Jung Hoon Park

Yonsei University Hospital, Seoul, Seoul, South Korea

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Publications (20)26.69 Total impact

  • [show abstract] [hide abstract]
    ABSTRACT: Next-generation sequencing (NGS) has enabled the high-throughput discovery of germline and somatic mutations. However, NGS-based variant detection is still prone to errors, resulting in inaccurate variant calls. Here, we categorized the variants detected by NGS according to total read depth (TD) and SNP quality (SNPQ), and performed Sanger sequencing with 348 selected non-synonymous single nucleotide variants (SNVs) for validation. Using the SAMtools and GATK algorithms, the validation rate was positively correlated with SNPQ but showed no correlation with TD. In addition, common variants called by both programs had a higher validation rate than caller-specific variants. We further examined several parameters to improve the validation rate, and found that strand bias (SB) was a key parameter. SB in NGS data showed a strong difference between the variants passing validation and those that failed validation, showing a validation rate of more than 92% (filtering cutoff value: alternate allele forward [AF]≥20 and AF<80 in SAMtools, SB<-10 in GATK). Moreover, the validation rate increased significantly (up to 97-99%) when the variant was filtered together with the suggested values of mapping quality (MQ), SNPQ and SB. This detailed and systematic study provides comprehensive recommendations for improving validation rates, saving time and lowering cost in NGS analyses.
    PLoS ONE 01/2014; 9(1):e86664. · 3.73 Impact Factor
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    ABSTRACT: Introduction The development of reliable gene expression profiling technology increasingly impacts our understanding of lung cancer biology. Here, we used RNA sequencing (RNA-Seq) to compare the transcriptomes of non-small cell lung cancer (NSCLC) and normal lung tissues and to investigate expression in lung cancer tissues. Methods We enrolled 88 male patients (mean age, 61.2 years) with NSCLC. RNA-Seq was performed on 88 pairs of NSCLC tumor tissue and non-tumor tissue from 54 patients with adenocarcinoma and 34 patients with squamous cell carcinoma. Immunohistochemistry was performed to validate differential candidate gene expression in a different NSCLC group. Results RNA-Seq produced 25.41 × 106 (± 8.90 × 106) reads in NSCLC tissues and 24.70 × 106 (± 4.70 × 106) reads in normal lung tissues [mean (± standard deviation)]. Among the genes expressed in both tissues, 335 were upregulated and 728 were downregulated ≥ 2-fold (P < 0.001). Four upregulated genes–CBX3, GJB2, CRABP2, and DSP–not previously reported in lung cancer were studied further. Their altered expression was verified by immunohistochemistry in a different set of NSCLC tissues (n = 154). CBX3 was positive in 90.3% (139 cases) of the samples; GJB2, in 22.7% (35 cases); CRABP2, in 72.1% (111 cases); and DSP, in 17.5% (27 cases). The positive rate of CRABP2 was higher in adenocarcinoma than squamous cell carcinoma (p < 0.01). Conclusions CBX3 and CRABP2 expression was markedly increased in lung cancer tissues and especially CRABP2 may be promising candidate genes in lung adenocarcinoma.
    Lung Cancer. 01/2014;
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    ABSTRACT: Plants are photosynthetic organisms that depend on sunlight for energy. Plants respond to light through different photoreceptors and show photomorphogenic development. Apart from Photosynthetically Active Radiation (PAR; 400-700 nm), plants are exposed to UV light, which is comprised of UV-C (below 280 nm), UV-B (280-320 nm) and UV-A (320-390 nm). The atmospheric ozone layer protects UV-C radiation from reaching earth while the UVR8 protein acts as a receptor for UV-B radiation. Low levels of UV-B exposure initiate signaling through UVR8 and induce secondary metabolite genes involved in protection against UV while higher dosages are very detrimental to plants. It has also been reported that genes involved in MAPK cascade help the plant in providing tolerance against UV radiation. The important targets of UV radiation in plant cells are DNA, lipids and proteins and also vital processes such as photosynthesis. Recent studies showed that, in response to UV radiation, mitochondria and chloroplasts produce a reactive oxygen species (ROS). Arabidopsis metacaspase-8 (AtMC8) is induced in response to oxidative stress caused by ROS, which acts downstream of the radical induced cell death (AtRCD1) gene making plants vulnerable to cell death. The studies on salicylic and jasmonic acid signaling mutants revealed that SA and JA regulate the ROS level and antagonize ROS mediated cell death. Recently, molecular studies have revealed genes involved in response to UV exposure, with respect to programmed cell death (PCD).
