Tag: statistics

Proc Natl Acad Sci U S A. 2025 Aug 5;122(31):e2410949122. doi: 10.1073/pnas.2410949122. Epub 2025 Jul 28.

ABSTRACT

Genomic sequence data harbor valuable information concerning the history of species divergence and interspecific gene flow and may offer important insights into conservation of endangered species. However, extracting such information from genomic data requires powerful statistical inference methods. A recent analysis of genomic sequence data found little evidence for gene flow from domestic Bactrian camels into the endangered wild Bactrian species. Nevertheless, the methods used to infer gene flow are based on data summaries and lack the power and precision to represent the complex phylogenetic history of the species with gene flow. Here, we apply Bayesian methods to genomic sequence data to test for both recent and ancient gene flow among the three species in the genus Camelus and to estimate the strength and timing of gene flow. We detect a strong signal of gene flow from domestic into wild Bactrian camels, confirming early evidence based on mitochondrial DNA and the Y chromosome. Overall gene flow appears to affect the autosomal genome uniformly, with similar effective rates of gene flow for exonic and noncoding regions. Estimation of species divergence times is seriously affected if gene flow is not accommodated in the analysis. Our results highlight the power of the coalescent model in analysis of genomic data and the utility of the coding as well as noncoding parts of the genome in elucidating the evolutionary history of modern species.

PMID:40720656 | DOI:10.1073/pnas.2410949122

Proc Natl Acad Sci U S A. 2025 Aug 5;122(31):e2410934122. doi: 10.1073/pnas.2410934122. Epub 2025 Jul 28.

ABSTRACT

Reticulate evolution has long been recognized as a key mechanism that contributes to genetic and trait diversity. With the widespread availability of genomic data, investigating historical reticulate evolution across taxa has gained significant attention, driven by the rapid development of statistical methods for detecting nontreelike patterns. Phylogenetic networks provide a biologically intuitive approach to depicting evolutionary processes such as hybrid speciation and introgressive hybridization, which result in signatures of historical gene flow. Interpreting phylogenetic networks is especially critical for groups of conservation concern that lack reference genome resources and explicit hypotheses from prior investigation, such as those based on molecular data, morphology, or species distributions. Here, we highlight recent advances in computational methods for inferring networks from genome-scale data and offer guidelines for deriving biological insights from phylogenetic networks. Particular emphasis is placed on modeling hybridization and whole-genome duplication in the context of allopolyploidization. Practical recommendations for empirical studies and the limitations of commonly used methods are discussed throughout. We anticipate that phylogenetic networks will influence conservation biology and biodiversity research, emphasizing the need for careful consideration of reticulate evolution inferred from these networks in the near future. Networks will accelerate other pressing avenues of biodiversity research, especially investigations of orphan crops and climate change resilience in natural systems. The promise of phylogenetic networks connects with broader themes in the special feature Monitoring and restoring gene flow in the increasingly fragmented ecosystems of the Anthropocene by providing an emerging probabilistic framework for inferring historical connectivity between species and populations.

PMID:40720655 | DOI:10.1073/pnas.2410934122

Proc Natl Acad Sci U S A. 2025 Aug 5;122(31):e2426815122. doi: 10.1073/pnas.2426815122. Epub 2025 Jul 28.

ABSTRACT

A central question in the study of language change is whether or not such change is generational. If a language changes over time generation-by-generation, the process looks as follows: New generations of speakers introduce innovations, while older speakers conserve their usage patterns, and the language changes as new generations replace older ones. At the opposite extreme, language change could be a zeitgeist phenomenon, in which changes are universally adopted by speakers simultaneously, regardless of age or generational cohort. This paper asks this question in the context of word meaning change. We analyze meaning change in over 100 words across more than 7.9 million U.S. congressional speeches, to observe whether, when a word sense rises or falls in prominence, adult speakers from different generations uniformly adopt it, or those from older generations conserve their prior usage. Using language model-based word sense induction methods, we identify different senses of each word, and then model the prevalence of each of these word senses as a function of time and speaker age. We find that most words show a small but statistically significant effect of speaker age; across almost 140 y of Congress, older speakers typically take longer than younger speakers to follow changes in word usage, but nevertheless do so within a few years. Our findings indicate that despite minor age-based differences, word meaning change among mature speakers is likely not a generational process, but rather a zeitgeist process, in which older adult speakers can readily adopt new word usage patterns.

