Outbreak of SARS-CoV-2 in a teenage discotheque in Northern Ireland-November 2021.

OBJECTIVES: To report key findings associated with an outbreak of SARS-CoV-2 following a teenage disco in Northern Ireland. STUDY DESIGN: Observational case series. METHODS: A case was defined as an individual who attended the event with a positive SARS-CoV-2 result between 6th and 20th November 2021. Demographic and clinical information, including symptom status, date of onset and school attended, were recorded during contact tracing. Vaccination status was derived from the COVID-19 Vaccine Management System. Forty-five samples associated with the outbreak were sequenced as part of the NI Whole Genome Sequencing (WGS) programme. RESULTS: Only 2.4% (5/205) of cases received a COVID-19 vaccine more than 14 days before the event. 84.9% (174/205) had received no vaccine at the time of the event and 12.7% (26/205) had been vaccinated within 14 days, offering only limited disease protection. The AY4.2.2 lineage of two cases who attended the event after symptom onset was found in 69% of sequenced outbreak cases. CONCLUSIONS: This study demonstrates extensive COVID-19 transmission in largely unvaccinated teenagers in an indoor venue with limited social distancing, close social contact and mixing, limited ventilation and singing and shouting. Public Health authorities developing COVID-19 entertainment regulations should consider congregations of teenagers in these settings, especially if vaccination rates are low in this group or they are not eligible for vaccination at that time. Public communications should be developed to ensure young people with COVID-19 symptoms follow public guidance regarding self-isolation and in particular avoid indoor events with larger numbers.

Software tool for internal standard based normalization of lipids, and effect of data-processing strategies on resulting values.

BACKGROUND: Lipidomics, the comprehensive measurement of lipids within a biological system or substrate, is an emerging field with significant potential for improving clinical diagnosis and our understanding of health and disease. While lipids diverse biological roles contribute to their clinical utility, the diversity of lipid structure and concentrations prove to make lipidomics analytically challenging. Without internal standards to match each lipid species, researchers often apply individual internal standards to a broad range of related lipids. To aid in standardizing and automating this relative quantitation process, we developed LipidMatch Normalizer (LMN) http://secim.ufl.edu/secim-tools/ which can be used in most open source lipidomics workflows. RESULTS: LMN uses a ranking system (1-3) to assign lipid standards to target analytes. A ranking of 1 signifies that both the lipid class and adduct of the internal standard and target analyte match, while a ranking of 3 signifies that neither the adduct or class match. If multiple internal standards are provided for a lipid class, standards with the closest retention time to the target analyte will be chosen. The user can also signify which lipid classes an internal standard represents, for example indicating that ether-linked phosphatidylcholine can be semi-quantified using phosphatidylcholine. LMN is designed to work with any lipid identification software and feature finding software, and in this study is used to quantify lipids in NIST SRM 1950 human plasma annotated using LipidMatch and MZmine. CONCLUSIONS: LMN can be integrated into an open source workflow which completes all data processing steps including feature finding, annotation, and quantification for LC-MS/MS studies. Using LMN we determined that in certain cases the use of peak height versus peak area, certain adducts, and negative versus positive polarity data can have major effects on the final concentration obtained.

Examining the relationship between obesity and mental health outcomes among individuals admitted to a level I trauma centre.

