Uncertainty of modelled bioenergy with carbon capture and storage due to variability of input data

Open Access via Jisc Wiley Open Access Agreement Funding information Natural Environment Research Council, Grant/Award Number: NE/M019691/1; UK Research and Innovation, Grant/Award Number: EP/S029575/1 ACKNOWLEDGEMENTS We were able to test climate and soil effects on BECCS, as part of the UKERC (UK Energy Research Centre) Phase 4 research programme, funded by UK Research and Innovation (EP/S029575/1). Model development was also made possible by ADVENT (ADdressing Valuation by the UK Natural environment Research Council (NE/M019691/1).Peer reviewedPublisher PD

A Systematic Review and Meta-analysis on Omentoplasty for the Management of Abdominoperineal Defects in Patients Treated for Cancer

Objective: The objective of this systematic review and meta-analysis was to examine the effects of omentoplasty on pelviperineal morbidity following abdominoperineal resection (APR) in patients with cancer. Background: Recent studies have questioned the use of omentoplasty for the prevention of perineal wound complications. Methods: A systematic review of published literature since 2000 on the use of omentoplasty during APR for cancer was undertaken. The authors were requested to share their source patient data. Meta-analyses were conducted using a random-effects model. Results: Fourteen studies comprising 1894 patients (n ¼ 839 omentoplasty) were included. The majority had APR for rectal cancer (87%). Omentoplasty was not significantly associated with the risk of presacral abscess formation in the overall population (RR 1.11; 95% CI 0.79–1.56), nor in planned subgroup analysis (n ¼ 758) of APR with primary perineal closure for nonlocally advanced rectal cancer (RR 1.06; 95% CI 0.68–1.64). No overall differences were found for complicated perineal wound healing within 30 days (RR 1.30; 95% CI 0.92–1.82), chronic perineal sinus (RR 1.08; 95% CI 0.53–2.20), and pelviperineal complication necessitating reoperation (RR 1.06; 95% CI 0.80– 1.42) as well. An increased risk of developing a perineal hernia was found for patients submitted to omentoplasty (RR 1.85; 95% CI 1.26–2.72). Complications related to the omentoplasty were reported in 4.6% (95% CI 2.5%– 8.6%). Conclusions: This meta-analysis revealed no beneficial effect of omentoplasty on presacral abscess formation and perineal wound healing after APR, while it increases the likelihood of developing a perineal hernia. These findings do not support the routine use of omentoplasty in APR for cancer

Inferring stabilizing mutations from protein phylogenies : application to influenza hemagglutinin

One selection pressure shaping sequence evolution is the requirement that a protein fold with sufficient stability to perform its biological functions. We present a conceptual framework that explains how this requirement causes the probability that a particular amino acid mutation is fixed during evolution to depend on its effect on protein stability. We mathematically formalize this framework to develop a Bayesian approach for inferring the stability effects of individual mutations from homologous protein sequences of known phylogeny. This approach is able to predict published experimentally measured mutational stability effects (ΔΔG values) with an accuracy that exceeds both a state-of-the-art physicochemical modeling program and the sequence-based consensus approach. As a further test, we use our phylogenetic inference approach to predict stabilizing mutations to influenza hemagglutinin. We introduce these mutations into a temperature-sensitive influenza virus with a defect in its hemagglutinin gene and experimentally demonstrate that some of the mutations allow the virus to grow at higher temperatures. Our work therefore describes a powerful new approach for predicting stabilizing mutations that can be successfully applied even to large, complex proteins such as hemagglutinin. This approach also makes a mathematical link between phylogenetics and experimentally measurable protein properties, potentially paving the way for more accurate analyses of molecular evolution

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

BACKGROUND: Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared. Moreover, a comprehensive pipeline is needed to produce a non-redundant library of TEs for species lacking this resource to generate whole-genome TE annotations. RESULTS: We benchmark existing programs based on a carefully curated library of rice TEs. We evaluate the performance of methods annotating long terminal repeat (LTR) retrotransposons, terminal inverted repeat (TIR) transposons, short TIR transposons known as miniature inverted transposable elements (MITEs), and Helitrons. Performance metrics include sensitivity, specificity, accuracy, precision, FDR, and F1. Using the most robust programs, we create a comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) that produces a filtered non-redundant TE library for annotation of structurally intact and fragmented elements. EDTA also deconvolutes nested TE insertions frequently found in highly repetitive genomic regions. Using other model species with curated TE libraries (maize and Drosophila), EDTA is shown to be robust across both plant and animal species. CONCLUSIONS: The benchmarking results and pipeline developed here will greatly facilitate TE annotation in eukaryotic genomes. These annotations will promote a much more in-depth understanding of the diversity and evolution of TEs at both intra- and inter-species levels. EDTA is open-source and freely available: https://github.com/oushujun/EDTA

Advances in methods for detection of anaerobic ammonium oxidizing (anammox) bacteria

Anaerobic ammonium oxidation (anammox), the biochemical process oxidizing ammonium into dinitrogen gas using nitrite as an electron acceptor, has only been recognized for its significant role in the global nitrogen cycle not long ago, and its ubiquitous distribution in a wide range of environments has changed our knowledge about the contributors to the global nitrogen cycle. Currently, several groups of methods are used in detection of anammox bacteria based on their physiological and biochemical characteristics, cellular chemical composition, and both 16S rRNA gene and selective functional genes as biomarkers, including hydrazine oxidoreductase and nitrite reductase encoding genes hzo and nirS, respectively. Results from these methods coupling with advances in quantitative PCR, reverse transcription of mRNA genes and stable isotope labeling have improved our understanding on the distribution, diversity, and activity of anammox bacteria in different environments both natural and engineered ones. In this review, we summarize these methods used in detection of anammox bacteria from various environments, highlight the strengths and weakness of these methods, and also discuss the new development potentials on the existing and new techniques in the future

Mental fatigue after very severe closed head injury: Sustained performance, mental effort, and distress at two levels of work-load in a driving simulator

In patients with very severe closed head injury (CHI), returning to work is often problematic. The present study focuses on a persistent complaint of these patients, viz. mental fatigue. To study this, the effect of sustained workload is assessed in a continuous dynamic divided attention task. Three types of measures are employed: performance loss with time-on-task, and subjective reports and cardiovascular measures of mental effort and distress. Eight very severe CHI patients (mean post-traumatic amnesia duration 51 days, mean age 23 years, (SD 6.4) and eight hospital controls (mean age 29 years, (SD 5.9) were tested. No differences were found between the patients and controls in the effects of task load on performance and the amount of mental effort, even in very demanding simulated work conditions. This parallels previous findings in less demanding laboratory tasks of sustained attention. Effects of CHI were found on both subjective and physiological indicators of distress. Compared to the controls, patients showed stronger effects on systolic blood pressure and subjectively experienced load

Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments