NURBS enhanced virtual element methods for the spatial discretization of the multigroup neutron diffusion equation on curvilinear polygonal meshes

The Continuous Galerkin Virtual Element Method (CG-VEM) is a recent innovation in spatial discretization methods that can solve partial differential equations (PDEs) using polygonal (2D) and polyhedral (3D) meshes. Recently, a new formulation of CG-VEM was introduced which can construct VEM spaces on polygons with curvilinear edges. This paper presents the application of the curved VEM to the multigroup neutron diffusion equation and demonstrates its benefits over the conventional straight-sided VEM for a number of benchmark verification test cases with curvilinear domains. These domains were constructed using a topological data-structure developed as part of this paper, based on the doubly-connected edge list, with curves and surfaces both represented using non-uniform rational B-splines (NURBS). This data-structure is used both to specify the geometry of the reactor and to represent the curvilinear polygonal mesh. We also present two separate methods of performing integrations on curvilinear polygons, one for homogeneous functions and one for non-homogeneous functions

The estimation and projection package age-sex model and the r-hybrid model: new tools for estimating HIV incidence trends in sub-Saharan Africa.

OBJECTIVES: Improve models for estimating HIV epidemic trends in sub-Saharan Africa (SSA). DESIGN: Mathematical epidemic model fit to national HIV survey and ANC sentinel surveillance (ANC-SS) data. METHODS: We modified EPP to incorporate age and sex stratification (EPP-ASM) to more accurately capture the shifting demographics of maturing HIV epidemics. Secondly, we developed a new functional form for the HIV transmission rate, termed 'r-hybrid', which combines a four-parameter logistic function for the initial epidemic growth, peak, and decline followed by a first-order random walk for recent trends after epidemic stabilization. We fitted the r-hybrid model along with previously developed r-spline and r-trend models to HIV prevalence data from household surveys and ANC-SS in 177 regions in 34 SSA countries. We used leave-one-out cross validation with household survey HIV prevalence to compare model predictions. RESULTS: The r-hybrid and r-spline models typically provided similar HIV prevalence trends, but sometimes qualitatively different assessments of recent incidence trends because of different structural assumptions about the HIV transmission rate. The r-hybrid model had the lowest average continuous ranked probability score, indicating the best model predictions. Coverage of 95% posterior predictive intervals was 91.5% for the r-hybrid model, versus 87.2 and 85.5% for r-spline and r-trend, respectively. CONCLUSION: The EPP-ASM and r-hybrid models improve consistency of EPP and Spectrum, improve the epidemiological assumptions underpinning recent HIV incidence estimates, and improve estimates and short-term projections of HIV prevalence trends. Countries that use general population survey and ANC-SS data to estimate HIV epidemic trends should consider using these tools

Edible crabs “Go West”: migrations and incubation cycle of Cancer pagurus revealed by electronic tags

Crustaceans are key components of marine ecosystems which, like other exploited marine taxa, show seasonable patterns of distribution and activity, with consequences for their availability to capture by targeted fisheries. Despite concerns over the sustainability of crab fisheries worldwide, difficulties in observing crabs’ behaviour over their annual cycles, and the timings and durations of reproduction, remain poorly understood. From the release of 128 mature female edible crabs tagged with electronic data storage tags (DSTs), we demonstrate predominantly westward migration in the English Channel. Eastern Channel crabs migrated further than western Channel crabs, while crabs released outside the Channel showed little or no migration. Individual migrations were punctuated by a 7-month hiatus, when crabs remained stationary, coincident with the main period of crab spawning and egg incubation. Incubation commenced earlier in the west, from late October onwards, and brooding locations, determined using tidal geolocation, occurred throughout the species range. With an overall return rate of 34%, our results demonstrate that previous reluctance to tag crabs with relatively high-cost DSTs for fear of loss following moulting is unfounded, and that DSTs can generate precise information with regards life-history metrics that would be unachievable using other conventional means

Equity in utilization of antiretroviral therapy for HIV-infected people in South Africa: a systematic review

