riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow.

MOTIVATION: Ribosome profiling, or Ribo-seq, is the state-of-the-art method for quantifying protein synthesis in living cells. Computational analysis of Ribo-seq data remains challenging due to the complexity of the procedure, as well as variations introduced for specific organisms or specialized analyses. RESULTS: We present riboviz 2, an updated riboviz package, for the comprehensive transcript-centric analysis and visualization of Ribo-seq data. riboviz 2 includes an analysis workflow built on the Nextflow workflow management system for end-to-end processing of Ribo-seq data. riboviz 2 has been extensively tested on diverse species and library preparation strategies, including multiplexed samples. riboviz 2 is flexible and uses open, documented file formats, allowing users to integrate new analyses with the pipeline. AVAILABILITY AND IMPLEMENTATION: riboviz 2 is freely available at github.com/riboviz/riboviz.

Interventions to improve hearing aid use in adult auditory rehabilitation.

BACKGROUND: Acquired adult-onset hearing loss is a common long-term condition for which the most common intervention is hearing aid fitting. However, up to 40% of people fitted with a hearing aid either fail to use it or may not gain optimal benefit from it. This is an update of a review first published in The Cochrane Library in 2014. OBJECTIVES: To assess the long-term effectiveness of interventions to promote the use of hearing aids in adults with acquired hearing loss fitted with at least one hearing aid. SEARCH METHODS: The Cochrane ENT Information Specialist searched the Cochrane ENT Trials Register; Central Register of Controlled Trials (CENTRAL 2016, Issue 5); PubMed; EMBASE; CINAHL; Web of Science; ClinicalTrials.gov; ICTRP and additional sources for published and unpublished trials. The date of the search was 13 June 2016. SELECTION CRITERIA: We included randomised controlled trials (RCTs) of interventions designed to improve or promote hearing aid use in adults with acquired hearing loss compared with usual care or another intervention. We excluded interventions that compared hearing aid technology. We classified interventions according to the 'chronic care model' (CCM). The primary outcomes were hearing aid use (measured as adherence or daily hours of use) and adverse effects (inappropriate advice or clinical practice, or patient complaints). Secondary patient-reported outcomes included quality of life, hearing handicap, hearing aid benefit and communication. Outcomes were measured over the short ( 12 to < 52 weeks) and long term (one year plus). DATA COLLECTION AND ANALYSIS: We used the standard methodological procedures expected by Cochrane. MAIN RESULTS: We included 37 studies involving a total of 4129 participants. Risk of bias across the included studies was variable. We judged the GRADE quality of evidence to be very low or low for the primary outcomes where data were available.The majority of participants were over 65 years of age with mild to moderate adult-onset hearing loss. There was a mix of new and experienced hearing aid users. Six of the studies (287 participants) assessed long-term outcomes.All 37 studies tested interventions that could be classified using the CCM as self-management support (ways to help someone to manage their hearing loss and hearing aid(s) better by giving information, practice and experience at listening/communicating or by asking people to practise tasks at home) and/or delivery system design interventions (just changing how the service was delivered). Self-management support interventions We found no studies that investigated the effect of these interventions on adherence, adverse effects or hearing aid benefit. Two studies reported daily hours of hearing aid use but we were unable to combine these in a meta-analysis. There was no evidence of a statistically significant effect on quality of life over the medium term. Self-management support reduced short- to medium-term hearing handicap (two studies, 87 participants; mean difference (MD) -12.80, 95% confidence interval (CI) -23.11 to -2.48 (0 to 100 scale)) and increased the use of verbal communication strategies in the short to medium term (one study, 52 participants; MD 0.72, 95% CI 0.21 to 1.23 (0 to 5 scale)). The clinical significance of these statistical findings is uncertain. It is likely that the outcomes were clinically significant for some, but not all, participants. Our confidence in the quality of this evidence was very low. No self-management support studies reported long-term outcomes. Delivery system design interventionsThese interventions did not significantly affect adherence or daily hours of hearing aid use in the short to medium term, or adverse effects in the long term. We found no studies that investigated the effect of these interventions on quality of life. There was no evidence of a statistically or clinically significant effect on hearing handicap, hearing aid benefit or the use of verbal communication strategies in the short to medium term. Our confidence in the quality of this evidence was low or very low. Long-term outcome measurement was rare. Combined self-management support/delivery system design interventionsOne combined intervention showed evidence of a statistically significant effect on adherence in the short term (one study, 167 participants, risk ratio (RR) 1.06, 95% CI 1.00 to 1.12). However, there was no evidence of a statistically or clinically significant effect on daily hours of hearing aid use over the long term, or the short to medium term. No studies of this type investigated adverse effects. There was no evidence of an effect on quality of life over the long term, or short to medium term. These combined interventions reduced hearing handicap in the short to medium term (15 studies, 728 participants; standardised mean difference (SMD) -0.26, 95% CI -0.48 to -0.04). This represents a small-moderate effect size but there is no evidence of a statistically significant effect over the long term. There was evidence of a statistically, but not clinically, significant effect on long-term hearing aid benefit (two studies, 69 participants, MD 0.30, 95% CI 0.02 to 0.58 (1 to 5 scale)), but no evidence of an effect over the short to medium term. There was evidence of a statistically, but not clinically, significant effect on the use of verbal communication strategies in the short term (four studies, 223 participants, MD 0.45, 95% CI 0.15 to 0.74 (0 to 5 scale)), but not the long term. Our confidence in the quality of this evidence was low or very low.We found no studies that assessed the effect of other CCM interventions (decision support, the clinical information system, community resources or health system changes). AUTHORS' CONCLUSIONS: There is some low to very low quality evidence to support the use of self-management support and complex interventions combining self-management support and delivery system design in adult auditory rehabilitation. However, effect sizes are small. The range of interventions that have been tested is relatively limited. Future research should prioritise: long-term outcome assessment; development of a core outcome set for adult auditory rehabilitation; and study designs and outcome measures that are powered to detect incremental effects of rehabilitative healthcare system changes.

