Estimation in Dirichlet random effects models

We develop a new Gibbs sampler for a linear mixed model with a Dirichlet process random effect term, which is easily extended to a generalized linear mixed model with a probit link function. Our Gibbs sampler exploits the properties of the multinomial and Dirichlet distributions, and is shown to be an improvement, in terms of operator norm and efficiency, over other commonly used MCMC algorithms. We also investigate methods for the estimation of the precision parameter of the Dirichlet process, finding that maximum likelihood may not be desirable, but a posterior mode is a reasonable approach. Examples are given to show how these models perform on real data. Our results complement both the theoretical basis of the Dirichlet process nonparametric prior and the computational work that has been done to date.Comment: Published in at http://dx.doi.org/10.1214/09-AOS731 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

The complete chloroplast genome sequence of Abies nephrolepis (Pinaceae: Abietoideae)

AbstractThe plant chloroplast (cp) genome has maintained a relatively conserved structure and gene content throughout evolution. Cp genome sequences have been used widely for resolving evolutionary and phylogenetic issues at various taxonomic levels of plants. Here, we report the complete cp genome of Abies nephrolepis. The A. nephrolepis cp genome is 121,336 base pairs (bp) in length including a pair of short inverted repeat regions (IRa and IRb) of 139 bp each separated by a small single copy (SSC) region of 54,323 bp (SSC) and a large single copy region of 66,735 bp (LSC). It contains 114 genes, 68 of which are protein coding genes, 35 tRNA and four rRNA genes, six open reading frames, and one pseudogene. Seventeen repeat units and 64 simple sequence repeats (SSR) have been detected in A. nephrolepis cp genome. Large IR sequences locate in 42-kb inversion points (1186 bp). The A. nephrolepis cp genome is identical to Abies koreana’s which is closely related to taxa. Pairwise comparison between two cp genomes revealed 140 polymorphic sites in each. Complete cp genome sequence of A. nephrolepis has a significant potential to provide information on the evolutionary pattern of Abietoideae and valuable data for development of DNA markers for easy identification and classification

Genomic profile of metastatic breast cancer patient-derived xenografts established using percutaneous biopsy.

BACKGROUND: Metastatic breast cancer (mBC) is a complex and life-threatening disease and although it is difficult to cure, patients can benefit from sequential anticancer treatment, including endocrine therapy, targeted therapy and cytotoxic chemotherapy. The patient-derived xenograft (PDX) model is suggested as a practical tool to predict the clinical outcome of this disease as well as to screen novel drugs. This study aimed to establish PDX models in Korean patients and analyze their genomic profiles and utility for translational research. METHODS: Percutaneous core needle biopsy or punch biopsy samples were used for xenotransplantation. Whole exome sequencing and transcriptome analysis were performed to assess the genomic and RNA expression profiles, respectively. Copy number variation and mutational burden were analyzed and compared with other metastatic breast cancer genomic results. Mutational signatures were also analyzed. The antitumor effect of an ATR inhibitor was tested in the relevant PDX model. RESULTS: Of the 151 cases studied, 40 (26%) PDX models were established. Notably, the take rate of all subtypes, including the hormone receptor-positive (HR +) subtype, exceeded 20%. The PDX model had genomic fidelity and copy number variation that represented the pattern of its donor sample. TP53, PIK3CA, ESR1, and GATA3 mutations were frequently found in our samples, with TP53 being the most frequently mutated, and the somatic mutations in these genes strengthened their frequency in the PDX model. The ESR1 mutation, CCND1 amplification, and the APOBEC signature were significant features in our HR + HER2- PDX model. Fulvestrant in combination with palbociclib showed a partial response to the relevant patient\u27s tumor harboring the ESR1 mutation, and CCND1 amplification was found in the PDX model. AZD6738, an ATR inhibitor, delayed tumor growth in a relevant PDX model. CONCLUSIONS: Our PDX model was established using core needle biopsy samples from primary and metastatic tissues. Genomic profiles of the samples reflected their original tissue characteristics and could be used for the interpretation of clinical outcomes

Work-related musculoskeletal disorders, reporting attitudes, and reporting behavior among direct care workers in long-term care facilities in South Korea

