76
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Murphy MK, Yue L, Pan R, Boliar S, Sethi A, Karita E, Allen SA, Cormier E, Robinson JE, Gnanakaran S, Hunter E, Kong X, Derdeyn CA. Sequential exposure to specific antibody escape mutations may program neutralization breadth during subtype A HIV-1 infection. Retrovirology 2012. [PMCID: PMC3441627 DOI: 10.1186/1742-4690-9-s2-p104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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77
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Pan R, Sampson JM, Chen Y, Vaine M, Wang S, Lu S, Kong X. Structural analyses of antigen binding similarities and differences between rabbit and human anti-gp120 V3 mAbs. Retrovirology 2012. [PMCID: PMC3442065 DOI: 10.1186/1742-4690-9-s2-p76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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78
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Sampson JM, Killikelly A, Zhang H, Gorny MK, Zolla-Pazner S, Kong X. High-resolution crystal structure of the Fv of quaternary neutralizing epitope mAb 2909 reveals atomic details of its antigen-binding site. Retrovirology 2012. [PMCID: PMC3442074 DOI: 10.1186/1742-4690-9-s2-p79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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79
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O'Connell O, Repik A, Reeves JD, Gonzalez-Perez MP, Quitadamo B, Duenas-Decamp M, Peters P, Lin R, Anton ED, Zolla-Pazner S, Corti D, Wallace A, Wang S, Kong X, Lu S, Clapham PR. The efficiency of bridging sheet recruitment determines HIV-1 R5 envelope sensitivity to soluble CD4 and macrophage tropism. Retrovirology 2012. [PMCID: PMC3441583 DOI: 10.1186/1742-4690-9-s2-p141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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80
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Chen Y, Vaine M, Kong X, Montefiori D, Wang S, Lu S. A novel rabbit monoclonal antibody platform to dissect the diverse repertoire of antibody epitopes for HIV-1 Env immunogen design. Retrovirology 2012. [PMCID: PMC3442079 DOI: 10.1186/1742-4690-9-s2-p83] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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81
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Chiu Y, Jiang X, Kumar R, Hioe CE, Zolla-Pazner S, Kong X. Skin tattooing as an effective tool for delivering DNA and protein vaccine immunogens. Retrovirology 2012. [PMCID: PMC3441817 DOI: 10.1186/1742-4690-9-s2-p338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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82
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Spurrier B, Pan R, Sampson J, Williams C, Gorny M, Zolla-Pazner S, Kong X. Crystal structure analysis of anti-V2 mAb 2158 suggests a conformational epitope involving an N-linked glycan. Retrovirology 2012. [PMCID: PMC3442101 DOI: 10.1186/1742-4690-9-s2-p70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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83
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Kong X, Clausen C, Wang S. SU-E-T-598: Clinical Experience of Configuration, Commission and Implementation for SmartArc with MOSAIQ R&V System. Med Phys 2012; 39:3843. [DOI: 10.1118/1.4735687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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84
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Ma Y, Zhou T, Kong X, C. Hider R. Chelating Agents for the Treatment of Systemic Iron Overload. Curr Med Chem 2012; 19:2816-27. [DOI: 10.2174/092986712800609724] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 01/18/2012] [Accepted: 01/19/2012] [Indexed: 11/22/2022]
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85
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Shen Y, Wang Y, Sheng K, Fei X, Guo Q, Larner J, Kong X, Qiu Y, Mi J. Serine/threonine protein phosphatase 6 modulates the radiation sensitivity of glioblastoma. Cell Death Dis 2011; 2:e241. [PMID: 22158480 PMCID: PMC3252736 DOI: 10.1038/cddis.2011.126] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Increasing the sensitivity of glioblastoma cells to radiation is a promising approach to improve survival in patients with glioblastoma multiforme (GBM). This study aims to determine if serine/threonine phosphatase (protein phosphatase 6 (PP6)) is a molecular target for GBM radiosensitization treatment. The GBM orthotopic xenograft mice model was used in this study. Our data demonstrated that the protein level of PP6 catalytic subunit (PP6c) was upregulated in the GBM tissue from about 50% patients compared with the surrounding tissue or control tissue. Both the in vitro survival fraction of GBM cells and the patient survival time were highly correlated or inversely correlated with PP6c expression (R2=0.755 and −0.707, respectively). We also found that siRNA knockdown of PP6c reduced DNA-dependent protein kinase (DNA-PK) activity in three different GBM cell lines, increasing their sensitivity to radiation. In the orthotopic mice model, the overexpression of PP6c in GBM U87 cells attenuated the effect of radiation treatment, and reduced the survival time of mice compared with the control mice, while the PP6c knocking-down improved the effect of radiation treatment, and increased the survival time of mice. These findings demonstrate that PP6 regulates the sensitivity of GBM cells to radiation, and suggest small molecules disrupting or inhibiting PP6 association with DNA-PK is a potential radiosensitizer for GBM.
