A Method for Generating New Datasets Based on Copy Number for Cancer Analysis

Kim, Shinuk,Kon, Mark,Kang, Hyunsik Hindawi Publishing Corporation 2015 BioMed research international Vol.2015 No.-

<P>New data sources for the analysis of cancer data are rapidly supplementing the large number of gene-expression markers used for current methods of analysis. Significant among these new sources are copy number variation (CNV) datasets, which typically enumerate several hundred thousand CNVs distributed throughout the genome. Several useful algorithms allow systems-level analyses of such datasets. However, these rich data sources have not yet been analyzed as deeply as gene-expression data. To address this issue, the extensive toolsets used for analyzing expression data in cancerous and noncancerous tissue (e.g., gene set enrichment analysis and phenotype prediction) could be redirected to extract a great deal of predictive information from CNV data, in particular those derived from cancers. Here we present a software package capable of preprocessing standard Agilent copy number datasets into a form to which essentially all expression analysis tools can be applied. We illustrate the use of this toolset in predicting the survival time of patients with ovarian cancer or glioblastoma multiforme and also provide an analysis of gene- and pathway-level deletions in these two types of cancer.</P>

Surface Modification of a ZnO Electron-Collecting Layer Using Atomic Layer Deposition to Fabricate High-Performing Inverted Organic Photovoltaics

Kim, Kwang-Dae,Lim, Dong Chan,Hu, Jinhee,Kwon, Jung-Dae,Jeong, Myung-Geun,Seo, Hyun Ook,Lee, Joo Yul,Jang, Ka-Young,Lim, Jae-Hong,Lee, Kyu Hwan,Jeong, Yongsoo,Kim, Young Dok,Cho, Shinuk American Chemical Society 2013 ACS APPLIED MATERIALS & INTERFACES Vol.5 No.17

<P>A ripple-structured ZnO film as the electron-collecting layer (ECL) of an inverted organic photovoltaic (OPV) was modified by atomic layer deposition (ALD) to add a ZnO thin layer. Depositing a thin ZnO layer by ALD on wet-chemically prepared ZnO significantly increased the short-circuit current (<I>J</I><SUB>sc</SUB>) of the OPV. The highest power conversion efficiency (PCE) of 7.96% with <I>J</I><SUB>sc</SUB> of 17.9 mA/cm<SUP>2</SUP> was observed in the inverted OPV with a 2-nm-thick ALD-ZnO layer, which quenched electron–hole recombination at surface defects of ZnO ripples. Moreover, an ALD-ZnO layer thinner than 2 nm made the distribution of electrical conductivity on the ZnO surface more uniform, enhancing OPV performance. In contrast, a thicker ALD-ZnO layer (5 nm) made the two-dimensional distribution of electrical conductivity on the ZnO surface more heterogeneous, reducing the PCE. In addition, depositing an ALD-ZnO thin layer enhanced OPV stability and initial performance. We suggest that the ALD-ZnO layer thickness should be precisely controlled to fabricate high-performing OPVs.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/aamick/2013/aamick.2013.5.issue-17/am402403x/production/images/medium/am-2013-02403x_0009.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/am402403x'>ACS Electronic Supporting Info</A></P>

Synthesis and characterization of indeno[1,2-b]fluorene-based low bandgap copolymers for photovoltaic cells

Kim, Jinseck,Kim, Sun Hee,Jung, In Hwan,Jeong, Eunjae,Xia, Yangjun,Cho, Shinuk,Hwang, In-Wook,Lee, Kwanghee,Suh, Hongsuk,Shim, Hong-Ku,Woo, Han Young Royal Society of Chemistry 2010 Journal of materials chemistry Vol.20 No.8