PMID:40720652 | DOI:10.1073/pnas.2426815122

Nutr Rev. 2025 Jul 28:nuaf123. doi: 10.1093/nutrit/nuaf123. Online ahead of print.

ABSTRACT

CONTEXT: The phase angle (PhA) of bioimpedance is a noninvasive parameter that has been reported to reflect the health and integrity of cells. Data on how PhA is related to cardiovascular risk factors are controversial.

OBJECTIVE: This systematic review and meta-analysis aims to explore the association between PhA and cardiovascular risk factors in participants over 18 years old.

DATA SOURCES: A systematic search was conducted in PubMed, Scopus, and Web of Science (2000-2024) to identify studies reporting the relationship between PhA and cardiovascular risk factors, including lipid profile, glycemic control, blood pressure, central obesity, and serum uric acid.

DATA EXTRACTION: Meta-analysis was performed using a random-effects model due to high heterogeneity (I2 statistic). Subgroup analyses by gender and health status, as well as meta-regressions, were conducted to explore heterogeneity. Publication bias was assessed using funnel plots and Egger’s test. Of 812 identified studies, 27 met the inclusion criteria.

DATA ANALYSIS: There were varied associations between PhA and key health markers. For lipid profiles, a significant negative correlation was observed with total cholesterol (r = -0.10, P = .02) in individuals with chronic conditions. With regard to glycemic control, PhA showed a significant negative correlation with fasting blood glucose (r = -0.18, P < .001) and homeostatic model assessment for insulin resistance (HOMA-IR) (r = -0.17, P = .02) in men. Diastolic blood pressure was positively correlated with PhA in the males and healthy subgroups (P < .05), while a significant negative correlation with systolic blood pressure was identified in unhealthy individuals (r = -0.10, P < .001). No significant correlations were found between PhA and other cardiovascular risk factors (P > .05).

CONCLUSION: This meta-analysis identified the potential of PhA as a noninvasive tool for cardiovascular risk assessment; however, the inconsistent findings necessitate further research considering other potential confounders as well as recruiting larger samples in other populations.

SYSTEMATIC REVIEW REGISTRATION: PROSPERO registration no. CRD42024597723.

PMID:40720635 | DOI:10.1093/nutrit/nuaf123

J Craniofac Surg. 2025 Jul 28. doi: 10.1097/SCS.0000000000011690. Online ahead of print.

ABSTRACT

This study aimed to evaluate the impact of psychometric properties on patients’ postoperative self-esthetic scores following orthognathic surgery using the Chinese version of the Depression Anxiety Stress Scale 21 (DASS-21). The research involved patients diagnosed with dentofacial deformities who underwent orthognathic surgery. A comprehensive questionnaire was administered, covering 3 key areas: clinical characteristics, self-awareness of esthetics and expectations, and psychometric parameters assessed through the Chinese version of DASS-21. Patients completed the questionnaire both before and after surgery, and the data were analyzed using the R statistical package. The findings revealed that preoperative anxiety scores, anxiety grades, and changes in anxiety levels from presurgery to postsurgery were independent factors influencing the self-perceived outcomes postorthognathic surgery (SPOPO) score. In addition, patients with asymmetrical deformities reported lower SPOPO scores, while the discrepancy between preoperative expectations and self-cognition was positively associated with SPOPO. The study concluded that postoperative satisfaction in orthognathic surgery is influenced by multiple factors, including the type of deformity, patients’ self-awareness and expectations, and their anxiety state. The Chinese version of DASS-21 emerged as a valuable tool for orthognathic surgeons in predicting patients’ postoperative esthetic satisfaction.

