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Microfluidic concentration-on-demand combinatorial dilutions

Kangsun Lee, Choong Kim, Youngeun Kim, Byungwook Ahn, Jaehoon Bang, Jungkwun Kim, Rajagopal Panchapakesan, Yong-Kyu Yoon, Ji Yoon Kang, Kwang W. Oh
2011 Microfluidics and Nanofluidics  
In this paper, we presented a straightforward strategy to generate 15 combinations with 3 samples, using single-layer microfluidic network. First, we investigated the performance of the single-layer based design by computational simulation (CFD-ACE + ). The simulated output concentrations were extremely close to the expected values within absolute error < 1%. Based on the simulated design, a PDMS device was fabricated by soft-lithography and tested with fluorescent dye (sodium salt). The
more » ... torial mixing results for 15 combinations showed good performance with absolute error less than 4%. In addition, we have also conceptually presented two liquid handing methods (bottom-up and top-down) for high-throughput screening and assay.
doi:10.1007/s10404-011-0775-8 fatcat:t6atgt4fqzesxkcf63pmo5jnoa

Invasive Lactuca serriola seeds contain endophytic bacteria that contribute to drought tolerance

Seorin Jeong, Tae-Min Kim, Byungwook Choi, Yousuk Kim, Eunsuk Kim
2021 Scientific Reports  
Kee Dae Kim for their insightful comments. We also thank the associate editor and anonymous reviewers for valuable comments on the manuscript.  ... 
doi:10.1038/s41598-021-92706-x pmid:34172799 fatcat:iejbwzqhwngzbmecp2iad2pejq

Gelatin-Alginate Coacervates Optimized by DOE to Improve Delivery of bFGF for Wound Healing

ByungWook Kim, Eunmi Ban, Aeri Kim
2021 Pharmaceutics  
Metabolic disorders in diabetic patients are associated with altered protein and lipid metabolism and defects in granulation tissue formation, resulting in non-healing wounds such as diabetic foot ulcers (DFU). Growth factors have essential roles in tissue re-epithelization and angiogenesis during wound healing. In this study, a complex coacervate was evaluated as an enhanced delivery system for fibroblast growth factor (bFGF) to control its release rate and protect it from proteases.
more » ... s composed of gelatin Type A (GA) and sodium alginate (SA) were optimized by the Design of Experiments (DOE), with the polymer ratio and the medium's pH as the independent variables, and turbidity, particle size, polydispersity index, and encapsulation efficiency (EE, %) as the responses. The optimized coacervate protected bFGF from trypsin digestion and showed controlled release compared with bFGF in solution or a physical mixture of GA and SA. It enhanced the viability, migration, and procollagen I C-terminal propeptide synthesis of human dermal fibroblasts in hyperglycemic conditions. In summary, the DOE approach was successfully applied to optimize bFGF GA-SA coacervates as a potential novel therapeutic modality to treat DFU.
doi:10.3390/pharmaceutics13122112 pmid:34959393 pmcid:PMC8705889 fatcat:jl6ghlbpbfar5g7mrz72rtqc24

Identification of genetic variants regulating the abundance of clinically relevant plasma proteins using the Diversity Outbred mouse model [article]

Stéphanie Philtjens, Dominic James Acri, Byungwook Kim, Hyewon Kim, Jungsu Kim
2020 bioRxiv   pre-print
Although there have been numerous expression quantitative trait loci (eQTL) studies, the effect of genetic variants on the levels of multiple plasma proteins still warrants more systematic investigation. To identify genetic modifiers that influence the levels of clinically relevant plasma proteins, we performed protein quantitative trait locus (pQTL) mapping on 92 proteins using the Diversity Outbred (DO) mouse population and identified 12 significant cis and 6 trans pQTL. Among them, we
more » ... red coding variants in a cis-pQTL in Ahr and a trans-pQTL in Rfx1 for the IL-17A protein. Our study reports an innovative pipeline for the identification of genetic modifiers that may be targeted for drug development.
doi:10.1101/2020.11.04.367938 fatcat:sd3wxhjpbncaff5rh75k7mknce

