The 28S rRNA RT-qPCR assay for host depletion evaluation to enhance avian virus detection in Illumina and Nanopore sequencing

Abundant host and bacterial sequences can obscure the detection of less prevalent viruses in untargeted next-generation sequencing (NGS). Efficient removal of these non-targeted sequences is vital for accurate viral detection. This study presents a novel 28S ribosomal RNA (rRNA) RT-qPCR assay designed to assess the efficiency of avian rRNA depletion before conducting costly NGS for the detection of avian RNA viruses. The comprehensive evaluation of this 28S-test focuses on substituting DNase I with alternative DNases in our established depletion protocols and finetuning essential parameters for reliable host rRNA depletion. To validate the effectiveness of the 28S-test, we compared its performance with NGS results obtained from both Illumina and Nanopore sequencing platforms. This evaluation utilized swab samples from chickens infected with highly pathogenic avian influenza virus, subjected to established and modified depletion protocols. Both methods significantly reduced host rRNA levels, but using the alternative DNase had superior performance. Additionally, utilizing the 28S-test, we explored cost- and time-effective strategies, such as reduced probe concentrations and other alternative DNase usage, assessed the impact of filtration pre-treatment, and evaluated various experimental parameters to further optimize the depletion protocol. Our findings underscore the value of the 28S-test in optimizing depletion methods for advancing improvements in avian disease research through NGS.

T-wave alternans poorly prognostic in primary prophylactic ICD patients: a prospective EU-CERT-ICD study

Background

New methods to identify patients who truly benefit from primary prophylactic implantable cardioverter defibrillation (ICD) are urgently needed. T-wave alternans (TWA) represents a beat-to-beat fluctuation in the morphology of the ST-segment and T-wave. It has been shown to associate with arrhythmogenesis of heart and sudden cardiac death [1]. We hypothised that TWA might associate with benefit from ICD implantation in primary prevention.

Methods

In EU-CERT-ICD study, we prospectively enrolled 2327 primary prophylactic ICD candidates from 15 European countries. A 24-hours Holter-monitoring was taken from all recruited patients at enrolment. TWA was assessed from Holter-monitoring using MMA method with Getemed Cardioday software. To assess the benefit from ICD treatment, we used outcomes all-cause mortality, appropriate shock and survival benefit. We conducted Cox regression model, competing risk regression model and propensity score adjusted Cox regression model. TWA was assessed both as contiguous variable and with cut-off points <47 μV and <60 μV.

Results

Final cohort included 1,734 valid T-wave alternans samples, 1,211 patients with ICD and 523 control patients with conservative treatment, with mean follow-up time 2.3 years. TWA <60 μV predicted lower all-cause mortality in ICD patients in univariate cox regression model (HR 1.484, 95% CI 1.024–2.151, p=0.0374). In multivariate models, TWA did not predict death or appropriate shocks in ICD patients. In addition, TWA did not predict death in control patients. In propensity score adjusted Cox regression model, TWA did not predict ICD benefit.

Conclusion

T-wave alternans is poorly prognostic in primary prophylactic ICD patients. Altough it may predict life-threatening arrhythmias and sudden cardiac death in several patient populations, it cannot be used in assessing benefit from implantable cardioverter defibrillator in primary prevention among patients with ejection fraction ≤35%.

Funding Acknowledgement

Type of funding sources: Public grant(s) – EU funding. Main funding source(s): European Community's 7th Framework Program FP7/2007-2013

Exploring what is important to patients with regards to quality of life after experiencing a lower limb reconstructive procedure: a qualitative evidence synthesis

BACKGROUND

Patient reported outcome measures (PROMs) are used to understand the impact of lower limb reconstruction surgery on patients' quality of life (QOL). Existing measures have not been developed to specifically capture patient experiences amongst adults with lower limb conditions that require reconstruction surgery. This review aimed to synthesise qualitative evidence to identify what is important to patients requiring, undergoing, or following reconstructive surgery for lower limb conditions.

METHODS

MEDLINE, Embase, PsychINFO and Cinahl were searched from inception until November 2020. Studies were included if they employed qualitative research methods, involved patients requiring, undergoing or following lower limb reconstruction and explored patients' experiences of care, treatment, recovery and QOL. Mixed methods studies that did not separately report qualitative findings, mixed population studies that were not separately reported and studies in languages other than English were excluded. Included studies were analysed using thematic synthesis. The Critical Appraisal Skills Programme qualitative studies checklist was used to undertake quality assessment.

