TY - JOUR AB - Whether or not evolutionary change is inherently irreversible remains a controversial topic. Some examples of evolutionary irreversibility are known; however, this question has not been comprehensively addressed at the molecular level. Here, we use data from 221 human genes with known pathogenic mutations to estimate the rate of irreversibility in protein evolution. For these genes, we reconstruct ancestral amino acid sequences along the mammalian phylogeny and identify ancestral amino acid states that match known pathogenic mutations. Such cases represent inherent evolutionary irreversibility because, at the present moment, reversals to these ancestral amino acid states are impossible for the human lineage. We estimate that approximately 10% of all amino acid substitutions along the mammalian phylogeny are irreversible, such that a return to the ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes with high rates of irreversibility, as much as 40% of all amino acid evolution was estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes, the molecular nature of the high rate of irreversibility in proteins is best explained by evolution with a high prevalence of compensatory, epistatic interactions between amino acid sites. Under such mode of protein evolution, once an amino acid substitution is fixed, the probability of its reversal declines as the protein sequence accumulates changes that affect the phenotypic manifestation of the ancestral state. The prevalence of epistasis in evolution indicates that the observed high rate of irreversibility in protein evolution is an inherent property of protein structure and function. AU - Soylemez, Onuralp AU - Fyodor Kondrashov ID - 846 IS - 12 JF - Genome Biology and Evolution TI - Estimating the rate of irreversibility in protein evolution VL - 4 ER - TY - JOUR AB - The 1H dipolar network, which is the major obstacle for applying proton detection in the solid-state, can be reduced by deuteration, employing the RAP (Reduced Adjoining Protonation) labeling scheme, which yields random protonation at non-exchangeable sites. We present here a systematic study on the optimal degree of random sidechain protonation in RAP samples as a function of the MAS (magic angle spinning) frequency. In particular, we compare 1H sensitivity and linewidth of a microcrystalline protein, the SH3 domain of chicken α-spectrin, for samples, prepared with 5–25 % H2O in the E. coli growth medium, in the MAS frequency range of 20–60 kHz. At an external field of 19.96 T (850 MHz), we find that using a proton concentration between 15 and 25 % in the M9 medium yields the best compromise in terms of sensitivity and resolution, with an achievable average 1H linewidth on the order of 40–50 Hz. Comparing sensitivities at a MAS frequency of 60 versus 20 kHz, a gain in sensitivity by a factor of 4–4.5 is observed in INEPT-based 1H detected 1D 1H,13C correlation experiments. In total, we find that spectra recorded with a 1.3 mm rotor at 60 kHz have almost the same sensitivity as spectra recorded with a fully packed 3.2 mm rotor at 20 kHz, even though ~20× less material is employed. The improved sensitivity is attributed to 1H line narrowing due to fast MAS and to the increased efficiency of the 1.3 mm coil. AU - Asami, Sam AU - Szekely, Kathrin AU - Schanda, Paul AU - Meier, Beat H. AU - Reif, Bernd ID - 8463 IS - 2 JF - Journal of Biomolecular NMR SN - 0925-2738 TI - Optimal degree of protonation for 1H detection of aliphatic sites in randomly deuterated proteins as a function of the MAS frequency VL - 54 ER - TY - JOUR AB - We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond time scales can be detected and quantified by solid-state NMR spectroscopy. We show two independent approaches that measure the effect of conformational exchange on transverse relaxation parameters, namely Carr–Purcell–Meiboom–Gill relaxation-dispersion experiments and measurement of differential multiple-quantum coherence decay. Long coherence lifetimes, as required for these experiments, are achieved by the use of highly deuterated samples and fast magic-angle spinning. The usefulness of the approaches is demonstrated by application to microcrystalline ubiquitin. We detect a conformational exchange process in a region of the protein for which dynamics have also been observed in solution. Interestingly, quantitative analysis of the data reveals that the exchange process