INTRODUCTION: About half a million people in South Africa are deprived of antiretroviral therapy (ART), and there is little systematic knowledge on who they are – e.g. by severity of disease, sex, or socio-economic status (SES). We performed a systematic review to determine the current quantitative evidence-base on equity in utilization of ART among HIV-infected people in South Africa. METHOD: We conducted a literature search based on the Cochrane guidelines. A study was included if it compared for different groups of HIV infected people (by sex, age, severity of disease, area of living, SES, marital status, ethnicity, religion and/or sexual orientation (i.e. equity criteria)) the number initiating/adhering to ART with the number who did not. We considered ART utilization inequitable for a certain criterion (e.g. sex) if between groups (e.g. men versus women) significant differences were reported in ART initiation/adherence. RESULTS: Twelve studies met the inclusion criteria. For sex, 2 out of 10 studies that investigated this criterion found that men are less likely than women to utilize ART, while the other 8 found no differences. For age, 4 out of 8 studies found inequities and reported less utilization for younger people. For area of living, 3 out of 4 studies showed that those living in rural areas or certain provinces have less access and 2 out of 6 studies looking at SES found that people with lower SES have less access. One study which looked at the marital status found that those who are married are less likely to utilize ART. For severity of disease, 5 out of 6 studies used more than one outcome measure for disease stage and reported within their study contradicting results. One of the studies reported inconclusive findings for ethnicity and no study had looked at religion and sexual orientation. CONCLUSION: It seems that men, young people, those living in certain provinces or rural areas, people who are unemployed or with a low educational level, and those being unmarried have less access to ART. As studies stem from different contexts and use different methods conclusions should be taken with caution

Low metabolic activity of biofilm formed by Enterococcus faecalis isolated from healthy humans and wild mallards (Anas platyrhynchos)

It is widely known that Enterococcus faecalis virulence is related to its biofilm formation. Although Enterococci are common commensal organisms of the gastrointestinal tract, the difference between commensal and pathogen strains remain unclear. In this study, we compare the biochemical profile of the biofilms formed by two groups of medical and two groups of commensal strains. The medical strains were isolated as pathogens from infections of urinary tract and other infections (wounds, pus and bedsores), and the commensal strains were taken from faeces of healthy volunteers and faeces of wild mallards (Anas platyrhynchos) living in an urban environment. The properties of biofilms formed by medical and commensal strains differed significantly. Commensal strains showed lower metabolic activity and glucose uptake and higher biofilm biomass than the medical ones. Consistent with glucose uptake experiments, we found that the glucose dehydrogenase gene was more expressed in medical strains. These results indicate that higher metabolic activity and lower protein concentration of E. faecalis cells within biofilms are formed during infections.This work was supported by the Medical University of Gdansk research grant (GUMed W-65) and was financed partly by University of Gdansk research grant (BW 1440-5-0099-7). We are grateful to Katarzyna Zolkos for her help in catching mallards and Magdalena Remisiewicz for correcting the English. Catarina Seabra helped in preparing assays

Endogenous cholinergic inputs and local circuit mechanisms govern the phasic mesolimbic dopamine response to nicotine

Nicotine exerts its reinforcing action by stimulating nicotinic acetylcholine receptors (nAChRs) and boosting dopamine (DA) output from the ventral tegmental area (VTA). Recent data have led to a debate about the principal pathway of nicotine action: direct stimulation of the DAergic cells through nAChR activation, or disinhibition mediated through desensitization of nAChRs on GABAergic interneurons. We use a computational model of the VTA circuitry and nAChR function to shed light on this issue. Our model illustrates that the α4β2-containing nAChRs either on DA or GABA cells can mediate the acute effects of nicotine. We account for in vitro as well as in vivo data, and predict the conditions necessary for either direct stimulation or disinhibition to be at the origin of DA activity increases. We propose key experiments to disentangle the contribution of both mechanisms. We show that the rate of endogenous acetylcholine input crucially determines the evoked DA response for both mechanisms. Together our results delineate the mechanisms by which the VTA mediates the acute rewarding properties of nicotine and suggest an acetylcholine dependence hypothesis for nicotine reinforcement.Peer reviewe

Current trends in the surgical management of Dupuytren’s disease in Europe: an analysis of patient charts

Introduction: Dupuytren's disease (DD) causes progressive digital flexion contracture and is more common in men of European descent. Methods: Orthopaedic and plastic surgeons in 12 European countries (the Czech Republic, Denmark, Finland, France, Germany, Hungary, Italy, The Netherlands, Poland, Spain, Sweden and the UK) with >3 and <30 years experience reviewed the medical charts of five consecutive patients they had treated surgically for DD in 2008. Descriptive statistics are reported. Results: In total, 3,357 patient charts were reviewed. Mean (standard deviation) patient age was 61.9 (10.2) years; 81% were men. At the time of the procedure, 11% of patients were at Tubiana stage Ia (0-20° total flexion); 30%, stage Ib (21-45°); 34%, stage II (46-90°); 17%, stage III (91-135°); and 5%, stage IV (&135°). Percutaneous needle fasciotomy was performed in 10%, fasciotomy in 13%, fasciectomy in 69% and dermofasciectomy (DF) in 6% of patients. After surgery, fingers improved a mean of 1.9 Tubiana stages, and 54% of patients had no nodules or contracture. The rate of reported complications during the procedure was 4% overall (11% in patients undergoing DF). The most common postoperative complications reported were haematoma (8%), wound healing complications (6%) and pain (6%). No postoperative complications were reported in 77% of patients. Conclusions: In this European study of more than 3,000 patients with DD, most patients were diagnosed at Tubiana stage I or II, the majority received fasciectomy and more than half had no nodules or contracture remaining after surgery

