Computational models for lncRNA function prediction and functional similarity calculation.

From transcriptional noise to dark matter of biology, the rapidly changing view of long non-coding RNA (lncRNA) leads to deep understanding of human complex diseases induced by abnormal expression of lncRNAs. There is urgent need to discern potential functional roles of lncRNAs for further study of pathology, diagnosis, therapy, prognosis, prevention of human complex disease and disease biomarker detection at lncRNA level. Computational models are anticipated to be an effective way to combine current related databases for predicting most potential lncRNA functions and calculating lncRNA functional similarity on the large scale.

On the Relationship Between Sensory Eye Dominance and Stereopsis in the Normal-Sighted Adult Population: Normative Data.

The extent of sensory eye dominance, a reflection of the interocular suppression in binocular visual processing, can be quantitatively measured using the binocular phase combination task. In this study, we aimed to provide a normative dataset for sensory eye dominance using this task. Based on that, we also assessed the relationship between perceptual eye dominance and stereopsis.

Dopamine Receptor Subtypes Mediate Opposing Effects on Form Deprivation Myopia in Pigmented Guinea Pigs.

Purpose: We reported previously that changes in dopamine receptor (DR) subtype activation modulate spontaneous myopia progression in albino guinea pigs. To determine if DR control of refractive error development is different than in its normal counterpart, we evaluated the contribution of dopaminergic pathways to emmetropization and form deprivation myopia (FDM) progression in pigmented guinea pigs.

Methods: Monocular myopia was induced by unilateral form-deprivation (FD).

Role of Cyclic Adenosine Monophosphate in Myopic Scleral Remodeling in Guinea Pigs: A Microarray Analysis.

Purpose: Myopia induction accompanies increased scleral cyclic adenosine phosphate (cAMP) levels and collagen degradation in mammalian models. We compared the scleral gene expression changes following monocular form deprivation (FD) with those induced by adenylate cyclase activation with forskolin (FSK) in guinea pigs.

Methods: Guinea pigs were assigned to FD, FSK-treated, and age-matched (AM) control groups.

MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction.

Recently, a growing number of biological research and scientific experiments have demonstrated that microRNA (miRNA) affects the development of human complex diseases. Discovering miRNA-disease associations plays an increasingly vital role in devising diagnostic and therapeutic tools for diseases. However, since uncovering associations via experimental methods is expensive and time-consuming, novel and effective computational methods for association prediction are in demand.

Identifying and Exploiting Potential miRNA-Disease Associations With Neighborhood Regularized Logistic Matrix Factorization.

With the rapid development of biological research, microRNAs (miRNA) have become an attractive topic because lots of experimental studies have revealed the significant associations between miRNAs and diseases. However, considering that experiments are expensive and time-consuming, computational methods for predicting associations between miRNAs and diseases have become increasingly crucial. In this study, we proposed a neighborhood regularized logistic matrix factorization method for miRNA-disease association prediction (NRLMFMDA) by integrating miRNA functional similarity, disease semantic similarity, Gaussian interaction profile kernel similarity, and experimentally validation of disease-miRNA association.

An Autism-Related, Nonsense Foxp1 Mutant Induces Autophagy and Delays Radial Migration of the Cortical Neurons.

Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that has a strong genetic component. Disruptions of FOXP1, a transcription factor expressed in the developing cerebral cortex, were associated with ASD. FOXP1(R525X) is a de novo heterozygous mutation found in patients with autism and severe mental retardation.

Microporous N,P-Codoped Graphitic Nanosheets as an Efficient Electrocatalyst for Oxygen Reduction in Whole pH Range for Energy Conversion and Biosensing Dissolved Oxygen.

Microporous N,P-codoped graphitic nanosheets (N,P-CMP-1000) were synthesized by thermal annealing (1000 °C) of as-synthesized conjugated microporous polymers (CMPs) in the presence of phytic acid, which can be used as an effective metal-free electrocatalyst for the oxygen reduction reaction (ORR) for energy conversion. In the whole pH range (i.e.