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86
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Kong X, Ristić J, Sanchez-Garcia MA, Calleja E, Trampert A. Polarity determination by electron energy-loss spectroscopy: application to ultra-small III-nitride semiconductor nanocolumns. NANOTECHNOLOGY 2011; 22:415701. [PMID: 21914935 DOI: 10.1088/0957-4484/22/41/415701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Channeling-enhanced electron energy-loss spectroscopy is applied to determine the polarity of ultra-small nitride semiconductor nanocolumns in transmission electron microscopy. The technique demonstrates some practical advantages in the nanostructure analysis, especially for feature sizes of less than 50 nm. We have studied GaN and (Al, Ga)N nanocolumns grown in a self-assembled way by molecular beam epitaxy directly on bare Si(111) substrates and on AlN buffer layers, respectively. The GaN nanocolumns on Si show an N polarity, while the (Al, Ga)N nanocolumns on an AlN buffer exhibit a Ga polarity. The different polarities of nanocolumns grown in a similar procedure are interpreted in terms of the specific interface bonding configurations. Our investigation contributes to the understanding of polarity control in III-nitride nanocolumn growth.
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87
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Fan YX, Song J, Shen HB, Kong X. PredCSF: an integrated feature-based approach for predicting conotoxin superfamily. Protein Pept Lett 2011; 18:261-7. [PMID: 20955172 DOI: 10.2174/092986611794578341] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Accepted: 10/08/2010] [Indexed: 11/22/2022]
Abstract
Conotoxins are small disulfide-rich peptides that are invaluable channel-targeted peptides and target neuronal receptors. They show prospects for being potent pharmaceuticals in the treatment of Alzheimer's disease, Parkinson's disease, and epilepsy. Accurate and fast prediction of conotoxin superfamily is very helpful towards the understanding of its biological and pharmacological functions especially in the post-genomic era. In the present study, we have developed a novel approach called PredCSF for predicting the conotoxin superfamily from the amino acid sequence directly based on fusing different kinds of sequential features by using modified one-versus-rest SVMs. The input features to the PredCSF classifiers are composed of physicochemical properties, evolutionary information, predicted second structure and amino acid composition, where the most important features are further screened by random forest feature selection to improve the prediction performance. The prediction results show that PredCSF can obtain an overall accuracy of 90.65% based on a benchmark dataset constructed from the most recent database, which consists of 4 main conotoxin superfamilies and 1 class of non-conotoxin class. Systematic experiments also show that combing different features is helpful for enhancing the prediction power when dealing with complex biological problems. PredCSF is expected to be a powerful tool for in silico identification of novel conotonxins and is freely available for academic use at http://www.csbio.sjtu.edu.cn/bioinf/PredCSF.
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88
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Song K, Nelson MR, Aponte J, Manas ES, Bacanu SA, Yuan X, Kong X, Cardon L, Mooser VE, Whittaker JC, Waterworth DM. Sequencing of Lp-PLA2-encoding PLA2G7 gene in 2000 Europeans reveals several rare loss-of-function mutations. THE PHARMACOGENOMICS JOURNAL 2011; 12:425-31. [PMID: 21606947 PMCID: PMC3449231 DOI: 10.1038/tpj.2011.20] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Elevated plasma levels of lipoprotein-associated phospholipase A2 (Lp-PLA2) activity have been shown to be associated with increased risk of coronary heart disease and an inhibitor of this enzyme is under development for the treatment of that condition. A Val279Phe null allele in this gene, that may influence patient eligibility for treatment, is relatively common in East Asians but has not been observed in Europeans. We investigated the existence and functional effects of low frequency alleles in a Western European population by re-sequencing the exons of PLA2G7 in 2000 samples. In all, 19 non-synonymous single-nucleotide polymorphisms (nsSNPs) were found, 14 in fewer than four subjects (minor allele frequency <0.1%). Lp-PLA2 activity was significantly lower in rare nsSNP carriers compared with non-carriers (167.8±63.2 vs 204.6±41.8, P=0.01) and seven variants had enzyme activities consistent with a null allele. The cumulative frequency of these null alleles was 0.25%, so <1 in 10 000 Europeans would be expected to be homozygous, and thus not potentially benefit from treatment with an Lp-PLA2 inhibitor.
