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MS and NMR analysis of isotopically-labelled chloramination disinfection by-products
Get PDFFT-ICR MS and NMR analysis of an isotopically-labelled complex mixture of water disinfection by-products formed
by chloramine disinfection of model phenolic acids is described. A new molecular formula assignment procedure using the CoreMS Python library able to assign isotopically-enriched formulae is proposed. Statistical analysis of the assigned formulae showed that the number of compounds, the diversity of the mixture and the chlorine count increase during the chloramination reaction. The complex reaction mixture was investigated as a network of reactions using PageRank and Reverse PageRank algorithms. Independent of the MS signal intensities, the PageRank algorithm calculated the formulae with highest probability at convergence of the reaction; these were chlorinated and nitrated derivatives of the starting materials. The Reverse PageRank revealed that the most probable chemical transformations in the complex mixture were chlorination and decarboxylation. This agreed with the data obtained from INADEQUATE NMR spectra and literature data, indicating that the above approach could be applied to gain insight into reactions pathways taking place in complex mixtures without any prior knowledge
Analysis of AT7519 and acetaminophen in a mouse model of acute inflammation by LC-MS/MS
No full textThis dataset is the LC-MS/MS analysis of quantities of acetaminophen (APAP) and the drug AT7519 in a preclinical study, as described. Neutrophils are crucial innate immune cells required for host pathogen defense, with multifaceted roles, recognized both in disease pathogenesis and increasingly during tissue repair. Neutrophil actions during acetaminophen (APAP)-induced acute liver injury (ALI), the leading cause of acute liver failure-induced death in the western world, are controversial. Most publications indicate neutrophils contribute to APAP-ALI, but recent reports highlight their reparative function, and no studies evaluate both injury and repair times.
Through a combination of pharmacological (AT7519) neutrophil depletion and genetic prevention of formylated peptide receptor 1 induction of neutrophil activation and chemotaxis, we show that they contribute both to hepatic damage and repair during APAP-ALI. We highlight APAP-ALI neutrophil reparative roles include hepatic extracellular matrix remodeling, angiogenesis and an anti-inflammatory monocyte/macrophage phenotype. This study resolves the time dependent dichotomous role of neutrophils in APAP-ALI, and informs future therapeutic strategies to modulate neutrophil function in APAP-ALI.README_AT7519_APAP_Mouse_2024_NZM
Reviving the Trinity: Laser Scanning (LIDAR) Survey of Trinity College Kirk, Edinburgh, UK
Get PDFThe dataset consists of a group of point cloud models of Trinity College Kirk in Edinburgh, UK. These were generated from a laser scanning (LIDAR) survey conducted on 3rd July 2024. The survey was undertaken as part of the Reviving the Trinity Stones project, funded by the Old Edinburgh Club’s Jean Guild Award. The project’s Principal Investigator is Jill Harrison, an Honorary Research Associate at the Open University. This survey was conducted by James Hillson during the time was a Lecturer in Architectural History at the University of Edinburgh (2023-24), with the assistance of Jill Harrison, Lizzie Swarbrick and James Cook. The aim of the survey was to use laser scanning data to record the interior of Trinity College Kirk, with the aim of producing a set of point cloud models which could be used for future research. This dataset consists of the resulting RAW scanning data and processed point clouds, made publicly available in .e57 format for any non-commercial purpose. Further details regarding the dataset and the surveying process can be found in the accompanying .xlsx spreadsheet
Development of an impedance assay-based model highlighting the crucial role of hypermucoviscosity in hypervirulent K. pneumoniae pathophysiology
No full textBackground
Hypervirulent Klebsiella pneumoniae (HvKp) cause pyogenic liver abscesses (PLA) in otherwise healthy people. Molecular surveillance of HvKp reveal that the global dissemination of HvKp poses an urgent threat to human health. The key microbiological property associated with the hypervirulence is capsule production resulting in the hypermucoviscous phenotype necessary for infection. Whilst pathogenesis occurs in the liver, HvKp are thought to colonise the gut before causing disease. We sought to establish the pathogenic process as current studies provide no definitive causes to explain the switch from “gut-located HvKp” and “pathogenic liver abscess HvKp”.
