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  • 1
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    Cell-Dock: high-performance protein-protein docking (2012)
    Oxford University Press
    Details
    Publication Date: 2012-09-08
    Description: : The application of docking to large-scale experiments or the explicit treatment of protein flexibility are part of the new challenges in structural bioinformatics that will require large computer resources and more efficient algorithms. Highly optimized fast Fourier transform (FFT) approaches are broadly used in docking programs but their optimal code implementation leaves hardware acceleration as the only option to significantly reduce the computational cost of these tools. In this work we present Cell-Dock, an FFT-based docking algorithm adapted to the Cell BE processor. We show that Cell-Dock runs faster than FTDock with maximum speedups of above 200 x , while achieving results of similar quality. Availability and implementation: The source code is released under GNU General Public License version 2 and can be downloaded from http://mmb.pcb.ub.es/~cpons/Cell-Dock . Contact: djimenez@ac.upc.edu or juanf@bsc.es Supplementary Information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    A neural network approach for identifying particle pitch angle distributions in Van Allen Probes data (2016)
    Wiley
    Details
    Publication Date: 2016-03-12
    Description: Analysis of particle pitch angle distributions (PADs) has been used as a mean to comprehend a multitude of different physical mechanisms that lead to flux variations in the Van Allen belts and also to particle precipitation into the upper atmosphere. In this work we developed a neural network-based data clustering methodology that automatically identifies distinct PAD types in an unsupervised way using particle flux data. One can promptly identify and locate three well-known PAD types in both time and radial distance, namely 90°-peaked, butterfly, and flattop distributions. In order to illustrate the applicability of our methodology we used relativistic electron flux data from the whole month of November, 2014, acquired from the Relativistic Electron-Proton Telescope (REPT) instrument onboard the Van Allen Probes, but it is emphasized that our approach can also be used with multi-platform spacecraft data. Our PAD classification results are in reasonably good agreement with those obtained by standard statistical fitting algorithms. The proposed methodology has a potential use for Van Allen belt's monitoring.
    Print ISSN: 1539-4964
    Electronic ISSN: 1542-7390
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
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    Comparative study of three reconnection X-line models at the Earth's dayside magnetopause using in situ observations (2017)
    Wiley
    Details
    Publication Date: 2017-03-29
    Description: This work examines the large-scale aspects of magnetic field reconnection at the Earth's dayside magnetopause. We use two sets of reconnection events, which are identified mostly by the in situ detection of accelerated and Alfvénic plasma flows. We intercompare three analytical models that predict the reconnection X-line location and orientation, namely the Trattner et al. [2007] and Swisdak and Drake [2007] models, and also a modified version of the component merging model [ Gonzalez and Mozer , 1974; Sonnerup, 1974]. In the first set of reconnection observations, we show three fortuitous, quasi-simultaneous dayside magnetopause crossing events where two widely separated spacecraft detect reconnection signatures, and the X-line location and orientation can be inferred from the observations. We compare X-line model predictions to those inferred from observations. These three reconnection events indicate the presence of an extended (〉7 Earth radii in length), component-type reconnection X-line on Earth's dayside magnetopause connecting and structuring the reconnection signatures at locations far apart. In the second set of reconnection events, we analyze the X-line models' performance in predicting the observed reconnection outflow direction, i.e., its north-south and/or east-west senses, in a total of 75 single, rather than multiple and quasi-simultaneous, magnetopause crossing events, where reconnection-associated plasma flows were clearly present. We found that the Swisdak and Drake [2007]'s X-line model performs slightly better, albeit not statistically significant, when predicting both accelerated plasma flow north-south and east-west components in 73% and 53% of the cases, respectively, as compared to the Trattner et al. [2007] model (70% north-south, 42% east-west), and the modified component merging model (66% north-south, 50% east-west).
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
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    Primary non-Hodgkin's lymphoma of the central nervous system. Results of radiotherapy in 15 cases (1983)
    Wiley
    Details
    Publication Date: 1983-06-01
    Print ISSN: 0008-543X
    Electronic ISSN: 1097-0142
    Topics: Biology , Medicine
    Published by Wiley on behalf of American Cancer Society.
