Category: Statistics

Proc Natl Acad Sci U S A. 2025 May 20;122(20):e2412978122. doi: 10.1073/pnas.2412978122. Epub 2025 May 14.

ABSTRACT

Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a comprehensive population tree and is distorted by survivorship and sampling biases. Inferring evolutionary parameters from ascertained trees requires modeling both the underlying population dynamics and the ascertainment process. A crucial component of this phylodynamic modeling involves tree simulation, which is used to benchmark probabilistic inference methods. To simulate an ascertained tree, one must first simulate the full population tree and then prune unobserved lineages. Consequently, the computational cost is determined not by the size of the final simulated tree, but by the size of the population tree in which it is embedded. In most biological scenarios, simulations of the entire population are prohibitively expensive due to computational demands placed on lineages without sampled descendants. Here, we address this challenge by proving that, for any partially ascertained process from a general multitype birth-death-mutation-sampling model, there exists an equivalent process with complete sampling and no death, a property which we leverage to develop a highly efficient algorithm for simulating trees. Our algorithm scales linearly with the size of the final simulated tree and is independent of the population size, enabling simulations from extremely large populations beyond the reach of current methods but essential for various biological applications. We anticipate that this massive speedup will significantly advance the development of novel inference methods that require extensive training data.

PMID:40366686 | DOI:10.1073/pnas.2412978122

JAMA Netw Open. 2025 May 1;8(5):e259840. doi: 10.1001/jamanetworkopen.2025.9840.

ABSTRACT

IMPORTANCE: Patients with sporadic breast cancer have comparable prognoses after undergoing either breast-conserving treatment (BCT) or mastectomy. However, there are limited and inconsistent data on the assessment of oncologic outcomes between BCT and mastectomy in patients with pathogenic variants in BRCA1 or BRCA2.

OBJECTIVE: To investigate the outcomes of BCT on recurrence and survival in patients with breast cancer with BRCA1 or BRCA2 pathogenic variants.

DESIGN, SETTING, AND PARTICIPANTS: This retrospective multicenter cohort study analyzed patients from 13 institutions in South Korea with primary breast cancer with BRCA1 or BRCA2 pathogenic variants who underwent either BCT or mastectomy from January 2008 through December 2015. The median (IQR) follow-up period was 8.3 (6.4-9.6) years. Data were analyzed from September 2023 to August 2024.

EXPOSURE: BRCA1 or BRCA2 pathogenic variant and BCT.

MAIN OUTCOMES AND MEASURES: Primary outcomes were logoregional recurrence-free survival, distant recurrence-free survival, and overall survival. Propensity score matching (PSM) using the greedy nearest neighbor method was performed to match covariates to minimize potential selection bias.

RESULTS: A total of 575 female patients with BRCA1 or BRCA2 pathogenic variants were identified, all of whom were South Korean with a mean (SD) age of 42.0 (9.7) years. Among them, 367 patients (66.2%) received BCT and 186 (33.8%) were treated with mastectomy. BCT was not a factor associated with oncologic outcomes, including locoregional recurrence, compared with mastectomy. After adjusting for clinicopathologic characteristics through 1:1 PSM, there were still no statistically significant differences in oncologic outcomes between the BCT group and the mastectomy group. Multivariate analysis showed that the type of breast surgery was not significantly associated with oncologic outcomes. In subgroup analysis among matched patients based on BRCA1 or BRCA2 status, tumor size, lymph node metastasis, histologic grade, and subtype, BCT was also not a factor associated with risk for recurrence.

CONCLUSIONS AND RELEVANCE: The findings from this cohort study of patients with BRCA1 or BRCA2 pathogenic variants suggested that there were no significant differences in oncologic outcomes between patients who underwent BCT and those who underwent mastectomy. Therefore, breast conservation with close surveillance can be considered a viable treatment option for BRCA1 or BRCA2 pathogenic variant carriers. Further studies incorporating prospectively collected data are warranted to validate our findings.

PMID:40366658 | DOI:10.1001/jamanetworkopen.2025.9840

JAMA Netw Open. 2025 May 1;8(5):e2510173. doi: 10.1001/jamanetworkopen.2025.10173.

