cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2106
title: SUPERSEDED - Effects of perceptual similarity but not semantic association on false recognition in aging

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/2233 ## This study investigated semantic and perceptual influences on false recognition in older and young adults in a variant on the Deese-Roediger-McDermott paradigm. In two experiments, participants encoded intermixed sets of semantically associated words, and sets of unrelated words. Each set was presented in a shared distinctive font. Older adults were no more likely to falsely recognize semantically associated lure words compared to unrelated lures also presented in studied fonts. However, they showed an increase in false recognition of lures which were related to studied items only by a shared font. The data show that older adults do not always rely more on prior knowledge in episodic memory tasks. They converge with other findings suggesting that older adults may also be more prone to perceptually-driven errors.
description: Expt1_data.csv - Experiment 1 data file Expt1_data_key.csv - key to the Experiment 1 data file Expt2_data.csv - Experiment 2 data file Expt2_data_key.csv - key to the Experiment 2 data file
DOI: 10.7488/ds/2745
title: Edinburgh Tall Building Fire Tests Analysis

description: Six experiments from the Edinburgh Tall Building Fire Tests are analysed in order to understand the effects of ventilation on the characteristic thermal behaviour of large open-plan spaces, typical of contemporary architecture and tall buildings. These experiments systematically vary the fire spread mode and the ventilation characteristic to identify the resultant fire behaviour. The data herein includes semi-processed data, and the code used to analyse the data in order to quantify the distribution of energy and characteristic fire dynamics for each experiment.
description: Two folders are included, one with the data and the other with the code to analyse the data. Users are instructed to refer to the data/data_legend.txt file to find the legend and details of the experiments and the scripts/readme.txt file to find details of each script used in the analysis of the data.
DOI: 10.7488/ds/2583
title: Data supporting the article "Significant climate impacts of aerosol changes driven by growth in energy use and advances in emissions control technology"

description: This dataset contains six files numbered in order. All data are preprocessed from the fully-coupled Community Earth System Model 1 (CESM1) simulations, produced and can be read using the Python cPickle package. File01: The global distributions of1970-2010 changes in sulphate, black carbon and organic carbon aerosol burdens, File02; The effective radiative forcing (ERF) of 1970-2010 changes in sulphate, black carbon and organic carbon aerosols File03: The global distribution of 1970-2010 changes in total aerosol optical depth (AOD), and those attributed to the emission drivers including growth in energy use and advances in emission control technology File04: The same as File03, but for ERF File05: The same as File03, but for annual mean surface air temperature File06: The same as File03, but for annual mean precipitation Note that these data files are to support the article submitted to the Journal Atmospheric Chemistry and Physics, and may be edited under peer-review processes. Any inquiries go to alcide.zhao@ed.ac.uk
DOI: 10.7488/ds/2093
title: Analysis of TCSPC data: a comparative evaluation of deterministic and probabilistic approaches

description: These files contain data and the MATLAB code for data analysis associated with our paper "Analysis of TCSPC data: a comparative evaluation of deterministic and probabilistic approaches", Darren A Smith, Grant McKenzie, Anita C Jones and Trevor A Smith, Methods Appl. Fluoresc. 2017. AnalysisCode.zip contains all MATLAB code files used to perform fitting analysis, with the exception of SparseLab files (which can be downloaded from http://sparselab.stanford.edu/). The file structure given in the accompanying pdf Guide to Supplementary Files should be maintained to ensure that the MATLAB code runs properly (note the code has only been tested on a Windows machine and requires some MATLAB toolboxes, such as the Statistical Toolbox). No liability will be taken for any consequences that occur through the use of the code provided. SummaryData.zip contains a summary of all decay fitting performed for the preparation of the manuscript. Fits are provided in terms of both lifetime and rates. The folder also contains raw decay input files that were either simulated or recorded experimentally. Parameters used to generate simulated decays are also provided. The folder/file structure from both parent folders (AnalysisCode/SummaryData) is given in the accompanying pdf Guide to Supplementary Files.
DOI: 10.7488/ds/2404
title: Simplified biochemical model of synaptic plasticity, extended with Calcium-Induced Calcium Release

