De novo analysis of the transcriptome of Pratylenchus zeae to identify transcripts for proteins required for structural integrity, sensation, locomotion and parasitism

The root lesion nematode Pratylenchus zeae, a migratory endoparasite, is an economically important pest of major crop plants (e.g. cereals, sugarcane). It enters host roots, migrates through root tissues and feeds from cortical cells, and defends itself against biotic and abiotic stresses in the soil and in host tissues. We report de novo sequencing of the P. zeae transcriptome using 454 FLX, and the identification of putative transcripts encoding proteins required for movement, response to stimuli, feeding and parasitism. Sequencing generated 347 443 good quality reads which were assembled into 10 163 contigs and 139 104 singletons: 65% of contigs and 28% of singletons matched sequences of free-living and parasitic nematodes. Three-quarters of the annotated transcripts were common to reference nematodes, mainly representing genes encoding proteins for structural integrity and fundamental biochemical processes. Over 15 000 transcripts were similar to Caenorhabditis elegans genes encoding proteins with roles in mechanical and neural control of movement, responses to chemicals, mechanical and thermal stresses. Notably, 766 transcripts matched parasitism genes employed by both migratory and sedentary endoparasites in host interactions, three of which hybridized to the gland cell region, suggesting that they might be secreted. Conversely, transcripts for effectors reported to be involved in feeding site formation by sedentary endoparasites were conspicuously absent. Transcripts similar to those encoding some secretory-excretory products at the host interface of Brugia malayi, the secretome of Meloidogyne incognita and products of gland cells of Heterodera glycines were also identified. This P. zeae transcriptome provides new information for genome annotation and functional analysis of possible targets for control of pratylenchid nematodes

Attitudes of parents towards the ‘Fit Together’ childhood obesity prevention programme: a qualitative study

Background: The latest available data for England show that childhood obesity continues to be a major public health concern with 9.3% of 4–5 years old and 18.9% of 10–11 years old children found to be obese (1). The aim of the study was to explore attitudes towards a community based childhood obesity prevention project among parents participating in the programme. Methods: The ‘Fit Together’ programme was provided in socio-economically deprived areas of Leeds which, at the time of the research study, was in its final year of running. The programme was delivered for 2 hours each week over a six week period by community health educators, and involved health education and cooking sessions. A convenience sample of parents who had attended at least one session of the Fit Together programme, delivered between November-December 2014, were recruited from a children’s centre (where families access health advice and related activities with their children aged 0– 5yr) and a primary school. Semi-structured interviews were conducted using a topic schedule with prompts, and were digitally recorded. A short screening questionnaire was completed to obtain demographic information. Three parents were present in each of the two Fit Together sessions allocated for recruitment. These six parents were recruited to the study and were interviewed. Interviews were transcribed verbatim, transcripts manually coded and thematic analysis conducted using a framework approach. Ethical approval for the study was obtained from the Faculty of Health & Social Sciences Local Research Ethics Coordinator, Leeds Beckett University. Results: Participants were all mothers with 1–3 children, and mean age was 27 years. Four participants self-defined their ethnicity as White British and the remaining two as Pakistani. Themes emerging from the interview data suggested that participants’ appraisal of the programme was positive and they reported benefits in behaviour change relevant to addressing childhood obesity. Parents felt the programme was logistically suitable, and had appropriate content and leaders. All participants would recommend the programme and highlighted the development of their cooking skills, which related to an increase in home cooking and in fruit and vegetable consumption. The opportunity to involve their children and spend time with them learning skills was a strongly held view among respondents. Parents felt the programme had also increased their awareness of nutrition content and children’s dietary habits. However, the view that an extended programme and subsequent follow-up were needed was commonly held. Additional benefits beyond behaviour change were also expressed. For example, the importance of social interaction was clear, with respondents reporting the alleviation of boredom and isolation while attending the programme, as this participant states: “Something to do ain’t it? Gets you out. There’s nothing else to go to” (White British, 23yr, 2 children). Participants also reported exchanging cultural beliefs and learning new styles of cooking from people from different backgrounds. Discussion: The findings of this first exploration of parents’ attitudes to Fit Together supports existing literature on the value of community educators in delivering health interventions (2). Beneficial behaviour change such as increased homecooking was consistent with previous programmes (3). Conclusion: Attitudes towards Fit Together were positive, with mothers viewing the programme as acceptable and bene- ficial. References 1. Stevens. L., & Nelson, M. The contribution of school meals and packed lunch to food consumption and nutrient intakes in UK primary school children from a low income population. Journal of Human Nutrition and Dietetics, 24; 223–232. 2011. 2. Evans, C., & Harper, C. A History and Review of school meals standards in the UK. Journal of Human Nutrition and Dietetics, 89–99. 2009. 3. Lop ez Nomdedeu, C. Agencia Espanola de Seguridad Alimentaria y Nutricion. Ministerio de Sanidad y Consum. La alimentacion de tus ni nos. Nutrici ~ on Saludable de la Infan- cia a la Adolescencia. Madrid: Fiselgraf, S.L. 2002