Current process in hearing-aid fitting appointments: An analysis of audiologists' use of behaviour change techniques using the behaviour change technique taxonomy (v1).

OBJECTIVES: To observe and analyse the range and nature of behaviour change techniques (BCTs) employed by audiologists during hearing-aid fitting consultations to encourage and enable hearing-aid use. DESIGN: Non-participant observation and qualitative thematic analysis using the behaviour change technique taxonomy (version 1) (BCTTv1). STUDY SAMPLE: Ten consultations across five English NHS audiology departments. RESULTS: Audiologists engage in behaviours to ensure the hearing-aid is fitted to prescription and is comfortable to wear. They provide information, equipment, and training in how to use a hearing-aid including changing batteries, cleaning, and maintenance. There is scope for audiologists to use additional BCTs: collaborating with patients to develop a behavioural plan for hearing-aid use that includes goal-setting, action-planning and problem-solving; involving significant others; providing information on the benefits of hearing-aid use or the consequences of non-use and giving advice about using prompts/cues for hearing-aid use. CONCLUSIONS: This observational study of audiologist behaviour in hearing-aid fitting consultations has identified opportunities to use additional behaviour change techniques that might encourage hearing-aid use. This information defines potential intervention targets for further research with the aim of improving hearing-aid use amongst adults with acquired hearing loss.

Outcome Measurement in Adult Auditory Rehabilitation: A Scoping Review of Measures Used in Randomized Controlled Trials.

OBJECTIVES: This review documented the range and nature of reported outcome measures in the context of adult auditory rehabilitative research. DESIGN: A scoping review conducted as a part of the development of a systematic review of the effect of interventions to improve hearing aid use. The authors searched the Cochrane Ear, Nose and Throat Disorders Group Trials Register; the Cochrane Central Register of Controlled Trials; PubMed; EMBASE; CINAHL; Web of Science; Cambridge Scientific Abstracts; ICTRP; and additional sources for published and unpublished randomized control trials. The date of the search was November 6, 2013. Outcomes were grouped using a framework suggested by the Cochrane Effective Practice and Organization of Care group. RESULTS: Patient outcomes included adherence to hearing aid use, daily hours of aid use, hearing handicap, hearing aid benefit, quality of life, and communication and psychological outcome. Satisfaction and speech perception were frequent secondary outcomes. There was diversity in measures used to report patient outcomes. Outcome categories other than patient health status and behavior were rarely reported. The timing of outcome measurement was often short term (<12 weeks), with a relative lack of evidence on long-term outcomes (>1 year). CONCLUSIONS: This review has highlighted considerable diversity in patient-reported outcome measurements in randomized control trials in the context of adult auditory rehabilitation. In addition, there are gaps in the literature with respect to measurement of other outcome types of potential interest to stakeholders, including policymakers and commissioners. Long-term outcome assessment is rare.