ABSTRACT

IMPORTANCE: Little is known about patterns (forms, frequency, and reasons) and factors associated with cannabis use in older veterans (aged ≥65 years).

OBJECTIVE: To examine factors associated with past 30-day cannabis use and cannabis use disorder (CUD) in older veterans.

DESIGN, SETTING, AND PARTICIPANTS: In this cross-sectional study, community-dwelling adults aged 65 to 84 years who used Veterans Health Administration care were interviewed between February 5, 2020, and August 29, 2023.

EXPOSURE: Sociodemographic, behavioral, and health-related characteristics.

MAIN OUTCOMES AND MEASURES: Past 30-day cannabis use (smoking, vaping, dabbing, or edibles) and any CUD (≥2 criteria based on Diagnostic and Statistical Manual of Mental Disorders [Fifth Edition]) were assessed using weighted multivariable logistic regressions.

RESULTS: Of the 4503 participants (weighted mean age, 73.3 years [95% CI, 73.0-73.5 years]; 85.4% [95% CI, 83.6%-87.2%] men), 58.2% (95% CI, 55.3%-61.0%) had ever used cannabis, 28.9% (95% CI, 26.0%-31.8%) of whom reported using cannabis for medical reasons, most commonly for pain (56.4%; 95% CI, 50.9%-61.9%), mood or mental health (18.4%; 95% CI, 14.7%-22.1%), and sleep (16.0%; 95% CI, 11.9%-20.0%). More than 1 in 10 reported past 30-day cannabis use (10.3%; 95% CI, 8.9%-11.7%), with 52.4% (95% CI, 45.4%-59.4%) of these using cannabis for 20 days or more; smoking (72.4%; 95% CI, 65.4%-79.3%) and edibles (36.9%; 95% CI, 29.8%-43.9%) were the most common forms of use. Characteristics associated with past 30-day use included younger age (65-75 years), economic hardship, tobacco and illicit drug use, and residing in a state with recreationally legal cannabis. Among those with past 30-day cannabis use, 36.3% (95% CI, 30.1%-42.6%) screened positive for CUD, with higher odds among younger respondents, those reporting anxiety, those with 1 or more deficits in activities of daily living, those with illicit drug use, those with frequent cannabis use, and those using cannabis recreationally. Past 30-day inhaled cannabis use, compared with edibles only, was associated with increased odds of any CUD (adjusted odds ratio, 3.56; 95% CI, 1.12-11.26).

CONCLUSIONS AND RELEVANCE: In this cross-sectional study of cannabis use in older veterans, use was common, and more than one-third who used in the past 30 days had any CUD. The prevalence of past 30-day cannabis use was close to tobacco use prevalence, and risk factors for cannabis use were similar to those observed in other populations. Frequent and inhaled cannabis use was associated with higher odds of any CUD. Routine health screening for cannabis use in Veterans Health Administration clinical settings is necessary to identify older adults with cannabis use.

PMID:40366653 | DOI:10.1001/jamanetworkopen.2025.10173

JAMA Netw Open. 2025 May 1;8(5):e2510298. doi: 10.1001/jamanetworkopen.2025.10298.

ABSTRACT

IMPORTANCE: Patients with dementia have considerable supportive care needs. Specialist palliative care may be beneficial, but it is unclear which patients are most appropriate for referral and when they should be referred.

OBJECTIVE: To identify a set of consensus referral criteria for specialist palliative care for patients with dementia.

DESIGN, SETTING, AND PARTICIPANTS: In this survey study using 3 rounds of Delphi surveys, an international, multidisciplinary panel of clinicians from 5 continents with expertise in the integration of dementia and palliative care were asked to rate 83 putative referral criteria (generated from a previous systematic review and steering committee discussion). Specialist palliative care was defined as an interdisciplinary team consisting of practitioners with advanced knowledge and skills in palliative medicine offering consultative services for specialist-level palliative care in (nonhospice) inpatient, outpatient, community, and home-based settings.