Smoking and life expectancy among HIV-infected individuals on antiretroviral therapy in Europe and North America.

BACKGROUND: Cardiovascular disease and non-AIDS malignancies have become major causes of death among HIV-infected individuals. The relative impact of lifestyle and HIV-related factors are debated. METHODS: We estimated associations of smoking with mortality more than 1 year after antiretroviral therapy (ART) initiation among HIV-infected individuals enrolled in European and North American cohorts. IDUs were excluded. Causes of death were assigned using standardized procedures. We used abridged life tables to estimate life expectancies. Life-years lost to HIV were estimated by comparison with the French background population. RESULTS: Among 17 995 HIV-infected individuals followed for 79 760 person-years, the proportion of smokers was 60%. The mortality rate ratio (MRR) comparing smokers with nonsmokers was 1.94 [95% confidence interval (95% CI) 1.56-2.41]. The MRRs comparing current and previous smokers with never smokers were 1.70 (95% CI 1.23-2.34) and 0.92 (95% CI 0.64-1.34), respectively. Smokers had substantially higher mortality from cardiovascular disease, non-AIDS malignancies than nonsmokers [MRR 6.28 (95% CI 2.19-18.0) and 2.67 (95% CI 1.60-4.46), respectively]. Among 35-year-old HIV-infected men, the loss of life-years associated with smoking and HIV was 7.9 (95% CI 7.1-8.7) and 5.9 (95% CI 4.9-6.9), respectively. The life expectancy of virally suppressed, never-smokers was 43.5 years (95% CI 41.7-45.3), compared with 44.4 years among 35-year-old men in the background population. Excess MRRs/1000 person-years associated with smoking increased from 0.6 (95% CI -1.3 to 2.6) at age 35 to 43.6 (95% CI 37.9-49.3) at age at least 65 years. CONCLUSION: Well treated HIV-infected individuals may lose more life years through smoking than through HIV. Excess mortality associated with smoking increases markedly with age. Therefore, increases in smoking-related mortality can be expected as the treated HIV-infected population ages. Interventions for smoking cessation should be prioritized

Evaluation of a semi-automated software program for the identification of vertebral fractures in children.

AIM: To assess observer reliability and diagnostic accuracy in children, of a semi-automated six-point technique developed for vertebral fracture (VF) diagnosis in adults, which records percentage loss of vertebral body height. MATERIALS AND METHODS: Using a semi-automated software program, five observers independently assessed T4 to L4 from the lateral spine radiographs of 137 children and adolescents for VF. A previous consensus read by three paediatric radiologists using a simplified algorithm-based qualitative technique (i.e., no software involved) served as the reference standard. RESULTS: Of a total of 1,781 vertebrae, 1,187 (67%) were adequately visualised according to three or more observers. Interobserver agreement in vertebral readability for each vertebral level for five observers ranged from 0.05 to 0.47 (95% CI: -0.19, 0.76). Intra-observer agreement using the intraclass correlation coefficient (ICC) ranged from 0.25 to 0.61. The overall sensitivity and specificity were 18% (95% CI: 14-22) and 97% (95% CI: 97-98), respectively. CONCLUSION: In contrast to adults, the six-point technique assessing anterior, middle, and posterior vertebral height ratios is neither satisfactorily reliable nor sensitive for VF diagnosis in children. Training of the software on paediatric images is required in order to develop a paediatric standard that incorporates not only specific vertebral body height ratios but also the age-related physiological changes in vertebral shape that occur throughout childhood

