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  • Articles  (47)
  • Science  (14)
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  • Articles  (47)
  • 1
    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
    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
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  • 3
    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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  • 4
    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〉
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    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
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    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
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  • 7
    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
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  • 8
    Publication Date: 1998-01-31
    Description: Several ion channels are reportedly redox responsive, but the molecular basis for the changes in activity is not known. The mechanism of nitric oxide action on the cardiac calcium release channel (ryanodine receptor) (CRC) in canines was explored. This tetrameric channel contains approximately 84 free thiols and is S-nitrosylated in vivo. S-Nitrosylation of up to 12 sites (3 per CRC subunit) led to progressive channel activation that was reversed by denitrosylation. In contrast, oxidation of 20 to 24 thiols per CRC (5 or 6 per subunit) had no effect on channel function. Oxidation of additional thiols (or of another class of thiols) produced irreversible activation. The CRC thus appears to be regulated by poly-S-nitrosylation (multiple covalent attachments), whereas oxidation can lead to loss of control. These results reveal that ion channels can differentiate nitrosative from oxidative signals and indicate that the CRC is regulated by posttranslational chemical modification(s) of sulfurs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, L -- Eu, J P -- Meissner, G -- Stamler, J S -- HL-27430/HL/NHLBI NIH HHS/ -- HL52529/HL/NHLBI NIH HHS/ -- HL59130/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1998 Jan 9;279(5348):234-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of North Carolina, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9422697" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/*metabolism ; Cyclic GMP/metabolism ; Cysteine/analogs & derivatives/pharmacology ; Dithiothreitol/pharmacology ; Dogs ; Electric Conductivity ; Ethylmaleimide/pharmacology ; Glutathione/analogs & derivatives/pharmacology ; Liposomes/metabolism ; *Mercaptoethanol ; Molsidomine/analogs & derivatives/pharmacology ; Myocardium/*metabolism ; Nitric Oxide/*metabolism ; Nitrosation ; Nitroso Compounds/*metabolism/pharmacology ; Oxidation-Reduction ; Proteolipids/metabolism ; Ryanodine Receptor Calcium Release Channel/drug effects/*metabolism ; S-Nitrosoglutathione ; *S-Nitrosothiols ; Sulfhydryl Compounds/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2010-07-22
    Description: The rapid dissemination of the 2009 pandemic influenza virus underscores the need for universal influenza vaccines that elicit protective immunity to diverse viral strains. Here, we show that vaccination with plasmid DNA encoding H1N1 influenza hemagglutinin (HA) and boosting with seasonal vaccine or replication-defective adenovirus 5 vector encoding HA stimulated the production of broadly neutralizing influenza antibodies. This prime/boost combination increased the neutralization of diverse H1N1 strains dating from 1934 to 2007 as compared to either component alone and conferred protection against divergent H1N1 viruses in mice and ferrets. These antibodies were directed to the conserved stem region of HA and were also elicited in nonhuman primates. Cross-neutralization of H1N1 subtypes elicited by this approach provides a basis for the development of a universal influenza vaccine for humans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wei, Chih-Jen -- Boyington, Jeffrey C -- McTamney, Patrick M -- Kong, Wing-Pui -- Pearce, Melissa B -- Xu, Ling -- Andersen, Hanne -- Rao, Srinivas -- Tumpey, Terrence M -- Yang, Zhi-Yong -- Nabel, Gary J -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Aug 27;329(5995):1060-4. doi: 10.1126/science.1192517. Epub 2010 Jul 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892-3005, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20647428" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Neutralizing/biosynthesis/*immunology ; Antibodies, Viral/biosynthesis/*immunology ; *Cross Protection ; Female ; Ferrets ; Genetic Vectors ; Hemagglutinin Glycoproteins, Influenza Virus/genetics/*immunology ; Humans ; Immunization, Secondary ; Influenza A Virus, H1N1 Subtype/*immunology ; Influenza A Virus, H2N2 Subtype/immunology ; Influenza A Virus, H3N2 Subtype/immunology ; Influenza A Virus, H5N1 Subtype/immunology ; Influenza Vaccines/*administration & dosage/*immunology ; Influenza, Human/immunology/prevention & control ; Macaca mulatta ; Male ; Mice ; Mice, Inbred BALB C ; Mutant Proteins/immunology ; Orthomyxoviridae Infections/immunology/prevention & control ; Plasmids ; Vaccination ; Vaccines, DNA/administration & dosage/immunology
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  • 10
    Publication Date: 2010-07-10
    Description: Cross-reactive neutralizing antibodies (NAbs) are found in the sera of many HIV-1-infected individuals, but the virologic basis of their neutralization remains poorly understood. We used knowledge of HIV-1 envelope structure to develop antigenically resurfaced glycoproteins specific for the structurally conserved site of initial CD4 receptor binding. These probes were used to identify sera with NAbs to the CD4-binding site (CD4bs) and to isolate individual B cells from such an HIV-1-infected donor. By expressing immunoglobulin genes from individual cells, we identified three monoclonal antibodies, including a pair of somatic variants that neutralized over 90% of circulating HIV-1 isolates. Exceptionally broad HIV-1 neutralization can be achieved with individual antibodies targeted to the functionally conserved CD4bs of glycoprotein 120, an important insight for future HIV-1 vaccine design.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965066/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965066/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Xueling -- Yang, Zhi-Yong -- Li, Yuxing -- Hogerkorp, Carl-Magnus -- Schief, William R -- Seaman, Michael S -- Zhou, Tongqing -- Schmidt, Stephen D -- Wu, Lan -- Xu, Ling -- Longo, Nancy S -- McKee, Krisha -- O'Dell, Sijy -- Louder, Mark K -- Wycuff, Diane L -- Feng, Yu -- Nason, Martha -- Doria-Rose, Nicole -- Connors, Mark -- Kwong, Peter D -- Roederer, Mario -- Wyatt, Richard T -- Nabel, Gary J -- Mascola, John R -- Z99 AI999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Aug 13;329(5993):856-61. doi: 10.1126/science.1187659. Epub 2010 Jul 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20616233" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Antibodies, Monoclonal/*immunology/isolation & purification ; Antibodies, Neutralizing/*immunology/isolation & purification ; Antibody Specificity ; Antigens, CD4/immunology/metabolism ; B-Lymphocytes/immunology ; Binding Sites, Antibody ; Cross Reactions ; Drug Design ; Enzyme-Linked Immunosorbent Assay ; Epitopes/immunology ; Genes, Immunoglobulin Heavy Chain ; Genes, Immunoglobulin Light Chain ; HIV Antibodies/*immunology/isolation & purification ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology/virology ; HIV-1/genetics/*immunology ; Humans ; Molecular Sequence Data ; Neutralization Tests ; Protein Engineering ; Recombinant Proteins/chemistry/immunology/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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