Publications by authors named "Jin-Dong Kim"

73 Publications

Editor's introduction to the special section on the 7th Biomedical Linked Annotation Hackathon (BLAH7).

Genomics Inform 2021 Sep 30;19(3):e20. Epub 2021 Sep 30.

Center for Convergence Research of Advanced Technologies, Ewha Womans University, Seoul 03760, Korea.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5808/gi.19.3.e1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510870PMC
September 2021

A Cross-Sectional Study of the Effects of Physical Activity and Nutrient Intakes on Blood Glucose Control Rates in Middle-Aged and Elderly Diabetes Patients: Korean National Health and Nutrition Examination Survey 2015-2017.

Inquiry 2021 Jan-Dec;58:469580211035727

A&P Lab, Inc., Research Institute of Consilience, Seoul, Republic of Korea.

This study aimed to investigate factors affecting blood glucose control among middle-aged and older diabetic patients taking medications or receiving insulin therapy. In 2015-2017 data obtained from the Korean National Health and Nutrition Examination Survey (KNHANES), 1257 patients with diabetes were divided into a controlled group and an uncontrolled group based on blood glucose levels (cutoff ≥126 mg/dL). After adjusting for confounding factors, the BMI, total cholesterol level, and triglycerides level of the uncontrolled group were significantly higher than the controlled group. The total amount of moderate-intensity activity in controlled patients was significantly higher than that of the controlled group. Total energy, fat, saturated fatty acids, and cholesterol intakes were found to be significantly higher in the uncontrolled than controlled group. Intakes of calcium, phosphorus, potassium, riboflavin, niacin, and vitamin C were significantly lower in the uncontrolled than controlled group. Adequate nutrition intake and physical activity of patients undergoing diabetes therapy are required for effective blood glucose management for both diabetic drug and insulin therapies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1177/00469580211035727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8461118PMC
October 2021

Bridging heterogeneous mutation data to enhance disease gene discovery.

Brief Bioinform 2021 09;22(5)

Hubei Key Lab of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei Province, P.R. China.

Bridging heterogeneous mutation data fills in the gap between various data categories and propels discovery of disease-related genes. It is known that genome-wide association study (GWAS) infers significant mutation associations that link genotype and phenotype. However, due to the differences of size and quality between GWAS studies, not all de facto vital variations are able to pass the multiple testing. In the meantime, mutation events widely reported in literature unveil typical functional biological process, including mutation types like gain of function and loss of function. To bring together the heterogeneous mutation data, we propose a 'Gene-Disease Association prediction by Mutation Data Bridging (GDAMDB)' pipeline with a statistic generative model. The model learns the distribution parameters of mutation associations and mutation types and recovers false-negative GWAS mutations that fail to pass significant test but represent supportive evidences of functional biological process in literature. Eventually, we applied GDAMDB in Alzheimer's disease (AD) and predicted 79 AD-associated genes. Besides, 12 of them from the original GWAS, 60 of them are supported to be AD-related by other GWAS or literature report, and rest of them are newly predicted genes. Our model is capable of enhancing the GWAS-based gene association discovery by well combining text mining results. The positive result indicates that bridging the heterogeneous mutation data is contributory for the novel disease-related gene discovery.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/bib/bbab079DOI Listing
September 2021

An empirical evaluation of electronic annotation tools for Twitter data.

Genomics Inform 2020 Jun 17;18(2):e24. Epub 2020 Jun 17.

Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Despite a growing number of natural language processing shared-tasks dedicated to the use of Twitter data, there is currently no ad-hoc annotation tool for the purpose. During the 6th edition of BLAH, after a short review of 19 generic annotation tools, we adapted GATE and TextAE for annotating Twitter timelines. Although none of the tools reviewed allow the annotation of all information inherent of Twitter timelines, a few may be suitable provided the willingness by annotators to compromise on some functionality.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5808/GI.2020.18.2.e24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7362942PMC
June 2020

Extending TextAE for annotation of non-contiguous entities.

Genomics Inform 2020 Jun 15;18(2):e15. Epub 2020 Jun 15.

Database Center for Life Science, Research Organization of Information and Systems, Kashiwa 277-0871, Japan.

