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  • Oxford University Press  (11)
  • American Physical Society (APS)  (7)
  • American Chemical Society (ACS)
  • Seismological Society of America (SSA)
  • 2010-2014  (18)
  • 1
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    Distinct in-plane resistivity anisotropy in a detwinned FeTe single crystal: Evidence for a Hund's metal (2013)
    American Physical Society (APS)
    Details
    Publication Date: 2013-09-18
    Description: Author(s): Juan Jiang (姜娟), C. He (贺诚), Y. Zhang (张焱), M. Xu (徐敏), Q. Q. Ge (葛青亲), Z. R. Ye (叶子荣), F. Chen (陈飞), B. P. Xie (谢斌平), and D. L. Feng (封东来) The in-plane resistivity anisotropy has been studied with the Montgomery method on the detwinned parent compound of the iron-based superconductor FeTe. The observed resistivity in the antiferromagnetic (AFM) direction is larger than that in the ferromagnetic (FM) direction, which is different from t... [Phys. Rev. B 88, 115130] Published Tue Sep 17, 2013
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 2
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    Interfacial Ferromagnetism and Exchange Bias in CaRuO_{3}/CaMnO_{3} Superlattices (2012)
    American Physical Society (APS)
    Details
    Publication Date: 2012-11-08
    Description: Author(s): C. He, A. J. Grutter, M. Gu, N. D. Browning, Y. Takamura, B. J. Kirby, J. A. Borchers, J. W. Kim, M. R. Fitzsimmons, X. Zhai, V. V. Mehta, F. J. Wong, and Y. Suzuki We have found ferromagnetism in epitaxially grown superlattices of CaRuO 3 /CaMnO 3 that arises in one unit cell at the interface. Scanning transmission electron microscopy and electron energy loss spectroscopy indicate that the difference in magnitude of the Mn valence states between the center of the... [Phys. Rev. Lett. 109, 197202] Published Wed Nov 07, 2012
    Keywords: Condensed Matter: Electronic Properties, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 3
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    Symmetry breaking via orbital-dependent reconstruction of electronic structure in detwinned NaFeAs (2012)
    American Physical Society (APS)
    Details
    Publication Date: 2012-02-23
    Description: Author(s): Y. Zhang, C. He, Z. R. Ye, J. Jiang, F. Chen, M. Xu, Q. Q. Ge, B. P. Xie, J. Wei, M. Aeschlimann, X. Y. Cui, M. Shi, J. P. Hu, and D. L. Feng The superconductivity discovered in iron pnictides is intimately related to a nematic ground state, where the C 4 rotational symmetry is broken via the structural and magnetic transitions. We here study the nematicity in NaFeAs with polarization-dependent angle-resolved photoemission spectroscopy. A ... [Phys. Rev. B 85, 085121] Published Wed Feb 22, 2012
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 4
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    New insight into the shape coexistence and shape evolution of ^{157} Yb (2011)
    American Physical Society (APS)
    Details
    Publication Date: 2011-01-29
    Description: Author(s): C. Xu, H. Hua, X. Q. Li, J. Meng, Z. H. Li, F. R. Xu, Y. Shi, H. L. Liu, S. Q. Zhang, Z. Y. Li, L. H. Zhu, X. G. Wu, G. S. Li, C. Y. He, S. G. Zhou, S. Y. Wang, Y. L. Ye, D. X. Jiang, T. Zheng, J. L. Lou, L. Y. Ma, E. H. Wang, Y. Y. Cheng, and C. He High-spin states in ^{157} Yb have been populated in the ^{144} Sm( ^{16} O,3n) ^{157} Yb fusion-evaporation reaction at a beam energy of 85 MeV. Two rotational bands built on the νf_{7/2} and νh_{9/2} intrinsic states, respectively, have been established for the first time. The newly observed νf... [Phys. Rev. C 83, 014318] Published Fri Jan 28, 2011
    Keywords: Nuclear Structure
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
    Published by American Physical Society (APS)
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  • 5
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    Fingerprinting protein structures effectively and efficiently (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-28
    Description: Motivation:  One common task in structural biology is to assess the similarities and differences among protein structures. A variety of structure alignment algorithms and programs has been designed and implemented for this purpose. A major drawback with existing structure alignment programs is that they require a large amount of computational time, rendering them infeasible for pairwise alignments on large collections of structures. To overcome this drawback, a fragment alphabet learned from known structures has been introduced. The method, however, considers local similarity only, and therefore occasionally assigns high scores to structures that are similar only in local fragments. Method:  We propose a novel approach that eliminates false positives, through the comparison of both local and remote similarity, with little compromise in speed. Two kinds of contact libraries (ContactLib) are introduced to fingerprint protein structures effectively and efficiently. Each contact group of the contact library consists of one local or two remote fragments and is represented by a concise vector. These vectors are then indexed and used to calculate a new combined hit-rate score to identify similar protein structures effectively and efficiently. Results:  We tested our method on the high-quality protein structure subset of SCOP30 containing 3297 protein structures. For each protein structure of the subset, we retrieved its neighbor protein structures from the rest of the subset. The best area under the Receiver-Operating Characteristic curve, archived by ContactLib, is as high as 0.960. This is a significant improvement compared with 0.747, the best result achieved by FragBag. We also demonstrated that incorporating remote contact information is critical to consistently retrieve accurate neighbor protein structures for all- query protein structures. Availability and implementation:   https://cs.uwaterloo.ca/~xfcui/contactlib/ . Contact:   shuaicli@cityu.edu.hk or mli@uwaterloo.ca
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 6
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    Matrix completion via an alternating direction method (2012)
    Oxford University Press
    Details
    Publication Date: 2012-01-20
    Description: The matrix completion problem is to complete an unknown matrix from a small number of entries, and it captures many applications in diversified areas. Recently, it was shown that completing a low-rank matrix can be successfully accomplished by solving its convex relaxation problem using the nuclear norm. This paper shows that the alternating direction method (ADM) is applicable for completing a low-rank matrix including the noiseless case, the noisy case and the positive semidefinite case. The ADM approach for the matrix completion problem is easily implementable and very efficient. Numerical comparisons of the ADM approach with some state-of-the-art methods are reported.
