Category: Nevin Manimala

Proc Natl Acad Sci U S A. 2024 Nov 26;121(48):e2322887121. doi: 10.1073/pnas.2322887121. Epub 2024 Nov 18.

ABSTRACT

Cultural evolution applies evolutionary concepts and tools to explain the change of culture over time. Despite advances in both theoretical and empirical methods, the connections between cultural evolutionary theory and evidence are often vague, limiting progress. Theoretical models influence empirical research but rarely guide data collection and analysis in logical and transparent ways. Theoretical models themselves are often too abstract to apply to specific empirical contexts and guide statistical inference. To help bridge this gap, we outline a quality-assurance computational workflow that starts from generative models of empirical phenomena and logically connects statistical estimates to both theory and real-world explanatory goals. We emphasize and demonstrate validation of the workflow using synthetic data. Using the interplay between conformity, migration, and cultural diversity as a case study, we present coded and repeatable examples of directed acyclic graphs, tailored agent-based simulations, a probabilistic transmission model for longitudinal data, and an approximate Bayesian computation model for cross-sectional data. We discuss the assumptions, opportunities, and pitfalls of different approaches to generative modeling and show how each can be used to improve data analysis depending on the structure of available data and the depth of theoretical understanding. Throughout, we highlight the significance of ethnography and of collecting basic cultural and demographic information about study populations and call for more emphasis on logical and theory-driven workflows as part of science reform.

PMID:39556723 | DOI:10.1073/pnas.2322887121

JMIR Pediatr Parent. 2024 Nov 18;7:e59283. doi: 10.2196/59283.

ABSTRACT

BACKGROUND: The Singapore integrated 24-hour activity guide for children and adolescents was introduced to promote healthy lifestyle behaviors, including physical activity, sedentary behavior, sleep, and diet, to enhance metabolic health and prevent noncommunicable diseases. To support the dissemination and implementation of these recommendations, a user-friendly online resource was created to help children and adolescents adopt these behaviors in Singapore.

OBJECTIVE: This study aimed to assess the acceptability of the online resource in the adoption of healthier lifestyle behaviors, and the change in the users’ behaviors with the use of this online resource.

METHODS: Participants aged 7-17 years were required to log their activity levels of the past 7 days at the beginning and at the end of a 3-month period using the browser-based online resource, including information on the duration and frequency of moderate- to vigorous-intensity physical activity (MVPA), length of sedentary behavior, duration and regularity of sleep, and food portions. User satisfaction, on the length, ease of use, and relevance of the online resource, was also recorded using a 10-point Likert scale. Descriptive statistics and statistical analyses, including the Wilcoxon signed rank test and McNemar test, were carried out at baseline and at the end of 3 months.

RESULTS: A total of 46 participants were included for analysis. For physical activity, the number of days of MVPA increased from a median of 3 (IQR 2-5) days to 4 (IQR 2-5) days (P=.01). For sedentary behavior, the median daily average screen time decreased from 106 (IQR 60-142.5) minutes to 90 (IQR 60-185) minutes. For sleep, 10% (5/46) more participants met the recommended duration, and the number of days with regular sleep increased from a median of 6 (IQR 5-7) days to 7 (IQR 5-7) days (P=.03). For diet, there was a decrease in the portion of carbohydrates consumed from a median of 42% (IQR 30-50) to 40% (IQR 30-48.5; P=.03), and the number of days of water and unsweetened beverage consumption remained stable at a median of 5 days but with a higher IQR of 4-7 days (P=.04). About 90% (39-41/46) of the participants reported that the online resource was relevant and easy to use, and the rating for user satisfaction remained favorable at a median of 8 with a higher IQR of 7-9 (P=.005).

CONCLUSIONS: The findings support the development of a dedicated online resource to assist the implementation of healthy lifestyle behaviors based on the Singapore integrated 24-hour activity guide for children and adolescents. This resource received favorable ratings and its use showed the adoption of healthier behaviors, including increased physical activity and sleep, as well as decreased sedentary time and carbohydrate consumption, at the end of a 3-month period.

PMID:39556715 | DOI:10.2196/59283

Circulation. 2024 Nov 19;150(21):1741-1744. doi: 10.1161/CIRCULATIONAHA.124.069792. Epub 2024 Nov 18.

NO ABSTRACT

PMID:39556651 | DOI:10.1161/CIRCULATIONAHA.124.069792

PLoS Comput Biol. 2024 Nov 18;20(11):e1012606. doi: 10.1371/journal.pcbi.1012606. Online ahead of print.