is more than 1 order of magnitude slower than in solution, and this points to the impact of the crystalline environment on free energy barriers. AU - Tollinger, Martin AU - Sivertsen, Astrid C. AU - Meier, Beat H. AU - Ernst, Matthias AU - Schanda, Paul ID - 8465 IS - 36 JF - Journal of the American Chemical Society SN - 0002-7863 TI - Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy VL - 134 ER - TY - JOUR AB - Recent advances in NMR spectroscopy and the availability of high magnetic field strengths now offer the possibility to record real-time 3D NMR spectra of short-lived protein states, e.g., states that become transiently populated during protein folding. Here we present a strategy for obtaining sequential NMR assignments as well as atom-resolved information on structural and dynamic features within a folding intermediate of the amyloidogenic protein β2-microglobulin that has a half-lifetime of only 20 min. AU - Rennella, Enrico AU - Cutuil, Thomas AU - Schanda, Paul AU - Ayala, Isabel AU - Forge, Vincent AU - Brutscher, Bernhard ID - 8466 IS - 19 JF - Journal of the American Chemical Society SN - 0002-7863 TI - Real-time NMR characterization of structure and dynamics in a transiently populated protein folding intermediate VL - 134 ER - TY - JOUR AB - Partial deuteration is a powerful tool to increase coherence life times and spectral resolution in proton solid-state NMR. The J coupling to deuterium needs, however, to be decoupled to maintain the good resolution in the (usually indirect) 13C dimension(s). We present a simple and reversible way to expand a commercial 1.3 mm HCN MAS probe with a 2H channel with sufficient field strength for J-decoupling of deuterium, namely 2–3 kHz. The coil is placed at the outside of the stator and requires no significant modifications to the probe. The performance and the realizable gains in sensitivity and resolution are demonstrated using perdeuterated ubiquitin, with selectively CHD2-labeled methyl groups. AU - Huber, Matthias AU - With, Oliver AU - Schanda, Paul AU - Verel, René AU - Ernst, Matthias AU - Meier, Beat H. ID - 8467 JF - Journal of Magnetic Resonance SN - 1090-7807 TI - A supplementary coil for 2H decoupling with commercial HCN MAS probes VL - 214 ER - TY - JOUR AB - The famous ergodic hypothesis suggests that for a typical Hamiltonian on a typical energy surface nearly all trajectories are dense. KAM theory disproves it. Ehrenfest (The Conceptual Foundations of the Statistical Approach in Mechanics. Ithaca, NY: Cornell University Press, 1959) and Birkhoff (Collected Math Papers. Vol 2, New York: Dover, pp 462–465, 1968) stated the quasi-ergodic hypothesis claiming that a typical Hamiltonian on a typical energy surface has a dense orbit. This question is wide open. Herman (Proceedings of the International Congress of Mathematicians, Vol II (Berlin, 1998). Doc Math 1998, Extra Vol II, Berlin: Int Math Union, pp 797–808, 1998) proposed to look for an example of a Hamiltonian near H0(I)=⟨I,I⟩2 with a dense orbit on the unit energy surface. In this paper we construct a Hamiltonian H0(I)+εH1(θ,I,ε) which has an orbit dense in a set of maximal Hausdorff dimension equal to 5 on the unit energy surface. AU - Kaloshin, Vadim AU - Saprykina, Maria ID - 8502 IS - 3 JF - Communications in Mathematical Physics KW - Mathematical Physics KW - Statistical and Nonlinear Physics SN - 0010-3616 TI - An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension VL - 315 ER - TY - JOUR AB - ackground: The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of stop codons in bacterial genomes.Results: We show that in bacteria stop codons evolve slower than synonymous sites, suggesting the action of weak negative selection. However, the frequency of stop codons relative to genomic nucleotide content indicated that this selection regime is not straightforward. The frequency of TAA and TGA stop codons is GC-content dependent, with TAA decreasing and TGA increasing with GC-content, while TAG frequency is independent of GC-content. Applying a formal, analytical model to these data we found that the relationship between stop codon frequencies and nucleotide content cannot be explained by mutational biases or selection on nucleotide content. However, with weak nucleotide content-dependent selection on TAG, -0.5 < Nes < 1.5, the model fits all of the data and recapitulates the relationship between TAG and nucleotide content. For biologically