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Now showing items 81 - 96 of 2568

  • A distribution free summarization method for Affymetrix GeneChip(R) arrays

    Chen, Z.   McGee, M.   Liu, Q.   Scheuermann, R. H.  

    Motivation: Affymetrix GeneChip arrays require summarization in order to combine the probe-level intensities into one value representing the expression level of a gene. However, probe intensity measurements are expected to be affected by different levels of non-specific- and cross-hybridization to non-specific transcripts. Here, we present a new summarization technique, the Distribution Free Weighted method (DFW), which uses information about the variability in probe behavior to estimate the extent of non-specific and cross-hybridization for each probe. The contribution of the probe is weighted accordingly during summarization, without making any distributional assumptions for the probe-level data. Results: We compare DFW with several popular summarization methods on spike-in datasets, via both our own calculations and the 'Affycomp II' competition. The results show that DFW outperforms other methods when sensitivity and specificity are considered simultaneously. With the Affycomp spike-in datasets, the area under the receiver operating characteristic curve for DFW is nearly 1.0 (a perfect value), indicating that DFW can identify all differentially expressed genes with a few false positives. The approach used is also computationally faster than most other methods in current use.
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  • An SPH model for multiphase flows with complex interfaces and large density differences

    Chen, Z.   Zong, Z.   Liu, M.B.   Zou, L.   Li, H.T.   Shu, C.  

    In this paper, an improved SPH model for multiphase flows with complex interfaces and large density differences is developed. The multiphase SPH model is based on the assumption of pressure continuity over the interfaces and avoids directly using the information of neighboring particles' densities or masses in solving governing equations. In order to improve computational accuracy and to obtain smooth pressure fields, a corrected density re-initialization is applied. A coupled dynamic solid boundary treatment (SBT) is implemented both to reduce numerical oscillations and to prevent unphysical particle penetration in the boundary area. The density correction and coupled dynamics SBT algorithms are modified to adapt to the density discontinuity on fluid interfaces in multiphase simulation. A cut-off value of the particle density is set to avoid negative pressure, which can lead to severe numerical difficulties and may even terminate the simulations. Three representative numerical examples, including a Rayleigh-Taylor instability test, a non-Boussinesq problem and a dam breaking simulation, are presented and compared with analytical results or experimental data. It is demonstrated that the present SPH model is capable of modeling complex multiphase flows with large interfacial deformations and density ratios. (C) 2014 Elsevier Inc. All rights reserved.
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  • Strongly coupled surface plasmons on thin shallow metallic gratings

    Chen, Z.   Hooper, I. R.   Sambles, J. R.  

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  • Hydrothermal synthesized nanostructure Bi–Sb–Te thermoelectric materials

    Chen, Z.   lin, M.Y.   Xu, G.D.   Chen, S.   Zhang, J.H.   Wang, M.M.  

    Nanostructure p-type Bi0.4Sb1.6Te3 was successfully prepared by adopting a feasible hydrothermal synthesis method. The crystallinity, particle size, morphology and chemical composition were characterized by XRD, FE-SEM, EDS respectively. Thermoelectric properties were also measured and a maximum ZT value up to 1.26 has been obtained at 398 K in prepared nanostructure sample. The achieved higher ZT value is attributed to the unique nanostructures which increase phonon scattering in the nanostructured materials to effectively reduce thermal conductivity. It is suggested that the as-prepared nanostructure Bi0.4Sb1.6Te3 has high potential for thermoelectric energy conversion application. (C) 2013 Elsevier B. V. All rights reserved.
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  • A mechanistic model of lateral rail head deflection based on fastening system parameters

    Chen, Z.   Andrawes, B.  

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  • A novel multilateral teleoperation scheme with power-based time-domain passivity control

    Chen, Z.   Pan, Y.-J.   Gu, J.   Forbrigger, S.  

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  • Activation of mTORC1 in Collecting Ducts Causes Hyperkalemia

    Chen, Z.   Dong, H.   Jia, C.   Song, Q.   Chen, J.   Zhang, Y.   Lai, P.   Fan, X.   Zhou, X.   Liu, M.   Lin, J.   Yang, C.   Li, M.   Gao, T.   Bai, X.  

