MISC: missing imputation for single-cell RNA sequencing data.

Background: Single-cell RNA sequencing (scRNA-seq) technology provides an effective way to study cell heterogeneity. However, due to the low capture efficiency and stochastic gene expression, scRNA-seq data often contains a high percentage of missing values. It has been showed that the missing rate can reach approximately 30% even after noise reduction.

Increased AURKA promotes cell proliferation and predicts poor prognosis in bladder cancer.

Background: Bladder cancer (BC) is the most common cancer of the urinary bladder and upper tract, in which the clinical management is limited. AURKA (aurora kinase A) has been identified as an oncogene in cancer development; however, its potential role and underlying mechanisms in the progression of BC remain unknown.

Results: In this study, we evaluated Aurora kinase A (AURKA) expression in patient samples by performing gene expression profiling, and found that AURKA expression levels were significantly higher in BC tissues than in normal tissues.

The emerging role of microRNA-4487/6845-3p in Alzheimer's disease pathologies is induced by Aβ25-35 triggered in SH-SY5Y cell.

Background: Accumulation of amyloid β-peptide (Aβ) is implicated in the pathogenesis and development of Alzheimer's disease (AD). Neuron-enriched miRNA was aberrantly regulated and may be associated with the pathogenesis of AD. However, regarding whether miRNA is involved in the accumulation of Aβ in AD, the underlying molecule mechanism remains unclear.

Colorectal premalignancy is associated with consensus molecular subtypes 1 and 2.

Background: Gene expression-based profiling of colorectal cancer (CRC) can be used to identify four molecularly homogeneous consensus molecular subtype (CMS) groups with unique biologic features. However, its applicability to colorectal premalignant lesions remains unknown.

Patients And Methods: We assembled the largest transcriptomic premalignancy dataset by integrating different public and proprietary cohorts of adenomatous and serrated polyps from sporadic (N = 311) and hereditary (N = 78) patient populations and carried out a comprehensive analysis of carcinogenesis pathways using the CMS random forest (RF) classifier.

Late-Onset T1DM and Older Age Predict Risk of Additional Autoimmune Disease.

Objective: Type 1 diabetes (T1DM) is associated with other autoimmune diseases (AIDs), which may have serious health consequences. The epidemiology of AIDs in T1DM is not well defined in adults with T1DM. In this cross-sectional cohort study, we sought to characterize the incident ages and prevalence of AIDs in adults with T1DM across a wide age spectrum.

Drug-Induced Rhabdomyolysis Atlas (DIRA) for idiosyncratic adverse drug reaction management.

Drug-induced rhabdomyolysis (DIR) is an idiosyncratic and fatal adverse drug reaction (ADR) characterized in severe muscle injuries accompanied by multiple-organ failure. Limited knowledge regarding the pathophysiology of rhabdomyolysis is the main obstacle to developing early biomarkers and prevention strategies. Given the lack of a centralized data resource to curate, organize, and standardize widespread DIR information, here we present a Drug-Induced Rhabdomyolysis Atlas (DIRA) that provides DIR-related information, including: a classification scheme for DIR based on drug labeling information; postmarketing surveillance data of DIR; and DIR drug property information.

Correction to: Identification and characterization of conserved lncRNAs in human and rat brain.

After publication of the original article [1], it was noticed that the Acknowledgement statement was incorrect. The original statement reads.

Erratum: Dan Li et al.; Transcription Factor and lncRNA Regulatory Networks Identify Key Elements in Lung Adenocarcinoma. Genes 2018, 9, 12.

The authors wish to make the following change to their paper [...

A Knowledge Base Completion Model Based on Path Feature Learning.

Large-scale knowledge bases, as the foundations for promoting the development of artificial intelligence, have attracted increasing attention in recent years. These knowledge bases contain billions of facts in triple format; yet, they suffer from sparse relations between entities. Researchers proposed the path ranking algorithm (PRA) to solve this fatal problem.

Transcription Factor and lncRNA Regulatory Networks Identify Key Elements in Lung Adenocarcinoma.

Lung cancer is the second most commonly diagnosed carcinoma and is the leading cause of cancer death. Although significant progress has been made towards its understanding and treatment, unraveling the complexities of lung cancer is still hampered by a lack of comprehensive knowledge on the mechanisms underlying the disease. High-throughput and multidimensional genomic data have shed new light on cancer biology.

Identification and characterization of conserved lncRNAs in human and rat brain.

Background: Long noncoding RNAs (lncRNAs) are involved in diverse biological processes and play an essential role in various human diseases. The number of lncRNAs identified has increased rapidly in recent years owing to RNA sequencing (RNA-Seq) technology. However, presently, most lncRNAs are not well characterized, and their regulatory mechanisms remain elusive.

Population-based birth defects data in the United States, 2010-2014: A focus on gastrointestinal defects.

Background: Gastrointestinal defects are a phenotypically and etiologically diverse group of malformations. Despite their combined prevalence and clinical impact, little is known about the epidemiology of these birth defects. Therefore, the objective of the 2017 National Birth Defects Prevention Network (NBDPN) data brief was to better describe the occurrence of gastrointestinal defects.

High-throughput state-machine replication using software transactional memory.

State-machine replication is a common way of constructing general purpose fault tolerance systems. To ensure replica consistency, requests must be executed sequentially according to some total order at all non-faulty replicas. Unfortunately, this could severely limit the system throughput.

A multicenter, randomized study of decitabine as epigenetic priming with induction chemotherapy in children with AML.