Background: Work-related musculoskeletal disorders among direct care workers have been a major concern in long-term care facilities worldwide. However, many work-related musculoskeletal disorders went unreported due to perceived barriers of direct care workers. Workers are encouraged to report even minor injury or near misses to their managements in many countries, but in Korea, the injury reporting responsibility of workers is not defined or described.Methods: This dissertation study used cross-sectional survey data from 377 direct care workers in 19 long-term care facilities in South Korea from May 2022 ~ August 2022. Long-term care facilities included long-term care hospitals and nursing homes in three cities in Gyeonggi, which is one out of eight provinces and represents 26% of Korean population. In the study, direct care workers refer to trained care staffs providing the most direct personal care such as feeding, bathing, dressing, and toileting regardless of the certification. Direct care workers who were employed for at least three months or longer in their current job, and able to read, write, and understand Korean were eligible to participate in the study. Results: A systematic review showed a high level of underreporting of work-related injuries or illnesses to management or Workers’ Compensation programs, ranging 20%-91% in the United States and identified contributing factors and reasons for underreporting of work-related injuries or illnesses. Analysis of the survey data from direct care workers in long-term care facilities showed that more than half of direct care workers had a work-related musculoskeletal disorder in the past 12 months, but only 13.5% of them reported it to their management. Also, half of direct care workers had no intention to report their symptoms. Direct care workers’ reporting behavior was associated with their attitudes toward reporting, safety climate, symptom severity, and witnessing injury reporting of others. Direct care workers’ reporting attitudes were associated with duration of work, work arrangement, safety training, safety climate, experience of work-related musculoskeletal disorders, and frequency and severity of symptoms. Direct care workers having positive reporting attitudes were more likely to have intention to reporting and actual reporting of work-related musculoskeletal disorders. Conclusion: This study provides important insight into workers’ reporting behaviors and attitudes of work-related musculoskeletal disorders and informs future efforts to reduce underreporting and underestimation of occupational health problems

Associations of iron deficiency and depressive symptoms among young adult males and Females: NHANES 2017 to 2020

Depression is one of the most prevalent mental health conditions throughout the lifespan. Notable differences in the prevalence of depression among females and males arise during adolescence and may peak during young adulthood. Since iron deficiency is a treatable condition that may contribute to depression, this topic among youth (18 to 25 years of age) needs to be further explored. Thus, our study examines the associations between three measures of iron (ferritin, serum iron, and transferrin saturation levels) with Patient Health Questionnaire-9 (PHQ-9) depressive symptoms and depression among young adult males and females using the National Health and Nutrition Examination Survey (NHANES) 2017–2020. Using multivariable Poisson and logistic regression models, adjusting for several demographic and clinical variables, we report 1) the prevalence of depression and 2) the associations between iron deficiency and depressive symptoms and depression among males and females. 917 participants were included in our study. More females (12.5 %) than males (6.8 %) had PHQ-9 depression. Males with ferritin (adjusted odds ratio [AOR] = 14.13, 95 % confidence interval [CI]: 1.51, 132.21), serum iron (AOR = 4.84, 95 % CI: 1.02, 22.92), and transferrin (AOR = 13.79, 95 % CI: 3.59, 53.06) deficiencies were at higher risk for depression, while females with ferritin deficiency (AOR = 0.34, 95 % CI: 0.11, 0.97) had a lower risk for depression. Our study highlights the need to focus on depression screening among young adults as well as risk factors for depression among this age group. Identifying risk factors and screening for iron deficiency, especially among females, should be considered as well

Maximum Likelihood Estimation for Directional Conditionally Autoregressive Models

A spatial process observed over a lattice or a set of irregular regions is usu-ally modeled using a conditionally autoregressive (CAR) model. The neighbor-hoods within a CAR model are generally formed using only the inter-distances between the regions. To accommodate the effect of directions, a new class of spatial models is developed using different weights given to neighbors in dif-ferent directions. The proposed model generalizes the usual CAR model by accounting for spatial anisotropy. Maximum likelihood estimators are derived and shown to be consistent under some regularity conditions. Simulation stud-ies are presented to evaluate the finite sample performance of the new model as compared to CAR model. Finally the method is illustrated using a data set on the crime rates of Columbus, OH