    Mutation of TSC (encoding tuberous sclerosis complex protein) and activation of mammalian target of rapamycin (mTOR) have been implicated in the pathogenesis of several renal diseases, such as diabetic nephropathy and polycystic kidney disease. However, the role of mTOR in renal potassium excretion and hyperkalemia is not known. We showed that mice with collecting-duct (CD)-specific ablation of TSC1 (CDTsc1KO) had greater mTOR complex 1 (mTORC1) activation in the CD and demonstrated features of pseudohypoaldosteronism, including hyperkalemia, hyperaldosteronism, and metabolic acidosis. mTORC1 activation caused endoplasmic reticulum stress, columnar cell lesions, and dedifferentiation of CD cells with loss of aquaporin-2 and epithelial-mesenchymal transition-like phenotypes. Of note, mTORC1 activation also reduced the expression of serum- and glucocorticoid-inducible kinase 1, a crucial regulator of potassium homeostasis in the kidney, and decreased the expression and/or activity of epithelial sodium channel-, renal outer medullary potassium channel, and Na+, K+-ATPase in the CD, which probably contributed to the aldosterone resistance and hyperkalemia in these mice. Rapamycin restored these phenotypic changes. Overall, this study identifies a novel function of mTORC1 in regulating potassium homeostasis and demonstrates that loss of TSC1 and activation of mTORC1 results in dedifferentiation and dysfunction of the CD and causes hyperkalemia. The CDTsc1KO mice provide a novel model for hyperkalemia induced exclusively by dysfunction of the CD.
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  • Fast Collocation Methods for High-Dimensional Weakly Singular Integral Equations

    Chen, Z.   Wu, B.   Xu, Y.  

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  • Directed evolution of homing endonuclease I-SceI with altered sequence specificity

    Chen, Z.   Wen, F.   Sun, N.   Zhao, H.  

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  • Transient crystalline superlattice generated by a photoacoustic transducer

    Loether, A.   Gao, Y.   Chen, Z.   DeCamp, M.F.   Dufresne, E.M.   Walko, D.A.   Wen, H.  

    Designing an efficient and simple method for modulating the intensity of x-ray radiation on a picosecond time-scale has the potential to produce ultrafast pulses of hard x-rays. In this work, we generate a tunable transient superlattice, in an otherwise perfect crystal, by photoexciting a metal film on a crystalline substrate. The resulting transient strain has amplitudes approaching 1%, wavevectors greater than 0.002 Aring-1, and lifetimes approaching 1 ns. This method has the potential to generate isolated picosecond x-ray bursts with scattering efficiencies in excess of 10%.
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  • Effect of mesenchymal stem cells on renal injury in rats with severe acute pancreatitis

    Chen, Z.   Lu, F.   Fang, H.   Huang, H.  

    The aim of this study was to preliminarily investigate the effect of bone marrow mesenchymal stem cells (MSCs) on structural change of capillary endothelial barrier and expression variation of aquaporin 1 (AQP1) in kidney at the onset of renal injury caused by severe acute pancreatitis (SAP). Ninety male Sprague-Dawley (SD) rats were divided into the control group, the SAP group in which animals received induction of SAP and the MSCs-treated group in which SAP-induced animals were injected with MSCs. They were further subdivided according to the time point that the animals were killed; 6 h, 12 h and 24 h after the closure of the incision, serum, pancreatic and renal samples were collected, respectively. The level of serum amylase (AMY), creatinine (Cr) and blood urea nitrogen (BUN) were analysed, the change of pancreatic histology was assessed, the structural change of the renal interstitial capillaries was evaluated using the transmission electron microscope (TEM) and the location and expression of AQP1 in kidney were analysed using immunohistochemistry, quantitative polymerase chain reaction and Western blot. The outcomes showed that the level of serum AMY, Cr, BUN elevated, the damage of pancreatic tissue and renal capillary endothelial barrier was aggravated and the expression of AQP1 was reduced significantly after induced pancreatitis. But after treatments with MSCs, the elevation of AMY, Cr and BUN was inhibited, the damage of pancreatic tissue and renal interstitial capillary barrier was alleviated and the down-regulation of AQP1 was reversed. In summary, the MSCs therapy could alleviate renal injury in rats with SAP, the mechanism of which might be related to reduction of the damage to renal interstitial capillary endothelial barrier, and up-expression of AQP1 in kidney.
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  • Cost-effectiveness of lipid lowering with statins and ezetimibe in chronic kidney disease

    Schlackow, Iryna   Kent, Seamus   Herrington, William   Emberson, Jonathan   Haynes, Richard   Reith, Christina   Collins, Rory   Landray, Martin J.   Gray, Alastair   Baigent, Colin   Mihaylova, Borislava   Collins, R.   Baigent, C.   Landray, M.J.   Bray, C.   Chen, Y.   Baxter, A.   Young, A.   Hill, M.   Knott, C.   Cass, A.   Feldt-Rasmussen, B.   Fellström, B.   Grobbee, D.E.   Grönhagen-Riska, C.   Haas, M.   Holdaas, H.   Hooi, L.S.   Jiang, L.   Kasiske, B.   Krairittichai, U.   Levin, A.   Massy, Z.A.   Tesar, V.   Walker, R.   Wanner, C.   Wheeler, D.C.   Wiecek, A.   Dasgupta, T.   Herrington, W.   Lewis, D.   Mafham, M.   Majoni, W.   Reith, C.   Emberson, J.   Parish, S.   Simpson, D.   Strony, J.   Musliner, T.   Agodoa, L.   Armitage, J.   Chen, Z.   Craig, J.   de Zeeuw, D.   Gaziano, J.M.   Grimm, R.   Krane, V.   Neal, B.   Ophascharoensuk, V.   Pedersen, T.   Sleight, P.   Tobert, J.   Tomson, C.  

