Simultaneous identification of long similar substrings in large sets of sequences

<p>Abstract</p> <p>Background</p> <p>Sequence comparison faces new challenges today, with many complete genomes and large libraries of transcripts known. Gene annotation pipelines match these sequences in order to identify genes and their alternative splice forms. However, the software currently available cannot simultaneously compare sets of sequences as large as necessary especially if errors must be considered.</p> <p>Results</p> <p>We therefore present a new algorithm for the identification of almost perfectly matching substrings in very large sets of sequences. Its implementation, called ClustDB, is considerably faster and can handle 16 times more data than VMATCH, the most memory efficient exact program known today. ClustDB simultaneously generates large sets of exactly matching substrings of a given minimum length as seeds for a novel method of match extension with errors. It generates alignments of maximum length with a considered maximum number of errors within each overlapping window of a given size. Such alignments are not optimal in the usual sense but faster to calculate and often more appropriate than traditional alignments for genomic sequence comparisons, EST and full-length cDNA matching, and genomic sequence assembly. The method is used to check the overlaps and to reveal possible assembly errors for 1377 <it>Medicago truncatula </it>BAC-size sequences published at <url>http://www.medicago.org/genome/assembly_table.php?chr=1</url>.</p> <p>Conclusion</p> <p>The program ClustDB proves that window alignment is an efficient way to find long sequence sections of homogenous alignment quality, as expected in case of random errors, and to detect systematic errors resulting from sequence contaminations. Such inserts are systematically overlooked in long alignments controlled by only tuning penalties for mismatches and gaps.</p> <p>ClustDB is freely available for academic use.</p

IMPlementing IMProved Asthma self-management as RouTine (IMP2ART) in primary care: study protocol for a cluster randomised controlled implementation trial

BACKGROUND: Asthma is a common long-term condition and major public health problem. Supported self-management for asthma that includes a written personalised asthma action plan, supported by regular professional review, reduces unscheduled consultations and improves asthma outcomes and quality of life. However, despite unequivocal inter/national guideline recommendations, supported self-management is poorly implemented in practice. The IMPlementing IMProved Asthma self-management as RouTine (IMP2ART) implementation strategy has been developed to address this challenge. The aim of this implementation trial is to determine whether facilitated delivery of the IMP2ART strategy increases the provision of asthma action plans and reduces unscheduled care in the context of routine UK primary care. METHODS: IMP2ART is a parallel group, cluster randomised controlled hybrid II implementation trial. One hundred forty-four general practices will be randomly assigned to either the IMP2ART implementation strategy or control group. Following a facilitation workshop, implementation group practices will receive organisational resources to help them prioritise supported self-management (including audit and feedback; an IMP2ART asthma review template), training for professionals and resources to support patients to self-manage their asthma. The control group will continue with usual asthma care. The primary clinical outcome is the between-group difference in unscheduled care in the second year after randomisation (i.e. between 12 and 24 months post-randomisation) assessed from routine data. Additionally, a primary implementation outcome of asthma action plan ownership at 12 months will be assessed by questionnaire to a random sub-group of people with asthma. Secondary outcomes include the number of asthma reviews conducted, prescribing outcomes (reliever medication and oral steroids), asthma symptom control, patients' confidence in self-management and professional support and resource use. A health economic analysis will assess cost-effectiveness, and a mixed methods process evaluation will explore implementation, fidelity and adaptation. DISCUSSION: The evidence for supported asthma self-management is overwhelming. This study will add to the literature regarding strategies that can effectively implement supported self-management in primary care to reduce unscheduled consultations and improve asthma outcomes and quality of life. TRIAL REGISTRATION: ISRCTN15448074. Registered on 2 December 2019

Reduced functional measure of cardiovascular reserve predicts admission to critical care unit following kidney transplantation

Background: There is currently no effective preoperative assessment for patients undergoing kidney transplantation that is able to identify those at high perioperative risk requiring admission to critical care unit (CCU). We sought to determine if functional measures of cardiovascular reserve, in particular the anaerobic threshold (VO2AT) could identify these patients. Methods: Adult patients were assessed within 4 weeks prior to kidney transplantation in a University hospital with a 37-bed CCU, between April 2010 and June 2012. Cardiopulmonary exercise testing (CPET), echocardiography and arterial applanation tonometry were performed. Results: There were 70 participants (age 41.7614.5 years, 60% male, 91.4% living donor kidney recipients, 23.4% were desensitized). 14 patients (20%) required escalation of care from the ward to CCU following transplantation. Reduced anaerobic threshold (VO2AT) was the most significant predictor, independently (OR = 0.43; 95% CI 0.27–0.68; p,0.001) and in the multivariate logistic regression analysis (adjusted OR = 0.26; 95% CI 0.12–0.59; p = 0.001). The area under the receiveroperating- characteristic curve was 0.93, based on a risk prediction model that incorporated VO2AT, body mass index and desensitization status. Neither echocardiographic nor measures of aortic compliance were significantly associated with CCU admission. Conclusions: To our knowledge, this is the first prospective observational study to demonstrate the usefulness of CPET as a preoperative risk stratification tool for patients undergoing kidney transplantation. The study suggests that VO2AT has the potential to predict perioperative morbidity in kidney transplant recipients

