Nevin Manimala

Trials. 2021 Sep 6;22(1):600. doi: 10.1186/s13063-021-05547-4.

ABSTRACT

BACKGROUND: Canadians of South Asian (SA) origin comprise the largest racialized group in Canada, representing 25.6% of what Statistics Canada terms “visible minority populations”. South Asian Canadians are disproportionately impacted by the social determinants of health, and this can result in high rates of mood and anxiety disorders. These factors can negatively impact mental health and decrease access to care, thereby increasing mental health inequities. Cognitive Behavioural Therapy (CBT) in its current form is not suitable for persons from the non-western cultural backgrounds. Culturally adapted Cognitive Behavioural Therapy (CaCBT) is an evidence-based practice. CaCBT is more effective than standard CBT and can reduce dropouts from therapy compared with standard CBT. Thus, CaCBT can increase access to mental health services and improve outcomes for immigrant, refugee and ethno-cultural and racialized populations. Adapting CBT for growing SA populations in Canada will ensure equitable access to effective and culturally appropriate interventions.

METHODS: The primary aim of the study is to develop and evaluate CaCBT for Canadian South Asian persons with depression and anxiety and to gather data from stakeholders to develop guidelines to culturally adapt CBT. This mixed methods study will use three phases: (1) cultural adaptation of CBT, (2) pilot feasibility of CaCBT and (3) implementation and evaluation of CaCBT. Phase 1 will use purposive sampling to recruit individuals from four different groups: (1) SA patients with depression and anxiety, (b) caregivers and family members of individuals affected by anxiety and depression, (c) mental health professionals and (d) SA community opinion leaders. Semi-structured interviews will be conducted virtually and analysis of interviews will be informed by an ethnographic approach. Phase 2 will pilot test the newly developed CaCBT for feasibility, acceptability and effectiveness via quantitative methodology and a randomized controlled trial, including an economic analysis. Phase 3 will recruit therapists to train and evaluate them in the new CaCBT.

DISCUSSION: The outcome of this trial will benefit health services in Canada, in terms of helping to reduce the burden of depression and anxiety and provide better care for South Asians. We expect the results to help guide the development of better services and tailor existing services to the needs of other vulnerable groups.

TRIAL REGISTRATION: ClinicalTrials.gov NCT04010890. Registered on July 8, 2019.

PMID:34488853 | DOI:10.1186/s13063-021-05547-4

Trials. 2021 Sep 6;22(1):597. doi: 10.1186/s13063-021-05526-9.

ABSTRACT

BACKGROUND: Randomised controlled trials (RCTs) are the gold standard for demonstrating the efficacy of new therapies. However, issues of external validity often affect result application to real-world settings. Using registries to conduct RCTs is a reasonably new practice, but is appealing because it combines the benefits of both observational studies and RCTs. There is limited literature on patient motivators, barriers, and consent to registries for conducting RCTs. The purpose of our study was to establish the factors that motivate and/or inhibit patients from joining a registry for RCTs and to determine what information matters to patients when making an enrolment decision to participate in such a registry.

METHODS: We conducted a cross-sectional questionnaire-based study at a dialysis centre in Southwest Ireland representing a catchment patient population of approximately 430,000. Quantitative data were coded and analysed in SPSS (v16). Descriptive statistics were produced, and open-ended questions were analysed by thematic analysis.

RESULTS: Eighty-seven patients completed the questionnaire. Reasons for participation in a registry included personal and altruistic benefits. Barriers to participation were time and travel requirements associated with registry participation, data safety concerns, risks, side effects, and concerns that registry participation would impact current treatment. Although 29.8% of patients expressed concern regarding their data being stored in a registry, 79.3% were still willing to consent to have their data uploaded and stored in a registry for conducting RCTs. It was important to patients to have their GP (general practitioner) involved in the decision to participate, despite little day-to-day contact with their GP for renal dialysis management.

CONCLUSION: Challenges to recruitment to registries for RCTs exist, but addressing the identified concerns of potential participants may aid patients in making a more informed enrolment decision and may improve recruitment to registries, and by extension, to RCTs conducted using the registry.

