cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2346
title: Carbon Nanotube/PVA Aerogels Impregnated with PEI: Solid Adsorbents for CO2 Capture

description: Experimental data associated with the manuscript "Carbon Nanotube/PVA Aerogels Impregnated with PEI: Solid Adsorbents for CO2 Capture" A. V. Gromov, A. Kulur, J.A.A. Gibson, E. Mangano, S. Brandani, E.E.B. Campbell, accepted for publication in Sustainable Energy & Fuels.
description: The data are grouped in 2 excel files (labbook records and/or ASCII files imported to MS Excel 2013): - aerogel synthesis measuremens raw data; - CO2 uptake TGA raw data.
DOI: 10.7488/ds/3412
title: Data from paper: Reducing voltage-dependent potassium channel Kv3.4 levels ameliorates synapse loss in a mouse model of Alzheimer’s disease

description: Synapse loss is associated with cognitive decline in Alzheimer’s disease (AD) and owing to their plastic nature, synapses are an ideal target for therapeutic intervention. Oligomeric amyloid beta (Abeta) around amyloid plaques is known to contribute to synapse loss in mouse models and is associated with synapse loss in human AD brain tissue, but the mechanisms leading from Aβ to synapse loss remain unclear. Recent data suggest that the fast-activating and -inactivating voltage-gated potassium channel subtype 3.4 (Kv3.4) may play a role in Abeta-mediated neurotoxicity. Here, we tested whether this channel could also be involved in Aβ synaptotoxicity. Using adeno-associated virus and CRISPR (clustered regularly interspaced short palindromic repeats) technology, we reduced Kv3.4 expression in neurons of the somatosensory cortex of APP/PS1 mice. These mice express human familial AD associated mutations in amyloid precursor protein and presenilin 1 and develop amyloid plaques and plaque-associated synapse loss similar to that observed in AD brain. We observe that reducing Kv3.4 levels ameliorates dendritic spine loss and changes spine morphology compared to control virus. In support of translational relevance, Kv3.4 protein was observed in human AD and control brain and is associated with synapses in human iPSC-derived cortical neurons. Interestingly, we observe a decrease in Kv3.4 expression in iPSC derived cortical neurons when they are challenged with human Alzheimer’s disease derived brain homogenate either containing Abeta or immunodepleted to remove Abeta These results suggest that approaches to reduce Kv3.4 expression and/or function could be protective against Abeta-induced synaptic alterations. This dataset includes the .csv files and R studio scripts for generating graphs and statistical analyses for the published paper.
description: Yeap_stats_to_share_2.rmd - R studio notebook file ('R Markdown' format) that calls the other files for analysis; Kv3.4 intensity_v4.csv - intensity dataset called by R studio notebook; MR6_control_cohort-JY4.csv - spine density dataset called by R studio notebook; RNA_Results_KV3.4.csv - iPSC RNA dataset called by R studio notebook ; Tortuosity.csv - iPSC curvature dataset called by R studio notebook
DOI: 10.7488/ds/1499
title: Datasets supporting "Characterisation of a New Family of Carboxyl Esterases with an OsmC domain"

description: These data support the publication "Characterisation of a New Family of Carboxyl Esterases with an OsmC domain". Proteins in the serine esterase family are widely distributed in bacterial phyla and display activity against a range of biologically produced and chemically synthesized esters. A serine esterase from the psychrophilic bacterium Pseudoalteromonas arctica with a C-terminal OsmC-like domain was recently characterized; here we report on the identification and characterization of further putative esterases with OsmC-like domains constituting a new esterase family that is found in a variety of bacterial species from different environmental niches. All of these proteins contained the Ser-Asp-His motif common to serine esterases and a highly conserved pentapeptide nucleophilic elbow motif. We produced these proteins heterologously in Escherichia coli and demonstrate their activity against a range of esterase substrates. Two of the esterases characterized have activity of over two orders of magnitude higher than other members of the family, and are active over a wide temperature range. We determined the crystal structure of the esterase domain of the protein from Rhodothermus marinus and show that it conforms to the classical α/β hydrolase fold with an extended ‘lid’ region, which occludes the active site of the protein in the crystal. The expansion of characterized members of the esterase family and demonstration of activity over a wide range of temperatures could be of use in biotechnological applications such as the pharmaceutical, detergent, bioremediation and dairy industries.
DOI: 10.7488/ds/2772
title: Informal dwelling fires, 2009 - 2015, City of Cape Town

