A Review of Web-Based Metagenomics Platforms for Analysing Next-Generation Sequence Data.

Metagenomics has now evolved as a promising technology for understanding the microbial population in the environment. By metagenomics, a number of extreme and complex environment has been explored for their microbial population. Using this technology, researchers have brought out novel genes and their potential characteristics, which have robust applications in food, pharmaceutical, scientific research, and other biotechnological fields. A sequencing platform can provide a sequence of microbial populations in any given environment. The sequence needs to be analysed computationally to derive meaningful information. It is presumed that only bioinformaticians with extensive computational skills can process the sequencing data till the downstream end. However, numerous open-source software and online servers are available to analyse the metagenomic data developed for a biologist with less computational skills. This review is focused on bioinformatics tools such as Galaxy, CSI-NGS portal, ANASTASIA and SHAMAN, EBI- metagenomics, IDseq, and MG-RAST for analysing metagenomic data.

CRISPR detection in metagenome-assembled genomes (MAGs) of coal mine.

Bacterial and archaeal CRISPR-Cas systems provide adaptive immune protection against foreign mobile genetic elements. When viruses infect bacteria, a small portion of the viral DNA is inserted into the bacterial DNA in a specific pattern to produce segments known as CRISPR arrays. Metagenome assembled genomes (MAGs) were used in our study to identify the CRISPR sequence for determining the interacted phage. Metagenomic data from a coal mine was used to perform a computational study. From raw reads, 206151 contigs were assembled. Then contigs were clustered into 150 Metagenome assembled genomes from which 78 non-redundant MAGs were selected. Using the CHECKM standard, seven MAGs were found to have >80 completeness and <20 contaminations. Those MAGs were analyzed for the presence of CRISPR elements. Out of seven MAGs, four MAGs have the CRISPR elements and are searched against the VIROblast database. CRISPR arrays have 4, 1, 3, and 7 spacer sequences in the MAGs of Burkholderia, Acinetobacter, Oxalobacteraceae, and Burkholderia multivorans respectively. The uncultured Caudovirales phage genomic regions were present in the genomes of Burkholderia, Oxalobacteriaceae, and Burkholderia multivorans. This study follows the unconventional metagenomics workflow to provide a better understanding of bacteria and phage interactions.

Efficacy of various forms of acupuncture for the treatment of urinary incontinence in women: A systematic review and meta-analysis.

BACKGROUND AND PURPOSE: Evidence regarding the efficacy of various forms of acupuncture for the treatment of urinary incontinence (UI) in women is outdated and inconclusive. This review aims to determine the efficacy of different forms of acupuncture for the treatment of UI in women. METHODS: Multiple databases were searched from inception to June 2020. Randomized controlled trials that compared various forms of acupuncture to control were included. RESULTS: Ten trials were included in this review. The pooled analysis demonstrated that an increased proportion of women with stress UI (SUI) reported fewer UI episodes (1.73 [95% CI 1.46, 2.04]; p < 0.00001) in the electroacupuncture group than in the sham group. The meta-analysis also revealed a significantly increased number of women who reported the complete cure of SUI in the electroacupuncture combined with pelvic floor muscle training group than in the medication group (RR 2.67 [95% CI 1.51, 4.71]; p = 0.0007). Body and laser acupuncture caused significant decreases in the number of urge accidents (-2.70 [95% CI -4.86, -0.54]; p = 0.01) and the occurrence of urgency symptoms (-3.60[95% CI -5.34, -1.86]; p < 0.0001), compared with sham acupuncture. CONCLUSIONS: Based on the findings of this review, electroacupuncture may be able to improve SUI in women in clinical settings. This review also identified evidence supporting the use of body, electro,- and laser acupuncture for the treatment of urge UI; however, these results were obtained from single studies, and further research remains necessary to confirm the effects of these interventions on the treatment of urge UI in women.

Effectiveness of pelvic floor muscle training alone or combined with either a novel biofeedback device or conventional biofeedback for improving stress urinary incontinence: A randomized controlled pilot trial.