PMID:34488851 | DOI:10.1186/s13063-021-05526-9

Trials. 2021 Sep 6;22(1):601. doi: 10.1186/s13063-021-05558-1.

ABSTRACT

BACKGROUND: Over 200 million individuals worldwide are infected with Schistosoma species, with over half of infections occurring in children. Many children experience first infections early in life and this impacts their growth and development; however praziquantel (PZQ), the drug used worldwide for the treatment of schistosomiasis, only has regulatory approval among adults and children over the age of four, although it is frequently used “off label” in endemic settings. Furthermore, pharmacokinetic/pharmacodynamics (PK/PD) evidence suggests the standard PZQ dose of 40 mg/kg is insufficient in preschool-aged children (PSAC). Our goal is to understand the best approaches to optimising the treatment of PSAC with intestinal schistosomiasis.

METHODS: We will conduct a randomised, controlled phase II trial in a Schistosoma mansoni endemic region of Uganda and a Schistosoma japonicum endemic region of the Philippines. Six hundred children, 300 in each setting, aged 12-47 months with Schistosoma infection will be randomised in a 1:1:1:1 ratio to receive either (1) 40 mg/kg PZQ at baseline and placebo at 6 months, (2) 40 mg/kg PZQ at baseline and 40 mg/kg PZQ at 6 months, (3) 80 mg/kg PZQ at baseline and placebo at 6 months, or (4) 80 mg/kg PZQ at baseline and 80 mg/kg PZQ at 6 months. Following baseline treatment, children will be followed up for 12 months. The co-primary outcomes will be cure rate and egg reduction rate at 4 weeks. Secondary outcomes include drug efficacy assessed by novel antigenic endpoints at 4 weeks, actively collected adverse events and toxicity for 12 h post-treatment, morbidity and nutritional outcomes at 6 and 12 months, biomarkers of inflammation and environmental enteropathy and PZQ PK/PD parameters.

DISCUSSION: The trial will provide valuable information on the safety and efficacy of the 80 mg/kg PZQ dose in PSAC, and on the impact of six-monthly versus annual treatment, in this vulnerable age group.

TRIAL REGISTRATION: ClinicalTrials.gov NCT03640377 . Registered on 21 Aug 2018.

PMID:34488846 | DOI:10.1186/s13063-021-05558-1

Genome Biol. 2021 Sep 6;22(1):258. doi: 10.1186/s13059-021-02451-7.

ABSTRACT

BACKGROUND: Standard preprocessing of single-cell RNA-seq UMI data includes normalization by sequencing depth to remove this technical variability, and nonlinear transformation to stabilize the variance across genes with different expression levels. Instead, two recent papers propose to use statistical count models for these tasks: Hafemeister and Satija (Genome Biol 20:296, 2019) recommend using Pearson residuals from negative binomial regression, while Townes et al. (Genome Biol 20:295, 2019) recommend fitting a generalized PCA model. Here, we investigate the connection between these approaches theoretically and empirically, and compare their effects on downstream processing.

RESULTS: We show that the model of Hafemeister and Satija produces noisy parameter estimates because it is overspecified, which is why the original paper employs post hoc smoothing. When specified more parsimoniously, it has a simple analytic solution equivalent to the rank-one Poisson GLM-PCA of Townes et al. Further, our analysis indicates that per-gene overdispersion estimates in Hafemeister and Satija are biased, and that the data are in fact consistent with the overdispersion parameter being independent of gene expression. We then use negative control data without biological variability to estimate the technical overdispersion of UMI counts, and find that across several different experimental protocols, the data are close to Poisson and suggest very moderate overdispersion. Finally, we perform a benchmark to compare the performance of Pearson residuals, variance-stabilizing transformations, and GLM-PCA on scRNA-seq datasets with known ground truth.

CONCLUSIONS: We demonstrate that analytic Pearson residuals strongly outperform other methods for identifying biologically variable genes, and capture more of the biologically meaningful variation when used for dimensionality reduction.

