Tag: statistics

Eur J Orthod. 2023 May 30:cjad007. doi: 10.1093/ejo/cjad007. Online ahead of print.

ABSTRACT

OBJECTIVES: To assess the changes in compliance with the Consolidated Standards of Reporting Trials (CONSORT) guidelines for randomized controlled trials (RCTs) in four orthodontic journals. To assess whether reporting of randomization, concealment, and blinding has improved.

METHODS: Electronic hand searching was undertaken to identify orthodontic RCTs published in four orthodontic journals from January 2016 to June 2017 (T1) and from January 2019 to June 2020 (T2). The journals were the American Journal of Orthodontics and Dentofacial Orthopaedics (AJO-DO), Angle Orthodontist (AO), European Journal of Orthodontics (EJO), and Journal of Orthodontics (JO). Each item on the CONSORT checklist was scored as either reported, not reported, or not applicable for each paper reporting an RCT.

RESULTS: The study included 69 papers reporting an RCT published in T1 and 64 RCTs published in T2. The median CONSORT score in T1 was 48.7% (interquartile range [IQR] 27.6%, 68.6%) and 67% in T2 (IQR 43.9%, 79.5%). This increase was statistically significant (P = 0.001) and largely attributable to improved reporting in AO (P = 0.016) and EJO (P = 0.023). Reporting did not change significantly in AJO-DO (P = 0.13) or in JO (P = 1.0). Reporting of random allocation sequence generation (OR 2.09; 95% CI 1.01, 4.29) and concealment of allocation (OR 2.27%, 95% CI 1.12, 4.57) were significantly higher in T2 compared with T1. Reporting of blinding did not change significantly.

CONCLUSION: Overall reporting of CONSORT items in reports of orthodontic RCTs published in the AJO-DO, AO, EJO, and JO, improved significantly from 2016-17 to 2019-20. This could be improved further by authors, journal referees, and editors adhering to the guidelines.

PMID:37253055 | DOI:10.1093/ejo/cjad007

PLoS One. 2023 May 30;18(5):e0286321. doi: 10.1371/journal.pone.0286321. eCollection 2023.

ABSTRACT

BACKGROUND: COVID-19 caused severe effects on the psychological well-being of Chinese students overseas (COS). Physical activity (PA) is critical to strengthen immunity, prevent infection, and reduce the psychological burden caused by COVID-19. However, there is a severe lack of effective PA intervention for mental health in most countries, and COS have limited access to mental healthcare during the pandemic.

OBJECTIVE: We aim to examine the effects of PA on COS’ mental health during the pandemic abroad and to better understand that certain types of PA might be associated with a greater reduction in psychological burdens during the pandemic.

METHODS AND RESULTS: In a multi-country cross-sectional analysis, a questionnaire was distributed to COS living in 37 foreign countries via WeChat Subscription using a snowball sampling strategy. A total of 10,846 participants were included. Descriptive statistics and Binary logistic regression analysis were used for statistical analysis. We found that COS had negative psychology during the pandemic, especially with fear (2.90, 95% CI 2.88-2.92), anxiety (2.84, 95% CI 2.82-2.85), and stress (2.71, 95% CI 2.69-2.73). PA had meaningful effects on reducing COS self-reported mental health burdens (3.42, 95% CI 3.41-3.44) during the pandemic. The largest associations were seen for recreational and home-based PA (i.e., family games, home aerobic exercise), individual outdoor PA (i.e., walking or running, rope skipping), and PA with a duration of 30 to 70 min per session at frequencies of 4 to 6 times and a total of 150 to 330 min of moderate and vigorous intensity per week tends to be an optimal choice during social distancing times.

CONCLUSIONS: COS had several poor mental health conditions during the pandemic. The improvement of PA on COS’ psychology was positively effective during the pandemic. Specific types, intensities, durations, and frequencies of PA might have advantages over others for improving COS’ mental health during periods of public health emergencies, and the topic may merit interventional study to reveal multiple factors causing COS’ psychological burdens and enrich the PA forms for all COS’ mental health improvement (i.e., infected, recovered, and asymptomatic COS).