Gastric Pathology Image Classification Using Stepwise Fine-Tuning for Deep Neural Networks.

Deep learning using convolutional neural networks (CNNs) is a distinguished tool for many image classification tasks. Due to its outstanding robustness and generalization, it is also expected to play a key role to facilitate advanced computer-aided diagnosis (CAD) for pathology images. However, the shortage of well-annotated pathology image data for training deep neural networks has become a major issue at present because of the high-cost annotation upon pathologist's professional observation.

Corneal Collagen Cross-Linking With Riboflavin and UVA Regulates Hemangiogenesis and Lymphangiogenesis in Rats.

Purpose: The purpose of this study was to determine whether corneal collagen crosslinking (CXL) inhibits hemangiogenesis and lymphangiogenesis during acute corneal inflammation in an in vivo rat model.

Methods: Inflammatory corneal neovascularization was induced by suture placement into a rat cornea. At day 3 after suture, a CXL protocol using riboflavin and UVA was administered after mechanical epithelial debridement.

Genipin-Crosslinked Donor Sclera for Posterior Scleral Contraction/Reinforcement to Fight Progressive Myopia.

Purpose: Myopia has become a global public health problem, particularly in East Asia where myopic retinopathy has become one of the leading causes of blindness and visual impairment in the elderly population. The purpose of this study was to evaluate the efficacy of posterior scleral contraction/reinforcement (PSCR) surgery on controlling the progressive elongation of axial length of highly myopic eyes in young patients.

Methods: This is a prospective self-controlled interventional case series.

TLHNMDA: Triple Layer Heterogeneous Network Based Inference for MiRNA-Disease Association Prediction.

In recent years, microRNAs (miRNAs) have been confirmed to be involved in many important biological processes and associated with various kinds of human complex diseases. Therefore, predicting potential associations between miRNAs and diseases with the huge number of verified heterogeneous biological datasets will provide a new perspective for disease therapy. In this article, we developed a novel computational model of Triple Layer Heterogeneous Network based inference for MiRNA-Disease Association prediction (TLHNMDA) by using the experimentally verified miRNA-disease associations, miRNA-long noncoding RNA (lncRNA) interactions, miRNA function similarity information, disease semantic similarity information and Gaussian interaction profile kernel similarity for lncRNAs into an triple layer heterogeneous network to predict new miRNA-disease associations.

Scleral hypoxia is a target for myopia control.

Worldwide, myopia is the leading cause of visual impairment. It results from inappropriate extension of the ocular axis and concomitant declines in scleral strength and thickness caused by extracellular matrix (ECM) remodeling. However, the identities of the initiators and signaling pathways that induce scleral ECM remodeling in myopia are unknown.

Hyperosmotic Stress-Induced TRPM2 Channel Activation Stimulates NLRP3 Inflammasome Activity in Primary Human Corneal Epithelial Cells.

Purpose: The purpose of this study was to determine whether either a hyperosmotic or oxidative stress induces NLRP3 inflammasome activation and increases in bioactive IL-1β secretion through transient receptor potential melastatin 2 (TRPM2) activation in primary human corneal epithelial cells (PHCECs).

Methods: Real-time PCR, Western blots, and immunofluorescent staining were used to evaluate TRPM2 and NLRP3, ASC, caspase-1, and IL-1β mRNA and protein expression levels, respectively. A CCK-8 assay evaluated cell viability.

Inferring potential small molecule-miRNA association based on triple layer heterogeneous network.

Recently, many biological experiments have indicated that microRNAs (miRNAs) are a newly discovered small molecule (SM) drug targets that play an important role in the development and progression of human complex diseases. More and more computational models have been developed to identify potential associations between SMs and target miRNAs, which would be a great help for disease therapy and clinical applications for known drugs in the field of medical research. In this study, we proposed a computational model of triple layer heterogeneous network based small molecule-MiRNA association prediction (TLHNSMMA) to uncover potential SM-miRNA associations by integrating integrated SM similarity, integrated miRNA similarity, integrated disease similarity, experimentally verified SM-miRNA associations and miRNA-disease associations into a heterogeneous graph.