description: Synaptic plasticity is a cellular process that leads to strengthening (LTP) or weakening(LTD) of a neuronal synapse and is highly associated with learning and memory. These events are dependent on calcium entering the cell: high calcium influx activates the CaMKII pathway that leads to LTP, whereas low influx triggers the calcineurin pathway that leads to LTD. The outcome of these cascades is represented by phosphorylation of AMPA receptors, prevalent feature of LTP. This model represents the aforementioned biochemical mechanisms based on calcium concentrations and it is a simplified version of Li et al (2012)* model of synaptic plasticity. Additionally, it was extended by the addition of a pathway activated by glutamate binding to mGluR5 that leads to calcium-induced calcium release, through activation of IP3 receptors. This extended version better depicts calcium dynamics in the cell. Both models can be found as SBML files and they were originally created to run in COPASI software. Simulations can be run as time courses (here of 500 sec) or parameter scans for various molecular concentrations. Apart from my co-authors whom I'd like to thank for their support and contribution to this model, I am very grateful to Richard Fitzpatrick for his precious advice and help during my project. *Li et al. (2012) "Calcium Input Frequency, Duration and Amplitude Differentially Modulate the Relative Activation of Calcineurin and CaMKII". PLoS One. 2012; 7(9): e43810. doi: 10.1371/journal.pone.0043810
DOI: 10.7488/ds/2336
title: High Pressure Synthesis, Crystal Growth and Magnetic Properties of TiOF

description: Data to accompany publication; High Pressure Synthesis, Crystal Growth and Magnetic Properties of TiOF J. Cumby, M. B. Burchell and J. P. Attfield Solid State Sciences (2018) Single crystal data files for TiOF at 90 and 200 K. cif files and standard formats used by the SHELX package are provided.
DOI: 10.7488/ds/2520
title: Listening-test materials for "Modern speech synthesis for phonetic sciences: a discussion and an evaluation"

description: This data release contains listening-test materials associated with the paper "Modern speech synthesis for phonetic sciences: a discussion and an evaluation", presented at ICPhS 2019 in Melbourne, Australia.
description: See readme.txt
DOI: 10.7488/ds/2755
title: Methods to quantify and visualize venules using structural magnetic resonance imaging scans
title: Brain venular visual assessment methods developed up to July 2019

description: These data were part of a project to design and validate a clinically relevant method to visually assess venules from magnetic resonance imaging (MRI) structural scans, conducted primarily by Miss. Angela C.C. Jochems, supervised by Dr. Maria del C. Valdés Hernández and Prof. Joanna M. Wardlaw. Cerebral venules remain understudied in general, perhaps due to difficulties in visualising or differentiating venules from arterioles using MRI. Recent advances in MRI allow visualisation of cerebral venules since the deoxygenated venous blood provides an intrinsic contrast agent on T2*-weighted sequences such as gradient echo (GRE), and on susceptibility weighted imaging (SWI). This has led to several visual and computational venular quantification methods being described in individuals with multiple sclerosis, sporadic small vessel disease-related features, moyamoya disease, sickle cell anaemia, neurosarcoidosis, early Alzheimer’s disease and amnestic mild cognitive impairment, cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), healthy individuals, and hypertensive rats. These studies use different regions of interest (ROI), field strengths and venular quantification metrics. We extracted these data to give an overview of the state-of-art of the brain venular assessment methods developed up to July 2019 (date of completion of this project).
DOI: 10.7488/ds/2416
title: Sub-regional classification of the IPCC Europe region

description: The IPCC sub-regional classification of the IPCC Europe region is based on a combination of the Environmental Stratification of Europe (Metzger at al. 2005), which covers the map up to 32° East, and an extension for Eastern Europe which was constructed using the same statistical methods. The combined dataset distinguishes 17 zones. To reduce the complexity, the zones have been aggregated to five main zones which were used in the IPCC 5th Assessment Reports Working Group 2 Europe Chapter (Kovats et al. 2014). Significant variation in climate, and (agro-) ecosystems remains within these zones, and further subdivision may make sense when assessing particular climate change impact. One obvious candidate for further subdivision is the ‘Southern zone’, which includes Mediterranean mountains and uplands in Anatolia that contrast starkly with other parts of the zone.
description: This dataset contains: 1) IPCC_Europe_subregions.zip - the ESRI shape files for the IPCC Europe regions and country boundaries 2) IPCC_Europe_subregions.jpg - image of the regions 2) readme.pdf - description of the creation of the dataset
DOI: 10.7488/ds/366
title: Eddy diffusivity diagnostics data

description: Coarse resolution numerical ocean models must typically include a parameterisation for mesoscale turbulence. A common recipe for such parameterisations is to invoke down-gradient mixing, or diffusion, of some tracer quantity, such as potential vorticity or buoyancy. However, it is well known that eddy fluxes include large rotational components which necessarily do not lead to any mixing; eddy diffusivities diagnosed from unfiltered fluxes are thus contaminated by the presence of these rotational components.
DOI: 10.7488/ds/2226
title: Computational modelling and simulation of the interaction between NMDA receptors and CaMKII in the postsynaptic neuron

