Impact of Gene Annotation on RNA-seq Data Analysis

RNA-seq has become increasingly popular in transcriptome profiling. One of the major challenges in RNA-seq data analysis is the accurate mapping of junction reads to their genomic origins. To detect splicing sites in short reads, many RNA-seq aligners use reference transcriptome to inform placement of junction reads. However, no systematic evaluation has been performed to assess or quantify the benefits of incorporating reference transcriptome in mapping RNA-seq reads. Meanwhile, there exist multiple human genome annotation databases, including RefGene (RefSeq Gene), Ensembl, and the UCSC annotation database. The impact of the choice of an annotation on estimating gene expression remains insufficiently investigated

Regulation of Osteoclastogenesis and Bone Resorption by miRNAs

Osteoclasts are specialized bone-resorbing cells that contribute to physiological bone development and remodeling in bone metabolism throughout life. Abnormal production and activation of osteoclasts lead to excessive bone resorption in pathological conditions, such as in osteoporosis and in arthritic diseases with bone destruction. Recent epigenetic studies have shed novel insight into the dogma of the regulation of gene expression. microRNAs belong to a category of epigenetic regulators, which post-transcriptionally regulate and silence target gene expression, and thereby control a variety of biological events. In this review, we discuss miRNA biogenesis, the mechanisms utilized by miRNAs, several miRNAs that play important roles in osteoclast differentiation, function, survival and osteoblast-to-osteoclast communication, and their translational potential and challenges in bone biology and skeletal diseases

Cloud Computing for Next-Generation Sequencing Data Analysis

High-throughput next-generation sequencing (NGS) technologies have evolved rapidly and are reshaping the scope of genomics research. The substantial decrease in the cost of NGS techniques in the past decade has led to its rapid adoption in biological research and drug development. Genomics studies of large populations are producing a huge amount of data, giving rise to computational issues around the storage, transfer, and analysis of the data. Fortunately, cloud computing has recently emerged as a viable option to quickly and easily acquire the computational resources for large-scale NGS data analyses. Some cloud-based applications and resources have been developed specifically to address the computational challenges of working with very large volumes of data generated by NGS technology. In this chapter, we will review some cloud-based systems and solutions for NGS data analysis, discuss the practical hurdles and limitations in cloud computing, including data transfer and security, and share the lessons we learned from the implementation of Rainbow, a cloud-based tool for large-scale genome sequencing data analysis

Attribute-based concurrent signatures

This paper introduces the notion of attribute-based concurrent signatures. This primitive can be considered as an interesting extension of concurrent signatures in the attribute-based setting. It allows two parties fairly exchange their signatures only if each of them has convinced the opposite party that he/she possesses certain attributes satisfying a given signing policy. Due to this new feature, this primitive can find useful applications in online contract signing, electronic transactions and so on. We formalize this notion and present a con-struction which is secure in the random oracle model under the Strong Dif-fie-Hellman assumption and the eXternal Diffie-Hellman assumption

Median mandibular flexure—the unique physiological phenomenon of the mandible and its clinical significance in implant restoration

Mandibular flexure, characterized by unique biomechanical behaviors such as elastic bending and torsion under functional loading, has emerged as a crucial factor in oral clinical diagnosis and treatment. This paper presents a comprehensive review of the current research status on mandibular flexure, drawing insights from relevant studies retrieved from the PubMed database (www.ncbi.nlm.nih.gov/pubmed), including research conclusions, literature reviews, case reports, and authoritative reference books. This paper thoroughly explores the physiological mechanisms underlying mandibular flexure, discussing different concurrent deformation types and the essential factors influencing this process. Moreover, it explores the profound implications of mandibular flexure on clinical aspects such as bone absorption around dental implants, the precision of prosthesis fabrication, and the selection and design of superstructure materials. Based on the empirical findings, this review provides crucial clinical recommendations. Specifically, it is recommended to exert precise control over the patients mouth opening during impression-taking. Those with a high elastic modulus or bone-tissue-like properties should be prioritized when selecting superstructure materials. Moreover, this review underscores the significance of customizing framework design to accommodate individual variations in facial morphology and occlusal habits. Future research endeavors in this field have the potential to advance clinical diagnosis and treatment approaches, providing opportunities for improvement

Bioinformatics for RNA‐Seq Data Analysis

While RNA sequencing (RNA‐seq) has become increasingly popular for transcriptome profiling, the analysis of the massive amount of data generated by large‐scale RNA‐seq still remains a challenge. RNA‐seq data analyses typically consist of (1) accurate mapping of millions of short sequencing reads to a reference genome, including the identification of splicing events; (2) quantifying expression levels of genes, transcripts, and exons; (3) differential analysis of gene expression among different biological conditions; and (4) biological interpretation of differentially expressed genes. Despite the fact that multiple algorithms pertinent to basic analyses have been developed, there are still a variety of unresolved questions. In this chapter, we review the main tools and algorithms currently available for RNA‐seq data analyses, and our goal is to help RNA‐seq data analysts to make an informed choice of tools in practical RNA‐seq data analysis. In the meantime, RNA‐seq is evolving rapidly, and newer sequencing technologies are briefly introduced, including stranded RNA‐seq, targeted RNA‐seq, and single‐cell RNA‐seq

Bone Protection by Inhibition of MicroRNA-182

Targeting microRNAs recently shows significant therapeutic promise; however, such progress is underdeveloped in treatment of skeletal diseases with osteolysis, such as osteoporosis and rheumatoid arthritis (RA). Here, we identified miR-182 as a key osteoclastogenic regulator in bone homeostasis and diseases. Myeloid-specific deletion of miR-182 protects mice against excessive osteoclastogenesis and bone resorption in disease models of ovariectomy-induced osteoporosis and inflammatory arthritis. Pharmacological treatment of these diseases with miR-182 inhibitors completely suppresses pathologic bone erosion. Mechanistically, we identify protein kinase double-stranded RNA-dependent (PKR) as a new and essential miR-182 target that is a novel inhibitor of osteoclastogenesis via regulation of the endogenous interferon (IFN)-β-mediated autocrine feedback loop. The expression levels of miR-182, PKR, and IFN-β are altered in RA and are significantly correlated with the osteoclastogenic capacity of RA monocytes. Our findings reveal a previously unrecognized regulatory network mediated by miR-182-PKR-IFN-β axis in osteoclastogenesis, and highlight the therapeutic implications of miR-182 inhibition in osteoprotection