Category: Statistics

G3 (Bethesda). 2025 Jan 30:jkaf018. doi: 10.1093/g3journal/jkaf018. Online ahead of print.

ABSTRACT

Genetic studies of Plasmodium parasites increasingly feature relatedness estimates. However, various aspects of malaria parasite relatedness estimation are not fully understood. For example, relatedness estimates based on whole-genome-sequence (WGS) data often exceed those based on sparser data types. Systematic bias in relatedness estimation is well documented in the literature geared towards diploid organisms, but largely unknown within the malaria community. We characterise systematic bias in malaria parasite relatedness estimation using three complementary approaches: theoretically, under a non-ancestral statistical model of pairwise relatedness; numerically, under a simulation model of ancestry; and empirically, using data on parasites sampled from Guyana and Colombia. We show that allele frequency estimates encode, locus-by-locus, relatedness averaged over the set of sampled parasites used to compute them. Plugging sample allele frequencies into models of pairwise relatedness can lead to systematic underestimation. However, systematic underestimation can be viewed as population-relatedness calibration, i.e., a way of generating measures of relative relatedness. Systematic underestimation is unavoidable when relatedness is estimated assuming independence between genetic markers. It is mitigated when relatedness is estimated using WGS data under a hidden Markov model (HMM) that exploits linkage between proximal markers. The extent of mitigation is unknowable when a HMM is fit to sparser data, but downstream analyses that use high relatedness thresholds are relatively robust regardless. In summary, practitioners can either resolve to use relative relatedness estimated under independence, or try to estimate absolute relatedness under a HMM. We propose various tools to help practitioners evaluate their situation on a case-by-case basis.

PMID:39883524 | DOI:10.1093/g3journal/jkaf018

Pulmonology. 2025 Dec 31;31(1):2411806. doi: 10.1080/25310429.2024.2411806. Epub 2024 Oct 30.

ABSTRACT

New ultrathin bronchoscopes (UTBs) enable the inspection and biopsy of small airways, potentially offering diagnostic advantages in sarcoidosis. In this prospective study, patients with suspected sarcoidosis underwent airway inspection with a UTB. Observed airway abnormalities were categorised into six predefined patterns. UTB-directed small airway biopsies (SABs) were collected from the upper lobes following a standardised procedure. We evaluated the prevalence and patterns of SAAs, as well as the diagnostic yield of UTB-directed SAB. Among 79 participants, 65 (82.3%) were diagnosed with sarcoidosis. Small airway abnormalities were identified in 26/65 (40%) patients, predominantly in those with parenchymal involvement on CT compared to those with lymphadenopathy only (58.1% VS. 23.5%, P = 0.005). The diagnostic yield of SABs for detecting granulomas was significantly higher in patients with SAAs than in those without (65.4% VS. 23.1%, P = 0.001) and in patients with parenchymal disease on CT compared to those without (54.8% VS. 26.5%, P = 0.02). Notably, random biopsies taken under direct visualisation from small airway carinas revealed peribronchiolar parenchyma in 23% of the patients. Small airway abnormalities are prevalent in sarcoidosis patients with parenchymal involvement, and biopsying these abnormalities yields a high rate of granuloma detection.

PMID:39883493 | DOI:10.1080/25310429.2024.2411806

Pulmonology. 2025 Dec 31;31(1):2423541. doi: 10.1080/25310429.2024.2423541. Epub 2024 Nov 8.

ABSTRACT

Guidelines for the follow-up of pulmonary subsolid nodule (SSN) vary in terms of frequency and criteria for discontinuation. We aimed to evaluate the growth risk of SSNs and define appropriate follow-up intervals and endpoints. The immediate risk (IR) and cumulative risk (CR) of SSN growth were assessed using the Kaplan-Meier method according to nodule consistency and size. Follow-up plans were proposed based on optimal growth risk threshold of 5%. 892 SSNs, comprising 833 pure ground-glass nodules (pGGNs) and 59 part-solid nodules (PSNs) were included. For pGGNs ≤ 6.6 mm, the CR exceeded 5% at every 3-year interval in the first 9 years. For pGGNs measuring 6.6-8.8 mm and >8.8 mm, the IR remained above 5% for the first 2-7 years, and the 2-year CR for pGGNs measuring 6.6-8.8 mm in the 8th and 9th years achieved 6.66%. For PSNs, the IR peaked in the 4th year (44%) and then declined. Therefore, triennial follow-up for 9 years is recommended for pGGNs ≤ 6.6 mm, annual follow-up for 7 years followed by biennial follow-up for 2 years for pGGNs measuring 6.6-8.8 mm, annual follow-up for 7 years for pGGNs > 8.8 mm, and continuous annual follow-up until nodule growth for PSNs.