plausible rates of mutations we show that, in bacteria, TAG stop codon is universally associated with lower fitness, with TAA being the optimal for G-content < 16% while for G-content > 16% TGA has a higher fitness than TAG.Conclusions: Our data indicate that TAG codon is universally suboptimal in the bacterial lineage, such that TAA is likely to be the preferred stop codon for low GC content while the TGA is the preferred stop codon for high GC content. The optimization of stop codon usage may therefore be useful in genome engineering or gene expression optimization applications.Reviewers: This article was reviewed by Michail Gelfand, Arcady Mushegian and Shamil Sunyaev. For the full reviews, please go to the Reviewers' Comments section. AU - Povolotskaya, Inna AU - Fyodor Kondrashov AU - Ledda, Alice AU - Vlasov, Peter K ID - 858 JF - Biology Direct TI - Stop codons in bacteria are not selectively equivalent VL - 7 ER - TY - JOUR AB - The main forces directing long-term molecular evolution remain obscure. A sizable fraction of amino-acid substitutions seem to be fixed by positive selection, but it is unclear to what degree long-term protein evolution is constrained by epistasis, that is, instances when substitutions that are accepted in one genotype are deleterious in another. Here we obtain a quantitative estimate of the prevalence of epistasis in long-term protein evolution by relating data on amino-acid usage in 14 organelle proteins and 2 nuclear-encoded proteins to their rates of short-term evolution. We studied multiple alignments of at least 1,000 orthologues for each of these 16 proteins from species from a diverse phylogenetic background and found that an average site contained approximately eight different amino acids. Thus, without epistasis an average site should accept two-fifths of all possible amino acids, and the average rate of amino-acid substitutions should therefore be about three-fifths lower than the rate of neutral evolution. However, we found that the measured rate of amino-acid substitution in recent evolution is 20 times lower than the rate of neutral evolution and an order of magnitude lower than that expected in the absence of epistasis. These data indicate that epistasis is pervasive throughout protein evolution: about 90 per cent of all amino-acid substitutions have a neutral or beneficial impact only in the genetic backgrounds in which they occur, and must therefore be deleterious in a different background of other species. Our findings show that most amino-acid substitutions have different fitness effects in different species and that epistasis provides the primary conceptual framework to describe the tempo and mode of long-term protein evolution. AU - Breen, Michael S AU - Kemena, Carsten AU - Vlasov, Peter K AU - Notredame, Cédric AU - Fyodor Kondrashov ID - 900 IS - 7421 JF - Nature TI - Epistasis as the primary factor in molecular evolution VL - 490 ER - TY - JOUR AB - In this Letter, we explore experimentally the phase behavior of a dense active suspension of self-propelled colloids. In addition to a solidlike and gaslike phase observed for high and low densities, a novel cluster phase is reported at intermediate densities. This takes the form of a stationary assembly of dense aggregates—resulting from a permanent dynamical merging and separation of active colloids—whose average size grows with activity as a linear function of the self-propelling velocity. While different possible scenarios can be considered to account for these observations—such as a generic velocity weakening instability recently put forward—we show that the experimental results are reproduced mathematically by a chemotactic aggregation mechanism, originally introduced to account for bacterial aggregation and accounting here for diffusiophoretic chemical interaction between colloidal swimmers. AU - Theurkauff, I. AU - Cottin-Bizonne, C. AU - Palacci, Jérémie A AU - Ybert, C. AU - Bocquet, L. ID - 9014 IS - 26 JF - Physical Review Letters SN - 00319007 TI - Dynamic clustering in active colloidal suspensions with chemical signaling VL - 108 ER - TY - JOUR AB - We demonstrate how to appropriately estimate the zero-frequency (static) hyperpolarizability of an organic molecule from its charge distribution, and we explore applications of these estimates for identifying and evaluating new organic nonlinear optical (NLO) materials. First, we calculate hyperpolarizabilities