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  • Anisotropic Debye model for the thermal boundary conductance

    Chen, Z.   Wei, Z.   Chen, Y.   Dames, C.  

    Most standard models for the thermal boundary conductance (TBC) assume isotropic properties and thus are inappropriate for layered and chainlike materials such as graphite, Bi2Te3, and high-density polyethylene (HDPE). To model such anisotropic materials, here a framework is introduced whereby the first Brillouin zone and the isoenergy surfaces of the Debye dispersion relation are both generalized from spherical to ellipsoidal. This model is checked by comparison with the experimental specific heat capacity of graphite and HDPE, as well as the phonon irradiation of graphite calculated from lattice dynamics. The anisotropic TBC model performs at least six times better than the standard isotropic diffuse mismatch model at explaining the measured TBC between graphite and various metals reported by Schmidt et al. [J. Appl. Phys. 107, 104907 (2010)]. The model further reveals an unexpected guideline to engineer the TBC: due to phonon focusing effects, in many cases the TBC across an interface can be increased by reducing a phonon velocity component parallel to the plane of the interface. DOI: 10.1103/PhysRevB.87.125426
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  • Immunoglobulin G expression in carcinomas and cancer cell lines

    Chen, Z.   Gu, J.  

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  • Key factors to understand in-situ behavior of Cs in Callovo–Oxfordian clay-rock (France)

    Chen, Z.   Montavon, G.   Ribet, S.   Guo, Z.   Robinet, J.C.   David, K.   Tournassat, C.   Grambow, B.   Landesman, C.  

    Understanding the behavior of Cs-137 and Cs-135 in soils and geological formations is of considerable interest in the context of nuclear accidents and nuclear waste repositories. Although the clay fraction is known to be responsible for sorption, there are still unanswered questions raised by the literature data concerning (i) the reversibility of the sorption process(es), (ii) the validity of the additivity rule (the overall distribution coefficient (Kd) for a radionuclide on a mixture of minerals is predicted from the distribution coefficients measured on individual minerals) and (iii) the validity of model transposition from dispersed systems to consolidated/intact systems. Because of these uncertainties, the validity of sorption models at equilibrium under in-situ conditions and for very long-term interaction is still pending. These different issues are studied in the present work for the Callovo-Oxfordian (COx) clay-rich rock Formation, which is under investigation in France as a geological barrier for a long-term nuclear waste repository. The work is based on sorption data measured on thirteen samples of different mineralogy taken from five different boreholes at several depths within the COx sedimentary layer. To our knowledge, it is the most extended Cs sorption dataset that has been published for a single clay formation in term of (i) sample locations (and thus natural variability), (ii) sorption conditions (powder dispersed in suspension, compacted powders and intact samples) and (iii) equilibration time (from one week to five years). Moreover, for the first time ever, radioactive Cs sorption results were compared to the natural distribution of non-radioactive Cs isotopes between pore water and the solid phase. The experimental system appeared to be in chemical equilibrium as much as can be expected for an ion-exchange reaction. More particularly, no kinetically-controlled process leading to partial Cs irreversibility was observed, in contrary to what was found in the literature for soils. This difference in behavior may be related to the difference in the illite studied, i.e. a soil-type illite which would be more altered than a sedimentary formation-type illite. No decrease in site capacity was observed between dispersed and intact/compacted states. A model based on exchange reactions with cations interacting with illite (frayed edge, type-II and planar sites) and mixed layer illite-smectite (I/S) (planar sites) using parameters published in the literature enabled the Kd variation to be described as a function of Cs concentration, the mineralogy of the samples, the change in water composition and the temperature (22-80 degrees C). Our study clearly demonstrates that no frayed edge sites should be considered on the illite fraction of I/S, thus emphasizing the difference of sorption properties between an I/S mixed layer mineral and a corresponding mechanical mix of illite and smectite minerals. The robustness of the model was confirmed by data analysis describing the behavior of naturally-occurring Cs in the formation thereby demonstrating the effectiveness of the Cs sorption processes in a very long-time period prospective. Lastly, the model was used to predict the sorption of trace concentrations of Cs in the COx Formation on the time-scale relevant for nuclear waste disposal performance assessment. As expected, the retention was significant with Kd values ranging from 100 to 2000 L/kg whatever the conditions that were probed and a simulation covering a period of over 105 years could show that the COx Formation is an efficient barrier to prevent Cs transport from the storage facility to the surrounding environment. (C) 2014 Elsevier B.V. All rights reserved.
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  • A simplified thermal lattice Boltzmann method without evolution of distribution functions

    Chen, Z.   Shu, C.   Tan, D.  

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