Quantification of damage to plasmid DNA from 35 MeV electrons, 228 MeV protons and 300 kVp X-rays in varying hydroxyl radical scavenging environments.

The pBR322 plasmid DNA was irradiated with 35 MeV electrons, 228 MeV protons and 300 kVp X-rays to quantify DNA damage and make comparisons of DNA damage between radiation modalities. Plasmid was irradiated in a medium containing hydroxyl radical scavengers in varying concentrations. This altered the amount of indirect hydroxyl-mediated DNA damage, to create an environment that is more closely associated with a biological cell.

Breath Biopsy to Identify Exhaled Volatile Organic Compounds Biomarkers for Liver Cirrhosis Detection.

Background And Aims: The prevalence of chronic liver disease in adults exceeds 30% in some countries and there is significant interest in developing tests and treatments to help control disease progression and reduce healthcare burden. Breath is a rich sampling matrix that offers non-invasive solutions suitable for early-stage detection and disease monitoring. Having previously investigated targeted analysis of a single biomarker, here we investigated a multiparametric approach to breath testing that would provide more robust and reliable results for clinical use.

The influence of neighbourhood equity on parkrunners in a British city.

Physical activity benefits both physical and mental health. Specific events may augment participation in physical activity at a population level. Parkrun is a popular, free, weekly, timed 5 km run or walk in public spaces located in five continents.

C-SEQer: An Open-Source de Novo Glycan Identification Tool in C+.

Glycans play an important role in many biochemical processes, including protein function and cell signaling. Mass spectrometry (MS) provides the potential for high-throughput, high-sensitivity analysis of glycans but relies heavily on computational interpretation of experimental results. Open-source, stand-alone algorithms for de novo glycan MS analysis are few.

Breath Biopsy Assessment of Liver Disease Using an Exogenous Volatile Organic Compound-Toward Improved Detection of Liver Impairment.

Introduction: Liver cirrhosis and its complication - hepatocellular carcinoma (HCC) - have been associated with increased exhaled limonene. It is currently unclear whether this increase is more strongly associated with the presence of HCC or with the severity of liver dysfunction.

Methods: We compared the exhaled breath of 40 controls, 32 cirrhotic patients, and 12 cirrhotic patients with HCC using the Breath Biopsy platform.

XFlow: An algorithm for extracting ion chromatograms.

Mass spectrometry is a fundamental tool for modern proteomics. The increasing availability of mass spectrometry data paired with the increasing sensitivity and fidelity of the instruments necessitates new and more potent analytical methods. To that end, we have created and present XFlow, a feature detection algorithm for extracting ion chromatograms from MS1 LC-MS data.

A web-based system for creating, viewing, and editing precursor mass spectrometry ground truth data.

Background: Mass spectrometry (MS) uses mass-to-charge ratios of measured particles to decode the identities and quantities of molecules in a sample. Interpretation of raw MS depends upon data processing algorithms that render it human-interpretable. Quantitative MS workflows are complex experimental chains and it is crucial to know the performance and bias of each data processing method as they impact accuracy, coverage, and statistical significance of the result.

Exploring Perspectives on Antimicrobial Use in Livestock: A Mixed-Methods Study of UK Pig Farmers.

Increasing levels of antimicrobial resistance in human and veterinary medicine have raised concerns over the irresponsible use of antimicrobials. The role of administering antimicrobials in food producing animals most frequently falls to the farmer, therefore it is essential that their use of antimicrobials is both optimal and responsible. This study sought in-depth information on the drivers behind antimicrobial use behaviors and farmer attitudes to responsible use using a mixed-methodological approach.

Identifying critically important vascular access outcomes for trials in haemodialysis: an international survey with patients, caregivers and health professionals.

Background: Vascular access outcomes reported across haemodialysis (HD) trials are numerous, heterogeneous and not always relevant to patients and clinicians. This study aimed to identify critically important vascular access outcomes.

Method: Outcomes derived from a systematic review, multi-disciplinary expert panel and patient input were included in a multilanguage online survey.

XNet: A Bayesian Approach to Extracted Ion Chromatogram Clustering for Precursor Mass Spectrometry Data.

Liquid chromatography mass spectrometry is a popular technique for high throughput analysis of biological samples. Identification and quantification of molecular species via mass spectrometry output requires postexperimental computational analysis of the raw instrument output. While tandem mass spectrometry remains a primary method for identification and quantification, species-resolved precursor data provides a rich source of unexploited information.

