Category: Nevin Manimala

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

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

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

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

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

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

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

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

AIDS Behav. 2023 Dec 7. doi: 10.1007/s10461-023-04233-7. Online ahead of print.

ABSTRACT

Exposure to discrimination has been linked to lower HIV antiretroviral therapy (ART) adherence and poor HIV care outcomes among Black Americans. Coping has been shown to mitigate the harmful effects of discrimination on health behaviors, but the use of cultural relevant Africultural coping strategies is understudied as a moderator of the association between intersectional discrimination and ART adherence among Black Americans. We used adjusted logistic regression to test whether Africultural coping strategies (cognitive/emotional debriefing; collective; spiritual-centered; ritual-centered) moderated associations between multiple forms of discrimination (HIV, sexual orientation, race) and good ART adherence (minimum of 75% or 85% of prescribed doses taken, as measured by electronic monitoring in separate analyses) among 92 sexual minority Black Americans living with HIV. Mean adherence was 66.5% in month 8 after baseline (36% ≥ 85% adherence; 49% ≥ 75% adherence). Ritual-centered coping moderated the relationship between each of the three types of discrimination at baseline and good ART adherence in month 8 (regardless of the minimum threshold for good adherence); when use of ritual coping was low, the association between discrimination and adherence was statistically significant. The other three coping scales each moderated the association between racial discrimination and good ART adherence (defined by the 75% threshold); cognitive/emotional debriefing was also a moderator for both HIV- and race-related discrimination at the 85% adherence threshold. These findings support the benefits of Africultural coping, particularly ritual-centered coping, to help sexual minority Black Americans manage stressors associated with discrimination and to adhere well to ART.

PMID:38060112 | DOI:10.1007/s10461-023-04233-7

J Autism Dev Disord. 2023 Dec 7. doi: 10.1007/s10803-023-06177-2. Online ahead of print.

ABSTRACT

PURPOSE: Autistic children are reported to display higher levels of externalizing and internalizing behaviors than neurotypical children, and their parents report more stress than parents of neurotypical children. It is unclear whether child behavior difficulties contribute to increased parenting stress, whether parenting stress contributes to child behavior difficulties, or whether the relationship may be bidirectional.

METHODS: We investigated prospective bidirectional associations between parenting stress and child externalizing and internalizing behaviors when autistic children were aged on average 3.5, 4.5, and 5.5 years. Data collected at these three timepoints were examined across two panels: Time 1 to Time 2 (n = 38 parent-child dyads) and Time 2 to Time 3 (n = 27 dyads).

RESULTS: Across Time 1 to Time 2, early parenting stress was significantly associated with later child externalizing behavior, and cross-lagged panel analysis supported a uni- rather than a bidirectional association between these factors. There was some evidence of a bidirectional association between parenting stress and child internalizing behavior, though this was non-significant when the strong stability of child internalizing behavior was statistically controlled. In contrast, across Time 2 to Time 3, there were no significant prospective associations found between variables, highlighting the importance of considering the impact of parenting stress early in the course of childhood autism.

CONCLUSION: Our results add to research indicating that support targeting parent characteristics, especially parenting stress, could ameliorate subsequent outcomes for both parents and children.

PMID:38060104 | DOI:10.1007/s10803-023-06177-2