PMID:34488842 | DOI:10.1186/s13059-021-02451-7

Genome Biol. 2021 Sep 6;22(1):257. doi: 10.1186/s13059-021-02479-9.

ABSTRACT

Polygenic risk scores (PRSs) have wide applications in human genetics research, but often include tuning parameters which are difficult to optimize in practice due to limited access to individual-level data. Here, we introduce PUMAS, a novel method to fine-tune PRS models using summary statistics from genome-wide association studies (GWASs). Through extensive simulations, external validations, and analysis of 65 traits, we demonstrate that PUMAS can perform various model-tuning procedures using GWAS summary statistics and effectively benchmark and optimize PRS models under diverse genetic architecture. Furthermore, we show that fine-tuned PRSs will significantly improve statistical power in downstream association analysis.

PMID:34488838 | DOI:10.1186/s13059-021-02479-9

J Orthop Surg Res. 2021 Sep 7;16(1):550. doi: 10.1186/s13018-021-02692-z.

ABSTRACT

BACKGROUND: Lumbar spinal stenosis (LSS) is a common degenerative condition of the spine that causes back pain radiating to the lower extremity. Surgical treatment is indicated to treat progressive radical symptoms. Obesity has been associated with inferior results in the domains of quality of life (QoL) following an LSS operation, but the research findings have been limited. This paper aims to identify whether obesity affects QoL due to back pain among patients who underwent an operation for LSS.

METHODS: This study is based on a series of patients operated on for LSS between 2012 and 2018. Operated patients who returned for follow-up forms within the first or second years were included. A total of 359 patients were selected, 163 males (45%) and 196 females (55%). The mean age was 68.9 years. The EuroQol five-dimension scale (EQ-5D) questionnaire was chosen to measure QoL and the Oswestry Disability Index (ODI) for functional disability.

RESULTS: QoL, as measured by EQ-5D, was preoperatively lower in those patients with a BMI ≥ 30. One year after the operation, all groups had a similar trend of improved QoL. At the second year, the results in all groups levelled off even though there was no statistical difference in clinical outcomes (p = 0.92). The ODI was preoperatively statistically higher in patients with a BMI ≥ 30 (p < 0.001). Two years after the surgery, all groups had improved ODI scores, but there was no statistical difference in ODI between the BMI groups (p = 0.54).

CONCLUSION: Surgical intervention for debilitating or longstanding symptoms of LSS should be considered as a treatment option for suitable patients in spite of an elevated BMI.

PMID:34488826 | DOI:10.1186/s13018-021-02692-z

World J Emerg Surg. 2021 Sep 6;16(1):44. doi: 10.1186/s13017-021-00391-y.

ABSTRACT

BACKGROUND: Acute appendicitis is one of the most frequent abdominal surgical emergencies. Intra-abdominal abscess is a frequent post-operative complication. The aim of this meta-analysis was to compare peritoneal irrigation and suction versus suction only when performing appendectomy for complicated appendicitis.

METHODS: According to PRISMA guidelines, a systematic review was conducted and registered into the Prospero register (CRD42020186848). The risk of bias was defined to be from low to moderate.

RESULTS: Seventeen studies (9 RCTs and 8 CCTs) were selected, including 5315 patients. There was no statistical significance in post-operative intra-abdominal abscess in open (RR 1.27, 95% CI 0.75-2.15; I² = 74%) and laparoscopic group (RR 1.51, 95% CI 0.73-3.13; I² = 83%). No statistical significance in reoperation rate in open (RR 1.27, 95% CI 0.04-2.49; I² = 18%) and laparoscopic group (RR 1.42, 95% CI 0.64-2.49; I² = 18%). In both open and laparoscopic groups, operative time was lower in the suction group (RR 7.13, 95% CI 3.14-11.12); no statistical significance was found for hospital stay (MD – 0.39, 95% CI – 1.07 to 0.30; I² = 91%) and the rate of wound infection (MD 1.16, 95% CI 0.56-2.38; I² = 71%).

