@inproceedings{3203, abstract = {In recent years the Markov Random Field (MRF) has become the de facto probabilistic model for low-level vision applications. However, in a maximum a posteriori (MAP) framework, MRFs inherently encourage delta function marginal statistics. By contrast, many low-level vision problems have heavy tailed marginal statistics, making the MRF model unsuitable. In this paper we introduce a more general Marginal Probability Field (MPF), of which the MRF is a special, linear case, and show that convex energy MPFs can be used to encourage arbitrary marginal statistics. We introduce a flexible, extensible framework for effectively optimizing the resulting NP-hard MAP problem, based around dual-decomposition and a modified mincost flow algorithm, and which achieves global optimality in some instances. We use a range of applications, including image denoising and texture synthesis, to demonstrate the benefits of this class of MPF over MRFs.}, author = {Woodford, Oliver J and Rother, Carsten and Vladimir Kolmogorov}, pages = {2319 -- 2326}, publisher = {IEEE}, title = {{A global perspective on MAP inference for low level vision}}, doi = {10.1109/ICCV.2009.5459434}, year = {2009}, } @inproceedings{3230, abstract = {We present a new approach to the design of IND-CCA2 secure hybrid encryption schemes in the standard model. Our approach provides an efficient generic transformation from 1-universal to 2-universal hash proof systems. The transformation involves a randomness extractor based on a 4-wise independent hash function as the key derivation function. Our methodology can be instantiated with efficient schemes based on standard intractability assumptions such as Decisional Diffie-Hellman, Quadratic Residuosity, and Paillier's Decisional Composite Residuosity. Interestingly, our framework also allows to prove IND-CCA2 security of a hybrid version of 1991's Damgård's ElGamal public-key encryption scheme under the DDH assumption. }, author = {Kiltz, Eike and Krzysztof Pietrzak and Stam, Martijn and Yung, Moti}, pages = {590 -- 609}, publisher = {Springer}, title = {{A new randomness extraction paradigm for hybrid encryption}}, doi = {10.1007/978-3-642-01001-9_34}, volume = {5479}, year = {2009}, } @inproceedings{3231, abstract = {We investigate the security of "padding-based" encryption schemes in the standard model. This class contains all public-key encryption schemes where the encryption algorithm first applies some invertible public transformation to the message (the "padding"), followed by a trapdoor permutation. In particular, this class contains OAEP and its variants. Our main result is a black-box impossibility result showing that one cannot prove any such padding-based scheme chosen-ciphertext secure even assuming the existence of ideal trapdoor permutations. The latter is a strong ideal abstraction of trapdoor permutations which inherits all security properties of uniform random permutations. }, author = {Kiltz, Eike and Krzysztof Pietrzak}, pages = {389 -- 406}, publisher = {Springer}, title = {{On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model}}, doi = {10.1007/978-3-642-01001-9_23}, volume = {5479}, year = {2009}, } @inproceedings{3232, abstract = {A weak pseudorandom function (wPRF) is a cryptographic primitive similar to - but weaker than - a pseudorandom function: for wPRFs one only requires that the output is pseudorandom when queried on random inputs.We show that unlike "normal" PRFs, wPRFs are seedincompressible, in the sense that the output of a wPRF is pseudorandom even if a bounded amount of information about the key is leaked. As an application of this result we construct a simple mode of operation which - when instantiated with any wPRF - gives a leakage-resilient stream-cipher. The implementation of such a cipher is secure against every side-channel attack, as long as the amount of information leaked per round is bounded, but overall can be arbitrary large. The construction is simpler than the previous one (Dziembowski-Pietrzak FOCS'08) as it only uses a single primitive (a wPRF) in a straight forward manner. }, author = {Krzysztof Pietrzak}, pages = {462 -- 482}, publisher = {Springer}, title = {{A leakage resilient mode of operation}}, doi = {10.1007/978-3-642-01001-9_27}, volume = {5479}, year = {2009}, } @article{3292, abstract = {Galactofuranose (Galf) containing molecules have been described at the cell surface of several eukaryotes and shown to contribute to the virulence of the parasite Leishmania major and the fungus Aspergillus fumigatus. It is anticipated that a number of the surface glycoconjugates such as N-glycans or glycolipids are galactofuranosylated in the Golgi apparatus. This raises the question of how the substrate for galactofuranosylation reactions, UDP-Galf, which is synthesized in the cytosol, translocates into the organelles of the secretory pathway. Here we report the first identification of a Golgi-localized nucleotide sugar transporter, named GlfB, with specificity for a UDP-Galf. In vitro transport assays established binding of UDP-Galf to GlfB and excluded transport of several other nucleotide sugars. Furthermore, the implication of glfB in the galactofuranosylation of A. fumigatus glycoconjugates and galactomannan was demonstrated by a targeted gene deletion approach. Our data reveal a direct connection between galactomannan and the organelles of the secretory pathway that strongly suggests that the cell wall-bound polysaccharide originates from its glycosylphosphatidylinositol-anchored form.}, author = {Engel, Jakob and Schmalhorst, Philipp S and Dörk Bousset, Thilo and Ferrières, Vincent and Routier, Françoise}, journal = {Journal of Biological Chemistry}, number = {49}, pages = {33859 -- 33868}, publisher = {American Society for Biochemistry and Molecular Biology}, title = {{A single UDP galactofuranose transporter is required for galactofuranosylation in Aspergillus fumigatus}}, doi = {10.1074/jbc.M109.070219 }, volume = {284}, year = {2009}, } @article{3293, abstract = {Chemotactic responses of Drosophila to certain esters and alcohols are experience dependent. When the flies are exposed after eclosion to these chemicals, the odorants become strongly attractive. We show that behavioral conditioning is accompanied by an increase in the electrophysiological responses of single neurons in sensilla basiconica. Sensitization involves odorants that act on a common olfactory receptor. The possible mechanism of imaginal conditioning and its ecological and evolutionary significance are discussed.}, author = {Chakraborty Tuhin, Subhra and Sarit Goswami and Siddiqi, Obaid}, journal = {Journal of Neurogenetics}, number = {1-2}, pages = {210 -- 9}, publisher = {Informa Healthcare}, title = {{Sensory correlates of imaginal conditioning in Drosophila melanogaster}}, doi = {10.1080/01677060802491559 }, volume = {23}, year = {2009}, } @article{3304, abstract = {Complex traits often involve interactions between different genetic loci. This can lead to sign epistasis, whereby mutations that are individually deleterious or neutral combine to confer a fitness benefit. In order to acquire the beneficial genotype, an asexual population must cross a fitness valley or plateau by first acquiring the deleterious or neutral intermediates. Here, we present a complete, intuitive theoretical description of the valley-crossing process across the full spectrum of possible parameter regimes. We calculate the rate at which a population crosses a fitness valley or plateau of arbitrary width, as a function of the mutation rates, the population size, and the fitnesses of the intermediates. We find that when intermediates are close to neutral, a large population can cross even wide fitness valleys remarkably quickly, so that valley-crossing dynamics may be common even when mutations that directly increase fitness are also possible. Thus the evolutionary dynamics of large populations can be sensitive to the structure of an extended region of the fitness landscape — the population may not take directly uphill paths in favor of paths across valleys and plateaus that lead eventually to fitter genotypes. In smaller populations, we find that below a threshold size, which depends on the width of the fitness valley and the strength of selection against intermediate genotypes, valley-crossing is much less likely and hence the evolutionary dynamics are less influenced by distant regions of the fitness landscape.