TIME-CoExpress: Temporal Trajectory Modeling of Dynamic Gene Co-expression Patterns Using Single-Cell Transcriptomics Data.

The rapid advancements of single-cell RNA sequencing (scRNAseq) technology provide high-resolution views of transcriptomic activity within a single cell. Most routine analyses of scRNAseq data focus on individual genes; however, the one-gene-at-a-time analysis is likely to miss meaningful genetic interactions. Gene co-expression analysis addresses this issue by identifying coordinated gene expression changes in response to cellular conditions, such as developmental or temporal trajectory.

Genome-wide search algorithms for identifying dynamic gene co-expression via Bayesian variable selection.

A wealth of gene expression data generated by high-throughput techniques provides exciting opportunities for studying gene-gene interactions systematically. Gene-gene interactions in a biological system are tightly regulated and are often highly dynamic. The interactions can change flexibly under various internal cellular signals or external stimuli.

Long-term patient-reported donor-site morbidity after free peroneal fasciocutaneous flap in head and neck reconstruction.

Objective: Fasciocutaneous free flap based on the peroneal artery (boneless version) is an option in our practice for head and neck reconstruction. However, the associated donor-site morbidity has rarely been discussed. Thus, this study investigated the long-term patient-reported donor-site morbidity associated with peroneal flaps.

Flexible copula model for integrating correlated multi-omics data from single-cell experiments.

With recent advances in technologies to profile multi-omics data at the single-cell level, integrative multi-omics data analysis has been increasingly popular. It is increasingly common that information such as methylation changes, chromatin accessibility, and gene expression are jointly collected in a single-cell experiment. In biomedical studies, it is often of interest to study the associations between various data types and to examine how these associations might change according to other factors such as cell types and gene regulatory components.

Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq.

Among single-cell analysis technologies, single-cell RNA-seq (scRNA-seq) has been one of the front runners in technical inventions. Since its induction, scRNA-seq has been well received and undergone many fast-paced technical improvements in cDNA synthesis and amplification, processing and alignment of next generation sequencing reads, differentially expressed gene calling, cell clustering, subpopulation identification, and developmental trajectory prediction. scRNA-seq has been exponentially applied to study global transcriptional profiles in all cell types in humans and animal models, healthy or with diseases, including cancer.

Haematogenous Klebsiella pneumoniae osteomyelitis.

Objectives: Klebsiella pneumoniae infection has been associated with alcoholic and diabetic patient populations, especially in Asian populations. K. pneumonia wound infection is common, but K.

Modeling dynamic correlation in zero-inflated bivariate count data with applications to single-cell RNA sequencing data.

Interactions between biological molecules in a cell are tightly coordinated and often highly dynamic. As a result of these varying signaling activities, changes in gene coexpression patterns could often be observed. The advancements in next-generation sequencing technologies bring new statistical challenges for studying these dynamic changes of gene coexpression.

Coexposure to Inhaled Aldehydes or Carbon Dioxide Enhances the Carcinogenic Properties of the Tobacco-Specific Nitrosamine 4-Methylnitrosamino-1-(3-pyridyl)-1-butanone in the A/J Mouse Lung.

Tobacco smoke is a complex mixture of chemicals, many of which are toxic and carcinogenic. Hazard assessments of tobacco smoke exposure have predominantly focused on either single chemical exposures or the more complex mixtures of tobacco smoke or its fractions. There are fewer studies exploring interactions between specific tobacco smoke chemicals.

Bisphosphonate-Related Osteonecrosis of the Jaw.

Objectives: Antiresorptive agents for bone pain were widely used to treat patients with advanced osteoporosis, multiple myeloma, and bone metastatic cancer. In recent years, however, bisphosphonate-related osteonecrosis of the jaw (BRONJ) has been a rare but major complication of this therapy. Most patients with BRONJ undergo dental procedures during treatment with antiresorptive agents.

Flexible bivariate correlated count data regression.

Multivariate count data are common in many disciplines. The variables in such data often exhibit complex positive or negative dependency structures. We propose three Bayesian approaches to modeling bivariate count data by simultaneously considering covariate-dependent means and correlation.

The Arabidopsis transcription factor AINTEGUMENTA orchestrates patterning genes and auxin signaling in the establishment of floral growth and form.

Understanding how flowers form is an important problem in plant biology, as human food supply depends on flower and seed production. Flower development also provides an excellent model for understanding how cell division, expansion and differentiation are coordinated during organogenesis. In the model plant Arabidopsis thaliana, floral organogenesis requires AINTEGUMENTA (ANT) and AINTEGUMENTA-LIKE 6 (AIL6)/PLETHORA 3 (PLT3), two members of the Arabidopsis AINTEGUMENTA-LIKE/PLETHORA (AIL/PLT) transcription factor family.

Using sufficient direction factor model to analyze latent activities associated with breast cancer survival.

High-dimensional gene expression data often exhibit intricate correlation patterns as the result of coordinated genetic regulation. In practice, however, it is difficult to directly measure these coordinated underlying activities. Analysis of breast cancer survival data with gene expressions motivates us to use a two-stage latent factor approach to estimate these unobserved coordinated biological processes.

Clinical Importance and Risk Factors for Postoperative Late-Onset Pneumonia After Major Oral Cancer Surgery With Microvascular Reconstruction.

Background: Pulmonary complications are common among patients who have undergone major oral cancer surgery with microvascular reconstruction. Current literatures focused on early-onset pneumonia in the postoperative acute stage. In contrast, we are aiming to identify the clinical importance and the risk factors associated with late-onset pneumonia in oral cancer patients after acute stage.

