• Genomics & Informatics
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• v.18 no.2
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• pp.17.1-17.4
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• 2020

The amount of content on social media platforms such as Twitter is expanding rapidly. Simultaneously, the lack of patient information seriously hinders the diagnosis and treatment of rare/intractable diseases. However, these patient communities are especially active on social media. Data from social media could serve as a source of patient-centric knowledge for these diseases complementary to the information collected in clinical settings and patient registries, and may also have potential for research use. To explore this question, we attempted to extract patient-centric knowledge from social media as a task for the 3-day Biomedical Linked Annotation Hackathon 6 (BLAH6). We selected amyotrophic lateral sclerosis and multiple sclerosis as use cases of rare and intractable diseases, respectively, and we extracted patient histories related to these health conditions from Twitter. Four diagnosed patients for each disease were selected. From the user timelines of these eight patients, we extracted tweets that might be related to health conditions. Based on our experiment, we show that our approach has considerable potential, although we identified problems that should be addressed in future attempts to mine information about rare/intractable diseases from Twitter.

• Genomics & Informatics
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• v.18 no.1
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• pp.3.1-3.8
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• 2020

Patient-derived xenograft (PDX) mouse models are frequently used to test the drug efficacy in diverse types of cancer. They are known to recapitulate the patient characteristics faithfully, but a systematic survey with a large number of cases is yet missing in lung cancer. Here we report the comparison of genomic characters between mouse and patient tumor tissues in lung cancer based on exome sequencing data. We established PDX mouse models for 132 lung cancer patients and performed whole exome sequencing for trio samples of tumor-normal-xenograft tissues. Then we computed the somatic mutations and copy number variations, which were used to compare the PDX and patient tumor tissues. Genomic and histological conclusions for validity of PDX models agreed in most cases, but we observed eight (~7%) discordant cases. We further examined the changes in mutations and copy number alterations in PDX model production and passage processes, which highlighted the clonal evolution in PDX mouse models. Our study shows that the genomic characterization plays complementary roles to the histological examination in cancer studies utilizing PDX mouse models.

• Genomics & Informatics
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• v.17 no.4
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• pp.41.1-41.12
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• 2019

Survival analysis mainly deals with the time to event, including death, onset of disease, and bankruptcy. The common characteristic of survival analysis is that it contains "censored" data, in which the time to event cannot be completely observed, but instead represents the lower bound of the time to event. Only the occurrence of either time to event or censoring time is observed. Many traditional statistical methods have been effectively used for analyzing survival data with censored observations. However, with the development of high-throughput technologies for producing "omics" data, more advanced statistical methods, such as regularization, should be required to construct the predictive survival model with high-dimensional genomic data. Furthermore, machine learning approaches have been adapted for survival analysis, to fit nonlinear and complex interaction effects between predictors, and achieve more accurate prediction of individual survival probability. Presently, since most clinicians and medical researchers can easily assess statistical programs for analyzing survival data, a review article is helpful for understanding statistical methods used in survival analysis. We review traditional survival methods and regularization methods, with various penalty functions, for the analysis of high-dimensional genomics, and describe machine learning techniques that have been adapted to survival analysis.

• Genomics & Informatics
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• v.13 no.1
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• pp.2-6
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• 2015

Pathogenic bacteria survive in iron-limited host environments by using several iron acquisition mechanisms. Acinetobacter baumannii, causing serious infections in compromised patients, produces an iron-chelating molecule, called acinetobactin, which is composed of equimolar quantities of 2,3-dihydroxybenzoic acid (DHBA), L-threonine, and N-hydroxyhistamine, to compete with host cells for iron. Genes that are involved in the production and transport of acinetobactin are clustered within the genome of A. baumannii. A recent study showed that entA, located outside of the acinetobactin gene cluster, plays important roles in the biosynthesis of the acinetobactin precursor DHBA and in bacterial pathogenesis. Therefore, understanding the genes that are associated with the biosynthesis and transport of acinetobactin in the bacterial genome is required. This review is intended to provide a general overview of the genes in the genome of A. baumannii that are required for acinetobactin biosynthesis and transport.

• Genomics & Informatics
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• v.12 no.1
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• pp.42-47
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• 2014

Asian populations contain a variety of ethnic groups that have ethnically specific genetic differences. Ethnic variants may be highly relevant in disease and human differentiation studies. Here, we identified ethnically specific variants and then investigated their distribution across Asian ethnic groups. We obtained 58,960 Pan-Asian single nucleotide polymorphisms of 1,953 individuals from 72 ethnic groups of 11 Asian countries. We selected 9,306 ethnic variant single nucleotide polymorphisms (ESNPs) and 5,167 ethnic variant copy number polymorphisms (ECNPs) using the nearest shrunken centroid method. We analyzed ESNPs and ECNPs in 3 hierarchical levels: superpopulation, subpopulation, and ethnic population. We also identified ESNP- and ECNP-related genes and their features. This study represents the first attempt to identify Asian ESNP and ECNP markers, which can be used to identify genetic differences and predict disease susceptibility and drug effectiveness in Asian ethnic populations.