<P>Two types of indenofluorene-based low bandgap conjugated polymers, poly(6,6′,12,12′-tetraoctylindeno[1,2-b]fluorene-co-4,7-bis(2-thienyl)-2,1,3-benzothiadiazole) (<B>PIF-DBT</B>) and poly(6,6′,12,12′-tetraoctylindeno[1,2-b]fluorene-co-5,7-dithien-2-yl-thieno[3,4-b]pyrazine) (<B>PIF-DTP</B>), were synthesized and characterized for use in plastic solar cells. The optical, electrochemical, charge carrier mobility, morphological and photovoltaic characteristics were investigated. The number-average molecular weights of the polymers measured by gel permeation chromatography ranged from 19 000 to 27 000 g mol<SUP>−1</SUP>. The polymers were fairly soluble in common organic solvents and formed optical-quality films by spin casting. Photophysical studies revealed a low bandgap of ∼1.9 eV for <B>PIF-DBT</B> and ∼1.6 eV for <B>PIF-DTP</B>, respectively, which could harvest the broad solar spectrum covering from 300 nm to 650 nm (<B>PIF-DBT</B>), and from 300 nm to 800 nm (<B>PIF-DTP</B>) in film. An electrochemical study confirmed the desirable HOMO/LUMO levels of the copolymers, which enable efficient electron transfer and a high open circuit voltage when blending them with fullerene derivatives. The field effect mobility measurements showed a hole mobility of 10<SUP>−5</SUP>∼10<SUP>−3</SUP> cm<SUP>2</SUP> V<SUP>−1</SUP> s<SUP>−1</SUP> for the copolymers. The film surface morphology was also studied by atomic force microscopy. Among the polyindenofluorene copolymers, <B>PIF-DBT50</B> (containing 50 mol% DBT) showed the best photovoltaic performance with an open circuit voltage of 0.77 V, a short circuit current of 5.50 mA cm<SUP>−2</SUP> and a power conversion efficiency of 1.70% when the polymers were blended with PC<SUB>71</SUB>BM, under air mass 1.5 global (AM 1.5G, 100 mW cm<SUP>−2</SUP>) illumination conditions.</P> <P>Graphic Abstract</P><P>The indenofluorene-based copolymers were synthesized and their photovoltaic properties were investigated. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=b919033c'> </P>

Easily Attainable Phenothiazine-BasedPolymers forPolymer Solar Cells: Advantage of Insertion of <i>S</i>,<i>S</i>-dioxides into its Polymer for Inverted Structure SolarCells

Kim, Gyoungsik,Yeom, Hye Rim,Cho, Shinuk,Seo, Jung Hwa,Kim, Jin Young,Yang, Changduk American ChemicalSociety 2012 Macromolecules Vol.45 No.4

<P>Two donor– (D−) acceptor (A) type polymersbasedon a soluble chromophore of phenothiazine (PT) unit that is a tricyclicnitrogen–sulfur heterocycle, have been synthesized by introducingan electron-deficient benzothiadiazole (BT) building block copolymerizedwith either PT or phenothiazine-<I>S</I>,<I>S</I>-dioxide (PT-<I>SS</I>) unit as an oxidized form of PT.The resulting polymers, <B>PPTDTBT</B> and <B>PPTDTBT-</B><I><B>SS</B></I> are fully characterized by UV–visabsorption, electrochemical cyclic voltammetry, X-ray diffraction(XRD), and DFT theoretical calculations. We find that the maximumabsorption of <B>PPTDTBT</B> is not only markedly red-shiftedwith respect to that of <B>PPTDTBT-</B><I><B>SS</B></I> but also its band gap as well as molecular energy levelsare readily tuned by the insertion of <I>S</I>,<I>S</I>-dioxides into the polymer. The main interest is focused on the electronicapplications of the two polymers in organic field-effect transistors(OFETs) as well as conventional and inverted polymeric solar cells(PSCs). <B>PPTDTBT</B> is a typical p-type polymer semiconductorfor OFETs and conventional PSCs based on this polymer and PC<SUB>71</SUB>BM show a power conversion efficiency (PCE) of 1.69%. In case of <B>PPTDTBT-</B><I><B>SS</B></I>, the devices characteristicsresult in: (i) 1 order of magnitude higher hole mobility (μ= 6.9 × 10<SUP>–4</SUP> cm<SUP>2</SUP> V<SUP>–1</SUP> s<SUP>–1</SUP>) than that obtained with <B>PPTDTBT</B> and (ii) improved performance of the inverted PSCs (1.22%), comparedto its conventional devices. Such positive features can be accountedfor in terms of closer packing molecular characteristics owing eitherto the effects of dipolar intermolecular interactions orientated fromthe sulfonyl groups or the relatively high coplanarity of <B>PPTDTBT-</B><I><B>SS</B></I> backbone.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/mamobx/2012/mamobx.2012.45.issue-4/ma202661b/production/images/medium/ma-2011-02661b_0011.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ma202661b'>ACS Electronic Supporting Info</A></P>

