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Nevin Manimala Statistics

The Reporting and Methodological Quality of Systematic Reviews Underpinning Clinical Practice Guidelines Focused on the Management of Cutaneous Melanoma: Cross-Sectional Analysis

JMIR Dermatol. 2023 Dec 7;6:e43821. doi: 10.2196/43821.

ABSTRACT

BACKGROUND: Clinical practice guidelines (CPGs) inform evidence-based decision-making in the clinical setting; however, systematic reviews (SRs) that inform these CPGs may vary in terms of reporting and methodological quality, which affects confidence in summary effect estimates.

OBJECTIVE: Our objective was to appraise the methodological and reporting quality of the SRs used in CPGs for cutaneous melanoma and evaluate differences in these outcomes between Cochrane and non-Cochrane reviews.

METHODS: We conducted a cross-sectional analysis by searching PubMed for cutaneous melanoma guidelines published between January 1, 2015, and May 21, 2021. Next, we extracted SRs composing these guidelines and appraised their reporting and methodological rigor using the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) and AMSTAR (A Measurement Tool to Assess Systematic Reviews) checklists. Lastly, we compared these outcomes between Cochrane and non-Cochrane SRs. All screening and data extraction occurred in a masked, duplicate fashion.

RESULTS: Of the SRs appraised, the mean completion rate was 66.5% (SD 12.29%) for the PRISMA checklist and 44.5% (SD 21.05%) for AMSTAR. The majority of SRs (19/50, 53%) were of critically low methodological quality, with no SRs being appraised as high quality. There was a statistically significant association (P<.001) between AMSTAR and PRISMA checklists. Cochrane SRs had higher PRISMA mean completion rates and higher methodological quality than non-Cochrane SRs.

CONCLUSIONS: SRs supporting CPGs focused on the management of cutaneous melanoma vary in reporting and methodological quality, with the majority of SRs being of low quality. Increasing adherence to PRISMA and AMSTAR checklists will likely increase the quality of SRs, thereby increasing the level of evidence supporting cutaneous melanoma CPGs.

PMID:38060306 | DOI:10.2196/43821

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Nevin Manimala Statistics

Assessing the Impact of a Serious Game (MedSMARxT: Adventures in PharmaCity) in Improving Opioid Safety Awareness Among Adolescents and Parents: Quantitative Study

JMIR Form Res. 2023 Dec 7;7:e51812. doi: 10.2196/51812.

ABSTRACT

BACKGROUND: The opioid crisis continues to worsen across the United States, affecting people of all demographics. Few evidence-based interventions exist for educating families, particularly those with adolescents, about opioid prescription safety. Serious games have demonstrated impacts in improving medication-related outcomes for various health conditions. The characterizing goal of this serious game is to improve opioid safety knowledge and awareness among adolescents and their families.

OBJECTIVE: This study evaluated the impact of a serious game, MedSMARxT: Adventures in PharmaCity, designed to foster opioid safety awareness among adolescents and their parents.

METHODS: A national sample of parents and their adolescent children was recruited through Qualtrics research panels, social media, listservs, and snowball sampling. Eligible participants were adolescents aged between 12 and 18 years and their parents. Study participants were required to reside in the United States; speak, read, and understand English; and have access to a computer with a webcam. Parent-child dyads completed pregame and postgame surveys and participated in gameplay for up to 30 minutes. Primary outcome scales have been previously evaluated by the study team.

RESULTS: A total of 60 adolescent participants and 68 parent participants met full attention criteria for inclusion in this study. Statistical analysis confirmed that both adolescents’ and parents’ concept scores improved from baseline regarding opioid safety self-efficacy (adolescent: mean 0.35, SD 0.60; P<.001; parent: mean 0.28, SD 0.42; P<.001), perceived knowledge (adolescent: mean 1.08, SD 1.04; P<.001; parent: mean 0.56, SD 0.55; P<.001), behavioral intent (adolescent: mean 0.26, SD 0.39; P<.001; parent: mean 0.25, SD 0.32; P<.001), safe storage (adolescent: mean 0.12, SD 0.27; P<.001; parent: mean 0.03, SD 0.11; P=.03), disposal knowledge (adolescent: mean 0.10, SD 0.27; P=.006; parent: mean 0.07, SD 0.16; P<.001), and knowledge about misuse behavior (adolescent: mean 0.05, SD 0.14; P=.002; parent: mean 0.04, SD 0.10; P<.001). Participant groups, stratified by who completed and who did not complete gameplay, improved their knowledge and awareness, with no significant differences between subgroups.

CONCLUSIONS: The use of this serious game to improve opioid prescription safety practices among parents and adolescents was supported by the study findings. MedSMARxT: Adventures in PharmaCity is an intervention with the capability of teaching parents and adolescents about safe opioid prescription practices. Further studies and game refinement are needed to demonstrate the effectiveness of a game-based intervention in clinical settings and community pharmacies.

