CosinorTest: An R Shiny App for Cosinor-model-based circadian and differential analysis in transcriptomic applications.

Summary: 'CosinorTest' application is an interactive R Shiny tool designed to facilitate circadian and differential circadian analysis with transcriptomic data using Cosinor-model-based methods. This novel application integrates multiple major statistical algorithms to identify circadian rhythmicity in gene expression data and enables the comparison of differential circadian patterns between two experimental conditions. Key features of the 'CosinorTest' app include circadian rhythmicity detection, differential patterns assessment, circadian and differential analyses with repeated measurement, and interactive data visualization, all contributing to a comprehensive understanding of underlying biological mechanisms.

A Bayesian Framework for Genome-wide Circadian Rhythmicity Biomarker Detection.

Circadian rhythms are endogenous ∼24-hour cycles that significantly influence physiological and behavioral processes. These rhythms are governed by a transcriptional-translational feedback loop of core circadian genes and are essential for maintaining overall health. The study of circadian rhythms has expanded into various omics datasets, necessitating accurate analytical methodology for circadian biomarker detection.

The value of synthetic MRI in detecting the brain changes and hearing impairment of children with sensorineural hearing loss.

Introduction: Sensorineural hearing loss (SNHL) can arise from a diverse range of congenital and acquired factors. Detecting it early is pivotal for nurturing speech, language, and cognitive development in children with SNHL. In our study, we utilized synthetic magnetic resonance imaging (SyMRI) to assess alterations in both gray and white matter within the brains of children affected by SNHL.

Examining Reactivity and Recovery Patterns of Pain-Evoked Cortisol and Alpha-Amylase Trajectories: Relations Between Psychological Markers of Risk and Resilience.

Chronic low back pain (cLBP) is one of the leading causes of disability globally and represents an enormous burden to aging adults. While numerous factors contribute to cLBP, dysregulation in the hypothalamic-pituitary-adrenal axis and autonomic nervous system functioning have been implicated in its pathogenesis. It is well documented that negative psychological states can modulate biological stress responsivity in chronic pain; however, little is known regarding the influence of positive psychological factors in this relationship.

Quantitative Relaxometry Assessment of Brain Microstructural Abnormality of Preschool Children With Autism Spectrum Disorder With Synthetic Magnetic Resonance Imaging.

Objective: This study aimed to perform an assessment of brain microstructure in children with autism aged 2 to 5 years using relaxation times acquired by synthetic magnetic resonance imaging.

Materials And Methods: Thirty-four children with autism spectrum disorder (ASD) (ASD group) and 17 children with global developmental delay (GDD) (GDD group) were enrolled, and synthetic magnetic resonance imaging was performed to obtain T1 and T2 relaxation times. The differences in brain relaxation times between the 2 groups of children were compared, and the correlation between significantly changed T1/T2 and clinical neuropsychological scores in the ASD group was analyzed.

Improved Differential Diagnosis Based on BI-RADS Descriptors and Apparent Diffusion Coefficient for Breast Lesions: A Multiparametric MRI Analysis as Compared to Kaiser Score.

Rationale And Objectives: To develop the nomogram utilizing the American College of Radiology BI-RADS descriptors, clinical features, and apparent diffusion coefficient (ADC) to differentiate benign from malignant breast lesions.

Materials And Methods: A total of 341 lesions (161 malignant and 180 benign) were included. Clinical data and imaging features were reviewed.

Pain interference mediates the association between epigenetic aging and grip strength in middle to older aged males and females with chronic pain.

Introduction: Chronic pain is one of the leading causes of disability that may accelerate biological aging and reduce physical function. Epigenetic clocks provide an estimate of how the system ages and can predict health outcomes such as physical function. Physical function declines may be attributed to decreases in muscle quality due to disuse that can be measured quickly and noninvasively using grip strength.

Vitamin D Metabolism Genes Are Differentially Methylated in Individuals with Chronic Knee Pain.

Introduction: Recent evidence suggests that vitamin D may interact with the epigenome and play a role in the pain experience. In order for proper functioning to occur, there must be an adequate level of vitamin D present, made possible by enzymatic reactions that allow vitamin D to be biologically active. The purpose of this study was to explore the epigenetic landscape of genes involved in vitamin D metabolism in individuals with and without chronic knee pain.