ABSTRACT

The time-resolved scRNA-seq (tscRNA-seq) provides the possibility to infer physically meaningful kinetic parameters, e.g., the transcription, splicing or RNA degradation rate constants with correct magnitudes, and RNA velocities by incorporating temporal information. Previous approaches utilizing the deterministic dynamics and steady-state assumption on gene expression states are insufficient to achieve favorable results for the data involving transient process. We present a dynamical approach, Storm (Stochastic models of RNA metabolic-labeling), to overcome these limitations by solving stochastic differential equations of gene expression dynamics. The derivation reveals that the new mRNA sequencing data obeys different types of cell-specific Poisson distributions when jointly considering both biological and cell-specific technical noise. Storm deals with measured counts data directly and extends the RNA velocity methodology based on metabolic labeling scRNA-seq data to transient stochastic systems. Furthermore, we relax the constant parameter assumption over genes/cells to obtain gene-cell-specific transcription/splicing rates and gene-specific degradation rates, thus revealing time-dependent and cell-state-specific transcriptional regulations. Storm will facilitate the study of the statistical properties of tscRNA-seq data, eventually advancing our understanding of the dynamic transcription regulation during development and disease.

PMID:39556617 | DOI:10.1371/journal.pcbi.1012606

PLoS One. 2024 Nov 18;19(11):e0313927. doi: 10.1371/journal.pone.0313927. eCollection 2024.

ABSTRACT

Wastewater-Based Epidemiology (WBE) has become a powerful tool for assessing disease occurrence in communities. This study investigates the coronavirus disease 2019 (COVID-19) epidemic in the United States during 2023-2024 using wastewater data from 189 wastewater treatment plants in 40 states and the District of Columbia. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and pepper-mild mottle virus normalized SARS-CoV-2 RNA concentration data were compared with COVID-19 hospitalization admission data at both national and state levels. We further investigate temporal features in wastewater viral RNA abundance, with peak timing and cross-correlation lag analyses indicating that wastewater SARS-CoV-2 RNA concentrations precede hospitalization admissions by 2 to 12 days. Lastly, we demonstrate that wastewater treatment plant size has a significant effect on the variability of measured SARS-CoV-2 RNA concentrations. This study highlights the effectiveness of WBE as a non-invasive, timely and resource-efficient disease monitoring strategy, especially in the context of declining COVID-19 clinical reporting.

PMID:39556598 | DOI:10.1371/journal.pone.0313927

PLoS One. 2024 Nov 18;19(11):e0311058. doi: 10.1371/journal.pone.0311058. eCollection 2024.

ABSTRACT

The mutation-selection mechanism of Darwinian evolution gives rise not only to adaptation to environmental conditions but also to the enhancement of robustness against mutations. When two or more phenotypes have the same fitness value, the robustness distribution for different phenotypes can vary. Thus, we expect that some phenotypes are favored in evolution and that some are hardly selected because of a selection bias for mutational robustness. In this study, we investigated this selection bias for phenotypes in a model of gene regulatory networks (GRNs) using numerical simulations. The model had one input gene accepting a signal from the outside and one output gene producing a target protein, and the fitness was high if the output for the full signal was much higher than that for no signal. The model exhibited three types of responses to changes in the input signal: monostable, toggle switch, and one-way switch. We regarded these three response types as three distinguishable phenotypes. We constructed a randomly generated set of GRNs using the multicanonical Monte Carlo method originally developed in statistical physics and compared it to the outcomes of evolutionary simulations. One-way switches were strongly suppressed during evolution because of their lack of mutational robustness. By examining one-way switch GRNs in detail, we found that mutationally robust GRNs obtained by evolutionary simulations and non-robust GRNs obtained by McMC have different network structures. While robust GRNs have a common core motif, non-robust GRNs lack this motif. The bistability of non-robust GRNs is considered to be realized cooperatively by many genes, and these cooperative genotypes have been suppressed by evolution.

PMID:39556585 | DOI:10.1371/journal.pone.0311058

PLOS Glob Public Health. 2024 Nov 18;4(11):e0003959. doi: 10.1371/journal.pgph.0003959. eCollection 2024.