Methods
Using HvKp strains, SGH10 and SGH10-p (loss of the virulence plasmid resulting in a no hypermucoviscosity) and Ecl8 (neither hypercapsulated or hypermucoviscous), we infected Caco2 (ileocolic cells), HepaRG (hepatocytes and cholangiocytes) and HUVEC (endothelial cells) cell lines. To dissect the cell-pathogen interactions, we employed the impedance- based assay, ECIS (Electrical cell-impedance system), to measure the variations in cellular electrical resistance in the presence or absence of pathogen. Pathogen-mediated damage when measured at low or high frequency using ECIS reflects damage to the integrity of the intracellular tight junctions or general cellular integrity respectively. Transepithelial (TEER) assays and western blot confirmation of the levels of tight junction scaffold protein, Zonula Occludens-1 (ZOI) were undertaken to confirm the ECIS data.
Results
SGH10 adhered and internalised less significantly to Caco2, HepaRG and HUVEC cell lines than SGH10-p and Ecl8. However, ECIS analyses shows that, despite being less adherent and internalised, SGH10 had a significantly greater effect on Caco2 cells by producing TJ disruption at least 2-3hrs relative to SGH10- and Ecl8. As expected, this trend was also mirrored in HepaRG. No differences were noted with HUVEC cells. TEER analyses and western blot analyses for ZO1 confirm the ECIS data in Caco2 cells where SGH10 results in significantly lower ZO1 TJ protein expression relative to SGH10p- and Ecl8.
Conclusions
Our data demonstrates that SGH10 elicits rapid damage of gut epithelial Caco2 cells by disrupting TJ interactions. This suggests that HvKp do not simply “colonise” the gut to gain access to the hepatic environment, providing new insights into the gut-liver axis in the pathophysiology of HvKp
Genotype data for commercial T451A Sasso chickens raised in Ethiopia
No full textThis dataset pertains to genotypes of individual Sasso chickens that were raised in semi-scavenging conditions in Ethiopia as part of a project collaboration with ILRI to study these commercial chickens. Data pertains to individual SNPs obtained from imputed sequences after quality control procedures (described in the attached readme.txt file).
This dataset contains the genotypes, in PLINK binary format, for 2,358 individuals genotypes with around 2.9 million SNPs across the genome. This data has been already through quality control procedures with the following steps: only bi-allelic markers, minor allele frequency threshold of 0.02, genotype and sample call rates of 0.9 and linkage disequilibrium pruning (r2 > 0.80). Also, samples with IBS > 0.98 were removed due to being considered as duplicates
Blood-based epigenome-wide analyses of chronic low-grade inflammation across diverse population cohorts - Bayesian EWAS and CRP Predictors
No full textThis dataset contains four files that are separated into two groups based on the analyses they inform in the manuscript by Hillary et al. entitled ‘Blood-based epigenome-wide analyses of chronic low-grade inflammation across diverse population cohorts’. The manuscript is available as: https://doi.org/10.1101/2023.11.02.23298000.
The first group contains one file called ‘crp_bayespr_basic_model_hillaryetal.csv’. This file contains the output of a Bayesian penalised regression model that was used to perform an epigenome-wide association study on blood C-reactive protein or CRP levels in Generation Scotland participants (N=17,936). The model examined the association between 752,722 CpG sites and log-transformed blood CRP levels. CRP levels were adjusted for age and sex prior to entry into the models. CpG beta-values were regressed on age, sex, estimated white blood cell proportions and experimental batch. Residuals were scaled to mean zero and unit variance and entered into the Bayesian model. The coefficients reflect these standardised variables. Results from a standard linear epigenome-wide association study are available on the EWAS Catalog.