Combination of ultrafast dynamic contrast-enhanced MRI-based radiomics and artificial neural network in assessing BI-RADS 4 breast lesions: Potential to avoid unnecessary biopsies.

Objectives: To investigate whether combining radiomics extracted from ultrafast dynamic contrast-enhanced MRI (DCE-MRI) with an artificial neural network enables differentiation of MR BI-RADS 4 breast lesions and thereby avoids false-positive biopsies.

Methods: This retrospective study consecutively included patients with MR BI-RADS 4 lesions. The ultrafast imaging was performed using Differential sub-sampling with cartesian ordering (DISCO) technique and the tenth and fifteenth postcontrast DISCO images (DISCO-10 and DISCO-15) were selected for further analysis.

Magnetic resonance imaging radiomics to differentiate ovarian sex cord-stromal tumors and primary epithelial ovarian cancers.

Objective: To evaluate the diagnostic ability of magnetic resonance imaging (MRI) based radiomics and traditional characteristics to differentiate between Ovarian sex cord-stromal tumors (SCSTs) and epithelial ovarian cancers (EOCs).

Methods: We consecutively included a total of 148 patients with 173 tumors (81 SCSTs in 73 patients and 92 EOCs in 75 patients), who were randomly divided into development and testing cohorts at a ratio of 8:2. Radiomics features were extracted from each tumor, 5-fold cross-validation was conducted for the selection of stable features based on development cohort, and we built radiomics model based on these selected features.

Defining the age-dependent and tissue-specific circadian transcriptome in male mice.

Cellular circadian clocks direct a daily transcriptional program that supports homeostasis and resilience. Emerging evidence has demonstrated age-associated changes in circadian functions. To define age-dependent changes at the systems level, we profile the circadian transcriptome in the hypothalamus, lung, heart, kidney, skeletal muscle, and adrenal gland in three age groups.

Enrichment of genomic pathways based on differential DNA methylation profiles associated with knee osteoarthritis pain.

Our study aimed to identify differentially methylated regions (i.e., genomic region where multiple adjacent CpG sites show differential methylation) and their enriched genomic pathways associated with knee osteoarthritis pain (KOA).

Evaluation of the differentiation of benign and malignant breast lesions using synthetic relaxometry and the Kaiser score.

Objective: To investigate whether there is added value of quantitative parameters from synthetic magnetic resonance imaging (SyMRI) as a complement to the Kaiser score (KS) to differentiate benign and malignant breast lesions.

Materials And Methods: In this single-institution study, 122 patients who underwent breast MRI from March 2020 to May 2021 were retrospectively analyzed. SyMRI and dynamic contrast-enhanced MRI were performed using a 3.

Epigenetic age predictors in community-dwelling adults with high impact knee pain.

Gerontological research reveals considerable interindividual variability in aging phenotypes, and emerging evidence suggests that high impact chronic pain may be associated with various accelerated biological aging processes. In particular, epigenetic aging is a robust predictor of health-span and disability compared to chronological age alone. The current study aimed to determine whether several epigenetic aging biomarkers were associated with high impact chronic pain in middle to older age adults (44-78 years old).

Epigenetic Aging Mediates the Association between Pain Impact and Brain Aging in Middle to Older Age Individuals with Knee Pain.

Chronic musculoskeletal pain is a health burden that may accelerate the aging process. Accelerated brain aging and epigenetic aging have separately been observed in those with chronic pain. However, it is unknown whether these biological markers of aging are associated with each other in those with chronic pain.

Single-cell profiling of microenvironment components by spatial localization in pancreatic ductal adenocarcinoma.

The biology of the pancreatic ductal adenocarcinoma (PDAC) is heterogenous, but how heterogenity of the tumor microenvironment contributes to disparate patient outcomes remains essentially unstudied. A strategy employing multiplex digital spatial profiling (mplxDSP) technology was employed to evaluate the nature and dynamics of microenvironment components including cancer associated fibroblasts (CAFs) and infiltrating immune cells at the single-cell level based upon their spatial relationship within the tumor. We report that myofibroblasts directly adjacent to PDAC tumors comparatively overexpress genes (BATF3, IL12B, ITGB8, CD4 and IFNAR1), constructing pathways prone to stimulating an adaptive immune response.

