• Molecules and Cells
• /
• v.44 no.11
• /
• pp.843-850
• /
• 2021

The rapid increase in collateral omics and phenotypic data has enabled data-driven studies for the fast discovery of cancer targets and biomarkers. Thus, it is necessary to develop convenient tools for general oncologists and cancer scientists to carry out customized data mining without computational expertise. For this purpose, we developed innovative software that enables user-driven analyses assisted by knowledge-based smart systems. Publicly available data on mutations, gene expression, patient survival, immune score, drug screening and RNAi screening were integrated from the TCGA, GDSC, CCLE, NCI, and DepMap databases. The optimal selection of samples and other filtering options were guided by the smart function of the software for data mining and visualization on Kaplan-Meier plots, box plots and scatter plots of publication quality. We implemented unique algorithms for both data mining and visualization, thus simplifying and accelerating user-driven discovery activities on large multiomics datasets. The present Q-omics software program (v0.95) is available at http://qomics.sookmyung.ac.kr.

• Journal of Korean Traditional Oncology
• /
• v.25 no.1
• /
• pp.11-24
• /
• 2020

Objective : Radiodermatitis is a common sequelae in 95% of patients receiving radiation therapy, which is important to be well managed as it can affect the patient's quality of life as well as the cancer treatment schedule. The aim of this study is to review and summarize the interventions available for the treatment of acute radiodermatitis, including traditional Korean medicine, and to propose treatment algorithms for clinicians. Methods : To collect studies about managements for radiodermatitis, domestic and foreign database were used such as Korean journal of traditional knowledge portal (KTKP), Korean studies information service system (KISS), national discovery or science leaders (NDSL), and oriental medicine advance searching integrated system (OASIS), Pubmed, Google scholar and Scopus. Results : Thirty-two studies were selected. There were nine studies on usual care and dressing, eleven studies on chemical agents, two studies on biological preparations, and ten studies on herbal medicines. Conclusion : Hygienic options and dressings have proved to be useful in the management of radiodermatitis. Chemical agents such as corticosteroid, statin, and topical antibiotic agent have proved to alleviate symptoms and severity, regenerate damaged skin, and prevent secondary infection. In biological preparations, EGF (epidermal growth factor) and GM-CSF (granulocyte-macrophage colony-stimulating factor) could be used to protect skin and prevent radiodermatitis. For herbal medicines, Calendula, catechin, β-sitosterol, and Jaungo (紫雲膏) may be effective for symptoms including pain, itching, and burning sensation induced by radiation therapy. Because of some research with conflicting results, further studies are needed to propose an algorithm for more optimal treatments.

• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.10
• /
• pp.5263-5272
• /
• 2012

Background: Gastric cancer (GC) is one of the most common cancers in China. Adjuvant chemotherapy (AC) is a routine auxiliary treatment for GC recommended by the guidelines issued in 2011 by the Ministry of Health of the People's Republic of China, but the relevant credible consequences in China have been insufficient because of China's late start and ethical concerns. Methods: A series of databases, including Cochrane Library, MEDLINE, EMBASE, the Chinese database of the National Knowledge Infrastructure and the VIP database, were searched by 2 reviewers independently for studies investigating AC for GC through March 2012. The retrieved literature was screened according to the eligibility criteria. Results: A total of 35 randomized control trials (RCTs) were subjected to the final analysis, including 4,043 patients in treatment group and 3,884 in the control group, as well as 4 clinical-control trials (CCTs), which accessed the final analysis with 238 and 252 patients, respectively. AC reduced the risk of death as a protective treatment with statistical significance (HR=0.91, 95%CI: [0.85, 0.97], P=0.002), and it seemed more effective for Asian than non-Asian patients. The effects of AC were not influenced by the starting time (P>0.05). D2 lymphadenectomy-based chemotherapy was effective (HR=0.89, 95%CI: [0.80, 0.99], P=0.04). Oral S-1 40 mg/m2 after D2 lymphadenectomy might be a better choice for Asians with advanced GC and might result in a greater reduction of adverse events than in non-Asian patients. GRADE quality assessment determined that the strength of the evidence from foreign studies from Europe, the United States and Asian countries other than China was high, while it was moderate for Chinese studies. Conclusion: AC was effective or even curative in Chinese patients in general, although it is still necessary to optimize a targeted AC scheme for Chinese patients with GC.