The increased incidence of obesity in the general population translates into clinicians caring for an increased number of trauma patients with obesity. Previous research has documented the unique anatomical and physiological challenges that clinicians face when caring for trauma patients with obesity; however, little is known about psychological challenges that trauma patients with obesity may also experience in the months following injury. The aim of this study is to determine the relationship between obesity and (i) mental health, (ii) demographic and injury-related variables and (iii) quality-of-life outcomes among trauma patients between hospitalization and 3-months post-injury. This is a prospective, longitudinal study conducted between March 2012 and May 2014 at a single, level I trauma centre in the southwest United States. Inclusion criteria for this convenience sample consisted of patients who were admitted to the trauma or orthopaedic trauma service ≥24 h, medically stable, spoke English or Spanish and ≥18 years of age. In total, 455 eligible patients were consented and enrolled; 343 (70.87%) completed 3-month follow-up. The objective of this study is to investigate the relationship between obesity and mental health among trauma patients in the months following injury. Demographic and injury-related data were also collected; patients' height and weight were used to determine body mass index. Health outcomes were assessed during initial hospitalization and at 3-month follow-up and included depression, post-traumatic stress symptoms, pain and return to work. Prior to data collection, it was hypothesized that obesity would have a negative effect on mental health outcomes among patients 3 months post-injury. The final sample consisted of 343 participants; average age was 46.4 ± 17.3 years; majority male (n = 213, 63%) and Caucasian (n = 231, 69%). Patients with obesity had higher odds of screening positive for depression (odds ratio [OR] = 2.36, P = 0.02) and overweight patients had lower odds of returning to work (OR = 0.31, P = 0.01) 3 months post-injury compared to patients of normal weight (65% vs. 40%). No other significant differences were found. Results of the current study are novel in that they identify psychological challenges that overweight and trauma patients with obesity may experience. These results demonstrate the need for mental health professionals to be involved in follow-up care to extending in the months following injury.

LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data.

BACKGROUND: Lipids are ubiquitous and serve numerous biological functions; thus lipids have been shown to have great potential as candidates for elucidating biomarkers and pathway perturbations associated with disease. Methods expanding coverage of the lipidome increase the likelihood of biomarker discovery and could lead to more comprehensive understanding of disease etiology. RESULTS: We introduce LipidMatch, an R-based tool for lipid identification for liquid chromatography tandem mass spectrometry workflows. LipidMatch currently has over 250,000 lipid species spanning 56 lipid types contained in in silico fragmentation libraries. Unique fragmentation libraries, compared to other open source software, include oxidized lipids, bile acids, sphingosines, and previously uncharacterized adducts, including ammoniated cardiolipins. LipidMatch uses rule-based identification. For each lipid type, the user can select which fragments must be observed for identification. Rule-based identification allows for correct annotation of lipids based on the fragments observed, unlike typical identification based solely on spectral similarity scores, where over-reporting structural details that are not conferred by fragmentation data is common. Another unique feature of LipidMatch is ranking lipid identifications for a given feature by the sum of fragment intensities. For each lipid candidate, the intensities of experimental fragments with exact mass matches to expected in silico fragments are summed. The lipid identifications with the greatest summed intensity using this ranking algorithm were comparable to other lipid identification software annotations, MS-DIAL and Greazy. For example, for features with identifications from all 3 software, 92% of LipidMatch identifications by fatty acyl constituents were corroborated by at least one other software in positive mode and 98% in negative ion mode. CONCLUSIONS: LipidMatch allows users to annotate lipids across a wide range of high resolution tandem mass spectrometry experiments, including imaging experiments, direct infusion experiments, and experiments employing liquid chromatography. LipidMatch leverages the most extensive in silico fragmentation libraries of freely available software. When integrated into a larger lipidomics workflow, LipidMatch may increase the probability of finding lipid-based biomarkers and determining etiology of disease by covering a greater portion of the lipidome and using annotation which does not over-report biologically relevant structural details of identified lipid molecules.

A Robust Lipidomics Workflow for Mammalian Cells, Plasma, and Tissue Using Liquid-Chromatography High-Resolution Tandem Mass Spectrometry.