Gelatin-Alginate Complexes for EGF Encapsulation: Effects of H-Bonding and Electrostatic Interactions

Seonghee Jeong, ByungWook Kim, Hui-Chong Lau, Aeri Kim
2019 Pharmaceutics  
Gelatin Type A (GA) and sodium alginate (SA) complexes were explored to encapsulate epidermal growth factor (EGF), and thereby to circumvent its proteolytic degradation upon topical application to chronic wounds. Phase diagrams were constructed based on turbidity as a function of GA to SA ratio and pH. Various GA-SA mixtures were compared for polydispersity index, zeta potential, Z-average, and ATR-FTIR spectra. Trypsin digestion and human dermal fibroblast scratch wound assay were done to
more » ... ate the effects of EGF encapsulation. The onset pH values for coacervation and precipitation were closer together in high molecular weight GA (HWGA)-SA reaction mixtures than in low molecular weight GA (LWGA)-SA, which was attributed to strong H-bonding interactions between HWGA and SA probed by ATR-FTIR. EGF incorporation in both HWGA-SA precipitates and LWGA-SA coacervates below the isoelectric point of EGF, but not above it, suggests the contribution of electrostatic interactions between EGF and SA. EGF encapsulated in LWGA-SA coacervates was effectively protected from trypsin digestion and showed better in vitro scratch wound activity compared to free EGF. LWGA-SA coacervates are suggested as a novel delivery system for topical application of EGF to chronic wounds.
doi:10.3390/pharmaceutics11100530 pmid:31614977 pmcid:PMC6835588 fatcat:mxhos56wovfwnb64neqvbvee6i

Improved Diabetic Wound Healing by EGF Encapsulation in Gelatin-Alginate Coacervates

Seonghee Jeong, ByungWook Kim, Minwoo Park, Eunmi Ban, Soo-Hyeon Lee, Aeri Kim
2020 Pharmaceutics  
Kim et al. showed that decreased levels of TNF-α and IL-1 after treatment with EGF and hyaluronate-EGF conjugate on the skin wound in normal (non-diabetic) rats [15] .  ... 
doi:10.3390/pharmaceutics12040334 pmid:32276508 pmcid:PMC7238057 fatcat:5z7aovz2tfezvimumiaj4gash4

Optimal Color Lighting for Scanning Images of Flat Panel Display using Simplex Search

HyungTae Kim, EungJoo Ha, KyungChan Jin, ByungWook Kim
2018 Journal of Imaging  
A system for inspecting flat panel displays (FPDs) acquires scanning images using multiline charge-coupled device (CCD) cameras and industrial machine vision. Optical filters are currently installed in front of these inspection systems to obtain high-quality images. However, the combination of optical filters required is determined manually and by using empirical methods; this is referred to as passive color control. In this study, active color control is proposed for inspecting FPDs. This
more » ... ction scheme requires the scanning of images, which is achieved using a mixed color light source and a mixing algorithm. The light source utilizes high-power light emitting diodes (LEDs) of multiple colors and a communication port to dim their level. Mixed light illuminates an active-matrix organic light-emitting diode (AMOLED) panel after passing through a beam expander and after being shaped into a line beam. The image quality is then evaluated using the Tenenbaum gradient after intensity calibration of the scanning images. The dimming levels are determined using the simplex search method which maximizes the image quality. The color of the light was varied after every scan of an AMOLED panel, and the variation was iterated until the image quality approached a local maximization. The number of scans performed was less than 225, while the number of dimming level combinations was 20484. The proposed method can reduce manual tasks in setting-up inspection machines, and hence is useful for the inspection machines in FPD processes.
doi:10.3390/jimaging4110133 fatcat:2vp2u7ezvbab5kw2vrpgwkflty