A study of the relationship between the video head impulse test and air calorics.

The video head impulse test (vHIT) has been proposed as an objective approach to detect peripheral vestibular disorder in a clinical setting. Data from several studies indicate that the vHIT is a useful addition to the vestibular test battery and can give complementary information to caloric testing. This study explores the relationship between lateral canal vestibular occular reflex gain measured using the vHIT system and canal paresis indicated using air calorics in a sample of patients attending a clinic for balance disorder. Sensitivity and specificity of the vHIT test relative to calorics was studied for a clinical sample of 51 patients (20 male, 31 female) who attended a private clinic for balance disorders. vHIT gains were compared to the manufacturer's normative range and to data from a normative study using 30 young volunteers. Of 14 patients in the clinical sample that had significant canal paresis indicated by air calorics, only 4 showed a significant abnormality in either canal using a measurement of vHIT gain. vHIT gain does not correlate with canal paresis as indicated by air caloric testing. vHIT gain appears relatively insensitive to peripheral vestibular disorder as indicated by air caloric testing, although patients that had no caloric response on one side showed abnormal vHIT gain. vHIT testing may be a useful addition to the existing vestibular test battery, but it does not appear to be an alternative to it.

Interventions to improve hearing aid use in adult auditory rehabilitation.

BACKGROUND: Acquired adult-onset hearing loss is a common long-term condition for which the most common intervention is hearing aid fitting. However, up to 40% of people fitted with a hearing aid either fail to use it or may not gain optimal benefit from it. OBJECTIVES: To assess the long-term effectiveness of interventions to promote the use of hearing aids in adults with acquired hearing loss fitted with at least one hearing aid. SEARCH METHODS: We searched the Cochrane ENT Disorders Group Trials Register; CENTRAL; PubMed; EMBASE; CINAHL; Web of Science; Cambridge Scientific Abstracts; ICTRP and additional sources for published and unpublished trials. The date of the search was 6 November 2013. SELECTION CRITERIA: We included randomised controlled trials (RCTs) of interventions designed to improve or promote hearing aid use in adults with acquired hearing loss compared with usual care or another intervention. We excluded interventions that compared hearing aid technology. We classified interventions according to the 'chronic care model' (CCM). The primary outcomes were hearing aid use (measured as adherence or daily hours of use) and adverse effects (inappropriate advice or clinical practice, or patient complaints). Secondary patient-reported outcomes included quality of life, hearing handicap, hearing aid benefit and communication. Outcomes were measured over the short ( 12 to < 52 weeks) and long term (one year plus). DATA COLLECTION AND ANALYSIS: We used the standard methodological procedures expected by The Cochrane Collaboration. MAIN RESULTS: We included 32 studies involving a total of 2072 participants. The risk of bias across the included studies was variable. We judged the GRADE quality of evidence to be very low or low for the primary outcomes where data were available.The majority of participants were over 65 years of age with mild to moderate adult-onset hearing loss. There was a mix of new and experienced hearing aid users. Six of the studies (1018 participants) were conducted in a military veteran population. Six of the studies (287 participants) assessed long-term outcomes.All 32 studies tested interventions that could be classified as self management support (ways to help someone to manage their hearing loss and hearing aid(s) better by giving information, practice and experience at listening/communicating or by asking people to practise tasks at home) and/or delivery system design interventions (just changing how the service was delivered) according to the CCM. Self management support interventions We found no studies that investigated the effect of these interventions on adherence, adverse effects or hearing aid benefit. Two studies reported daily hours of hearing aid use but we were unable to combine these in a meta-analysis. There was no evidence of a statistically significant effect on quality of life over the medium term. Self management support reduced short- to medium-term hearing handicap (two studies, 87 participants; mean difference (MD) -12.80, 95% confidence interval (CI) -23.11 to -2.48 (0 to 100 scale)) and increased the use of verbal communication strategies in the short to medium term (one study, 52 participants; MD 0.72, 95% CI 0.21 to 1.23 (0 to 5 scale)). The clinical significance of these statistical findings is uncertain but it is likely that the outcomes were clinically significant for some, but not all, participants. Our confidence in the quality of this evidence was very low. No self management support studies reported long-term outcomes. Delivery system design interventions These interventions did not significantly affect adherence or daily hours of hearing aid use in the short to medium term, or adverse effects in the long term. We found no studies that investigated the effect of these interventions on quality of life. There was no evidence of a statistically or clinically significant effect on hearing handicap, hearing aid benefit or the use of verbal communication strategies in the short to medium term. Our confidence in the quality of this evidence was low or very low. Long-term outcome measurement was rare. Combined self management support/delivery system design interventions We found no studies that investigated the effect