ABSTRACT

Healthcare workers continue to experience high levels of work-related stress which continue to negatively affect their psychological, physical, and emotional well-being. This is even more prevalent among healthcare workers who work in surgical specialities, with the surgical operation room becoming a known stressor at hospitals. This study aims to assess work-related stress among surgical team members at Ahmadu Bello University Teaching Hospital in Zaria between January 2021-2022. Data analysis involved descriptive and inferential statistical approaches using the Statistical Package for Social Science (SPSS) version 23.0. The study found an overall high prevalence of work-related stress, with 65% of participants reporting moderate levels of stress. The majority of the participants have a mean age of 39.4 ± 7.8 years, most of them being physicians (66.3%), being males (59.9%), and identified with a Hausa ethnic tribe. Notably, the multiple regression analysis found that tribe (p = 0.008), professional cadres (p = 0.001) and age/years of experience (p = 0.0035) emerged as significant predictors of work-related stress. Key determinants of work-related stress among surgical team members include workload, complexity of work, and conflicting cognitive job demands that continue to subject professionals to increasing workloads and constant decision-making about their job. Organizational factors, such as job policy and procedure, communication problems, and the nature of facilities, were identified as the highest contributors to work-related stress in organizational, interpersonal, and physical/environmental dimensions. The findings lead to the conclusion that a considerable proportion of surgical team members experience a relatively high level of work-related stress, primarily attributed to workload and cognitive demands. In light of these results, urgent efforts are recommended to improve the working conditions and environment for surgical team members. Furthermore, the integration of stress management measures into the educational programs for the surgical team is emphasized to effectively address and mitigate the impact of work-related stress.

PMID:39556579 | DOI:10.1371/journal.pgph.0003959

PLoS One. 2024 Nov 18;19(11):e0301111. doi: 10.1371/journal.pone.0301111. eCollection 2024.

ABSTRACT

OBJECTIVE: Peer review frequently follows a process where reviewers first provide initial reviews, authors respond to these reviews, then reviewers update their reviews based on the authors’ response. There is mixed evidence regarding whether this process is useful, including frequent anecdotal complaints that reviewers insufficiently update their scores. In this study, we aim to investigate whether reviewers anchor to their original scores when updating their reviews, which serves as a potential explanation for the lack of updates in reviewer scores.

DESIGN: We design a novel randomized controlled trial to test if reviewers exhibit anchoring. In the experimental condition, participants initially see a flawed version of a paper that is corrected after they submit their initial review, while in the control condition, participants only see the correct version. We take various measures to ensure that in the absence of anchoring, reviewers in the experimental group should revise their scores to be identically distributed to the scores from the control group. Furthermore, we construct the reviewed paper to maximize the difference between the flawed and corrected versions, and employ deception to hide the true experiment purpose.

RESULTS: Our randomized controlled trial consists of 108 researchers as participants. First, we find that our intervention was successful at creating a difference in perceived paper quality between the flawed and corrected versions: Using a permutation test with the Mann-Whitney U statistic, we find that the experimental group’s initial scores are lower than the control group’s scores in both the Evaluation category (Vargha-Delaney A = 0.64, p = 0.0096) and Overall score (A = 0.59, p = 0.058). Next, we test for anchoring by comparing the experimental group’s revised scores with the control group’s scores. We find no significant evidence of anchoring in either the Overall (A = 0.50, p = 0.61) or Evaluation category (A = 0.49, p = 0.61). The Mann-Whitney U represents the number of individual pairwise comparisons across groups in which the value from the specified group is stochastically greater, while the Vargha-Delaney A is the normalized version in [0, 1].

PMID:39556577 | DOI:10.1371/journal.pone.0301111

JAMA Netw Open. 2024 Nov 4;7(11):e2445309. doi: 10.1001/jamanetworkopen.2024.45309.

ABSTRACT

IMPORTANCE: Cardiovascular-kidney-metabolic (CKM) syndrome-a novel, multistage, multisystem disorder as defined by the American Heart Association-is highly prevalent in the US. However, the prevalence of CKM stages by social determinants of health (SDOH) remains unclear.

OBJECTIVE: To investigate whether the prevalence of CKM stages varies by SDOH in US adults.

DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study used data from the National Health and Nutrition Examination Survey (1999-2018) and included a nationally representative sample of adults aged 30 to 79 years through complex, multistage probability sampling. Data were analyzed from April 1 to June 15, 2024.

EXPOSURES: The exposures included 5 CKM stages (ie, stages 0-4) reflecting progressive pathophysiology, with advanced (stages 3 or 4) and nonadvanced (stages 0, 1, or 2) disease. CKM stages were defined based on risk factors for metabolic syndrome, cardiovascular disease, and chronic kidney disease.

MAIN OUTCOME AND MEASURES: The main outcome was the age-standardized prevalence of CKM stages and advanced CKM stages across SDOH, including education, marital status, family income, food security, health insurance, employment, home ownership, and health care access.