CONCLUSIONS: This systematic review has failed to demonstrate the statistical superiority of employing intra-operative peritoneal irrigation and suction over suction-only to reduce the rate of post-operative complications after appendectomy, but all the articles report clinical superiority in terms of post-operative abscess, wound infection and operative times in suction-only group.

PMID:34488825 | DOI:10.1186/s13017-021-00391-y

Radiat Oncol. 2021 Sep 6;16(1):171. doi: 10.1186/s13014-021-01895-2.

ABSTRACT

BACKGROUND: To compare the dosimetric, normal tissue complication probability (NTCP), secondary cancer complication probabilities (SCCP), and excess absolute risk (EAR) differences of volumetric modulated arc therapy (VMAT) and intensity-modulated radiation therapy (IMRT) for left-sided breast cancer after mastectomy.

METHODS AND MATERIALS: Thirty patients with left-sided breast cancer treated with post-mastectomy radiation therapy (PMRT) were randomly enrolled in this study. Both IMRT and VMAT treatment plans were created for each patient. Planning target volume (PTV) doses for the chest wall and internal mammary nodes, PTV1, and PTV of the supraclavicular nodes, PTV2, of 50 Gy were prescribed in 25 fractions. The plans were evaluated based on PTV1 and PTV2 coverage, homogeneity index (HI), conformity index, conformity number (CN), dose to organs at risk, NTCP, SCCP, EAR, number of monitors units, and beam delivery time.

RESULTS: VMAT resulted in more homogeneous chest wall coverage than did IMRT. The percent volume of PTV1 that received the prescribed dose of VMRT and IMRT was 95.9 ± 1.2% and 94.5 ± 1.6%, respectively (p < 0.001). The HI was 0.11 ± 0.01 for VMAT and 0.12 ± 0.02 for IMRT, respectively (p = 0.001). The VMAT plan had better conformity (CN: 0.84 ± 0.02 vs. 0.78 ± 0.04, p < 0.001) in PTV compared with IMRT. As opposed to IMRT plans, VMAT delivered a lower mean dose to the ipsilateral lung (11.5 Gy vs 12.6 Gy) and heart (5.2 Gy vs 6.0 Gy) and significantly reduced the V₅, V₁₀, V_20, V_30, and V₄₀ of the ipsilateral lung and heart; only the differences in V₅ of the ipsilateral lung did not reach statistical significance (p = 0.409). Although the volume of the ipsilateral lung and heart encompassed by the 2.5 Gy isodose line (V_2.5) was increased by 6.7% and 7.7% (p < 0.001, p = 0.002), the NTCP was decreased by 0.8% and 0.6%, and SCCP and EAR were decreased by 1.9% and 0.1% for the ipsilateral lung. No significant differences were observed in the contralateral lung/breast V_2.5, V_5, V₁₀, V₂₀, mean dose, SCCP, and EAR. Finally, VMAT reduced the number of monitor units by 31.5% and the treatment time by 71.4%, as compared with IMRT.

CONCLUSIONS: Compared with IMRT, VMAT is the optimal technique for PMRT patients with left-sided breast cancer due to better target coverage, a lower dose delivered, NTCP, SCCP, and EAR to the ipsilateral lung and heart, similar doses delivered to the contralateral lung and breast, fewer monitor units and a shorter delivery time.

PMID:34488817 | DOI:10.1186/s13014-021-01895-2

Global Health. 2021 Sep 6;17(1):103. doi: 10.1186/s12992-021-00756-7.

ABSTRACT

BACKGROUND: Refugees often face psychosocial complexity and multi-dimensional healthcare needs. Community-Based Participatory Research (CBPR) methods have been previously employed in designing health programs for refugee communities and in building strong research partnerships in refugee communities. However, the extent to which these communities are involved remains unknown.

OBJECTIVE: To review the evidence on the involvement of refugees in CBPR processes to inform healthcare research.