    Print ISSN: 0272-4979
    Electronic ISSN: 1464-3642
    Topics: Mathematics
    Published by Oxford University Press
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  • 7
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    Direct activation of human and mouse Oct4 genes using engineered TALE and Cas9 transcription factors (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-15
    Description: The newly developed transcription activator-like effector protein (TALE) and clustered regularly interspaced short palindromic repeats/Cas9 transcription factors (TF) offered a powerful and precise approach for modulating gene expression. In this article, we systematically investigated the potential of these new tools in activating the stringently silenced pluripotency gene Oct4 ( Pou5f1 ) in mouse and human somatic cells. First, with a number of TALEs and sgRNAs targeting various regions in the mouse and human Oct4 promoters, we found that the most efficient TALE-VP64s bound around –120 to –80 bp, while highly effective sgRNAs targeted from –147 to –89-bp upstream of the transcription start sites to induce high activity of luciferase reporters. In addition, we observed significant transcriptional synergy when multiple TFs were applied simultaneously. Although individual TFs exhibited marginal activity to up-regulate endogenous gene expression, optimized combinations of TALE-VP64s could enhance endogenous Oct4 transcription up to 30-fold in mouse NIH3T3 cells and 20-fold in human HEK293T cells. More importantly, the enhancement of OCT4 transcription ultimately generated OCT4 proteins. Furthermore, examination of different epigenetic modifiers showed that histone acetyltransferase p300 could enhance both TALE-VP64 and sgRNA/dCas9-VP64 induced transcription of endogenous OCT4 . Taken together, our study suggested that engineered TALE-TF and dCas9-TF are useful tools for modulating gene expression in mammalian cells.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Metal-insulator transitions in epitaxial LaVO_{3} and LaTiO_{3} films (2012)
    American Physical Society (APS)
    Details
    Publication Date: 2012-08-02
    Description: Author(s): C. He, T. D. Sanders, M. T. Gray, F. J. Wong, V. V. Mehta, and Y. Suzuki We have demonstrated that epitaxial films of LaVO 3 and LaTiO 3 can exhibit metallicity though their bulk counterparts are Mott insulators. When LaTiO 3 films are compressively strained on SrTiO 3 substrates, we observe metallicity that is attributed largely to epitaxial strain-induced electronic struct... [Phys. Rev. B 86, 081401] Published Wed Aug 01, 2012
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 9
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    Young intragenic miRNAs are less coexpressed with host genes than old ones: implications of miRNA-host gene coevolution (2012)
    Oxford University Press
    Details
    Publication Date: 2012-05-13
    Description: MicroRNAs (miRNAs) have emerged as key regulators of gene expression. Intragenic miRNAs account for ~50% of mammalian miRNAs. Classic studies reported that they are usually coexpressed with host genes. Here, using genome-wide miRNA and gene expression profiles from five sample sets, we show that evolutionarily conserved (‘old’) intragenic miRNAs tend to be coexpressed with host genes, but non-conserved (‘young’) ones rarely do so. This result is robust: in all sample sets, the coexpression rate of young miRNAs is significantly lower than that of conserved ones even after controlling for abundance. As a result, although young miRNAs dominate in human genome, the majority of intragenic miRNAs that show coexpression with host genes are phylogenetically old ones. For younger miRNAs, extrapolation of their expression profiles from those of their host genes should be treated with caution. We propose a model to explain this phenomenon in which the majority of young miRNAs are unlikely to be coexpressed with host genes; however, for some fraction of young miRNAs coexpression with their host genes, initially imbued by chromatin level effects, is advantageous and these are the ones likely to embed into the system and evolve ever higher levels of coexpression, possibly by evolving piggybacking mechanisms.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Genome-Wide Analyses of a Plant-Specific LIM-Domain Gene Family Implicate Its Evolutionary Role in Plant Diversification (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-01
    Description: The Arabidopsis DA1 genes appear to have multiple functions in regulating organ size and abiotic stress response, but the biological roles of its closely related genes remain unknown. Evolutionary analyses might provide some clues to aid in an understanding of their functional diversification. In this work, we characterized the molecular evolution and expressional diversification of DA1 -like genes. Surveying 354 sequenced genomes revealed 142 DA1 -like genes only in plants, indicating plant-specificity of these genes. The DA1-like protein modular structure was composed of two UIMs (ubiquitin interaction motifs), one LIM-domain (from lin-11 , isl-1 , and mec-3 ), and a conserved C-terminal, and was distinguishable from the already defined three groups of LIM-domain proteins. We further found that the DA1 -like genes diverged into Classes I and II at the ancestor of seed plants and acquired 13 clade-specific residues during their evolutionary history. Moreover, diverse intron size evolution was noted following the transition from size-expandable introns to minimal ones, accompanying the emergence and diversification of angiosperms. Functional diversification as it relates to gene expression was further investigated in soybean. Glycine max DA1 genes showed diverse tissues expression patterns during development and had substantially varied abiotic stress response expression. Thus, variations in the coding regions, intron size, and gene expression contributed to the functional diversification of this gene family. Our data suggest that the evolution of the DA1 -like genes facilitated the development of diverse molecular and functional diversification patterns to accompany the successful radiation of plants into diverse environments during evolution.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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