MAIN OUTCOMES AND MEASURES: Consensus was defined a priori as at least 70% agreement among experts. A criterion was coded as major if the experts advocated that meeting 1 criterion alone was satisfactory to justify a referral. Data were summarized using descriptive statistics.

RESULTS: Of the 63 invited and eligible panelists, the response rate was 58 (92.1%) in round 1, 58 (92.1%) in round 2, and 60 (95.2%) in round 3. Of the 58 panelists who provided demographic data in round 1, most were aged 40 to 49 years (28 of 58 [48.3%]), and 29 panelists (50%) each were men and women. Panelists achieved consensus on 15 major and 42 minor criteria for specialist palliative care referral. The 15 major criteria were grouped under 5 categories, including dementia type (eg, rapidly progressive dementia), symptom distress (eg, severe physical symptoms), psychosocial factors or decision-making (eg, request for hastened death, assisted suicide, or euthanasia), comorbidities or complications (eg, ≥2 episodes of aspiration pneumonia in the past 12 months); and hospital use (eg, ≥2 hospitalizations within the past 3 months).

CONCLUSIONS AND RELEVANCE: In this Delphi survey study, international experts reached consensus on a range of criteria for referral to specialist palliative care. With testing and validation, these criteria may be used to standardize specialist palliative care access for patients with dementia across various care settings.

PMID:40366652 | DOI:10.1001/jamanetworkopen.2025.10298

JAMA Dermatol. 2025 May 14. doi: 10.1001/jamadermatol.2025.1190. Online ahead of print.

ABSTRACT

IMPORTANCE: Hidradenitis suppurativa (HS) is a chronic inflammatory skin condition. Risk factors for developing HS (eg smoking and obesity) are influenced by social drivers of health at the neighborhood level. However, the association of neighborhood-level socioeconomic status (nSES) and HS has not been adequately assessed.

OBJECTIVE: To evaluate the association of nSES with new HS diagnoses among dermatology patients within a single health system.

DESIGN, SETTING, AND PARTICIPANTS: This was a cross-sectional study of patients of the dermatology clinics at the University of California San Francisco health system between August 1, 2019, and May 31, 2024, who were also residents of the San Francisco Bay Area at index visit. Data analyses were performed from June 1, 2024, to February 11, 2025.

EXPOSURE: Census tract-level index measure of nSES that incorporated income, poverty, housing cost, rental cost, education, occupation, and employment. Quintiles of nSES were assigned based on nSES distribution in the San Francisco Bay Area counties.

MAIN OUTCOMES AND MEASURES: A new HS diagnosis during the study period, identified by the International Statistical Classification of Diseases and Related Health Problems, Tenth Revision code, and confirmed by medical record review. Logistic regression models were constructed and fit by generalized estimating equations accounting for clustering by census tract with nSES quintile as the primary exposure (reference used was quintile 5, the highest nSES quintile); new HS diagnosis as the binary outcome; and age, sex, and race and ethnicity as confounders. In secondary analyses, smoking status, obesity, and health insurance type were assessed as possible mediators.

RESULTS: The analyses included a total of 65 766 patients (mean [SD] age, 50.4 [18.3] years; 41.8% female), of whom 485 (0.7%) had a new HS diagnosis. Greater odds of a new HS diagnosis were observed in lower-SES neighborhoods (Q1-Q4)-after adjusting for age, sex, and race and ethnicity, odds ratio for Q1 was 3.32 (95% CI, 2.46-4.49); Q2, 2.25 (95% CI, 1.62-3.12); Q3, 1.97 (95% CI, 1.46-2.66); and Q4, 1.44 (95% CI, 1.06-1.96) (P <.001 [linear trend]). In race-stratified analyses, greater odds of a new HS diagnosis were observed among patients residing in lower-SES neighborhoods, although this pattern did not reach statistical significance at the 5% level in all racial and ethnic groups.

CONCLUSIONS AND RELEVANCE: This cross-sectional study found that nSES was independently associated with a new diagnosis of HS among dermatology patients. This finding supports the hypothesis that neighborhood-level factors may influence the development of HS.

PMID:40366644 | DOI:10.1001/jamadermatol.2025.1190

J Urban Health. 2025 May 14. doi: 10.1007/s11524-025-00977-w. Online ahead of print.