    International Journal of Molecular Sciences 01/2013; 14(1):1608-28. · 2.46 Impact Factor
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    ABSTRACT: Peroxiredoxins (Prxs), which are classified into three isotypes in plants, play important roles in protection systems as peroxidases or molecular chaperones. The three Prx isotypes of Chinese cabbage, namely C1C-Prx, C2C-Prx, and C-PrxII, have recently been identified and characterized. The present study compares their molecular properties and biochemical functions to gain insights into their concerted roles in plants. The three Prx isotype genes were differentially expressed in tissue- and developmental stage-specific manners. The transcript level of the C1C-Prx gene was abundant at the seed stage, but rapidly decreased after imbibitions. In contrast, the C2C-Prx transcript was not detected in the seeds, but its expression level increased at germination and was maintained thereafter. The C-PrxII transcript level was mild at the seed stage, rapidly increased for 10 days after imbibitions, and gradually disappeared thereafter. In the localization analysis using GFP-fusion proteins, the three isotypes showed different cellular distributions. C1C-Prx was localized in the cytosol and nucleus, whereas C2C-Prx and C-Prx were found mainly in the chloroplast and cytosol, respectively. In vitro thiol-dependent antioxidant assays revealed that the relative peroxidase activities of the isotypes were CPrxII > C2C-Prx > C1C-Prx. C1C-Prx and C2C-Prx, but not C-PrxII, prevented aggregation of malate dehydrogenase as a molecular chaperone. Taken together, these results suggest that the three isotypes of Prx play specific roles in the cells in timely and spatially different manners, but they also cooperate with each other to protect the plant.
    Molecules and Cells 01/2012; 33(1):27-33. · 2.21 Impact Factor
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    ABSTRACT: Zinc finger-homeodomain proteins (ZF-HDs) have been identified in many plant species. In soybean (Glycine max), GmZF-HD1 functions as a transcription factor that activates the soybean calmodulin isoform-4 (GmCaM-4) gene in response to pathogens. Recently, we reported specific binding of GmZF-HD1 to a 30-nt A/T-rich cis-element which constitutes two repeats of a conserved homeodomain binding site, ATTA, within -1207 to -1128bp of the GmCaM-4 promoter. Herein, homeodomain sequences of the GmZF-HD1 protein were compared to those of other homeodomain proteins and characterized the specificity of DNA sequences in the interaction of the GmCaM-4 promoter with GmZF-HD1 protein. Considering the conservation of homeodomains in plants, the AG sequence within a 30-nt A/T-rich cis-element is required for binding of the GmZF-HD1 protein. Approximately 25-bp of A/T-rich DNA sequences containing an AG sequence is necessary for effective binding to the GmZF-HD1 protein. Taken together, the results support the notion that the GmZF-HD1 protein specifically functions in plant stress signalling by interacting with the promoter of GmCaM-4.
    Phytochemistry 11/2010; 71(16):1832-8. · 3.05 Impact Factor
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    ABSTRACT: One of the sites most frequently invaded by gastric cancer is the mesocolon; however, the UICC does not mention this anatomical site as an adjacent structure involved in gastric cancer. The purpose of this study was to characterize and classify mesocolon invasion from gastric cancer. We examined 806 patients who underwent surgery for advanced gastric carcinoma from 1992 to 2007 at the Department of Surgery, Gangnam Severance Hospital, Korea. Among these, patients who showed macroscopically direct invasion into the mesocolon were compared to other patients with advanced gastric cancer. The curability, number and extent of nodal metastasis, and the survival of the mesocolon invasion group were significantly worse than these factors in the T3 group. However, the survival of the mesocolon invasion group after curative resection was much better than that of patients who had incurable factors. Mesocolon invasion should be included in T4 for the staging of gastric cancer.