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  • 5
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    The Chlamydomonas genome reveals the evolution of key animal and plant functions (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-13
    Description: Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087/" 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/PMC2875087/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Merchant, Sabeeha S -- Prochnik, Simon E -- Vallon, Olivier -- Harris, Elizabeth H -- Karpowicz, Steven J -- Witman, George B -- Terry, Astrid -- Salamov, Asaf -- Fritz-Laylin, Lillian K -- Marechal-Drouard, Laurence -- Marshall, Wallace F -- Qu, Liang-Hu -- Nelson, David R -- Sanderfoot, Anton A -- Spalding, Martin H -- Kapitonov, Vladimir V -- Ren, Qinghu -- Ferris, Patrick -- Lindquist, Erika -- Shapiro, Harris -- Lucas, Susan M -- Grimwood, Jane -- Schmutz, Jeremy -- Cardol, Pierre -- Cerutti, Heriberto -- Chanfreau, Guillaume -- Chen, Chun-Long -- Cognat, Valerie -- Croft, Martin T -- Dent, Rachel -- Dutcher, Susan -- Fernandez, Emilio -- Fukuzawa, Hideya -- Gonzalez-Ballester, David -- Gonzalez-Halphen, Diego -- Hallmann, Armin -- Hanikenne, Marc -- Hippler, Michael -- Inwood, William -- Jabbari, Kamel -- Kalanon, Ming -- Kuras, Richard -- Lefebvre, Paul A -- Lemaire, Stephane D -- Lobanov, Alexey V -- Lohr, Martin -- Manuell, Andrea -- Meier, Iris -- Mets, Laurens -- Mittag, Maria -- Mittelmeier, Telsa -- Moroney, James V -- Moseley, Jeffrey -- Napoli, Carolyn -- Nedelcu, Aurora M -- Niyogi, Krishna -- Novoselov, Sergey V -- Paulsen, Ian T -- Pazour, Greg -- Purton, Saul -- Ral, Jean-Philippe -- Riano-Pachon, Diego Mauricio -- Riekhof, Wayne -- Rymarquis, Linda -- Schroda, Michael -- Stern, David -- Umen, James -- Willows, Robert -- Wilson, Nedra -- Zimmer, Sara Lana -- Allmer, Jens -- Balk, Janneke -- Bisova, Katerina -- Chen, Chong-Jian -- Elias, Marek -- Gendler, Karla -- Hauser, Charles -- Lamb, Mary Rose -- Ledford, Heidi -- Long, Joanne C -- Minagawa, Jun -- Page, M Dudley -- Pan, Junmin -- Pootakham, Wirulda -- Roje, Sanja -- Rose, Annkatrin -- Stahlberg, Eric -- Terauchi, Aimee M -- Yang, Pinfen -- Ball, Steven -- Bowler, Chris -- Dieckmann, Carol L -- Gladyshev, Vadim N -- Green, Pamela -- Jorgensen, Richard -- Mayfield, Stephen -- Mueller-Roeber, Bernd -- Rajamani, Sathish -- Sayre, Richard T -- Brokstein, Peter -- Dubchak, Inna -- Goodstein, David -- Hornick, Leila -- Huang, Y Wayne -- Jhaveri, Jinal -- Luo, Yigong -- Martinez, Diego -- Ngau, Wing Chi Abby -- Otillar, Bobby -- Poliakov, Alexander -- Porter, Aaron -- Szajkowski, Lukasz -- Werner, Gregory -- Zhou, Kemin -- Grigoriev, Igor V -- Rokhsar, Daniel S -- Grossman, Arthur R -- GM07185/GM/NIGMS NIH HHS/ -- GM42143/GM/NIGMS NIH HHS/ -- R01 GM032843/GM/NIGMS NIH HHS/ -- R01 GM042143/GM/NIGMS NIH HHS/ -- R01 GM042143-09/GM/NIGMS NIH HHS/ -- R01 GM060992/GM/NIGMS NIH HHS/ -- R01 GM062915-06/GM/NIGMS NIH HHS/ -- R37 GM030626/GM/NIGMS NIH HHS/ -- R37 GM042143/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 12;318(5848):245-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17932292" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/*genetics/*physiology ; Animals ; *Biological Evolution ; Chlamydomonas reinhardtii/*genetics/physiology ; Chloroplasts/metabolism ; Computational Biology ; DNA, Algal/genetics ; Flagella/metabolism ; Genes ; *Genome ; Genomics ; Membrane Transport Proteins/genetics/physiology ; Molecular Sequence Data ; Multigene Family ; Photosynthesis/genetics ; Phylogeny ; Plants/genetics ; Proteome ; Sequence Analysis, DNA
    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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  • 6
    Electronic Resource
    Electronic Resource
    Maximum-likelihood models for mapping genetic markers showing segregation distortion. 2. F2 populations (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 81-89 
    Details
    ISSN: 1432-2242
    Keywords: Genetic mapping ; Maximum-likelihood ; Molecular markers ; Gametic selection ; Zygotic selection
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In F2 populations, gametic and zygotic selection may affect the analysis of linkage in different ways. Therefore, specific likelihood equations have to be developed for each case, including dominant and codominant markers. The asymptotic bias of the “classical” estimates are derived for each case, in order to compare them with the standard errors of the suggested estimates. We discuss the utility and the efficiency of a previous model developed for dominant markers. We show that dominant markers provide very poor information in the case of segregation distortion and, therefore, should be used with circumspection. On the other hand, the estimation of recombination fractions between codominant markers is less affected by selection than is that for dominant markers. We also discuss the analysis of linkage between dominant and codominant markers.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00220999