description: This data collates fires of an "informal" nature obtained from the City of Cape Town Fire Incidence database (https://web1.capetown.gov.za/web1/OpenDataPortal/DatasetDetail?DatasetName=Fire%20incidence). The dataset differs from the original in that: (1) only fires deemed to be informal in nature are included. This was established either through the categorisation of informal in the original data or where the description of what was burning included statements such as "wood and iron structures". The data is likely therefore to include both informal settlements as well as the so called "backyard dweller" where an informal structure is erected within a formal urban environment. (2) the number of structure affected are included as a separate field. This information was manually obtained through the original data's descriptive fields. (3) The location of the fire was reported in the original dataset as grid cells corresponding to a map reference used in the Cape Town book of maps, published by MapStudio. These grids (approximately 1 km x 1 km) are recorded as individual fields to allow for linking to GIS. It is acknowledged that this is not an accurate spatial method of capture since for some fires up to 6 map cells are given. Fields: Date: The date of the fire Structures: Number of structures affected by the fire described in point (2) above. Callers_Statement: The statement as recorded in the original dataset and used to determine if structures affected were "informal". Grid1...Grid6: Map reference as described in point (3) above. Weather: Weather conditions as recorded in the original dataset. Wind: As recorded in the original dataset. Temperature: As recorded in the original dataset. What_was_burning: As recorded in the original dataset and used to determine the number of structures affected and if fire affected informal structures. Damage: As recorded in the original dataset and used to determine the number of structures affected and if fire affected informal structures.
DOI: 10.7488/ds/2713
title: Houwers_data

description: Serological data from Houwers, D. J. and van der Molen, E. J. (1987). A five-year serological study of natural transmission of maedi-visna virus in a flock of sheep, completed with post mortem investigation. Journal of Veterinary Medicine, Series B, 34:421–431
DOI: 10.7488/ds/2714
title: Peterson_data

description: Serological data from Peterson, K., Stegeman, A., Colenbrander, B., and Houwers, D. J. (2007). Comparative quantification of the lateral transmission of Maedi Visna virus in two flocks of sheep of different genetic constitution. In Peterson, K. (2007). Dissertation. Aspects of reproduction and lentivirus epidemiology in small ruminants, pages 64–75. Utrecht University.
description: Peterson_data.xlsx
DOI: 10.7488/ds/3411
title: GenOMICC WGS summary statistics
title: GWAS summary statistics for GenOMICC all ancestries

description: GWAS summary statistics from 7,491 critically ill patients from COVID-19 and 48,400 population controls: European(EUR) 5,989/42,891; South Asian(SAS) 788/3,793; African(AFR) 440/1,350; East Asian(EAS) 274/366. GWAS models were calculated with SAIGE using a logisitic mixed-model regression. A trans-ancestry meta-analysis was performed using inverse-variant weighted fixed-effects. Ancestry-specific and trans-ancestry summary statistics are available with MAF&gt;0.01. TWAS was performed using GTEx v8 gene expression data for lung and blood and an all-tissue meta-analysis. Summary statistics for tissue-specific and meta-TWAS are available
description: The file README_GenOMICC.txt includes a description of datasets with column name definition. files genomic_[XX].txt.gz are severe COVID-19 GWAS summary statistics for specific ancestries where [XX] is the ancestry. genomicc_metaanalysis.gz is the meta-analysis of all ancestries files twas_[XX].csv are severe COVID-19 TWAS summary statistics from European population where [XX] is the tissue (models constructed from GTExv8 data). file metatwas.csv is an all-tissues meta-analysis using GTExv8
DOI: 10.7488/ds/2503
title: Use of Isotopically Labelled Substrates Reveals Kinetic Differences Between Human and Bacterial Serine Palmitoyltransferase

description: Please see the associated journal publication for contextual information.
DOI: 10.7488/ds/72
title: The reduced kinome of Ostreococcus tauri: core eukaryotic signalling components in a tractable model species