3DIV: A 3D-genome Interaction Viewer and database

Dongchan Yang, Insu Jang, Jinhyuk Choi, Min-Seo Kim, Andrew J Lee, Hyunwoong Kim, Junghyun Eom, Dongsup Kim, Inkyung Jung, Byungwook Lee
2017 Nucleic Acids Research  
Three-dimensional (3D) chromatin structure is an emerging paradigm for understanding gene regulation mechanisms. Hi-C (high-throughput chromatin conformation capture), a method to detect long-range chromatin interactions, allows extensive genome-wide investigation of 3D chromatin structure. However, broad application of Hi-C data have been hindered by the level of complexity in processing Hi-C data and the large size of raw sequencing data. In order to overcome these limitations, we constructed
more » ... a database named 3DIV (a 3D-genome Interaction Viewer and database) that provides a list of long-range chromatin interaction partners for the queried locus with genomic and epigenomic annotations. 3DIV is the first of its kind to collect all publicly available human Hi-C data to provide 66 billion uniformly processed raw Hi-C read pairs obtained from 80 different human cell/tissue types. In contrast to other databases, 3DIV uniquely provides normalized chromatin interaction frequencies against genomic distance dependent background signals and a dynamic browsing visualization tool for the listed interactions, which could greatly advance the interpretation of chromatin interactions. '3DIV' is available at http://kobic.kr/3div.
doi:10.1093/nar/gkx1017 pmid:29106613 pmcid:PMC5753379 fatcat:l3ypzvmt7na6fm7hhompag6nge

Design a High-Level Language for Large Network Security Management [chapter]

Jangha Kim, Byungwook Song, Kanghee Lee, Sangwook Kim, Daesik Choi, Jungtaek Seo
2004 Lecture Notes in Computer Science  
A common breach of network security is the class of attacks called Worm-virus. This paper proposes a language called Triton whose goal is to efficiently and effectively safeguard large network security for management system. We represent abstract language that supports various functions. This high-level language abstracts the control behavior of the network nodes, which has various setting-up methodology. We shall describe the feature of Triton language and give some example of the preliminary Triton implementation on the test-bed.
doi:10.1007/978-3-540-30470-8_4 fatcat:tazgf6i4evacngfkq72gwnpkiy

Genetic Landscape of Open Chromatin in Yeast

Kibaick Lee, Sang Cheol Kim, Inkyung Jung, Kwoneel Kim, Jungmin Seo, Heun-Sik Lee, Gireesh K. Bogu, Dongsup Kim, Sanghyuk Lee, Byungwook Lee, Jung Kyoon Choi, Hunter Fraser
2013 PLoS Genetics  
Chromatin regulation underlies a variety of DNA metabolism processes, including transcription, recombination, repair, and replication. To perform a quantitative genetic analysis of chromatin accessibility, we obtained open chromatin profiles across 96 genetically different yeast strains by FAIRE (formaldehyde-assisted isolation of regulatory elements) assay followed by sequencing. While 5,10% of open chromatin region (OCRs) were significantly affected by variations in their underlying DNA
more » ... ces, subtelomeric areas as well as gene-rich and gene-poor regions displayed high levels of sequenceindependent variation. We performed quantitative trait loci (QTL) mapping using the FAIRE signal for each OCR as a quantitative trait. While individual OCRs were associated with a handful of specific genetic markers, gene expression levels were associated with many regulatory loci. We found multi-target trans-loci responsible for a very large number of OCRs, which seemed to reflect the widespread influence of certain chromatin regulators. Such regulatory hotspots were enriched for known regulatory functions, such as recombinational DNA repair, telomere replication, and general transcription control. The OCRs associated with these multi-target trans-loci coincided with recombination hotspots, telomeres, and gene-rich regions according to the function of the associated regulators. Our findings provide a global quantitative picture of the genetic architecture of chromatin regulation.
doi:10.1371/journal.pgen.1003229 pmid:23408895 pmcid:PMC3567132 fatcat:4xhpaubxljgyzm2piterhodgpe

Identification of Ethnically Specific Genetic Variations in Pan-Asian Ethnos

Jin Ok Yang, Sohyun Hwang, Woo-Yeon Kim, Seong-Jin Park, Sang Cheol Kim, Kiejung Park, Byungwook Lee
2014 Genomics & Informatics  
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
more » ... 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.
doi:10.5808/gi.2014.12.1.42 pmid:24748860 pmcid:PMC3990765 fatcat:mev6eodmbbbppnku3zc523zdce

