Using a prisoner advisory group to develop diversity research in a maximum-security prison

This paper addresses groupwork processes with a group of prisoners advising a research project in a maximum-security prison in England. The research project (Appreciative Inquiry into the Diversity Strategy of HMP Wakefield. RES-000-22-3441) was funded by the Economic and Social Research Council (ESRC) and lasted 9 months. The research explored the experiences of prisoners in diverse minority groupings and the strategies of the prison to accommodate the complex needs of these groups. The Prisoner Advisory Group (PAG) was made up of representatives from Black and Minority Ethnic (BME) prisoners; older prisoners (over 60s); Disabled prisoners (with physical disabilities, learning difficulties; and mental health problems); Gay, Bi-sexual and Transgender prisoners; and prisoners affiliated to Faith groups. It met regularly during the research. The paper considers the forming norming and performing aspects of establishing an effective participant voice in a prison-based project. It considers the contribution of the PAG to developing a research strategy that engaged prisoners in the research. It reflects on the nature of ‘participative research’ in general and whether such research is possible within a high-security prison environment

Telomeric expression sites are highly conserved in trypanosoma brucei

Subtelomeric regions are often under-represented in genome sequences of eukaryotes. One of the best known examples of the use of telomere proximity for adaptive purposes are the bloodstream expression sites (BESs) of the African trypanosome Trypanosoma brucei. To enhance our understanding of BES structure and function in host adaptation and immune evasion, the BES repertoire from the Lister 427 strain of T. brucei were independently tagged and sequenced. BESs are polymorphic in size and structure but reveal a surprisingly conserved architecture in the context of extensive recombination. Very small BESs do exist and many functioning BESs do not contain the full complement of expression site associated genes (ESAGs). The consequences of duplicated or missing ESAGs, including ESAG9, a newly named ESAG12, and additional variant surface glycoprotein genes (VSGs) were evaluated by functional assays after BESs were tagged with a drug-resistance gene. Phylogenetic analysis of constituent ESAG families suggests that BESs are sequence mosaics and that extensive recombination has shaped the evolution of the BES repertoire. This work opens important perspectives in understanding the molecular mechanisms of antigenic variation, a widely used strategy for immune evasion in pathogens, and telomere biology

Evaluation of a Melanocortin-4 Receptor (MC4R) agonist (Setmelanotide) in MC4R deficiency

$\textbf{Objective:}$ Pro-opiomelanocortin (POMC)-derived peptides act on neurons expressing the Melanocortin 4 receptor (MC4R) to reduce body weight. Setmelanotide is a highly potent MC4R agonist that leads to weight loss in diet-induced obese animals and in obese individuals with complete POMC deficiency. While POMC deficiency is very rare, 1e5% of severely obese individuals harbor heterozygous mutations in MC4R. We sought to assess the efficacy of Setmelanotide in human MC4R deficiency. $\textbf{Methods:}$ We studied the effects of Setmelanotide on mutant MC4Rs in cells and the weight loss response to Setmelanotide administration in rodent studies and a human clinical trial. We annotated the functional status of 369 published MC4R variants. $\textbf{Results:}$ In cells, we showed that Setmelanotide is significantly more potent at MC4R than the endogenous ligand alpha-melanocyte stimulating hormone and can disproportionally rescue signaling by a subset of severely impaired MC4R mutants. Wild-type rodents appear more sensitive to Setmelanotide when compared to MC4R heterozygous deficient mice, while MC4R knockout mice fail to respond. In a 28-day Phase 1b clinical trial, Setmelanotide led to weight loss in obese MC4R variant carriers. Patients with POMC defects upstream of MC4R show significantly more weight loss with Setmelanotide than MC4R deficient patients or obese controls. $\textbf{Conclusions:}$ Setmelanotide led to weight loss in obese people with MC4R deficiency; however, further studies are justified to establish whether Setmelanotide can elicit clinically meaningful weight loss in a subset of the MC4R deficient obese population.This work was supported by the Wellcome Trust (I.S.F.), the National Institute for Health Research Cambridge Biomedical Research Centre (S.O’R., I.S.F.), the Bernard Wolfe Health Neuroscience Fund (I.S.F.), the European Research Council (I.S.F.), and the Swiss National Science Foundation (PBLAP3-145870, P3SMP3-155318, PZ00P3-167826 to T.-H.C.). Funds were also obtained from the Clinical Research Programs on Obesity (Assistance Publique-Hôpitaux de Paris, and the Direction of Clinical Research (CRC) (PHRC 02076 to K.C.), as well as the Institut Benjamin Delessert and the Fondation pour la Recherche Médicale and the National Agency of Research (program “Investissements d’Avenir” with the reference ANR-10-IAHU-05). The clinical trial was supported by Rhythm Pharmaceuticals