Predicting miRNA-disease association based on inductive matrix completion.

Motivation: It has been shown that microRNAs (miRNAs) play key roles in variety of biological processes associated with human diseases. In Consideration of the cost and complexity of biological experiments, computational methods for predicting potential associations between miRNAs and diseases would be an effective complement.

Results: This paper presents a novel model of Inductive Matrix Completion for MiRNA-Disease Association prediction (IMCMDA).

A Single Multiplex crRNA Array for FnCpf1-Mediated Human Genome Editing.

Cpf1 has been harnessed as a tool for genome manipulation in various species because of its simplicity and high efficiency. Our recent study demonstrated that FnCpf1 could be utilized for human genome editing with notable advantages for target sequence selection due to the flexibility of the protospacer adjacent motif (PAM) sequence. Multiplex genome editing provides a powerful tool for targeting members of multigene families, dissecting gene networks, modeling multigenic disorders in vivo, and applying gene therapy.

Dopamine D1 Receptors Contribute Critically to the Apomorphine-Induced Inhibition of Form-Deprivation Myopia in Mice.

Purpose: To determine the roles of dopamine D2 receptors (D2Rs) and dopamine D1 receptors (D1Rs) in the inhibition of form-deprivation myopia (FDM) by the nonselective dopamine agonist apomorphine (APO) in D2R-knockout (D2R-KO) and D1R-KO mice.

Methods: Retinal layer thicknesses and electroretinograms (ERGs) were analyzed in KO mice and in D2R and D1R antagonist-treated mice. D2R-KO or D1R-KO mice and wild-type (WT) littermates were subjected to form deprivation during postnatal weeks 5 to 8.

Cause and Effect Relationship between Changes in Scleral Matrix Metallopeptidase-2 Expression and Myopia Development in Mice.

Myopia is a serious sight-compromising condition in which decreases in scleral biomechanical strength are associated with protease up-regulation resulting in thinning of its collagenous framework and changes in the extracellular matrix composition. Matrix metallopeptidase (MMP)-2 is one of the known proteases mediating these alterations. To determine whether MMP-2 up-regulation precedes myopia development, the direct effects of gain and loss in Mmp2 gene function were evaluated on refractive development and form deprivation myopia in mice.

Therapeutic Angiogenesis of Chinese Herbal Medicines in Ischemic Heart Disease: A Review.

Ischemic heart disease (IHD) is one of the primary causes of death around the world. Therapeutic angiogenesis is a promising innovative approach for treating IHD, improving cardiac function by promoting blood perfusion to the ischemic myocardium. This treatment is especially important for targeting patients that are unable to undergo angioplasty or bypass surgery.

Prospective Study on Ex-PRESS Implantation Combined with Phacoemulsification in Primary Angle-Closure Glaucoma Coexisting Cataract: 3-Year Results.

Purpose: To evaluate the feasibility, efficacy, and safety of Ex-PRESS implantation combined with phacoemulsification surgery in primary angle-closure glaucoma (PACG) with cataract.

Materials And Methods: This is a prospective, nonrandomized study. A total of 34 eyes of 34 subjects were enrolled.

Continuous-light versus pulsed-light accelerated corneal crosslinking with ultraviolet-A and riboflavin.

Purpose: To determine whether the pulsed-light ultraviolet-A (UVA) accelerated corneal crosslinking (CXL) procedure is more efficacious and selective than its continuous-light counterpart in rabbits.

Setting: School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.

Design: Experimental study.

Antioxidant effects and mechanism of silymarin in oxidative stress induced cardiovascular diseases.

Cardiovascular diseases (CVDs) are considered as the major reason for mortality and morbidity worldwide. Substantial evidence suggests that increased oxidative stress plays a significant role in the pathogenesis of CVDs, including atherosclerosis, hypertension, vascular endothelial dysfunction and ischemic heart disease. Cellular oxidative stress results in the release of toxic free radicals by endothelial cells and vascular smooth muscle cells that interact with cell components such as protein, DNA or lipid resulting in cardiovascular pathology.