}, author = {Daniel Weissman and Desai, Michael M and Fisher, Daniel S and Feldman, Marcus W}, journal = {Theoretical Population Biology}, number = {4}, pages = {286 -- 300}, publisher = {Academic Press}, title = {{The rate at which asexual populations cross fitness valleys}}, doi = {10.1016/j.tpb.2009.02.006}, volume = {75}, year = {2009}, } @article{3309, abstract = { Mastitis, a worldwide endemic disease of dairy cows, is an important cause of decreased efficiency in milk production. Early medical treatment can reduce the nonreversible losses in milk production caused by this infection. Various diagnostic tests for mastitis are available, including a test measuring the electrical conductivity of milk (MEC test), the industry standard of somatic cell counting (SCC test), a bacteriological test, and a recently developed test measuring mammary associated amyloid A (MAA test). None of these tests is considered a gold standard, however. The aim of the present study was to determine which of these tests provides the best results, and at what cost, to improve the efficiency of milk production. For this study, 25 cows were tested at all four quarters of the udder with each of the aforementioned mastitis diagnostic tests. Based on the data, the disease prevalence as well as the sensitivity and the specificity of the four tests were estimated with a Bayesian approach by extending the Hui and Walter model with two independent tests and two populations to a model with four partially dependent tests and one population. This model was further combined with a receiver operating characteristics analysis to estimate the overall test accuracy.}, author = {Caroline Uhler}, journal = {Journal of Agricultural Biological and Environmental Statistics}, number = {1}, pages = {79 -- 98}, publisher = {Springer}, title = {{Mastitis in dairy production: Estimation of sensitivity, specificity and disease prevalence in the absence of a gold standard}}, doi = {10.1198/jabes.2009.0005}, volume = {14}, year = {2009}, } @article{110, abstract = {In order to better understand magnetic reconnection and particle acceleration in solar flares, we compare the RHESSI hard X-ray (HXR) footpoint motions of three flares with a detailed study of the corresponding topology given by a Magnetic Charge Topology model. We analyze the relationship between the footpoint motions and topological spine lines and find that the examined footpoint sources move along spine lines. We present a three-dimensional topological model in which this movement can be understood. As reconnection proceeds, flux is transferred between the reconnecting domains, causing the separator to move. The movement of the separator\'s chromospheric ends, identified with the HXR footpoints, is along those spine lines on which the separator ends.}, author = {Des Jardins, Angela and Canfield, Richard and Longcope, Dana and Fordyce, Crystal and Waitukaitis, Scott R}, journal = {The Astrophysical Journal}, number = {2}, pages = {1628 -- 1636}, publisher = {IOP Publishing Ltd.}, title = {{Reconnection in three dimensions: The role of spines in three eruptive flares}}, doi = {10.1088/0004-637X/693/2/1628}, volume = {693}, year = {2009}, } @article{111, abstract = {Thin streams of liquid commonly break up into characteristic droplet patterns owing to the surface-tension-driven PlateauRayleigh instability 1-3. Very similar patterns are observed when initially uniform streams of dry granular material break up into clusters of grains4-6, even though flows of macroscopic particles are considered to lack surface tension7,8. Recent studies on freely falling granular streams tracked fluctuations in the stream profile9, but the clustering mechanism remained unresolved because the full evolution of the instability could not be observed. Here we demonstrate that the cluster formation is driven by minute, nanoNewton cohesive forces that arise from a combination of van der Waals interactions and capillary bridges between nanometre-scale surface asperities. Our experiments involve high-speed video imaging of the granular stream in the co-moving frame, control over the properties of the grain surfaces and the use of atomic force microscopy to measure grain-grain interactions. The cohesive forces that we measure correspond to an equivalent surface tension five orders of magnitude below that, of ordinary liquids. We find that, the shapes of these weakly cohesive, non-thermal clusters of macroscopic particles closely resemble droplets resulting from thermally induced rupture of liquid nanojets 10-12.