of complex interventions combining components of self management support and delivery system design on adherence or adverse effects. There was no evidence of a statistically or clinically significant effect on daily hours of hearing aid use over the long term, or the short to medium term. Similarly, there was no evidence of an effect on quality of life over the long term, or short to medium term. These combined interventions reduced hearing handicap in the short to medium term (13 studies, 485 participants, standardised mean difference (SMD) -0.27, 95% CI -0.49 to -0.06). This represents a small-moderate effect size but there is no evidence of a statistically significant effect over the long term. There was evidence of a statistically, but not clinically, significant effect on long-term hearing aid benefit (two studies, 69 participants, MD 0.30, 95% CI 0.02 to 0.58 (1 to 5 scale)), but no evidence of effect over the short to medium term. There was evidence of a statistically, but not clinically, significant effect on the use of verbal communication strategies in the short term (four studies, 223 participants, MD 0.45, 95% CI 0.15 to 0.74 (0 to 5 scale)), but not the long term. Our confidence in the quality of this evidence was low or very low.We found no studies that assessed the effect of other CCM interventions (decision support, the clinical information system, community resources or health system changes). AUTHORS' CONCLUSIONS: There is some low to very low quality evidence to support the use of self management support and complex interventions combining self management support and delivery system design in adult auditory rehabilitation. However, effect sizes are small and the range of interventions that have been tested is relatively limited. Priorities for future research should be assessment of long-term outcome a year or more after the intervention, development of a core outcome set for adult auditory rehabilitation and development of study designs and outcome measures that are powered to detect incremental effects of rehabilitative healthcare system changes over and above the provision of a hearing aid.

Mixed-method exploratory study of general practitioner and nurse perceptions of a new community based nurse-led heart failure service.

INTRODUCTION: The treatment of patients with chronic heart failure (CHF) remains sub-optimal. Specialist CHF nurses are proven to improve care and reduce admission but developing such services, especially in remote areas, can be difficult. This study aimed: first, to assess the perceived acceptability and effectiveness of a new community based nurse-led heart failure service by general practitioners (GPs) in an area with a dispersed population; second, to assess the knowledge and learning needs of GPs; and third, to assess perceptions of the use of national guidelines and telehealth on heart failure management. METHODS: The study was conducted in the Scottish Highlands, a large geographical area in the north of the UK which includes both rural and urban populations. The area has a total population of 240 000, approximately 60% of whom are within 1 hour travel time of the largest urban centre. A postal survey of all GPs (n = 260) and structured email survey of all CHF specialist nurses (n = 3) was performed. All responses were entered into a Microsoft Excel spreadsheet, summarised and subjected to thematic analysis. Differences between GPs in 'rural', 'urban' or both 'urban & rural' was investigated using an F-test for continuous variables and a three-sample test for equality of proportions for nominal data. RESULTS: Questionnaires were returned from 83 GPs (32%) and all three CHF specialist nurses. In this sample there were only a few differences between GPs from 'rural', 'urban' and 'urban & rural'. There also appeared to be little difference in responses between those who had the experience of the CHF nurse service and those who had not. Overall, 32 GPs (39%) wished better, local access to echocardiography, while 63 (76%) wished access to testing for brain natriuretic peptide (BNP). Only 27 GPs (33%) referred all patients with CHF to hospital. A number of GPs stated that this was dependant on individual circumstances and the patient's ability to travel. The GPs were confident to initiate standard heart failure drugs although only 54 (65%) were confident in the initiation of beta-blockers. Most GPs (69%) had had experience of the CHF specialist nurse service and the responses were mixed. The GPs who had experienced the service appeared less confident that it would lead to reduced admission of patients to hospital (51% vs 77%, p = 0.046). Three main themes emerged from the nurse responses: service planning, communication and attitudinal changes after service embedment. CONCLUSIONS: This study demonstrates that a community based heart failure nurse service was not universally valued. Differences between urban and rural localities (communication) suggest that models of care derived from evidence based practice in urban areas may not be directly transferable to remote areas. Clearly, good communication among staff groups at all stages of implementation is important; however, despite best efforts and clinical trial evidence, specialist nurse services will not be welcomed by all doctors. Service providers and commissioners should be cognisant of the different roles of urban and rural GPs when designing such services. Among GPs there was a high degree of confidence with initiation and titration of drugs for heart failure with the exception of beta-blockers so clearly this is an area of ongoing educational need and support. Education and support should focus on ensuring that all doctors who care for patients with CHF have the skills and confidence to use medical therapies and specialist services as appropriate.