RESULTS: Among 29 722 participants (weighted mean [SE] age, 50.8 [0.1] years; weighted 50.7% male), the age-standardized prevalence of CKM stages 0 to 4 was 13.6% (95% CI, 13.0%-14.3%), 29.9% (95% CI, 29.1%-30.7%), 43.7% (95% CI, 42.9%-44.5%), 4.7% (95% CI, 4.4%-5.0%), and 8.1% (95% CI, 7.6%-8.5%), respectively. Significant differences were observed in the prevalence of CKM stages across all unfavorable SDOH of interest compared with their favorable counterparts, with unemployment (18.8% [95% CI, 17.7%-20.1%] vs 11.4% [95% CI, 11.0%-11.9%]), low family income (16.1% [95% CI, 15.4%-16.8%] vs 10.1% [95% CI, 9.5%-10.7%]), and food insecurity (18.3% [95% CI, 17.1%-19.6%] vs 11.7% [95% CI, 11.2%-12.2%]) associated with an increased likelihood of advanced CKM stages. Participants with 2 or more unfavorable SDOH were more likely to have advanced CKM stages (age-standardized prevalence, 15.8% [95% CI, 15.2%-16.5%] vs 10.5% [95% CI, 9.9%-11.1%] with <2 unfavorable SDOH). Living in a rented home (15.9% [95% CI, 14.7%-17.0%] vs 9.3% [95% CI, 8.7%-9.9%] owning the home) or not living with a partner (13.2% [95% CI, 12.3%-14.3%] vs 9.2% [95% CI, 8.5%-9.8%] living with a partner) increased the likelihood of advanced CKM stages in female but not male participants.

CONCLUSIONS AND RELEVANCE: In this cross-sectional study, disparities in the prevalence of CKM stages by SDOH, particularly family income, food security, and employment, with notable sex differences, were observed in US adults. These findings highlight the need to address inequities in CKM syndrome through targeted interventions.

PMID:39556396 | DOI:10.1001/jamanetworkopen.2024.45309

JAMA Netw Open. 2024 Nov 4;7(11):e2445525. doi: 10.1001/jamanetworkopen.2024.45525.

ABSTRACT

IMPORTANCE: The burden of liver cancer varies worldwide. An upward trend in both hepatocellular carcinoma (HCC) incidence and mortality in the past 2 decades has been observed.

OBJECTIVE: To assess observed HCC-related age-standardized mortality rates (ASMRs) in the US for 2006 to 2022 and provide ASMR projections through 2040.

DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study used data from the National Vital Statistics System, which is accessible through the Centers for Disease Control and Prevention Wide-Ranging Online Data for Epidemiologic Research website. Data on deaths attributed to HCC (from January 1, 2006, to December 31, 2022) were obtained for adults 25 years or older and were stratified by liver disease etiology, age, sex, and race and ethnicity. Etiologies included alcohol-associated liver disease (ALD), hepatitis B virus (HBV), hepatitis C virus (HCV), and metabolic dysfunction-associated steatotic liver disease (MASLD).

MAIN OUTCOMES AND MEASURES: The main outcomes were (1) observed ASMRs of HCC per 100 000 persons using Joinpoint regression (National Cancer Institute) to assess trends during 2006 to 2022 and (2) ASMRs projected for 2023 to 2040 using Prophet and AutoARIMA modeling.

RESULTS: This study included 188 280 HCC-related deaths from 2006 to 2022. Most deaths occurred among males (77.4%). The annual percentage change was 4.1% (95% CI, 2.2% to 7.7%) for 2006 to 2009 and decreased to 1.8% (95% CI, 0.7% to 2.0%) for 2009 to 2022, with an overall observed ASMR of 5.03 per 100 000 persons in 2022 and a projected ASMR of 6.39 per 100 000 persons by 2040, with consistent trends for both sexes. By etiology, ASMRs decreased for HCV- and HBV-related mortality but increased for ALD- and MASLD-related mortality. In 2022, MASLD surpassed HBV as the third-leading cause of HCC-related death and was projected to overtake HCV in 2032 as the second-leading cause; ALD was projected to be the leading cause of HCC-related death in 2026. In 2022, the ASMR was higher among individuals aged 65 years or older compared with those aged 25 to 64 years (18.37 vs 1.79 per 100 000 persons). The American Indian or Alaska Native population had the largest increase in projected ASMR by 2040 (14.71 per 100 000 persons) compared with the Asian population (3.03 per 100 000 persons).

CONCLUSIONS AND RELEVANCE: In this cross-sectional study, ASMRs for ALD- and MASLD-related HCC death increased rapidly from 2006 to 2022; ALD-related HCC was projected to be the leading cause by 2026, with MASLD as the second-leading cause by 2032. These findings may serve as a reference for public health decision-making and timely identification of groups at high risk of HCC death.

PMID:39556395 | DOI:10.1001/jamanetworkopen.2024.45525