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89
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Xie X, Guo F, Song X, Zhang Q, Kong X, Li C, Li Z, Qu S, Liu Z, Piao Y, Zheng Z. Efficacy and toxicity of sorafenib in patients with advanced renal cell cancer in northeast China: A multicenter study. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.e15046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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90
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Li Y, Li M, Yao G, Geng N, Xie Y, Feng Y, Zhang P, Kong X, Xue J, Cheng S, Zhou J, Xiao L. Telomerase inhibition strategies by siRNAs against either hTR or hTERT in oral squamous cell carcinoma. Cancer Gene Ther 2011; 18:318-25. [PMID: 21233858 DOI: 10.1038/cgt.2010.81] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human telomerase RNA (hTR) and human telomerase reverse transcriptase (hTERT) are considered effective molecular targets for current anticancer therapy. In this study, we investigated the therapeutic effects of targeting hTR and hTERT individually or in combination by recombinant adenovirus-delivered small interfering RNA (siRNA) in oral squamous cell carcinoma (OSCC) Tca8113. Further, we screened the optimal strategy for RNA interference. Our results show that these different recombinant adenoviruses specifically reduced the levels of hTR mRNA, hTERT mRNA, hTERT protein and telomerase activity in Tca8113 cells. Moreover, they successfully inhibited xenograft tumor growth in nude mice. The potency of their antitumor activities was ranked as follows: anti-hTR >anti-hTR+anti-hTERT >anti-hTERT. Therefore, we demonstrated that the siRNA-expressing recombinant adenoviruses were an effective anticancer tool for treatment of OSCC. Furthermore, the anticancer effect of solely targeting hTR was more direct and efficient, compared with the effect of targeting hTR and hTERT in combination, or hTERT exclusively. The mechanism of this anticancer effect in OSCC was not only related to the inhibition of cell proliferation and the induction of cell apoptosis, but might also involve the inhibition of tumor angiogenesis.
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91
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Ye R, Zhang X, Kong X, Han J, Yang Q, Zhang Y, Chen Y, Li P, Liu J, Shi M, Xiong L, Zhao G. Ginsenoside Rd attenuates mitochondrial dysfunction and sequential apoptosis after transient focal ischemia. Neuroscience 2011; 178:169-80. [PMID: 21219973 DOI: 10.1016/j.neuroscience.2011.01.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 12/23/2010] [Accepted: 01/02/2011] [Indexed: 10/18/2022]
Abstract
We previously found that ginsenoside Rd (Rd), one of the major active ingredients in Panax ginseng, protects neuronal cells from hydrogen peroxide and oxygen-glucose deprivation, an in vitro model of cerebral ischemia. In this study, we examined the protective effects of Rd in an animal model of focal cerebral ischemia. Rats administered with Rd or vehicle were subjected to transient middle cerebral artery occlusion (MCAO). Rd (50 mg/kg) significantly reduced the infarct volume by 52.8%. This reduction of injury volume was associated with an improvement in neurological function and was sustained for at least 2 weeks after the induction of ischemia. To evaluate the underlying mechanisms of Rd against stroke, brain tissues were assayed for mitochondrial enzyme activities, mitochondrial membrane potential (MMP), production of reactive oxygen species (ROS), energy metabolites, and apoptosis. Rd markedly protected mitochondria as indicated by preserved respiratory chain complex activities and aconitase activity, lowered mitochondrial hydrogen peroxide production, and hyperpolarized MMP. Microdialysis results illustrated that Rd significantly decreased the accumulation of lactate, the end product of anaerobic glycolysis, and increased pyruvate, the end product of aerobic glycolysis, hence inducing a lower lactate/pyruvate ratio. Additionally, in vitro studies further exhibited that Rd protected isolated mitochondria from calcium-induced damage by attenuating mitochondrial swelling, preserving MMP and decreasing ROS production. Moreover, Rd treatment reduced mitochondrial release of cytochrome c (CytoC) and apoptosis-inducing factor (AIF), thereby minimizing mitochondria-mediated apoptosis following ischemia. In conclusion, these findings demonstrated that Rd exerts neuroprotective effects in transient focal ischemia, which may involve an integrated process of the mitochondrial protection, energy restoration and inhibition of apoptosis.
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92
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Kong X, Domier CW, Luhmann NC. Antenna development for high field plasma imaging. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2010; 81:10D923. [PMID: 21033955 DOI: 10.1063/1.3479117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Electron cyclotron emission imaging (ECEI) and microwave imaging reflectometry (MIR) are two microwave nonperturbing plasma visualization techniques that employ millimeter-wave imaging arrays with lens-coupled planar antennas, yielding time-resolved images of temperature (via ECEI) and electron density (via MIR) fluctuations within high temperature magnetic fusion plasmas. A series of new planar antennas have been developed that extend this technology to frequencies as high as 220 GHz for use on high field plasma devices with toroidal fields in excess of 3 T. Antenna designs are presented together with theoretical calculations, simulations, and experimental measurements.
