A wave of new technologies has created opportunities for the cost-effective generation of high-throughput profiles of biological systems, foreshadowing a "data-driven science" era. The large variety of data available from biological research is also a rich resource that can be used for innovative endeavors. However, we are facing considerable challenges in big data deposition, integration, and translation due to the complexity of biological data and its production at unprecedented exponential rates. To address these problems, in 2020, the Korean government officially announced a national strategy to collect and manage the biological data produced through national R&D fund allocations and provide the collected data to researchers. To this end, the Korea Bioinformation Center (KOBIC) developed a new biological data repository, the Korea BioData Station (K-BDS), for sharing data from individual researchers and research programs to create a data-driven biological study environment. The K-BDS is dedicated to providing free open access to a suite of featured data resources in support of worldwide activities in both academia and industry.

The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent years. Leveraging these big data requires researchers to use large-scale computational resources and analysis pipelines. A promising solution for addressing this computational challenge is cloud computing, where CPUs, memory, storage, and programs are accessible in the form of virtual machines. Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets. Bio-Express is loaded with predefined multi-omics data analysis pipelines, which are divided into genome, transcriptome, epigenome, and metagenome pipelines. Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating downstream analysis of genome data. Bio-Express web service is freely available at https://www.bioexpress.re.kr/.

The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent years. Leveraging these big data requires researchers to use large-scale computational resources and analysis pipelines. A promising solution for addressing this computational challenge is cloud computing, where CPUs, memory, storage, and programs are accessible in the form of virtual machines. Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets. Bio-Express is loaded with predefined multi-omics data analysis pipelines, which are divided into genome, transcriptome, epigenome, and metagenome pipelines. Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating downstream analysis of genome data. Bio-Express web service is freely available at https://www.bioexpress.re.kr/.

OBJECTIVES: Since Korea is geographically close to China (the origin site for Asian sand dust [ASD]) the health influence of ASD event will be still greater in Korea. We aimed to evaluate the effect of PM₁₀ (particulate matter with aerodynamic diameter <10 μm, below 150 μg/m³) on the clinical course of allergic rhinitis (AR). METHODS: We enrolled 47 healthy volunteers (group A) and 108 AR patients sensitized to house dust mites (group B). For 120 consecutive days (from February 1st to May 30th, 2012), all subjects reported their daily nasal symptoms and performed 2 peak flowmeter readings to measure peak nasal inspiratory flow (PNIF). We evaluated the correlation between the daily concentration of PM₁₀, symptoms, and PNIF of patients. We also investigated changes in symptoms and PNIF 2 days before and after ‘dusty’ days (daily concentration of PM₁₀>100 μg/m³) RESULTS: There was no significant difference between group A and B in nasal symptoms and PNIF during the 120-day period. Changes in nasal symptoms and PNIF were not statistically significant before or after a PM₁₀ concentration rise above 100 μg/m³. CONCLUSION: Low concentration PM10 does not have significant effect on nasal symptoms and PNIF in AR patients.
Asian Continental Ancestry Group ; China ; Dust ; Flowmeters ; Healthy Volunteers ; Humans ; Korea ; Mites ; Particulate Matter ; Pyroglyphidae ; Reading ; Rhinitis, Allergic*

Immunoglobulin G4 (IgG4)-related disease is a newly recognized condition characterized by fibroinflammatory lesions with dense lymphoplasmacytic infiltration, storiform-type fibrosis and obliterative phlebitis. The pathogenesis is not fully understood but multiple immune-mediated mechanisms are believed to contribute. This rare disease can involve various organs and pleural involvement is even rarer. We report a case of IgG4-related disease involving pleura. A 66-year-old man presented with cough and sputum production for a week. Chest radiography revealed consolidation and a pleural mass at right hemithorax. Treatment with antibiotics resolved the consolidation and respiratory symptoms disappeared, but the pleural mass was unchanged. Video-assisted thoracoscopic surgery was performed. Histopathology revealed dense lymphoplasmacytic infiltration and storiform fibrosis with numerous IgG4-bearing plasma cells. The serum IgG4 level was also elevated. Further examination ruled out the involvement of any other organ. The patient was discharged without further treatment and there is no evidence of recurrence to date.
Aged ; Anti-Bacterial Agents ; Autoimmune Diseases ; Cough ; Fibrosis ; Humans ; Immunoglobulin G ; Immunoglobulins* ; Phlebitis ; Plasma Cells ; Pleura ; Pleural Neoplasms ; Radiography ; Rare Diseases ; Recurrence ; Sputum ; Thoracic Surgery, Video-Assisted ; Thorax

BACKGROUND/AIMS: This study assessed the efficacy of a rifaximin plus levofloxacin-based rescue regimen in patients that had failed both triple and quadruple standard regimens for the eradication of Helicobacter pylori. METHODS: We treated patients for H. pylori between August 2009 and April 2011. The triple regimen consisted of combined treatment with amoxicillin, clarithromycin, and pantoprazole for 1 week. For failed cases, a quadruple regimen of tetracycline, metronidazole, bismuth dicitrate, and lansoprazole for 1 week was administered. The rescue regimen for persistently refractory cases was rifaximin 200 mg t.i.d., levofloxacin 500 mg q.d., and lansoprazole 15 mg b.i.d. for 1 week. RESULTS: In total, 482 patients were enrolled in this study. The eradication rates associated with the first and second regimens were 58% and 60%, respectively. Forty-seven out of 58 patients who failed with the second-line regimen received rifaximin plus levofloxacin-based third-line therapy. The eradication rate for the third regimen was 65%. The cumulative eradication rates were 58%, 85%, and 96% for each regimen, respectively. CONCLUSIONS: A rifaximin plus levofloxacin-based regimen could be an alternative rescue therapy in patients with resistance to both triple and quadruple regimens for the eradication of H. pylori.
2-Pyridinylmethylsulfinylbenzimidazoles ; Amoxicillin ; Bismuth ; Clarithromycin ; Helicobacter ; Helicobacter pylori ; Humans ; Metronidazole ; Ofloxacin ; Rifamycins ; Tetracycline

