Beschreibung: In many bacteria, the ability to modulate biofilm production relies on specific signaling molecules that are either self-produced or made by neighboring microbes within the ecological niche. We analyzed the potential interspecies signaling effect of the Burkholderia diffusible signal factor (BDSF) on Francisella novicida , a model organism for Francisella tularensis , and demonstrated that BDSF both inhibits the formation and causes the dispersion of Francisella biofilm. Specificity was demonstrated for the cis versus the trans form of BDSF. Using transcriptome sequencing, quantitative reverse transcription-PCR, and activity assays, we found that BDSF altered the expression of many F. novicida genes, including genes involved in biofilm formation, such as chitinases. Using a chitinase inhibitor, the antibiofilm activity of BDSF was also shown to be chitinase dependent. In addition, BDSF caused an increase in RelA expression and increased levels of (p)ppGpp, leading to decreased biofilm production. These results support our observation that exposure of F. novicida to BDSF causes biofilm dispersal. Furthermore, BDSF upregulated the genes involved in iron acquisition ( figABCD ), increasing siderophore production. Thus, this study provides evidence for a potential role and mechanism of diffusible signal factor (DSF) signaling in the genus Francisella and suggests the possibility of interspecies signaling between Francisella and other bacteria. Overall, this study suggests that in response to the interspecies DSF signal, F. novicida can alter its gene expression and regulate its biofilm formation.

Beschreibung: Objectives The study sought to identify key design features that could be used to create a new framework for group-based health interventions. We designed and tested the first session of a group intervention for stroke survivors with aphasia which was aimed at nurturing new psychological connections between group members. Setting The intervention session, a participant focus group and interviews with intervention facilitators were held in a local community music centre in the South West of England. Participants A convenience sample of 10 community-dwelling people with poststroke aphasia participated in the session. Severity of aphasia was not considered for inclusion. Intervention Participants took part in a 90-min group singing session which involved singing songs from a specially prepared song book. Musical accompaniment was provided by the facilitators. Primary and secondary outcome measures Participants and group facilitators reported their experiences of participating in the session, with a focus on activities within the session related to the intervention aims. Researcher observations of the session were also made. Results Two themes emerged from the analysis, concerning experiences of the session (‘developing a sense of group belonging’) and perceptions of its design and delivery (‘creating the conditions for engagement’). Participants described an emerging sense of shared social identity as a member of the intervention group and identified fixed (eg, group size, session breaks) and flexible (eg, facilitator responsiveness) features of the session which contributed to this emergence. Facilitator interviews and researcher observations corroborated and expanded participant reports. Conclusions Engagement with health intervention content may be enhanced in group settings when intervention participants begin to establish positive and meaningful psychological connections with other group members. Understanding and actively nurturing these connections should be a core feature of a general framework for the design and delivery of group interventions.

Beschreibung: Introduction The Rehabilitation Training (ReTrain) intervention aims to improve functional mobility, adherence to poststroke exercise guidelines and quality of life for people after stroke. A definitive randomised controlled trial (RCT) is required to assess the clinical and cost-effectiveness of ReTrain, which is based on Action for Rehabilitation from Neurological Injury (ARNI). The purpose of this pilot study is to assess the feasibility of such a definitive trial and inform its design. Methods and analysis A 2-group, assessor-blinded, randomised controlled external pilot trial with parallel mixed-methods process evaluation and economic evaluation. 48 participants discharged from clinical rehabilitation despite residual physical disability will be individually randomised 1:1 to ReTrain (25 sessions) or control (exercise advice booklet). Outcome assessment at baseline, 6 and 9 months include Rivermead Mobility Index; Timed Up and Go Test; modified Patient-Specific Functional Scale; 7-day accelerometry; Stroke Self-efficacy Questionnaire, exercise diary, Fatigue Assessment Scale, exercise beliefs and self-efficacy questionnaires, SF-12, EQ-5D-5L, Stroke Quality of Life, Carer Burden Index and Service Receipt Inventory. Feasibility, acceptability and process outcomes include recruitment and retention rates; with measurement burden and trial experiences being explored in qualitative interviews (20 participants, 3 intervention providers). Analyses include descriptive statistics, with 95% CI where appropriate; qualitative themes; intervention fidelity from videos and session checklists; rehearsal of health economic analysis. Ethics and dissemination National Health Service (NHS) National Research Ethics Service approval granted in April 2015; recruitment started in June. Preliminary studies suggested low risk of serious adverse events; however (minor) falls, transitory muscle soreness and high levels of postexercise fatigue are expected. Outputs include pilot data to inform whether to proceed to a definitive RCT and support a funding application; finalised Trainer and Intervention Delivery manuals for multicentre replication of ReTrain; presentations at conferences, public involvement events; internationally recognised peer-reviewed journal publications, open access sources and media releases. Trial registration number NCT02429180 ; Pre-results.