PMID:37253054 | DOI:10.1371/journal.pone.0286321

PLoS One. 2023 May 30;18(5):e0285463. doi: 10.1371/journal.pone.0285463. eCollection 2023.

ABSTRACT

Species Distribution Models often include spatial effects which may improve prediction at unsampled locations and reduce Type I errors when identifying environmental drivers. In some cases ecologists try to ecologically interpret the spatial patterns displayed by the spatial effect. However, spatial autocorrelation may be driven by many different unaccounted drivers, which complicates the ecological interpretation of fitted spatial effects. This study aims to provide a practical demonstration that spatial effects are able to smooth the effect of multiple unaccounted drivers. To do so we use a simulation study that fit model-based spatial models using both geostatistics and 2D smoothing splines. Results show that fitted spatial effects resemble the sum of the unaccounted covariate surface(s) in each model.

PMID:37253039 | DOI:10.1371/journal.pone.0285463

PLoS One. 2023 May 30;18(5):e0286012. doi: 10.1371/journal.pone.0286012. eCollection 2023.

ABSTRACT

Structural features and the heterogeneity of disease transmissions play an essential role in the dynamics of epidemic spread. But these aspects can not completely be assessed from aggregate data or macroscopic indicators such as the effective reproduction number. We propose in this paper an index of effective aggregate dispersion (EffDI) that indicates the significance of infection clusters and superspreading events in the progression of outbreaks by carefully measuring the level of relative stochasticity in time series of reported case numbers using a specially crafted statistical model for reproduction. This allows to detect potential transitions from predominantly clustered spreading to a diffusive regime with diminishing significance of singular clusters, which can be a decisive turning point in the progression of outbreaks and relevant in the planning of containment measures. We evaluate EffDI for SARS-CoV-2 case data in different countries and compare the results with a quantifier for the socio-demographic heterogeneity in disease transmissions in a case study to substantiate that EffDI qualifies as a measure for the heterogeneity in transmission dynamics.

PMID:37253038 | DOI:10.1371/journal.pone.0286012

PLoS One. 2023 May 30;18(5):e0285977. doi: 10.1371/journal.pone.0285977. eCollection 2023.

ABSTRACT

This study sought to investigate prevalence of urogenital and intestinal schistosomiasis among school age children 6-13 years in selected communities in the Okavango Delta. The termination of the Botswana national schistosomiasis control program in 1993 contributed to its neglect. An outbreak of schistosomiasis in 2017 at one of the primary schools in the northeastern part of the country resulted in 42 positive cases, indicating that the disease exists. A total of 1,611 school age children 6-13 years were randomly selected from school registers in 10 primary schools; from which 1603 urine and 1404 stool samples were collected. Macroscopic examination of urine and stool for color, odor, blood; viscosity, consistency, and the presence of worms. Urine filtration and centrifugation methods were used to increase sensitivity of detecting parasite ova. Kato-Katz and Formalin-Ether were used for the examination of stool samples. Data were analyzed using SPSS version 25. Results were expressed as odds ratio (OR) with their 95% CI and statistical significance set at p < 0.05. A total of (n = 1611) school age children 6-13 years participated in the study, mean age 9.7years (SD 2.06), females (54%) and males (46%). Results indicated an overall prevalence of SS. hematobium and S.mansoni at 8.7% and 0.64% respectively. Intensity of SS. hematobium was generally light (97.6%) and heavy intensity (2.4%). Results also revealed a knowledge deficit, about 58% of children had never heard of bilharzia even though they lived in communities where the disease was previously endemic. Learners who had a family member who previously suffered from schistosomiasis had higher knowledge than those who did not. Interestingly, these learners were likely to engage in risky behaviors compared to those with lower knowledge of the disease. An integrated approach that emphasizes health education, mass drug administration, water, sanitation, and hygiene infrastructure should be prioritized for prevention and control of schistosomiasis.