RESULTS

Nine studies met the inclusion criteria. The thematic synthesis identified two overarching themes: (1) areas of living key to QOL for lower limb reconstruction patients and (2) moving towards a new normal. The way in which lower limb reconstruction affects an individual's QOL and their recovery is complex and is influenced by a range of inter-related factors, which will affect patients to varying degrees depending on their individual circumstances. We identified these factors as: pain, daily functioning and lifestyle, identity, income, emotional wellbeing, support, the ability to adapt and adjust and the ability to move forwards.

CONCLUSIONS

The way patients' QOL is affected after a lower limb reconstruction is complex, may change over time and is strongly linked to their recovery. These findings will aid us in developing a conceptual framework which identifies the outcomes important to patients and those that should be included in a PROM. Further research is then required to establish whether the range of factors we identified are captured by existing PROMs. Depending on the outcome of this work, a new PROM for patients following lower limb reconstruction may be required.

Systematic review of the limited evidence base for treatments of Eustachian tube dysfunction: a health technology assessment

BACKGROUND

The Health Technology Assessment programme commissioned a wide-ranging review of treatments for adult Eustachian tube dysfunction. Treatments range from advice and observation and pharmacological treatments to surgical options.

OBJECTIVE

(i) To assess the evidence for interventions for adults with a clinical diagnosis of Eustachian tube dysfunction and (ii) to identify priorities for future research.

TYPE OF REVIEW

Systematic review (PROSPERO registration CRD42012003035) adhering to PRISMA guidance.

SEARCH

An extensive search of 15 databases including MEDLINE, EMBASE and CENTRAL (up to October 2012).

EVALUATION METHOD

Controlled and uncontrolled studies of interventions for adult Eustachian tube dysfunction were included. Because of insufficient data, the protocol was amended to also include controlled studies with mixed adult/child populations. Risk of bias was assessed. Narrative synthesis was employed due to high clinical heterogeneity.

RESULTS

Interventions assessed were pharmacological treatments [two randomised controlled trials (RCTs), one controlled non-randomised trial (CCT), 159 patients]; mechanical pressure equalisation devices (one randomised controlled trial, one CCT, 48 patients); and surgery, including laser tuboplasty (seven case series, 192 patients), balloon dilatation (three case series, 103 patients), myringotomy without grommet insertion (two case series, 121 patients), transtubal steroids (one case series, 11 patients) and laser coagulation (one retrospective controlled study, 40 patients). All studies had high risk of bias except two pharmacological trials; one had low risk and one unclear risk. No evidence was found for many treatments. The single low risk of bias RCT (n = 91; 67% adults) showed no effect of nasal steroids and favoured placebo for improved middle ear function (RR 1.20, 95% CI 0.91-1.58) and symptoms (P = 0.07). Other studies showed improvements in middle ear function for mechanical devices, antihistamine/ephedrine and nasal decongestant, but they had significant methodological weaknesses including insufficient length of follow-up. None of the surgical studies were adequately controlled, and many reported high levels of co-intervention. Therefore, observed benefits for tuboplasty and balloon dilatation in symptoms, middle ear function or hearing could not be reliably attributed to the interventions assessed. There was variability in definitions of the condition.

CONCLUSION

Eustachian tube dysfunction is a poorly defined condition. Due to the limited and poor-quality evidence, it is inappropriate to make conclusions on the effectiveness of any intervention; the evidence base is insufficient to guide recommendations for a trial of any particular intervention. Consensus on diagnostic criteria for Eustachian tube dysfunction is required to inform inclusion criteria of future trials.

Acupuncture and other physical treatments for the relief of pain due to osteoarthritis of the knee: network meta-analysis

OBJECTIVE

To compare the effectiveness of acupuncture with other relevant physical treatments for alleviating pain due to knee osteoarthritis.

DESIGN

Systematic review with network meta-analysis, to allow comparison of treatments within a coherent framework. Comprehensive searches were undertaken up to January 2013 to identify randomised controlled trials in patients with osteoarthritis of the knee, which reported pain.