The second group contains three files called ‘elastic_net_predictor_for_crp.csv’, ‘bayespr_predictor_for_crp.csv’ and ‘pca_elnet_prediction_object_for_crp.rds’. These files contain CpG sites and their weights from three different prediction methods. The methods were elastic net regression, Bayesian penalised regression and elastic net combined with principal component analysis, respectively. The predictors for C-reactive protein levels were trained in Generation Scotland and can be applied to external cohorts. Prediction scripts and the predictors (grouped together) are available in the following repository: https://doi.org/10.5281/zenodo.10154736
Kermadec 2021 refined earthquake catalogue and slip models
No full textEarthquake catalogue and slip models for 2021 Kermadec earthquake sequence. From Lythgoe et al, Earth and Planetary Science Letters (Accepted). The ruptures of the 2021 Mw7.4 and Mw8.1 doublet earthquake sequence in the Kermadec subduction zone are investigated and compared to the 1976 doublet that occurred at the same location. We find that although the 2021 mainshock likely re-ruptured the same asperity as the 1976 Mw7.9 event, the detailed slip distribution is different. Other ruptures in the doublets also differ in character and location. Our observations indicate the variability between large earthquakes on the same segment of the plate boundary in each earthquake cycle. This high-seismicity segment is coincident with an isolated forearc sedimentary basin, possibly formed by basal erosion related to seismogenesis, suggesting that seismic slip has persisted here for several million years. Refined up-dip aftershock and background seismicity focal mechanisms have a steeper dip angle than the slab interface, suggesting these events are located within the subducting oceanic slab, possibly forming a rougher plate interface that facilitates basal erosion. We conclude that the stress heterogeneity within this bounded seismogenic zone is long-lived and has produced a rich spectrum of earthquake ruptures
OxygenData4
No full textThis study focus on oxygen sensing which was based on luminescence quenching of metalloporphyrins by oxygen. Polymerisable metalloporphyrins were developed, and photo- polymerised at the end of an optical fibre. The fabricated oxygen sensors were dual emissions upon excitation, allowing self-referencing for ratiometric oxygen analysis. For oxygen measurements inside an ex vivo lung model, the polymer was immobilised at the distal end of an etched 4-core optical fibre, and showed robust oxygen measurements in agreement with on-bench calibration and the internal lung measurements. The sensor showed different oxygen emission signal at different oxygen concentrations, and this successful demonstration showed the potential for in vivo application of the sensor.
This dataset consists of 4 set of data (i.e. 4 separated files) namely OxygenData1, OxygenData2, OxygenData3 and OxygenData4. OxygenData1 is the oxygen sensor data on 19-cores optical fibre whereas OyxgenData2 is the oxygen sensor data on 4-cores optical fibre. Both data show fluorescence emission of oxygen sensor at different oxygen saturation. OxygenData3 contains absorbance data of compound palladium-metalloporphyrins (compound 3), and data analysis of oxygen sensor experiments conducted at different temperatures (emission-temperature dependent experiments), photostability of oxygen sensors and time response of the sensors. OxygenData4 is the emission data of oxygen sensor conducted inside the sheep lung for ex-vivo analysis
SHARE-MH
No full textThe SHARE Mental Health (SHARE-MH) cohort was established to address the paucity of clinical and genetic data available for mental health research. The cohort brings together detailed mental health questionnaire responses, routinely-collected electronic health data and genetic data to provide researchers with an unprecedented linkable dataset. This data represents the mental health survey that was sent to participants of the SHARE research register, and which forms the basis for the SHARE-MH cohort. It provides research-grade individual-level data on mental health and the experiences of those interacting with healthcare services.Readme.txt - An overview of the dataset and description of how it was created.
Processed Data Dictionary.csv - Data dictionary
SHARE-MH Mental Health Survey.pdf - Copy of the mental health survey presented to participants
LAG - Maˈya (Laganyan dialect: ISO 369-3: lcc, Glottocode: lege1241) segmented files
No full textThis dataset contains segmented audio files from two of the three recordings in the Maˈya (Laganyan dialect: ISO 369-3: lcc, Glottocode: lege1241) collection. The full collection is available here: https://datashare.ed.ac.uk/handle/10283/8591. These segmented files are designed to facilitate searches for a particular word or construction in the Laganyan Maˈya collection. Full information on how to navigate these segmented files using the filenames is given in the Documentation file. The audio files in this dataset come from recordings that were made between 1 and 2 March 2023, in Waisai town (Waigeo island, Raja Ampat regency, Southwest Papua province, Indonesia). This dataset relates to the British Academy Postdoctoral Fellowship 'Synchronic and diachronic investigations in Raja Ampat-South Halmahera, a little-known subbranch of Austronesian' (PF19\100004); additional fieldwork funds were provided by a British Academy Small Grant (SG1920\100342). Further deposits are available in the related DataShare sub-community (https://datashare.ed.ac.uk/handle/10283/8573)