from Hartree-Fock-derived charge distributions and find order-of-magnitude agreement with experimental values. We show that these simple arithmetic calculations will enable systematic searches for new organic NLO molecules. Second, we derive hyperpolarizabilities from crystallographic data using a multipolar charge-density analysis and find good agreement with empirical calculations. This demonstrates an experimental determination of the full static hyperpolarizability tensor in a solid-state sample. AU - Higginbotham, Andrew P AU - Cole, Jacqueline AU - Blood Forsythe, Martin AU - Hickstein, Daniel ID - 91 IS - 3 JF - Journal of Applied Physics TI - Identifying and evaluating organic nonlinear optical materials via molecular moments VL - 111 ER - TY - JOUR AB - In models of radiative–convective equilibrium it is known that convection can spontaneously aggregate into one single localized moist region if the domain is large enough. The large changes in the mean climate state and radiative fluxes accompanying this self-aggregation raise questions as to what simulations at lower resolutions with parameterized convection, in similar homogeneous geometries, should be expected to produce to be considered successful in mimicking a cloud-resolving model. The authors investigate this self-aggregation in a nonrotating, three-dimensional cloud-resolving model on a square domain without large-scale forcing. It is found that self-aggregation is sensitive not only to the domain size, but also to the horizontal resolution. With horizontally homogeneous initial conditions, convective aggregation only occurs on domains larger than about 200km and with resolutions coarser than about 2km in the model examined. The system exhibits hysteresis, so that with aggregated initial conditions, convection remains aggregated even at our finest resolution, 500m, as long as the domain is greater than 200–300km. The sensitivity of self-aggregation to resolution and domain size in this model is due to the sensitivity of the distribution of low clouds to these two parameters. Indeed, the mechanism responsible for the aggregation of convection is the dynamical response to the longwave radiative cooling from low clouds. Strong longwave cooling near cloud top in dry regions forces downward motion, which by continuity generates inflow near cloud top and near-surface outflow from dry regions. This circulation results in the net export of moist static energy from regions with low moist static energy, yielding a positive feedback. AU - Muller, Caroline J AU - Held, Isaac M. ID - 9142 IS - 8 JF - Journal of the Atmospheric Sciences KW - Atmospheric Science SN - 0022-4928 TI - Detailed investigation of the self-aggregation of convection in cloud-resolving simulations VL - 69 ER - TY - JOUR AB - The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations. AU - Ibarra, Christian A. AU - Feng, Xiaoqi AU - Schoft, Vera K. AU - Hsieh, Tzung-Fu AU - Uzawa, Rie AU - Rodrigues, Jessica A. AU - Zemach, Assaf AU - Chumak, Nina AU - Machlicova, Adriana AU - Nishimura, Toshiro AU - Rojas, Denisse AU - Fischer, Robert L. AU - Tamaru, Hisashi AU - Zilberman, Daniel ID - 9451 IS - 6100 JF - Science SN - 0036-8075 TI - Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes VL - 337 ER - TY - JOUR AB - The most well-studied function of DNA methylation in eukaryotic cells is the transcriptional silencing of genes and transposons. More recent results showed that many eukaryotes methylate the bodies of genes as well and that this methylation correlates with transcriptional activity rather than repression. The purpose of gene body methylation remains mysterious, but is potentially related to the histone variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and other investigators have shown that this relationship is likely to be the result of an ancient but unknown mechanism by which DNA methylation prevents the incorporation of H2A.Z. Recently, we discovered strong correlations between the presence of H2A.Z within gene bodies, the degree to which a gene's expression varies across tissue types or environmental conditions, and transcriptional misregulation in an h2a.z mutant. We propose that one basal function of gene body methylation is the establishment of constitutive expression patterns within housekeeping genes by excluding H2A.Z from their bodies. AU - Coleman-Derr, D. AU - Zilberman, Daniel ID - 9535 JF - Cold Spring