[Correlation of polymorphisms of DNA double-strand break repair genes XRCC5, LIG4 and glioma].

Objective: To assess the association of DNA double-strand break repair genes XRCC5 and LIG4 with glioma.

Methods: 126 patients with glioma (case group) and 120 healthy volunteers (control group) were enrolled. The polymorphisms of XRCC5 loci rs828704 and rs9288516, LIG4 loci rs3093737, rs3093739 and rs10131 were detected, and their association with the susceptibility to glioma was analyzed.

Epigenetic aging, knee pain and physical performance in community-dwelling middle-to-older age adults.

Knee pain is a leading cause of disability in the aging population and may indirectly accelerate biological aging processes. Chronological aging increases the risk of developing of knee pain and knee pain reduces physical function; however, limited data exist on how epigenetic aging, a known hallmark of biological aging shown to predict health span and mortality, may influence this relationship. The purpose of this study was to examine whether decreased physical performance associated with knee pain is mediated by markers of epigenetic aging.

Differential DNA methylation in Black and White individuals with chronic low back pain enrich different genomic pathways.

Unlabelled: Compared to Non-Hispanic Whites (NHWs), individuals who self-identify as Non-Hispanic Blacks (NHBs) in the United States experience more severe and disabling chronic low back pain (cLBP). We hypothesized that differences in DNA methylation (DNAm) play a role in racial disparities in cLBP.

Purpose: To determine the relationship between DNAm levels and racial group differences in adults with cLBP.

A Comparative Assessment of MR BI-RADS 4 Breast Lesions With Kaiser Score and Apparent Diffusion Coefficient Value.

Objectives: To investigate the diagnostic performance of the Kaiser score and apparent diffusion coefficient (ADC) to differentiate Breast Imaging Reporting and Data System (BI-RADS) Category 4 lesions at dynamic contrast-enhanced (DCE) MRI.

Methods: This was a single-institution retrospective study of patients who underwent breast MRI from March 2020 to June 2021. All image data were acquired with a 3-T MRI system.

Likelihood-based tests for detecting circadian rhythmicity and differential circadian patterns in transcriptomic applications.

Circadian rhythmicity in transcriptomic profiles has been shown in many physiological processes, and the disruption of circadian patterns has been found to associate with several diseases. In this paper, we developed a series of likelihood-based methods to detect (i) circadian rhythmicity (denoted as LR_rhythmicity) and (ii) differential circadian patterns comparing two experimental conditions (denoted as LR_diff). In terms of circadian rhythmicity detection, we demonstrated that our proposed LR_rhythmicity could better control the type I error rate compared to existing methods under a wide variety of simulation settings.

BCL11B is positioned upstream of PLZF and RORγt to control thymic development of mucosal-associated invariant T cells and MAIT17 program.

Mucosal-associated invariant T (MAIT) cells recognize microbial riboflavin metabolites presented by MR1 and play role in immune responses to microbial infections and tumors. We report here that absence of the transcription factor (TF) Bcl11b in mice alters predominantly MAIT17 cells in the thymus and further in the lung, both at steady state and following infection. Transcriptomics and ChIP-seq analyses show direct control of TCR signaling program and position BCL11B upstream of essential TFs of MAIT17 program, including RORγt, ZBTB16 (PLZF), and MAF.

Effects of obesity on breast aromatase expression and systemic metabo-inflammation in women with BRCA1 or BRCA2 mutations.

Obesity is associated with an increased risk of breast cancer in post-menopausal women and decreased risk in pre-menopausal women. Conversely, in BRCA1/2 mutation carriers, pre-menopausal obesity is associated with early-onset breast cancer. Here we show that obese, pre-menopausal BRCA1/2 mutation carriers have increased levels of aromatase and inflammation in the breast, as occurs in post-menopausal women.

Effects of Adiposity and Exercise on Breast Tissue and Systemic Metabo-Inflammatory Factors in Women at High Risk or Diagnosed with Breast Cancer.

Excess body fat and sedentary behavior are associated with increased breast cancer risk and mortality, including in normal weight women. To investigate underlying mechanisms, we examined whether adiposity and exercise impact the breast microenvironment (e.g.