A phylogenetic approach to comparative genomics.

Comparative genomics, whereby the genomes of different species are compared, has the potential to address broad and fundamental questions at the intersection of genetics and evolution. However, species, genomes and genes cannot be considered as independent data points within statistical tests. Closely related species tend to be similar because they share genes by common descent, which must be accounted for in analyses.

Mortality prediction after major surgery in a mixed population through machine learning: a multi-objective symbolic regression approach.

Introduction: Understanding 1-year mortality following major surgery offers valuable insights into patient outcomes and the quality of peri-operative care. Few models exist that predict 1-year mortality accurately. This study aimed to develop a predictive model for 1-year mortality in patients undergoing complex non-cardiac surgery using a novel machine-learning technique called multi-objective symbolic regression.

Does it run in the family? - Improving radiological risk assessment in the coastal environment using taxonomic and phylogenetic perspectives in macroalgae species.

Marine macroalgae are widely used indicator species for monitoring environmental radioactivity. Empirical studies have demonstrated a range in radionuclide transfer coefficients, or concentration ratios (CRs), between taxonomic groups, however the CR values used for dose estimation assume that macroalgae are a homogenous group, represented by a single CR. This study demonstrates the presence of a taxonomic signal in macroalgae CRs for multiple anthropogenic and naturally occurring radionuclides (Cs, Am, Pu, Po) based on a collation of available data.

Exploring the use of Rasch modelling in "common content" items for multi-site and multi-year assessment.

Rasch modelling is a powerful tool for evaluating item performance, measuring drift in difficulty over time, and comparing students who sat assessments at different times or at different sites. Here, we use data from thirty UK medical schools to describe the benefits of Rasch modelling in quality assurance and the barriers to using it. Sixty "common content" multiple choice items were offered to all UK medical schools in 2016-17, and a further sixty in 2017-18, with five available in both years.

Bacterial lifestyle shapes pangenomes.

Pangenomes vary across bacteria. Some species have fluid pangenomes, with a high proportion of genes varying between individual genomes. Other species have less fluid pangenomes, with different genomes tending to contain the same genes.

Evaluation of a hospital-initiated tobacco dependence treatment service: uptake, smoking cessation, readmission and mortality.

Background: The National Health Service in England aims to implement tobacco dependency treatment services in all hospitals by 2024. We aimed to assess the uptake of a new service, adapted from the Ottawa Model of Smoking Cessation, and its impact on 6-month quit rates and readmission or death at 1-year follow-up.

Methods: We conducted a pragmatic service evaluation of a tobacco dependency service implemented among 2067 patients who smoked who were admitted to 2 acute hospitals in London, England, over a 12-month period from July 2020.

Genes for cooperation are not more likely to be carried by plasmids.

Cooperation is prevalent across bacteria, but risks being exploited by non-cooperative cheats. Horizontal gene transfer, particularly via plasmids, has been suggested as a mechanism to stabilize cooperation. A key prediction of this hypothesis is that genes which are more likely to be transferred, such as those on plasmids, should be more likely to code for cooperative traits.

Preoperative aerobic fitness and perioperative outcomes in patients undergoing cystectomy before and after implementation of a national lockdown.

Background: Lower fitness is a predictor of adverse outcomes after radical cystectomy. Lockdown measures during the COVID-19 pandemic affected daily physical activity. We hypothesised that lockdown during the pandemic was associated with a reduction in preoperative aerobic fitness and an increase in postoperative complications in patients undergoing radical cystectomy.

SOCfinder: a genomic tool for identifying social genes in bacteria.

Bacteria cooperate by working collaboratively to defend their colonies, share nutrients, and resist antibiotics. Nevertheless, our understanding of these remarkable behaviours primarily comes from studying a few well-characterized species. Consequently, there is a significant gap in our understanding of microbial social traits, particularly in natural environments.

Signatures of kin selection in a natural population of the bacteria .

Laboratory experiments have suggested that bacteria perform a range of cooperative behaviors, which are favored because they are directed toward relatives (kin selection). However, there is a lack of evidence for cooperation and kin selection in natural bacterial populations. Molecular population genetics offers a promising method to study natural populations because the theory predicts that kin selection will lead to relaxed selection, which will result in increased polymorphism and divergence at cooperative genes.

Development and implementation of the lung volume reduction pulmonary rehabilitation tool to identify eligibility for lung volume reduction in people with chronic obstructive pulmonary disease during pulmonary rehabilitation.

Background: Completion of pulmonary rehabilitation is recognised in chronic obstructive pulmonary disease (COPD) guidelines as a key opportunity to consider systematically whether a respiratory review to assess potential suitability for a lung volume reduction (LVR) procedure might be appropriate. We describe the development of a simple decision-support tool (the LVR-PR tool) to aid clinicians working in pulmonary rehabilitation, to operationalise this process.

Methods: We took an iterative mixed methods approach, which was partnership-based and involved an initial consensus survey, focus groups and an observational study cohort at multiple pulmonary rehabilitation centres.

Enhancing radiological monitoring of Cs in coastal environments using taxonomic signals in brown seaweeds.

With the rapidly expanding global nuclear industry, more efficient and direct radiological monitoring approaches are needed to ensure the associated environmental health impacts and risk remain fully assessed and undertaken as robustly as possible. Conventionally, radiological monitoring in the environment consists of measuring a wide range of anthropogenically enhanced radionuclides present in selected environmental matrices and using generic transfer values for modelling and prediction that are not necessarily suitable in some situations. Previous studies have found links between taxonomy and radionuclide uptake in terrestrial plants and freshwater fish, but the marine context remains relatively unexplored.

