Discriminatory power of RNA family models

Motivation: RNA family models group nucleotide sequences that share a common biological function. These models can be used to find new sequences belonging to the same family. To succeed in this task, a model needs to exhibit high sensitivity as well as high specificity. As model construction is guided by a manual process, a number of problems can occur, such as the introduction of more than one model for the same family or poorly constructed models. We explore the Rfam database to discover such problems

Workplace support for newly qualified doctors and secondary school teachers: A comparative analysis

This is the final version. Available on open access from Wiley via the DOI in this recordData availability statement: We intend that the data collected during this study, from 11 newly qualified teachers, will be uploaded to the UK Data Service archive, in anonymised form. The secondary analysis drew up already existing data.Doctors and teachers in their first year of practice face steep learning curves and increased stress, which can induce poor mental health, burnout and attrition. Informal workplace support from colleagues can help smooth transitions and aid professional development. A three-phase comparative research design was used to explore who provides informal workplace support to early-career professionals, types of support and influencing factors. Phase 1 was a systematic secondary analysis of interviews and audio diaries from 52 UK doctors in their first year of foundation training (F1s). Phase 2 involved new narrative interviews with 11 newly qualified teachers (NQTs) from English secondary schools. Phase 3 was a comparative analysis to produce a model of workplace support. Given barriers to accessing senior doctors, F1 doctors drew upon nurses, pharmacists, microbiologists, peers/near-peers and allied healthcare professionals for support. NQTs gained support from allocated mentors and seniors within subject departments, as well as teaching assistants, allied support staff and wider professional networks. Support types for both professions included information and advice on practice, orientation to local settings, collaborative development activities, observation and feedback, and socioemotional support. Influencing factors included variable departmental cultures, limited opportunities for informal contact, sometimes negative inter-group perceptions and the agentic responses of novices. The resulting workplace model of support could underpin future research and evaluations of support in similar ‘hot-action’ environments. In medicine and teaching, greater utilisation of near-peers and allied staff, improved role understanding and communication, increased informal contact and sharing successful strategies across professions could enhance supportive relationships.Economic and Social Research Council (ESRC

Genome-wide analysis of long noncoding RNA stability

Transcriptomic analyses have identified tens of thousands of intergenic, intronic, and cis-antisense long noncoding RNAs (lncRNAs) that are expressed from mammalian genomes. Despite progress in functional characterization, little is known about the post-transcriptional regulation of lncRNAs and their half-lives. Although many are easily detectable by a variety of techniques, it has been assumed that lncRNAs are generally unstable, but this has not been examined genome-wide. Utilizing a custom noncoding RNA array, we determined the half-lives of ∼800 lncRNAs and ∼12,000 mRNAs in the mouse Neuro-2a cell line. We find only a minority of lncRNAs are unstable. LncRNA half-lives vary over a wide range, comparable to, although on average less than, that of mRNAs, suggestive of complex metabolism and widespread functionality. Combining half-lives with comprehensive lncRNA annotations identified hundreds of unstable (half-life 16 h). Analysis of lncRNA features revealed that intergenic and cis-antisense RNAs are more stable than those derived from introns, as are spliced lncRNAs compared to unspliced (single exon) transcripts. Subcellular localization of lncRNAs indicated widespread trafficking to different cellular locations, with nuclear-localized lncRNAs more likely to be unstable. Surprisingly, one of the least stable lncRNAs is the well-characterized paraspeckle RNA Neat1, suggesting Neat1 instability contributes to the dynamic nature of this subnuclear domain. We have created an online interactive resource (http://stability. matticklab.com) that allows easy navigation of lncRNA and mRNA stability profiles and provides a comprehensive annotation of ∼7200 mouse lncRNAs

Understanding surgical antimicrobial prescribing behaviour in the hospital setting: a systematic review and meta-ethnography protocol.

This is the final version. Available from BMC via the DOI in this record. Availability of data and materials: Not applicable.BACKGROUND: Surgical specialities use extensive amounts of antimicrobials, and misuse has been widely reported, making them a key target for antimicrobial stewardship initiatives. Interventions informed by, and tailored to, a clear understanding of the contextual barriers to appropriate antimicrobial use are more likely to successfully improve practice. However, this approach has been under utilised. Our aim is to synthesise qualitative studies on surgical antimicrobial prescribing behaviour (APB) in hospital settings to explain how and why contextual factors act and interact to influence APB amongst surgical teams. We will develop new theory to advance understanding and identify knowledge gaps to inform further research. METHODS: The meta-ethnography will follow the seven-phase method described by Noblit and Hare. We will conduct a comprehensive search using eight databases (AMED, CINAHL, EMBASE, MEDLINE, MEDLINE-in-process, Web of Science, Cochrane Library and PsycINFO) with no date restrictions; forwards and backwards citation searches; and contacting first authors of relevant papers. Studies will be dual screened and included if they use recognised qualitative methods and analysis; focus on contextual factors associated with surgical APB within hospital settings; are available in full in English; and are relevant to the research question. Any disagreements between reviewers will be resolved through discussion to reach consensus. Included studies will be read repeatedly to illuminate key concepts and the relationship between key concepts across studies. Then, key concepts will be sorted into conceptual categories or 'piles' which will be further abstracted to form a conceptual framework explaining surgical APB. During the synthesis, emerging interpretations will be discussed with stakeholders (including authors of included studies where possible; surgical and stewardship practitioners; and patient representatives) to ensure new knowledge is meaningful. DISCUSSION: This research has several strengths: (1) the protocol has been written with reference to established guidance maximising rigour and transparency; (2) the multi-disciplinary research team bring varied interpretative repertoires and relevant methodological skills; and (3) stakeholders will be involved to ensure that findings are relevant, and disseminated via suitable channels, to support improved patient care. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42020184343.Health Education England/National Institute for Health Researc

Receptor Quaternary Organization Explains G Protein-Coupled Receptor Family Structure.