Named entity recognition tools are used to identify mentions of biomedical entities in free text and are essential components of high-quality information retrieval and extraction systems. Without good entity recognition, methods will mislabel searched text and will miss important information or identify spurious text that will frustrate users. Most tools do not capture non-contiguous entities which are separate spans of text that together refer to an entity, e.g., the entity "type 1 diabetes" in the phrase "type 1 and type 2 diabetes." This type is commonly found in biomedical texts, especially in lists, where multiple biomedical entities are named in shortened form to avoid repeating words. Most text annotation systems, that enable users to view and edit entity annotations, do not support non-contiguous entities. Therefore, experts cannot even visualize non-contiguous entities, let alone annotate them to build valuable datasets for machine learning methods. To combat this problem and as part of the BLAH6 hackathon, we extended the TextAE platform to allow visualization and annotation of non-contiguous entities. This enables users to add new subspans to existing entities by selecting additional text. We integrate this new functionality with TextAE's existing editing functionality to allow easy changes to entity annotation and editing of relation annotations involving non-contiguous entities, with importing and exporting to the PubAnnotation format. Finally, we roughly quantify the problem across the entire accessible biomedical literature to highlight that there are a substantial number of non-contiguous entities that appear in lists that would be missed by most text mining systems.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5808/GI.2020.18.2.e15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7362949PMC
June 2020

Editor's introduction to the special issue of the 6th Biomedical Linked Annotation Hackathon (BLAH6).

Genomics Inform 2020 Jun 24;18(2):e12. Epub 2020 Jun 24.

Center for Convergence Research of Advanced Technologies, Ewha Womans University, Seoul 03760, Korea.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5808/GI.2020.18.2.e12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7362940PMC
June 2020

BioHackathon 2015: Semantics of data for life sciences and reproducible research.

F1000Res 2020 24;9:136. Epub 2020 Feb 24.

St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, Australia.

We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.12688/f1000research.18236.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7141167PMC
February 2021

Towards cross-platform interoperability for machine-assisted text annotation.

Genomics Inform 2019 Jun 26;17(2):e19. Epub 2019 Jun 26.

Vassar College, Poughkeepsie, NY 12604-0520, USA.

In this paper we investigate cross-platform interoperability for natural language processing (NLP) and, in particular, annotation of textual resources, with an eye toward identifying the design elements of annotation models and processes that are particularly problematic for, or amenable to, enabling seamless communication across different platforms. The study is conducted in the context of a specific annotation methodology, namely machine-assisted interactive annotation (also known as human-in-the-loop annotation). This methodology requires the ability to freely combine resources from different document repositories, access a wide array of NLP tools that automatically annotate corpora for various linguistic phenomena, and use a sophisticated annotation editor that enables interactive manual annotation coupled with on-the-fly machine learning. We consider three independently developed platforms, each of which utilizes a different model for representing annotations over text, and each of which performs a different role in the process.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5808/GI.2019.17.2.e19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6808624PMC
June 2019

Introduction to BLAH5 special issue: recent progress on interoperability of biomedical text mining.

Genomics Inform 2019 Jun 27;17(2):e12. Epub 2019 Jun 27.

Institute of Computational Linguistics, University of Zurich, Zurich CH-8050, Switzerland.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5808/GI.2019.17.2.e12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6808629PMC
June 2019

GOF/LOF knowledge inference with tensor decomposition in support of high order link discovery for gene, mutation and disease.

Math Biosci Eng 2019 02;16(3):1376-1391

College of Informatics, Huazhong Agricultural University, 430070, Wuhan, China.

For discovery of new usage of drugs, the function type of their target genes plays an important role, and the hypothesis of "Antagonist-GOF" and "Agonist-LOF" has laid a solid foundation for supporting drug repurposing. In this research, an active gene annotation corpus was used as training data to predict the gain-of-function or loss-of-function or unknown character of each human gene after variation events. Unlike the design of(entity, predicate, entity) triples in a traditional three way tensor, a four way and a five way tensor, GMFD-/GMAFD-tensor, were designed to represent higher order links among or among part of these entities: genes(G), mutations(M), functions(F), diseases( D) and annotation labels(A). A tensor decomposition algorithm, CP decomposition, was applied to the higher order tensor and to unveil the correlation among entities. Meanwhile, a state-of-the-art baseline tensor decomposition algorithm, RESCAL, was carried on the three way tensor as a comparing method. The result showed that CP decomposition on higher order tensor performed better than RESCAL on traditional three way tensor in recovering masked data and making predictions. In addition, The four way tensor was proved to be the best format for our issue. At the end, a case study reproducing two disease-gene-drug links(Myelodysplatic Syndromes-IL2RA-Aldesleukin, Lymphoma- IL2RA-Aldesleukin) presented the feasibility of our prediction model for drug repurposing.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3934/mbe.2019067DOI Listing
February 2019

Open Agile text mining for bioinformatics: the PubAnnotation ecosystem.

Bioinformatics 2019 11;35(21):4372-4380

Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.

Motivation: Most currently available text mining tools share two characteristics that make them less than optimal for use by biomedical researchers: they require extensive specialist skills in natural language processing and they were built on the assumption that they should optimize global performance metrics on representative datasets. This is a problem because most end-users are not natural language processing specialists and because biomedical researchers often care less about global metrics like F-measure or representative datasets than they do about more granular metrics such as precision and recall on their own specialized datasets. Thus, there are fundamental mismatches between the assumptions of much text mining work and the preferences of potential end-users.

