504 research outputs found
Metabolic Analysis of Escherichia coli in response to Environmental and Genetic Alterations
No full text九州工業大学博士学位論文 学位記番号:情工博甲第145号 学位授与年月日:平成16年9月30日対象論文(1)：p.10-37収録論文「Applied Microbiology and Biotechnology」Vol.61, issue 2, pp.163-178,Springer Berlin / Heidelberg, 2003.4.掲載-[Title]：Global metabolic regulation analysis for Escherichia coli K12 based on protein expression by 2-dimensional electrophoresis and enzyme activity measurement[Author(s)]:L. Peng and K. Shimizu@@@対象論文(2)：p.38-55当該部分削除（著作権規定不明のため当該部分を削除）収録論文「Proceedings of Asian Pacific Biochemical Engineering Conference」8,Asian Pacific Biochemical Engineering Conference, 2003掲載-[Title]：Effect of ppc gene knockout on the metabolism of Escherichia coli in view of gene expressions, enzyme activities and intracellular metabolite concentrations[Author(s)]:Peng, Lifeng|Shimizu, Kazuyuki@@@対象論文(3)：p.80-99 当該部分削除（著作権規定不明のため当該部分を削除）収録論文 Vol.235, issue 1, pp.17-23 FEMS Microbiology Letters © 2008 Federation of European Microbiological Societies/Blackwell Publishing Ltd , 2004 掲載-[Title]：Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements[Author(s)]:Peng, Lifeng|Arauzo-Bravo, Marcos J|Shimizu, KazuyukiThe final publication is available at www.springerlink.com平成16年
CCDC 1956266: Experimental Crystal Structure Determination
No full textFUVFAG : catena-(bis(μ-4,4'-(1,4-phenylene)dipyridine)-copper(ii) closo-dodecaborate unknown solvate) Space Group: I m a 2 (46), Cell: a 19.8856(17)Å b 22.4095(18)Å c 21.0263(16)Å, α 90° β 90° γ 90° Related Article: Yuanbin Zhang, Jianbo Hu, Rajamani Krishna, Lingyao Wang, Lifeng Yang, Xili Cui, Simon Duttwyler, Huabin Xing|2020|Angew.Chem.,Int.Ed.|59|17664|doi:10.1002/anie.20200768
sj-pdf-1-tct-10.1177_15330338231152350 - Supplemental material for A Randomized Phase III Study of Anlotinib Versus Bevacizumab in Combination With CAPEOX as First-Line Therapy for <i>RAS/BRAF</i> Wild-Type Metastatic Colorectal Cancer: A Clinical Trial Protocol
No full textSupplemental material, sj-pdf-1-tct-10.1177_15330338231152350 for A Randomized Phase III Study of Anlotinib Versus Bevacizumab in Combination With CAPEOX as First-Line Therapy for RAS/BRAF Wild-Type Metastatic Colorectal Cancer: A Clinical Trial Protocol by Jinjie He, Yue Liu, Chengcheng Liu, Hanguang Hu, Lifeng Sun, Dong Xu, Jun Li, Junye Wang, Xiaobing Chen, Rongbo Lin, Yi Jiang, Yanqiao Zhang, Weisheng Zhang, Ying Cheng, Xiaohong Wu, Mingzhi Fang, Enxiao Li, Ye Xu, Ye Chen, Jiayi Li, Yanyan Cui, Zhanyu Pan, Songnan Zhang, Ying Yuan and Kefeng Ding in Technology in Cancer Research & Treatment</p
CCDC 1545670: Experimental Crystal Structure Determination
No full textPESVIV : catena-(bis(μ-4,4'-dipyridylacetylene)-(μ-hexafluorosilicato)-copper(ii) sulfur dioxide) Space Group: I 4/m m m (139), Cell: a 13.731496Å b 13.731496Å c 8.210038Å, α 90.0000° β 90.0000° γ 90.0000° Related Article: Xili Cui, Qiwei Yang, Lifeng Yang, Rajamani Krishna, Zhiguo Zhang, Zongbi Bao, Hui Wu, Qilong Ren, Wei Zhou, Banglin Chen and Huabin Xing|2017|Adv.Mater.|29|1606929|doi:10.1002/adma.201606929,An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
CCDC 1545669: Experimental Crystal Structure Determination
No full textPESVER : catena-(bis(μ-4,4'-bipyridine)-(μ-hexafluorosilicato)-copper(ii) sulfur dioxide) Space Group: P 4 2 2 (89), Cell: a 11.134845Å b 11.134845Å c 8.004745Å, α 90.0000° β 90.0000° γ 90.0000° Related Article: Xili Cui, Qiwei Yang, Lifeng Yang, Rajamani Krishna, Zhiguo Zhang, Zongbi Bao, Hui Wu, Qilong Ren, Wei Zhou, Banglin Chen and Huabin Xing|2017|Adv.Mater.|29|1606929|doi:10.1002/adma.201606929,An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Tandem Desulfurization/C–C Coupling Reaction of Tetrathienylbenzenes on Cu(111): Synthesis of Pentacene and an Exotic Ladder Polymer
No full textSurface-confined reactions represent a powerful approach for the precise synthesis of low-dimensional organic materials. A complete understanding of the pathways of surface reactions would enable the rational synthesis of a wide range of molecules and polymers. Here, we report different reaction pathways of tetrathienylbenzene (T1TB) and its extended congener tetrakis(dithienyl)benzene (T2TB) on Cu(111), investigated using scanning tunneling microscopy, X-ray photoelectron spectroscopy, and density functional theory calculations. Both T1TB and T2TB undergo desulfurization when deposited on Cu(111) at room temperature. Deposition of T1TB at 453 K yields pentacene through desulfurization, hydrogen transfer, and a cascade of intramolecular cyclization. In contrast, for T2TB the intramolecular cyclization stops at anthracene and the following intermolecular C–C coupling produces a conjugated ladder polymer. We show that tandem desulfurization/C–C coupling provides a versatile approach for growing carbon-based nanostructures on metal surfaces