}, author = {Royer, John and Evans, Daniel and Oyarte, Loreto and Guo, Qiti and Kapit, Eliot and Möbius, Matthias and Waitukaitis, Scott R and Jaeger, Heinrich}, journal = {Nature}, number = {7250}, pages = {1110 -- 1113}, publisher = {Nature Publishing Group}, title = {{High-speed tracking of rupture and clustering in freely falling granular streams}}, doi = {10.1038/nature08115}, volume = {459}, year = {2009}, } @article{11103, abstract = {Over the last decade, the nuclear envelope (NE) has emerged as a key component in the organization and function of the nuclear genome. As many as 100 different proteins are thought to specifically localize to this double membrane that separates the cytoplasm and the nucleoplasm of eukaryotic cells. Selective portals through the NE are formed at sites where the inner and outer nuclear membranes are fused, and the coincident assembly of ∼30 proteins into nuclear pore complexes occurs. These nuclear pore complexes are essential for the control of nucleocytoplasmic exchange. Many of the NE and nuclear pore proteins are thought to play crucial roles in gene regulation and thus are increasingly linked to human diseases.}, author = {HETZER, Martin W and Wente, Susan R.}, issn = {1534-5807}, journal = {Developmental Cell}, keywords = {Developmental Biology, Cell Biology, General Biochemistry, Genetics and Molecular Biology, Molecular Biology}, number = {5}, pages = {606--616}, publisher = {Elsevier}, title = {{Border control at the nucleus: Biogenesis and organization of the nuclear membrane and pore complexes}}, doi = {10.1016/j.devcel.2009.10.007}, volume = {17}, year = {2009}, } @article{11105, abstract = {Nuclear-pore complexes (NPCs) are large protein channels that span the nuclear envelope (NE), which is a double membrane that encloses the nuclear genome of eukaryotes. Each of the typically 2,000–4,000 pores in the NE of vertebrate cells is composed of multiple copies of 30 different proteins known as nucleoporins. The evolutionarily conserved NPC proteins have the well-characterized function of mediating the transport of molecules between the nucleoplasm and the cytoplasm. Mutations in nucleoporins are often linked to specific developmental defects and disease, and the resulting phenotypes are usually interpreted as the consequences of perturbed nuclear transport activity. However, recent evidence suggests that NPCs have additional functions in chromatin organization and gene regulation, some of which might be independent of nuclear transport. Here, we review the transport-dependent and transport-independent roles of NPCs in the regulation of nuclear function and gene expression.}, author = {Capelson, Maya and HETZER, Martin W}, issn = {1469-3178}, journal = {EMBO reports}, keywords = {Genetics, Molecular Biology, Biochemistry}, number = {7}, pages = {697--705}, publisher = {EMBO}, title = {{The role of nuclear pores in gene regulation, development and disease}}, doi = {10.1038/embor.2009.147}, volume = {10}, year = {2009}, } @article{11106, abstract = {Formation of the nuclear envelope (NE) around segregated chromosomes occurs by the reshaping of the endoplasmic reticulum (ER), a reservoir for disassembled nuclear membrane components during mitosis. In this study, we show that inner nuclear membrane proteins such as lamin B receptor (LBR), MAN1, Lap2β, and the trans-membrane nucleoporins Ndc1 and POM121 drive the spreading of ER membranes into the emerging NE via their capacity to bind chromatin in a collaborative manner. Despite their redundant functions, decreasing the levels of any of these trans-membrane proteins by RNAi-mediated knockdown delayed NE formation, whereas increasing the levels of any of them had the opposite effect. Furthermore, acceleration of NE formation interferes with chromosome separation during mitosis, indicating that the time frame over which chromatin becomes membrane enclosed is physiologically relevant and regulated. These data suggest that functionally distinct classes of chromatin-interacting membrane proteins, which are present at nonsaturating levels, collaborate to rapidly reestablish the nuclear compartment at the end of mitosis.