A randomised controlled trial and cost-effectiveness evaluation of "booster" interventions to sustain increases in physical activity in middle-aged adults in deprived urban neighbourhoods

Background: Systematic reviews have identified a range of brief interventions which increase physical activity in previously sedentary people. There is an absence of evidence about whether follow up beyond three months can maintain long term physical activity. This study assesses whether it is worth providing motivational interviews, three months after giving initial advice, to those who have become more active. Methods/Design: Study candidates (n = 1500) will initially be given an interactive DVD and receive two telephone follow ups at monthly intervals checking on receipt and use of the DVD. Only those that have increased their physical activity after three months (n = 600) will be randomised into the study. These participants will receive either a "mini booster" (n = 200), "full booster" (n = 200) or no booster (n = 200). The "mini booster" consists of two telephone calls one month apart to discuss physical activity and maintenance strategies. The "full booster" consists of a face-to-face meeting with the facilitator at the same intervals. The purpose of these booster sessions is to help the individual maintain their increase in physical activity. Differences in physical activity, quality of life and costs associated with the booster interventions, will be measured three and nine months from randomisation. The research will be conducted in 20 of the most deprived neighbourhoods in Sheffield, which have large, ethnically diverse populations, high levels of economic deprivation, low levels of physical activity, poorer health and shorter life expectancy. Participants will be recruited through general practices and community groups, as well as by postal invitation, to ensure the participation of minority ethnic groups and those with lower levels of literacy. Sheffield City Council and Primary Care Trust fund a range of facilities and activities to promote physical activity and variations in access to these between neighbourhoods will make it possible to examine whether the effectiveness of the intervention is modified by access to community facilities. A one-year integrated feasibility study will confirm that recruitment targets are achievable based on a 10% sample.Discussion: The choice of study population, study interventions, brief intervention preceding the study, and outcome measure are discussed

Accumulation of Endogenous LITAF in Aggresomes

LITAF is a 161 amino acid cellular protein which includes a proline rich N-terminus and a conserved C-terminal domain known as the simple-like domain. Mutations in LITAF have been identified in Charcot-Marie tooth disease, a disease characterized by protein aggregates. Cells transfected with cellular LITAF reveal that LITAF is localized to late endosomes/lysosomes. Here we investigated the intracellular localization of endogenous LITAF. We demonstrated that endogenous LITAF accumulates at a discrete cytoplasmic site in BGMK cells that we identify as the aggresome. To determine the domain within LITAF that is responsible for the localization of LITAF to aggresomes, we created a construct that contained the C-terminal simple-like domain of LITAF and found that this construct also localizes to aggresomes. These data suggest the simple-like domain is responsible for targeting endogenous LITAF to the aggresome

Molecular analysis of the Acinetobacter baumannii biofilm-associated protein

Acinetobacter baumannii is a multidrug-resistant pathogen associated with hospital outbreaks of infection across the globe, particularly in the intensive care unit. The ability of A. baumannii to survive in the hospital environment for long periods is linked to antibiotic resistance and its capacity to form biofilms. Here we studied the prevalence, expression, and function of the A. baumannii biofilm-associated protein (Bap) in 24 carbapenem-resistant A. baumannii ST92 strains isolated from a single institution over a 10-year period. The bap gene was highly prevalent, with 22/24 strains being positive for bap by PCR. Partial sequencing of bap was performed on the index case strain MS1968 and revealed it to be a large and highly repetitive gene approximately 16 kb in size. Phylogenetic analysis employing a 1,948-amino-acid region corresponding to the C terminus of Bap showed that Bap(MS1968) clusters with Bap sequences from clonal complex 2 (CC2) strains ACICU, TCDC-AB0715, and 1656-2 and is distinct from Bap in CC1 strains. By using overlapping PCR, the bap(MS1968) gene was cloned, and its expression in a recombinant Escherichia coli strain resulted in increased biofilm formation. A Bap-specific antibody was generated, and Western blot analysis showed that the majority of A. baumannii strains expressed an similar to 200-kDa Bap protein. Further analysis of three Bap-positive A. baumannii strains demonstrated that Bap is expressed at the cell surface and is associated with biofilm formation. Finally, biofilm formation by these Bap-positive strains could be inhibited by affinity-purified Bap antibodies, demonstrating the direct contribution of Bap to biofilm growth by A. baumannii clinical isolates