RESULTS

Of 156 eligible studies, 114 trials (covering 22 treatments and 9,709 patients) provided data suitable for analysis. Most trials studied short-term effects and many were classed as being of poor quality with high risk of bias, commonly associated with lack of blinding (which was sometimes impossible to achieve). End of treatment results showed that eight interventions: interferential therapy, acupuncture, TENS, pulsed electrical stimulation, balneotherapy, aerobic exercise, sham acupuncture, and muscle-strengthening exercise produced a statistically significant reduction in pain when compared with standard care. In a sensitivity analysis of satisfactory and good quality studies, most studies were of acupuncture (11 trials) or muscle-strengthening exercise (9 trials); both interventions were statistically significantly better than standard care, with acupuncture being statistically significantly better than muscle-strengthening exercise (standardised mean difference: 0.49, 95% credible interval 0.00-0.98).

CONCLUSIONS

As a summary of the current available research, the network meta-analysis results indicate that acupuncture can be considered as one of the more effective physical treatments for alleviating osteoarthritis knee pain in the short-term. However, much of the evidence in this area of research is of poor quality, meaning there is uncertainty about the efficacy of many physical treatments.

The clinical effectiveness and cost-effectiveness of low-intensity psychological interventions for the secondary prevention of relapse after depression: a systematic review

BACKGROUND

Depression is the most common mental disorder in community settings and a major cause of disability across the world. The objective of treatment is to achieve remission or at least adequate control of depressive symptoms; however, even after successful treatment, the risk of relapse after remission is significant. Although the effectiveness of low-intensity interventions has been extensively evaluated to treat primary symptoms of psychological difficulties, there has been substantially less research examining the use of these interventions as a relapse prevention strategy.

OBJECTIVE

To systematically review the clinical effectiveness and cost-effectiveness of low-intensity psychological or psychosocial interventions to prevent relapse or recurrence in patients with depression. As the broader definition of 'low-intensity' psychological intervention is somewhat contested, the review was conducted in two parts: A, a systematic review of all evaluations of 'low-intensity' interventions that were delivered by para-professionals, peer supporters or psychological well-being practitioners as defined by the Improving Access to Psychological Therapies programme; and B, a scoping review of relevant evaluations of interventions involving qualified mental health professionals (e.g. psychiatrists, clinical psychologists, cognitive behavioural therapists) involving < 6 hours of contact per patient.

DATA SOURCES

Comprehensive literature searches were developed; electronic databases were searched from inception until September 2010 (including MEDLINE, MEDLINE In-Process & Other Non-Indexed Citations, PsycINFO, EMBASE, The Cochrane Library), internet resources were used to identify guidelines on the treatment of depression, and the bibliographies of relevant reviews, guidelines and included studies were scrutinised.

REVIEW METHODS

Two reviewers independently screened titles and abstracts; data were extracted independently by one reviewer using a standardised data extraction form and checked by another. Discrepancies were resolved by consensus, with involvement of a third reviewer when necessary. The inclusion criteria were population - adults or adolescents who had received treatment for depression; intervention - part A, low-intensity interventions, specifically any unsupported psychological/psychosocial interventions or any supported interventions that did not involve highly qualified mental health professionals, and, part B, interventions carried out by qualified mental health professionals that involved < 6 hours of contact per patient; comparator - any, including no treatment, placebo, psychological or pharmacological interventions; outcomes - relapse or recurrence, other outcomes (e.g. social function, quality of life) were recorded where reported; and study design - for clinical effectiveness, randomised, quasi-randomised and non-randomised studies with concurrent control patients. For cost-effectiveness, full economic evaluations that compared two or more treatment options and considered both costs and consequences. No studies met the main part A inclusion criteria.

RESULTS

For the clinical effectiveness review, 17 studies (14 completed, three ongoing), reported in 27 publications, met the part B inclusion criteria. These studies were clinically and methodologically diverse, and reported differing degrees of efficacy for the evaluated interventions. One randomised controlled trial (RCT), which evaluated a collaborative care-type programme, was potentially relevant to part A; this study reported no difference between patients receiving the intervention and those receiving usual care in terms of relapse of depression over 12 months. For the cost-effectiveness review, two studies met the criteria for part B. One of these was an economic evaluation of the RCT above, which was potentially relevant to part A. This evaluation found that the intervention may be a cost-effective use of resources when compared with usual care; however, it was unclear how valid these estimates were for the NHS.

