Bayesian modeling

BACKGROUND: Volatile organic compounds (VOCs) encompass hundreds of high production volume chemicals and have been reported to be associated with adverse respiratory outcomes such as chronic obstructive pulmonary disease (COPD). However, research on the combined toxic effects of exposure to various VOCs on COPD is lacking. We aimed to assess the effect of VOC metabolite mixture on COPD risk in a large population sample. METHODS: We assessed the effect of VOC metabolite mixture on COPD risk in 5997 adults from the National Health and Nutrition Examination Survey (NHANES) from 2011 to 2020 (pre-pandemic) using multivariate logistic regression, Bayesian weighted quantile sum regression (BWQS), quantile-based g-Computation method (Qgcomp), and Bayesian kernel machine regression (BKMR)...

BACKGROUND: Survival prediction using high-dimensional molecular data is a hot topic in the field of genomics and precision medicine, especially for cancer studies. Considering that carcinogenesis has a pathway-based pathogenesis, developing models using such group structures is a closer mimic of disease progression and prognosis. Many approaches can be used to integrate group information; however, most of them are single-model methods, which may account for unstable prediction. METHODS: We introduced a novel survival stacking method that modeled using group structure information to improve the robustness of cancer survival prediction in the context of high-dimensional omics data...

Individuals with high environmental sensitivity have nervous systems that are disproportionately receptive to both the protective and imperilling aspects of the environment, suggesting their mental health is strongly context-dependent. However, there have been few consolidated attempts to examine putative markers of sensitivity, across different levels of analysis, within a single cohort of individuals with high-priority mental health needs. Here, we examine psychological (self-report), physiological (hair hormones) and genetic (polygenic scores) markers of sensitivity in a large cohort of 1591 Syrian refugee children across two waves of data...

OBJECTIVES: Sjögren disease (SjD) diagnosis often requires either positive anti-SSA antibodies or a labial salivary gland biopsy with a positive focus score (FS). One-third of patients with SjD lack anti-SSA antibodies (SSA-), requiring a positive FS for diagnosis. Our objective was to identify novel autoantibodies to diagnose 'seronegative' SjD. METHODS: IgG binding to a high-density whole human peptidome array was quantified using sera from SSA- SjD cases and matched non-autoimmune controls...

Excess abdominal fat is a sexually dimorphic risk factor for cardio-metabolic disease and is approximated by the waist-to-hip ratio adjusted for body mass index (WHRadjBMI ). Whereas this trait is highly heritable, few causal genes are known. We aimed to identify novel drivers of WHRadjBMI using systems genetics. We used two independent cohorts of adipose tissue gene expression and constructed sex- and depot-specific Bayesian networks to model gene-gene interactions from 8,492 genes. Using key driver analysis, we identified genes that, in silico and putatively in vitro, regulate many others...

BACKGROUND: Inappropriate medication utilization among older adults is a pressing concern in the United States, owing to its high prevalence and the consequential detrimental impact it engenders. The adverse effects stemming from the inappropriate use of medication may be unequally borne by racial/ethnic minority populations, calling for greater efforts towards promoting equity in healthcare. The study objective was to assess the cost-effectiveness of Medication Therapy Management (MTM) services among Medicare beneficiaries and across racial/ethnic groups...

INTRODUCTION: Antenatal care (ANC) visit is a proxy for maternal and neonatal health. The ANC is a key indicator of access and utilization of health care for pregnant women. Recently, eight times ANC visits have been recommended during the pregnancy period. However, nearly 57% of women received less than four ANC visits in Ethiopia. Therefore, the objective of this study is to identify factors associated withthe number of ANC visits in Ethiopia. METHODS: A community-based cross-sectional study design was conducted from March 21 to June 28/2019...

BACKGROUND: Copper exposure is reported to be associated with increased risk of stroke. However, the association of copper exposure with subclinical carotid atherosclerosis remains unclear. METHODS AND RESULTS: This observational study included consecutive participants from Xinqiao Hospital between May 2020 and August 2021. Blood metals were measured using inductively coupled plasma mass spectrometry and carotid atherosclerosis was assessed using ultrasound. Modified Poisson regression was performed to evaluate the associations of copper and other metals with subclinical carotid plaque presence...

Joint modeling of longitudinal data and survival data has gained great attention in the last two decades. However, most of the existing studies have focused on right-censored survival data. In this article, we study joint analysis of longitudinal data and interval-censored survival data and conduct Bayesian variable selection in this framework. A new joint model is proposed with a shared frailty to characterize the dependence between the two types of responses, where the longitudinal response is modeled with a semiparametric linear mixed-effects submodel and the survival time is modeled by a semiparametric normal fraility probit sub-model...