PMID:40720615 | DOI:10.1097/SCS.0000000000011690

Behav Res Methods. 2025 Jul 25;57(9):234. doi: 10.3758/s13428-025-02756-6.

ABSTRACT

Extreme response style (ERS), the tendency of participants to select extreme item categories regardless of the item content, has frequently been found to decrease the validity of Likert-type questionnaire results (e.g., Moors, European Journal of Work and Organizational Psychology, 21, 271-298, 2012). For this reason, detecting ERS at both the group and individual levels is of paramount importance. While various approaches to detecting ERS exist, these may conflate ERS with the trait of interest, require additional questionnaires to be administered, or require the use of mixture or multidimensional IRT models. As an alternative approach to detecting ERS, Bayesian posterior predictive checks (PPCs) may be a viable option. Posterior predictive checking offers a highly customizable framework for detecting model misfit, which can be directly applied to frequently used unidimensional IRT models. Critically, the use of PPCs to detect ERS does not require strong assumptions regarding the nature of ERS, such as ERS being a continuous dimension or a categorical trait. In this paper, we thus apply PPCs to a generalized partial credit model to detect model misfit related to ERS on both the group and person levels. We propose various possible PPCs tailored to ERS, which are illustrated in an empirical example, and their performance in detecting ERS is examined under various conditions. Suggestions for practical applications are provided, and avenues for future research are explored.

PMID:40715867 | DOI:10.3758/s13428-025-02756-6

Support Care Cancer. 2025 Jul 25;33(8):721. doi: 10.1007/s00520-025-09772-4.

ABSTRACT

PURPOSE: Few remote-delivered physical activity (PA) interventions leverage a community-academic partnership, which may impact sustainability. The current study aimed to assess the satisfaction with a community-based remote-delivered group-based PA program (2Unstoppable Strong) among women diagnosed with cancer and the preliminary impact of the intervention on exploratory outcomes (PA levels, perceived social support, exercise self-efficacy, barrier self-efficacy, and health-related quality of life).

METHODS: Online questionnaires were administered at baseline (T0), post-program (T1), and follow-up (T2). Quantitative analyses included descriptive statistics and repeated measures analyses of variance. Open responses at the end of the questionnaire were used to identify areas of improvement. Content analysis was used to analyze the open response data.

RESULTS: Participants rated 2Unstoppable Strong as satisfactory (M_score = 4.7, SD = 0.54; M_range = 2.93 to 5.00). Moderate-to-vigorous physical activity significantly increased from T0 to T1 to T2 (F (2, 34) = 3.5, p < .05). From T0 to T1 to T2, both perceived social support quantity (F (2, 34) = 18.6, p < .001) and quality (F (2, 34) = 13.9, p < .001) significantly increased. All exploratory outcomes did not significantly change. Participants enjoyed interacting with the trustworthy instructors and found the videoconferencing software convenient to use. Areas for improvement included facilitating social interaction within the exercise group, increasing the intervention duration, and providing additional sessions.

CONCLUSIONS: Based on the promising findings, future hybrid implementation-effectiveness studies with larger and more-diverse populations are needed to examine the impact of 2Unstoppable Strong on cancer-related outcomes.

PMID:40715849 | DOI:10.1007/s00520-025-09772-4

J Math Biol. 2025 Jul 26;91(2):20. doi: 10.1007/s00285-025-02251-8.

ABSTRACT

The paper aims to study the constructive role of noise in tumor dynamics. Mathematical investigation of this problem is carried out on the basis of a model of dynamic interaction between effector and tumor cells under conditions of chemotherapy. For the deterministic variant of the model, zones of mono-, bi-, and tristability are defined depending on the bifurcation parameter of treatment intensity. We find equilibrium and oscillatory attractors associated with active, dormant and zero tumor states. The paper studies how, depending on the chemotherapy intensity, random disturbances transform the active tumor mode into the dormant, or even zero state providing the main target of treatment. We also find conditions generating stochastic transitions of the tumor-immune system from the dormant tumor to the regime of active tumor. In the mathematical study of the positive and negative role of random noise, along with direct numerical simulation and statistical processing, we use the analytical confidence domain method.