PMID:39883492 | DOI:10.1080/25310429.2024.2423541

JAMA Netw Open. 2025 Jan 2;8(1):e2457300. doi: 10.1001/jamanetworkopen.2024.57300.

ABSTRACT

IMPORTANCE: Rising prescription medication costs under Medicaid have led to increased procedural prescription denials by health plans. The effect of unresolved denials on chronic condition exacerbation and subsequent acute care utilization remains unclear.

OBJECTIVE: To examine whether procedural prescription denials are associated with increased net spending through downstream acute care utilization among Medicaid patients not obtaining prescribed medication following a denial.

DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study used Medicaid claims data from 2022 to 2023 for patients at inpatient, outpatient, and pharmacy sites of care across 2 states (Virginia and Washington) and 2 independent health plans. Patients with at least 1 prescription denial in the study period (January 1 through July 31, 2023) were matched to those without denials in a given medication class, based on demographics, health plan data, chronic condition history, and health care utilization. Rates of and spending for physiologically related acute care visits in the 60 days following a medication fill or denial were compared for the study period.

MAIN OUTCOMES AND MEASURES: The main outcomes were all-cause acute care utilization and total medical spending (in 2023 US dollars per member per year [PMPY]) for principal diagnoses physiologically related to each medication class, in the 60 days following a medication fill or denial. Sensitivity analyses were performed to check for spurious associations or unmeasured confounders.

RESULTS: The 19 725 patients in this study had a median age of 41 (IQR, 29-55) years, and most (60.7%) were female. Patients had a mean (SD) of 3.3 (16.1) comorbidities, 1.0 (2.6) all-cause acute care visits, and 5.6 (7.8) primary care visits during the baseline period. Patients experiencing specific procedural prescription denials had a higher risk of physiologically related emergency department visits and hospitalizations compared with those without a denial in the subsequent 60 days (adjusted odds ratio, 1.40 [95% CI, 1.03-1.88] minimum vs 1.75 [95% CI, 1.39-2.20] maximum for exposure and control groups across the 7 medication classes with significant differences). Denials in 6 medication classes were associated with net total medical spending increases, ranging from $624 (95% CI, $435-$813) to $3016 (95% CI, $1483-$4550) in additional expense PMPY after accounting for both prescription and medical costs attributed to denials.

CONCLUSIONS AND RELEVANCE: The findings of this cross-sectional study suggest that although procedural prescription denials aimed to curb immediate drug costs, some denials prompted heightened acute care utilization and costs that outweighed the short-term prescription budget savings. Health plans should incorporate this potential unintended consequence when shaping prescription coverage policies. Future research should systematically review all medication classes across plans nationally.

PMID:39883462 | DOI:10.1001/jamanetworkopen.2024.57300

J Appl Psychol. 2025 Jan 30. doi: 10.1037/apl0001266. Online ahead of print.

ABSTRACT

Do unions facilitate or hamper the effectiveness of high-performance work systems (HPWS)? Despite the long-standing interest among labor and human resource scholars on this matter, relevant studies are limited and dated. This research investigates whether and how the interplay between HPWS and unions affects both organizational performance and employee well-being outcomes. The authors argue while unions may attenuate the HPWS effects on organizational performance due to decreased performance climate, the overall impacts of unions are likely beneficial, as they facilitate cooperative climate that contributes to organizational performance and enhances employee well-being, which positively affects longer term organizational outcomes. Analyzing longitudinal data with 934 observations from 287 South Korean firms, the authors show that unions indeed facilitate the positive effects of HPWS on organizational performance and employee well-being, mediated by enhanced cooperative climate. They did not find statistically meaningful evidence that unions mitigate HPWS’ effects on performance climate and subsequent organizational performance. (PsycInfo Database Record (c) 2025 APA, all rights reserved).

