ECgene: genome annotation for alternative splicing

ECgene provides annotation for gene structure, function and expression, taking alternative splicing events into consideration. The gene-modeling algorithm combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. The website provides several viewers and applications that have many unique features useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. We also provide two unique ways of analyzing gene expression. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publically. Furthermore, the cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns. It should be noted that the ECgene website provides annotation for the whole transcriptome, not just the alternatively spliced genes. Currently, ECgene supports the human, mouse and rat genomes. The ECgene suite of tools and programs is available at http://genome.ewha.ac.kr/ECgene/

ECgene: an alternative splicing database update

ECgene () was developed to provide functional annotation for alternatively spliced genes. The applications encompass the genome-based transcript modeling for alternative splicing (AS), domain analysis with Gene Ontology (GO) annotation and expression analysis based on the EST and SAGE data. We have expanded the ECgene's AS modeling and EST clustering to nine organisms for which sufficient EST data are available in the GenBank. As for the human genome, we have also introduced several new applications to analyze differential expression. ECprofiler is an ontology-based candidate gene search system that allows users to select an arbitrary combination of gene expression pattern and GO functional categories. DEGEST is a database of differentially expressed genes and isoforms based on the EST information. Importantly, gene expression is analyzed at three distinctive levels—gene, isoform and exon levels. The user interfaces for functional and expression analyses have been substantially improved. ASviewer is a dedicated java application that visualizes the transcript structure and functional features of alternatively spliced variants. The SAGE part of the expression module provides many additional features including SNP, differential expression and alternative tag positions

ADAS-viewer: web-based application for integrative analysis of multi-omics data in Alzheimer’s disease

Alzheimer’s disease (AD) is a neurodegenerative disorder and is represented by complicated biological mechanisms and complexity of brain tissue. Our understanding of the complicated molecular architecture that contributes to AD progression benefits from performing comprehensive and systemic investigations with multi-layered molecular and biological data from different brain regions. Since recently different independent studies generated various omics data in different brain regions of AD patients, multi-omics data integration can be a useful resource for better comprehensive understanding of AD. Here we present a web platform, ADAS-viewer, that provides researchers with the ability to comprehensively investigate and visualize multi-omics data from multiple brain regions of AD patients. ADAS-viewer offers means to identify functional changes in transcript and exon expression (i.e., alternative splicing) along with associated genetic or epigenetic regulatory effects. Specifically, it integrates genomic, transcriptomic, methylation, and miRNA data collected from seven different brain regions (cerebellum, temporal cortex, dorsolateral prefrontal cortex, frontal pole, inferior frontal gyrus, parahippocampal gyrus, and superior temporal gyrus) across three independent cohort datasets. ADAS-viewer is particularly useful as a web-based application for analyzing and visualizing multi-omics data across multiple brain regions at both transcript and exon level, allowing the identification of candidate biomarkers of Alzheimer’s disease

A standardized pathology report for gastric cancer: 2nd edition

The first edition of ‘A Standardized Pathology Report for Gastric Cancer’ was initiated by the Gastrointestinal Pathology Study Group of the Korean Society of Pathologists and published 17 years ago. Since then, significant advances have been made in the pathologic diagnosis, molecular genetics, and management of gastric cancer (GC). To reflect those changes, a committee for publishing a second edition of the report was formed within the Gastrointestinal Pathology Study Group of the Korean Society of Pathologists. This second edition consists of two parts: standard data elements and conditional data elements. The standard data elements contain the basic pathologic findings and items necessary to predict the prognosis of GC patients, and they are adequate for routine surgical pathology service. Other diagnostic and prognostic factors relevant to adjuvant therapy, including molecular biomarkers, are classified as conditional data elements to allow each pathologist to selectively choose items appropriate to the environment in their institution. We trust that the standardized pathology report will be helpful for GC diagnosis and facilitate large-scale multidisciplinary collaborative studies

A Study on the Plan of Activation of Library by Utilizing the Virtual Reality and Augmented Reality

In this study, in line with the era of the fourth industrial revolution, general concepts, technologies, trends, and examples of virtual reality and augmented reality were examined, and based on this, a plan that could be applied to libraries in the future was proposed. As a result of the study, first, it is necessary to construct a smart space as an experiential play space that can satisfy cultural desires transcending time and space by providing immersive contents using 4th technology such as VR and AR. Second, it is necessary to expand experiential cultural support services through VR, AR and MR. Third, to develop educational contents based on augmented reality technology. In order to apply and activate virtual reality and augmented reality in libraries in the future, based on a survey of librarians and users of public libraries, a survey on the application status, satisfaction, and demand of current public libraries should be conducted