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  • 7
    Electronic Resource
    Electronic Resource
    Maximum-likelihood models for mapping genetic markers showing segregation distortion. 1. Backcross populations (1995)
    Springer
    Theoretical and applied genetics 90 (1995), S. 73-80 
    Details
    ISSN: 1432-2242
    Keywords: Genetic mapping ; Segregation distortion ; Maximum-likelihood ; Linkage ; Molecular markers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A maximum-likelihood approach is used in order to estimate recombination fractions between markers showing segregation distortion in backcross populations. It is assumed that the distortions are induced by viability differences between gametes or zygotes due to one or more selected genes. We show that Bailey's (1949) estimate stays consistent and efficient under more general assumptions than those defined by its author. This estimate should therefore be used instead of the classical maximum-likelihood estimate. The question of detection of linkage is also discussed. We show that the order of markers on linkage groups may be affected by segregation distortion.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00220998
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  • 8
    Electronic Resource
    Electronic Resource
    Gel filtration and high-performance liquid chromatographic analysis of phosphotungstic acid soluble peptides from blue cheeses (1987)
    Springer
    Chromatographia 23 (1987), S. 764-766 
    Details
    ISSN: 1612-1112
    Keywords: Column liquid chromatography ; Gel permeation chromatography ; Cheese peptides ; Amino acids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The nitrogen fraction from cheese, soluble in phosphotungstic acid has been analyzed by gel permeation and high performance liquid chromatography. Elution profiles of this fraction on Sephadex G-10 show that there are no peptides of molecular weight higher than 700 daltons. Six fractions have been obtained. The first one has the peptides and some amino acids. Fractions II to VI contains mostly free amino acids. Fraction I has been separated into many peaks by HPLC. Six or seven of these peaks are presumed to correspond to peptides.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02312670
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  • 9
    Electronic Resource
    Electronic Resource
    Einfluß der Reaktionsbedingungen bei der Chlormethylierung von Styrol (1982)
    Weinheim : Wiley-Blackwell
    Angewandte Makromolekulare Chemie 105 (1982), S. 91-97 
    Details
    ISSN: 0003-3146
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Description / Table of Contents: The influence of trioxane, inhibitor (CuCl2), solvent (isopropanol), water, and catalyst concentration, and temperature in the chloromethylation of styrene has been studied. A two level statistical design of experiments was used. Conversion and selectivity were fitted by multiple linear regression. Two equations have been obtained. The influence of the conditions in the reaction is shown in these two equations.
    Notes: Es wurde der Einfluß der Trioxan-, Inhibitor- (CuCl2), Lösungsmittel-(Isopropanol), Wasser- und Katalysatormenge (ZnCl2) und der Temperatur bei der Chlormethylierung von Styrol untersucht. Dabei wurde ein 2m-q Teilfaktor-Versuchsplan verwendet. Der Umsetzungsgrad und die Selektivität wurden nach einer linearen multiplen Regression korreliert. Die erhaltenen zwei Regressionsgleichungen zeigen den Einfluß der Reaktionsbedingungen bei der Chlormethylierung von Styrol.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/apmc.1982.051050110
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  • 10
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    Genetic Diversity, Specific Combining Ability, and Heterosis in Tropical Maize under Stress and Nonstress Environments (2003)
    Wiley
    Details
    Publication Date: 2003-05-01
    Print ISSN: 0011-183X
    Electronic ISSN: 1435-0653
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Wiley
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