Results: This article introduces the concept of Agile text mining, and presents the PubAnnotation ecosystem as an example implementation. The system approaches the problems from two perspectives: it allows the reformulation of text mining by biomedical researchers from the task of assembling a complete system to the task of retrieving warehoused annotations, and it makes it possible to do very targeted customization of the pre-existing system to address specific end-user requirements. Two use cases are presented: assisted curation of the GlycoEpitope database, and assessing coverage in the literature of pre-eclampsia-associated genes.

Availability And Implementation: The three tools that make up the ecosystem, PubAnnotation, PubDictionaries and TextAE are publicly available as web services, and also as open source projects. The dictionaries and the annotation datasets associated with the use cases are all publicly available through PubDictionaries and PubAnnotation, respectively.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btz227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821251PMC
November 2019

A Model to Predict 1-Month Risk of Transplant or Death in Hepatitis A-Related Acute Liver Failure.

Hepatology 2019 08 17;70(2):621-629. Epub 2019 Feb 17.

Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India.

Acute liver failure (ALF) caused by hepatitis A is a rare but fatal disease. Here, we developed a model to predict outcome in patients with ALF caused by hepatitis A. The derivation set consisted of 294 patients diagnosed with hepatitis A-related ALF (ALFA) from Korea, and a validation set of 56 patients from Japan, India, and United Kingdom. Using a multivariate proportional hazard model, a risk-prediction model (ALFA score) consisting of age, international normalized ratio, bilirubin, ammonia, creatinine, and hemoglobin levels acquired on the day of ALF diagnosis was developed. The ALFA score showed the highest discrimination in the prediction of liver transplant or death at 1 month (c-statistic, 0.87; 95% confidence interval [CI], 0.84-0.92) versus King's College criteria (KCC; c-statistic, 0.56; 95% CI, 0.53-0.59), U.S. Acute Liver Failure Study Group index specific for hepatitis A virus (HAV-ALFSG; c-statistic, 0.70; 95% CI, 0.65-0.76), the new ALFSG index (c-statistic, 0.79; 95% CI, 0.74-0.84), Model for End-Stage Liver Disease (MELD; c-statistic, 0.79; 95% CI, 0.74-0.84), and MELD including sodium (MELD-Na; c-statistic, 0.78; 95% CI, 0.73-0.84) in the derivation set (all P < 0.01). In the validation set, the performance of the ALFA score (c-statistic, 0.84; 95% CI, 0.74-0.94) was significantly better than that of KCC (c-statistic, 0.65; 95% CI, 0.52-0.79), MELD (c-statistic, 0.74; 95% CI, 0.61-0.87), and MELD-Na (c-statistic, 0.72; 95% CI, 0.58-0.85) (all P < 0.05), and better, but not statistically significant, than that of the HAV-ALFSG (c-statistic, 0.76; 95% CI, 0.61-0.90; P = 0.28) and new ALFSG indices (c-statistic, 0.79; 95% CI, 0.65-0.93; P = 0.41). The model was well-calibrated in both sets. Conclusion: Our disease-specific score provides refined prediction of outcome in patients with ALF caused by hepatitis A.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/hep.30262DOI Listing
August 2019

PubCaseFinder: A Case-Report-Based, Phenotype-Driven Differential-Diagnosis System for Rare Diseases.

Am J Hum Genet 2018 09 30;103(3):389-399. Epub 2018 Aug 30.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo-to, 113-0032, Japan.

Recently, to speed up the differential-diagnosis process based on symptoms and signs observed from an affected individual in the diagnosis of rare diseases, researchers have developed and implemented phenotype-driven differential-diagnosis systems. The performance of those systems relies on the quantity and quality of underlying databases of disease-phenotype associations (DPAs). Although such databases are often developed by manual curation, they inherently suffer from limited coverage. To address this problem, we propose a text-mining approach to increase the coverage of DPA databases and consequently improve the performance of differential-diagnosis systems. Our analysis showed that a text-mining approach using one million case reports obtained from PubMed could increase the coverage of manually curated DPAs in Orphanet by 125.6%. We also present PubCaseFinder (see Web Resources), a new phenotype-driven differential-diagnosis system in a freely available web application. By utilizing automatically extracted DPAs from case reports in addition to manually curated DPAs, PubCaseFinder improves the performance of automated differential diagnosis. Moreover, PubCaseFinder helps clinicians search for relevant case reports by using phenotype-based comparisons and confirm the results with detailed contextual information.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ajhg.2018.08.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6128307PMC
September 2018

Serum cystatin C level: An excellent predictor of mortality in patients with cirrhotic ascites.

J Gastroenterol Hepatol 2018 Apr 26;33(4):910-917. Epub 2018 Jan 26.

Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea.

Background And Aim: Although serum cystatin C level is considered a more accurate marker of renal function in patients with liver cirrhosis, its prognostic efficacy remains uncertain. This study aimed to evaluate the prognostic efficacy of serum cystatin C level in patients with cirrhotic ascites.

Methods: Patients with cirrhotic ascites from 15 hospitals were prospectively enrolled between September 2009 and March 2013. Cox regression analyses were performed to identify independent predictive factors of mortality and development of type 1 hepatorenal syndrome (HRS-1).

Results: In total, 350 patients were enrolled in this study. The mean age was 55.4 ± 10.8 years, and 267 patients (76.3%) were men. The leading cause of liver cirrhosis was alcoholic liver disease (64.3%), followed by chronic viral hepatitis (29.7%). Serum creatinine and cystatin C levels were 0.9 ± 0.4 mg/dL and 1.1 ± 0.5 mg/L, respectively. Multivariate analyses revealed that international normalized ratio and serum bilirubin, sodium, and cystatin C levels were independent predictors of mortality and international normalized ratio and serum sodium and cystatin C levels were independent predictors of the development of HRS-1. Serum creatinine level was not significantly associated with mortality and development of HRS-1 on multivariate analysis.

Conclusion: Serum cystatin C level was an independent predictor of mortality and development of HRS-1 in patients with cirrhotic ascites, while serum creatinine level was not. Predictive models based on serum cystatin C level instead of serum creatinine level would be more helpful in the assessment of the condition and prognosis of patients with cirrhotic ascites.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/jgh.13983DOI Listing
April 2018

Exploring biomedical ontology mappings with graph theory methods.

PeerJ 2017 2;5:e2990. Epub 2017 Mar 2.

Database Center for Life Science, Research Organization of Information and Systems , Tokyo , Japan.

Background: In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patterns in BioPortal, a comprehensive publicly available repository of live science ontologies.

Methods: We report an analysis of biomedical ontology mapping data over time. We apply graph theory methods such as Modularity Analysis and Betweenness Centrality to analyse data gathered at five different time points. We identify communities, i.e., sets of overlapping ontologies, and define similar and closest communities. We demonstrate evolution of identified communities over time and identify core ontologies of the closest communities. We use BioPortal project and category data to measure community coherence. We also validate identified communities with their mutual mentions in scientific literature.

Results: With comparing mapping data gathered at five different time points, we identified similar and closest communities of overlapping ontologies, and demonstrated evolution of communities over time. Results showed that anatomy and health ontologies tend to form more isolated communities compared to other categories. We also showed that communities contain all or the majority of ontologies being used in narrower projects. In addition, we identified major changes in mapping data after migration to BioPortal Version 4.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.2990DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5337086PMC
March 2017

Diagnostic performance of gadoxetic acid (Primovist)-enhanced MR imaging versus CT during hepatic arteriography and portography for small hypervascular hepatocellular carcinoma.

Medicine (Baltimore) 2016 Sep;95(39):e4903

aDivision of Gastroenterology and Hepatology, Department of Internal Medicine Sungbuk-ku bDepartment of Radiology cDivision of Gastroenterology and Hepatology, Department of Internal Medicine, Cheju Halla General Hospital, Jeju-do dDepartment of Surgery eDepartment of Biostatistics, Korea University College of Medicine, Seoul, Republic of Korea.

To compare the diagnostic performance of gadoxetic acid-enhanced magnetic resonance imaging (MRI) with that of computed tomography (CT) during hepatic arteriography and arterial portography (CT HA/AP) for detecting hepatocellular carcinoma (HCC) from small hypervascular nodules.This retrospective study included 38 patients with 131 hypervascular nodules (≤2 cm) who had underwent MRI and CT HA/AP within a 2-week interval. Two observers analyzed MRI while other 2 observers analyzed CT HA/AP. Thereafter, MRI observers reviewed the CT HA/AP and magnetic resonance (MR) images again using both modalities. HCC was diagnosed by pathologic or imaging studies according to American Association for the Study of Liver Diseases (AASLD) criteria. Alternative free-response receiver operating characteristic (ROC) analysis was performed on a lesion-by-lesion basis. Diagnostic accuracy (area under the ROC curve [Az]), sensitivity, specificity, and positive and negative predictive values were calculated.The pooled Az was significantly higher for the combined modalities (0.946) than for MRI alone (0.9, P = 0.004), and for MRI than for CT HA/AP alone (0.827, P = 0.0154). Subgroup analysis for HCC ≤1 cm showed the sensitivity of the combined modalities (79.4%) was significantly higher than for MRI (52.9%) and CT HA/AP alone (50%) (both, P < 0.005). The specificity of the combined modalities was not different from MRI alone (98.8% vs. 97.3%, P = 0.5), but was significantly higher than for CT HA/AP alone (98.8% vs. 92.5%, P = 0.022).Hypervascular HCCs >1 to 2 cm can be diagnosed sufficiently by MRI. The combined modalities increased the diagnostic accuracy of HCCs ≤1 cm, compared with MRI or CT HA/AP alone.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/MD.0000000000004903DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5265917PMC
September 2016

Extending the evaluation of Genia Event task toward knowledge base construction and comparison to Gene Regulation Ontology task.