Tissue-Specific RNA Localization in the Uterus During Implantation, Decidualization and Placentation: Technical Nuances of Various Labeling Approaches.

In situ hybridization (ISH) is a sensitive method used to localize a specific sequence of DNA or RNA in biological samples, including cells, tissue sections or whole organs. RNA ISH can be used to determine spatial gene expression using a single-stranded probe with a reverse-complementary sequence. Cell-specific gene expression has been studied using mRNA and protein levels.

Is cooperation favored by horizontal gene transfer?

It has been hypothesized that horizontal gene transfer on plasmids can facilitate the evolution of cooperation, by allowing genes to jump between bacteria, and hence increase genetic relatedness at the cooperative loci. However, we show theoretically that horizontal gene transfer only appreciably increases relatedness when plasmids are rare, where there are many plasmid-free cells available to infect (many opportunities for horizontal gene transfer). In contrast, when plasmids are common, there are few opportunities for horizontal gene transfer, meaning relatedness is not appreciably increased, and so cooperation is not favored.

An unanticipated discourse of HB-EGF with VANGL2 signaling during embryo implantation.

Implantation is the first direct encounter between the embryo and uterus during pregnancy, and is the earliest known molecular signaling for embryo-uterine crosstalk during implantation. The downstream effectors of heparin-binding EGF (HB-EGF) in implantation remain elusive due to the complexity of EGF receptor family. This study shows that the formation of implantation chamber (crypt) triggered by HB-EGF is disrupted by uterine deletion of a key planar cell polarity component (PCP).

Heart Rate Recovery Assessed by Cardiopulmonary Exercise Testing in Patients with Cardiovascular Disease: Relationship with Prognosis.

Background: The use of exercise testing has expanded in recent decades and there is a wealth of information examining the prognostic significance of exercise variables, such as peak oxygen consumption or ventilatory measures whilst exercising. However, a paucity of research has investigated the use of recovery-derived parameters after exercise cessation. Heart rate recovery (HRR) has been considered a measure of the function of the autonomic nervous system and its dysfunction is associated with cardiovascular risk.

Dietary Costs among Midwestern Adult Food-Pantry Users by Food-Security Status.

Evidence of the relationship between dietary cost, diet quality, and socio-economic status is mixed. No studies have directly evaluated food-security status and dietary cost. This study investigated whether food-pantry clients with low and very low food-security status had less expensive daily diets than food-secure clients by comparing total cost, cost per gram, and cost per calorie of total daily dietary intake both per person and by individual food item, followed by evaluations of each food group.

Gene transferability and sociality do not correlate with gene connectivity.

The connectivity of a gene, defined as the number of interactions a gene's product has with other genes' products, is a key characteristic of a gene. In prokaryotes, the complexity hypothesis predicts that genes which undergo more frequent horizontal transfer will be less connected than genes which are only very rarely transferred. We tested the role of horizontal gene transfer, and other potentially important factors, by examining the connectivity of chromosomal and plasmid genes, across 134 diverse prokaryotic species.

Physicians' Conceptions of the Dying Patient: Scoping Review and Qualitative Content Analysis of the United Kingdom Medical Literature.

Most people in high income countries experience dying while receiving healthcare, yet dying has no clear beginning, and contexts influence how dying is conceptualised. This study investigates how UK physicians conceptualise the dying patient. We employed Scoping Study Methodology to obtain medical literature from 2006-2021, and Qualitative Content Analysis to analyse stated and implied meanings of language used, informed by social-materialism.

Targeted depletion of uterine glandular Foxa2 induces embryonic diapause in mice.

Embryonic diapause is a reproductive strategy in which embryo development and growth is temporarily arrested within the uterus to ensure the survival of neonates and mothers during unfavorable conditions. Pregnancy is reinitiated when conditions become favorable for neonatal survival. The mechanism of how the uterus enters diapause in various species remains unclear.

Kin selection for cooperation in natural bacterial populations.

Bacteria produce a range of molecules that are secreted from the cell and can provide a benefit to the local population of cells. Laboratory experiments have suggested that these "public goods" molecules represent a form of cooperation, favored because they benefit closely related cells (kin selection). However, there is a relative lack of data demonstrating kin selection for cooperation in natural populations of bacteria.

A seafood risk tool for assessing and mitigating chemical and pathogen hazards in the aquaculture supply chain.

Intricate links between aquatic animals and their environment expose them to chemical and pathogenic hazards, which can disrupt seafood supply. Here we outline a risk schema for assessing potential impacts of chemical and microbial hazards on discrete subsectors of aquaculture-and control measures that may protect supply. As national governments develop strategies to achieve volumetric expansion in seafood production from aquaculture to meet increasing demand, we propose an urgent need for simultaneous focus on controlling those hazards that limit its production, harvesting, processing, trade and safe consumption.

Plasmids do not consistently stabilize cooperation across bacteria but may promote broad pathogen host-range.

Horizontal gene transfer via plasmids could favour cooperation in bacteria, because transfer of a cooperative gene turns non-cooperative cheats into cooperators. This hypothesis has received support from theoretical, genomic and experimental analyses. By contrast, we show here, with a comparative analysis across 51 diverse species, that genes for extracellular proteins, which are likely to act as cooperative 'public goods', were not more likely to be carried on either: (1) plasmids compared to chromosomes; or (2) plasmids that transfer at higher rates.