A Study on Perception of Librarian's Job Prospects

The purpose of this study is to investigate awareness of librarian’s job prospects, and to do this a survey was conducted with 502 college students in 14 Departments of Library and Information Science around Korea and 753 librarians in libraries and related agencies. The study results are as follows. First, satisfaction with educational curriculum was higher in students than librarians. Second, both students and librarians regarded workplace based practical training as employment requirements and also evaluated certifications and academic performance as important requirements. Third, both groups asked that information on employment rates be available in a timely manner, and perceived that the librarian’s job prospects were not bright. Therefore, in order to improve employment of librarians, it will be necessary to establish a job information system, reorganize the current educational curriculum into a practice-oriented curriculum, and introduce the national curriculum statements (NCS)-based curriculum

Medium Effect on the α-Effect for Nucleophilic Substitution Reactions of p-Nitrophenyl Acetate with Benzohydroxamates and m-Chlorophenoxide in DMSO-H2O Mixtures as Contrasts with MeCN-H2O Mixtures: Comparing Two Very Different Polar Aprotic Solvent Components

A kinetic study is reported on nucleophilic substitution reactions of p-nitrophenyl acetate (1a) with three α-effect nucleophiles, benzohydroxamate (BHA‒), p-methylbenzohydroxamate (MBHA‒) and p-methyl-N-methylbenzohydroxamate (M2BHA‒), and a reference nucleophile, m-chlorophenoxide (m-ClPhO‒) in DMSO-H2O mixtures of varying compositions at 25.0 ± 0.1 oC. Second-order rate constants for the reactions with BHA‒ and MBHA‒ decrease upon addition of DMSO to the reaction medium up to 60 mol % DMSO and then increase thereafter only a little. In contrast, M2BHA‒ and m-ClPhO‒ become much more reactive as the DMSO content in the medium increases. Such contrasting medium effects on reactivity are consistent with the report that hydroxamic acids behave as OH acids in H2O but as NH acids in dipolar aprotic solvents (e.g., DMSO and MeCN). It has been concluded that BHA‒ and MBHA‒ form an equilibrium of a reactive form I with less reactive species II in DMSO-H2O mixtures and the position of the equilibrium is dependent on solvent compositions. BHA‒ and MBHA‒ exhibit the α-effect in H2O but not in in 90 mol % DMSO. In contrast, the α-effect yielded by M2BHA‒ increases steeply up to 70 mol % DMSO and then levels off thereafter.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Interleukin-31, Interleukin-31RA, and OSMR Expression Levels in Post-burn Hypertrophic Scars

Background Although several studies have shown the role of interleukin-31 (IL-31) and its receptors in inducing pruritus in certain skin disorders, knowledge of its role in post-burn hypertrophic scars is insufficient. Therefore, the histopathological expression levels of IL-31, IL-31 receptor alpha (IL-31RA), and oncostatin M receptor (OSMR) in post-burn hypertrophic scar tissues were investigated and compared with normal tissue expression levels. Methods Samples of hypertrophic scar tissue were obtained from 20 burn patients through punch biopsy. Normal samples were obtained from areas adjacent to the burn injury site of the same patients. Samples were placed in 10% neutral buffered formalin, embedded in paraplast, and processed into serial 5-μm sections. Immunohistochemistry results were semi-quantitatively evaluated for IL-31, IL-31RA, and OSMR. By hematoxylin and eosin staining, epidermal and dermal thickness were assessed with a microscope and digital camera. Intensities were rated on a scale of 1 to 4. Results Percentages for IL-31, IL-31RA, and OSMR in the epidermal basal layer cell cytoplasm were significantly greater in the burn scar tissue compared to normal skin, as well as the dermal and epidermal thickness (p < .05). There was a significant difference in IL-31 epidermal basal layer intensity in burn scar tissue compared to normal skin (p < .05). Besides the OSMR basal layer intensity, IL-31 and IL-31RA intensities between the burn scar and normal tissues were not significant. However, correlations were significant, indicating that the greater the infiltration percentage, the higher the intensity (p < .05). Conclusions IL-31, IL-31RA, and OSMR expression levels are increased in hypertrophic scars compared with normal tissue