Harbor Symposia on Quantitative Biology SN - 0091-7451 TI - DNA methylation, H2A.Z, and the regulation of constitutive expression VL - 77 ER - TY - JOUR AB - Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”). AU - Konrad, Matthias AU - Vyleta, Meghan AU - Theis, Fabian AU - Stock, Miriam AU - Tragust, Simon AU - Klatt, Martina AU - Drescher, Verena AU - Marr, Carsten AU - Ugelvig, Line V AU - Cremer, Sylvia ID - 3242 IS - 4 JF - PLoS Biology TI - Social transfer of pathogenic fungus promotes active immunisation in ant colonies VL - 10 ER - TY - GEN AB - Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”). AU - Konrad, Matthias AU - Vyleta, Meghan AU - Theis, Fabian AU - Stock, Miriam AU - Klatt, Martina AU - Drescher, Verena AU - Marr, Carsten AU - Ugelvig, Line V AU - Cremer, Sylvia ID - 9755 TI - Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies ER - TY - GEN AB - We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction. AU - Aeschbacher, Simon AU - Futschik, Andreas AU - Beaumont, Mark ID - 9758 TI - Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates ER - TY - GEN AB - To fight infectious diseases, host immune defences are employed at multiple levels. Sanitary behaviour, such as pathogen avoidance and removal, acts as a first line of defence to prevent infection [1] before activation of the physiological immune system. Insect societies have evolved a wide range of collective hygiene measures and intensive health care towards pathogen-exposed group members [2]. One of the most common behaviours is allogrooming, in which nestmates remove infectious particles from the body surfaces of exposed individuals [3]. Here we show that, in invasive garden ants, grooming of fungus-exposed brood is effective beyond the sheer mechanical removal of fungal conidiospores as it also includes chemical disinfection through the application of poison produced by the ants themselves. Formic acid is the main active component of the poison. It inhibits fungal growth of conidiospores remaining on the brood surface after grooming and also those collected in the mouth of the grooming ant. This dual function is achieved by uptake of the poison droplet into the mouth through acidopore self-grooming and subsequent application onto the infectious brood via brood grooming. This extraordinary behaviour extends current understanding of grooming and the establishment of social immunity in insect societies. AU - Tragust, Simon AU - Mitteregger, Barbara AU - Barone, Vanessa AU - Konrad, Matthias AU - Ugelvig, Line V AU - Cremer, Sylvia ID - 9757 TI - Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison ER - TY - JOUR AB - In this paper we present a surprising example of a Cr unimodal map of an interval f:I→I whose number of periodic points Pn(f)=∣{x∈I:fnx=x}∣ grows faster than any ahead given sequence along a subsequence nk=3k. This example also shows that ‘non-flatness’ of critical points is necessary for the Martens–de Melo–van Strien theorem [M. Martens, W. de Melo and S. van Strien. Julia–Fatou–Sullivan theory for real one-dimensional dynamics. Acta Math.168(3–4) (1992), 273–318] to hold. AU - Kaloshin, Vadim AU - KOZLOVSKI, O. S. ID - 8504 IS - 1 JF - Ergodic Theory and Dynamical Systems KW - Applied Mathematics KW - General Mathematics SN - 0143-3857 TI - A Cr unimodal map with an arbitrary fast growth of the number of periodic points VL - 32 ER - TY - JOUR AB - We prove there are finitely many isometry classes of planar central configurations (also called relative equilibria) in the Newtonian 5-body problem, except perhaps if the 5-tuple of positive masses belongs to a given codimension 2 subvariety of the mass space. AU - Albouy, Alain AU - Kaloshin, Vadim ID - 8503 IS - 1 JF - Annals of Mathematics SN - 0003-486X TI - Finiteness of central configurations of five bodies in the plane VL - 176 ER - TY - JOUR AB - A subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. Concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. At this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. Nevertheless, enough examples have accumulated in the literature that such a possibility should be considered. Here, I review the recent examples of adaptive gene duplications and make an attempt to draw generalizations on what types of genes may be particularly prone to be selected for under certain environmental conditions. The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve our understanding of gene duplications as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications. AU - Fyodor Kondrashov ID - 887 IS - 1749 JF - Proceedings of the Royal Society of London Series B Biological Sciences TI - Gene duplication as a mechanism of genomic adaptation to a changing environment VL - 279 ER - TY - JOUR AB - Diffusiophoretic motion of colloids and macromolecules under salt gradients exhibits a logarithmic-sensing, i.e. the particle velocity is proportional to the spatial gradient of the logarithm of the salt concentration, as VDP = DDP∇logc. Here we explore experimentally the implications of this log-sensing behavior, on the basis of a hydrogel microfluidic device allowing to build spatially and temporally controlled gradients. We first demonstrate that the non-linearity of the salt-taxis leads to a trapping of particles under concentration gradient oscillations via a rectification of the motion. As an alternative, we make use of the high sensitivity of diffusiophoretic migration to vanishing salt concentration due to the log-sensing: in a counter-intuitive way, a vanishing gradient can lead to measurable velocity provided that the solute concentration is low enough, thus keeping ∇c/c finite. We show that this leads to a strong segregation of particles in osmotic shock configuration, resulting from a step change of the salt concentration at the boundaries. These various phenomena are rationalized on the basis of a theoretical description for the time-dependent Smoluchowski equation for the colloidal density. AU - Palacci, Jérémie A AU - Cottin-Bizonne, Cécile AU - Ybert, Christophe AU - Bocquet, Lydéric ID - 9049 IS - 4 JF - Soft Matter SN - 1744-683X TI - Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis VL - 8 ER - TY - JOUR AB - We study theoretically the morphologies of biological tubes affected by various pathologies. When epithelial cells grow, the negative tension produced by their division provokes a buckling instability. Several shapes are investigated: varicose, dilated, sinuous, or sausagelike. They are all found in pathologies of tracheal, renal tubes, or arteries. The final shape depends crucially on the mechanical parameters of the tissues: Young's modulus, wall-to-lumen ratio, homeostatic pressure. We argue that since tissues must be in quasistatic mechanical equilibrium, abnormal shapes convey information as to what causes the pathology. We calculate a phase diagram of tubular instabilities which could be a helpful guide for investigating the underlying genetic regulation. AU - Hannezo, Edouard B AU - Prost, Jacques AU - Joanny, Jean ID - 922 IS - 1 JF - Physical Review Letters TI - Mechanical instabilities of biological tubes VL - 109 ER - TY - JOUR AB - EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment levels of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying cell fates during growth and differentiation. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism. AU - Kim, Sang Yeol AU - Lee, Jungeun AU - Eshed-Williams, Leor AU - Zilberman, Daniel AU - Sung, Z. Renee ID - 9499 IS - 3 JF - PLoS Genetics SN - 1553-7390 TI - EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development VL - 8 ER - TY - JOUR AB - The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes. AU - Coleman-Derr, Devin AU - Zilberman, Daniel ID - 9497 IS - 10 JF - PLoS Genetics SN - 1553-7390 TI - Deposition of histone variant H2A.Z within gene bodies regulates responsive genes VL - 8 ER - TY - JOUR AB - Accumulating evidence points toward diverse functions for plant chromatin. Remarkable progress has been made over the last few years in elucidating the mechanisms for a number of these functions. Activity of the histone demethylase IBM1 accurately targets DNA methylation to silent repeats and transposable elements, not to genes. A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes in sensing precise differences in ambient temperature and consequent gene regulation. Precise maintenance of chromosome number is assured by a histone modification that suppresses inappropriate DNA replication and by centromeric histone H3 regulation of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS C, the expression of which quantitatively measures the duration of cold exposure, functioning as memory of winter. These findings are a testament to the power of using plants to research chromatin organization, and demonstrate examples of how chromatin