PMID:38060287 | DOI:10.2196/51812

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Nevin Manimala Statistics

LMdist: Local Manifold distance accurately measures beta diversity in ecological gradients

Bioinformatics. 2023 Dec 7:btad727. doi: 10.1093/bioinformatics/btad727. Online ahead of print.

ABSTRACT

MOTIVATION: Differentiating ecosystems poses a complex, high-dimensional problem constrained by capturing relevant variation across species profiles. Researchers use pairwise distances and subsequent dimensionality reduction to highlight variation in a few dimensions. Despite popularity in analysis of ecological data, these low-dimensional visualizations can contain geometric abnormalities such as “arch” and “horseshoe” effects, potentially obscuring the impact of environmental gradients. These abnormalities appear in ordination but are in fact a product of oversaturated large pairwise distances.

RESULTS: We present Local Manifold distance (LMdist), an unsupervised algorithm which adjusts pairwise beta diversity measures to better represent true ecological distances between samples. Beta diversity measures can have a bounded dynamic range in depicting long environmental gradients with high species turnover. Using a graph structure, LMdist projects pairwise distances onto a manifold and traverses the manifold surface to adjust pairwise distances at the upper end of the beta diversity measure’s dynamic range. This allows for values beyond the range of the original measure. Not all datasets will have oversaturated pairwise distances, nor will capture variation that resembles a manifold, so LMdist adjusts only those pairwise values which may be undervalued in the presence of a sampled gradient. The adjusted distances serve as input for ordination and statistical testing. We demonstrate on real and simulated data that LMdist effectively recovers distances along known gradients and along complex manifolds such as the Swiss roll dataset. LMdist enables more powerful statistical tests for gradient effects and reveals variation orthogonal to the gradient.

AVAILABILITY: Available on GitHub at https://github.com/knights-lab/LMdist.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:38060267 | DOI:10.1093/bioinformatics/btad727

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Nevin Manimala Statistics

FunctanSNP: an R package for functional analysis of dense SNP data (with interactions)

Bioinformatics. 2023 Dec 7:btad741. doi: 10.1093/bioinformatics/btad741. Online ahead of print.

ABSTRACT

SUMMARY: Densely measured SNP data is routinely analyzed but faces challenges due to its high dimensionality, especially when gene-environment (G-E) interactions are incorporated. In recent literature, a functional analysis strategy has been developed, which treats dense SNP measurements as a realization of a genetic function and can “bypass” the dimensionality challenge. However, there is a lack of portable and friendly software, which hinders practical utilization of these functional methods. We fill this knowledge gap and develop the R package FunctanSNP. This comprehensive package encompasses estimation, identification, and visualization tools and has undergone extensive testing using both simulated and real data, confirming its reliability. FunctanSNP can serve as a convenient and reliable tool for analyzing SNP and other densely measured data.

AVAILABILITY: The package is available at https://CRAN.R-project.org/package=FunctanSNP.

SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.

PMID:38060266 | DOI:10.1093/bioinformatics/btad741

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Nevin Manimala Statistics

Effectiveness of Aerobic Exercise and Tai Chi Interventions on Sleep Quality in Patients With Advanced Lung Cancer: A Randomized Clinical Trial

JAMA Oncol. 2023 Dec 7. doi: 10.1001/jamaoncol.2023.5248. Online ahead of print.

ABSTRACT

IMPORTANCE: Sleep disturbances prevalent among patients with advanced lung cancer can aggravate physical and psychological symptoms, contributing to decreased quality of life and survival.

OBJECTIVE: To compare the effectiveness of 2 physical activities of different modalities and intensities, namely aerobic exercise (AE) and tai chi (TC), on subjective sleep quality, physical and psychological outcomes, and survival in patients with advanced lung cancer.

DESIGN, SETTING, AND PARTICIPANTS: This assessor-blinded, randomized clinical trial was conducted in 3 public hospitals in Hong Kong between December 19, 2018, and September 7, 2022. A total of 226 patients with advanced lung cancer were recruited and randomized 1:1:1 to AE, TC, or the control group.

INTERVENTIONS: For 16 weeks, the AE group received two 60-minute supervised group exercise sessions and home-based exercises per month, and the TC group received 60-minute group sessions twice weekly. The control group received physical activity guidelines.

MAIN OUTCOMES AND MEASURES: The primary outcome was subjective sleep quality. Secondary outcomes included objective sleep measures, anxiety, depression, fatigue, quality of life, physical function, circadian rhythm, and 1-year survival. Assessments were conducted at baseline, 16 weeks (T1), and 1 year (T2).

