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  • Articles  (78)
  • Physical Review B  (19)
  • Science  (14)
  • Royal Society Open Science  (5)
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  • Articles  (78)
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  • 1
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    Accelerating adaptive inverse distance weighting interpolation algorithm on a graphics processing unit (2017)
    Royal Society
    Details
    Publication Date: 2017-09-21
    Description: This paper focuses on designing and implementing parallel adaptive inverse distance weighting (AIDW) interpolation algorithms by using the graphics processing unit (GPU). The AIDW is an improved version of the standard IDW, which can adaptively determine the power parameter according to the data points’ spatial distribution pattern and achieve more accurate predictions than those predicted by IDW. In this paper, we first present two versions of the GPU-accelerated AIDW, i.e. the naive version without profiting from the shared memory and the tiled version taking advantage of the shared memory. We also implement the naive version and the tiled version using two data layouts, structure of arrays and array of aligned structures, on both single and double precision. We then evaluate the performance of parallel AIDW by comparing it with its corresponding serial algorithm on three different machines equipped with the GPUs GT730M, M5000 and K40c. The experimental results indicate that: (i) there is no significant difference in the computational efficiency when different data layouts are employed; (ii) the tiled version is always slightly faster than the naive version; and (iii) on single precision the achieved speed-up can be up to 763 (on the GPU M5000), while on double precision the obtained highest speed-up is 197 (on the GPU K40c). To benefit the community, all source code and testing data related to the presented parallel AIDW algorithm are publicly available.
    Keywords: computer modelling and simulation
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by Royal Society
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  • 2
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    Teosinte ligule allele narrows plant architecture and enhances high-density maize yields (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉Increased planting densities have boosted maize yields. Upright plant architecture facilitates dense planting. Here, we cloned 〈i〉UPA1〈/i〉 (〈i〉Upright Plant Architecture1〈/i〉) and 〈i〉UPA2〈/i〉, two quantitative trait loci conferring upright plant architecture. 〈i〉UPA2〈/i〉 is controlled by a two-base sequence polymorphism regulating the expression of a B3-domain transcription factor (〈i〉ZmRAVL1〈/i〉) located 9.5 kilobases downstream. 〈i〉UPA2〈/i〉 exhibits differential binding by DRL1 (DROOPING LEAF1), and DRL1 physically interacts with LG1 (LIGULELESS1) and represses LG1 activation of 〈i〉ZmRAVL1〈/i〉. 〈i〉ZmRAVL1〈/i〉 regulates 〈i〉brd1〈/i〉 (〈i〉brassinosteroid C-6 oxidase1〈/i〉), which underlies 〈i〉UPA1〈/i〉, altering endogenous brassinosteroid content and leaf angle. The 〈i〉UPA2〈/i〉 allele that reduces leaf angle originated from teosinte, the wild ancestor of maize, and has been lost during maize domestication. Introgressing the wild 〈i〉UPA2〈/i〉 allele into modern hybrids and editing 〈i〉ZmRAVL1〈/i〉 enhance high-density maize yields.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Electrical control of quantum-dot fine-structure splitting for high-fidelity hole spin initialization (2016)
    American Physical Society (APS)
    Details
    Publication Date: 2016-01-29
    Description: Author(s): J. D. Mar, J. J. Baumberg, X. L. Xu, A. C. Irvine, and D. A. Williams We demonstrate electrical control of the neutral exciton fine-structure splitting in a single InAs/GaAs self-assembled quantum dot by significantly reducing the splitting to near zero through the application of a vertical electric field in the fast electron tunneling regime. This is verified by perf… [Phys. Rev. B 93, 045316] Published Wed Jan 27, 2016
    Keywords: Semiconductors II: surfaces, interfaces, microstructures, and related topics
    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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    Bias-controlled single-electron charging of a self-assembled quantum dot in a two-dimensional-electron-gas-based n-i-Schottky diode (2011)
    American Physical Society (APS)
    Details
    Publication Date: 2011-02-15
    Description: Author(s): J. D. Mar, X. L. Xu, J. J. Baumberg, F. S. F. Brossard, A. C. Irvine, C. Stanley, and D. A. Williams We present bias-dependent micro-photoluminescence (μ-PL) spectroscopy of the neutral (X^{0} ) and singly negatively-charged (X^{-} ) excitons in single InAs/GaAs self-assembled quantum dots (QDs) embedded in the intrinsic region of an n-i-Schottky diode based on a two-dimensional electron gas (2DEG... [Phys. Rev. B 83, 075306] Published Mon Feb 14, 2011
    Keywords: Semiconductors II: surfaces, interfaces, microstructures, and related topics
