• Proceedings of the Korean Society for Bioinformatics Conference
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• 2006.02a
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• pp.83-89
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• 2006

Cellular functions are carried out by a concerted action of biochemical pathways whose components have genetic interactions. Abnormalities in the activity of the genes that constitute or modulate these pathways frequently have oncogenic implications. Therefore, identifying the upstream regulatory genes for major biochemical pathways and defining their roles in carcinogenesis can have important consequences in establishing an effective target-oriented antitumor strategy We have analyzed the gene expression profiles of human liver cancer samples using cDNA microarray chips enriched in liver and/or stomach-expressed cDNA elements, and identified groups of genes that can tell tumors from non-tumors or normal liver, or classify tumors according to clinical parameters such as tumor grade, age, and inflammation grade. We also set up a high-throughput cell-based assay system (cell chip) that can monitor the activity of major biochemical pathways through a reporter assay. Then, we applied the cell chip platform for the analysis of the HCC-associated genes discovered from transcriptome profiling, and found a number of cancer marker genes having a potential of modulating the activity of cancer-related biochemical pathways such as E2F, TCF, p53, Stat, Smad, AP-1, c-Myc, HIF and NF-kB. Some of these marker genes were previously blown to modulate these pathways, while most of the others not. Upon a fast-track phenotype analysis, a subset of the genes showed increased colony forming abilities in soft agar and altered cell morphology or adherence characteristics in the presence of purified matrix proteins. We are currently analyzing these selected marker genes in more detail for their effects on various biological Processes and for Possible clinical roles in liver cancer development.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.15 no.4
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• pp.913-920
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• 2011

In this paper, a logic process based 1-kbit EEPROM IP for RFID tag chips of 900MHz is designed. The cell array of the designed 1-kbit EEPROM IP is arranged in a form of four blocks of 16 rows x 16 columns, that is in a two-dimensional arrangement of one-word EEPROM phantom cells. We can reduce the IP size by making four memory blocks share CG (control gate) and TG (tunnel gate) driver circuits. We propose a TG switch circuit to supply respective TG bias voltages according to operational modes and to keep voltages between devices within 5.5V in terms of reliability in order to share the TG driver circuit. Also, we can reduce the power consumption in the read mode by using a partial activation method to activate just one of four memory blocks. Furthermore, we can reduce the access time by making BL (bit line) switching times faster in the read mode from reduced number of cells connected to each column. We design and compare two 1-kbit EEPROM IPs, two blocks of 32 rows ${\times}$ 16 columns and four blocks of 16 rows ${\times}$ 16 columns, which use Tower's $0.18{\mu}m$ CMOS process. The four-block IP is smaller by 11.9% in the layout size and by 51% in the power consumption in the read mode than the two-block counterpart.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.206-212
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• 2019

Propionibacterium acnes (P. acnes) lives in the hair follicles and pores, and it uses cell debris, sebum and metabolic byproducts of surrounding skin tissues as energy and nutrients. Increased production of sebum due to sebaceous hyperplasia or blockage of the follicle can cause growth and proliferation of P. acnes. The rapid growth of P. acnes in follicles produces cell damage, metabolic byproducts and bacterial chips, which can cause inflammation. In this study, we examined the possibility of Senecio iscoensis Hieron. (S. iscoensis) extract to regulate P. acnes-induced inflammatory signaling pathways. We observed that S. iscoensis extract effectively inhibited P. acnes-induced pro-inflammatory cytokine expressions such as IL-$1{\beta}$, TNF-${\alpha}$, and iNOS in mouse macrophage cell line Raw 264.7. The inhibitory effect of S. iscoensis in pro-inflammatory cytokine levels was accompanied by the inhibition of the transcription factors NF-${\kappa}B$ and NF-AT. However, S. iscoensis did not alter the P. acnes-induced MAPK signaling pathways. This study first suggests the potential of using S. iscoensis extract as an alternative agent for the treatment of acne.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.5
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• pp.2519-2525
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• 2016