BMC Bioinformatics 2015 13;16 Suppl 10:S3. Epub 2015 Jul 13.

Background: The third edition of the BioNLP Shared Task was held with the grand theme "knowledge base construction (KB)". The Genia Event (GE) task was re-designed and implemented in light of this theme. For its final report, the participating systems were evaluated from a perspective of annotation. To further explore the grand theme, we extended the evaluation from a perspective of KB construction. Also, the Gene Regulation Ontology (GRO) task was newly introduced in the third edition. The final evaluation of the participating systems resulted in relatively low performance. The reason was attributed to the large size and complex semantic representation of the ontology. To investigate potential benefits of resource exchange between the presumably similar tasks, we measured the overlap between the datasets of the two tasks, and tested whether the dataset for one task can be used to enhance performance on the other.

Results: We report an extended evaluation on all the participating systems in the GE task, incoporating a KB perspective. For the evaluation, the final submission of each participant was converted to RDF statements, and evaluated using 8 queries that were formulated in SPARQL. The results suggest that the evaluation may be concluded differently between the two different perspectives, annotation vs. KB. We also provide a comparison of the GE and GRO tasks by converting their datasets into each other's format. More than 90% of the GE data could be converted into the GRO task format, while only half of the GRO data could be mapped to the GE task format. The imbalance in conversion indicates that the GRO is a comprehensive extension of the GE task ontology. We further used the converted GRO data as additional training data for the GE task, which helped improve GE task participant system performance. However, the converted GE data did not help GRO task participants, due to overfitting and the ontology gap.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-16-S10-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511578PMC
February 2016

Total Colonic Decompression After Colonoscopy Decreases Postcolonoscopy Abdominal Pain: A Randomized Double-Blind Controlled Trial.

J Clin Gastroenterol 2016 Jan;50(1):59-65

*Department of Internal Medicine, Institute of Gastroenterology, Hallym University College of Medicine, Hallym University Dongtan Sacred Heart Hospital, Gyeonggi-do †Department of Internal Medicine, Digestive Disease Center, Cheju Halla General Hospital, Jeju, Korea.

Goals: The purpose of this study was to determine whether total colonic decompression after colonoscopy decreased postcolonoscopy abdominal pain.

Background: Abdominal pain that occurs after a colonoscopy may cause significant discomfort in some patients, and residual bowel gas is thought to be a key contributor to this abdominal pain.

Study: Asymptomatic 300 patients who underwent colonoscopy under sedation were randomized to either the decompression group or the control group. Initial colonoscopic procedure was performed uniformly in both the groups. After the colonoscopy examination was completed, the colonoscope was reinserted into the cecum, and the intraluminal air was aspirated during withdrawal in the decompression group. Abdominal pain was assessed before discharge and 24 to 48 hours after colonoscopy using a 10-point visual analogue scale (VAS).

Results: The 2 groups were similar with regard to clinical, demographic, and procedural factors. Among 288 patients, the incidence of abdominal pain (VAS≥1) after colonoscopy was 38 (26.6%) of 143 patients in the decompression group and 95 (65.5%) of 145 patients in the control group (VAS 0.68±1.35 vs. 2.14±2.15, P<0.001). There was an 86.1% reduction rate of abdominal pain by colonic decompression, based on multivariate analysis (odds ratio 0.139 [95% confidence interval, 0.077-0.250], P<0.001). Furthermore, independent factors for abdominal pain included female gender and total duration of procedure >800 seconds. There were no reinsertion-related complications in the decompression group.

Conclusion: Total colonic decompression after colonoscopy has a beneficial effect and can reduce postcolonoscopy abdominal pain without additional complications.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/MCG.0000000000000329DOI Listing
January 2016

Outcome of transarterial chemoembolization-based multi-modal treatment in patients with unresectable hepatocellular carcinoma.

World J Gastroenterol 2015 Feb;21(8):2395-404

Do Seon Song, Soon Woo Nam, Si Hyun Bae, Jeong Won Jang, Myeong Jun Song, Sung Won Lee, Hee Yeon Kim, Jong Young Choi, Seung Kew Yoon, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul 137-701, South Korea.

Aim: To investigate the efficacy and safety of transarterial chemoembolization (TACE)-based multimodal treatment in patients with large hepatocellular carcinoma (HCC).