functions to achieve biological accuracy, precision, and memory. AU - Huff, Jason T. AU - Zilberman, Daniel ID - 9528 IS - 2 JF - Current Opinion in Genetics and Development SN - 0959-437X TI - Regulation of biological accuracy, precision, and memory by plant chromatin organization VL - 22 ER - TY - JOUR AB - Motivated by recent experiments on Ba3NiSb2O 9, we investigate possible quantum spin liquid ground states for spin S=1 Heisenberg models on the triangular lattice. We use variational Monte Carlo techniques to calculate the energies of microscopic spin liquid wave functions where spin is represented by three flavors of fermionic spinon operators. These energies are compared with the energies of various competing three-sublattice ordered states. Our approach shows that the antiferromagnetic Heisenberg model with biquadratic term and single-ion anisotropy does not have a low-temperature spin liquid phase. However, for an SU(3)-invariant model with sufficiently strong ring-exchange terms, we find a paired chiral quantum spin liquid with a Fermi surface of deconfined spinons that is stable against all types of ordering patterns we considered. We discuss the physics of this exotic spin liquid state in relation to the recent experiment and suggest new ways to test this scenario. AU - Bieri, Samuel AU - Maksym Serbyn AU - Senthil, Todadri S AU - Lee, Patrick ID - 966 IS - 22 JF - Physical Review B - Condensed Matter and Materials Physics TI - Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice VL - 86 ER - TY - JOUR AB - Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and-using triplet alignments of intronic loci-quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. © 2012 Blackwell Publishing Ltd. AU - Lohse, Konrad AU - Barton, Nicholas H AU - Melika, George AU - Stone, Graham ID - 2968 IS - 18 JF - Molecular Ecology TI - A likelihood based comparison of population histories in a parasitoid guild VL - 21 ER - TY - GEN AB - Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and - using triplet alignments of intronic loci - quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. AU - Lohse, Konrad AU - Barton, Nicholas H AU - Stone, Graham AU - Melika, George ID - 13075 TI - Data from: A likelihood-based comparison of population histories in a parasitoid guild ER - TY - JOUR AB - We show that diamagnetic particles can be remotely manipulated by a magnet by the reversible adsorption of dual-responsive, light-switchable/superparamagnetic nanoparticles down to their surface. Adsorption occurs upon exposure to UV light, and can be reversed thermally or by ambient light. The dynamic self-assembly of thin films of the dual-responsive nanoparticles induces attractive interactions between diamagnetic particles. We demonstrate that catalytic amounts of the dual-responsive nanoparticles are sufficient to magnetically guide and deliver the diamagnetic particles to desired locations, where they can then be released by disassembling the dynamic layers of superparamagnetic nanoparticles with visible light. AU - Chovnik, Olga AU - Balgley, Renata AU - Goldman, Joel R. AU - Klajn, Rafal ID - 13407 IS - 48 JF - Journal of the American Chemical Society KW - Colloid and Surface Chemistry KW - Biochemistry KW - General Chemistry KW - Catalysis SN - 0002-7863 TI - Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets VL - 134 ER - TY - JOUR AB - Well-defined metallic nanobowls can be prepared by extending the concept of a protecting group to colloidal synthesis. Magnetic nanoparticles are employed as “protecting groups” during the galvanic replacement of silver with gold. The replacement reaction is accompanied by spontantous dissociation of the protecting groups, leaving behind metallic nanobowls. AU - Ridelman, Yonatan AU - Singh, Gurvinder AU - Popovitz-Biro, Ronit AU - Wolf, Sharon G. AU - Das, Sanjib AU - Klajn, Rafal ID - 13408 IS - 5 JF - Small KW - Biomaterials KW - Biotechnology KW - General Materials Science KW - General Chemistry SN - 1613-6810 TI - Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles VL - 8 ER - TY - CONF AB - We propose a logic-based framework for automated reasoning about sequential programs manipulating singly-linked lists and arrays with unbounded data. We introduce the logic SLAD, which allows combining shape constraints, written in a fragment of Separation Logic, with data and size constraints. We address the problem of checking the entailment