    Journal of Surgical Oncology 03/2010; 101(3):205-8. · 2.64 Impact Factor
  • Jung Hoon Park, Ki Young Kim, Sang Do Park
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    ABSTRACT: An oxygen transport ceramic membrane was prepared with La0.6Sr0.4TixFe1−xO3−δ (x = 0.2 and 0.3) oxides which was synthesized by polymerized complex method. In order to investigate the effects of Ti substitutions into lanthanum–strontium ferrites, material property, thermal expansion coefficient, oxygen permeation, electrical conductivity and phase stability were examined according to Ti contents. The thermal expansion coefficients of LSTF6428 and LSTF6437 were 25.76 × 10−6 K−1 and 21.32 × 10−6 K−1 in the temperature range of 973−1273 K, respectively. The oxygen permeation fluxes through a disk type dense membrane of LSTF6428 and LSTF6437 with 1.6 mm thickness increased exponentially with increasing temperature and were 0.17 mL min−1cm–2 and 0.13 mL min−1cm−2 with Ph = 0.21 atm (O2 rich side) and Pl = 10−5 atm (lean side) at 1223 K, respectively. In the result of phase stability test with various conditions such as He, H2/N2 and CO2 atmosphere, La0.6Sr0.4TixFe1−xO3−δ was confirmed to be more stable than La0.6Sr0.4Ti0.2Fe0.8O3−δ through XRD and SEM analysis.
    Desalination. 01/2009;
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    ABSTRACT: The estimation of disturbance torque in the safety window system is important for peoplepsilas convenience. Mostly, this kind of system can estimate the torque of window traveling system using the output of a hall sensor. To set up a window torque estimation system, however, is normally complicate and expensive. In addition, the calculation process of a window torque from the hall sensor output has usually inaccuracy because of various noises. To tackle this inherent problems of the previous approaches, a new sensorless DC drive disturbance torque estimator based on the Kalman estimator is proposed. Aside from the existing methods which utilize a torque from the hall sensor output, the proposed algorithm detects the pinched condition using the a motor driving current. The suggested scheme is also able to produce more a reliable pinch alarm in stead of the previous method.
    Control, Automation and Systems, 2008. ICCAS 2008. International Conference on; 11/2008
  • Jung hoon Park, Sang do Park
    Journal of Chemical Engineering of Japan - J CHEM ENG JPN. 01/2008; 41(7):590-596.
  • Jung hoon Park, Sang do Park
    Journal of Chemical Engineering of Japan - J CHEM ENG JPN. 01/2008; 41(7):631-638.
  • Jung Hoon Park, Sang Do Park
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    ABSTRACT: La0.6Sr0.4Co0.2Fe0.8O3−δ oxides were synthesized by citrate method and hydrothermal method. The oxides prepared by citrate method are perovskite type structure, while the oxides by hydrothermal method have a small amount of secondary phase in the powder. Pyrex glass seal and Ag melting seal provided reliable gas-tight sealing of disk type dense membrane in the range of operation temperature, but commercial ceramic binder could not be removed from the support tube without damage to the tube or membrane. Though the degree of gas tightness increases in the order of glass>Ag>ceramic binder, in the case of glass seal, the undesired spreading of glass leads to an interfacial reaction between it and the membrane and reduction of effective permeation area. The oxygen flux of La0.6Sr0.4Co0.2Fe0.8O3−δ membrane increases with increasing temperature and decreasing thickness, and the oxygen permeation flux through 1.0 mm membrane exposed to flowing air (P h =0.21 atm) and helium (P1=0.037 atm) is ca. 0.33 ml/cm2·min at 950 °C. X-ray diffraction analysis for the membrane after permeation test over 160 h revealed that La2O3 and unknown compound were formed on the surface of membrane. The segregation compounds of surface elements formed on both surfaces of membrane irrespective of spreading of glass sealing material.