PMID:37253026 | DOI:10.1371/journal.pone.0285977

Proc Natl Acad Sci U S A. 2023 Jun 6;120(23):e2212154120. doi: 10.1073/pnas.2212154120. Epub 2023 May 30.

ABSTRACT

The personality trait neuroticism is tightly linked to mental health, and neurotic people experience stronger negative emotions in everyday life. But, do their negative emotions also show greater fluctuation? This commonsensical notion was recently questioned by [Kalokerinos et al. Proc Natl Acad Sci USA 112, 15838-15843 (2020)], who suggested that the associations found in previous studies were spurious. Less neurotic people often report very low levels of negative emotion, which is usually measured with bounded rating scales. Therefore, they often pick the lowest possible response option, which severely constrains the amount of emotional variability that can be observed in principle. Applying a multistep statistical procedure that is supposed to correct for this dependency, [Kalokerinos et al. Proc Natl Acad Sci USA 112, 15838-15843 (2020)] no longer found an association between neuroticism and emotional variability. However, like other common approaches for controlling for undesirable effects due to bounded scales, this method is opaque with respect to the assumed mechanism of data generation and might not result in a successful correction. We thus suggest an alternative approach that a) takes into account that emotional states outside of the scale bounds can occur and b) models associations between neuroticism and both the mean and variability of emotion in a single step with the help of Bayesian censored location-scale models. Simulations supported this model over alternative approaches. We analyzed 13 longitudinal datasets (2,518 individuals and 11,170 measurements in total) and found clear evidence that more neurotic people experience greater variability in negative emotion.

PMID:37253012 | DOI:10.1073/pnas.2212154120

Proc Natl Acad Sci U S A. 2023 Jun 6;120(23):e2302107120. doi: 10.1073/pnas.2302107120. Epub 2023 May 30.

ABSTRACT

Helping strangers at a cost to oneself is a hallmark of many human interactions, but difficult to justify from the viewpoint of natural selection, particularly in anonymous one-shot interactions. Reputational scoring can provide the necessary motivation via “indirect reciprocity,” but maintaining reliable scores requires close oversight to prevent cheating. We show that in the absence of such supervision, it is possible that scores might be managed by mutual consent between the agents themselves instead of by third parties. The space of possible strategies for such “consented” score changes is very large but, using a simple cooperation game, we search it, asking what kinds of agreement can i) invade a population from rare and ii) resist invasion once common. We prove mathematically and demonstrate computationally that score mediation by mutual consent does enable cooperation without oversight. Moreover, the most invasive and stable strategies belong to one family and ground the concept of value by incrementing one score at the cost of the other, thus closely resembling the token exchange that underlies money in everyday human transactions. The most successful strategy has the flavor of money except that agents without money can generate new score if they meet. This strategy is evolutionarily stable, and has higher fitness, but is not physically realizable in a decentralized way; when conservation of score is enforced more money-like strategies dominate. The equilibrium distribution of scores under any of this family of strategies is geometric, meaning that agents with score 0 are inherent to money-like strategies.

PMID:37253000 | DOI:10.1073/pnas.2302107120

Proc Natl Acad Sci U S A. 2023 Jun 6;120(23):e2216932120. doi: 10.1073/pnas.2216932120. Epub 2023 May 30.

ABSTRACT

Dietary flavanols are food constituents found in certain fruits and vegetables that have been linked to cognitive aging. Previous studies suggested that consumption of dietary flavanols might specifically be associated with the hippocampal-dependent memory component of cognitive aging and that memory benefits of a flavanol intervention might depend on habitual diet quality. Here, we tested these hypotheses in the context of a large-scale study of 3,562 older adults, who were randomly assigned to a 3-y intervention of cocoa extract (500 mg of cocoa flavanols per day) or a placebo [(COcoa Supplement and Multivitamin Outcomes Study) COSMOS-Web, NCT04582617]. Using the alternative Healthy Eating Index in all participants and a urine-based biomarker of flavanol intake in a subset of participants [n = 1,361], we show that habitual flavanol consumption and diet quality at baseline are positively and selectively correlated with hippocampal-dependent memory. While the prespecified primary end point testing for an intervention-related improvement in memory in all participants after 1 y was not statistically significant, the flavanol intervention restored memory among participants in lower tertiles of habitual diet quality or habitual flavanol consumption. Increases in the flavanol biomarker over the course of the trial were associated with improving memory. Collectively, our results allow dietary flavanols to be considered in the context of a depletion-repletion paradigm and suggest that low flavanol consumption can act as a driver of the hippocampal-dependent component of cognitive aging.