IMPlementing IMProved Asthma self-management as RouTine (IMP2ART) in primary care: study protocol for a cluster randomised controlled implementation trial.

BACKGROUND: Asthma is a common long-term condition and major public health problem. Supported self-management for asthma that includes a written personalised asthma action plan, supported by regular professional review, reduces unscheduled consultations and improves asthma outcomes and quality of life. However, despite unequivocal inter/national guideline recommendations, supported self-management is poorly implemented in practice. The IMPlementing IMProved Asthma self-management as RouTine (IMP2ART) implementation strategy has been developed to address this challenge. The aim of this implementation trial is to determine whether facilitated delivery of the IMP2ART strategy increases the provision of asthma action plans and reduces unscheduled care in the context of routine UK primary care. METHODS: IMP2ART is a parallel group, cluster randomised controlled hybrid II implementation trial. One hundred forty-four general practices will be randomly assigned to either the IMP2ART implementation strategy or control group. Following a facilitation workshop, implementation group practices will receive organisational resources to help them prioritise supported self-management (including audit and feedback; an IMP2ART asthma review template), training for professionals and resources to support patients to self-manage their asthma. The control group will continue with usual asthma care. The primary clinical outcome is the between-group difference in unscheduled care in the second year after randomisation (i.e. between 12 and 24 months post-randomisation) assessed from routine data. Additionally, a primary implementation outcome of asthma action plan ownership at 12 months will be assessed by questionnaire to a random sub-group of people with asthma. Secondary outcomes include the number of asthma reviews conducted, prescribing outcomes (reliever medication and oral steroids), asthma symptom control, patients' confidence in self-management and professional support and resource use. A health economic analysis will assess cost-effectiveness, and a mixed methods process evaluation will explore implementation, fidelity and adaptation. DISCUSSION: The evidence for supported asthma self-management is overwhelming. This study will add to the literature regarding strategies that can effectively implement supported self-management in primary care to reduce unscheduled consultations and improve asthma outcomes and quality of life. TRIAL REGISTRATION: ISRCTN15448074. Registered on 2 December 2019

Evaluation of recruitment methods for a trial targeting childhood obesity: Families for Health randomised controlled trial

Background: Recruitment to trials evaluating the effectiveness of childhood obesity management interventions is challenging. We report our experience of recruitment to the Families for Health study, a randomised controlled trial evaluating the effectiveness of a family-based community programme for children aged 6–11 years, versus usual care. We evaluated the effectiveness of active recruitment (contacting eligible families directly) versus passive recruitment (informing the community through flyers, public events, media). Methods: Initial approaches included passive recruitment via the media (newspapers and radio) and two active recruitment methods: National Child Measurement Programme (letters to families with overweight children) and referrals from health-care professionals. With slow initial recruitment, further strategies were employed, including active (e.g. targeted letters from general practices) and passive (e.g. flyers, posters and public events) methods. At first enquiry from a potential participant, families were asked where they heard about the study. Further quantitative (questionnaire) and qualitative data (one-to-one interviews with parents/carers), were collected from recruited families at baseline and 3-month follow-up and included questions about recruitment. Results: In total, 194 families enquired about Families for Health, and 115 (59.3 %) were recruited and randomised. Active recruitment yielded 85 enquiries, with 43 families recruited (50.6 %); passive recruitment yielded 99 enquiries with 72 families recruited (72.7 %). Information seen at schools or GP surgeries accounted for over a quarter of enquiries (28.4 %) and over a third (37.4 %) of final recruitment. Eight out of ten families who enquired this way were recruited. Media-led enquiries were low (5 %), but all were recruited. Children of families recruited actively were more likely to be Asian or mixed race. Despite extensive recruitment methods, the trial did not recruit as planned, and was awarded a no-cost extension to complete the 12-month follow-up. Conclusions: The higher number of participants recruited through passive methods may be due to the large number of potential participants these methods reached and because participants may see the information more than once. Recruiting to a child obesity treatment study is complex and it is advisable to use multiple recruitment strategies, some aiming at blanket coverage and some targeted at families with children who are overweight