Methods: A total of 146 consecutive patients were included in the analysis, and their medical records and radiological data were reviewed retrospectively.

Results: In total, 119 patients received TACE-based multi-modal treatments, and the remaining 27 received conservative management. Overall survival (P<0.001) and objective tumor response (P=0.003) were significantly better in the treatment group than in the conservative group. After subgroup analysis, survival benefits were observed not only in the multi-modal treatment group compared with the TACE-only group (P=0.002) but also in the surgical treatment group compared with the loco-regional treatment-only group (P<0.001). Multivariate analysis identified tumor stage (P<0.001) and tumor type (P=0.009) as two independent pre-treatment factors for survival. After adjusting for significant pre-treatment prognostic factors, objective response (P<0.001), surgical treatment (P=0.009), and multi-modal treatment (P=0.002) were identified as independent post-treatment prognostic factors.

Conclusion: TACE-based multi-modal treatments were safe and more beneficial than conservative management. Salvage surgery after successful downstaging resulted in long-term survival in patients with large, unresectable HCC.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3748/wjg.v21.i8.2395DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4342916PMC
February 2015

Gastrectomy for the treatment of refractory gastric ulceration after radioembolization with 90Y microspheres.

Clin Mol Hepatol 2014 Sep 25;20(3):300-5. Epub 2014 Sep 25.

Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea.

Transcatheter arterial radioembolization (TARE) with Yttrium-90 ((90)Y)-labeled microspheres has an emerging role in treatment of patients with unresectable hepatocellular carcinoma. Although complication of TARE can be minimized by aggressive pre-evaluation angiography and preventive coiling of aberrant vessels, radioembolization-induced gastroduodenal ulcer can be irreversible and can be life-threatening. Treatment of radioembolization-induced gastric ulcer is challenging because there is a few reported cases and no consensus for management. We report a case of severe gastric ulceration with bleeding that eventually required surgery due to aberrant deposition of microspheres after TARE.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3350/cmh.2014.20.3.300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4197179PMC
September 2014

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

J Biomed Semantics 2014 Feb 5;5(1). Epub 2014 Feb 5.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/2041-1480-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978116PMC
February 2014

Percutaneous cholecystostomy is appropriate as definitive treatment for acute cholecystitis in critically ill patients: a single center, cross-sectional study.

Korean J Gastroenterol 2014 Jan;63(1):32-8

Digestive Disease Center, Department of Internal Medicine, Cheju Halla General Hospital, Doreongno 65, Jeju 690-766, Korea.

Background/aims: Percutaneous cholecystostomy (PC) is an effective treatment for cholecystitis in high-risk surgical patients. However, there is no definitive agreement on the need for additional cholecystectomy in these patients.

Methods: All patients who were admitted to Cheju Halla General Hospital (Jeju, Korea) for acute cholecystitis and who underwent ultrasonography-guided PC between 2007 and 2012 were consecutively enrolled in this study. Among 82 total patients enrolled, 35 underwent laparoscopic cholecystectomy after recovery and 47 received the best supportive care (BSC) without additional surgery.

Results: The technical and clinical success rates for PC were 100% and 97.5%, respectively. The overall mean survival was 12.8 months. In the BSC group, mean survival was 5.4 months, and in the cholecystectomy group, mean survival was 22.4 months (p<0.01). However, there was no significant difference between these groups in multivariate analysis (relative risk [RR]=1.92; 95% CI, 0.77-4.77; p=0.16). However, advanced age (RR=1.05; 95% CI, 1.02-1.08; p=0.001) and higher class in the American Society of Anesthesiologists' physical status (RR=3.06; 95% CI, 1.37-6.83, p=0.006) were significantly associated with survival in the multivariate analysis. Among the 47 patients in the BSC group, the cholecystostomy tube was removed in 31 patients per protocol. Recurrent cholecystitis was not observed in either group of patients during the follow-up period.

Conclusions: In high-risk surgical patients, PC without additional cholecystectomy might be the best definitive management. Furthermore, the cholecystostomy drainage catheter can be safely removed in certain patients.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.4166/kjg.2014.63.1.32DOI Listing
January 2014

Clinical significance of hepatitis B virus precore and core promoter variants in Korean patients with chronic hepatitis B.

J Clin Gastroenterol 2015 Jan;49(1):61-8

*Department of Internal Medicine, Division of Gastroenterology and Hepatology, Korea University College of Medicine, Seoul †Department of Internal Medicine, Division of Gastroenterology and Hepatology, Cheju Halla General Hospital, Cheju, Korea.

Background/aim: We aimed to clarify the clinical significance of precore (preC)/core promoter (CP) variants of hepatitis B virus (HBV) in chronic hepatitis B (CHB) patients.

