Detection of Differentially Expressed Gene Sets in a Partially Paired Microarray Data Set

Lim, Johan,Kim, Jayoun,Kim, Sang-cheol,Yu, Donghyeon,Kim, Kyunga,Kim, Byung Soo Walter de Gruyter GmbH 2012 Statistical applications in genetics and molecular Vol.11 No.3

<P>Partially paired data sets often occur in microarray experiments (Kim et al., 2005; Liu, Liang and Jang, 2006). Discussions of testing with partially paired data are found in the literature (Lin and Stivers 1974; Ekbohm, 1976; Bhoj, 1978). Bhoj (1978) initially proposed a test statistic that uses a convex combination of paired and unpaired t statistics. Kim et al. (2005) later proposed the t3 statistic, which is a linear combination of paired and unpaired t statistics, and then used it to detect differentially expressed (DE) genes in colorectal cancer (CRC) cDNA microarray data. In this paper, we extend Kim et al.'s t3 statistic to the Hotelling's T2 type statistic Tp for detecting DE gene sets of size p. We employ Efron's empirical null principle to incorporate inter-gene correlation in the estimation of the false discovery rate. Then, the proposed Tp statistic is applied to Kim et al's CRC data to detect the DE gene sets of sizes p=2 and p=3. Our results show that for small p, particularly for p=2 and marginally for p=3, the proposed Tp statistic compliments the univariate procedure by detecting additional DE genes that were undetected in the univariate test procedure. We also conduct a simulation study to demonstrate that Efron's empirical null principle is robust to the departure from the normal assumption.</P>

Quantum Electron-Exchange Effects on the Buneman Instability in Quantum Plasmas

Hong, Woo-Pyo,Jamil, Muhammad,Rasheed, Abdur,Jung, Young-Dae De Gruyter 2015 Zeitschrift für Naturforschung. A, A journal Vol.70 No.6

<P><B>Abstract</B></P><P>The quantum-mechanical electron-exchange effects on the Buneman instability are investigated in quantum plasmas. The growth rate and wave frequency of the Buneman instability for the quantum plasma system composed of the moving electron fluid relative to the ion fluid are obtained as functions of the electron-exchange parameter, de Broglie’s wave length, Debye’s length, and wave number. The result shows that the electron-exchange effect suppresses the growth rate of the quantum Buneman instability in quantum plasmas. It is also shown that the influence of electron exchange reduces the instability domain of the wave number in quantum plasmas. However, the instability domain enlarges with an increase in the ratio of the Debye length to the de Broglie wave length. In addition, the electron-exchange effect on the growth rate of the Buneman instability increases with an increase in the ratio of the Debye length to the de Broglie wave length. The variation in the growth rate of the Buneman instability due to the change in the electron-exchange effect and plasma parameters is also discussed.</P>

Quantum Shielding Effects on the Eikonal Collision Cross Section in Strongly Coupled Two-temperature Plasmas

Lee, Myoung-Jae,Jung, Young-Dae De Gruyter 2017 Zeitschrift für Naturforschung. A, A journal Vol.72 No.5

<P><B>Abstract</B></P><P>The influence of nonisothermal and quantum shielding on the electron-ion collision process is investigated in strongly coupled two-temperature plasmas. The eikonal method is employed to obtain the eikonal scattering phase shift and eikonal cross section as functions of the impact parameter, collision energy, electron temperature, ion temperature, Debye length, and de Broglie wavelength. The results show that the quantum effect suppresses the eikonal scattering phase shift for the electron-ion collision in two-temperature dense plasmas. It is also found that the differential eikonal cross section decreases for small impact parameters. However, it increases for large impact parameters with increasing de Broglie wavelength. It is also found that the maximum position of the differential eikonal cross section is receded from the collision center with an increase in the nonisothermal character of the plasma. In addition, it is found that the total eikonal cross sections in isothermal plasmas are always greater than those in two-temperature plasmas. The variations of the eikonal cross section due to the two-temperature and quantum shielding effects are also discussed.</P>

Harnack inequality for a class of functionals with non-standard growth via De Giorgi’s method

De Gruyter 2018 Advances in nonlinear analysis Vol.7 No.2

<P><B>Abstract</B></P><P>We study the regularity theory of quasi-minimizers of functionals with[FORMULA OMISSION]-growth. In particular, we prove the Harnack inequality and, in addition, the local boundedness and the Hölder continuity of the quasi-minimizers. We directly prove our results via De Giorgi’s method.</P>

Approximation solvability for a system of implicit nonlinear variational inclusions with Η-monotone operators

Kim, Jong Kyu,Bhat, Muhammad Iqbal De Gruyter 2018 Demonstratio mathematica Vol.51 No.1

<P><B>Abstract</B></P><P>In this paper, we introduce and study a new system of variational inclusions which is called a system of nonlinear implicit variational inclusion problems with A-monotone and H-monotone operators in semi-inner product spaces. We define the resolvent operator associated with A-monotone and H-monotone operators and prove its Lipschitz continuity. Using resolvent operator technique, we prove the existence and uniqueness of solution for this new system of variational inclusions. Moreover, we suggest an iterative algorithm for approximating the solution of this system and discuss the convergence analysis of the sequences generated by the iterative algorithm under some suitable conditions.</P>

Anthropological-semiotics of rhythm and animating modernity in China: A rhythmanalysis of <i>Princess Iron Fan</i>