PURPOSE: To (i) compare the acceptance of a newly developed, novel biofeedback device (PelviSense) with that of conventional biofeedback (CB) using an intravaginal probe for the treatment of stress urinary incontinence (SUI) in women, (ii) examine the feasibility and safety of using the PelviSense device as a pelvic floor muscle (PFM) training (PFMT) adjunct, and (iii) compare the PFMT adherence and effectiveness of CB, the PelviSense device, with PFMT alone for women with SUI. METHODS: An assessor-blinded, three-arm, randomized controlled pilot trial was conducted among 51 women with SUI. Women were randomly allocated to one of three study groups (PelviSense-assisted PFMT, CB-assisted PFMT, or PFMT alone [control]). Outcome measures included the International Consultation on Incontinence Questionnaire-Short Form, the 1-h pad test, and the Modified Oxford Scale. RESULTS: Participants in the PelviSense-assisted PFMT group expressed good device acceptance. PFMT adherence was greater in the PelviSense-assisted PFMT group than in the unassisted or CB-assisted PFMT groups. Between-groups analysis revealed significant effects on improved SUI symptoms, urine loss severity, and PFM strength for the PelviSense-assisted PFMT group compared with the CB-assisted and PFMT alone groups. CONCLUSIONS: The pilot trial results demonstrated moderate to high PFMT adherence in the PelviSense-assisted PFMT group and supported the safety of using the PelviSense device. The preliminary results of the pilot trial showed that PelviSense-assisted PFMT was more effective for reducing SUI symptoms among women than unassisted or CB-assisted PFMT. TRIAL REGISTRATION: This trial was registered in http://ClinicalTrials.gov (reference number: NCT04638348) before the recruitment of the first participant.

Efficacy of physical therapy interventions on quality of life and upper quadrant pain severity in women with post-mastectomy pain syndrome: a systematic review and meta-analysis.

PURPOSE: To determine the efficacy of physical therapy interventions on quality of life (QoL) and pain severity in post-mastectomy pain syndrome (PMPS). METHODS: Multiple databases were searched from database inception to October 2020. Searches were limited to human studies published in either English or Chinese in peer-reviewed journals with full text available for randomized controlled trials conducted on females. Trials comparing the effectiveness of physical therapy interventions against control conditions on QoL and pain were included. RESULTS: Eighteen trials were included in the review. The pooled analysis of the four exercise trials revealed a significant effect of the intervention on general [standardized mean difference [SMD]: 0.87 (95%CI: 0.36, 1.37); p = 0.001], physical [SMD: 0.34 (95%CI: 0.01, 0.66); p = 0.044], and mental health components [SMD: 0.27 (95%CI: 0.03, 0.51); p = 0.027] of QoL compared with the control condition. Meta-analyses of six exercise trials, two myofascial release trials, and two acupuncture trials revealed a significant improvement in pain severity in the treatment group than in the control group. However, meta-analyses of two studies revealed a non-significant effect of compression therapy compared to control on pain severity. CONCLUSION: Our meta-analyses found that exercise is beneficial for improving the QoL and pain severity of women with PMPS. Future studies are needed to determine the optimal parameters for exercise interventions designed to improve QoL and pain severity in women with PMPS. The effect of acupuncture, myofascial release, and compression therapy remains inconclusive, and future research is required to validate the effect of these interventions on PMPS.

The efficacy of different forms of acupuncture for the treatment of nocturnal enuresis in children: A systematic review and meta-analysis.

BACKGROUND: The efficacy of different forms of acupuncture for the treatment of nocturnal enuresis in children is not known. OBJECTIVE: To determine the efficacy of different forms of acupuncture, such as manual acupuncture, laser/electroacupuncture, acupoint injection, and moxibustion, for the treatment of nocturnal enuresis. METHODS: A literature search was conducted on Medline, EMBASE, Web of Science, CINAHL, PubMed, Physiotherapy Evidence Database, and Scopus from database inception to September 2020. The Cochrane risk of bias tool was utilised to evaluate the risk of bias in each included study. The quality of the evidence was evaluated using the Grading of Recommendations, Assessment, Development, and Evaluation tool. RESULTS: Thirteen trials (n = 890) were included. Meta-analyses revealed significantly greater numbers of children reporting improved nocturnal enuresis in the moxibustion (p = 0.004), acupoint injection (p = 0.020), and laser acupuncture (p = 0.001) groups than in the control groups. Meta-analyses showed no significant differences in the numbers of children reporting the complete cure of nocturnal enuresis between laser acupuncture and desmopressin (p = 0.57). CONCLUSIONS: The review identified moxibustion, acupoint injections, and laser acupuncture as effective treatments for nocturnal enuresis in children. However, the evidence for these interventions is limited and of very-low-grade quality. The effects of laser acupuncture compared with desmopressin remain inconclusive.

Yoga and Pilates compared to pelvic floor muscle training for urinary incontinence in elderly women: A randomised controlled pilot trial.