ABSTRACT

Few existing data sources quantify the magnitude of court-ordered and illegal residential evictions, among historically marginalized groups. We describe the Social Epidemiology to Combat Unjust Residential Evictions (SECURE) Study (2021-2024; n = 1,428; 91.1% response rate) methodology and participant characteristics. Univariable and multivariable statistics including Spearman correlations were used to describe data. Unadjusted and adjusted modified Poisson regression with robust error variance estimated relative risk (RR) and associated 95% confidence intervals (95% CI) for associations between five eviction measures and self-rated health (SRH), and self-rated health relative to most similarly aged peers (RSRH). A quarter of the participants reported experiencing an eviction as a child (n = 354). Over half of the study sample reported ever experiencing a court-ordered (n = 432) and/or an illegal eviction (n = 360). In the past 2 years, 15.2% of the sample reported experiencing a court-ordered (n = 122) and/or illegal eviction (n = 95). Eviction during childhood, and ever experiencing both court-ordered and/or illegal eviction was associated with between 12 and 17% higher risk of poor SRH, and childhood eviction and ever experiencing illegal eviction was associated with between 34 and 37% higher risk of worse RSRH among reproductive age Black women. More community-partnered research using participatory action research methods are needed to understand and intervene upon the health impacts of residential evictions among disproportionately impacted groups.

PMID:40366613 | DOI:10.1007/s11524-025-00977-w

Eur J Epidemiol. 2025 May 14. doi: 10.1007/s10654-025-01236-7. Online ahead of print.

ABSTRACT

Renal cell carcinoma (RCC) management has advanced due to increased imaging-based diagnoses and improved therapies for metastatic disease. This nationwide registry-based cohort study examines changes in the number of primary RCC cases, stage at diagnosis, prognosis during the past 30 years in Denmark, and how these are associated with sex and age. All Danish patients aged 18 and older diagnosed with primary RCC from 1992 to 2021 with no prior cancer history (except non-melanoma skin cancer) were included and followed from diagnosis until death or end of follow-up (31-12-2023). Statistical analyses included Pearson’s χ2, Cramer’s V, Wilcoxon rank-sum test, Kruskal-Wallis, competing risk regression, Cox proportional hazard regression, and Kaplan-Meier. 17,423 RCC patients were identified. Primary RCC cases increased from 2,244 in 1992-1996 to 3,947 in 2017-2021. In this period, the proportion of male patients increased from 59 to 72% (P < 0.001). Male patients were younger at diagnosis than female patients (median age 65 vs. 69 years, P < 0.001). Localized cancer cases increased from 44% (N = 983) in 1992-1996 to 70% (N = 2,766) in 2017-2021, while metastatic cases declined from 29% (N = 640) to 17% (N = 652). Median survival for metastatic RCC improved from 4.1 months in 1992-1996 to 13.3 months in 2017-2021. Over three decades, RCC incidence in Denmark has grown, particularly among men, largely due to localized disease, adding pressure on urological departments. The number of metastatic cases remained stable, but survival improved, reflecting advances in early detection and treatment.

PMID:40366611 | DOI:10.1007/s10654-025-01236-7

Eur J Epidemiol. 2025 May 14. doi: 10.1007/s10654-025-01227-8. Online ahead of print.