description: NMDAR and CaMKII interactions in the postsynaptic neuron play crucial roles that underlie our ability to learn and form memories. Their activity varies with time and space, and elucidating this matter is important for understanding how memory works. We develop a computer model that creates realistic 3D movements and reactions of molecules within a cell. It is an isolated model that enables us to look specifically at our molecules of interest, NMDARs and CaMKII. The report aims to answer three main questions which should address: the validity of our model against previous knowledge, the effects of sub-cellular localization on CaMKII and the effects on CaMKII by abolishing CaMKII/NMDAR binding. For the first question, we compared results with published literature. Secondly, counting boxes were added to the cell to assess if PSD regions were associated with higher molecule levels compared to cytosolic regions. Lastly, a mutant model was created to account for effects of CaMKII/NMDAR binding impairments. These experiments found that our model is consistent with what is known about sequence of molecule reactions and timeline of CaMKII activation. We could not conclude that space affects CaMKII activity as suggested, but we found that abolishing the interaction between NMDARs and CaMKII increased levels of free, phosphorylated CaMKII. This item supersedes and replaces the one which can be found at http://hdl.handle.net/10283/2726.
description: This fileset contains three zip archives: (1) "Mutant and WT models.zip" (which was *not* included in http://hdl.handle.net/10283/2726) ... and the following two zip archives which *were* present in the earlier version http://hdl.handle.net/10283/2726: (2) "Postsynaptic cell, mutant NMDAR-CaMKII interactions.zip" (3) "Postsynaptic cell, NMDAR-CaMKII interactions.zip"
DOI: 10.7488/ds/2112
title: A high resolution atlas of gene expression in the domestic sheep (Ovis aries)

description: Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of guilt by association was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.
description: This dataset contains three .txt files - S1_Dataset.txt, S2_Dataset.txt and S3_Dataset.txt - corresponding to three supplemental files published as Clark, et al. (2017) A high resolution atlas of gene expression in the domestic sheep (Ovis aries). These supplemental files are expression atlases, respectively listing the: (1) expression level per gene per tissue per replicate, (2) average expression level per tissue per developmental stage, and (3) female:male expression ratio per gene. In all cases, expression level is quantified as transcripts per million (TPM).
DOI: 10.7488/ds/2342
title: Multi-snapshot Gel Electrophoresis Traces

description: Multi-snapshot gel-electrophoresis data, acquired in the studies of improving gel electrophoresis resolution.
DOI: 10.7488/ds/2104
title: Stabilization of ammonia-rich hydrate inside icy planets

description: The interior structure of the giant ice planets Uranus and Neptune, but also of newly discovered exoplanets, is loosely constrained, because limited observational data can be satisfied with various interior models. Although it is known that their mantles comprise large amounts of water, ammonia, and methane ices, it is unclear how these organize themselves within the planets -- as homogeneous mixtures, with continuous concentration gradients, or as well-separated layers of specific composition. While individual ices have been studied very detailed under pressure, the properties of their mixtures are much less explored. We show here, using first-principles calculations, that the 2:1 ammonia hydrate, (H2O)(NH3)2, is stabilized at icy planet mantle conditions due to a remarkable structural evolution. Above 65 GPa, we predict it to transform from a hydrogen-bonded molecular solid into a fully ionic phase O2-(NH4+)2, where all water molecules are completely deprotonated, an unexpected bonding phenomenon not seen before. Ammonia hemihydrate is stable in a sequence of ionic phases up to 500 GPa, pressures found deep within Neptune-like planets, and thus at higher pressures than any other ammonia-water mixture. This suggests it precipitates out of any ammonia-water mixture at sufficiently high pressures and thus forms an important component of icy planets.
description: See Readme file.
DOI: 10.7488/ds/2116
title: Osmotaxis in E. coli through changes in motor speed - Osmotic shock dataset

description: Osmotic shock data presented in Figure 2 and 3 of the paper: "Osmotaxis in E. coli through changes in motor speed" (in press). These are raw (X,Y) voltages from the position sensitive detector as decribed in the Methods section of the paper.
description: Dataset contains 69 .zip archives, each containing a single cell (single motor) rotation measurement. A single measurement contains 120 or more text files ordered chronologically, in order of an ascending integer count.
DOI: 10.7488/ds/2581
title: Genetic and epigenetic architectures of neurological protein biomarkers in the Lothian Birth Cohort 1936 - EWAS

