Deep Learning on High-Throughput Transcriptomics to Predict Drug-Induced Liver Injury.

Drug-induced liver injury (DILI) is one of the most cited reasons for the high drug attrition rate and drug withdrawal from the market. The accumulated large amount of high throughput transcriptomic profiles and advances in deep learning provide an unprecedented opportunity to improve the suboptimal performance of DILI prediction. In this study, we developed an eight-layer Deep Neural Network (DNN) model for DILI prediction using transcriptomic profiles of human cell lines (LINCS L1000 dataset) with the current largest binary DILI annotation data [i.

Genome sequences of antibiotic-resistant Streptococcus suis strains isolated from human patients and diseased and asymptomatic pigs in Thailand.

Streptococcus suis, a zoonotic bacterial pathogen, has negative economic impacts on both intensive swine production and human health worldwide. Whole-genome sequencing and comparative genomic analysis have been widely used for comprehensive classification and investigation of the genetic basis of several S. suis strains obtained from distinct hosts in different geographic areas, revealing great genetic diversity of this zoonotic pathogen.

KITSUNE: A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis.

Genomic DNA is the best "unique identifier" for organisms. Alignment-free phylogenomic analysis, simple, fast, and efficient method to compare genome sequences, relies on looking at the distribution of small DNA sequence of a particular length, referred to as k-mer. The k-mer approach has been explored as a basis for sequence analysis applications, including assembly, phylogenetic tree inference, and classification.

L-leucine improves anemia and growth in patients with transfusion-dependent Diamond-Blackfan anemia: Results from a multicenter pilot phase I/II study from the Diamond-Blackfan Anemia Registry.

Background: Diamond-Blackfan anemia (DBA) is an inherited bone marrow failure syndrome characterized by anemia, short stature, congenital anomalies, and cancer predisposition. Most cases are due to mutations in genes encoding ribosomal proteins (RP) leading to RP haploinsufficiency. Effective treatments for the anemia of DBA include chronic red cell transfusions, long-term corticosteroid therapy, or hematopoietic stem cell transplantation.

Genetics and genomics of SARS-CoV-2: A review of the literature with the special focus on genetic diversity and SARS-CoV-2 genome detection.

The outbreak of 2019-novel coronavirus disease (COVID-19), caused by SARS-CoV-2, started in late 2019; in a short time, it has spread rapidly all over the world. Although some possible antiviral and anti-inflammatory medications are available, thousands of people are dying daily. Well-understanding of the SARS-CoV-2 genome is not only essential for the development of new treatments/vaccines, but it also can be used for improving the sensitivity and specificity of current approaches for virus detection.

A Uromodulin Mutation Drives Autoimmunity and Kidney Mononuclear Phagocyte Endoplasmic Reticulum Stress.

We identified a family with a UMOD gene mutation (C106F) resulting in glomerular inflammation and complement deposition. To determine if the observed phenotype is due to immune system activation by mutant uromodulin, a mouse strain with a homologous cysteine to phenylalanine mutation (C105F) in the UMOD gene was generated using CRISPR-Cas9 gene editing and the effect of this mutation on mononuclear phagocytic cells was examined. Mutant mice developed high levels of intracellular and secreted aggregated uromodulin, resulting in anti-uromodulin antibodies and circulating uromodulin containing immune complexes with glomerular deposition and kidney fibrosis with aging.

Divergence in aerobic capacity impacts bile acid metabolism in young women.

Liver adaptations may be critical for regular exercise and high aerobic capacity to protect against metabolic disease, but mechanisms remain unknown. Bile acids (BAs) synthesized in the liver are bioactive and can putatively modify energy metabolism. Regular exercise influences BA metabolism in rodents, but effects in humans are unknown.

Design and Synthesis of Novel Hybrid 8-Hydroxy Quinoline-Indole Derivatives as Inhibitors of Aβ Self-Aggregation and Metal Chelation-Induced Aβ Aggregation.

A series of novel hybrid 8-hydroxyquinoline-indole derivatives (, and ) were synthesized and screened for inhibitory activity against self-induced and metal-ion induced Aβ aggregation as potential treatments for Alzheimer's disease (AD). In vitro studies identified the most inhibitory compounds against self-induced Aβ aggregation as , and (EC = 1.72, 1.

Drug Repositioning for Noonan and LEOPARD Syndromes by Integrating Transcriptomics With a Structure-Based Approach.

Noonan and LEOPARD syndromes (NS and LS) belong to a group of related disorders called RASopathies characterized by abnormalities of multiple organs and systems including hypertrophic cardiomyopathy and dysmorphic facial features. There are no approved drugs for these two rare diseases, but it is known that a missense mutation in PTPN11 genes is associated with approximately 50% and 70% of NS and LS cases, respectively. In this study, we implemented a hybrid computational drug repositioning framework by integrating transcriptomic and structure-based approaches to explore potential treatment options for NS and LS.

Dimension Reduction and Clustering Models for Single-Cell RNA Sequencing Data: A Comparative Study.

With recent advances in single-cell RNA sequencing, enormous transcriptome datasets have been generated. These datasets have furthered our understanding of cellular heterogeneity and its underlying mechanisms in homogeneous populations. Single-cell RNA sequencing (scRNA-seq) data clustering can group cells belonging to the same cell type based on patterns embedded in gene expression.

Pathogenic and protective roles of cytokines in pemphigus: A systematic review.

Pemphigus is a rare and life-threatening group of blistering autoimmune diseases that affects the skin and mucous membranes. There are two major subtypes of pemphigus, including pemphigus vulgaris (PV) and pemphigus foliaceus (PF); each has different clinical manifestations. Pemphigus cannot be considered as a single disease and each patient may have a specific immunological profile.