Enhanced Stability of Organic Photovoltaics by Additional ZnO Layers on Rippled ZnO Electron-collecting Layer using Atomic Layer Deposition

Kim, Kwang-Dae,Lim, Dong Chan,Jeong, Myung-Geun,Seo, Hyun Ook,Seo, Bo Yeol,Lee, Joo Yul,Song, Youngsup,Cho, Shinuk,Lim, Jae-Hong,Kim, Young Dok Korean Chemical Society 2014 Bulletin of the Korean Chemical Society Vol.35 No.2

We fabricated organic photovoltaic (OPV) based on ZnO ripple structure on indium tin oxide as electron-collecting layers and PTB7-F20 as donor polymer. In addition, atomic layer deposition (ALD) was used for preparing additional ZnO layers on rippled ZnO. Addition of 2 nm-thick ALD-ZnO resulted in enhanced initial OPV performance and stability. Based on photoluminescence results, we suggest that ALD-ZnO layers reduced number of surface defect sites on ZnO, which can act as electron-hole recombination center of OPV, and increased resistance of ZnO towards surface defect formation.

Comparisons of cancer classifiers based on RNA_seq and miRNA_seq

Kim, Shinuk,Lee, Hyowon,Kon, Mark Inderscience Enterprises Ltd. 2017 International journal of data mining and bioinform Vol.17 No.4

Ladder-type heteroacene polymers bearing carbazole and thiophene ring units and their use in field-effect transistors and photovoltaic cells

Cheedarala, Ravi Kumar,Kim, Gi-Hwan,Cho, Shinuk,Lee, Junghoon,Kim, Jonggi,Song, Hyun-Kon,Kim, Jin Young,Yang, Changduk Royal Society of Chemistry 2011 Journal of materials chemistry Vol.21 No.3

<P>A family of ladder-type π-excessive conjugated monomer (dicyclopentathienocarbazole (DCPTCz)) integrating the structural components of carbazole and thiophene into a single molecular entity is synthesized and polymerized by oxidative coupling to yield poly(dicyclopentathienocarbazole) (PDCPTCz). Moreover, through the careful selection of 2,1,3-benzothiadiazole unit as a π-deficient building block, the dicyclopentathienocarbazole-based donor–acceptor copolymer (poly(dicyclopentathienocarbazole-<I>alt</I>-2,1,3-benzothiadiazole) (PDCPTCz-BT)) is prepared by Suzuki polycondensation. The optical, electrochemical, and field-effect charge transport properties of the resulting polymers (PDCPTCz and PDCPTCz-BT) are not only characterized in detail but also their bulk-heterojunction (BHJ) solar cell in combination with PC<SUB>71</SUB>BM are evaluated. The values of field-effect mobility (<I>µ</I>) for PDCPTCz and PDCPTCz-BT are 8.7 × 10<SUP>−6</SUP> cm<SUP>2</SUP> V<SUP>−1</SUP> s<SUP>−1</SUP> and 2.7 × 10<SUP>−4</SUP> cm<SUP>2</SUP> V<SUP>−1</SUP> s<SUP>−1</SUP>, respectively. A power conversion efficiency (PCE) of 1.57% is achieved on the PDCPTCz-BT<B>/</B>PC<SUB>71</SUB>BM device, implying that the push–pull copolymers based on ladder-type dicyclopentathienocarbazole as an electron-donating moiety are promising for organic electronic devices.</P> <P>Graphic Abstract</P><P>A series of ladder-type heteroacene polymers based on dicyclopentathienocarbazole, <I>i.e.</I> poly(dicyclopentathienocarbazole) (PDCPTCz) and poly(dicyclopentathienocarbazole-alt-2,1,3-benzothiadiazole) (PDCPTCz-BT), is described for use in electronic applications. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c0jm01897j'> </P>