Lipids have been analyzed in applications including drug discovery, disease etiology elucidation, and natural products. The chemical and structural diversity of lipids requires a tailored lipidomics workflow for each sample type. Therefore, every protocol in the lipidomics workflow, especially those involving sample preparation, should be optimized to avoid the introduction of bias. The coupling of ultra-high-performance liquid chromatography (UHPLC) with high-resolution mass spectrometry (HRMS) allows for the separation and identification of lipids based on class and fatty acid acyl chain. This work provides a comprehensive untargeted lipidomics workflow that was optimized for various sample types (mammalian cells, plasma, and tissue) to balance extensive lipid coverage and specificity with high sample throughput. For identification purposes, both data-dependent and data-independent tandem mass spectrometric approaches were incorporated, providing more extensive lipid coverage. Popular open-source feature detection, data processing, and identification software are also outlined.

Expanding Lipidome Coverage Using LC-MS/MS Data-Dependent Acquisition with Automated Exclusion List Generation.

Untargeted omics analyses aim to comprehensively characterize biomolecules within a biological system. Changes in the presence or quantity of these biomolecules can indicate important biological perturbations, such as those caused by disease. With current technological advancements, the entire genome can now be sequenced; however, in the burgeoning fields of lipidomics, only a subset of lipids can be identified. The recent emergence of high resolution tandem mass spectrometry (HR-MS/MS), in combination with ultra-high performance liquid chromatography, has resulted in an increased coverage of the lipidome. Nevertheless, identifications from MS/MS are generally limited by the number of precursors that can be selected for fragmentation during chromatographic elution. Therefore, we developed the software IE-Omics to automate iterative exclusion (IE), where selected precursors using data-dependent topN analyses are excluded in sequential injections. In each sequential injection, unique precursors are fragmented until HR-MS/MS spectra of all ions above a user-defined intensity threshold are acquired. IE-Omics was applied to lipidomic analyses in Red Cross plasma and substantia nigra tissue. Coverage of the lipidome was drastically improved using IE. When applying IE-Omics to Red Cross plasma and substantia nigra lipid extracts in positive ion mode, 69% and 40% more molecular identifications were obtained, respectively. In addition, applying IE-Omics to a lipidomics workflow increased the coverage of trace species, including odd-chained and short-chained diacylglycerides and oxidized lipid species. By increasing the coverage of the lipidome, applying IE to a lipidomics workflow increases the probability of finding biomarkers and provides additional information for determining etiology of disease. Graphical Abstract ᅟ.

Lipotoxicity in steatohepatitis occurs despite an increase in tricarboxylic acid cycle activity.

The hepatic tricarboxylic acid (TCA) cycle is central to integrating macronutrient metabolism and is closely coupled to cellular respiration, free radical generation, and inflammation. Oxidative flux through the TCA cycle is induced during hepatic insulin resistance, in mice and humans with simple steatosis, reflecting early compensatory remodeling of mitochondrial energetics. We hypothesized that progressive severity of hepatic insulin resistance and the onset of nonalcoholic steatohepatitis (NASH) would impair oxidative flux through the hepatic TCA cycle. Mice (C57/BL6) were fed a high-trans-fat high-fructose diet (TFD) for 8 wk to induce simple steatosis and NASH by 24 wk. In vivo fasting hepatic mitochondrial fluxes were determined by(13)C-nuclear magnetic resonance (NMR)-based isotopomer analysis. Hepatic metabolic intermediates were quantified using mass spectrometry-based targeted metabolomics. Hepatic triglyceride accumulation and insulin resistance preceded alterations in mitochondrial metabolism, since TCA cycle fluxes remained normal during simple steatosis. However, mice with NASH had a twofold induction (P< 0.05) of mitochondrial fluxes (µmol/min) through the TCA cycle (2.6 ± 0.5 vs. 5.4 ± 0.6), anaplerosis (9.1 ± 1.2 vs. 16.9 ± 2.2), and pyruvate cycling (4.9 ± 1.0 vs. 11.1 ± 1.9) compared with their age-matched controls. Induction of the TCA cycle activity during NASH was concurrent with blunted ketogenesis and accumulation of hepatic diacylglycerols (DAGs), ceramides (Cer), and long-chain acylcarnitines, suggesting inefficient oxidation and disposal of excess free fatty acids (FFA). Sustained induction of mitochondrial TCA cycle failed to prevent accretion of "lipotoxic" metabolites in the liver and could hasten inflammation and the metabolic transition to NASH.