    Korean Journal of Chemical Engineering 08/2007; 24(5):897-905. · 1.06 Impact Factor
  • Jung Hoon Park, Yong Ou Joung, Sang Do Park
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    ABSTRACT: Conversion and sulfur removal of coal in sub- and supercritical water was studied in a micro reactor in the temperature range of 340-400C and water density 0-0.27 g/cm3 for 0-90 min under N2 atmosphere. The experiments were conducted to investigate the effect of reaction temperature, pressure, time and density of water on the sulfur removal in gaseous and liquid effluents, respectively. The results show that supercritical condition is more effective than sub-critical condition to remove the sulfur from coal. It is possible to reduce 57.42% of the original sulfur in coal for the reaction time of 90 min at 400C and 30 MPa. The main gas containing sulfur in the gaseous effluent is not SO2 but H2S, irrespective of operating condition. The sulfur removal in liquid effluents is much greater than that in gas effluents. Compared with temperature, the influence of water density and pressure is less significant.
    Korean Journal of Chemical Engineering 01/2007; 24(2):314-318. · 1.06 Impact Factor
  • American Journal of Medical Genetics Part A 03/2006; 140(5):527-32. · 2.30 Impact Factor
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    ABSTRACT: To determine whether 5,10-methylenetetrahydrofolate reductase (MTHFR C677T and A1298C) genotype is associated with male infertility. Analysis of cytogenetic, Y chromosomal microdeletion assay (Yq), and the C677T and A1298C polymorphisms of the MTHFR gene by pyrosequencing and PCR-Restriction Fragment Length Polymorphism (RFLP) method. SAS 8.1 assessed the statistical risk of MTHFR genotype. The homozygous (T/T) C677T polymorphism of the MTHFR gene was present at a statistically high significance in unexplained infertile men with normal karyotype, instead at no significance in explained infertile men with chromosomal abnormality or Y chromosome deletion. There was no statistically significance of A1298C variation in infertile males. The MTHFR 677TT genotype may be a genetic risk factor for male infertility, especially with severe OAT and non-obstructive azoospermia in unexplained infertile males.
    Journal of Assisted Reproduction and Genetics 11/2005; 22(9-10):361-8. · 1.82 Impact Factor
  • Fertility and Sterility - FERT STERIL. 01/2003; 80:31-31.
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    ABSTRACT: Rheological properties of the polystyrene (PS) and poly(methyl methacrylate) (PMMA) blends were studied by Advanced Rheometric Expansion System (ARES). Storage modulus and loss modulus of the PS and PMMA blends were measured, and the interfacial tension of the PS and PMMA blends were obtained with various emulsion models by using the storage modulus and loss modulus of the blends. The value of interfacial tension estimated from the Palierne emulsion model was found to be 2.0 mN/m. Also, the interfacial tension between PS and PMMA was calculated by a theoretical model. The values of interfacial tension of the PS and PMMA blends obtained by the experiment and theoretical model were found to be in good agreement.
    Korean Journal of Chemical Engineering 02/2002; 19(2):337-341. · 1.06 Impact Factor
  • Jung Hoon Park, Sang Do Park
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    ABSTRACT: The effects of reaction temperature, pressure and residence time were investigated with a flow apparatus. Cellobiose decomposition kinetics and products in suband supercritical water were examined at temperatures from 320 to 420 °C at pressures from 25 to 40 MPa, and at residence times within 3 sec. Cellobiose was found to decompose via hydrolysis and pyrolysis. The yield of desired hydrolysis product, glucose, was the maximum value of 36.8% at 320 °C, 35 MPa, but the amount of 5-(hydroxymethyl)furfural (HMF), fermentation inhibitor increased too because residence time increased in the subcritical region owing to decrease of reaction rate. Meanwhile, though the yield of glucose is low in the supercritical region, the yield of HMF decreased compared with the subcritical region; and at the minimum yield of HMF (380 °C, 25 MPa), the yield of glucose was 21.4%. The decomposition of cellobiose followed first-order kinetics and the activation energy for the decomposition of cellobiose was 51.05 kJ/mol at 40MPa.