High dimensional statistical methods for gene-environment interactions
No full textThe genetic influences on complex disease traits generally depends on the joint effects of multiple genetic variants, environment factors, as well as their interplays. Geneenvironment (GE) interactions play vital roles in determining an individual's disease risk, but the underlying genetic machinery is poorly understood. Traditional analysis assuming linear relationship between genetic and environmental factors, along with their interactions, is commonly pursued under the regression-based framework to examine GE interactions. This assumption, however, could be violated due to nonlinear responses of genetic variants to environmental stimuli. As an extension to our previous work on continuous traits, we proposed a flexible varying-coefficient model for the detection of nonlinear GE interaction with binary disease traits. Varying coefficients were approximated by a non-parametric regression function through which one can assess the nonlinear response of genetic factors to environmental changes. A group of statistical tests were proposed to elucidate various mechanisms of GE interaction. The utility of the proposed method was illustrated via simulation and real data analysis with application to type 2 diabetes.It has been increasingly recognized the power of genetic variant set based association analysis over the single variant based approach. We develop a variant set based approach to examine how variants in a genetic system mediated by a common environment factor to affect the phenotype response. The problem can be approached from a high dimensional variable selection perspective. In particular, we can select genetic variants with varying, non-zero constant and zero coefficients, which are corresponding to cases of GE interactions, no GE interactions and no genetic effects, correspondingly. The procedure was implemented in a two stage iterative framework via Smoothly Clipped Absolute Deviation (SCAD) penalty. With proper regularity conditions, we can establish the consistency in variable selection and effect separation of our two stage iterative estimator, as well as the optimal convergence rates of the estimates for varying effect. In addition, it can be shown that the estimate of non-zero constant coefficient enjoys the oracle property. The utility of our procedure will be demonstrated through extensive simulation study and real data analysis.Due to the drawback of local quadratic approximations in the aforementioned two-stage framework, the approach is not efficient in handling cases when the dimension is very large. A group coordinate descent (GCD) based approach was proposed within the framework, which is computationally efficient particularly for high dimensional problems where , because the computational complexity increases only linearly with the number of predictor groups after basis expansion. The advantage of our method is demonstrated through extensive simulation study and real data analysis.Thesis (Ph. D.)--Michigan State University. Statistics, 2013Includes bibliographical references (pages 109-117
Statistical issues and novel strategies for expression quantitative trait loci mapping
No full textGene regulation is thought to play a pivotal role in determiningphysiological trait variability by promoting/reducing the expressionof functional genes directly or indirectly related to the phenotype.Expression quantitative trait loci (eQTL) mapping studies hold greatpromise in disentangling gene regulations and have become a popular research area recently. In this dissertation, I explore severalstatistical strategies, which are applied to eQTL mapping studies,aimed to have a better understanding on the biological mechanism of gene regulation.The major goal of eQTL studies is to identify genomic regions thatare likely to regulate gene expressions. Given that genes functionin a network basis, we consider the scenario that a geneticperturbation could lead to a cascade effects on the transcription ofmultiple genes which belongs to a gene set, e.g., network/pathway.We develop a statistical procedure which incorporates priorbiological gene set information (e.g. KEGG pathway, GO terms) intoeQTL mapping framework to elucidate gene regulation from a systems biology perspective. Pathway regulators which mediate the expression of genes in a pathway are detected by modeling multiple gene expressions as a multivariate response to test the joint variation changes among different genotype categories. We apply the proposed approach to a yeast eQTL data set. Novel pathway regulators and regulation hotspots are identified.Currently, most