• Journal of the Korean Academy of Child and Adolescent Psychiatry
• /
• v.5 no.1
• /
• pp.28-35
• /
• 1994

Research on biological aspects on adult depression has been subjected to more than 25 years of systematic research, while biologic investigations regarding childhood and adolescent depression are only now being initiated. Although no unifying, explanatory theory of the biologic etiology of childhood depression emerges from the results of studies reviewed above, the findings do support that biological factors may be involved in the genesis of childhood depression. The research reviewed in this paper suggests that age and pubertal factors have major effects in most biological markers of depression. Some of these markers, like sleep EEG and neuroendocrine markers should be broken down by decades during adult life span. Thus, although adult data are very valuable points of departure for biological research on child and adolescent depression, it is very hard to transfer the adult data to prepubertal children and adolescents, ignoring the biological changes that take place in growth and development, pubety and aging. A great deal of work in basic developmental neuroscience remains to be done. It will be crucial for further advances in this field to determine the normal patterns of neurotransmitter interaction in this age group and to study children at high risk for depression. It will be also crucial to use primate models of depressive illness in order to be able to answer the many queations that cannot be investigated in humans for ethical issues. Conclusively, much closer collaboration between developmental and neurobiological and behavioral studies in primates and in humans will be essential for further development.

• Korean Journal of Soil Science and Fertilizer
• /
• v.49 no.2
• /
• pp.144-156
• /
• 2016

Soil is a dynamic biological system, in which it is difficult to determine the composition of microbial communities. Knowledge of microbial diversity and function in soils are limited because of the taxonomic and methodological limitations associated with studying the organisms. In this review, approaches to measure microbial diversity in soil were discussed. Research on soil microbes can be categorized as structural diversity, functional diversity and genetic diversity studies, and these include cultivation based and cultivation independent methods. Cultivation independent technique to evaluate soil structural diversity include different techniques such as Phospholipid Fatty Acids (PLFA) and Fatty Acid Methyl Ester (FAME) analysis. Carbon source utilization pattern of soil microorganisms by Community Level Physiological Profiling (CLPP), catabolic responses by Substrate Induced Respiration technique (SIR) and soil microbial enzyme activities are discussed. Genetic diversity of soil microorganisms using molecular techniques such as 16S rDNA analysis Denaturing Gradient Gel Electrophoresis (DGGE) / Temperature Gradient Gel Electrophoresis (TGGE), Terminal Restriction Fragment Length Polymorphism (T-RFLP), Single Strand Conformation Polymorphism (SSCP), Restriction Fragment Length Polymorphism (RFLP) / Amplified Ribosomal DNA Restriction Analysis (ARDRA) and Ribosomal Intergenic Spacer Analysis (RISA) are also discussed. The chapter ends with a final conclusion on the advantages and disadvantages of different techniques and advances in molecular techniques to study the soil microbial diversity.

• Journal of Microbiology and Biotechnology
• /
• v.31 no.8
• /
• pp.1060-1068
• /
• 2021

Community-associated Methicillin-Resistant Staphylococcus aureus (CA-MRSA) is notorious as a leading cause of soft tissue infections. Despite several studies on the Agr regulator, the mechanisms of action of Agr on the virulence factors in different strains are still unknown. To reveal the role of Agr in different CA-MRSA, we investigated the LACΔagr mutant and the MW2Δagr mutant by comparing LAC (USA300), MW2 (USA400), and Δagr mutants. The changes of Δagr mutants in sensitivity to oxacillin and several virulence factors such as biofilm formation, pigmentation, motility, and membrane properties were monitored. LACΔagr and MW2Δagr mutants showed different oxacillin sensitivity and biofilm formation compared to the LAC and MW2 strains. Regardless of the strain, the motility was reduced in Δagr mutants. And there was an increase in the long chain fatty acid in phospholipid fatty acid composition of Δagr mutants. Other properties such as biofilm formation, pigmentation, motility, and membrane properties were different in both Δagr mutants. The Agr regulator may have a common role like the control of motility and straindependent roles such as antibiotic resistance, biofilm formation, change of membrane, and pigment production. It does not seem easy to control all MRSA by targeting the Agr regulator only as it showed strain-dependent behaviors.