PMID:40715848 | DOI:10.1007/s00285-025-02251-8

Int Orthop. 2025 Jul 26. doi: 10.1007/s00264-025-06620-2. Online ahead of print.

ABSTRACT

BACKGROUND: Total knee arthroplasty (TKA) is a highly effective procedure for end-stage knee osteoarthritis, but postoperative instability remains a major concern, impacting patient satisfaction and leading to potential revision surgeries. Understanding patient-related risk factors for instability is crucial for optimizing outcomes and minimizing complications.

METHODS: We conducted a retrospective cohort study of patients who underwent revision TKA at our clinic between 1996 and 2021, focusing on those who required revision specifically due to instability. We analyzed a dataset of 39,572 primary TKA patients without documented revisions and 859 revision patients. Data extraction included age, gender, body mass index (BMI), age-adjusted Charlson Comorbidity Index (CCI) score, and comorbidities. Statistical analyses, including binary logistic regression, were performed to identify independent risk factors for instability.

RESULTS: The instability group (n = 859) had a mean age of 65.7 years and a significantly lower proportion of males compared to the control group (mean age 67.5 years, p < 0.001; males 30.7% vs. 38.1%, p < 0.001). Notable risk factors included younger age, female gender, stroke, deep vein thrombosis (DVT), and scleroderma. Specifically, scleroderma was associated with a high risk of instability (P < 0.01 OR [odds ratio] 9.27, CI [confidence interval] 2.01 to 42.7), stroke (P = 0.01 OR 1.8, CI: 1.1 to 3.1), and DVT (p < 0.01 OR: 2.0, CI: 1.4 to 2.8).

CONCLUSION: Patient-related factors such as younger age, female gender, stroke, DVT, and scleroderma significantly influence the risk of instability following primary TKA. These findings highlight the multifactorial nature of TKA instability and underscore the importance of tailored preoperative assessment and postoperative care. Addressing these risk factors can improve patient outcomes and reduce the incidence of instability following TKA.

PMID:40715844 | DOI:10.1007/s00264-025-06620-2

Environ Geochem Health. 2025 Jul 26;47(9):339. doi: 10.1007/s10653-025-02585-8.

ABSTRACT

Urban air pollution caused by car emissions and industrial activities is one of the most salient causes of health threat in urban areas. Considering that taxi drivers are exposed to such pollutants all the time for several hours, the present study sought to determine the level of metal elements in the hair of this working population and to examine the determining factors.In this study, hair samples from 88 taxi drivers in Kerman city were analyzed for concentrations of iron, copper, chromium, cadmium, zinc, lead, aluminum, cobalt, and nickel using ICP-OES instrument. The relationship between metal elements (MEs) and influencing factors was investigated using Spearman’s test. Mean group differences were evaluated with Kruskal-Wallis and Mann-Whitney tests. Nickel had no strong correlation with chromium, cadmium and aluminum (rho = 0.2; Sig < 0.05). Other MEs exhibited strong positive correlations with each other, with iron showing the strongest correlation (rho = 0.34 to 0.84; Sig < 0.05), indicating that the elements may have originated from common sources. Age exhibited a significant positive correlation with nickel levels (rho = 0.47; Sig < 0.01). Using the Mann-Whitney U test, a significant difference was observed in the average nickel concentration between the hair of young and middle-aged drivers (Sig = 0.006). In addition, hair nickel levels were significantly different among drivers in the northern, western and eastern regions of the city (Sig < 0.03). However, there was no significant difference in nickel levels between drivers with less than a decade of work experience and those with over a decade (Sig > 0.05). About 75% of samples had lead concentrations below 18 mg/kg, while 25% had levels exceeding this.

PMID:40715843 | DOI:10.1007/s10653-025-02585-8