• Genomics & Informatics
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• 제20권1호
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• pp.11.1-11.20
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• 2022

Vibrio harveyi belongs to the Vibrio genus that causes vibriosis in marine and aquatic fish species through double-stranded DNA virus replication. In humans, around 12 Vibrio species can cause gastroenteritis (gastrointestinal illness). A large amount of virus particles can be found in the cytoplasm of infected cells, which may cause death. Despite these devastating complications, there is still no cure or vaccine for the virus. As a result, we used an immunoinformatics approach to develop a multi-epitope vaccine against most pathogenic hemolysin gene of V. harveyi. The immunodominant T- and B-cell epitopes were identified using the hemolysin protein. We developed a vaccine employing three possible epitopes: cytotoxic T-lymphocytes, helper T-lymphocytes, and linear B-lymphocyte epitopes, after thorough testing. The vaccine was developed to be antigenic, immunogenic, and non-allergenic, as well as having a better solubility. Molecular dynamics simulation revealed significant structural stiffness and binding stability. In addition, the immunological simulation generated by computer revealed that the vaccination might elicit immune reactions in the actual life after injection. Finally, using Escherichia coli K12 as a model, codon optimization yielded ideal GC content and a higher codon adaptation index value, which was then included in the cloning vector pET2+ (a). Altogether, our experiment implies that the proposed peptide vaccine might be a good option for vibriosis prophylaxis.

• Genomics & Informatics
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• 제19권3호
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• pp.31.1-31.9
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• 2021

Leptospirosis is a zoonotic disease caused by spirochetes from the genus Leptospira. In Thailand, Leptospira interrogans is a major cause of leptospirosis. Leptospirosis patients present with a wide range of clinical manifestations from asymptomatic, mild infections to severe illness involving organ failure. For better understanding the difference between Leptospira isolates causing mild and severe leptospirosis, illumina sequencing was used to sequence genomic DNA in both serotypes. DNA of Leptospira isolated from two patients, one with mild and another with severe symptoms, were included in this study. The paired-end reads were removed adapters and trimmed with Q30 score using Trimmomatic. Trimmed reads were constructed to contigs and scaffolds using SPAdes. Cross-contamination of scaffolds was evaluated by ContEst16s. Prokka tool for bacterial annotation was used to annotate sequences from both Leptospira isolates. Predicted amino acid sequences from Prokka were searched in EggNOG and David gene ontology database to characterize gene ontology. In addition, Leptospira from mild and severe patients, that passed the criteria e-value < 10e^-5 from blastP against virulence factor database, were used to analyze with Venn diagram. From this study, we found 13 and 12 genes that were unique in the isolates from mild and severe patients, respectively. The 12 genes in the severe isolate might be virulence factor genes that affect disease severity. However, these genes should be validated in further study.

• 한국정보통신학회논문지
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• 제26권12호
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• pp.1777-1785
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• 2022

본 연구는 국민 건강 검진 결과를 활용하여 건강점수 산출하는 새로운 방법을 제시하고 해당 결과의 타당성을 확인한 연구다. 건강점수(Health Score, 'HS')는 건강 검진 항목에 대한 임상적 기준과 통계적 장치를 적용하여 개인 건강 정도를 점수화한 지표로 특정 검진 항목이 건강변화량에 미치는 전체 크기와 건강변화량에 주는 영향력, 바이오마커가 정상 범위에서 벗어난 비율에 따른 가중치 변화율, 표준화 값으로 계산된다. 지표에 대한 검증은 선정된 질환에 대하여 질환 발생군과 미발생군 간의 HS를 비교하고, HS 순으로 나눈 구간에서 질환 발생률을 비교하여 타당성 검증을 시도하였다. 그 결과, 모든 선정 질환에서 질환의 유무에 따라 평균 HS 차이는 유의하였고, HS가 감소함에 따라 선정 질환의 발생률이 증가하는 경향을 보였다.

• Journal of Ginseng Research
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• 제46권3호
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• pp.337-347
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• 2022

Coronavirus disease 2019 (COVID-19) is currently a pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 are directly associated with hyper-activation of innate immune response that excessively produce pro-inflammatory cytokines and induce cytokine storm, leading to multi-organ-failure and significant morbidity/mortality. Currently, several antiviral drugs such as Paxlovid (nirmatrelvir and ritonavir) and molnupiravir are authorized to treat mild to moderate COVID-19, however, there are still no drugs that can specifically fight against challenges of SARS-CoV-2 variants. Panax ginseng, a medicinal plant widely used for treating various conditions, might be appropriate for this need due to its anti-inflammatory/cytokine/viral activities, fewer side effects, and cost efficiency. To review Panax ginseng and its pharmacologically active-ingredients as potential phytopharmaceuticals for treating cytokine storm of COVID-19, articles that reporting its positive effects on the cytokine production were searched from academic databases. Experimental/clinical evidences for the effectiveness of Panax ginseng and its active-ingredients in preventing or mitigating cytokine storm, especially for the cascade of cytokine storm, suggest that they might be beneficial as an adjunct treatment for cytokine storm of COVID-19. This review may provide a new approach to discover specific medications using Panax ginseng to control cytokine storm of COVID-19.

