• Molecules and Cells
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• v.42 no.9
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• pp.617-627
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• 2019

Brain organoids are an exciting new technology with the potential to significantly change our understanding of the development and disorders of the human brain. With step-by-step differentiation protocols, three-dimensional neural tissues are self-organized from pluripotent stem cells, and recapitulate the major millstones of human brain development in vitro. Recent studies have shown that brain organoids can mimic the spatiotemporal dynamicity of neurogenesis, the formation of regional neural circuitry, and the integration of glial cells into a neural network. This suggests that brain organoids could serve as a representative model system to study the human brain. In this review, we will overview the development of brain organoid technology, its current progress and applications, and future prospects of this technology.

• Molecules and Cells
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• v.46 no.1
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• pp.21-32
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• 2023

MicroRNAs (miRNAs) play cardinal roles in regulating biological pathways and processes, resulting in significant physiological effects. To understand the complex regulatory network of miRNAs, previous studies have utilized massivescale datasets of miRNA targeting and attempted to computationally predict the functional targets of miRNAs. Many miRNA target prediction tools have been developed and are widely used by scientists from various fields of biology and medicine. Most of these tools consider seed pairing between miRNAs and their mRNA targets and additionally consider other determinants to improve prediction accuracy. However, these tools exhibit limited prediction accuracy and high false positive rates. The utilization of additional determinants, such as RNA modifications and RNA-binding protein binding sites, may further improve miRNA target prediction. In this review, we discuss the determinants of functional miRNA targeting that are currently used in miRNA target prediction and the potentially predictive but unappreciated determinants that may improve prediction accuracy.

• IMMUNE NETWORK
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• v.22 no.1
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• pp.6.1-6.19
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• 2022

Chimeric antigen receptor (CAR) T cells, which express a synthetic receptor engineered to target specific antigens, have demonstrated remarkable potential to treat haematological malignancies. However, their transition beyond haematological malignancy has so far been unsatisfactory. Here, we discuss recent challenges and improvements for CAR T cell therapy against solid tumors: Antigen heterogeneity which provides an effective escape mechanism against conventional mono-antigen-specific CAR T cells; and the immunosuppressive tumor microenvironment which provides physical and molecular barriers that respectively prevent T cell infiltration and drive T cell dysfunction and hypoproliferation. Further, we discuss the application of CAR T cells in infectious disease and autoimmunity.

• Korean Journal of Biological Psychiatry
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• v.22 no.3
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• pp.101-108
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• 2015

Recent breakthroughs in functional neuroimaging techniques have launched the quest of mapping the connections of the human brain, otherwise known as the human connectome. Imaging connectomics is an umbrella term that refers to the neuroimaging techniques used to generate these maps, which recently has enabled comprehensive brain mapping of network connectivity combined with graph theoretic methods. In this review, we present an overview of the key concepts in functional connectomics. Furthermore, we discuss articles that applied task-based and/or resting-state functional magnetic resonance imaging to examine network deficits in post-traumatic stress disorder (PTSD). These studies have provided important insights regarding the etiology of PTSD, as well as the overall organization of the brain network. Advances in functional connectomics are expected to provide insight into the pathophysiology and the development of biomarkers for diagnosis and treatment of PTSD.

• International Journal of Control, Automation, and Systems
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• v.4 no.3
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• pp.382-393
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• 2006

Mechanical system dynamics plays an important role in the area of computational structural biology. Elastic network models (ENMs) for macromolecules (e.g., polymers, proteins, and nucleic acids such as DNA and RNA) have been developed to understand the relationship between their structure and biological function. For example. a protein, which is basically a folded polypeptide chain, can be simply modeled as a mass-spring system from the mechanical viewpoint. Since the conformational flexibility of a protein is dominantly subject to its chemical bond interactions (e.g., covalent bonds, salt bridges, and hydrogen bonds), these constraints can be modeled as linear spring connections between spatially proximal representatives in a variety of coarse-grained ENMs. Coarse-graining approaches enable one to simulate harmonic and anharmonic motions of large macromolecules in a PC, while all-atom based molecular dynamics (MD) simulation has been conventionally performed with an aid of supercomputer. A harmonic analysis of a macroscopic mechanical system, called normal mode analysis, has been adopted to analyze thermal fluctuations of a microscopic biological system around its equilibrium state. Furthermore, a structure-based system optimization, called elastic network interpolation, has been developed to predict nonlinear transition (or folding) pathways between two different functional states of a same macromolecule. The good agreement of simulation and experiment allows the employment of coarse-grained ENMs as a versatile tool for the study of macromolecular dynamics.