• Genomics & Informatics
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• v.12 no.1
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• pp.21-34
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• 2014

A visual analysis approach and the developed supporting technology provide a comprehensive solution for analyzing large and complex integrated genomic and biomedical data. This paper presents a methodology that is implemented as an interactive visual analysis technology for extracting knowledge from complex genetic and clinical data and then visualizing it in a meaningful and interpretable way. By synergizing the domain knowledge into development and analysis processes, we have developed a comprehensive tool that supports a seamless patient-to-patient analysis, from an overview of the patient population in the similarity space to the detailed views of genes. The system consists of multiple components enabling the complete analysis process, including data mining, interactive visualization, analytical views, and gene comparison. We demonstrate our approach with medical scientists on a case study of childhood cancer patients on how they use the tool to confirm existing hypotheses and to discover new scientific insights.

• Tuberculosis and Respiratory Diseases
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• v.80 no.1
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• pp.21-26
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• 2017

It is well established that health care workers (HCWs) have a considerably higher risk of occupationally acquired tuberculosis (TB). To reduce the transmission of TB to HCWs and patients, TB infection control programs should be implemented in health care settings. The first and most important level of all protection and control programs is administrative control. Its goals are to prevent HCWs, other staff, and patients from being exposed to TB, and to reduce the transmission of infection by ensuring rapid diagnosis and treatment of affected individuals. Administrative control measures recommended by the United States Centers for Disease Control and Prevention and the World Health Organization include prompt identification of people with TB symptoms, isolation of infectious patients, control of the spread of the pathogen, and minimization of time spent in health care facilities. Another key component of measures undertaken is the baseline and serial screening for latent TB infection in HCWs who are at risk of exposure to TB. Although the interferon-gamma release assay has some advantages over the tuberculin skin test, the former has serious limitations, mostly due to its high conversion rate.

• Journal of Korean Academy of Nursing
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• v.37 no.4
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• pp.529-539
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• 2007

Purpose: This quantitative meta analysis sought to determine the effectiveness of SMIs. Method: Forty-six experimental studies with a randomized or nonequivalent control group pre-post test design were included in the analysis. The selected studies were classified according to the sample characteristics, the types and methods of the interventions, and the types of outcome variables. Six intervention types were distinguished: cognitive-behavioral intervention(CBT), relaxation techniques(RT), exercise(EX), multimodal programs 1 and 2(MT1, 2), and organization-focused interventions(OTs). Effect sizes were calculated for the 4 outcome categories across intervention types: psycho-social outcome, behavioral-personal resources, physiologic, and organizational outcome. Results : Individual worker-focused interventions(ITs) were more effective than OTs. A small but significant overall effect was found A moderate effect was found for RT, and small effects were found for other ITs, The effect size for OTs was the smallest. The interventions involving CBT and RT appeared to be the preferred means of reducing worker's psycho-social and organizational outcomes. With regard to physiologic outcomes, RT appeared to be most effective. CBT appeared to be most effective in reducing psycho-social outcomes. The effects of OT were non-significant, except for the psycho-social outcomes. Conclusions: SMIs are effective. Interventions involving RT and CBT are more effective than other types.

• Journal of muscle and joint health
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• v.19 no.2
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• pp.107-119
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• 2012

Purpose: This study was conducted to extract international classification of functioning, disability, and health (ICF) core sets for measuring functional status in acute stroke patients, and to evaluate clinical applicability of the core sets. Methods: A set of 22 ICF items on functional status in acute stroke patients were extracted from the Korean general ICF core sets and ICF core sets for stroke patients. The extracted ICF functional items were assessed at the time of admission and discharge among 100 stroke patients who were admitted in a university hospital. Results: Comparing to functional status at admission of acute stroke patients, the overall functional status at discharge was improved. However, functions on defecation, skin protection, and relationship with immediate family at the time of discharge were not significantly changed. Conclusion: The set of ICF functional items identified in this study may be reliable and valid to assess acute stoke patients' body functions, activities and participation and environmental factors in the holistic and comprehensive nursing context. Nursing interventions on bowel elimination and skin protection for acute stroke patients need to be developed.

• Journal of Physiology & Pathology in Korean Medicine
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• v.33 no.6
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• pp.303-310
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• 2019

In order to search for the causes of having difficulty with the scientification task of the Korean medicine, the definition and conception of science were reviewed first and then formalization of reasoning scheme and a practical method of scientification were proposed. Science in its definition is meant by foundation of method and system for production of scientific knowledge not by knowledge of science itself. The formation of science is composed of complex processes including not only scientific knowledge but also politicosocial output containing activity of scientist society, spreading of social value and intercommunication. The production of scientific knowledge of Korean medicine is begun from logicality of the differential diagnosis and treatment theory through abductive verification of analogical inference by yinyang and 5 phase theory. For the commensurability between the various heterogenic theories within Korean medicine, the scientific activity of collecting, compiling, analyzing, distributing, and discussing the significant knowledge gained through abductive verification in the experiment and clinical process should be formed broadly. Based on these knowledge database, organization of scientist society with Korean medicine, life science, medical engineering, social expansion and generalization of pattern conception, and then social propagation and contribution for national health should be driven forward.