Facilitating implementation of research evidence (FIRE): A randomised controlled trial and process evaluation of two models of facilitation informed by the promoting action on research implementation in health services (PARIHS) framework

Background: The PARIHS framework proposes that successful implementation of research evidence results from the complex interplay between the evidence to be implemented, the context of implementation and the facilitation processes employed. Facilitation is defined as a role (the facilitator) and a process (facilitation strategies/methods). Empirical evidence comparing different facilitation approaches is limited; this paper reports a trial of two different types of facilitation represented in the PARIHS framework. Methods: A pragmatic cluster randomised controlled trial with embedded process evaluation was undertaken in 24 long-term nursing care settings in four European countries. In each country, sites were randomly allocated to standard dissemination of urinary incontinence guideline recommendations and one of two types of external-internal facilitation, labelled Type A and B. Type A facilitation was a less resource intensive approach, underpinned by improvement methodology; Type B was a more intensive, emancipatory model of facilitation, informed by critical social science. The primary outcome was percentage documented compliance with guideline recommendations. Process evaluation was framed by realist methodology and involved quantitative and qualitative data collection from multiple sources. Findings: Quantitative data were obtained from reviews of 2313 records. Qualitative data included over 332 hours of observations of care; 39 hours observation of facilitation activity; 471 staff interviews; 174 resident interviews; 120 next of kin/carer interviews; and 125 stakeholder interviews. There were no significant differences in the primary outcome between study arms and all study arms improved over time. Process data revealed three core mechanisms that influenced the trajectory of the facilitation intervention: alignment of the facilitation approach to the needs and expectations of the internal facilitator and colleagues; engagement of internal facilitators and staff in attitude and action; and learning over time. Data from external facilitators demonstrated that the facilitation interventions did not work as planned, issues were cumulative and maintenance of fidelity was problematic. Implications for D&I Research: Evaluating an intervention - in this case facilitation - that is fluid and dynamic within the methodology of a randomised controlled trial is complex and challenging. For future studies, we suggest a theoretical approach to fidelity, with a focus on mechanisms, as opposed to dose and intensity of the intervention

What is a β cell? - Chapter I in the Human Islet Research Network (HIRN) review series

BACKGROUND: The pancreatic β cell, as the sole source of the vital hormone insulin, has been under intensive study for more than a century. Given the potential of newly created insulin-producing cells as a treatment or even cure of type 1 diabetes (T1D) and possibly in severe cases of type 2 diabetes (T2D), multiple academic and commercial laboratories are working to derive surrogate glucose-responsive, insulin-producing cells. SCOPE OF REVIEW: The recent development of advanced phenotyping technologies, including molecular, epigenomic, histological, or functional, have greatly improved our understanding of the critical properties of human β cells. Using this information, here we summarize the salient features of normal, fully functional adult human β cells, and propose minimal criteria for what should rightfully be termed 'β cells' as opposed to insulin-producing but not fully-functional surrogates that we propose should be referred to as 'β-like' cells or insulin-producing cells. MAJOR CONCLUSIONS: Clear criteria can be established to differentiate fully functional, mature β cells from 'β-like' surrogates. In addition, we outline important knowledge gaps that must be addressed to enable a greater understanding of the β cell

Clinical and laboratory variability in a cohort of patients diagnosed with type 1 VWD in the United States