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 5
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    Theory of laser-induced demagnetization at high temperatures (2012)
    American Physical Society (APS)
    Details
    Publication Date: 2012-02-18
    Description: Author(s): A. Manchon, Q. Li, L. Xu, and S. Zhang Laser-induced demagnetization is theoretically studied by explicitly taking into account interactions among electrons, spins, and lattice. Assuming that the demagnetization processes take place during the thermalization of the subsystems, the temperature dynamics is given by the energy transfer betw... [Phys. Rev. B 85, 064408] Published Fri Feb 17, 2012
    Keywords: Magnetism
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 6
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    Differential use of CREB binding protein-coactivator complexes (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-02-21
    Description: CREB binding protein (CBP) functions as an essential coactivator of transcription factors that are inhibited by the adenovirus early gene product E1A. Transcriptional activation by the signal transducer and activator of transcription-1 (STAT1) protein requires the C/H3 domain in CBP, which is the primary target of E1A inhibition. Here it was found that the C/H3 domain is not required for retinoic acid receptor (RAR) function, nor is it involved in E1A inhibition. Instead, E1A inhibits RAR function by preventing the assembly of CBP-nuclear receptor coactivator complexes, revealing differences in required CBP domains for transcriptional activation by RAR and STAT1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kurokawa, R -- Kalafus, D -- Ogliastro, M H -- Kioussi, C -- Xu, L -- Torchia, J -- Rosenfeld, M G -- Glass, C K -- New York, N.Y. -- Science. 1998 Jan 30;279(5351):700-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Cellular and Molecular Medicine, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9445474" target="_blank"〉PubMed〈/a〉
    Keywords: Adenovirus E1A Proteins/*metabolism/pharmacology ; Animals ; Binding Sites ; CREB-Binding Protein ; Cell Differentiation ; Cell Line ; DNA-Binding Proteins/metabolism ; Histone Acetyltransferases ; Humans ; Mutation ; Nuclear Proteins/chemistry/genetics/*metabolism ; Nuclear Receptor Coactivator 1 ; Nuclear Receptor Coactivator 3 ; Protein Binding ; Receptors, Retinoic Acid/metabolism ; Recombinant Fusion Proteins/metabolism ; STAT1 Transcription Factor ; Trans-Activators/metabolism ; Transcription Factors/chemistry/genetics/*metabolism ; *Transcription, Genetic ; Transcriptional Activation ; Tretinoin/pharmacology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Direct synthesis of long single-walled carbon nanotube strands (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-05-04
    Description: In the processes that are used to produce single-walled nanotubes (electric arc, laser ablation, and chemical vapor deposition), the typical lengths of tangled nanotube bundles reach several tens of micrometers. We report that long nanotube strands, up to several centimeters in length, consisting of aligned single-walled nanotubes can be synthesized by the catalytic pyrolysis of n-hexane with an enhanced vertical floating technique. The long strands of nanotubes assemble continuously from arrays of nanotubes, which are intrinsically long.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, H W -- Xu, C L -- Wu, D H -- Wei, B Q -- Vajtai, R -- Ajayan, P M -- New York, N.Y. -- Science. 2002 May 3;296(5569):884-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Mechanical Engineering, Tsinghua University, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11988567" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Dnmt3L and the establishment of maternal genomic imprints (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-11-24
    Description: Complementary sets of genes are epigenetically silenced in male and female gametes in a process termed genomic imprinting. The Dnmt3L gene is expressed during gametogenesis at stages where genomic imprints are established. Targeted disruption of Dnmt3L caused azoospermia in homozygous males, and heterozygous progeny of homozygous females died before midgestation. Bisulfite genomic sequencing of DNA from oocytes and embryos showed that removal of Dnmt3L prevented methylation of sequences that are normally maternally methylated. The defect was specific to imprinted regions, and global genome methylation levels were not affected. Lack of maternal methylation imprints in heterozygous embryos derived from homozygous mutant oocytes caused biallelic expression of genes that are normally expressed only from the allele of paternal origin. The key catalytic motifs characteristic of DNA cytosine methyltransferases have been lost from Dnmt3L, and the protein is more likely to act as a regulator of imprint establishment than as a DNA methyltransferase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bourc'his, D -- Xu, G L -- Lin, C S -- Bollman, B -- Bestor, T H -- GM59377/GM/NIGMS NIH HHS/ -- HD37687/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2001 Dec 21;294(5551):2536-9. Epub 2001 Nov 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and Development, Transgenic Animal Facility, Herbert Irving Comprehensive Cancer Center, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11719692" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Autoantigens/genetics ; Catalytic Domain ; Crosses, Genetic ; DNA (Cytosine-5-)-Methyltransferase/chemistry/genetics/*physiology ; *DNA Methylation ; Embryo, Mammalian/cytology/*metabolism ; Female ; Gene Expression ; Gene Targeting ; *Genomic Imprinting ; Heterozygote ; Homozygote ; Male ; Mice ; Mutation ; Oocytes/*metabolism ; Oogenesis ; Phenotype ; *Ribonucleoproteins, Small Nuclear ; Stem Cells ; Testis/metabolism ; snRNP Core Proteins
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Distinct cellular interactions of secreted and transmembrane Ebola virus glycoproteins (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-03-07
    Description: The mechanisms by which Ebola virus evades detection and infects cells to cause hemorrhagic fever have not been defined, though its glycoprotein, synthesized in either a secreted or transmembrane form, is likely involved. Here the secreted glycoprotein was found to interact with neutrophils through CD16b, the neutrophil-specific form of the Fc gamma receptor III, whereas the transmembrane glycoprotein was found to interact with endothelial cells but not neutrophils. A murine retroviral vector pseudotyped with the transmembrane glycoprotein preferentially infected endothelial cells. Thus, the secreted glycoprotein inhibits early neutrophil activation, which likely affects the host response to infection, whereas binding of the transmembrane glycoprotein to endothelial cells may contribute to the hemorrhagic symptoms of this disease.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Z -- Delgado, R -- Xu, L -- Todd, R F -- Nabel, E G -- Sanchez, A -- Nabel, G J -- New York, N.Y. -- Science. 1998 Feb 13;279(5353):1034-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9461435" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; Ebolavirus/genetics/metabolism/*pathogenicity/physiology ; Endothelium, Vascular/cytology/*metabolism/virology ; Genes, Viral ; Genetic Vectors ; Glycoproteins/genetics/*metabolism/secretion ; Hemorrhagic Fever, Ebola/virology ; Humans ; L-Selectin/metabolism ; Membrane Glycoproteins/genetics/*metabolism ; Moloney murine leukemia virus/genetics/physiology ; Neutrophil Activation ; Neutrophils/immunology/*metabolism ; Receptors, IgG/metabolism ; Transfection ; Tumor Cells, Cultured ; Viral Matrix Proteins/genetics/*metabolism ; Viral Proteins/genetics/*metabolism/secretion
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Transcription factor-specific requirements for coactivators and their acetyltransferase functions (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-02-21
    Description: Different classes of mammalian transcription factors-nuclear receptors, cyclic adenosine 3',5'-monophosphate-regulated enhancer binding protein (CREB), and signal transducer and activator of transcription-1 (STAT-1)-functionally require distinct components of the coactivator complex, including CREB-binding protein (CBP/p300), nuclear receptor coactivators (NCoAs), and p300/CBP-associated factor (p/CAF), based on their platform or assembly properties. Retinoic acid receptor, CREB, and STAT-1 also require different histone acetyltransferase (HAT) activities to activate transcription. Thus, transcription factor-specific differences in configuration and content of the coactivator complex dictate requirements for specific acetyltransferase activities, providing an explanation, at least in part, for the presence of multiple HAT components of the complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Korzus, E -- Torchia, J -- Rose, D W -- Xu, L -- Kurokawa, R -- McInerney, E M -- Mullen, T M -- Glass, C K -- Rosenfeld, M G -- New York, N.Y. -- Science. 1998 Jan 30;279(5351):703-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093-0648, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9445475" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyltransferases/genetics/*metabolism ; CREB-Binding Protein ; Cell Cycle Proteins/genetics/*metabolism ; Cyclic AMP/metabolism ; Cyclic AMP Response Element-Binding Protein/metabolism ; DNA-Binding Proteins/metabolism ; Gene Expression Regulation ; HeLa Cells ; Histone Acetyltransferases ; Humans ; Ligands ; Mutation ; Nuclear Proteins/*metabolism ; Nuclear Receptor Co-Repressor 1 ; Nuclear Receptor Coactivator 1 ; Nuclear Receptor Coactivator 3 ; Promoter Regions, Genetic ; Receptors, Retinoic Acid/metabolism ; Repressor Proteins/metabolism ; STAT1 Transcription Factor ; *Saccharomyces cerevisiae Proteins ; Trans-Activators/metabolism ; Transcription Factors/genetics/*metabolism ; *Transcription, Genetic ; Transcriptional Activation ; p300-CBP Transcription Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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