BACKGROUND: and purpose: There is limited evidence from randomised controlled trials (RCTs) regarding the use of yoga and Pilates for the management of urinary incontinence (UI) in women. This study aims to investigate the preliminary effects of using Pilates and yoga to manage UI. MATERIALS AND METHODS: An assessor-blinded, prospective, three-arm parallel-group randomised controlled pilot trial was conducted in three elderly care centres in Hong Kong. Thirty women aged 60 years or above were included in the study. Study centres were randomly assigned to each of the three interventions (yoga, Pilates and pelvic floor muscle training [PFMT; standard care control]). Study interventions were provided once a week for four weeks, followed by unsupervised CD-guided home exercises for eight weeks. Outcomes included the International Consultation on Incontinence Questionnaire-Short Form (ICIQ-SF), 1-h pad test, and feasibility measures such as adherence to the intervention programme, recruitment and retention rates and safety. Outcomes were assessed at baseline, 4 and 12 weeks. Statistical analysis was performed using two-way repeated measures analysis of covariance. RESULTS: All three interventions demonstrated a statistically significant effect on ICIQ-SF scores from baseline to weeks 4 and 12. Significant effects in UI were reported for yoga compared with Pilates (mean: -2.93, 95% CI -5.35, -0.51; p = 0.02). CONCLUSION: Yoga poses intended to address the pelvic floor and core muscles were found to have superior benefits over Pilates exercises in terms of improved continence measured with the ICIQ-SF.

Effectiveness of physiotherapy interventions for improving erectile function and climacturia in men after prostatectomy: a systematic review and meta-analysis of randomized controlled trials.

OBJECTIVE: To determine the effectiveness of physiotherapy interventions for postprostatectomy erectile dysfunction and climacturia. DATA SOURCES: Multiple databases were searched from database inception to February 2019. REVIEW METHODS: Randomized controlled trials comparing physiotherapy interventions to control were included. RESULTS: The search yielded 127 potentially relevant articles; seven met the inclusion criteria and were included in the review. Meta-analysis of two studies revealed a statistically significant effect of pelvic floor muscle training (PFMT) plus biofeedback compared to the no treatment control group for erectile function at the12-month follow-up period (risk ratio (RR) = 3.65, 95% confidence interval (CI) = 1.02-13.05; P = 0.05). Data from one small study (n = 31) identified a greater number of men reporting improved climacturia in the PFMT plus electrical stimulation group compared to the no treatment control group, and the overall effect was significant (RR = 15.60, 95% CI = 0.95-254.91; P = 0.05). Meta-analyses of two studies found no statistically significant differences between groups receiving PFMT and no treatment control for erectile function or climacturia at long-term follow-up. CONCLUSIONS: PFMT augmented with biofeedback improves erectile function after prostatectomy. Data from a single study found PFMT combined with electrical stimulation to be beneficial for postprostatectomy climacturia. However, electrical stimulation is recommended for terminally ill people only. The effect of PFMT alone on postprostatectomy erectile dysfunction and climacturia remains inconclusive. However, this is likely to be affected by the participant adherence and physiotherapy supervision. High-quality trials providing intensive supervision and due consideration of adherence factors are recommended.

Can pre-screening vestibulocerebellar involvement followed by targeted training improve the outcomes of balance in cerebellar ataxia?

Balance problems and frequent falls are common among clients with Cerebellar Ataxia (CA). CA is not a disease by itself but a collection of symptoms due to the involvement of cerebellum or its pathways. Presently the treatment for balance problems for CA is not standardized. Interventions available to improve balance are not specific to symptoms presentation. Functionally the cerebellum is divided into the spinocerebellum, vestibulocerebellum and corticocerebellum. Each functional zone has a distinct role in maintaining balance. Therefore, the presentation of symptoms will vary according to the functional zone involved. Pre-screening clients with CA for identifying the part of cerebellum involved will facilitate clinicians to provide tailor-made interventions for targeting specific symptoms for better outcomes. Pre-screening clients with CA according to the part of cerebellum involved is not in practice and our study will introduce this concept. We hypothesize pre-screening participants with spinocerebellar ataxia (SCA) for the involvement vestibulocerebellum followed by prescribing vestibulocerebellum targeted exercises will have better outcomes when compared to conventional balance training. We plan to conduct two related studies. In study 1 we will screen participants with CA for the involvement of vestibulocerebellum. In study 2, the effects of vestibulocerebellum targeted balance exercises on balance will be studied. We will assess the Subjective Visual Vertical (SVV) deviation and postural sway pattern to screen participants into people with and without vestibulocerebellar involvement. SVV deviation will be estimated using a computerized Subjective Visual Vertical (cSVV) device and postural sway pattern will be assessed using the limits of stability program of the Bertec© Balance system. The obtained SVV deviation scores will be used to derive at cut-off scores to discriminate clients with and without vestibulocerebellar involvement. The second study will test the treatment effects of conventional exercises plus vestibulocerebellum targeted exercises to improve balance by correcting SVV deviation in SCA with vestibulocerebellar involvement. The intervention is planned as 12 one-to-one sessions over three months period. Participants will be reassessed after the intervention and 3 months post-intervention. The findings of this cutting-edge research are extremely important to the clinicians, researchers and clients with SCA.

Does Tai Chi improve balance and reduce falls incidence in neurological disorders? A systematic review and meta-analysis.