    Korean Journal of Chemical Engineering 01/2002; 19(6):960-966. · 1.06 Impact Factor
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    ABSTRACT: Blends of the linear bisphenol-A polycarbonate (L-PC) and randomly branched bisphenol-A polycarbonate (Br-PC), prepared by co-rotating twin screw extrusion, were investigated using differential scanning calorimetry (DSC), sag resistance time tester, extensional rheometry, and advanced rheometric expansion system (ARES). From the DSC results, the glass transition temperature (Tg) of the L-PC/Br-PC blend was increased with the increase of Br-PC in the blend, and the blend showed a singleTg, which suggests a miscible blend. The sag resistance time of the L-PC/Br-PC blend was increased with the increase of Br-PC in the blends. From the results of rheological measurements of the L-PC/Br-PC blends, the extensional viscosity and the complex viscosity of the blends were found to increase with the increase of Br-PC in the blends. The increase of extensional viscosity and complex viscosity was related with the increase of sag resistance time with the Br-PC in the L-PC/Br-PC blends.
    Macromolecular Research 01/2002; 10(3):135-139. · 1.64 Impact Factor
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    ABSTRACT: As a preliminary work for the preparation of nylon 6/clay nanocomposites by reactive extrusion, nylon 6/clay nanocomposites were prepared by anionic polymerization in a flask. In order to investigate the effect of the intercalation of clay layers, the clay feeding times, such as in pre-mixing where the clay was fed before initiation of polymerization and in after-mixing method where the clay was fed after initiation of polymerization, were changed. The appearance of the WAXD peak of nanocomposites prepared by the pre-mixing method was obvious and the tensile strength was decreased compared with that of pure nylon 6, which indicates that the clay layers were not dispersed and distributed. During the preparation of the nanocomposites by the after-mixing method, disordering of the clay layers was observed with increasing clay addition time and was suspected to result from the rapid polymerization of nylon 6 within the clay layers. Keywordsanionic polymerization–nanocomposite–intercalation–disordering–nylon
    Macromolecular Research 13(5):367-372. · 1.64 Impact Factor
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    ABSTRACT: A robust pinch detection algorithm which can be implemented in a cheap microprocessor is proposed for the development of a safety feature in the automotive power window system. To solve the problems caused by the performance degradation of a Hall sensor or real driving situations, the proposed algorithm makes use of the H ∞ state estimation technique. The motivation of this approach comes from the advantage that the H ∞ filter can minimize or bound the worst-case estimation error energy for all bounded energy disturbances. Herein, the pinch torque rate estimator is derived from applying the steady-state H ∞ filter to the augmented model, which includes the motor dynamics and an additional torque rate state. Then, to redesign an appropriate estimator for real-time implementation, the torque rate estimate can be calculated more efficiently than the previous method [1]. Experimental results verify that, with a small amount of computation, the proposed pinch detection algorithm provides fast pinch detection performance superior to the existing method. Furthermore, it guarantees robustness against the worst-case measurement noises.
    International Journal of Control Automation and Systems 7(2):185-192. · 0.95 Impact Factor

Publication Stats

60 Citations
26.69 Total Impact Points

Institutions

  • 2010
    • Yonsei University Hospital
      • Surgery
      Seoul, Seoul, South Korea
  • 2002–2009
    • Korea Institute of Energy Research
      Sŏul, Seoul, South Korea
    • Korea University
      • Department of Chemical and Biological Engineering
      Seoul, Seoul, South Korea
  • 2008
    • Yonsei University
      • Department of Electrical and Electronic Engineering
      Seoul, Seoul, South Korea
  • 2005–2006
    • CHA University
      • College of Medicine
      Sŏul, Seoul, South Korea