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TC1(C8orf4) is a novel endothelial inflammatory regulator enhancing NF-kappaB activity.
Kim, Jungtae,Kim, Yunlim,Kim, Hyun-Taek,Kim, Dong Wook,Ha, Yunhi,Kim, Jihun,Kim, Cheol-Hee,Lee, Inchul,Song, Kyuyoung Williams Wilkins 2009 JOURNAL OF IMMUNOLOGY Vol.183 No.6
<P>Endothelial inflammation is regulated by a complex molecular mechanism. TC1(C8orf4) is a novel regulator implicated in cancer and inflammation. It is a small protein conserved well among vertebrates. In zebrafish embryos, it is mostly expressed in angio-hematopoietic system and the overexpression induces edema. In human aortic endothelial cells and umbilical vein endothelial cells, TC1 transfection up-regulates key inflammatory cytokines, enzymes, and adhesion proteins including IL-6, IL-1alpha, COX-2, CXCL1, CCL5, CCL2, IL-8, ICAM1, VCAM1, and E-selectin, while TC1 knockdown down-regulates them. TC1 also enhances inflammatory parameters such as monocyte-endothelial adhesion and endothelial monolayer permeability. TC1 is up-regulated by IL-1beta, TNF-alpha, LPS, and phorbol ester, and the up-regulation is inhibited by I-kappaB-kinase inhibitors. TC1, in turn, enhances the nuclear translocation of RelA and the DNA binding activity, suggesting a biological role of amplifying NF-kappaB signaling via a positive feedback. Our findings suggest that TC1 is a novel endothelial inflammatory regulator that might be implicated in inflammatory vascular diseases.</P>
Semantic Signature: Comparative Interpretation of Gene Expression on a Semantic Space
Kim, Jihun,Kim, Keewon,Kim, Ju Han Hindawi Publishing Corporation 2016 Computational and mathematical methods in medicine Vol.2016 No.-
<P><I>Background</I>. Interpretation of microarray data remains challenging because biological meaning should be extracted from enormous numeric matrices and be presented explicitly. Moreover, huge public repositories of microarray dataset are ready to be exploited for comparative analysis. This study aimed to provide a platform where essential implication of a microarray experiment could be visually expressed and various microarray datasets could be intuitively compared.<I> Results</I>. On the semantic space, gene sets from Molecular Signature Database (MSigDB) were plotted as landmarks and their relative distances were calculated by Lin's semantic similarity measure. By formal concept analysis, a microarray dataset was transformed into a concept lattice with gene clusters as objects and Gene Ontology terms as attributes. Concepts of a lattice were located on the semantic space reflecting semantic distance from landmarks and edges between concepts were drawn; consequently, a specific geographic pattern could be observed from a microarray dataset. We termed a distinctive geography shared by microarray datasets of the same category as “semantic signature.”<I> Conclusions</I>. “Semantic space,” a map of biological entities, could serve as a universal platform for comparative microarray analysis. When microarray data were displayed on the semantic space as concept lattices, “semantic signature,” characteristic geography for a microarray experiment, could be discovered.</P>
Kim, Mijung,Park, Jihun,Ji, Sangyoon,Shin, Sung-Ho,Kim, So-Yun,Kim, Young-Cheon,Kim, Ju-Young,Park, Jang-Ung The Royal Society of Chemistry 2016 Nanoscale Vol.8 No.18
<P>Here we demonstrate fully-integrated, bezel-less transistor arrays using stretchable origami substrates and foldable conducting interconnects. Reversible folding of these arrays is enabled by origami substrates which are composed of rigid support fixtures and foldable elastic joints. In addition, hybrid structures of thin metal films and metallic nanowires worked as foldable interconnects which are located on the elastomeric joints.</P>
Kim, Jeong E.,Chun, Sung-Min,Hong, Yong S.,Kim, Kyu-pyo,Kim, Sun Y.,Kim, Jihun,Sung, Chang Ohk,Cho, Eun J.,Kim, Tae W.,Jang, Se Jin Elsevier 2019 The Journal of Molecular Diagnostics Vol.21 No.2
<P>Next-generation sequencing (NGS) panels are widely used for defining tumor mutation profiles and determining treatment approaches. We performed targeted NGS with 382 colorectal cancer genes with known microsatellite instability (MSI). After exclusion of germline alterations, the load of somatic mutations and small insertion/deletion (indel) alterations were determined. In the test set, 79 patients with 41 microsatellite-stable (MSS) and 38 MSI tumors were included. There were 120 MSS and eight MSI-high tumors in the validation set. The number of somatic mutations of whole samples were distinguished into three groups: mutant functional polymerase epsilon catalytic subunit, MSI, and MSS tumors. The median numbers of somatic and indel mutations in MSI tumors were higher. The indel mutation to whole mutation ratio (I index) was higher in MSI tumors. Hypermutation and low I index of polymerase epsilon catalytic subunit mutant tumors, a somatic mutation load cut-off of ≥40, and an I index of ≥9% were selected as the criteria for detecting MSI tumors with high sensitivity and specificity. With the analysis of alteration patterns of homopolymer genes, a higher median number of homopolymer mutations in MSI tumors was observed. Mutated homopolymer ≥5 was selected as the criterion for detecting MSI tumors. MSI in colorectal cancer can be detected by targeted NGS panels with high sensitivity and specificity using somatic mutation load and I index.</P>
Kim, Bohyun,Park, Seong Ho,Pickhardt, Perry J,Lee, Seung Soo,Ahn, Soyeon,Kim, Jihun,Kim, Jin Cheon,Yu, Chang Sik,Yang, Suk-Kyun,Kim, Ah Young,Ha, Hyun Kwon Radiological Society of North America 2014 Radiology Vol. No.
<P>To determine the postoperative incidence of adenomatous neoplasia in the colon proximal to an occlusive colorectal cancer where preoperative computed tomographic (CT) colonography findings were normal.</P>
SSD Performance Modeling Using Bottleneck Analysis
Kim, Jihun,Kim, Joonsung,Park, Pyeongsu,Kim, Jong,Kim, Jangwoo IEEE 2018 IEEE computer architecture letters Vol.17 No.1
<P>Solid-State Drives (SSDs) are widely deployed for high throughput and low latency. However, the unpredictable access latency of SSDs makes it difficult to satisfy quality-of-service requirements and fully achieve the performance potential. In fact, it has been a fundamental challenge to accurately predict the access latency of modern SSDs performing many non-disclosed, device-specific intra-SSD optimizations. In this paper, we propose SSDcheck, a novel SSD performance model which accurately predicts the latency of future SSD accesses. After first identifying write buffer (WB) and garbage collection (GC) as the key components in modeling the access latency, we develop diagnosis snippets to identify the target SSDs critical intra-SSD parameters (e.g., WB size). Finally, we construct the SSDs access-latency model with the identified parameters. Our system-level evaluations using five commodity SSDs show that SSDcheck achieves up to 93 percent prediction accuracy. Our real-world prototype applying an SSDcheck-aware system-level request scheduling can significantly improve both throughput and tail latency by up to 2.1x and 1.46x, respectively.</P>