Methods: We assessed serum HBeAg, HBV DNA levels, alanine transferase (ALT) levels, and progression of liver fibrosis in 226 Korean CHB patients, presumed to be infected with genotype C HBV, to analyze HBV variants in the preC region (G1896A) and CP regions (A1762T, G1764A).

Results: CP and preC variants were more frequently found in HBeAg-negative patients than in HBeAg-positive patients (P<0.05). HBeAg-positive patients with CP variants had higher ALT levels and more advanced fibrosis scores (all P<0.01) than those without variants; those with preC variant had lower HBV DNA levels (P=0.009), with no significant difference in ALT levels and fibrosis scores. However, no significant correlation was found between HBV variants and clinicopathologic findings in HBeAg-negative patients. Furthermore, multivariate analysis revealed that (1) progression of liver fibrosis (≥F2) was associated with older age in both HBeAg-positive and HBeAg-negative patients (P<0.05) and with CP variants in the HBeAg-positive group (P=0.007), and (2) HBV DNA levels were positively correlated with ALT levels, irrespective of HBeAg (P<0.05), whereas they were negatively correlated with the presence of preC variant in the HBeAg-positive group (P=0.004).

Conclusions: In HBeAg-positive CHB patients infected with genotype C HBV, preC variant was associated with enhanced host immune response with lower HBV DNA levels, whereas CP variants were associated with severe liver damage and liver fibrosis progression.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/MCG.0000000000000052DOI Listing
January 2015

Introducing glycomics data into the Semantic Web.

J Biomed Semantics 2013 Nov 26;4(1):39. Epub 2013 Nov 26.

Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba Central-2, Umezono 1-1-1, Tsukuba 305-8568, Japan.

Background: Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as "switches" that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases.

Results: In order to implement support for the Semantic Web most efficiently for glycomics research, the developers of major glycomics databases agreed on a minimal standard for representing glycan structure and annotation information using RDF (Resource Description Framework). Moreover, all of the participants implemented this standard prototype and generated preliminary RDF versions of their data. To test the utility of the converted data, all of the data sets were uploaded into a Virtuoso triple store, and several SPARQL queries were tested as "proofs-of-concept" to illustrate the utility of the Semantic Web in querying across databases which were originally difficult to implement.

Conclusions: We were able to successfully retrieve information by linking UniCarbKB, GlycomeDB and JCGGDB in a single SPARQL query to obtain our target information. We also tested queries linking UniProt with GlycoEpitope as well as lectin data with GlycomeDB through PDB. As a result, we have been able to link proteomics data with glycomics data through the implementation of Semantic Web technologies, allowing for more flexible queries across these domains.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/2041-1480-4-39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177142PMC
November 2013

Evaluation of SPARQL query generation from natural language questions.

Proc Conf Assoc Comput Linguist Meet 2013 Sep;2013:3-7

Database Center for Life Science.

SPARQL queries have become the standard for querying linked open data knowledge bases, but SPARQL query construction can be challenging and time-consuming even for experts. SPARQL query generation from natural language questions is an attractive modality for interfacing with LOD. However, how to evaluate SPARQL query generation from natural language questions is a mostly open research question. This paper presents some issues that arise in SPARQL query generation from natural language, a test suite for evaluating performance with respect to these issues, and a case study in evaluating a system for SPARQL query generation from natural language questions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7581285PMC
September 2013

Computed tomography findings for predicting severe acute hepatitis with prolonged cholestasis.

World J Gastroenterol 2013 Apr;19(16):2543-9

Department of Internal Medicine, College of Medicine, Korea University, Seoul 136-705, South Korea.

Aim: To evaluate the significance of computed tomography (CT) findings in relation to liver chemistry and the clinical course of acute hepatitis.

Methods: Four hundred and twelve patients with acute hepatitis who underwent enhanced CT scanning were enrolled retrospectively. Imaging findings were analyzed for the following variables: gallbladder wall thickness (GWT), arterial heterogeneity, periportal tracking, number and maximum size of lymph nodes, presence of ascites, and size of spleen. The serum levels of alanine aminotransferase, alkaline phosphatase, bilirubin, albumin, and prothrombin time were measured on the day of admission and CT scan, and laboratory data were evaluated every 2-4 d for all subjects during hospitalization.

Results: The mean age of patients was 34.4 years, and the most common cause of hepatitis was hepatitis A virus (77.4%). The mean GWT was 5.2 mm. The number of patients who had findings of arterial heterogeneity, periportal tracking, lymph node enlargement > 7 mm, and ascites was 294 (80.1%), 348 (84.7%), 346 (84.5%), and 56 (13.6%), respectively. On multivariate logistic regression, male gender [odds ratio (OR) = 2.569, 95%CI: 1.477-4.469, P = 0.001], toxic hepatitis (OR = 3.531, 95%CI: 1.444-8.635, P = 0.006), level of albumin (OR = 2.154, 95%CI: 1.279-3.629, P = 0.004), and GWT (OR = 1.061, 95%CI: 1.015-1.110, P = 0.009) were independent predictive factors for severe hepatitis. The level of bilirubin (OR = 1.628, 95%CI: 1.331-1.991, P < 0.001) and GWT (OR = 1.172, 95%CI: 1.024-1.342, P = 0.021) were independent factors for prolonged cholestasis in multivariate analysis.

