Books

Ask the Doctor. Hypertension By Vincent Friedewald. Pp. xiv + 120. R59.95. Kansas City:Andrews and McMeel. ISBN 0-8362-7022-3.How to Survive in Anaesthesia*By P Neville Robinson and George M Hall. Pp. xi + 172. £22.00.1997. London: BMJ. ISBN 0-7279-1066-3.Epidemiology. A Manual for South Africa* Edited by J M Katzenellenbogen, G Joubert and S S Abdool Karim. Pp. 295. R120. 1997. Cape Town: Oxford University Press. ISBN 0-19-571308-7

Communicating the uncertainty in estimated greenhouse gas emissions from agriculture

In an effort to mitigate anthropogenic effects on the global climate system, industrialised countries are required to quantify and report, for various economic sectors, the annual emissions of greenhouse gases from their several sources and the absorption of the same in different sinks. These estimates are uncertain, and this uncertainty must be communicated effectively, if government bodies, research scientists or members of the public are to draw sound conclusions. Our interest is in communicating the uncertainty in estimates of greenhouse gas emissions from agriculture to those who might directly use the results from the inventory. We tested six methods of communication. These were: a verbal scale using the IPCC calibrated phrases such as ‘likely’ and ‘very unlikely’; probabilities that emissions are within a defined range of values; confidence intervals for the expected value; histograms; box plots; and shaded arrays that depict the probability density of the uncertain quantity. In a formal trial we used these methods to communicate uncertainty about four specific inferences about greenhouse gas emissions in the UK. Sixty four individuals who use results from the greenhouse gas inventory professionally participated in the trial, and we tested how effectively the uncertainty about these inferences was communicated by means of a questionnaire. Our results showed differences in the efficacy of the methods of communication, and interactions with the nature of the target audience. We found that, although the verbal scale was thought to be a good method of communication it did not convey enough information and was open to misinterpretation. Shaded arrays were similarly criticised for being open to misinterpretation, but proved to give the best impression of uncertainty when participants were asked to interpret results from the greenhouse gas inventory. Box plots were most favoured by our participants largely because they were particularly favoured by those who worked in research or had a stronger mathematical background. We propose a combination of methods should be used to convey uncertainty in emissions and that this combination should be tailored to the professional grou

The low recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression

The low-recombining pericentromeric region of the barley genome contains roughly a quarter of the genes of the species, embedded in low-recombining DNA that is rich in repeats and repressive chromatin signatures. We have investigated the effects of pericentromeric region residency upon the expression, diversity and evolution of these genes. We observe no significant difference in average transcript level or developmental RNA specificity between the barley pericentromeric region and the rest of the genome. In contrast, all of the evolutionary parameters studied here show evidence of compromised gene evolution in this region. First, genes within the pericentromeric region of wild barley show reduced diversity and significantly weakened purifying selection compared with the rest of the genome. Second, gene duplicates (ohnolog pairs) derived from the cereal whole-genome duplication event ca. 60MYa have been completely eliminated from the barley pericentromeric region. Third, local gene duplication in the pericentromeric region is reduced by 29% relative to the rest of the genome. Thus, the pericentromeric region of barley is a permissive environment for gene expression but has restricted gene evolution in a sizeable fraction of barley's genes

Assessment of active tubulointerstitial nephritis in non-scarred renal cortex improves prediction of renal outcomes in patients with IgA nephropathy

Background: The addition of tubulointerstitial inflammation to the existing pathological classification of IgA nephropathy (IgAN) is appealing but was previously precluded due to reportedly wide inter-observer variability. We report a novel method to score percentage of non-atrophic renal cortex containing active tubulointerstitial inflammation (ATIN) in patients with IgAN and assess its utility to predict clinical outcomes. Methods: All adult patients with a native renal biopsy diagnosis of IgAN between 2010 and 2015 in a unit serving 1.5 million people were identified. Baseline characteristics, biopsy reports and outcome data were collected. ATIN was calculated by subtracting the percentage of atrophic cortex from the percentage of total cortex with tubulointerstitial inflammation, with ≥10% representing significant ATIN. The primary outcome was a composite of requiring renal replacement therapy or doubling of serum creatinine. Results: In total 153 new cases of IgAN were identified, of which 111 were eligible for inclusion. Of these, 76 (68%) were male and 54 (49%) had ATIN on biopsy. During a median follow-up of 2.3 years, 34 (31%) reached the primary outcome. On univariable Cox regression analysis, ATIN was associated with a five-fold increase in the primary outcome [hazard ratio (HR) (95% confidence interval) 4.9 (95% confidence interval (CI) 2.1–11.3)]. On multivariable analysis, mesangial hypercellularity, tubular atrophy and interstitial fibrosis and ATIN independently associated with renal outcome (P = 0.02 for ATIN). Inter-observer reproducibility revealed fair agreement in the diagnosis of ATIN (κ=0.43, P = 0.05). Conclusions: Within our centre, ATIN was significantly associated with renal outcome in patients with IgAN, independently of established histological features and baseline clinical characteristics