Beschreibung: The transition zone (TZ) of eukaryotic cilia and flagella is a structural intermediate between the basal body and the axoneme that regulates ciliary traffic. Mutations in genes encoding TZ proteins (TZPs) cause human inherited diseases (ciliopathies). Here, we use the trypanosome to identify TZ components and localize them to TZ...

Beschreibung: Motivation: We addressed the problem of inferring gene regulatory network (GRN) from gene expression data of knockout (KO) experiments. This inference is known to be underdetermined and the GRN is not identifiable from data. Past studies have shown that suboptimal design of experiments (DOE) contributes significantly to the identifiability issue of biological networks, including GRNs. However, optimizing DOE has received much less attention than developing methods for GRN inference. Results: We developed REDuction of UnCertain Edges (REDUCE) algorithm for finding the optimal gene KO experiment for inferring directed graphs (digraphs) of GRNs. REDUCE employed ensemble inference to define uncertain gene interactions that could not be verified by prior data. The optimal experiment corresponds to the maximum number of uncertain interactions that could be verified by the resulting data. For this purpose, we introduced the concept of edge separatoid which gave a list of nodes (genes) that upon their removal would allow the verification of a particular gene interaction. Finally, we proposed a procedure that iterates over performing KO experiments, ensemble update and optimal DOE. The case studies including the inference of Escherichia coli GRN and DREAM 4 100-gene GRNs, demonstrated the efficacy of the iterative GRN inference. In comparison to systematic KOs, REDUCE could provide much higher information return per gene KO experiment and consequently more accurate GRN estimates. Conclusions: REDUCE represents an enabling tool for tackling the underdetermined GRN inference. Along with advances in gene deletion and automation technology, the iterative procedure brings an efficient and fully automated GRN inference closer to reality. Availability and implementation: MATLAB and Python scripts of REDUCE are available on www.cabsel.ethz.ch/tools/REDUCE . Contact: rudi.gunawan@chem.ethz.ch Supplementary information: Supplementary data are available at Bioinformatics online.

Beschreibung: Autism spectrum disorder (ASD) is characterized by core social deficits. Prognosis is poor, in part, because existing medications target only associated ASD features. Emerging evidence suggests that the neuropeptide oxytocin (OXT) may be a blood-based biomarker of social functioning and a possible treatment for ASD. However, prior OXT treatment trials...

Beschreibung: Motivation Single cell transcriptional profiling opens up a new avenue in studying the functional role of cell-to-cell variability in physiological processes. The analysis of single cell expression profiles creates new challenges due to the distributive nature of the data and the stochastic dynamics of gene transcription process. The reconstruction of gene regulatory networks (GRNs) using single cell transcriptional profiles is particularly challenging, especially when directed gene-gene relationships are desired. Results We developed SINCERITIES (SINgle CEll Regularized Inference using TIme-stamped Expression profileS) for the inference of GRNs from single cell transcriptional profiles. We focused on time-stamped cross-sectional expression data, commonly generated from transcriptional profiling of single cells collected at multiple time points after cell stimulation. SINCERITIES recovers directed regulatory relationships among genes by employing regularized linear regression (ridge regression), using temporal changes in the distributions of gene expressions. Meanwhile, the modes of the gene regulations (activation and repression) come from partial correlation analyses between pairs of genes. We demonstrated the efficacy of SINCERITIES in inferring GRNs using in silico time-stamped single cell expression data and single cell transcriptional profiles of THP-1 monocytic human leukemia cells. The case studies showed that SINCERITIES could provide accurate GRN predictions, significantly better than other GRN inference algorithms such as TSNI, GENIE3 and JUMP3. Moreover, SINCERITIES has a low computational complexity and is amenable to problems of extremely large dimensionality. Finally, an application of SINCERITIES to single cell expression data of T2EC chicken erythrocytes pointed to BATF as a candidate novel regulator of erythroid development. Availability and implementation MATLAB and R version of SINCERITIES are freely available from the following websites: http://www.cabsel.ethz.ch/tools/sincerities.html and https://github.com/CABSEL/SINCERITIES . The single cell THP-1 and T2EC transcriptional profiles are available from the original publications ( Kouno et al. , 2013 ; Richard et al. , 2016 ). The in silico single cell data are available on SINCERITIES websites. Contact rudi.gunawan@chem.ethz.ch Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.