METHODS: A scoping review was performed, using Arksey & O’Malley’s methodological framework. A literature search in Medline, PubMed, PsycINFO, CINAHL, Embase, Global Health, Scopus, and Policy File Index for articles published until August 2020 was conducted. Articles were included if they focused on CBPR, had refugee involvement, and discussed healthcare/health policy.

RESULTS: 4125 articles were identified in the database searches. After removal of duplicates, 2077 articles underwent title and abstract review by two authors, yielding an inter-reviewer kappa-statistic of 0.85. 14 studies were included in the final analysis. The purpose of CBPR use for 6 (42.9%) of the articles was developing and implementing mental health/social support interventions, 5 (35.7%) focused on sexual and reproductive health interventions, 1 (7.1%) focused on domestic violence interventions, 1 (7.1%) focused on cardiovascular disease prevention and 1 (7.1%) focused on parenting interventions. In terms of refugee involvement in the various stages in the research process, 9 (64.3%) articles reported refugees having a role in the inception of the research, no articles reported including refugees in obtaining funding, all articles included refugees in the design of the research study, 10 (71.4%) articles reported having refugees involved in community engagement/recruitment, 8 (57.1%) articles reported involvement throughout the data collection process, 4 (28.6%) articles reported involvement in data analysis, 6 (42.9%) articles reported having refugees involved in knowledge translation/dissemination and 1 article (7.1%) reported having refugees contribute to scale up initiatives.

CONCLUSIONS: CBPR has been identified as a methodology with the potential to make substantial contributions to improving health and well-being in traditionally disenfranchised populations. As the needs of refugee communities are so diverse, efforts should be made to include refugees as partners in all stages of the research process.

PMID:34488810 | DOI:10.1186/s12992-021-00756-7

Ann Clin Microbiol Antimicrob. 2021 Sep 6;20(1):63. doi: 10.1186/s12941-021-00471-6.

ABSTRACT

BACKGROUND: Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae has become a public health concern. This study aimed to compare the clinical outcomes of patients with nonurinary source bacteraemia caused by ESBL-producing Escherichia coli (E. coli) or Klebsiella pneumoniae (ESBL-producing EK) receiving β-lactam/β-lactamase inhibitor combinations (BLICs) versus carbapenem treatment and assess the risk factors of mortality with these two drugs.

METHODS: We conducted a retrospective single-centre study of adult hospitalised patients with ESBL-producing EK bloodstream infection (BSI) from nonurinary source at our centre over a 4-year period. One hundred and eighty patients who received BLICs or carbapenems were included in the analysis. The outcome variables were 14-day treatment failure and 30-day mortality. For more reliable results, propensity score analysis was performed to compare the efficacy of the two drugs and analyse their risk factors for 30-day mortality.

RESULTS: Out of 180 patients, 114 received BLICs, and 66 received carbapenem therapy. Compared to carbapenem-treated patients, those treated with BLICs were older and had higher age-adjusted Charlson comorbidity index, but they had shorter stay in the hospital. Additionally, their Pitt bacteraemia score, SOFA score, rate of leukaemia, and immune compromise were lower. After propensity score matching (PSM), the baseline characteristics of patients in the two treatment groups were balanced. BLICs were associated with a higher 14-day treatment failure rate (20.6%, 13/63) than carbapenems (16.3%, 7/43), although the difference was not significant in either univariate analysis (P = 0.429) or multivariate analysis (P = 0.122). And the 30-day mortality rate in BTG (11.1%, 7/63) and CTG (11.6%, 5/43) did not significantly differ (univariate analysis, P = 0.926; multivariate analysis, P = 0.420). In the multivariate analysis, after PSM, leukaemia was the only independent predictor of mortality in both BTG and CTG.

CONCLUSIONS: Our study showed that BLICs had higher 14-day treatment failure rate compared with carbapenems, although there were no statistically significant differences because of the small number of patients, therefore, further evaluation of the efficacy of BLICs is needed.

PMID:34488786 | DOI:10.1186/s12941-021-00471-6