}, author = {Anderson, Daniel J. and Vargas, Jesse D. and Hsiao, Joshua P. and HETZER, Martin W}, issn = {1540-8140}, journal = {Journal of Cell Biology}, keywords = {Cell Biology}, number = {2}, pages = {183--191}, publisher = {Rockefeller University Press}, title = {{Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo}}, doi = {10.1083/jcb.200901106}, volume = {186}, year = {2009}, } @article{11107, abstract = {Nucleocytoplasmic transport occurs exclusively through nuclear pore complexes (NPCs) embedded in pores formed by inner and outer nuclear membrane fusion. The mechanism for de novo pore and NPC biogenesis remains unclear. Reticulons (RTNs) and Yop1/DP1 are conserved membrane protein families required to form and maintain the tubular endoplasmic reticulum (ER) and the postmitotic nuclear envelope. In this study, we report that members of the RTN and Yop1/DP1 families are required for nuclear pore formation. Analysis of Saccharomyces cerevisiae prp20-G282S and nup133Δ NPC assembly mutants revealed perturbations in Rtn1–green fluorescent protein (GFP) and Yop1-GFP ER distribution and colocalization to NPC clusters. Combined deletion of RTN1 and YOP1 resulted in NPC clustering, nuclear import defects, and synthetic lethality with the additional absence of Pom34, Pom152, and Nup84 subcomplex members. We tested for a direct role in NPC biogenesis using Xenopus laevis in vitro assays and found that anti-Rtn4a antibodies specifically inhibited de novo nuclear pore formation. We hypothesize that these ER membrane–bending proteins mediate early NPC assembly steps.}, author = {Dawson, T. Renee and Lazarus, Michelle D. and HETZER, Martin W and Wente, Susan R.}, issn = {1540-8140}, journal = {Journal of Cell Biology}, keywords = {Cell Biology}, number = {5}, pages = {659--675}, publisher = {Rockefeller University Press}, title = {{ER membrane–bending proteins are necessary for de novo nuclear pore formation}}, doi = {10.1083/jcb.200806174}, volume = {184}, year = {2009}, } @article{11108, abstract = {In dividing cells, nuclear pore complexes (NPCs) disassemble during mitosis and reassemble into the newly forming nuclei. However, the fate of nuclear pores in postmitotic cells is unknown. Here, we show that NPCs, unlike other nuclear structures, do not turn over in differentiated cells. While a subset of NPC components, like Nup153 and Nup50, are continuously exchanged, scaffold nucleoporins, like the Nup107/160 complex, are extremely long-lived and remain incorporated in the nuclear membrane during the entire cellular life span. Besides the lack of nucleoporin expression and NPC turnover, we discovered an age-related deterioration of NPCs, leading to an increase in nuclear permeability and the leaking of cytoplasmic proteins into the nucleus. Our finding that nuclear “leakiness” is dramatically accelerated during aging and that a subset of nucleoporins is oxidatively damaged in old cells suggests that the accumulation of damage at the NPC might be a crucial aging event.}, author = {D'Angelo, Maximiliano A. and Raices, Marcela and Panowski, Siler H. and HETZER, Martin W}, issn = {0092-8674}, journal = {Cell}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {2}, pages = {284--295}, publisher = {Elsevier}, title = {{Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells}}, doi = {10.1016/j.cell.2008.11.037}, volume = {136}, year = {2009}, } @inproceedings{11752, abstract = {We propose a model which suggests that structural martensitic transitions are related to significant changes in the electronic structure, and are effected by high-magnetic fields. The magnetic field dependence is considered unusual as many influential investigations of martensitic transitions have emphasized that the structural transitions are primarily lattice dynamical and are driven by the entropy due to the phonons. We provide a theoretical framework which can be used to describe the effect of high magnetic field on the transition and lattice dynamics in which the field dependence originates from the dielectric constant. The model is compared with some recent experimental results.