RESULTS: The 226 participants had a mean (SD) age of 61.41 (8.73) years, and 122 (54.0%) were female. Compared with the control group, participants in the AE and TC groups showed statistically significant improvements in subjective sleep quality from baseline to T1 (AE: between-group difference, -2.72; 95% CI, -3.97 to -1.46; P < .001; TC: between-group difference, -4.21; 95% CI, -5.48 to -2.94; P < .001) and T2 (AE: between-group difference, -1.75; 95% CI, -3.24 to -0.26; P = .02; TC: between-group difference, -3.95; 95% CI, -5.41 to -2.49; P < .001), psychological distress, physical function, step count, and circadian rhythm. The TC group had a statistically significant greater improvement in sleep than the AE group at T1 (between-group difference, -1.49; 95% CI, -2.77 to -0.22; P = .02) and T2 (between-group difference, -2.20; 95% CI, -3.57 to -0.83; P < .001). Participants in the TC group showed statistically significant improvement in survival compared with the control group.

CONCLUSIONS AND RELEVANCE: In this randomized clinical trial, AE and TC improved sleep, psychological distress, physical function, and circadian rhythm, with TC demonstrating greater benefits on sleep and survival. Both exercises, but particularly TC, can be incorporated into lung cancer survivorship care.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT04119778.

PMID:38060250 | DOI:10.1001/jamaoncol.2023.5248

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Nevin Manimala Statistics

Choroidal Vascularity Index Fluctuations in Epiretinal Membranes in Vitreoretinal Surgery: Comparison Between Idiopathic and Diabetic Ones

Transl Vis Sci Technol. 2023 Dec 1;12(12):9. doi: 10.1167/tvst.12.12.9.

ABSTRACT

PURPOSE: The aim of the study was to analyze choroidal vascularity index (CVI) fluctuations in patients with epiretinal membrane after vitreoretinal surgery, comparing idiopathic and secondary diabetic ones.

METHODS: Thirty eyes suffering from idiopathic ERMs (I-ERMS; n = 15) and diabetic ERMs (D-ERMS; n = 15) were analyzed in this observational prospective study. Anatomical (central macular thickness) and functional (best-corrected visual acuity) parameters were analyzed preoperatively and at 1 and 3 months after vitrectomy. Perfusion findings regarding CVI and luminal area were also calculated.

RESULTS: At 1 month after surgery, the luminal area and CVI significantly decreased in the I-ERMS group, whereas they were increased in the D-ERMS group. At the 3-month follow-up, the CVI tended to return to baseline values in I-ERMS and to reduce in D-ERMS, but without any statistical differences.

CONCLUSIONS: The significant change in the CVI after surgery seems to imply that the choroidal layer is affected by vitreomacular disease and can become a novel potential biomarker of predictiveness in vitreoretinal surgery.

TRANSLATIONAL RELEVANCE: The aim of the study was to focus on the early choroidal changes to better understand initial predictive elements of long-term functional postoperative outcomes.

PMID:38060233 | DOI:10.1167/tvst.12.12.9

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Nevin Manimala Statistics

Cross-Sectional Study of the Psychological Well-Being of Healthcare Workers in a Large European University Hospital after the COVID-19 Initial Wave

Med Lav. 2023 Dec 7;114(6):e2023051. doi: 10.23749/mdl.v114i6.14849.

ABSTRACT

BACKGROUND: The SARS-CoV-2 pandemic greatly impacted healthcare workers (HCWs) dedicated to caring for COVID-19 patients. The study was conducted in a large European hospital to study the psychological distress of HCWs engaged in COVID-19 wards in the early phase of the pandemic.

METHODS: A questionnaire was sent to 1229 HCWs aimed at collecting the following information: 1) sociodemographic data; 2) depression, anxiety, and stress scales (DASS-21); 3) event impact scale (IES-R); 4) perceived stress scale (PSS); and 5) work interface analysis. The responses were collected through Google® forms and then statistically analyzed. Regardless of the outcome of the questionnaire, all subjects were offered psychological support voluntarily.

RESULTS: Approximately two-thirds of the workers reported no symptoms according to the DASS-21 scales, while the IES-R and PSS scales showed 36% and 43%, respectively. There were no statistically significant differences in the levels of depression investigated through the different scales in the various occupational categories. Symptoms of anxiety, stress, and depression were more pronounced in women, while the highest stress levels were observed in the younger age groups. The highest scores were observed on the DAS-21 scales of anxiety and IES-R but not on the others. Only 51 workers, most of them with previous SARS-CoV-2 infection, sought clinical psychological counseling, and more than half received subsequent psychological support.

CONCLUSIONS: Our results agree with most of the literature data that anxiety, depression, and stress are associated with gender (female), age (18-44 vs. over 55), and having cared for patients with COVID-19.

