolution and improved imaging. We propose two algorithms: i) a modified back-projection algorithm, and ii) a compressed sensing based back-projection algorithm. We suggest techniques to reduce computational complexity of the proposed algorithms. Results of simulation and real-data experiments corroborate the validity of our proposed methodology and algorithms. The data (real-data) contains three files. The two .mat files contain data and the .m file is the matlab code. Running the matlab code by loading one of the data files generates a basic radar image. The paper basically uses this data to test our proposed methods.
DOI: 10.7488/ds/2448
title: CINIC-10 Is Not ImageNet or CIFAR-10

description: CINIC-10 is an augmented extension of CIFAR-10. It contains the images from CIFAR-10 (60,000 images, 32x32 RGB pixels) and a selection of ImageNet database images (210,000 images downsampled to 32x32). It was compiled as a 'bridge' between CIFAR-10 and ImageNet, for benchmarking machine learning applications. It is split into three equal subsets - train, validation, and test - each of which contain 90,000 images.
description: README.md: readme description of dataset and accompanying files imagenet-contributors.csv: list of contributing elements from ImageNet synsets-to-cifar-10-classes.txt: list of synsets to include into the CIFAR-10 classes train, valid, test: subset splits containing actual .png image files. (README.md has more details)
DOI: 10.7488/ds/2290
title: Stellate cells in medial entorhinal cortex are required for spatial learning

description: Spatial learning requires estimates of location that may be obtained by path integration or from positional cues. Grid and other spatial firing patterns of neurons in the superficial medial entorhinal cortex (MEC) suggest roles in behavioral estimation of location. However, distinguishing contributions of path integration and cue-based signals to spatial behaviors is challenging, and the roles of identified MEC neurons are unclear. We use virtual reality to dissociate linear path integration from other strategies for behavioral estimation of location. We find that mice learn to path integrate using motor-related self-motion signals, with accuracy that decreases steeply as a function of distance. We show that inactivation of stellate cells in superficial MEC impairs spatial learning in the virtual-reality task and in a real world object location recognition task. Our results quantify contributions of path integration to behavior and corroborate key predictions of models in which stellate cells contribute to location estimation.
DOI: 10.7488/ds/2379
title: Assemblies of the gyr falcon
title: Chromosome level genome assembly and comparative genomics between three falcon species reveals a pattern of genome organization not typical for birds

description: Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology including morphology, ecology and physiology and thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, the arrangement of its chromosomes, which can then be linked to the whole genome sequence to generate a so-called chromosome level assembly. Chromosome level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes as well as determining patterns of gross genomic evolution. To date only two falcon species have been sequenced and neither initially to chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date however published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purpose of this study was to generate analyzable karyotypes and ideograms of peregrine, saker and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n=50 for peregrine falcon and 2n=52 for saker and gyr through high quality banded chromosomes. Standard ideograms generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falcon, saker/gyr differed by 1 interchromosomal and 7 intrachromosomal rearrangements (a fusion plus 7 inversions) whereas peregrine and saker/gyr differ from the reference chicken genomes by 14/13 fusions (11 microchromosomal) and 6 fissions. The chromosomal differences between the species could possibly provide the basis of a screening test for hybrid animals. We have preserved these partial assemblies here for future use. The final assemblies for this genome will be submitted to the nucleotide archives GenBank/ENA.
description: falcon.contig.fasta.gz - version 0.1 of the assembly (contigs) falcon_contigs_260911.fasta.gz - version 0.2 of the assembly (contigs) falcon_scaffolds_260911.fasta.gz - version 0.2 of the assembly (scaffolds)
DOI: 10.7488/ds/2549
title: From nano to micro: evolution of magnetic domain structures in multi-domain magnetite

description: Micromagnetic models found in the paper "From nano to micro: evolution of magnetic domain structures in multi-domain magnetite". Reliability of magnetic recordings of the ancient magnetic field are strongly dependent on the magnetic mineralogy of natural samples. Theoretical estimates of long term stability of remanence was restricted to single-domain (SD) states, but micromagnetic models have recently demonstrated that the so-called single vortex (SV) domain structure can have even higher stability that SD grains. In larger grains (at approximately 10 μm in magnetite) the multidomain (MD) state dominates, so that large uniform magnetic domains are separated by narrow domain walls. In this study we use a parallelized micromagnetic finite element model to provide resolutions of many millions of elements allowing us, for the first time, to examine the evolution of magnetic structure from a uniform state, through the SV state up to the development of the domain walls indicative of MD states. For a cub-octahedral grain of magnetite, we identify clear domain walls in grains as small as ~3 μm with domain wall widths equal to that expected in large MD grains; we therefore put the SV to MD transition at ~3 μm for magnetite, and expect well defined, and stable, SV structures to be present until at least ~1 μm when reducing the grain size. Reducing the size further shows critical dependence on the history of domain structures, particularly with SV states that transition through a so-called "unstable zone" leading to the recently observed hard-aligned SV states that proceed to unwind to SD yet remain hard aligned.