description: ## Background ## The current knowledge of eukaryote signalling originates from phenotypically diverse organisms. There is a pressing need to identify conserved signalling components among eukaryotes, which will lead to the transfer of knowledge across kingdoms. Two useful properties of a eukaryote model for signalling are (1) reduced signalling complexity, (2) conservation of signalling components. The alga Ostreococcus tauri is described as the smallest free-living eukaryote. With less than 8,000 genes, it represents a highly constrained genomic palette. ## Results ## Our survey revealed 133 protein kinases and 34 protein phosphatases (1.7% and 0.4% of the proteome). We conducted phospho-proteomic experiments and constructed domain structures and phylogenies for the catalytic protein-kinases. For each of the major kinases families we review the completeness and divergence of O. tauri representatives in comparison to the well-studied kinomes of the laboratory models Arabidopsis thaliana and Saccharomyces cerevisiae, and of Homo sapiens. Many kinase clades in O. tauri were reduced to a single member, in preference to the loss of family diversity, whereas TKL and ABC1 clades were expanded. We also identified kinases that have been lost in A. thaliana but retained in O. tauri. For three, contrasting eukaryotic pathways – TOR, MAPK, and the circadian clock – we established the subset of conserved components and demonstrate conserved sites of substrate phosphorylation and kinase motifs. ## Conclusions ## We conclude that O. tauri satisfies our two central requirements. Several of its kinases are more closely related to H. sapiens orthologs than S. cerevisiae is to H. sapiens. The greatly reduced kinome of O. tauri is therefore a suitable model for signalling in free-living eukaryotes.
DOI: 10.7488/ds/2436
title: Non-invasive 19F NMR analysis of a protein-templated N- acylhydrazone dynamic combinatorial library. OBC 2018

description: Supplementary data to support the following publication (abstract): Dynamic combinatorial chemistry (DCC) is a powerful tool to identify ligands for biological targets. We used 19F NMR as an in situ, non-invasive technique for measuring the composition of a dynamic combinatorial library (DCL) of N-acylhydrazones (NAHs). An NAH DCL, constructed from a fluoro-aromatic aldehyde and a small set of hydrazides, was targetted at ecFabH, an essential enzyme in bacterial fatty acid biosynthesis. Our NMR analysis identified a tert-butyl NAH as the best binder which was confirmed by enzymatic assay.
DOI: 10.7488/ds/2632
title: Pulsed laser-induced nucleation of sodium chlorate at high energy densities

description: The dataset consists of measurements of the numbers of crystals of sodium chlorate obtained following pulsed laser induced nucleation. Aqueous sodium chlorate in supersaturated aqueous solutions were irriadated with focused nanosecond laser pulses at high energy densities (420 kJ cm–2). On irradiation with a single laser pulse, optical breakdown was observed in the form of a luminous plasma, and numerous microbubbles were produced. Based on the observations, we estimate the energy threshold for optical breakdown in the solutions to be 70 J cm–2. Remarkably, even at high energy densities, single laser pulses produced on average only one or two crystals. The mean number of crystals obtained was 1.5 (532 nm) and 1.8 (1064 nm) per sample (3 cm3). The effect of left circularly polarized (LCP) and right circularly polarized (RCP) light on the nucleation of dextrorotatory (d) versus levorotatory (l) enantiomorphs of cubic (phase I) sodium chlorate crystals was investigated. No significant correlation between the helicity of circular polarization and the chirality of enantiomorph was observed.
DOI: 10.7488/ds/2804
title: Data relevant to the publication "Evaporation of Li@C60", by Campbell, Chandler, Schaub, EPJD

description: Data relevant to the publication "Evaporation of Li@C60" by Campbell, Chandler, Schaub, published in European Journal of Physics D (2020). Mass spectra as a function of temperature and ionising laser power.
DOI: 10.7488/ds/1517
title: On the role of impurity nanoparticles in laser-induced nucleation of ammonium chloride

description: Data on dynamic light scattering (DLS): raw correlation functions, fitted distributions, raw data and analysis of counts of nuclei, inductively coupled plasma (ICP) mass spectrometry and optical emission spectroscopy data.
description: Zipfile extracting to folder containing 7 files. 4 files are comma delimited (CSV). 2 CSV files contain data on dynamic light scattering (DLS): raw correlation functions, fitted distributions. 2 CSV files contain raw data and analysis of counts of nuclei. 3 files are portable document format (PDF) containing inductively coupled plasma (ICP) mass spectrometry and optical emission spectroscopy data.
DOI: 10.7488/ds/1692
title: Polarization independence of laser-induced nucleation in supersaturated aqueous urea solutions