Completeness of reporting and risks of overstating impact in cluster randomised trials : a systematic review

Acknowledgments We received no funding specifically for this systematic review. ELT is funded in part by awards R01-AI141444 from the National Institute of Allergy and Infectious Diseases and R01-MH120649 from the US National Institute of Mental Health; both Institutes are part of the National Institutes of Health (NIH). JAG and ACP's support of this project was made possible (in part) by grant number UL1TR002553 from the National Center for Advancing Translational Sciences of the NIH, and the NIH Roadmap for Medical Research. JEM is supported by an Australian National Health and Medical Research Council Career Development Fellowship (APP1143429). SN was supported by an award that is jointly funded by the UK Medical Research Council (MRC) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement, and part of the EDCTP2 programme supported by the European Union (grant reference MR/R010161/1). ABF acknowledges funding support from the National Health and Medical Research Council of Australia (grant ID 1183303). KH is funded by a National Institute for Health Research Senior Research Fellowship SRF-2017-10-002. The contents of the research included in this manuscript are solely the responsibility of the authors and do not necessarily represent the official views of any of the funders. The research contributed by all authors of this manuscript are independent of their funders. Specifically, the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We wish to thank the three reviewers for their insightful comments and constructive feedback.Peer reviewedPublisher PD

Dissociation constants and thermodynamic properties of amines and alkanolamines from (293 to 353) K

The dissociation constants of protonated 2-amino-2-ethyl-l,3-propanediol, 2-amino-2-methyl-l-propanol, diethylmonoethanolamine, diisopropanolamine, dimethylmonoethanolamine, monoethanolamine, 1-amino-2-propanol, methylmonoethanolamine, triethanolamine, and the first and the second dissociation constants of piperazine and hydroxyethylpiperazine have been determined by electromotive force measurements from (293 to 353) K. The dissociation constants of protonated triethylamine have been determined with the same technique from (293 to 333) K. The experimental results and derived values of the standard state thermodynamic properties are reported and compared to available literature values. © 2009 American Chemical Society.

Dissociation constants and thermodynamic properties of alkanolamines

The dissociation constants of protonated 2-amino-2-ethyl-1,3-propanediol (AEPD), 2-amino-2-methyl-1-propanol (AMP), diethylmonoethanolamine (DEMEA), diisopropanolamine (DIPA), dimethylmonoethanolamine (DMMEA), monoethanolamine (MEA), 1-amino-2-propanol (MIPA), and methylmonoethanolamine (MMEA) have been determined by electromotive force measurements from (293 to 353) K. The experimental results and derived values of the standard state thermodynamic properties are reported. © 2009 Elsevier Ltd. All rights reserved.

Effectiveness of a volunteer befriending programme for patients with schizophrenia: randomised controlled trial.

BACKGROUND: Befriending by volunteers has the potential to reduce the frequent social isolation of patients with schizophrenia and thus improve health outcomes. However, trial-based evidence for its effectiveness is limited.AimsTo conduct a randomised controlled trial of befriending for patients with schizophrenia or related disorders. METHOD: Patients were randomised to a befriending programme for 1 year or to receive information about social activities only (trial registration: ISRCTN14021839). Outcomes were assessed masked to allocation at the end of the programme; at 12 months and at a 6-month follow-up. The primary outcome was daily time spent in activities (using the Time Use Survey (TUS)) with intention-to-treat analysis. RESULTS: A total of 124 patients were randomised (63 intervention, 61 active control) and 92 (74%) were followed up at 1 year. In the intervention group, 49 (78%) met a volunteer at least once and 31 (49%) had more than 12 meetings. At 1 year, mean TUS scores were more than three times higher in both groups with no significant difference between them (adjusted difference 8.9, 95% CI -40.7 to 58.5, P = 0.72). There were no significant differences in quality of life, symptoms or self-esteem. However, patients in the intervention group had significantly more social contacts than those in the control group at the end of the 12-month period. This difference held true at the follow-up 6 months later. CONCLUSIONS: Although no difference was found on the primary outcome, the findings suggest that befriending may have a lasting effect on increasing social contacts. It may be used more widely to reduce the social isolation of patients with schizophrenia.Declaration of interestNone.This work was supported by the National Institute for Health Research (NIHR) under its Programme Grants for Applied Research (Reference Number RP-PG-0611-20002). The views expressed are those of the authors and not necessarily those of the National Health Service, the NIHR or the Department of Health in the UK