Background: Decitabine is a deoxycytidine nucleoside derivative inhibitor of DNA-methyltransferases, which has been studied extensively and is approved for myelodysplastic syndrome in adults but with less focus in children. Accordingly, we conducted a phase 1 multicenter, randomized, open-label study to evaluate decitabine pre-treatment before standard induction therapy in children with newly diagnosed AML to assess safety and tolerability and explore a number of biologic endpoints.

Results: Twenty-four patients were fully assessable for all study objectives per protocol (10 in Arm A = epigenetic priming induction, 14 in Arm B = standard induction).

Effects of allergen sensitization on response to therapy in children with eosinophilic esophagitis.

Background: In children with eosinophilic esophagitis (EoE) foods are the most common disease triggers, but environmental allergens are also suspected culprits.

Objective: To determine the effects of environmental allergen sensitization on response to treatment in children with EoE in the southeastern United States.

Methods: Patients 2 to 18 years old who were referred to the Arkansas Children's Hospital Eosinophilic Gastrointestinal Disorders Clinic from January 2012 to January 2016 were enrolled in a prospective, longitudinal cohort study with collection of demographics, clinical symptoms, medical history, allergy sensitization profiles, and response to treatment over time.

Metabolic syndrome: pathophysiology, management, and modulation by natural compounds.

Metabolic syndrome (MetS) represents a cluster of metabolic abnormalities that include hypertension, central obesity, insulin resistance, and atherogenic dyslipidemia, and is strongly associated with an increased risk for developing diabetes and atherosclerotic and nonatherosclerotic cardiovascular disease (CVD). The pathogenesis of MetS involves both genetic and acquired factors that contribute to the final pathway of inflammation that leads to CVD. MetS has gained significant importance recently due to the exponential increase in obesity worldwide.

Multi-class computational evolution: development, benchmark evaluation and application to RNA-Seq biomarker discovery.

Background: A computational evolution system (CES) is a knowledge discovery engine that can identify subtle, synergistic relationships in large datasets. Pareto optimization allows CESs to balance accuracy with model complexity when evolving classifiers. Using Pareto optimization, a CES is able to identify a very small number of features while maintaining high classification accuracy.

Practical application of opt-out recruitment methods in two health services research studies.

Background: Participant recruitment is an ongoing challenge in health research. Recruitment may be especially difficult for studies of access to health care because, even among those who are in care, people using services least often also may be hardest to contact and recruit. Opt-out recruitment methods (in which potential participants are given the opportunity to decline further contact about the study (opt out) following an initial mailing, and are then contacted directly if they have not opted out within a specified period) can be used for such studies.

Biallelic mutations in human DCC cause developmental split-brain syndrome.

Motor, sensory, and integrative activities of the brain are coordinated by a series of midline-bridging neuronal commissures whose development is tightly regulated. Here we report a new human syndrome in which these commissures are widely disrupted, thus causing clinical manifestations of horizontal gaze palsy, scoliosis, and intellectual disability. Affected individuals were found to possess biallelic loss-of-function mutations in the gene encoding the axon-guidance receptor 'deleted in colorectal carcinoma' (DCC), which has been implicated in congenital mirror movements when it is mutated in the heterozygous state but whose biallelic loss-of-function human phenotype has not been reported.

Dalbavancin Pharmacokinetics and Safety in Children 3 Months to 11 Years of Age.

Background: Dalbavancin is a novel lipoglycopeptide antibiotic that has potent in vitro activity against Gram-positive microorganisms.

Methods: We performed a phase 1, open-label, multicenter study to investigate the pharmacokinetics (PK) and safety of a single dose of intravenous dalbavancin in hospitalized pediatric subjects 3 months to 11 years of age. We combined these data with previously collected adolescent PK data and performed a population PK analysis.

Proteins that accumulate with age in human skeletal-muscle aggregates contribute to declines in muscle mass and function in .

Protein aggregation increases with age in normal tissues, and with pathology and age in Alzheimer's hippocampus and mouse cardiac muscle. We now ask whether human skeletal muscle accumulates aggregates with age. Detergent-insoluble protein aggregates were isolated from biopsies from 5 young (23–27 years of age) and 5 older (64-80 years) adults.

A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models.

Ovarian carcinomas can be aggressive with a high mortality rate (e.g., high-grade serous ovarian carcinomas, or HGSOCs), or indolent with much better long-term outcomes (e.

The up-regulation of Myb may help mediate EGCG inhibition effect on mouse lung adenocarcinoma.

Background: Green tea polyphenol epigallocatechin-3-gallate (EGCG) has been demonstrated to inhibit cancer in experimental studies through its antioxidant activity and modulations on cellular functions by binding specific proteins. By means of computational analysis and functional genomic approaches, we previously identified a set of protein coding genes and microRNAs whose expressions were significantly modulated in response to the EGCG treatment in tobacco carcinogen-induced lung adenocarcinoma in A/J mice. However, to what degree these genes are involved in the cancer inhibition of EGCG remains unclear.

The clinical significance of snail protein expression in gastric cancer: a meta-analysis.

Background: Snail is a typical transcription factor that could induce epithelial-mesenchymal transition (EMT) and cancer progression. There are some related reports about the clinical significance of snail protein expression in gastric cancer. However, the published results were not completely consistent.

Association of six CpG-SNPs in the inflammation-related genes with coronary heart disease.

Background: Chronic inflammation has been widely considered to be the major risk factor of coronary heart disease (CHD). The goal of our study was to explore the possible association with CHD for inflammation-related single nucleotide polymorphisms (SNPs) involved in cytosine-phosphate-guanine (CpG) dinucleotides. A total of 784 CHD patients and 739 non-CHD controls were recruited from Zhejiang Province, China.