eQTL mapping studies focus on single markeranalysis. However, the variability of gene expression may be causedby the regulation of a set of variants that belong to a commongenetic system, and individually only with small or moderate effect.To study the roles of genetic systems in regulating geneexpressions, we propose a statistical p-value combination approachto combine individual signals across a pre-defined genetic system to form an overall signal, while considering correlations betweengenetic variants in the system. Results for simulation studies andthe application to the yeast eQTL data are presented.As part of the DNA sequence variation, gene-gene interaction orepistasis has been ubiquitously observed in nature where its role inshaping the development of an organism has been broadly recognized. Investigating genetic interactions related to mRNA expression is an important step on the path to elucidating the genetic architecture underlying gene expression and could provide valuable functional interpretation of gene regulation. As genes are the functional units in living organisms, we conceptually propose a gene-centric gene-gene interaction framework for genome-wide epistasis detection. Multiple genetic markers (e.g. SNPs) in a gene are modeled simultaneously as a testing unit. We develop a model-based kernel machine approach for detecting pairwise gene-gene interactions. Simulation study and applications of the proposed method to the yeast eQTL data indicate its feasibility to eQTL mapping. We further extend the model-based kernel machine method to binary phenotypic outcomes. Our models provide quantitative and testable framework for assessing the interplay between gene expression and gene regulation,and will have great implications for elucidating the geneticarchitecture of gene expression.Thesis (Ph. D.)--Michigan State University. Statistics, 2011Includes bibliographical reference
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Photoelectron spectroscopy studies on group IV semiconductor clusters and novel binary clusters
No full textClusters consisting of a few to a few hundred atoms (~ 2 nm) cover a critical size range, in which the finite-sized systems evolve from molecular-like species to nanoparticles. Photoelectron spectroscopy of size-selected cluster anions in gas phase is a powerful technique to investigate their electronic structure and follow the evolution from discrete molecular features to bulk band structures. Advances in our laboratory to improve the photoelectron energy resolution and to control cluster temperatures have enabled us to obtain well-resolved photoelectron spectra for a wide range of gas-phaseatomic clusters. This dissertation mainly focuses on studies of group IV semiconductor (Si, Ge, Sn) clusters. Several binary cluster systems, such as hydrogenated aluminum clusters and alkali and coinage metal alloy clusters were also investigated. We have confirmed a prolate-to-spherical structural transition with the increase of size for silicon clusters. A semiconductor-to-metal transition was elucidated for tin clusters as a function of size. More importantly, we discovered a stable 12-atom tin cluster Sn12 2-, which has ahighly symmetric icosahedral structure and is named stannashperene for its high stability, high symmetry and π-bonding characters. This icosahedral cage has a size comparable to that of C60 and can be considered as an inorganic analog of the fullerenes. Subsequently, we have synthesized a series of endohedral cage clusters M@Sn12 2-, where M is a transition metal atom. The doped atom in M@Sn12 - keeps its quasi-atomic nature with large magnetic moments. These endohedral cage clusters might thus be viewed as “superatoms”, yielding a rich class of new building blocks for cluster-assembled materials with tunable magnetic, electronic, and chemical properties
Si nanoparticle-decorated Si nanowire networks for Li-ion battery anodes
No full textWe designed and fabricated binder-free, 3D porous silicon nanostructures for Li-ion battery anodes, where Si nanoparticles electrically contact current collectors via vertically grown silicon nanowires. When compared with a Si nanowire anode, the areal capacity was increased by a factor of 4 without having to use long, high temperature steps under vacuum that vapour-liquid-solid Si nanowire growth entails. © 2011 The Royal Society of Chemistry.Y. Cui, L. Hu, H. Wu, and L-F. Cui acknowledge the support from the King Abdullah University of Science and Technology (KAUST) Investigator Award (No. KUS-l1-001-12). J. McDonough acknowledges the support from the National Defense Science and Engineering and National Science Foundation Graduate Research Fellowships
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