Network models are increasingly used to study infectious disease spread. Exponential Random Graph models have a history in this area, with scalable inference methods now available. An alternative approach uses mechanistic network models. Mechanistic network models directly capture individual behaviors, making them suitable for studying sexually transmitted diseases. Combining mechanistic models with Approximate Bayesian Computation allows flexible modeling using domain-specific interaction rules among agents, avoiding network model oversimplifications...

When modeling the dynamics of infectious disease, the incorporation of contact network information allows for the capture of the non-randomness and heterogeneity of realistic contact patterns. Oftentimes, it is assumed that the underlying contact pattern is known with perfect certainty. However, in realistic settings, the observed data often serves as an imperfect proxy of the actual contact patterns in the population. Furthermore, the epidemic in the real world are often not fully observed; event times such as infection and recovery times may be missing...

The classification system and the higher level phylogenetic relationships of Pentatomomorpha, the second largest infraorder of Heteroptera (Insecta: Hemiptera), have been debated and remain controversial over decades. In particular, the placement and phylogenetic relationship of Idiostoloidea are not well resolved, which hampers a better understanding of the evolutionary history of Pentatomomorpha. In this study, for the first time, we reported the complete mitochondrial genome for two narrowly distributed families of Idiostoloidea (including Idiostolidae and Henicocoridae), respectively...

BACKGROUND: For investigating the individual-environment interplay and individual differences in response to environmental exposures as captured by models of environmental sensitivity including Diathesis-stress, Differential Susceptibility, and Vantage Sensitivity, over the last few years, a series of statistical guidelines have been proposed. However, available solutions suffer of computational problems especially relevant when sample size is not sufficiently large, a common condition in observational and clinical studies...

AIMS: This study aimed to investigate environmental factors and genetic variant loci associated with hepatocellular carcinoma (HCC) in Chinese population and construct a weighted genetic risk score (wGRS) and polygenic risk score (PRS). METHODS: A case-control study was applied to confirm the single nucleotide polymorphisms (SNPs) and environmental variables linked to HCC in the Chinese population, which had been screened by meta-analyses. wGRS and PRS were built in training sets and validation sets...

INTRODUCTION: Plasminogen deficiency is an ultra rare disease whose patients may develop ligneous lesions if untreated. Prophylactic replacement therapy with plasma derived plasminogen, Ryplazim, is efficient in treating lesions and could benefit from pharmacokinetic (PK) tailoring. AIM: The objectives of this study are to develop, evaluate and integrate into the WAPPS-Hemo platform a Population PK model supporting prophylactic replacement therapy for Plasminogen deficient patients...

BACKGROUND: Recursive models are a category of structural equation models that propose a causal relationship between traits. These models are more parameterized than multiple trait models, and they require imposing restrictions on the parameter space to ensure statistical identification. Nevertheless, in certain situations, the likelihood of recursive models and multiple trait models are equivalent. Consequently, the estimates of variance components derived from the multiple trait mixed model can be converted into estimates under several recursive models through LDL' or block-LDL' transformations...

PURPOSE: The purpose of this work is to create a metric for evaluating the degree of laterality of the patella's entry into the trochlea, the entry point-trochlear groove (EP-TG) angle, and to evaluate if this laterality is associated with recurrent patella instability. METHODS: The time frame of the study was January 2020 to February 2023. The inclusion criteria were patients treated by the senior author (JPF) (with the exception of two patients who were treated by another provider at the institution who was aware of the study) who have been diagnosed with recurrent atraumatic patellar dislocations...

Persons living with HIV are known to be at increased risk of developing tuberculosis (TB) disease upon infection with Mycobacterium tuberculosis (Mtb). However, it has remained unclear how HIV co-infection affects subsequent Mtb transmission from these patients. Here, we customized a Bayesian phylodynamic framework to estimate the effects of HIV co-infection on the Mtb transmission dynamics from sequence data. We applied our model to four Mtb genomic datasets collected in sub-Saharan African countries with a generalized HIV epidemic...

OBJECTIVE: Several population pharmacokinetic models of tacrolimus in liver transplant patients were built, and their predictability was evaluated in their settings. However, the extrapolation in the prediction was unclear. This study aimed to evaluate the predictive performance of published tacrolimus models in adult liver transplant recipients using data from the Thai population as an external dataset. METHODS: The selected published models were systematically searched and evaluated for their quality...

BACKGROUND: China has the highest number of new cancer cases and deaths globally. Due to particularly low scores in health care quality for cutaneous squamous cell carcinoma (cSCC), the country's cSCC burden requires greater awareness. Consequently, we aimed to evaluate and predict the trend of the cSCC burden globally and in China from 1990 to 2030. METHODS: We retrieved data from the Global Burden of Disease 2019 study, which provided estimates of the incidence, mortality, prevalence, and disability-adjusted life years (DALYs) of cSCC from 1990 to 2019...