description: Excel spreadsheet (including PDF copy) containing raw data on angles measured for laser induced nucleation of urea, as published by the authors in doi:10.1039/C6CP07997K
description: Excel spreadsheet (including PDF copy) containing raw data on angles measured for laser induced nucleation of urea, as published by the authors in doi:10.1039/C6CP07997K
DOI: 10.7488/ds/2467
title: A novel fluorescein-bisphosphonate based diagnostic tool for the detection of hydroxyapatite in both cell and tissue models

description: A rapid and efficient method for the detection of hydroxyapatite (HAP) has been developed which shows superiority to existing well-established methods. This fluorescein-bisphosphonate probe is highly selective for HAP over other calcium minerals and is capable of detecting lower levels of calcification in cellular models than either hydrochloric acid-based calcium leaching assays or the Alizarin S stain. The probe has been shown to be effective in both in vitro vascular calcification models and in vitro bone calcification models. Moreover we have demonstrated binding of this probe to vascular calcification in rat aorta and to areas of microcalcification, in human vascular tissue, beyond the resolution of computed tomography in human atherosclerotic plaques. Fluorescein-BP is therefore a highly sensitive and specific imaging probe for the detection of vascular calcification, with the potential to improve not only ex vivo assessments of HAP deposition but also the detection of vascular microcalcification in humans.
DOI: 10.7488/ds/1338
title: Dataset for paper 'Advances in electroanalysis, sensing and monitoring in molten salts'

description: Microelectrodes have a number of advantages over macroelectrodes for quantitative electroanalysis and monitoring, including reduced iR drop, high signal to noise and reduced sensitivity to convection. Their use in molten salts has been generally precluded by the combined materials challenges of stresses associated with thermal cycling and physical and corrosive chemical degradation at the relatively high temperatures involved. We have shown that microfabrication, employing high precision photolithographic patterning in combination with the controlled deposition of materials, can be used to successfully address these challenges. The resulting molten salt compatible microelectrodes (MSMs) enable prolonged quantitative microelectrode measurements in molten salts (MSs). This paper reports the fabrication of novel MSM disc electrodes, chosen because they have an established ambient analytical response. It includes a detailed set of electrochemical characterisation studies which demonstrate both their enhanced capability over macroelectrodes and over commercial glass pulled microelectrodes, and their ability to extract quantitative electroanalytical information from MS systems. MSM measurements are then used to demonstrate their potential for shedding new light on the fundamental properties of, and processes in, MSs, such as mass transport, charge transfer reaction rates and the selective plating/stripping and alloying reactions of liquid Bi and other metals; this is will underpin the development of enhanced MS industrial processes, including pyrochemical spent nuclear fuel reprocessing.
DOI: 10.7488/ds/2445
title: A catch-and-release approach to selective modification of accessible tyrosine residues

description: The tyrosine side chain is amphiphilic leading to significant variations in the surface exposure of tyrosine residues in the folded structure of a native sequence protein. This variability can be exploited to give residue-selective functionalization of a protein substrate by using a highly reactive diazonium group tethered to an agarose-based resin. This novel catch-and-release approach to protein modification has been demonstrated for proteins with accessible tyrosine residues, which are compared with a control group of proteins in which there are no accessible tyrosine residues. MS analysis of the modified proteins showed that functionalization was highly selective, but reactivity was further attenuated by the electrostatic environment of any individual residue. Automated screening of PDB structures allows identification of potential candidates for selective modification by comparison with the accessibility of the tyrosine residue in a benchmark peptide (GYG).
DOI: 10.7488/ds/2118
title: Data for "Controlled core-to-core photo-polymerisation – fabrication of an optical fibre-based pH sensor"