Comparison of Levitt- and Zwislocki-type adaptive procedures for stimulus placement in human listeners.

The "3-down, 1-up" adaptive stimulus placement rules attributed to Levitt and Zwislocki were compared in the context of human interaural time difference discrimination, employing otherwise commonly used procedures (e.g., averaging reversals to estimate threshold). The Zwislocki rule typically accumulated over three more reversals than the Levitt rule but the rules were approximately equally efficient. This may be because the additional reversals did not provide additional information or that any additional information was countered by other factors, such as the lower theoretical asymptotic response probability (0.75 vs 0.794). Relative bias between rules was also explored with the aid of a simulation.

Speech recognition and comfort using hearing instruments with adaptive directional characteristics in asymmetric listening conditions.

OBJECTIVE: Hearing instruments with adaptive directional microphone systems attempt to maximize speech-to-noise ratio (SNR) and thereby improve speech recognition in noisy backgrounds. When instruments with adaptive systems are fitted bilaterally, there is the potential for adverse effects as they operate independently and may give confusing cues or disturbing effects. The present study compared speech recognition performance in 16 listeners fitted bilaterally with the Phonak Claro hearing instrument using omni-directional, fixed directional, and adaptive directional microphone settings as well as mixed microphone settings (an omni-directional microphone on one side and an adaptive directional microphone on the other). DESIGN: Under anechoic conditions, speech was always presented from a loudspeaker directly in front of the listener (0 degree azimuth) whereas noise was presented from one or two loudspeakers arranged either symmetrically (0, 180, 90 + 270 degrees) or asymmetrically (170 + 240 degrees and 120 + 190 degrees) in the horizontal plane. Adaptive sentence recognition in noise measurement was supplemented by quality ratings. RESULTS: With symmetrical omni-directional settings (Omni/Omni), performance was poorer than a control group of 14 listeners with normal hearing tested unaided: Aided listeners required 4.3 dB more favorable SNR for criterion performance. In all loudspeaker arrangements in which directional characteristics could be exploited, performance with symmetrical adaptive microphones (Adapt/Adapt) was similar to the control group. The mixed microphone settings did not appear to confer any particular disadvantage for speech recognition from their asymmetric nature, always giving scores significantly better than Omni/Omni. Quality rating scores were consistent with speech recognition performance, showing benefits in terms of clarity and comfort for the Adapt/Adapt and Fixed/Fixed microphone conditions over the Omni/Omni and mixed microphone conditions wherever directional characteristics could be used. Similarly, the mixed microphone conditions were rated more comfortable and quieter for the noise than Omni/Omni. CONCLUSIONS: It is concluded that bilateral hearing instruments with adaptive directional microphones confer benefits in terms of speech recognition in noise and sound quality. Independence of the two adaptive control systems does not appear to cause untoward effects.