There are several existing reports of microarray chip use for assessment of altered gene expression in different diseases. In fact, there have been over 1.5 million assays of this kind performed over the last twenty years, which have influenced clinical and translational research studies. The most commonly used DNA microarray platforms are Affymetrix GeneChip and Quality Control Software along with their GeneChip Probe Arrays. These chips are created using several quality controls to confirm the success of each assay, but their actual impact on gene expression profiles had not been previously analyzed until the appearance of several bioinformatics tools for this purpose. We here performed a data mining analysis, in this case specifically focused on ovarian cancer, as well as healthy ovarian tissue and ovarian cell lines, in order to confirm quality control results and associated variation in gene expression profiles. The microarray data used in our research were downloaded from ArrayExpress and Gene Expression Omnibus (GEO) and analyzed with Expression Console Software using RMA, MAS5 and Plier algorithms. The gene expression profiles were obtained using Partek Genomics Suite v6.6 and data were visualized using principal component analysis, heat map, and Venn diagrams. Microarray quality control analysis showed that roughly 40% of the microarray files were false negative, demonstrating over- and under-estimation of expressed genes. Additionally, we confirmed the results performing second analysis using independent samples. About 70% of the significant expressed genes were correlated in both analyses. These results demonstrate the importance of appropriate microarray processing to obtain a reliable gene expression profile.

• Journal of the Institute of Electronics Engineers of Korea SD
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• v.46 no.4
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• pp.15-20
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• 2009

In a detection system based on laser light scattering, focusing an excitation laser beam into a focal point of a channel in a microfluidic chip is important for obtaining the highest excitation intensity, and consequently for obtaining a laser light scattering signal using a photodetector with a high efficiency. In this paper, we present a polydimethylsiloxane (PDMS) microfluidic chip consisting of an integrated PDMS microlens for cell detection based on laser light scattering. We fabricated PDMS microlens for optical detection system by simply putting down on PDMS chips. The PDMS microlens was fabricated by photoresist reflow and replica molding. This fabrication technique is simple and has an excellent property in terms of the microlens and a high-dimensional accuracy. The PDMS microlens integrated on the PDMS microfluidic chip has been verified to improve the laser intensity, and accordingly, the signal-to-noise ratio and sensitivity of laser light scattering detection for red blood cells(RBCs)

• JSTS:Journal of Semiconductor Technology and Science
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• v.13 no.4
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• pp.291-302
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• 2013

NAND flash memory (NFM) based storage devices, e.g. Solid State Drive (SSD), are rapidly replacing conventional storage devices, e.g. Hard Disk Drive (HDD). As NAND flash memory technology advances, its specification has evolved to support denser cells and larger pages and blocks. However, efforts to fully understand their impacts on design objectives such as performance, power, and cost for various applications are often neglected. Our research shows this recent trend can adversely affect the design objectives depending on the characteristics of applications. Past works mostly focused on improving the specific design objectives of NFM based systems via various architectural solutions when the specification of NFM is given. Several other works attempted to model and characterize NFM but did not access the system-level impacts of individual parameters. To the best of our knowledge, this paper is the first work that considers the specification of NFM as the design parameters of NAND flash storage devices (NFSDs) and analyzes the characteristics of various synthesized and real traces and their interaction with design parameters. Our research shows that optimizing design parameters depends heavily on the characteristics of applications. The main contribution of this research is to understand the effects of low-level specifications of NFM, e.g. cell type, page size, and block size, on system-level metrics such as performance, cost, and power consumption in various applications with different characteristics, e.g. request length, update ratios, read-and-modify ratios. Experimental results show that the optimized page and block size can achieve up to 15 times better performance than the conventional NFM configuration in various applications. The results can be used to optimize the system-level objectives of a system with specific applications, e.g. embedded systems with NFM chips, or predict the future direction of NFM.

• Molecular & Cellular Toxicology
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• v.3 no.3
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• pp.165-171
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• 2007

Mitomycin C (MMC), an antitumor antibiotic isolated from Streptomyces caespitosus, is used in chemotherapy of gastric, bladder and colorectal cancer. MMC is activated in vivo to alkylate and crosslink DNA, via G-G interstrand bonds, thereby inhibiting DNA synthesis and transcription. This study investigates gene expression changes in response to MMC treatment in order to elucidate the mechanisms of MMC-induced toxicity. MMC was admistered with single dose (0.32 and 1.6 ${\mu}M$) to TK6 cells. Applied Biosystem's DNA chips were used for identifying the gene expression profile by MMC-induced toxicity. We identified up- or down-regulated 90 genes including cyclin M2, cyclin-dependent kinase inhibitor 1A (p21, cip1), programmed cell death 1, tumor necrosis factor (ligand) superfamily, member 9, et al. The regulated genes by MMC associated with the biological pathways apoptosis signaling pathway. Further characterization of these candidate markers related to the toxicity will be useful to understand the detailed mechanism of action of MMC.