Conclusion: In patients with acute hepatitis, GWT on CT scan was an independent predictor of severe hepatitis and prolonged cholestasis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3748/wjg.v19.i16.2543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646146PMC
April 2013

Clinical features and outcomes of gastric variceal bleeding: retrospective Korean multicenter data.

Clin Mol Hepatol 2013 Mar 25;19(1):36-44. Epub 2013 Mar 25.

Department of Internal Medicine and Cell Therapy and Tissue Engineering Center, Yonsei University Wonju College of Medicine, Wonju, Korea.

Background/aims: While gastric variceal bleeding (GVB) is not as prevalent as esophageal variceal bleeding, it is reportedly more serious, with high failure rates of the initial hemostasis (>30%), and has a worse prognosis than esophageal variceal bleeding. However, there is limited information regarding hemostasis and the prognosis for GVB. The aim of this study was to determine retrospectively the clinical outcomes of GVB in a multicenter study in Korea.

Methods: The data of 1,308 episodes of GVB (males:females=1062:246, age=55.0±11.0 years, mean±SD) were collected from 24 referral hospital centers in South Korea between March 2003 and December 2008. The rates of initial hemostasis failure, rebleeding, and mortality within 5 days and 6 weeks of the index bleed were evaluated.

Results: The initial hemostasis failed in 6.1% of the patients, and this was associated with the Child-Pugh score [odds ratio (OR)=1.619; P<0.001] and the treatment modality: endoscopic variceal ligation, endoscopic variceal obturation, and balloon-occluded retrograde transvenous obliteration vs. endoscopic sclerotherapy, transjugular intrahepatic portosystemic shunt, and balloon tamponade (OR=0.221, P<0.001). Rebleeding developed in 11.5% of the patients, and was significantly associated with Child-Pugh score (OR=1.159, P<0.001) and treatment modality (OR=0.619, P=0.026). The GVB-associated mortality was 10.3%; mortality in these cases was associated with Child-Pugh score (OR=1.795, P<0.001) and the treatment modality for the initial hemostasis (OR=0.467, P=0.001).

Conclusions: The clinical outcome for GVB was better for the present cohort than in previous reports. Initial hemostasis failure, rebleeding, and mortality due to GVB were universally associated with the severity of liver cirrhosis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3350/cmh.2013.19.1.36DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3622854PMC
March 2013

Literature mining solutions for life science research.

Adv Bioinformatics 2013 8;2013:320436. Epub 2013 Jan 8.

Disease Translational Informatics, F. Hoffmann-La Roche Inc., Nutley, NJ 07110, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1155/2013/320436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556398PMC
February 2013

Treatment strategies using adefovir dipivoxil for individuals with lamivudine-resistant chronic hepatitis B.

World J Gastroenterol 2012 Dec;18(47):6987-95

Department of Internal Medicine, Korea University College of Medicine, Seoul 136-705, South Korea.

Aim: To investigate retrospectively the long-term efficacy of various treatment strategies using adefovir dipivoxil (adefovir) in patients with lamivudine-resistant chronic hepatitis B.

Methods: We included 154 consecutive patients in two treatment groups: the "add-on" group (n = 79), in which adefovir was added to ongoing lamivudine treatment due to lamivudine resistance, and the "switch/combination" group (n = 75), in which lamivudine was first switched to adefovir and then re-added later as needed. The "switch/combination" group was then divided into two subgroups depending on whether participants followed (group A, n = 30) or violated (group B, n = 45) a proposed treatment strategy that determined whether to add lamivudine based on the serum hepatitis B virus (HBV) DNA levels (< 60 IU/mL or not) after 6 mo of treatment (roadmap concept).

Results: The cumulative probability of virologic response (HBV DNA < 60 IU/mL) was higher in group A than in the "add-on" group and in group B (P < 0.001). In contrast, the cumulative probability of virologic breakthrough was lower in the "add-on" group than in group B (P = 0.002). Furthermore, the risk of virologic breakthrough in the multivariate analysis was significantly lower in the "add-on" group than in group A (hazard ratio = 0.096; 95%CI, 0.015-0.629; P = 0.015).

Conclusion: The selective combination of adefovir with lamivudine based upon early treatment responses increased the odds of virologic breakthrough relative to the use of uniform combination therapy from the beginning of treatment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3748/wjg.v18.i47.6987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531684PMC
December 2012
-->