We report a rare case of a massive fatal embolism that occurred in the middle of endoscopic retrograde cholangiopancreatography (ERCP) and retrospectively examine the significant causes of the event. The patient was a 50-year old female with an uncertain history of previous abdominal surgery for multiple biliary stones 20 years prior. The patient presented with acute right upper quadrant pain. An abdominal computed tomographic (CT) scan revealed the presence of multiple stones in the common bile duct (CBD) and intra-hepatic duct (IHD) with biliary obstruction, multifocal liver abscesses, and air-biliarygram. Emergency ERCP showed a wide and straight opening of choledochoduodenostomy, which may have been created during a previous surgery, and multiple filling defects in the CBD. With the use of a forward endoscope, mud stones were extracted through the opening of the choledochoduodenostomy. Cardiac arrest suddenly developed during the procedure, and despite immediate resuscitation, the patient died due to a massive systemic air embolism. We reviewed previously reported fatal cases and accessed factors facilitating air embolisms in this case.
Cholangiopancreatography, Endoscopic Retrograde/*methods ; Choledochostomy/*methods ; Common Bile Duct/radiography ; Embolism, Air/*complications ; Fatal Outcome ; Female ; Humans ; Liver Abscess/pathology ; Middle Aged ; Tomography, X-Ray Computed

OBJECTIVES: We aimed to provide standard data of the individual tests in 7MS that could generalized for Korean elderly according to age and education. We also evaluated diagnostic efficacy of each test in 7MS. METHODS: Data on demographic characteristics of 311 normals were gathered for comparison. We also assessed two differences between normal and dementia group in individual tests of 7MS. RESULTS: All individual tests of 7MS showed significant differences in sex, age, and education, except for ECR. But there were no significant differences in sex controlling age and education. As a result of ROC curve, the ability of the ECR test to discriminate between AD and normal subject appeared superior. The scores of the individual tests of 7MS among CDR 0.5 and 1 group and normal group were compared. It was also found that the ECR test stands out among 7MS tests. CONCLUSION: The 7MS, particularly ECR, had the highest sensitivity and specificity for diagnosis of AD as well as early dementia. It suggests that the individual tests of 7MS are useful to predict early dementia, without using the complex logistic regression equation.
Aged ; Dementia ; Diagnosis ; Education ; Humans ; Logistic Models ; Mass Screening ; ROC Curve ; Sensitivity and Specificity

BACKGROUND: Non-erosive reflux disorder, which represents more than 60% of gastro-esophageal reflux disorders, lacks objective parameters for diagnosis. The purpose of this study was to evaluate the correlation between non-erosive minimal lesions at the lower esophagus and gastro-esophageal reflux disorder. METHODS: Patients were asked to answer a symptom questionnaire. The endoscopic findings were either graded by LA classification or recorded as non-erosive minimal lesions. Patients with minimal lesions were treated with rabeprazole or a placebo and responses were evaluated at weeks 1 and 4. RESULTS: In 8 centers, 3454 patients were screened. In patients with heartburn or acid regurgitation as the most bothersome symptom, 23.7% had endoscopy negative reflux disorder, 40.1% showed minimal lesions, and 36.2% had mucosal break esophagitis. Thirty-four percent of patients with minimal lesions and 39.1% of patients with LA 'grade A' mild esophagitis reported typical reflux symptoms as their main symptom. In patients with minimal lesions, medication with rabeprazole reduced symptoms significantly at weeks 1 and 4, but not with the placebo. CONCLUSION: Patients with non-erosive minimal esophageal lesions had similar reflux symptoms comparable to those with mild erosive reflux esophagitis, and reflux symptoms were improved with a short-term proton pump inhibitor. Thus, non-erosive minimal esophageal lesion constitutes a great part of gastro-esophageal reflux disorder.
2-Pyridinylmethylsulfinylbenzimidazoles ; Adult ; Aged ; Aged, 80 and over ; Anti-Ulcer Agents/*therapeutic use ; Benzimidazoles/*therapeutic use ; Enzyme Inhibitors/*therapeutic use ; Esophageal Diseases/*pathology ; Female ; Follow-Up Studies ; Gastroesophageal Reflux/drug therapy/epidemiology/*pathology ; Humans ; Korea/epidemiology ; Male ; Middle Aged ; Omeprazole/*analogs & derivatives/therapeutic use ; Prospective Studies ; Proton-Translocating ATPases/*antagonists & inhibitors ; Treatment Outcome

Diabetic gastroparesis is a pathologic condition of delayed gastric emptying with gastrointestinal symptoms such as nausea, early satiety and vomiting in the absence of mechanical obstruction in patients with diabetes mellitus. We report a case of diabetic gastroparesis who had diabetes mellitus for 13 years and suffered from nausea and vomiting with marked gastric dilatation of acute onset. Blood glucose level of the patient was very high and any mechanical obstruction was not found by gastroduodenal endoscopy, hypotonic duodenography, celiac angiography, electrogastrography and CT scan. Acute gastric dilatation was resolved with conservative treatment of gastric drainage, glucose control and hydration. Gastrointestinal symptoms of nausea and vomiting improved and diet was well tolerated thereafter.
Angiography ; Blood Glucose ; Diabetes Mellitus ; Diet ; Drainage ; Endoscopy ; Gastric Dilatation* ; Gastric Emptying ; Gastroparesis* ; Glucose ; Humans ; Nausea ; Tomography, X-Ray Computed ; Vomiting