PMID:38060210 | DOI:10.23749/mdl.v114i6.14849

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Nevin Manimala Statistics

The Search for System’s Parameters: Statistical and Dynamical Description from Complex Network Analysis

Methods Mol Biol. 2024;2745:21-30. doi: 10.1007/978-1-0716-3577-3_2.

ABSTRACT

The integration of physical and biological science styles is the key for facing the deluge of molecular level information that is becoming a real threat for knowledge advancement. In this work, I will indicate a possible integration path based on the network formalization of molecular knowledge by two different (here named flux and dynamical) perspectives. Some theoretical and applicative cases are presented, focusing on the different physical models implicit in the two network analysis approaches.

PMID:38060177 | DOI:10.1007/978-1-0716-3577-3_2

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Durability of Effectiveness Between Users of Once-Weekly Semaglutide and Dipeptidyl Peptidase 4 Inhibitors (DPP-4i) in US Adults with Type 2 Diabetes

Diabetes Ther. 2023 Dec 7. doi: 10.1007/s13300-023-01509-y. Online ahead of print.

ABSTRACT

INTRODUCTION: Long-term effectiveness and durability of glucose-lowering medications are important considerations in managing type 2 diabetes (T2D). This study aimed to compare durability of treatment efficacy of once-weekly (OW) semaglutide for T2D with that of the dipeptidyl peptidase 4 inhibitor (DPP-4i) class.

METHODS: This observational cohort study used 2017-2022 data from the Optum® Clinformatics® Data Mart to compare long-term clinical outcomes associated with semaglutide or DPP-4i in US adults with T2D. The primary outcomes were HbA1c at 2-year follow-up, change in HbA1c from baseline, and the odds of achieving HbA1c targets. BMI at 2-year follow-up, change in BMI from baseline, odds of reducing BMI category, and the need for treatment augmentation were exploratory outcomes. Bivariate and multivariate analyses were conducted using inverse probability of treatment weighting (IPTW) weighted descriptive statistics.

RESULTS: Weighted HbA1c and BMI cohorts included 865 and 642 semaglutide users and 779 and 537 DPP-4i users, respectively. In the weighted HbA1c cohort, semaglutide and DPP-4i users had an average age of 60 years and similar baseline characteristics including HbA1c level and comorbidity status. Two-year follow-up HbA1c with semaglutide was 0.56% lower than with DPP-4i; reduction in HbA1c from baseline was 0.61% greater. Odds of achieving HbA1c level < 7% were 2.16 times greater after covariate adjustment (all, p < 0.001). Semaglutide was associated with 1.03 kg/m2 greater reduction in BMI and 2.27 times greater odds of reducing BMI category vs DPP-4i (p < 0.001). Semaglutide users were less likely to add new glucose-lowering treatment (hazard ratio [HR] 0.57; p < 0.001) or initiate insulin (HR 0.49; p < 0.001) vs DPP-4i users.

CONCLUSION: Compared with DPP-4i, semaglutide was associated with lower follow-up HbA1c and BMI, greater reduction in HbA1c and BMI from baseline, and reduced likelihood of requiring treatment augmentation or insulin initiation to manage T2D in US adults, suggesting better durability of semaglutide vs DPP-4i. INFOGRAPHIC.

PMID:38060149 | DOI:10.1007/s13300-023-01509-y

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Exploration and Retrieval of Virus-Related Molecular Data Using ExTaxsI: The Monkeypox Use Case

Methods Mol Biol. 2024;2732:145-154. doi: 10.1007/978-1-0716-3515-5_10.

ABSTRACT

Retrieval and visualization of biological data are essential for understanding complex systems. With the increasing volume of data generated from high-throughput sequencing technologies, effective and optimized data visualization tools have become indispensable. This is particularly relevant in the COVID-19 postpandemic period, where understanding the diversity and interactions of microbial communities (i.e., viral and bacterial) constitutes an important asset to develop and plan suitable interventions.In this chapter, we show the usage and the potentials of ExTaxsI (Exploring Taxonomy Information) tool to retrieve viral biodiversity data stored in National Center for Biotechnology Information (NCBI) databases and create the related visualization. In addition, by integrating different functions and modules, the tool generates relevant types of visualization plots to facilitate the exploration of microbial biodiversity communities useful to deep dive into ecological and taxonomic relationships among different species and identify potential significant targets.Using the Monkeypox virus as a case study, this work points out significant perspectives on biological data visualization, which can be used to gain insights into the ecology, evolution, and pathogenesis of viruses. Accordingly, we show the potentiality of ExTaxsI to organize and describe the available/downloaded data in an easy, simple, and interpretable way allowing the user to interact dynamically with the visualization plots through specific filters, zoom, and explore functions.

PMID:38060123 | DOI:10.1007/978-1-0716-3515-5_10