description: The fabrication of fluorescence-based pH sensors, embedded into etched pits of an optical fibre via highly controllable and spatially selective photo-polymerisation is described and the sensors validated.
description: File Name - Data Set Analyst 2017 Excel files that include raw data from manuscript - Controlled Core-to-Core Photo-polymerisation - Fabrication of an Optical Fibre-Based pH Sensor
DOI: 10.7488/ds/2611
title: Dual Killing Strategy: Photocatalytic Generation of Singlet Oxygen with Concomitant Pt(IV) Prodrug Activation
DOI: 10.7488/ds/2394
title: Data for Angle-resolved Photoelectron Spectroscopy and Scanning Tunnel Spectroscopy Studies of the Endohedral Fullerene Li@C60

description: Data associated to the manuscript "Angle-resolved Photoelectron Spectroscopy and Scanning Tunnel Spectroscopy Studies of the Endohedral Fullerene Li@C60". Included are: (i) the raw data files of the photoelectron VMI (Velocity Map Imaging) images of Li@C60 and C60 using femtosecond laser pulses at 267 nm, 400 nm, 540 nm and 600 nm, and (ii) the mass spectroscopy data associated with Figure 3. -------------------------------------------------- ## Figures 4, 9, 10, S4, S5, S6, S7, S8, S9, S10, S11 - STM and DFT data by Dr Renald Schaub and coworkers ## STM raw data files can be opened using either (1) Createc Analysis Software, or (2) WSxM. Data files contain raw STM data (as acquired, i.e. unprocessed). For the purpose of this publication, data were processed through a home-developed analysis software based on Igor Pro.
description: Included are: (i) the raw data files of the photoelectron VMI (Velocity Map Imaging) images of Li@C60 and C60 using femtosecond laser pulses at 267 nm, 400 nm, 540 nm and 600 nm, and (ii) the mass spectroscopy data associated with Figure 3. -------------------------------------------------- ## Figures 4, 9, 10, S4, S5, S6, S7, S8, S9, S10, S11 - STM and DFT data by Dr Renald Schaub and coworkers ## STM raw data files can be opened using either (1) Createc Analysis Software, or (2) WSxM. Data files contain raw STM data (as acquired, i.e. unprocessed). For the purpose of this publication, data were processed through a home-developed analysis software based on Igor Pro.
DOI: 10.7488/ds/2364
title: Data for Blister-Based-Laser-Induced-Forward-Transfer: A Non-Contact, Dry Laser-Based Transfer Method for Nanomaterials

description: Data for: "Blister-Based-Laser-Induced-Forward-Transfer: A Non-Contact, Dry Laser-Based Transfer Method for Nanomaterials". We show that blister-based-laser-induced forward transfer (BB-LIFT) can be used to cleanly desorb and transfer nano- and micro-scale particles between substrates without exposing the particles to the laser radiation or to any chemical treatment that could damage the intrinsic electronic and optical properties of the materials. The technique uses laser pulses to induce the rapid formation of a blister on a thin metal layer deposited on glass via ablation at the metal/glass interface. Femtosecond laser pulses are advantageous for forming beams of molecules or small nanoparticles with well-defined velocity and narrow angular distributions. Both fs and ns laser pulses can be used to cleanly transfer larger nanoparticles including relatively fragile monolayer 2D transition metal dichalcogenide crystals and for direct transfer of nanoparticles from chemical vapour deposition (CVD) growth substrates, although the mechanisms for inducing blister formation are different. Data Set contains raw data pertaining to the measured velocity distributions, radial distributions and Raman spectra of the transferred nanomaterials.
description: All data is within an excel file with separate worksheets for the different data sets. The name of the worksheet describes the content.
DOI: 10.7488/ds/2392
title: Data associated with manuscript: A tripod anchor offers improved robustness of peptide-based electrochemical biosensors

description: Data associated to manuscript. Includes set of tables containing the data used for obtaining figures and results.
description: Design and evaluation of a robust electrochemical biosensor for protease activity employing self-assembled monolayers (SAM). A peptide-based probe has been designed and synthesised endowed with a tripod anchor for improved stability. A side-by-side comparison has been carried out with a monoanchor analogue.
DOI: 10.7488/ds/2066
title: Dataset for "BIMODAL FLUOROGENIC SENSING OF MATRIX PROTEOLYTIC SIGNATURES"

description: Dataset related to a bimodal fluorescent reporter for the simultaneous and highly specific detection of two independent protease families of biological importance, based on a dual, multiplexing, peptide FRET system.