• Journal of Ecology and Environment
• /
• v.48 no.3
• /
• pp.247-255
• /
• 2024

Background: To effectively understand and evaluate plant diversity in a specific area and make meaningful comparisons between regions, standardized methods that measure diversity irrespective of survey plot size are crucial. This study proposes a model equation for comparing plant species diversity using the modified Whittaker plots. Plant species diversity was measured in two Gotjawal areas on Jeju Island, where the coexistence of northern and southern limit species significantly impacts diversity. By analyzing the relationship between plant species diversity and environmental factors, the study clarified the characteristics of plant and habitat diversity in the Gotjawal ecosystem. Results: The species richness of vascular plants, herbaceous plants, and woody plants increased with area and was higher in Jeoji Gotjawal than in Seonheul Gotjawal. Similarly, the species turnover rate (slope value) was higher in Jeoji Gotjawal (4.37) than in Seonheul Gotjawal (3.85). This indicates that the species richness in Jeoji Gotjawal increases more with the expansion of the survey area (1-1,000 m²), reflecting a faster species turnover rate. Additionally, in Gotjawal areas, species richness increased with greater leaf litter depth, elevation, slope, and rock ratio. These results indicate that differences in plant species diversity were attributed to soil environmental factors. Conclusions: The plant species diversity of Gotjawal, surveyed using standardized methods, was lower than that of forested areas in the central region of South Korea where the same method was applied. Most previous studies on species diversity likely compared diversity without considering a consistent survey area. Therefore, when comparing plant species diversity domestically and globally, it emphasizes the need for the use of standardized survey methods.

• Animal cells and systems
• /
• v.14 no.1
• /
• pp.11-15
• /
• 2010

Long-term working memory (LTWM) is a subdivision concept of working memory and indicates the enhancement of performance in a working memory task. LTWM has been shown in humans who have been engaged in a specific task requiring working memory over a long time. However, there is very little understanding of the exact mechanism of LTWM because of limitations of experimental methods in human studies. We have modified the standard T-maze task, which is used to test working memory in mice, to demonstrate LTWM in an animal model. We observed an enhancement of performance by repeated experience with the same working memory load in mice, which can be regarded as an LTWM. This effect seems to depend on the condition wherein a delay was given. This task may be a good experimental protocol to assess LTWM in animal studies.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.10
• /
• pp.3265-3268
• /
• 2012

Nanoparticles (NPs) are increasingly used in consumer products, which have aroused many concerns and debates regarding their fate in biological systems from a point of their safety/toxicity. Although a number of studies on the biological effects of NPs have been published, these are often complicated by the possible toxicity of conventional NPs, caused by contamination with chemical precursors or additives during their synthesis and/or purification procedures. To explicitly understand the toxicity basis of NPs, it is necessary to directly address a main problem related to their intrinsic/inherent toxicity and/or incompatibility with biological objects. The present study is designed to take advantage of a novel laser-assisted method called laser ablation to generate Ag, Au, Co, and Cu NPs in biocompatible aqueous solution, and to evaluate the toxicity of the resulting ultra-pure NPs. Our results show that the ultra-pure NPs with nascent surfaces possess moderate cytotoxicity to human cells in a cell-dependent manner.

• BMB Reports
• /
• v.51 no.8
• /
• pp.369-370
• /
• 2018

In previous studies, memory storage was localized to engram cells distributed across the brain. While these studies have provided an individual cellular profile of engram cells, their synaptic connectivity, or whether they follow Hebbian mechanisms, remains uncertain. Therefore, our recent study investigated whether synapses between engram cells exhibit selectively enhanced structural and functional properties following memory formation. This was accomplished using a newly developed technique called "dual-eGRASP". We found that the number and size of spines on CA1 engram cells that receive inputs from CA3 engram cells were larger than at other synapses. We further observed that this enhanced connectivity correlated with induced memory strength. CA3 engram synapses exhibited increased release probability, while CA1 engram synapses produced enhanced postsynaptic responses. CA3 engram to CA1 engram projections showed strong occlusion of long-term potentiation. We demonstrated that the synaptic connectivity of CA3 to CA1 engram cells was strengthened following memory formation. Our results suggest that Hebbian plasticity occurs during memory formation among engram cells at the synapse level.