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A Stochastic Model for Microtubule Motors Describes the In Vivo Cytoplasmic Transport of Human Adenovirus
(2009)PLoS Computational BiologyCytoplasmic transport of organelles, nucleic acids and proteins on microtubules is usually bidirectional with dynein and kinesin motors mediating the delivery of cargoes in the cytoplasm. Here we combine live cell microscopy, single virus tracking and trajectory segmentation to systematically identify the parameters of a stochastic computational model of cargo transport by molecular motors on microtubules. The model parameters are identified ...Journal Article -
CARINA oxygen data in the Atlantic Ocean
(2009)Earth System Science DataIn the CARINA (Carbon dioxide in the Atlantic Ocean) project, a new dataset with many previously unpublished hydrographic data from the Atlantic, Arctic and Southern Ocean was assembled and subjected to careful quality control (QC) procedures. Here, we present the dissolved oxygen measurements in the Atlantic region of the dataset and describe in detail the secondary QC procedures that aim to ensure that the data are internally consistent. ...Journal Article -
ON/OFF and Beyond - A Boolean Model of Apoptosis
(2009)PLoS Computational BiologyApoptosis is regulated by several signaling pathways which are extensively linked by crosstalks. Boolean or logical modeling has become a promising approach to capture the qualitative behavior of such complex networks. Here we built a large-scale literature-based Boolean model of the central intrinsic and extrinsic apoptosis pathways as well as pathways connected with them. The model responds to several external stimuli such as Fas ligand, ...Journal Article -
Bound-to-continuum terahertz quantum cascade laser with a single-quantum-well phonon extraction/injection stage
(2009)New Journal of PhysicsA terahertz quantum cascade laser design that combines a wide gain bandwidth, large photon-driven transport and good high-temperature characteristics is presented. It relies on a diagonal transition between a bound state and doublet of states tunnel coupled to the upper state of a phonon extraction stage. The high optical efficiency of this design enables the observation of photon-driven transport over a wide current density range. The ...Journal Article -
A measurement of coherent neutral pion production in neutrino neutral current interactions in the NOMAD experiment
(2009)Physics Letters BWe present a study of exclusive neutral pion production in neutrino-nucleus Neutral Current interactions using data from the NOMAD experiment at the CERN SPS. The data correspond to 1.44 × 10 6 muon-neutrino Charged Current interactions in the energy range 2.5 ≤ E ν ≤ 300 GeV. Neutrino events with only one visible π 0 in the final state are expected to result from two Neutral Current processes: coherent π 0 production, ν + A → ν + A + π ...Journal Article -
Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology
(2009)PLoS Computational BiologyThe use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today's important nutritional research questions poses a ...Journal Article -
Combined molecular algorithms for the generation, equilibration and topological analysis of entangled polymers: Methodology and performance
(2009)International Journal of Molecular SciencesWe review the methodology, algorithmic implementation and performance characteristics of a hierarchical modeling scheme for the generation, equilibration and topological analysis of polymer systems at various levels of molecular description: from atomistic polyethylene samples to random packings of freely-jointed chains of tangent hard spheres of uniform size. Our analysis focuses on hitherto less discussed algorithmic details of the ...Journal Article -
Wheat domestication accelerated evolution and triggered positive selection in the beta-xylosidase enzyme of Mycosphaerella graminicola
(2009)PLoS ONEPlant cell wall degrading enzymes (PCWDEs) of plant pathogens are receiving increasing interest for their potential to trigger plant defense reactions. In an antagonistic co-evolutionary arms race between host and pathogen, PCWDEs could be under strong selection. Here, we tested the hypothesis that PCWDEs in the fungal wheat pathogen Mycosphaerella graminicola have been positively selected by analyzing ratios of non-synonymous and synonymous ...Journal Article -
Deeply virtual Compton scattering and its beam charge asymmetry in e±p collisions at HERA
(2009)Physics Letters BA measurement of elastic deeply virtual Compton scattering γ * p → γ p using e + p and e - p collision data recorded with the H1 detector at HERA is presented. The analysed data sample corresponds to an integrated luminosity of 306 pb -1, almost equally shared between both beam charges. The cross section is measured as a function of the virtuality Q 2 of the exchanged photon and the centre-of-mass energy W of the γ * p system in the ...Journal Article -
Metabolite Profiling Uncovers Plasmid-Induced Cobalt Limitation under Methylotrophic Growth Conditions
(2009)PLoS ONEBackground The introduction and maintenance of plasmids in cells is often associated with a reduction of growth rate. The reason for this growth reduction is unclear in many cases. Methodology/Principal Findings We observed a surprisingly large reduction in growth rate of about 50% of Methylobacterium extorquens AM1 during methylotrophic growth in the presence of a plasmid, pCM80 expressing the tetA gene, relative to the wild-type. ...Journal Article