Facilitating the elicitation of beliefs for use in Bayesian Belief modelling

Expert opinion is increasingly being used to inform Bayesian Belief Networks, in particular to define the conditional dependencies modelled by the graphical structure. The elicitation of such expert opinion remains a major challenge due to both the quantity of information required and the ability of experts to quantify subjective beliefs effectively. In this work, we introduce a method designed to initialise conditional probability tables based on a small number of simple questions that capture the overall shape of a conditional probability distribution before enabling the expert to refine their results in an efficient way. These methods have been incorporated into a software Application for Conditional probability Elicitation (ACE), freely available at https://github.com/KirstyLHassall/ACE Hassall (2019

3D RNA-seq:A powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists

RNA-sequencing (RNA-seq) analysis of gene expression and alternative splicing should be routine and robust but is often a bottleneck for biologists because of different and complex analysis programs and reliance on specialized bioinformatics skills. We have developed the ‘3D RNA-seq’ App, an R shiny App and web-based pipeline for the comprehensive analysis of RNA-seq data from any organism. It represents an easy-to-use, flexible and powerful tool for analysis of both gene and transcript-level gene expression to identify differential gene/transcript expression, differential alternative splicing and differential transcript usage (3D) as well as isoform switching from RNA-seq data. 3D RNA-seq integrates state-of-the-art differential expression analysis tools and adopts best practice for RNA-seq analysis. The program is designed to be run by biologists with minimal bioinformatics experience (or by bioinformaticians) allowing lab scientists to analyse their RNA-seq data. It achieves this by operating through a user-friendly graphical interface which automates the data flow through the programs in the pipeline. The comprehensive analysis performed by 3D RNA-seq is extremely rapid and accurate, can handle complex experimental designs, allows user setting of statistical parameters, visualizes the results through graphics and tables, and generates publication quality figures such as heat-maps, expression profiles and GO enrichment plots. The utility of 3D RNA-seq is illustrated by analysis of data from a time-series of cold-treated Arabidopsis plants and from dexamethasone-treated male and female mouse cortex and hypothalamus data identifying dexamethasone-induced sex- and brain region-specific differential gene expression and alternative splicing

Tablet—next generation sequence assembly visualization

Summary: Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine

Supervisor trainees' and their supervisors' perceptions of attainment of knowledge and skills. An empirical evaluation of a psychotherapy supervisor training programme

Objectives. This study aimed to evaluate the success of a two-year, part-time training programme for psychotherapy supervisors. A second aim was to examine factors that might contribute to perceived knowledge and skills attainment during the training course. Design. This is a naturalistic, longitudinal study where several measures are used to examine group process and outcome. Methods. Supervisor trainees’ (n=21) and their facilitators’ (n=6) ratings of learning (knowledge and skills), relations to the supervisor and supervision group, usage of the group, and supervisor style were completed at three time points. Results. The findings suggested that both trainees and their supervisors perceived that the trainees attained a substantial amount of knowledge and skills during the course. In accordance with the literature and expectations, the regression analysis suggested a strong negative association between a strong focus on group processes in the initial and middle phases of the training and perceived knowledge and skills attainment in the final phase of the training. The expected, positive role of relations among trainees in the supervision group in the first half of the training and perceived knowledge and skills attainment in the final part of the training was obtained, whilst the hypothesized significance of the relationship between trainee and supervisor did not receive support. Conclusions The supervisory course seemed to provide a training that allowed trainees to attain knowledge and skills that are necessary for psychotherapy supervisors. The results of this pilot study also emphasize the need of more research on learning in the context of group supervision in psychotherapy

Wearable near-infrared spectroscopy as a physiological monitoring tool for seals under anaesthesia

Chemical immobilisation of pinnipeds is a routine procedure in research and veterinary practice. Yet, there are inevitable risks associated with chemical immobilisation, and the physiological response to anaesthetic agents in pinnipeds remains poorly understood. The current study used wearable continuous-wave near-infrared spectroscopy (NIRS) data from 10 trials of prolonged anaesthesia (0.5 to 1.4 h) induced through ketamine and midazolam in five grey seals (Halichoerus grypus) involved in other procedures. The aim of this study was to (1) analyse the effect of each compound on heart rate, arterial oxygen saturation (SpO2), and relative concentration changes in oxygenated [ΔO2Hb] and deoxygenated haemoglobin [ΔHHb] in cerebral tissue and (2) to investigate the use of NIRS as a real-time physiological monitoring tool during chemical immobilisation. Average group responses of ketamine (n = 27) and midazolam (n = 11) administrations were modelled using generalised additive mixed models (GAMM) for each dependent variable. Following ketamine and midazolam administration, [ΔHHb] increased and [ΔO2Hb] remained relatively stable, which was indicative of apnoea. Periods of apnoea were confirmed from respiratory band data, which were simultaneously collected during drugging trials. Given that SpO2 remained at 97% during apnoea, we hypothesized that increasing cerebral [ΔHHb] was a result of venous congestion as opposed to decreased oxygen delivery. Changes in heart rate were limited and appeared to be driven by the individual pharmacological actions of each drug. Future research could include simultaneous measures of metabolic rate, such as the relative change in concentration of cytochrome-c-oxidase, to guide operators in determining when apnoea should be considered prolonged if changes in [ΔHHb] and [ΔO2Hb] occur beyond the limits recorded in this study. Our findings support the use of NIRS as real-time physiological monitoring tool during pinniped chemical immobilisation, which could assist veterinarians and researchers in performing safe anaesthetic procedures