A Peptide-Level Fully Annotated Data Set for Quantitative Evaluation of Precursor-Aware Mass Spectrometry Data Processing Algorithms.

Modern label-free quantitative mass spectrometry workflows are complex experimental chains for devising the composition of biological samples. With benchtop and in silico experimental steps that each have a significant effect on the accuracy, coverage, and statistical significance of the study result, it is crucial to understand the efficacy and biases of each protocol decision. Although many studies have been conducted on wet lab experimental protocols, postacquisition data processing methods have not been adequately evaluated in large part due to a lack of available ground truth data.

Quantitative Evaluation of Algorithms for Isotopic Envelope Extraction via Extracted Ion Chromatogram Clustering.

LC-MS precursor (MS1) data are used increasingly often in conjunction with MS/MS data for the quantification, validation, and other computational mass spectrometry tasks. The efficacy of MS1 data on downstream tasks is dependent on the coverage and accuracy of the MS1 isotopic envelope extraction algorithms that delineate them from the dense backgrounds common in complex samples. Although several algorithms for extracted ion chromatogram (XIC) clustering exist, their performance has not yet been quantified, in part due to the difficulty of obtaining, isolating, and running some algorithms and in part due to the lack of quantitative MS1 ground truth.

Novel application of the matched case-control design to compare food supply chains during an O157 outbreak, United Kingdom, 2016.

There is a need for innovative methods to investigate outbreaks of food-borne infection linked to produce with a complex distribution network. The investigation of a large outbreak of O157 PT34 infection in the United Kingdom in 2016 indicated that catering venues associated with multiple cases had used salad leaves sourced from one supplier. Our aim was to investigate whether catering venues linked to cases were more likely to have used salad leaves from this supplier.

Fast, axis-agnostic, dynamically summarized storage and retrieval for mass spectrometry data.

Mass spectrometry, a popular technique for elucidating the molecular contents of experimental samples, creates data sets comprised of millions of three-dimensional (m/z, retention time, intensity) data points that correspond to the types and quantities of analyzed molecules. Open and commercial MS data formats are arranged by retention time, creating latency when accessing data across multiple m/z. Existing MS storage and retrieval methods have been developed to overcome the limitations of retention time-based data formats, but do not provide certain features such as dynamic summarization and storage and retrieval of point meta-data (such as signal cluster membership), precluding efficient viewing applications and certain data-processing approaches.

JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals.

Background: Despite the ubiquity of mass spectrometry (MS), data processing tools can be surprisingly limited. To date, there is no stand-alone, cross-platform 3-D visualizer for MS data. Available visualization toolkits require large libraries with multiple dependencies and are not well suited for custom MS data processing modules, such as MS storage systems or data processing algorithms.

Scientific Opinion of the PPR Panel on the follow-up of the findings of the External Scientific Report 'Literature review of epidemiological studies linking exposure to pesticides and health effects'.

In 2013, EFSA published a comprehensive systematic review of epidemiological studies published from 2006 to 2012 investigating the association between pesticide exposure and many health outcomes. Despite the considerable amount of epidemiological information available, the quality of much of this evidence was rather low and many limitations likely affect the results so firm conclusions cannot be drawn. Studies that do not meet the 'recognised standards' mentioned in the Regulation (EU) No 1107/2009 are thus not suited for risk assessment.

Randomised clinical trial evaluating the effect of different timing and number of fixed timed artificial inseminations, following a seven-day progesterone-based protocol, on pregnancy outcomes in UK dairy heifers.

The objective of this study was to determine the effect on pregnancy outcome of either inseminating heifers twice (at 48 and 72 hours after withdrawal of a controlled internal drug release insert (CIDR) containing progesterone) or once (56 hours after CIDR withdrawal) following a seven-day CIDR synchronisation protocol. Dairy heifers (n=267) from five farms, with an age range of 388-736 days, were randomly assigned to one of two treatment groups (group A heifers were inseminated twice; group B heifers were inseminated once). Both groups received a CIDR on day (D) 0 and an intramuscular injection of d-cloprostenol on D6; the CIDR was withdrawn on D7.

Live births after embryo selection using morphokinetics versus conventional morphology: a retrospective analysis.

The increasing corpus of clinical studies using time-lapse imaging for embryo selection demonstrates considerable variation in study protocols and only limited-sized study cohorts. Outcome measures are based on implantation or clinical pregnancy; some predict blastulation from early cleavage-stage data, and few have evaluated live birth. Erroneously, most studies treat the embryos as independent variables and do not include patient or treatment variables in the statistical analyses.