Kinematic Analysis and Experimental Verification on the Locomotion of Gecko

Woochul Nam, TaeWon Seo, Byungwook Kim, Dongsu Jeon, Kyu-Jin Cho, Jongwon Kim
2009 Journal of Bionic Engineering  
This paper presents a kinematic analysis of the locomotion of a gecko, and experimental verification of the kinematic model. Kinematic analysis is important for parameter design, dynamic analysis, and optimization in biomimetic robot research. The proposed kinematic analysis can simulate, without iteration, the locomotion of gecko satisfying the constraint conditions that maintain the position of the contacted feet on the surface. So the method has an advantage for analyzing the climbing motion
more » ... of the quadruped mechanism in a real time application. The kinematic model of a gecko consists of four legs based on 7-degrees of freedom spherical-revolute-spherical joints and two revolute joints in the waist. The motion of the kinematic model is simulated based on measurement data of each joint. The motion of the kinematic model simulates the investigated real gecko's motion by using the experimental results. The analysis solves the forward kinematics by considering the model as a combination of closed and open serial mechanisms under the condition that maintains the contact positions of the attached feet on the ground. The motions of each joint are validated by comparing with the experimental results. In addition to the measured gait, three other gaits are simulated based on the kinematic model. The maximum strides of each gait are calculated by workspace analysis. The result can be used in biomimetic robot design and motion planning.
doi:10.1016/s1672-6529(08)60121-3 fatcat:okhdizbnhvhprclcs6kcfygeo4

Bioinformatics services for analyzing massive genomic datasets

Gunhwan Ko, Pan-Gyu Kim, Youngbum Cho, Seongmun Jeong, Jae-Yoon Kim, Kyoung Hyoun Kim, Ho-Yeon Lee, Jiyeon Han, Namhee Yu, Seokjin Ham, Insoon Jang, Byunghee Kang (+10 others)
2020 Genomics & Informatics  
Kim  ...  -0038-461X Jae-Yoon Kim: https://orcid.org/0000-0002-8557-0998 Kyoung Hyoun Kim: https://orcid.org/0000-0002-7652-1879 Ho-Yeon Lee: https://orcid.org/0000-0002-1026-1744 Jiyeon Han: https://orcid.org/0000  ... 
doi:10.5808/gi.2020.18.1.e8 fatcat:s6adhmxa4vamlpreykcejc3hcy

Bioinformatics services for analyzing massive genomic datasets

Gunhwan Ko, Pan-Gyu Kim, Youngbum Cho, Seongmun Jeong, Jae-Yoon Kim, Kyoung Hyoun Kim, Ho-Yeon Lee, Jiyeon Han, Namhee Yu, Seokjin Ham, Insoon Jang, Byunghee Kang (+10 others)
2020 Genomics & Informatics  
Kim  ...  -0038-461X Jae-Yoon Kim: https://orcid.org/0000-0002-8557-0998 Kyoung Hyoun Kim: https://orcid.org/0000-0002-7652-1879 Ho-Yeon Lee: https://orcid.org/0000-0002-1026-1744 Jiyeon Han: https://orcid.org/0000  ... 
doi:10.5808/gi.2020.18.1.e8 pmid:32224841 pmcid:PMC7120352 fatcat:upd22fio7rfqrc3ffaepatxeee

IntoPub: A Directory Server for Bioinformatics Tools and Databases

DongSoo Jung, Sanghyuk Lee, Ji Han Kim, Byungwook Lee
2011 Interdisciplinary Bio Central  
DJ thanks Jemin Kim for correcting and updating XML-parsing modules.  ...  Acknowled This work w gram and the K gy (MEST) und Kim for correct ACKNOWLEDGEMENTS This work was supported by the KRIBB Research Initiative Program and the Korean Ministry of Education, Science and Technology  ... 
doi:10.4051/ibc.2011.3.3.0012 fatcat:mjeqozq25ba3pjd2bwogcoonui
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