PMID:39883423 | DOI:10.1037/apl0001266

J Pers Soc Psychol. 2025 Jan;128(1):61-81. doi: 10.1037/pspa0000422.

ABSTRACT

Face stereotypes are prevalent, consequential, yet oftentimes inaccurate. How do false first impressions arise and persist despite counter-evidence? Building on the overgeneralization hypothesis, we propose a domain-general cognitive mechanism: insufficient statistical learning, or Insta-learn. This mechanism posits that humans are quick statistical learners but insufficient samplers. Humans extract statistical regularities from very few exemplars in their immediate context and prematurely decide to stop sampling, creating and perpetuating locally accurate-but globally inaccurate-impressions. Six experiments (N = 1,565) tested this hypothesis using novel pairs of computer-generated faces and social behaviors by fixing the population-level statistics of face-behavior associations to zero (i.e., no relationship). The initial sample contained either 11, five, or three examples with either a positive, zero, or negative linear relationship between facial features and social behaviors. The sampling procedure contained a free-sampling condition in which participants were free to decide when to stop viewing more examples and a fixed-sampling condition in which participants were forced to view all stimuli before making decisions. Consistent with the Insta-learn mechanism, participants learned novel face stereotypes quickly, with as few as three examples, and did not sample enough when they were given the freedom to do so. This domain-general cognitive mechanism provides one plausible origin of false face stereotypes, demonstrating negative consequences when people learn too much from too little. (PsycInfo Database Record (c) 2025 APA, all rights reserved).

PMID:39883402 | DOI:10.1037/pspa0000422

AIDS Behav. 2025 Jan 30. doi: 10.1007/s10461-025-04616-y. Online ahead of print.

ABSTRACT

Pre-exposure prophylaxis (PrEP) has proven to be a powerful tool in preventing HIV infection. There is limited information about the factors associated with willingness to use different PrEP modalities among adolescent girls and young women (AGYW) in Africa. We assessed willingness to use long-acting injectable PrEP (LAI-PrEP) among 14-24-year-old AGYW at high risk of HIV in Uganda, and associated factors determined using multivariable complementary log-log regression. Of the 285 participants, 69.8% of participants showed willingness to use LAI-PrEP despite only 3.9% having knowledge about it before enrolment. Report of recent transactional sex was high (92.6%). Participants that were divorced/separated (aOR = 1.74, 95% CI 1.03-2.92) and those with multiple sexual partners (aOR = 2.11, 95% CI 1.46-3.06) compared to those with one partner were more likely to be willing to use LAI-PrEP while those that were screened as heavy episodic drinkers (consuming 6 or more drinks on an occasion as per the AUDIT tool) were less likely to be willing to use LAI-PrEP (aOR = 0.61, 95% CI 0.42-0.87). LAI PrEP has shown efficacy in clinical trials; the product is approved for use by the Government of Uganda (MoH) and should be expedited for use by AGYW engaged in paid sex and those with multiple sexual partnerships. As it becomes available, we recommend PrEP education and counseling to increase awareness of LAI PrEP as an alternative HIV prevention method.

PMID:39883369 | DOI:10.1007/s10461-025-04616-y

J Nephrol. 2025 Jan 30. doi: 10.1007/s40620-025-02211-x. Online ahead of print.

ABSTRACT

BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is caused primarily by pathogenic variants in the PKD1 and PKD2 genes. Although the type of ADPKD variant can influence disease severity, rare, hypomorphic PKD1 variants have also been reported to modify disease severity or cause biallelic ADPKD. This study examines whether rare, additional, potentially protein-altering, non-pathogenic PKD1 variants contribute to ADPKD phenotypic outcomes.

METHODS: We investigated the prevalence of rare, additional, potentially protein-altering PKD1 variants in patients with PKD1-associated ADPKD. The association between rare, additional, potentially protein-altering variants and phenotypic outcomes, including progression to kidney failure, age at onset of hypertension and urological events, height-adjusted total kidney volume, and predicting renal outcomes in PKD (PROPKD) score, were examined.