• Journal of the Institute of Electronics Engineers of Korea SD
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• v.42 no.6 s.336
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• pp.39-48
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• 2005

This paper proposes a reconfigurable coprocessor for communication systems, which can perform high speed computations and various functions. The proposed reconfigurable coprocessor can easily implement communication operations, such as scrambling, interleaving, convolutional encoding, Viterbi decoding, FFT, etc. The proposed architecture has been modeled by VHDL and synthesized using the SEC 0.18$\mu$m standard cell library. The gate count is about 35,000 gates and the critical path is 3.84ns. The proposed coprocessor can reduced about $33\%$ for FFT operations and complex MAC, $37\%$ for Viterbi operations, and $48\%\~84\%$ for scrambling and convolutional encoding for the IEEE 802.11a WLAN standard compared with existing DSPs. The proposed coprocessor shows Performance improvements compared with existing DSP chips for communication algorithms.

• Transactions of Materials Processing
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• v.17 no.8
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• pp.594-599
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• 2008

This paper presents a micro air pump based on the synthetic jet to supply reactant at the cathode side for micro fuel cells. The synthetic jet is a zero mass flux device that converts electrical energy into the momentum. The synthetic jet actuation is usually generated by a traditional PZT-driven actuator, which consists of a small cylindrical cavity, orifices and PZT diaphragms. Therefore, it is very important that the design parameters are optimized because of the simple configuration. To design the synthetic jet micro air pump, a numerical analysis has been conducted for flow characteristics with respect to various geometries. From results of numerical analysis, the micro air pump has been fabricated by the PDMS replication process. The most important design factors of the micro air pump in micro fuel cells are the small size and low power consumption. To satisfy the design targets, we used SP4423 micro chip that is high voltage output DC-AC converter to control the PZT. The SP4423 micro chips can operate from $2.2{\sim}6V$ power supply(or battery) and is capable of supplying up to 200V signals. So it is possible to make small size controller and low power consumption under 0.1W. The size of micro air pump was $16{\times}13{\times}3mm^3$ and the performance test was conducted. With a voltage of 3V at 800Hz, the air pump's flow rate was 2.4cc/min and its power consumption was only 0.15W.

• Journal of Korean Neurosurgical Society
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• v.60 no.4
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• pp.397-403
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• 2017

Objective : Cranioplasty using a cryopreserved skull flap is a wide spread practice. The most well-known complications of cranioplasty are postoperative surgical infections and bone flap resorption. In order to find biological evidence of cryopreserved cranioplasty, we investigated microorganism contamination of cryopreserved skulls and cultured osteoblasts from cryopreserved skulls. Methods : Cryopreserved skull flaps of expired patients stored in a bone bank were used. Cryopreserved skulls were packaged in a plastic bag and wrapped with cotton cloth twice. After being crushed by a hammer, cancellous bone between the inner and outer table was obtained. The cancellous bone chips were thawed in a water bath of $30^{\circ}C$ rapidly. After this, osteoblast culture and general microorganism culture were executed. Osteoblast cultures were done for 3 weeks. Microorganism cultures were done for 72 hours. Results : A total of 47 cryopreserved skull flaps obtained from craniectomy was enrolled. Of the sample, 11 people were women, and the average age of patients was 55.8 years. Twenty four people had traumatic brain injuries, and 23 people had vascular diseases. Among the patients with traumatic brain injuries, two had fracture compound comminuted depressed. The duration of cryopreservation was, on average, 83.2 months (9 to 161 months). No cultured osteoblast was observed. No microorganisms were cultured. Conclusion : In this study, neither microorganisms nor osteoblasts were cultured. The biological validity of cryopreserved skulls cranioplasty was considered low. However, the usage of cryopreserved skulls for cranioplasty is worthy of further investigation in the aspect of cost-effectiveness and risk-benefit of post-cranioplasty infection.