OBJECTIVE: To evaluate the effect of Tai Chi on balance and reducing falls incidence in neurological disorders. DATA SOURCES: AMED, Embase, Web of Science, SCOPUS, EBSCO and Medline from inception until February 2018. REVIEW METHOD: Randomized controlled trials of Tai Chi compared with active or no treatment control, measuring balance with the Berg Balance Scale or the Timed Up and Go Test and number of falls in neurological disorders were included. Methodological quality was assessed using PEDro and quality of evidence using the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) system. RESULTS: A total of 10 studies involving 720 participants were reviewed. Seven studies were in Parkinson's disease and three in stroke. Seven studies were of high methodological quality and three were low. Meta-analyses of balance measured with the Timed Up and Go Test in Parkinson's disease revealed a statistically significant effect of Tai Chi compared to no treatment (weighted mean difference (WMD), -2.13; 95% confidence interval (CI), -3.26 to -1.00; P < 0.001) and was insignificant (WMD, -0.19; 95% CI, -1.74 to 1.35; P = 0.81) when compared with active treatment. Tai Chi significantly reduced falls incidence in Parkinson's disease (odds ratio (OR), 0.47; 95% CI, 0.29 to 0.77; P = 0.003) and stroke (OR, 0.21; 95% CI, 0.09 to 0.48; P < 0.001). Balance measured with the Timed Up and Go Test comparing Tai Chi and active treatment was insignificant (WMD, 0.45; 95% CI, -3.43 to 2.54; P = 0.77) in stroke. CONCLUSION: Tai Chi is effective in reducing falls incidence in Parkinson's disease and stroke. This systematic review did not find high-quality studies among other neurological disorders.

STRICTA: is it time to do more?

BACKGROUND: In order to facilitate the completeness and transparency of reporting on randomized controlled trials undertaken using acupuncture interventions, a consensus group of international experts developed the Standards for Reporting Interventions in Controlled Trials of Acupuncture (STRICTA) in 2002. This reporting guideline was updated in 2010, and was applicable to a broader range of acupuncture research, including uncontrolled trials and case reports. Subsequent evaluations have noted limitations on the impact of STRICTA in the reporting quality of acupuncture trials, and the description of acupuncture details remains poor. Thus improvement in the efficacy of the STRICTA guidelines is called for. DISCUSSION: We explored the STRICTA guidelines from four aspects, including the development procedure, validity assessment, endorsement and adherence, and citation situation. Based upon these findings, we provided five potential suggestions for further development of STRICTA. SUMMARY: STRICTA are valid reporting guidelines based on robust methodology and scientific content. However specific implementation strategies including: updating the STRICTA checklist; improving the STRICTA reporting efficiency; consistency with implementing the "Instructions for authors" for journals; establishing global STRICTA research centers; and expanding the STRICTA website, are needed. Such strategies will improve their utilization and impact positively on the quality of reporting on acupuncture research outcomes.

Some physiotherapy treatments may relieve menstrual pain in women with primary dysmenorrhea: a systematic review.

QUESTION: In women with primary dysmenorrhoea, what is the effect of physiotherapeutic interventions compared to control (either no treatment or placebo/sham) on pain and quality of life? DESIGN: Systematic review of randomised trials with meta-analysis. PARTICIPANTS: Women with primary dysmenorrhea. INTERVENTION: Any form of physiotherapy treatment. OUTCOME MEASURES: The primary outcome was menstrual pain intensity and the secondary outcome was quality of life. RESULTS: The search yielded 222 citations. Of these, 11 were eligible randomised trials and were included in the review. Meta-analysis revealed statistically significant reductions in pain severity on a 0-10 scale from acupuncture (weighted mean difference 2.3, 95% CI 1.6 to 2.9) and acupressure (weighted mean difference 1.4, 95% CI 0.8 to 1.9), when compared to a control group receiving no treatment. However, these are likely to be placebo effects because when the control groups in acupuncture/acupressure trials received a sham instead of no treatment, pain severity did not significantly differ between the groups. Significant reductions in pain intensity on a 0-10 scale were noted in individual trials of heat (by 1.8, 95% CI 0.9 to 2.7), transcutaneous electrical nerve stimulation (2.3, 95% CI 0.03 to 4.2), and yoga (3.2, 95% CI 2.2 to 4.2). Meta-analysis of two trials of spinal manipulation showed no significant reduction in pain. None of the included studies measured quality of life. CONCLUSION: Physiotherapists could consider using heat, transcutaneous electrical nerve stimulation, and yoga in the management of primary dysmenorrhea. While benefits were also identified for acupuncture and acupressure in no-treatment controlled trials, the absence of significant effects in sham-controlled trials suggests these effects are mainly attributable to placebo effects.