Comparison of blood plasma sample preparation methods for combined LC-MS lipidomics and metabolomics.

The goal of this research was to find the most comprehensive lipid extraction of blood plasma, while also providing adequate aqueous preparation for metabolite analysis. Comparisons have been made previously of the Folch, Bligh-Dyer, and Matyash lipid extractions; furthermore, this paper provides an additional comparison of a phospholipid removal plate for analysis. This plate was used for lipid extraction rather than its intended use in lipid removal for polar analysis, and it proves to be robust for targeted lipid analysis. Folch and Matyash provided reproducible recovery over a range of lipid classes, however the Matyash aqueous layer compared well to a typical methanol preparation for polar metabolite analysis. Thus, the Matyash method is the best choice for an untargeted biphasic extraction for metabolomics and lipidomics in blood plasma.

Pulmonary benign metastasising leiomyoma: response to treatment with goserelin.

Benign metastasising leiomyoma is a rare disease occurring predominantly in women of childbearing age and is hormonally influenced. The response of the disease to the luteinising hormone releasing hormone analogue goserelin is reported.

Metronidazole excretion in human milk and its effect on the suckling neonate.

1. Milk and plasma metronidazole and hydroxymetronidazole concentrations were measured in 12 breast-feeding patients following multiple doses of metronidazole (400 mg three times daily). All patients received metronidazole in combination with other broad spectrum antibiotics. 2. Plasma concentrations of both parent drug and metabolite were measured in seven suckling infants. Thirty-five infants were monitored for adverse reactions to maternal metronidazole therapy and two further groups of suckling infants, those whose mothers received either ampicillin alone or no drug therapy, were recruited as controls. 3. The mean milk to plasma ratio (M/P) was 0.9 for metronidazole and 0.76 for hydroxymetronidazole while the mean milk metronidazole concentrations (around Cmax) were 15.5 micrograms ml-1. The mean milk hydroxymetronidazole concentration was 5.7 micrograms ml-1. 4. Infant plasma metronidazole concentrations ranged from 1.27 micrograms ml-1 to 2.41 micrograms ml-1, and the corresponding hydroxymetronidazole concentrations from 1.1 to 2.4 micrograms ml-1. 5. There were no significant increases in adverse effects in infants which could be attributable to maternal metronidazole therapy. 6. Metronidazole was excreted in milk at concentrations which caused no serious reactions in the infants studied. The drug may therefore be administered at doses of 400 mg three times daily to mothers wishing to breast-feed their infants.

Correlation of scanning electron microscope and light microscope findings in uninflamed and pathologically involved human pulps.

The use of the scanning electron microscope has been investigated as a modality for pulpal diagnosis. Findings in ten normal, inflamed, and necrotic human pulps were correlated with light microscope findings. Inflammatory cell identification by SEM was found to be difficult. The inflammatory cells, especially lymphocytes, appeared in varying forms in SEM. Polymorphonuclear leukocytes and macrophages had similar surface structure. Degenerative changes of cells and fibers and dystrophic mineralizations were graphically depicted by SEM.

Ovarian pregnancies with Dalkon Shield IUCDs in situ: laparoscopic visualization.

Two ovarian pregnancies coexistent with intra-uterine contraceptive devices are described. In one case, the ovary appeared to contain a cyst at laparoscopy and rupture of the cyst and extrusion of the fetus were witnessed. In the second case, a hemorrhagic ovarian cyst bled at laparoscopy and laparotomy resulted in the diagnosis of ovarian pregnancy. These two cases reveal that laparoscopic examination could be misleading and result in inappropriate management if the diagnosis of ovarian pregnancy is not entertained. The cases described add to the growing number of reports of extrauterine pregnancies occurring in patients using intra-uterine contraceptive devices.