• Genomics & Informatics
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• 제21권1호
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• pp.4.1-4.18
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• 2023

Coronavirus disease 2019 (COVID-19) is an inflammatory and infectious disease caused by severe acute respiratory syndrome coronavirus 2 virus with a complex pathophysiology. While COVID-19 vaccines and boosters are available, treatment of the disease is primarily supportive and symptomatic. Several research have suggested the potential of herbal medicines as an adjunctive treatment for the disease. A popular herbal medicine approved in the Philippines for the treatment of acute respiratory disease is Vitex negundo L. In fact, the Department of Science and Technology of the Philippines has funded a clinical trial to establish its potential as an adjunctive treatment for COVID-19. Here, we utilized network pharmacology and molecular docking in determining pivotal targets of Vitex negundo compounds against COVID-19. The results showed that significant targets of Vitex negundo compounds in COVID-19 are CSB, SERPINE1, and PLG which code for cathepsin B, plasminogen activator inhibitor-1, and plasminogen, respectively. Molecular docking revealed that α-terpinyl acetate and geranyl acetate have good binding affinity in cathepsin B; 6,7,4-trimethoxyflavanone, 5,6,7,8,3',4',5'-heptamethoxyflavone, artemetin, demethylnobiletin, gardenin A, geranyl acetate in plasminogen; and 7,8,4-trimethoxyflavanone in plasminogen activator inhibitor-1. While the results are promising, these are bound to the limitations of computational methods and further experimentation are needed to completely establish the molecular mechanisms of Vitex negundo against COVID-19.

• Genomics & Informatics
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• 제21권1호
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• pp.13.1-13.8
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• 2023

Importance of accurate molecular diagnosis and quantification of particular disease-related pathogenic microorganisms is highlighted as an introductory step to prevent and care for diseases. In this study, we designed a primer/probe set for quantitative real-time polymerase chain reaction (qRT-PCR) targeting rgpA gene, known as the specific virulence factor of periodontitis-related pathogenic bacteria 'Porphyromonas gingivalis', and evaluated its diagnostic efficiency by detecting and quantifying relative bacterial load of P. gingivalis within saliva samples collected from clinical subjects. As a result of qRT-PCR, we confirmed that relative bacterial load of P. gingivalis was detected and quantified within all samples of positive control and periodontitis groups. On the contrary, negative results were confirmed in both negative control and healthy groups. Additionally, as a result of comparison with next-generation sequencing (NGS)-based 16S metagenome profiling data, we confirmed relative bacterial load of P. gingivalis, which was not identified on bacterial classification table created through 16S microbiome analysis, in qRT-PCR results. It showed that an approach to quantifying specific microorganisms by applying qRT-PCR method could solve microbial misclassification issues at species level of an NGS-based 16S microbiome study. In this respect, we suggest that P. gingivalis-specific primer/probe set introduced in present study has efficient applicability in various oral healthcare industries, including periodontitis-related microbial molecular diagnosis field.

• Genomics & Informatics
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• 제21권3호
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• pp.38.1-38.8
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• 2023

Non-small cell lung cancer (NSCLC) is an important cause of cancer-associated deaths worldwide. Therefore, the exact molecular mechanisms of NSCLC are unidentified. The present investigation aims to identify the miRNAs with predictive value in NSCLC. The two datasets were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs (DEmiRNA) and mRNAs (DEmRNA) were selected from the normalized data. Next, miRNA-mRNA interactions were determined. Then, co-expression network analysis was completed using the WGCNA package in R software. The co-expression network between DEmiRNAs and DEmRNAs was calculated to prioritize the miRNAs. Next, the enrichment analysis was performed for DEmiRNA and DEmRNA. Finally, the drug-gene interaction network was constructed by importing the gene list to dgidb database. A total of 3,033 differentially expressed genes and 58 DEmiRNA were recognized from two datasets. The co-expression network analysis was utilized to build a gene co- expression network. Next, four modules were selected based on the Z_summary score. In the next step, a bipartite miRNA-gene network was constructed and hub miRNAs (let-7a-2-3p, let-7d-5p, let-7b-5p, let-7a-5p, and let-7b-3p) were selected. Finally, a drug-gene network was constructed while SUNITINIB, MEDROXYPROGESTERONE ACETATE, DOFETILIDE, HALOPERIDOL, and CALCITRIOL drugs were recognized as a beneficial drug in NSCLC. The hub miRNAs and repurposed drugs may act a vital role in NSCLC progression and treatment, respectively; however, these results must validate in further clinical and experimental assessments.