}, author = {Yang, Xiaodong and Riseborough, Peter S and Modic, Kimberly A and Fisher, R A and Oppeil, C P and Finlayson, T R and Cooley, J C and Smith, J L and Goddard, P A and Silhanek, A V and Lashley, J C}, booktitle = {Journal of Physics: Conference Series}, issn = {1742-6596}, location = {Karlsruhe, Germany}, number = {3}, publisher = {IOP Publishing}, title = {{Influence of magnetic fields on structural martensitic transitions}}, doi = {10.1088/1742-6596/200/3/032062}, volume = {200}, year = {2009}, } @article{8026, abstract = {Recent theoretical work has provided a basic understanding of signal propagation in networks of spiking neurons, but mechanisms for gating and controlling these signals have not been investigated previously. Here we introduce an idea for the gating of multiple signals in cortical networks that combines principles of signal propagation with aspects of balanced networks. Specifically, we studied networks in which incoming excitatory signals are normally cancelled by locally evoked inhibition, leaving the targeted layer unresponsive. Transmission can be gated 'on' by modulating excitatory and inhibitory gains to upset this detailed balance. We illustrate gating through detailed balance in large networks of integrate-and-fire neurons. We show successful gating of multiple signals and study failure modes that produce effects reminiscent of clinically observed pathologies. Provided that the individual signals are detectable, detailed balance has a large capacity for gating multiple signals.}, author = {Vogels, Tim P and Abbott, L F}, issn = {1097-6256}, journal = {Nature Neuroscience}, number = {4}, pages = {483--491}, publisher = {Springer Nature}, title = {{Gating multiple signals through detailed balance of excitation and inhibition in spiking networks}}, doi = {10.1038/nn.2276}, volume = {12}, year = {2009}, } @article{8474, abstract = {Hydrogen bonds are ubiquitous interactions in proteins, and are important for their folding and functionality. Scalar coupling constants across hydrogen bonds in the protein backbone, some as small as 0.5 Hz, can be directly measured in the solid state by NMR spectroscopy (see figure). The nuclei on both sides of the hydrogen bond can be identified and the size of the coupling constant can be measured accurately.}, author = {Schanda, Paul and Huber, Matthias and Verel, René and Ernst, Matthias and Meier, Beat H.}, issn = {1433-7851}, journal = {Angewandte Chemie International Edition}, keywords = {General Chemistry, Catalysis}, number = {49}, pages = {9322--9325}, publisher = {Wiley}, title = {{Direct detection of 3hJN' hydrogen-bond scalar couplings in proteins by solid-state NMR spectroscopy}}, doi = {10.1002/anie.200904411}, volume = {48}, year = {2009}, } @article{8475, author = {Schanda, Paul}, issn = {0079-6565}, journal = {Progress in Nuclear Magnetic Resonance Spectroscopy}, number = {3}, pages = {238--265}, publisher = {Elsevier}, title = {{Fast-pulsing longitudinal relaxation optimized techniques: Enriching the toolbox of fast biomolecular NMR spectroscopy}}, doi = {10.1016/j.pnmrs.2009.05.002}, volume = {55}, year = {2009}, } @article{8476, abstract = {Atomic-resolution information on the structure and dynamics of nucleic acids is essential for a better understanding of the mechanistic basis of many cellular processes. NMR spectroscopy is a powerful method for studying the structure and dynamics of nucleic acids; however, solution NMR studies are currently limited to relatively small nucleic acids at high concentrations. Thus, technological and methodological improvements that increase the experimental sensitivity and spectral resolution of NMR spectroscopy are required for studies of larger nucleic acids or protein−nucleic acid complexes. Here we introduce a series of imino-proton-detected NMR experiments that yield an over 2-fold increase in sensitivity compared to conventional pulse schemes. These methods can be applied to the detection of base pair interactions, RNA−ligand titration experiments, measurement of residual dipolar 15N−1H couplings, and direct measurements of conformational transitions. These NMR experiments employ longitudinal spin relaxation enhancement techniques that have proven useful in protein NMR spectroscopy. The performance of these new experiments is demonstrated for a 10 kDa TAR-TAR*GA RNA kissing complex and a 26 kDa tRNA.}, author = {Farjon, Jonathan and Boisbouvier, Jérôme and Schanda, Paul and Pardi, Arthur and Simorre, Jean-Pierre and Brutscher, Bernhard}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {24}, pages = {8571--8577}, publisher = {American Chemical Society}, title = {{Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids in solution}}, doi = {10.1021/ja901633y}, volume = {131}, year = {2009}, }