• Molecules and Cells
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• v.42 no.2
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• pp.166-174
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• 2019

Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.

• Journal of Korean Biological Nursing Science
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• v.23 no.3
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• pp.170-179
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• 2021

Purpose: The aim of this study was to identify core keywords and topic groups in the 'Diabetes mellitus and mobile applications' field of research for better understanding research trends in the past 20 years. Methods: This study was a text-mining and topic modeling study including four steps such as 'collecting abstracts', 'extracting and cleaning semantic morphemes', 'building a co-occurrence matrix', and 'analyzing network features and clustering topic groups'. Results: A total of 789 papers published between 2002 and 2021 were found in databases (Springer). Among them, 435 words were extracted from 118 articles selected according to the conditions: 'analyzed by text network analysis and topic modeling'. The core keywords were 'self-management', 'intervention', 'health', 'support', 'technique' and 'system'. Through the topic modeling analysis, four themes were derived: 'intervention', 'blood glucose level control', 'self-management' and 'mobile health'. The main topic of this study was 'self-management'. Conclusion: While more recent work has investigated mobile applications, the highest feature was related to self-management in the diabetes care and prevention. Nursing interventions utilizing mobile application are expected to not only effective and powerful glycemic control and self-management tools, but can be also used for patient-driven lifestyle modification.

• Proceedings of the Microbiological Society of Korea Conference
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• 2005.05a
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• pp.152-153
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• 2005

• Animal cells and systems
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• v.13 no.3
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• pp.305-314
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• 2009

The control region of mitochondrial DNA (13516-14619) is located between srRNA and $tRNA^{lle}$ gene in swimming crab, Portunus trituberculatus. The present study was investigated the genetic polymorph isms of the control region in samples of P. trituberculatus collected at coastal waters of the Yellow Sea in Korea. A total of 300 substitution and indel polymorphic sites were identified. In addition to SNPs and indel variation, a hypervariable microsatellite motif was also identified at position from 14358 to 14391, which exhibited 10 alleles including 53 different suballeles. When the hypervariable microsatellite motif was removed from the alignment, 95 haplotypes were identified (93 unique haplotypes). The nucleotide and haplotype diversities were ranged from 0.024 to 0.028 and from 0.952 to 1.000, respectively. The statistically significant evidence for geographical structure was not detected from the analyses of neighbor-joining tree and minimum-spanning network, neither. This result suggest that population of P. trituberculatus are capable of extensive gene flow among populations. We believed that the polymorph isms of the control region will be used for informative markers to study phylogenetic relationships of P. trituberculatus.

• KSBB Journal
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• v.16 no.5
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• pp.452-458
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• 2001

Concentrations of ammonia in biological processes were controlled by PID controllers and also neural network based controllers (NN controllers). A flow injection analysis system has been to on-line monitor the concentrations of ammonia in a bioreactor. The effect of the analysis error and the residence time of samples on the control performance were studied. The optimal neural network structure was investigated by using computer simulation and found to be a 3(input layer)-2(hidden layer)-1(output layer). The NN controller is often time consuming, but it has advantage over the PID controller in sensitivity. The 3-2-1 NN controller has been applied to control the ammonia concentrations in a simulated bioprocess and also a real cultivation process of yeast. The good control performance showed that the 3-2-1 NN controller based on the FIA system can be used to control the concentration of substrates in biological processes very well.