description: Data supporting the paper Hillary et al. "Genetic and epigenetic architectures of neurological protein biomarkers in the Lothian Birth Cohort 1936" (In submission). Specifically EWAS proteins.
DOI: 10.7488/ds/2099
title: SUPERSEDED - Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/2296. ## The cow rumen is a specialised organ adapted for the efficient breakdown of plant material into energy and nutrients, and it is the rumen microbiome that encodes the enzymes responsible. Many of these enzymes are of huge industrial interest. Despite this, rumen microbes are under-represented in the public databases. Here we present 220 high quality bacterial and archaeal genomes assembled directly from 768 gigabases of rumen metagenomic sequence data. Comparative analysis with current publicly available genomes reveals that the majority of these represent previously unsequenced strains and species of bacteria and archaea. The genomes contain over 13,000 proteins predicted to be involved in carbohydrate metabolism, over 90% of which do not have a good match in the public databases. Inclusion of the 220 genomes presented here improves metagenomic read classification by 2-3-fold, both in our data and in other publicly available rumen datasets. This release improves the coverage of rumen microbes in the public databases, and represents a hugely valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome.
DOI: 10.7488/ds/98
title: QUANGO Watch - Survey of non-elected public bodies in Scotland, 1995

description: Nearly 500 non-departmental public bodies in Scotland were surveyed in late 1995, having been identified from publications such as HMSO's 'Public Bodies' and 'Scottish Regions'. One organisation questionnaire was sent initially, then, if the organisation fitted the 'quango' profile, a further organisation questionnaire was sent together with board member questionnaires. A QUANGO is a Quasi-Autonomous Non-Governmental Organisation. The replies were entered into two databases; one for organisations and one for board members. The databases contain details of over 250 organisations and approximately 600 individual members. The criteria for inclusion in the database are that the organisation receives public funds which it also disburses and that it's board members are not elected.
description: Raw ASCII members and quangos data files, equivalent data files in MS-Word (.doc). 2 x Perl script set-up files and ASCII README file (containing information about resurrecting the content in a web environment)
DOI: 10.7488/ds/1455
title: Cytokine stimulation of canine chondrocytes and osteoblasts
title: Joint Cells Stimulated with Cytokines (As in abstract)

description: In vitro modelling of osteoarthritis typically uses cytokines to induce a catabolic phenotype in joint cells. This model was used to identify the response to a cytokine parameter identified as most representative of early stage osteoarthritis. Canine cells were used, isolated from the humeral head of post-mortem subjects. The cartilage cells were stimulated with 5 ng/ml of IL8 for 2 hours, whilst the osteoblasts were stimulated with 500 pg/mL of IL1 and 500 pg/mL of IL8. After the indicated culture time, RNA was extracted and a microarray was performed to identify gene expression changes.
description: Files are .CEL format produced during Affymetrix Microarray Experiments. It is a widely used format for these experiments. A number of software packages are capable of opening these files, including Affymetrix Expression Console and Partek Genomics Suite.
DOI: 10.7488/ds/1459
title: Cyclic compression of canine joint cells - microarray data
title: Canine chondrocytes and osteoblasts cyclically compressed

description: Cells are agarose embedded and cyclically compressed on FXC compression bioreactor for 4 hours followed by 24 hours of recovery incubation. RNA extracted according to Bougault et al (2008) and canine microarray performed
DOI: 10.7488/ds/2419
title: A high resolution economic density zone map of Europe

description: Available data for gross domestic product (GDP) and population density are useful for defining divisions in socio-economic gradients across Europe, since economic power and human population pressure are recognised as two of the most critical factors causing ecosystem changes. To overcome both the limitations in data availability and in the distortions caused by using administrative regions, we decided to base the socio-economic dimension on an economic density indicator, defined as the income generated per square kilometre (€ km−2), which can be mapped at a 1km2 spatial resolution. Economic density forms an integrative indicator that is based on two key drivers that were identified above: economic power and human population pressure. The indicator, which has been used to rank countries by their level of development, can be considered a crude measure for impacts on the environment caused by economic activity. An economic density map (€ km−2) at 1 km2 spatial resolution was constructed by multiplying economic power (€ person−1) with population density (person km−2). Subsequent logarithmic divisions resulted in an aggregated map of four economic density zones. Although the map has a fine spatial resolution it has to be realised that they form a spatial disaggregation of coarser census statistics. Importantly, the finer resolution discerns regional gradients in human activity that are required for many environmental studies, whilst broad gradients in economic activity is also treated consistently across Europe. GDP and population density data used were for the year 2001. The dataset consists of GeoTiff files of the economic density map and the four economic density zones.
description: This dataset contains three files: 1) readme.pdf explains the construction of the dataset; 2) GeoTiff.zip contains GIS GeoTiff files for the economic density map and the economic density zones; 3) thumbnail.jpg provides an image of the economic density map.
DOI: 10.7488/ds/2488
title: Droplet Coalescence is Initiated by Thermal Motion

description: This data folder contains LAMMPS input files for molecular dynamics (MD) simulations and post-processing codes used in the study: Perumanath et al. https://journals.aps.org/prl/accepted/f6070Y62F8b1396f66d06f366e35c46518e21059e .