ABSTRACT

Emerging evidence suggests that exposure to air pollutants and road traffic noise triggers stress responses, which mediate physiological responses in multiple organs and tissues. However, epidemiological study in children is sparse. We aimed to evaluate whether outdoor air pollution and road traffic noise are associated with physiological response measured by allostatic load in children. We studied 919 children aged 6-11 years from the HELIX (Human Early Life Exposome) cohort in 6 European countries with 19 biomarkers assessed in four physiological systems-cardiovascular, metabolic, immune/inflammation, and neuroendocrine systems. We then calculated both count-based and continuous scores for each physiological system and generated allostatic load scores (range 0-19). Exposure to air pollution (NO₂, PM_2.5, PM₁₀, PM_2.5absorbance) and road traffic noise (L_DEN) based on participants’ home, school, and commuting route addresses were estimated for the year prior to outcome assessment. Higher exposure to all air pollutants was associated with a higher allostatic load, although only the association of PM₁₀ survived correction for multiple testing (for count-based allostatic load score: RR = 1.27, 95%CI: 1.08, 1.48; for continuous allostatic load score: β = 0.56, 95% CI: 0.27-0.84, per each 10 µg/m³ increase in PM₁₀). Examining physiological systems separately, higher exposure to air pollution was mainly associated with higher allostatic load in the immune/inflammatory and metabolic systems. No associations between road traffic noise and allostatic load were observed. Our findings suggest that air pollution act as a chronic stressor in manifesting multi-systemic physiological dysregulation in childhood, which may be a precursor of air pollution-related diseases.

PMID:40366609 | DOI:10.1007/s10654-025-01227-8

Ecotoxicology. 2025 May 14. doi: 10.1007/s10646-025-02886-9. Online ahead of print.

ABSTRACT

The European perch (Perca fluviatilis) is a fish species that can be a planktivorous, benthivorous and carnivorous at different life stages. Using the example of the perch population from White Lake (Northwest Russia) the connection between ontogenetic change of diet and mercury accumulation in fish muscle tissue is shown. Analysis of the gut contents of 223 perch indicated that the main food item of perch aged 4-6+ years is the lake form of European smelt (80-100%). Also, the lowest THg concentrations were observed in perch aged 4-5+ and 6+ years – 160 ± 47 and 172 ± 51 ng/g (wet weight), respectively. Starting from age 6+ pikeperch and ruff appear in the diet of perch. In fish aged 9+ the proportion of lake smelt in the diet is 25-33%, and the mercury content in muscles is 447 ± 44 and 462 ± 109 ng/g (wet weight) in individuals aged 9+ and 10-12+ years, respectively. An increased proportion of pikeperch and ruff in the diet, whose average mercury content is 2.5 times higher than that of smelt, lead to increased mercury concentrations in perch muscle. There was also a statistically significant linear regression between mercury content and δ¹⁵N in perch older than 7+ years (p = 0.002; r² = 0.38) and no correlation between mercury content and δ¹³C in fish of different ages. Concentrations exceeding the U.S. EPA recommended values (330 ng/g ww) were found in perch aged 9+ years and older, with body length greater than 25 cm. Therefore, the local people should not consume perch with body length greater than 25 cm from White Lake. Further measurements are needed to determine the mercury concentration in perch in nearby lakes and their suitability for human consumption. It is recommended that a similar study be conducted in a number of reservoirs within the study region in order to determine the factors influencing the intensive accumulation of mercury in fish.

PMID:40366607 | DOI:10.1007/s10646-025-02886-9

Andrology. 2025 May 14. doi: 10.1111/andr.70063. Online ahead of print.

ABSTRACT

OBJECTIVES: To evaluate the risk of priapism in patients undergoing Dynamic-Penile duplex ultrasound (D-PDU) who were referred to our Unit between January 2022 and December 2023.

PATIENTS AND METHODS: We enrolled 292 patients, of whom 268 underwent Dynamic-Penile duplex ultrasound for erectile dysfunction and 24 for Peyronie’s disease. The mean age of the patients was 56 ± 12 years, the mean alprostadil dose administered was 9.17 ± 5.59 mcg and the mean erection response was 79.55 ± 19.95%. To evaluate the occurrence of priapism, we considered i) patients who called our phone number within the first hours following the exam; ii) patients who were referred to our Emergency Department within the 24 h following Dynamic-Penile duplex ultrasound; iii) patients who reported to us the occurrence of priapism at subsequent follow-up visit; iv) patients who e-mailed us to report this side effect.

RESULTS: We found no cases of priapism (0/292 patients, 0%). Therefore, statistical analysis with correlation and regression analysis was not conducted.

CONCLUSIONS: In our opinion, the risk of priapism following Dynamic-Penile duplex ultrasound with alprostadil injection might be re-evaluated, as it appears to be a rare and preventable condition.

PMID:40366605 | DOI:10.1111/andr.70063