A Health Care Provider Intervention to Address Obesity in Patients with Diabetes.

An education program offered health care providers information to assess patients' daily calorie goal and prompted an increase in weight loss and dietician referrals.

Early acetaminophen-protein adducts predict hepatotoxicity following overdose (ATOM-5).

Background & Aims: Acetaminophen-protein adducts are specific biomarkers of toxic acetaminophen (paracetamol) metabolite exposure. In patients with hepatotoxicity (alanine aminotransferase [ALT] >1,000 U/L), an adduct concentration ≥1.0 nmol/ml is sensitive and specific for identifying cases secondary to acetaminophen.

Management of an odontoid synchondrosis fracture causing chronic translational anterior atlanto-axial subluxation in a child with autism: case report.

The authors report an unusual case of an odontoid synchondrosis fracture causing chronic translational anterior atlanto-axial subluxation and present a discussion of the unique management of this case. Traumatic translational anterior atlanto-axial subluxation is a rare manifestation within pediatrics. Patients with preexisting abnormalities in ligamentous or bony structures may present with unusual symptomatology, which could result in delay of treatment.

TGFβ1 single-nucleotide polymorphism C-509T alters mucosal cell function in pediatric eosinophilic esophagitis.

Eosinophilic esophagitis (EoE) is a chronic Th2 antigen-driven disorder associated with tissue remodeling. Inflammation and remodeling lead to esophageal rigidity, strictures, and dysphagia. TGFβ1 drives esophageal remodeling including epithelial barrier dysfunction and subepithelial fibrosis.

Comparing the Efficacy and Safety of Treating Chronic Hepatitis B Infection during Pregnancy with Lamivudine, Telbivudine, and Tenofovir: A Meta-analysis.

The perinatal transmission of hepatitis B virus (HBV) remains an important global health problem. Here, a systematic review and meta-analysis were conducted to evaluate the evidence regarding the efficacy and maternal/fetal safety of treating pregnant women with lamivudine, telbivudine (LdT), and tenofovir (TDF). A PubMed and Scopus search resulted in 1,076 records, which were reduced to 36, containing 7,717 pregnant women with chronic HBV infection and 7467 infants meeting the inclusion criteria.

Blood flow patterns regulate PCSK9 secretion via MyD88-mediated pro-inflammatory cytokines.

Aims: Blood flow patterns play an important role in the localization of atherosclerosis in the sense that low-flow state is pro-atherogenic, and helical flow is protective against atherosclerosis. Proprotein convertase subtilisin/kexin type 9 (PCSK9) regulates cholesterol metabolism via low-density lipoprotein receptor (LDLr) degradation and is highly expressed in the atherosclerotic tissues. This study was designed to investigate the role of different blood flow patterns in the regulation of PCSK9 expression.

Transcriptome analysis of Sézary syndrome and lymphocytic-variant hypereosinophilic syndrome T cells reveals common and divergent genes.

Sézary syndrome (SS) is an aggressive cutaneous T cell lymphoma with pruritic skin inflammation and immune dysfunction, driven by neoplastic, clonal memory T cells in both peripheral blood and skin. To gain insight into abnormal gene expression promoting T cell dysfunction, lymphoproliferation and transformation in SS, we first compared functional transcriptomic profiles of both resting and activated CD4CD45RO T cells from SS patients and normal donors to identified differential expressed genes. Next, a meta-analysis was performed to compare our SS data to public microarray data from a novel benign disease control, lymphocytic-variant hypereosinophilic syndrome (L-HES).

Invasive Pneumococcal Disease in Children's Hospitals: 2014-2017.

Background: The 13-valent pneumococcal conjugate vaccine (PCV13) was licensed in the United States in 2010. We describe invasive pneumococcal disease (IPD) in children at 8 children's hospitals in the US from 2014 to 2017.

Methods: Children with IPD occurring from 2014 to 2017 were identified from a prospective study.

Image Captioning with Bidirectional Semantic Attention-Based Guiding of Long Short-Term Memory.

Automatically describing contents of an image using natural language has drawn much attention because it not only integrates computer vision and natural language processing but also has practical applications. Using an end-to-end approach, we propose a bidirectional semantic attention-based guiding of long short-term memory (Bag-LSTM) model for image captioning. The proposed model consciously refines image features from previously generated text.

Single-nucleotide polymorphisms associated with pemphigus vulgaris: Potent markers for better treatment and personalized medicine.

Pemphigus vulgaris (PV) is a rare autoimmune blistering disorder, which could affect both skin and mucosal surfaces. There is increasing evidence that genetics plays a critical role in PV development, severity and prognosis. Single-nucleotide polymorphisms (SNPs) are the most common type of genetic variation among people and have been widely evaluated in most diseases.

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

It was highlighted that the original article [1] contained a typesetting error in the last name of Allon Canaan. This was incorrectly captured as Allon Canaann in the original article which has since been updated.

Role of meprin metalloproteinases in cytokine processing and inflammation.

Meprin metalloendopeptidases, comprising α and β isoforms, are widely expressed in mammalian cells and organs including kidney, intestines, lungs, skin, and bladder, and in a variety of immune cells and cancer cells. Meprins proteolytically process many inflammatory mediators, including cytokines, chemokines, and other bioactive proteins and peptides that control the function of immune cells. The knowledge of meprin-mediated processing of inflammatory mediators and other target substrates provides a pathophysiologic link for the involvement of meprins in the pathogenesis of many inflammatory disorders.

Systems biology analysis reveals new insights into invasive lung cancer.

Background: Adenocarcinoma in situ (AIS) is a pre-invasive lesion in the lung and a subtype of lung adenocarcinoma. The patients with AIS can be cured by resecting the lesion completely. In contrast, the patients with invasive lung adenocarcinoma have very poor 5-year survival rate.