Kim, Minhyoung,Kim, Sung-do De Gruyter 2016 SEMIOTICA Vol.2016 No.210

<P><B>Abstract</B></P><P>This article explores the contribution made by anthropological-semiotics of rhythm when it comes to comprehending visual modernity of East Asia, with a particular focus on China’s experience. From the humanistic foundations of rhythm including cultural anthropological perspectives, traditions of rhythmanalysis, and semiotic thinking of rhythm, this paper demonstrates the construction of a semiotic square of rhythm along with a topology of rhythmia; then provides a case study of rhythmanalysis surrounding the emergence of the first Chinese feature animated film entitled<I>Princess Iron Fan</I>; and ultimately presents the potential of establishing the multiplicity of modernities based on the transdisciplinary examination of rhythm in visual cultures of East Asia.</P>

Anatomical location of transcallosal sensorimotor fibers in the human brain: Diffusion tensor tractography study

Seo, Jung,Jang, Sung De Gruyter Open Sp. z o.o. 2013 Translational neuroscience Vol.4 No.3

<B>Abstract</B><P>Many diffusion tensor tractography (DTT) studies have reported on the topography of transcallosal fibers (TCF). However, little detailed anatomical information on TCF that can be easily applied for clinical purposes is known. Using probabilistic DTT, we attempted to determine the anatomical location of the TCF for motor and sensory function in the human brain. A total of 51 healthy subjects were recruited for this study. Diffusion tensor images (DTIs) were obtained at 1.5 T, and four TCF for the premotor cortex (PMC), the primary motor cortex (M1) for hand and leg, and the primary somatosensory cortex (S1) were obtained using FMRIB software. Locations of the TCF were defined as the highest probabilistic location on the midsagittal slice of the corpus callosum. We measured distances between the most anterior and posterior points of the corpus callosum. The relative mean distances of the highest probabilistic location for the precentral knob PMC (Brodmann area 6 anterior to the precentral knob), hand M1, leg M1, and precentral knob S1 (postcentral gyrus posterior to the precentral knob) TCF were 48.99%, 59.78%, 67.93%, and 73,48% from the most anterior point of the CC, respectively. According to our findings, the precentral knob PMC, hand M1, leg M1, and precentral knob S1 TCF were located at the anterior body, posterior body, posterior body, and isthmus according to Witelson’s classification, respectively.</P>

Chemical structure and physical properties of cyclic olefin copolymers (IUPAC Technical Report)

Shin, Ju Young,Park, Ji Yong,Liu, Chenyang,He, Jiasong,Kim, Sung Chul De Gruyter 2005 Pure and Applied Chemistry Vol.77 No.5

<P>Cyclic olefin copolymers comprise a new class of polymeric materials showing properties of high glass-transition temperature, optical clarity, low shrinkage, low moisture absorption, and low birefringence. There are several types of cyclic olefin copolymers based on different types of cyclic monomers and polymerization methods. In this work, we have analyzed the chemical structure of the currently commercialized cyclic olefin copolymers by<SUP>13</SUP>C NMR, and investigated their glass-transition temperatures and surface characteristics. It was observed that the glass-transition temperature,<I>T</I><SUB>g</SUB>, of cyclic olefin copolymers depended on the bulkiness of the main chain, and the number of rings had an important role in increasing the bulkiness of cyclic olefin copolymers. Cyclic olefin copolymers with polar substituents such as ester or ether groups showed high surface energy per area and peel strength.</P>

Brain plasticity, cognitive functions and neural stem cells: a pivotal role for the brain-specific neural master gene |-SRGAP2-FAM72-|

Ho, Nguyen Thi Thanh,Kutzner, Arne,Heese, Klaus De Gruyter 2018 Biological Chemistry Vol.399 No.1

<P><B>Abstract</B></P><P>Due to an aging society with an increased dementia-induced threat to higher cognitive functions, it has become imperative to understand the molecular and cellular events controlling the memory and learning processes in the brain. Here, we suggest that the novel master gene pair |-SRGAP2-FAM72-| (SLIT-ROBO Rho GTPase activating the protein 2, family with sequence similarity to 72) reveals a new dogma for the regulation of neural stem cell (NSC) gene expression and is a distinctive player in the control of human brain plasticity. Insight into the specific regulation of the brain-specific neural master gene |-SRGAP2-FAM72-| may essentially contribute to novel therapeutic approaches to restore or improve higher cognitive functions.</P>

Synthesis, characterization and application of polypyrrole-cellulose nanocomposite for efficient Ni(II) removal from aqueous solution: Box-Behnken design optimization

Rathika, R.,Byung-Taek, Oh,Vishnukumar, B.,Shanthi, K.,Kamala-Kannan, S.,Janaki, V. De Gruyter 2018 E-Polymers Vol.18 No.4

<P><B>Abstract</B></P><P>The role of polypyrrole-cellulose (PPy-Ce) nanocomposite for the removal of Ni(II) from aqueous solution was investigated by batch experiments. The PPy-Ce nanocomposite was prepared by chemical oxidate polymerization of pyrrole monomer with cellulose. Transmission electron micrography (TEM) showed the size of the particles varied from 80 to 95 nm. The characteristic C-O, O-H, C-N and C-C vibrations in the Fourier transform infrared (FTIR) spectra indicate that the cellulose successfully integrated with the pyrrole. Influence of experimental variables such as pH, contact time, adsorbent dose and initial Ni(II) concentration were optimized using the response surface methodology (RSM) based Box-Behnken design (BBD). The optimal conditions for maximum removal of Ni(II) were pH 8, time 65 min, adsorbent dose 0.3 mg/l and Ni(II) concentration 50 mg/l. The maximum removal efficiency under optimized conditions was >94%. The results indicate that BBD could be used to optimize experimental conditions for metal removal from aqueous solution.</P>