• Genomics & Informatics
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• 제21권3호
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• pp.30.1-30.13
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• 2023

Ephs belong to the largest family of receptor tyrosine kinase and are highly conserved both sequentially and structurally. The structural organization of Eph is similar to other receptor tyrosine kinases; constituting the extracellular ligand binding domain, a fibronectin domain followed by intracellular juxtamembrane kinase, and SAM domain. Eph binds to respective ephrin ligand, through the ligand binding domain and forms a tetrameric complex to activate the kinase domain. Eph-ephrin regulates many downstream pathways that lead to physiological events such as cell migration, proliferation, and growth. Therefore, considering the importance of Eph-ephrin class of protein in tumorigenesis, 7,620 clinically reported missense mutations belonging to the class of variables of unknown significance were retrieved from cBioPortal and evaluated for pathogenicity. Thirty-two mutations predicted to be pathogenic using SIFT, Polyphen-2, PROVEAN, SNPs&GO, PMut, iSTABLE, and PremPS in-silico tools were found located either in critical functional regions or encompassing interactions at the binding interface of Eph-ephrin. However, seven were reported in nonsmall cell lung cancer (NSCLC). Considering the relevance of receptor tyrosine kinases and Eph in NSCLC, these seven mutations were assessed for change in the folding pattern using molecular dynamic simulation. Structural alterations, stability, flexibility, compactness, and solvent-exposed area was observed in EphA3 Trp790Cys, EphA7 Leu749Phe, EphB1 Gly685Cys, EphB4 Val748Ala, and Ephrin A2 Trp112Cys. Hence, it can be concluded that the evaluated mutations have potential to alter the folding pattern and thus can be further validated by in-vitro, structural and in-vivo studies for clinical management.

• Archives of Plastic Surgery
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• 제50권6호
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• pp.541-549
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• 2023

Background Despite its many advantages, prepectoral breast reconstruction also carries the risk of implant rippling. The recent introduction of partial superior implant coverage using a pectoralis muscle slip in prepectoral direct-to-implant (DTI) breast reconstruction has shown the potential to minimize upper pole rippling. The purpose of this study was to identify factors associated with rippling and the effectiveness of our surgical technique. Methods In total, 156 patients (186 breasts) who underwent prepectoral DTI breast reconstruction between August 2019 and March 2021 were identified retrospectively. Patient data were analyzed from medical records. Univariable and multivariable logistic analyses were performed to contextualize the risks associated with rippling deformity relative to demographic characteristics and other clinical factors. Retrospective propensity-matched analysis was performed to identify the relationship between rippling deformity and the reconstruction method. Results Patients with body mass index (BMI; odds ratio [OR], 0.736; p < 0.001), those with a postoperative chemotherapy history (OR, 0.324; p = 0.027) and those who received breast reconstruction via the superior coverage technique (OR, 0.2; p = 0.004), were less likely to develop rippling deformity. The median follow-up period was 64.9 weeks, and there were no significant differences between patients in types of mastectomy, implant, or acellular dermal matrix. Patients who underwent superior coverage technique-based reconstruction showed significantly reduced rippling (OR, 0.083; p = 0.017) Conclusion Patients with higher BMI and prior postoperative chemotherapy were less likely to develop rippling deformity. The superior coverage technique can be effective in minimizing upper pole rippling.

• 보건의료생명과학 논문지
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• 제11권1호
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• pp.1-9
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• 2023

본 연구는 급변하는 환경에 대응하는 보건의료정보관리자들의 역할을 도출하고 학생들의 교육요구도를 분석하여 대학의 교육과정 개선방안을 제시하는 것을 목적으로 한다. 이를 위해 선행연구 및 NCS 등에서 제시하는 능력단위를 바탕으로 보건의료정보관리자의 역할들을 도출하여 설문지를 구성하고 설문조사를 실시하였다. 분석결과 첫째, 보건의료정보관리자들의 현재 역할에 있어 진료정보지원과 통계생성 및 활용, 규정관리에 대한 개선 필요성이 높은 것으로 나타났으며, 둘째, 미래역할에 대해서는 업무과정 설계자, 임상연구 코디네이터, 비즈니스 변화관리자에 대한 개선 우선순위가 높게 나타났다. 결과에서 나타난 학생들의 교육요구도를 반영하여 대학은 관련 교과목들의 유기적인 연계와 교수자들의 실습 과정 단계별 내용 분석과 피드백 노력이 필요하며, 실습 관련 교과목에 대해서는 병원정보시스템과 유사한 프로그램과 데이터베이스를 도입하여 학생들이 실무와 가장 유사하게 데이터를 활용하고 관리할 수 있는 교육 환경이 마련되어야 할 것이다.