PMID:37252983 | DOI:10.1073/pnas.2216932120

Proc Natl Acad Sci U S A. 2023 Jun 6;120(23):e2218200120. doi: 10.1073/pnas.2218200120. Epub 2023 May 30.

ABSTRACT

The distribution of fitness effects (DFE) of new mutations is key to our understanding of many evolutionary processes. Theoreticians have developed several models to help understand the patterns seen in empirical DFEs. Many such models reproduce the broad patterns seen in empirical DFEs but these models often rely on structural assumptions that cannot be tested empirically. Here, we investigate how much of the underlying “microscopic” biological processes involved in the mapping of new mutations to fitness can be inferred from “macroscopic” observations of the DFE. We develop a null model by generating random genotype-to-fitness maps and show that the null DFE is that with the largest possible information entropy. We further show that, subject to one simple constraint, this null DFE is a Gompertz distribution. Finally, we illustrate how the predictions of this null DFE match empirically measured DFEs from several datasets, as well as DFEs simulated from Fisher’s geometric model. This suggests that a match between models and empirical data is often not a very strong indication of the mechanisms underlying the mapping of mutation to fitness.

PMID:37252948 | DOI:10.1073/pnas.2218200120

PLoS Biol. 2023 May 30;21(5):e3001665. doi: 10.1371/journal.pbio.3001665. eCollection 2023 May.

ABSTRACT

Epithelial repair relies on the activation of stress signaling pathways to coordinate tissue repair. Their deregulation is implicated in chronic wound and cancer pathologies. Using TNF-α/Eiger-mediated inflammatory damage to Drosophila imaginal discs, we investigate how spatial patterns of signaling pathways and repair behaviors arise. We find that Eiger expression, which drives JNK/AP-1 signaling, transiently arrests proliferation of cells in the wound center and is associated with activation of a senescence program. This includes production of the mitogenic ligands of the Upd family, which allows JNK/AP-1-signaling cells to act as paracrine organizers of regeneration. Surprisingly, JNK/AP-1 cell-autonomously suppress activation of Upd signaling via Ptp61F and Socs36E, both negative regulators of JAK/STAT signaling. As mitogenic JAK/STAT signaling is suppressed in JNK/AP-1-signaling cells at the center of tissue damage, compensatory proliferation occurs by paracrine activation of JAK/STAT in the wound periphery. Mathematical modelling suggests that cell-autonomous mutual repression between JNK/AP-1 and JAK/STAT is at the core of a regulatory network essential to spatially separate JNK/AP-1 and JAK/STAT signaling into bistable spatial domains associated with distinct cellular tasks. Such spatial stratification is essential for proper tissue repair, as coactivation of JNK/AP-1 and JAK/STAT in the same cells creates conflicting signals for cell cycle progression, leading to excess apoptosis of senescently stalled JNK/AP-1-signaling cells that organize the spatial field. Finally, we demonstrate that bistable separation of JNK/AP-1 and JAK/STAT drives bistable separation of senescent signaling and proliferative behaviors not only upon tissue damage, but also in RasV12, scrib tumors. Revealing this previously uncharacterized regulatory network between JNK/AP-1, JAK/STAT, and associated cell behaviors has important implications for our conceptual understanding of tissue repair, chronic wound pathologies, and tumor microenvironments.

PMID:37252939 | DOI:10.1371/journal.pbio.3001665