Beschreibung: Objectives To assess acceptability and feasibility of trial processes and the Rehabilitation Training (ReTrain) intervention including an assessment of intervention fidelity. Design A two-group, assessor-blinded, randomised controlled trial with parallel mixed methods process and economic evaluations. Setting Community settings across two sites in Devon. Participants Eligible participants were: 18 years old or over, with a diagnosis of stroke and with self-reported mobility issues, no contraindications to physical activity, discharged from National Health Service or any other formal rehabilitation programme at least 1 month before, willing to be randomised to either control or ReTrain and attend the training venue, possessing cognitive capacity and communication ability sufficient to participate. Participants were individually randomised (1:1) via a computer-generated randomisation sequence minimised for time since stroke and level of functional disability. Only outcome assessors independent of the research team were blinded to group allocation. Interventions ReTrain comprised (1) an introductory one-to-one session; (2) ten, twice-weekly group classes with up to two trainers and eight clients; (3) a closing one-to-one session, followed by three drop-in sessions over the subsequent 3 months. Participants received a bespoke home-based training programme. All participants received treatment as usual. The control group received an exercise after stroke advice booklet. Outcome measures Candidate primary outcomes included functional mobility and physical activity. Results Forty-five participants were randomised (ReTrain=23; Control=22); data were available from 40 participants at 6 months of follow-up (ReTrain=21; Control=19) and 41 at 9 months of follow-up (ReTrain=21; Control=20). We demonstrated ability to recruit and retain participants. Participants were not burdened by the requirements of the study. We were able to calculate sample estimates for candidate primary outcomes and test procedures for process and health economic evaluations. Conclusions All objectives were fulfilled and indicated that a definitive trial of ReTrain is feasible and acceptable. Trial registration number NCT02429180 ; Results.

Beschreibung: Objective To identify factors influencing general practitioners' (GPs’) decisions about whether or not to remain in direct patient care in general practice and what might help to retain them in that role. Design Qualitative, in-depth, individual interviews exploring factors related to GPs leaving, remaining in and returning to direct patient care. Setting South West England, UK. Participants 41 GPs: 7 retired; 8 intending to take early retirement; 11 who were on or intending to take a career break; 9 aged under 50 years who had left or were intending to leave direct patient care and 6 who were not intending to leave or to take a career break. Plus 19 stakeholders from a range of primary care-related professional organisations and roles. Results Reasons for leaving direct patient care were complex and based on a range of job-related and individual factors. Three key themes underpinned the interviewed GPs’ thinking and rationale: issues relating to their personal and professional identity and the perceived value of general practice-based care within the healthcare system; concerns regarding fear and risk, for example, in respect of medical litigation and managing administrative challenges within the context of increasingly complex care pathways and environments; and issues around choice and volition in respect of personal social, financial, domestic and professional considerations. These themes provide increased understanding of the lived experiences of working in today’s National Health Service for this group of GPs. Conclusion Future policies and strategies aimed at retaining GPs in direct patient care should clarify the role and expectations of general practice and align with GPs’ perception of their own roles and identity; demonstrate to GPs that they are valued and listened to in planning delivery of the UK healthcare; target GPs’ concerns regarding fear and risk, seeking to reduce these to manageable levels and give GPs viable options to support them to remain in direct patient care.

Beschreibung: Author(s): H. Miao, W. H. Brito, Z. P. Yin, R. D. Zhong, G. D. Gu, P. D. Johnson, M. P. M. Dean, S. Choi, G. Kotliar, W. Ku, X. C. Wang, C. Q. Jin, S.-F. Wu, T. Qian, and H. Ding Here, we use angle-resolved photoemission spectroscopy to study superconductivity that emerges in two extreme cases, from a Fermi-liquid phase (LiFeAs) and an incoherent bad-metal phase ( FeTe 0.55 Se 0.45 ). We find that although the electronic coherence can strongly reshape the single-particle spectral... [Phys. Rev. B 98, 020502(R)] Published Mon Jul 09, 2018