The organization of Rhodopsin-family G protein-coupled receptors (GPCRs) at the cell surface is controversial. Support both for and against the existence of dimers has been obtained in studies of mostly individual receptors. Here, we use a large-scale comparative study to examine the stoichiometric signatures of 60 receptors expressed by a single human cell line. Using bioluminescence resonance energy transfer- and single-molecule microscopy-based assays, we found that a relatively small fraction of Rhodopsin-family GPCRs behaved as dimers and that these receptors otherwise appear to be monomeric. Overall, the analysis predicted that fewer than 20% of ∼700 Rhodopsin-family receptors form dimers. The clustered distribution of the dimers in our sample and a striking correlation between receptor organization and GPCR family size that we also uncover each suggest that receptor stoichiometry might have profoundly influenced GPCR expansion and diversification

NONCODE v2.0: decoding the non-coding

The NONCODE database is an integrated knowledge database designed for the analysis of non-coding RNAs (ncRNAs). Since NONCODE was first released 3 years ago, the number of known ncRNAs has grown rapidly, and there is growing recognition that ncRNAs play important regulatory roles in most organisms. In the updated version of NONCODE (NONCODE v2.0), the number of collected ncRNAs has reached 206 226, including a wide range of microRNAs, Piwi-interacting RNAs and mRNA-like ncRNAs. The improvements brought to the database include not only new and updated ncRNA data sets, but also an incorporation of BLAST alignment search service and access through our custom UCSC Genome Browser. NONCODE can be found under http://www.noncode.org or http://noncode.bioinfo.org.cn

Tipping the balance: A systematic review and meta-ethnography to unfold the complexity of surgical antimicrobial prescribing behavior in hospital settings.

This is the final version. Available from Public Library of Science via the DOI in this record. Data Availability Statement: All relevant data are within the paper and its Supporting Information filesSurgical specialties account for a high proportion of antimicrobial use in hospitals, and misuse has been widely reported resulting in unnecessary patient harm and antimicrobial resistance. We aimed to synthesize qualitative studies on surgical antimicrobial prescribing behavior, in hospital settings, to explain how and why contextual factors act and interact to influence practice. Stakeholder engagement was integrated throughout to ensure consideration of varying interpretive repertoires and that the findings were clinically meaningful. The meta-ethnography followed the seven phases outlined by Noblit and Hare. Eight databases were systematically searched without date restrictions. Supplementary searches were performed including forwards and backwards citation chasing and contacting first authors of included papers to highlight further work. Following screening, 14 papers were included in the meta-ethnography. Repeated reading of this work enabled identification of 48 concepts and subsequently eight overarching concepts: hierarchy; fear drives action; deprioritized; convention trumps evidence; complex judgments; discontinuity of care; team dynamics; and practice environment. The overarching concepts interacted to varying degrees but there was no consensus among stakeholders regarding an order of importance. Further abstraction of the overarching concepts led to the development of a conceptual model and a line-of-argument synthesis, which posits that social and structural mediators influence individual complex antimicrobial judgements and currently skew practice towards increased and unnecessary antimicrobial use. Crucially, our model provides insights into how we might 'tip the balance' towards more evidence-based antimicrobial use. Currently, healthcare workers deploy antimicrobials across the surgical pathway as a safety net to allay fears, reduce uncertainty and risk, and to mitigate against personal blame. Our synthesis indicates that prescribing is unlikely to change until the social and structural mediators driving practice are addressed. Furthermore, it suggests that research specifically exploring the context for effective and sustainable quality improvement stewardship initiatives in surgery is now urgent.Health Education England/National Institute for Health Researc

Buprenorphine versus dihydrocodeine for opiate detoxification in primary care: a randomised controlled trial

Background Many drug users present to primary care requesting detoxification from illicit opiates. There are a number of detoxification agents but no recommended drug of choice. The purpose of this study is to compare buprenorphine with dihydrocodeine for detoxification from illicit opiates in primary care. Methods Open label randomised controlled trial in NHS Primary Care (General Practices), Leeds, UK. Sixty consenting adults using illicit opiates received either daily sublingual buprenorphine or daily oral dihydrocodeine. Reducing regimens for both interventions were at the discretion of prescribing doctor within a standard regimen of not more than 15 days. Primary outcome was abstinence from illicit opiates at final prescription as indicated by a urine sample. Secondary outcomes during detoxification period and at three and six months post detoxification were recorded. Results Only 23% completed the prescribed course of detoxification medication and gave a urine sample on collection of their final prescription. Risk of non-completion of detoxification was reduced if allocated buprenorphine (68% vs 88%, RR 0.58 CI 0.35–0.96, p = 0.065). A higher proportion of people allocated to buprenorphine provided a clean urine sample compared with those who received dihydrocodeine (21% vs 3%, RR 2.06 CI 1.33–3.21, p = 0.028). People allocated to buprenorphine had fewer visits to professional carers during detoxification and more were abstinent at three months (10 vs 4, RR 1.55 CI 0.96–2.52) and six months post detoxification (7 vs 3, RR 1.45 CI 0.84–2.49). Conclusion Informative randomised trials evaluating routine care within the primary care setting are possible amongst drug using populations. This small study generates unique data on commonly used treatment regimens