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93
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Liang T, Tobias B, Kong X, Domier CW, Luhmann NC, Lee W, Yun GS, Park HK. Innovations in optical coupling of the KSTAR electron cyclotron emission imaging diagnostic. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2010; 81:10D909. [PMID: 21033941 DOI: 10.1063/1.3478637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The installation of a new electron cyclotron emission imaging diagnostic for the Korea Superconducting Tokamak Advanced Research (KSTAR) is underway, making use of a unique optical port cassette design, which allows placement of refractive elements inside the cryostat region without adverse effects. The result is unprecedented window access for the implementation of a state of the art imaging diagnostic. A dual-array optical design has been developed, capable of simultaneously imaging the high and low field sides of the plasma with independent features of focal plane translation, vertical zoom, and radial channel spacing. The number of translating optics has been minimized by making use of a zoom lens triplet and parabolic plasma facing lens for maximum channel uniformity over a continuous vertical zoom range of 3:1. The simulated performance of this design is presented along with preliminary laboratory characterization data.
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94
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Yun GS, Lee W, Choi MJ, Kim JB, Park HK, Domier CW, Tobias B, Liang T, Kong X, Luhmann NC, Donné AJH. Development of KSTAR ECE imaging system for measurement of temperature fluctuations and edge density fluctuations. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2010; 81:10D930. [PMID: 21033958 DOI: 10.1063/1.3483209] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The ECE imaging (ECEI) diagnostic tested on the TEXTOR tokamak revealed the sawtooth reconnection physics in unprecedented detail, including the first observation of high-field-side crash and collective heat transport [H. K. Park, N. C. Luhmann, Jr., A. J. H. Donné et al., Phys. Rev. Lett. 96, 195003 (2006)]. An improved ECEI system capable of visualizing both high- and low-field sides simultaneously with considerably better spatial coverage has been developed for the KSTAR tokamak in order to capture the full picture of core MHD dynamics. Direct 2D imaging of other MHD phenomena such as tearing modes, edge localized modes, and even Alfvén eigenmodes is expected to be feasible. Use of ECE images of the optically thin edge region to recover 2D electron density changes during L/H mode transitions is also envisioned, providing powerful information about the underlying physics. The influence of density fluctuations on optically thin ECE is discussed.
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95
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Tobias B, Domier CW, Liang T, Kong X, Yu L, Yun GS, Park HK, Classen IGJ, Boom JE, Donné AJH, Munsat T, Nazikian R, Van Zeeland M, Boivin RL, Luhmann NC. Commissioning of electron cyclotron emission imaging instrument on the DIII-D tokamak and first data. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2010; 81:10D928. [PMID: 21033956 DOI: 10.1063/1.3460456] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A new electron cyclotron emission imaging diagnostic has been commissioned on the DIII-D tokamak. Dual detector arrays provide simultaneous two-dimensional images of T(e) fluctuations over radially distinct and reconfigurable regions, each with both vertical and radial zoom capability. A total of 320 (20 vertical×16 radial) channels are available. First data from this diagnostic demonstrate the acquisition of coherent electron temperature fluctuations as low as 0.1% with excellent clarity and spatial resolution. Details of the diagnostic features and capabilities are presented.
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96
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Oledzka E, Kong X, Narine SS. Synthesis and characterization of novel lipid functionalized poly(ε-caprolactone)s. J Appl Polym Sci 2010. [DOI: 10.1002/app.32898] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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97
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Bakke PS, Zhu G, Gulsvik A, Kong X, Agusti AGN, Calverley PMA, Donner CF, Levy RD, Make BJ, Pare PD, Rennard SI, Vestbo J, Wouters EFM, Anderson W, Lomas DA, Silverman EK, Pillai SG. Candidate genes for COPD in two large data sets. Eur Respir J 2010; 37:255-63. [DOI: 10.1183/09031936.00091709] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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98
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Zhang W, Cao X, Chen D, Wang J, Yang H, Moahapatra S, Hellermann G, Kong X, Lockey R, Moahapatra S. Atrial Natriuretic Peptide Receptor Signaling Plays a Critical Role in Induction of Tolerogenic Dendritic Cells. J Allergy Clin Immunol 2010. [DOI: 10.1016/j.jaci.2009.12.889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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99
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Zolla-Pazner S, Kong X, Cardozo T, Hioe C, Cohen S, Jiang X, Gorny MK, Totrov M, Pinter A, Krachmarov C, Seaman MS, Wang S, Lu S. P04-09. Induction of cross-clade neutralizing antibodies with a prime/boost vaccine strategy focused on a neutralizing epitope. Retrovirology 2009. [PMCID: PMC2767881 DOI: 10.1186/1742-4690-6-s3-p37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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100
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Almond D, Kimura T, Kong X, Swetnam J, Zolla-Pazner S, Cardozo T. P19-21. Sequence variability in the crown of the V3 loop of the HIV-1 envelope is clustered within a small 3D structural zone. Retrovirology 2009. [PMCID: PMC2767850 DOI: 10.1186/1742-4690-6-s3-p341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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