Von Willebrand disease (VWD) is the most common inherited bleeding disorder, and type 1 VWD is the most common VWD variant. Despite its frequency, diagnosis of type 1 VWD remains the subject of much debate. In order to study the spectrum of type 1 VWD in the United States, the Zimmerman Program enrolled 482 subjects with a previous diagnosis of type 1 VWD without stringent laboratory diagnostic criteria. VWF laboratory testing and full length VWF gene sequencing were performed for all index cases and healthy control subjects in a central laboratory. Bleeding phenotype was characterized using the ISTH Bleeding Assessment Tool. At study entry, 64% of subjects had VWF:Ag or VWF:RCo below the lower limit of normal, while 36% had normal VWF levels. VWF sequence variations were most frequent in subjects with VWF:Ag < 30 IU/dL (82%) while subjects with type 1 VWD and VWF:Ag ≥ 30 IU/dL had an intermediate frequency of variants (44%). Subjects whose VWF testing was normal at study entry had a similar rate of sequence variations as the healthy controls at 14% of subjects. All subjects with severe type 1 VWD and VWF:Ag ≤ 5 IU/dL had an abnormal bleeding score, but otherwise bleeding score did not correlate with VWF:Ag level. Subjects with a historical diagnosis of type 1 VWD had similar rates of abnormal bleeding scores compared to subjects with low VWF levels at study entry. Type 1 VWD in the United States is highly variable, and bleeding symptoms are frequent in this population

In the social factory? Immaterial labour, precariousness and cultural work

This article introduces a special section concerned with precariousness and cultural work. Its aim is to bring into dialogue three bodies of ideas -- the work of the autonomous Marxist 'Italian laboratory'; activist writings about precariousness and precarity; and the emerging empirical scholarship concerned with the distinctive features of cultural work, at a moment when artists, designers and (new) media workers have taken centre stage as a supposed 'creative class' of model entrepreneurs. The paper is divided into three sections. It starts by introducing the ideas of the autonomous Marxist tradition, highlighting arguments about the autonomy of labour, informational capitalism and the 'factory without walls', as well as key concepts such as multitude and immaterial labour. The impact of these ideas and of Operaismo politics more generally on the precarity movement is then considered in the second section, discussing some of the issues that have animated debate both within and outside this movement, which has often treated cultural workers as exemplifying the experiences of a new 'precariat'. In the third and final section of the paper we turn to the empirical literature about cultural work, pointing to its main features before bringing it into debate with the ideas already discussed. Several points of overlap and critique are elaborated -- focusing in particular on issues of affect, temporality, subjectivity and solidarity

Measurement of the B0-anti-B0-Oscillation Frequency with Inclusive Dilepton Events

The $B^0$-$\bar B^0$ oscillation frequency has been measured with a sample of 23 million \B\bar B pairs collected with the BABAR detector at the PEP-II asymmetric B Factory at SLAC. In this sample, we select events in which both B mesons decay semileptonically and use the charge of the leptons to identify the flavor of each B meson. A simultaneous fit to the decay time difference distributions for opposite- and same-sign dilepton events gives $\Delta m_d = 0.493 \pm 0.012{(stat)}\pm 0.009{(syst)}$ ps$^{-1}$.Comment: 7 pages, 1 figure, submitted to Physical Review Letter

Search for a W' boson decaying to a bottom quark and a top quark in pp collisions at sqrt(s) = 7 TeV

Results are presented from a search for a W' boson using a dataset corresponding to 5.0 inverse femtobarns of integrated luminosity collected during 2011 by the CMS experiment at the LHC in pp collisions at sqrt(s)=7 TeV. The W' boson is modeled as a heavy W boson, but different scenarios for the couplings to fermions are considered, involving both left-handed and right-handed chiral projections of the fermions, as well as an arbitrary mixture of the two. The search is performed in the decay channel W' to t b, leading to a final state signature with a single lepton (e, mu), missing transverse energy, and jets, at least one of which is tagged as a b-jet. A W' boson that couples to fermions with the same coupling constant as the W, but to the right-handed rather than left-handed chiral projections, is excluded for masses below 1.85 TeV at the 95% confidence level. For the first time using LHC data, constraints on the W' gauge coupling for a set of left- and right-handed coupling combinations have been placed. These results represent a significant improvement over previously published limits.Comment: Submitted to Physics Letters B. Replaced with version publishe