RESULTS: Rare, additional, potentially protein-altering variants were detected in 6% of the 932 ADPKD patients in the study. The presence of rare, additional, potentially protein-altering variants was associated with 4 years earlier progression to kidney failure (hazard ratio (HR): 1.66; 95% confidence interval (CI): 1.18-2.34; P = 0.003), with in-trans rare, additional, potentially protein-altering variants (n = 13/894) showing a greater risk of kidney failure (HR: 1.83; 95% CI 1.00-3.33; P = 0.049). We did not detect statistically significant differences between rare, additional, potentially protein-altering variants and other phenotypic outcomes compared to those without rare, additional, potentially protein-altering variants.

CONCLUSIONS: In patients with PKD1-associated ADPKD, our findings suggest that rare, additional, potentially protein-altering variants in PKD1 may influence disease severity. These findings have potential clinical implications in counselling and treating patients with rare, additional, potentially protein-altering variants, but further investigation of such variants in larger, longitudinal cohorts with detailed, standardised phenotype data is required.

PMID:39883360 | DOI:10.1007/s40620-025-02211-x

Neurol Sci. 2025 Jan 30. doi: 10.1007/s10072-025-08020-1. Online ahead of print.

ABSTRACT

BACKGROUND: Non-motor symptoms, including depression, anxiety, sleep disturbances, pain and cognitive dysfunction, are a much more important predictor of quality of life than the severity of dystonia.

OBJECTIVES: To assess the effect of Botulinum toxin on non-motor symptoms and quality of life in patients with adult-onset idiopathic focal dystonia.

METHODS: Patients aged > 18 years diagnosed with idiopathic focal dystonia were recruited in this longitudinal cohort study. The severity of dystonia, non-motor symptoms, and quality of life were evaluated using the BFMDRS, DNMSQuest, and EQ-5D at baseline and 1 and 3 months after botulinum toxin.

RESULTS: 65 patients were recruited with a median age of 59 years. Blepharospasm was the most common phenomenology. 49.2% of patients had depression at baseline assessed using the Beck Depression Inventory (BDI). There was a significant negative correlation between baseline BFMDRS, DNMSQuest, BDI, and HAM-A scores and quality of life, but there was no relation with the type of focal dystonia. The mean percentage improvement in the BFMDRS-M, BFMDRS-D, DNMSQuest, BDI, HAM-A and EQ-5D was 25%, 52%, 16%,20%,23% and 23%, respectively, at one month. There was no statistically significant correlation between percentage change in motor scores compared to depression and quality of life scores at one month.

CONCLUSION: Botulinum toxin improved motor and non-motor scores and quality of life at 1 and 3 months after botulinum toxin therapy. The motor scores did not correlate with depression and DNMSQUEST scores but showed a weak positive correlation with anxiety scores.

PMID:39883352 | DOI:10.1007/s10072-025-08020-1

Bull Math Biol. 2025 Jan 30;87(3):37. doi: 10.1007/s11538-025-01414-4.

ABSTRACT

Compared to our closest primate relatives, human life history involves greater longevity, which includes a distinctive postmenopausal life stage. Given mammalian reproductive physiology in which females build a finite stock of cells that can become oocytes early in life, which then continuously deplete mostly through cell death while males produce new sperm throughout adulthood, the postmenopausal stage makes the sex ratio in the fertile pool, called the adult sex ratio (ASR), male biased. Additionally, this affects a more fine-grained ratio, the operational sex ratio (OSR), defined as the ratio of males to females currently able to conceive. Here, we construct an ODE model in which males compete for paternities using either a multiple-mating or mate-guarding strategy. Our focus is on investigating the differences of strategy choice between populations with varying life histories, which include a distinct post-fertile stage for adult females. By simulating the system, we determine the dominant strategy and its dependence on various parameter combinations. Our results show that an increase in OSR and ASR correlates well with a change in the dominant strategy from multiple mating to guarding.

PMID:39883339 | DOI:10.1007/s11538-025-01414-4