LIMITATIONS

Although any definition of 'brief' is likely to be somewhat arbitrary, an inclusion threshold of 6 hours contact per patient was used to select brief high-intensity intervention studies. Most excluded studies evaluated clearly resource-intensive interventions, though occasionally, studies were excluded on the basis of having only slightly more than 6 hours contact per patient.

CONCLUSIONS

There is inadequate evidence to determine the clinical effectiveness or cost-effectiveness of low-intensity interventions for the prevention of relapse or recurrence of depression. A scoping review of brief high-intensity therapies indicates that some approaches have shown promise in some studies, but findings have not been consistent. Many uncertainties remain and further primary research is required. Careful consideration should be given to the scope of such research; it is important to evaluate the broader patient pathway accounting for the heterogeneous patient groups of interest. Future RCTs conducted in a UK primary care setting should include adult participants in remission or recovery from depression, and evaluate the quality of the intervention and consistency of delivery across practitioners where appropriate. The occurrence of relapse or recurrence should be measured using established methods, and functional outcomes as well as symptoms should be measured; data on quality of life using a generic instrument, such as the European Quality of Life-5 Dimensions (EQ-5D), should be collected.

FUNDING

The National Institute for Health Research Health Technology Assessment programme.

The effectiveness of interventions in the management of patients with primary frozen shoulder

There are many types of treatment used to manage the frozen shoulder, but there is no consensus on how best to manage patients with this painful and debilitating condition. We conducted a review of the evidence of the effectiveness of interventions used to manage primary frozen shoulder using the Cochrane Database of Systematic Reviews, the Database of Abstracts of Reviews of Effects, the Physiotherapy Evidence Database, MEDLINE and EMBASE without language or date restrictions up to April 2009. Two authors independently applied selection criteria and assessed the quality of systematic reviews using the Assessment of Multiple Systematic Reviews (AMSTAR) tool. Data were synthesised narratively, with emphasis placed on assessing the quality of evidence. In total, 758 titles and abstracts were identified and screened, which resulted in the inclusion of 11 systematic reviews. Although these met most of the AMSTAR quality criteria, there was insufficient evidence to draw firm conclusions about the effectiveness of treatments commonly used to manage a frozen shoulder. This was mostly due to poor methodological quality and small sample size in primary studies included in the reviews. We found no reviews evaluating surgical interventions. More rigorous randomised trials are needed to evaluate the treatments used for frozen shoulder.

Non-contingent positive and negative reinforcement schedules of superstitious behaviors

The role of schedules of reinforcement on the development of superstitious conditioning was investigated in a college age population. Participants were randomly assigned to one of eight operant schedules and instructed to remove (escape), prevent and/or remove (avoidance and escape) or produce (positive) the appearance of a computer generated stimulus using a response pad. Results from the experiment indicate that concomitant (escape and avoidance) schedules of reinforcement are most effective in facilitating acquisition of superstitious behavior as measured by self-reports of participants.

Psychobiological effects of carbohydrates

The authors studied whether the fatiguing effects of eating lunch are greater for carbohydrate-rich meals than for other meals, and related the time course of behavioral change to plasma glucose, insulin, and amino acids. On different occasions, in counterbalanced order, normal women (N = 7) fasted overnight, ate a standard breakfast, and at lunch either continued to fast or ate a high-carbohydrate, low-protein meal; a hedonically similar meal containing both carbohydrate and protein; or a high-protein, low-carbohydrate meal. Meals were isocaloric and equated for fat content. Only the carbohydrate meal significantly increased fatigue, which could not be attributed to hypoglycemia because plasma glucose remained elevated. Fatigue began approximately, when the carbohydrate meal elevated the plasma tryptophan ratio but ended even though the ratio remained elevated. Fatigue after a high-carbohydrate lunch could not be explained by reactive hypoglycemia or sweet taste, and could partially be explained by the hypothesis that fatigue parallels an elevation of the tryptophan ratio.

Compliance of insulin-dependent diabetics with a low-fat diet

Compliance with medical therapy is widely researched yet unpredictable. When counseled by a dietitian to begin a low-fat (25%) diabetic diet, subjects significantly decreased fat intake but did not achieve the prescribed 25% fat level. The significantly lower fat intake after instruction identified the registered dietitian as an effective behavioral change agent. Six compliance predictors obtained at an initial interview accounted for 77% of the variance in compliance.