High-resolution analysis of multi-copy variant surface glycoprotein gene expression sites in African trypanosomes

BACKGROUND: African trypanosomes cause lethal diseases in humans and animals and escape host immune attack by switching the expression of Variant Surface Glycoprotein (VSG) genes. The expressed VSGs are located at the ends of telomeric, polycistronic transcription units known as VSG expression sites (VSG-ESs). Each cell has many VSG-ESs but only one is transcribed in bloodstream-form parasites and all of them are inactive upon transmission to the insect vector mid-gut; a subset of monocistronic metacyclic VSG-ESs are then activated in the insect salivary gland. Deep-sequence analyses have been informative but assigning sequences to individual VSG-ESs has been challenging because they each contain closely related expression-site associated genes, or ESAGs, thought to contribute to virulence. RESULTS: We utilised ART, an in silico short read simulator to demonstrate the feasibility of accurately aligning reads to VSG-ESs. Then, using high-resolution transcriptomes from isogenic bloodstream and insect-stage Lister 427 Trypanosoma brucei, we uncover increased abundance in the insect mid-gut stage of mRNAs from metacyclic VSG-ESs and of mRNAs from the unusual ESAG, ESAG10. Further, we show that the silencing associated with allelic exclusion involves repression focussed at the ends of the VSG-ESs. We also use the approach to report relative fitness costs following ESAG RNAi from a genome-scale screen. CONCLUSIONS: By assigning sequences to individual VSG-ESs we provide new insights into VSG-ES transcription control, allelic exclusion and impacts on fitness. Thus, deeper insights into the expression and function of regulated multi-gene families are more accessible than previously anticipated. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3154-8) contains supplementary material, which is available to authorized users

A turbulent decade for NSAIDs: update on current concepts of classification, epidemiology, comparative efficacy, and toxicity

Non-steroidal anti-inflammatory drugs (NSAIDs) represent a diverse class of drugs and are among the most commonly used analgesics for arthritic pain worldwide, though long-term use is associated with a spectrum of adverse effects. The introduction of cyclooxygenase-2-selective NSAIDs early in the last decade offered an alternative to traditional NSAIDs with similar efficacy and improved gastrointestinal tolerability; however, emerging concerns about cardiovascular safety resulted in the withdrawal of two agents (rofecoxib and valdecoxib) in the mid-2000s and, subsequently, in an overall reduction in NSAID use. It is now understood that all NSAIDs are associated with some varying degree of gastrointestinal and cardiovascular risk. Guidelines still recommend their use, but little is known of how patients use these agents. While strategies and guidelines aimed at reducing NSAID-associated complications exist, there is a need for evidence-based algorithms combining cardiovascular and gastrointestinal factors that can be used to aid treatment decisions at an individual patient level

Extending interaction overview diagrams with activity diagram constructs

UML2.0 introduced interaction overview diagrams (IODs) as a way of specifying relationships between UML interactions. IODs are a variant of activity diagrams that show control flow between a set of interactions. The nodes in an IOD are either inline interactions or references to an interaction. A number of recent papers have defined a formal semantics for IODs. These are restricted, however, to interactions that can be specified using basic sequence diagrams. This excludes the many rich modeling constructs available in activity diagrams such as interruptible regions, activity groups, concurrent node executions, and flow final nodes. It is non-trivial to allow such constructs in IODs because their meaning has to be interpreted in the context of interaction sequences rather than activities. In this paper, we consider how some of these activity diagram constructs can be used practically in IODs. We motivate the integration of these constructs into IODs using a NASA air traffic control subsystem and define a formal semantics for these constructs that builds on an existing semantics definition for IODs