Individual Differences in the Response of Human β-Lymphoblastoid Cells to the Cytotoxic, Mutagenic, and DNA-Damaging Effects of a DNA Methylating Agent, -Methylnitrosourethane.

Metabolic activation of many carcinogens leads to formation of reactive intermediates that form DNA adducts. These adducts are cytotoxic when they interfere with cell division. They can also cause mutations by miscoding during DNA replication.

Meta-analytic framework for modeling genetic coexpression dynamics.

Methods for exploring genetic interactions have been developed in an attempt to move beyond single gene analyses. Because biological molecules frequently participate in different processes under various cellular conditions, investigating the changes in gene coexpression patterns under various biological conditions could reveal important regulatory mechanisms. One of the methods for capturing gene coexpression dynamics, named liquid association (LA), quantifies the relationship where the coexpression between two genes is modulated by a third "coordinator" gene.

Whole-Blood Transcriptional Signatures Composed of Erythropoietic and NRF2-Regulated Genes Differ Between Cerebral Malaria and Severe Malarial Anemia.

Background: Among the severe malaria syndromes, severe malarial anemia (SMA) is the most common, whereas cerebral malaria (CM) is the most lethal. However, the mechanisms that lead to CM and SMA are unclear.

Methods: We compared transcriptomic profiles of whole blood obtained from Ugandan children with acute CM (n = 17) or SMA (n = 17) and community children without Plasmodium falciparum infection (n = 12) and determined the relationships among gene expression, hematological indices, and relevant plasma biomarkers.

A Bayesian hierarchical model for demand curve analysis.

Drug self-administration experiments are a frequently used approach to assess the abuse liability and reinforcing property of a compound. It has been used to assess the abuse liabilities of various substances such as psychomotor stimulants and hallucinogens, food, nicotine, and alcohol. The demand curve generated from a self-administration study describes how demand of a drug or non-drug reinforcer varies as a function of price.

A Bayesian hierarchical model for demand curve analysis.

Drug self-administration experiments are a frequently used approach to assessing the abuse liability and reinforcing property of a compound. It has been used to assess the abuse liabilities of various substances such as psychomotor stimulants and hallucinogens, food, nicotine, and alcohol. The demand curve generated from a self-administration study describes how demand of a drug or non-drug reinforcer varies as a function of price.

Daily and Nondaily Smoking Varies by Acculturation among English-Speaking, US Latino Men and Women.

Background: Higher smoking prevalence and quantity (cigarettes per day) has been linked to acculturation in the United States among Latinas, but not Latino men. Our study examines variation between a different and increasingly important target behavior, smoking level (nondaily vs daily) and acculturation by sex.

Methods: An online English-language survey was administered to 786 Latino smokers during July through August 2012.

Impact of a Prostate Specific Antigen Screening Decision Aid on Clinic Function.

Introduction: Decision aids (DAs) around prostate cancer screening can increase knowledge and shared decision making (SDM), but remain underutilized due to cost and time constraints that disrupt clinic flow. We examined the impact of a simple prostate specific antigen (PSA) screening DA distribution strategy on clinic flow as well as SDM in a diverse urban primary care clinic.

Methods: Men ages 50-75 viewed the DA while waiting for physicians.

Evaluation of the prebiotic effects of citrus pectin hydrolysate.

Citrus pectin enzyme hydrolysate (PEH) of different hydrolysis time intervals (6 hours, PEH-6; 12 hours, PEH-12; 24 hours, PEH-24; or 48 hours, PEH-48) or concentrations (1%, 2%, and 4%) was tested for its growth stimulation effect on two probiotics, Bifidobacterium bifidum and Lactobacillus acidophilus. Higher monosaccharide concentrations and smaller molecular weights of PEHs were obtained by prolonging the hydrolysis time. In addition, higher PEH concentrations resulted in significantly higher (p < 0.

Acquired Tamoxifen Resistance in MCF-7 Breast Cancer Cells Requires Hyperactivation of eIF4F-Mediated Translation.

While selective estrogen receptor modulators, such as tamoxifen, have contributed to increased survival in patients with hormone receptor-positive breast cancer, the development of resistance to these therapies has led to the need to investigate other targetable pathways involved in oncogenic signaling. Approval of the mTOR inhibitor everolimus in the therapy of secondary endocrine resistance demonstrates the validity of this approach. Importantly, mTOR activation regulates eukaryotic messenger RNA translation.

Meta-analytic framework for liquid association.

Motivation: Although coexpression analysis via pair-wise expression correlation is popularly used to elucidate gene-gene interactions at the whole-genome scale, many complicated multi-gene regulations require more advanced detection methods. Liquid association (LA) is a powerful tool to detect the dynamic correlation of two gene variables depending on the expression level of a third variable (LA scouting gene). LA detection from single transcriptomic study, however, is often unstable and not generalizable due to cohort bias, biological variation and limited sample size.

Contributing Factors for Complications and Outcomes in Patients With Snakebite: Experience in a Medical Center in Southern Taiwan.

Objectives: Snakebite usually results in various complications, such as significant soft tissue damage, infection, hematological, and neurological deficit. Surgical intervention, usually, is indicated in patients with tissue necrosis, infection, and compartment syndrome. To identify the contributing factors for complications and outcomes in different patients with snakebite so that outcomes can be evaluated and treatment of such patients can be initiated at the earliest.

Automatic health record review to help prioritize gravely ill Social Security disability applicants.

Objective: Every year, thousands of patients die waiting for disability benefits from the Social Security Administration. Some qualify for expedited service under the Compassionate Allowance (CAL) initiative, but CAL software focuses exclusively on information from a single form field. This paper describes the development of a supplemental process for identifying some overlooked but gravely ill applicants, through automatic annotation of health records accompanying new claims.