Downward self-polarization of lead-free (K_0.5 Na_0.5 )(Mn_0.005 Nb_0.995 )O₃ ferroelectric thin films on Nb:SrTiO₃ substrate

Seog, Hae Jin,Ahn, Chang Won,Cho, Shinuk,Kim, Kwang-Eun,Yang, Chan-Ho,Koo, Tae Yeong,Lee, Sun-Young,Kim, Jong Pil,Kim, Ill Won Wiley Blackwell (John Wiley Sons) 2017 Physica Status Solidi. Rapid Research Letters Vol.11 No.1

Effect of Annealing Time on the Performance of ZnO Nanoparticles-Assembled Microsphere-Based Dye-Sensitized Solar Cell

Nguyen Tri Khoa,Su Min CHOI,윤종원,Soon Wook KIM,박수정,Shinuk Cho,Sung Hong HAHN,Yong Soo KIM,Eui Jung Kim 한국물리학회 2016 새물리 Vol.66 No.10

We investigate the negative effect on the performance of t dye-sensitized solar cell (DSSC) due to increased annealing time of a ZnO nanoparticle-assembled microsphere-based photoanode. Annealing at 600 $^\circ$C for 30 to 300 min causes an increase in the oxygen interstitial (O$_i$) density to occur in the ZnO crystals. The ZnO crystals prepared with different annealing times are applied as photoanode layers in DSSCs to study the effect of annealing time on the efficiency of the DSSC. The efficiency of DSSCs decreases with increasing annealing time because (1) the O$_i$ defects generated in the ZnO crystal reduce the photocurrent density of the device by trapping the photo-excited electrons that diffuse from the dye to the photoanode layer, and (2) the improvement in the necking between ZnO nanoparticles with increasing annealing time causes the adsorption of dye on the ZnO surface to diminish.

An Empirical Interference Modeling for Link Reliability Assessment in Wireless Networks

Shinuk Woo,Hwangnam Kim IEEE 2013 IEEE/ACM transactions on networking Vol.21 No.1

<P>In recent years, it has been widely believed in the community that the link reliability is strongly related to received signal strength indicator (RSSI) [or signal-to-interference-plus-noise ratio (SINR)] and external interference makes it unpredictable, which is different from the previous understanding that there is no tight relationship between the link reliability and RSSI (or SINR), but multipath fading causes the unpredictability. However, both cannot fully explain why the unpredictability appears in the link state. In this paper, we unravel the following questions: 1) What causes frame losses that are directly related to intermediate link states? 2) Is RSSI or SINR a right criterion to represent the link reliability? 3) Is there a better measure to assess the link reliability? We first configured a testbed for performing a real measurement study to identify the causes of frame losses, and observed that link reliability depends on an intraframe SINR distribution, not a single value of RSSI (or SINR). We also learned that an RSSI value is not always a good indicator to estimate the link state. We then conducted a further investigation on the intraframe SINR distribution and the relationship between the SINR and link reliability with the ns-2 simulator. Based on these results, we finally propose an interference modeling framework for estimating link states in the presence of wireless interferences. We envision that the framework can be used for developing link-aware protocols to achieve their optimal performance in a hostile wireless environment.</P>