between SLAD formulas, which is crucial in performing pre-post condition reasoning. Although this problem is undecidable in general for SLAD, we propose a sound and powerful procedure that is able to solve this problem for a large class of formulas, beyond the capabilities of existing techniques and tools. We prove that this procedure is complete, i.e., it is actually a decision procedure for this problem, for an important fragment of SLAD including known decidable logics. We implemented this procedure and shown its preciseness and its efficiency on a significant benchmark of formulas. AU - Bouajjani, Ahmed AU - Dragoi, Cezara AU - Enea, Constantin AU - Sighireanu, Mihaela ID - 10903 SN - 0302-9743 T2 - Automated Technology for Verification and Analysis TI - Accurate invariant checking for programs manipulating lists and arrays with infinite data VL - 7561 ER - TY - CONF AB - Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP ∩ co−NP, but are not known to be in P. While the existence of polynomial-time algorithms has been a major open problem for decades, there is no algorithm that solves any non-trivial subclass in polynomial time. In this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several counter examples that show that many previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting graph structures need not help. AU - Chatterjee, Krishnendu AU - Henzinger, Monika H AU - Krinninger, Sebastian AU - Nanongkai, Danupon ID - 10905 SN - 0302-9743 T2 - Algorithms – ESA 2012 TI - Polynomial-time algorithms for energy games with special weight structures VL - 7501 ER - TY - CONF AB - HSF(C) is a tool that automates verification of safety and liveness properties for C programs. This paper describes the verification approach taken by HSF(C) and provides instructions on how to install and use the tool. AU - Grebenshchikov, Sergey AU - Gupta, Ashutosh AU - Lopes, Nuno P. AU - Popeea, Corneliu AU - Rybalchenko, Andrey ED - Flanagan, Cormac ED - König, Barbara ID - 10906 SN - 0302-9743 T2 - Tools and Algorithms for the Construction and Analysis of Systems TI - HSF(C): A software verifier based on Horn clauses VL - 7214 ER - TY - CHAP AU - Gupta, Ashutosh ID - 5745 SN - 0302-9743 T2 - Automated Technology for Verification and Analysis TI - Improved Single Pass Algorithms for Resolution Proof Reduction VL - 7561 ER - TY - CONF AB - Many infinite state systems can be seen as well-structured transition systems (WSTS), i.e., systems equipped with a well-quasi-ordering on states that is also a simulation relation. WSTS are an attractive target for formal analysis because there exist generic algorithms that decide interesting verification problems for this class. Among the most popular algorithms are acceleration-based forward analyses for computing the covering set. Termination of these algorithms can only be guaranteed for flattable WSTS. Yet, many WSTS of practical interest are not flattable and the question whether any given WSTS is flattable is itself undecidable. We therefore propose an analysis that computes the covering set and captures the essence of acceleration-based algorithms, but sacrifices precision for guaranteed termination. Our analysis is an abstract interpretation whose abstract domain builds on the ideal completion of the well-quasi-ordered state space, and a widening operator that mimics acceleration and controls the loss of precision of the analysis. We present instances of our framework for various classes of WSTS. Our experience with a prototype implementation indicates that, despite the inherent precision loss, our analysis often computes the precise covering set of the analyzed system. AU - Zufferey, Damien AU - Wies, Thomas AU - Henzinger, Thomas A ID - 3251 TI - Ideal abstractions for well structured transition systems VL - 7148 ER - TY - JOUR AB - Colorectal tumours that are wild type for KRAS are often sensitive to EGFR blockade, but almost always develop resistance within several months of initiating therapy. The mechanisms underlying this acquired resistance to anti-EGFR antibodies are largely unknown. This situation is in marked contrast to that of small-molecule targeted agents, such as inhibitors of ABL, EGFR, BRAF and MEK, in which mutations in the genes encoding the protein targets render the tumours resistant to the effects of the drugs. The simplest hypothesis to account for the development of resistance to EGFR blockade is that rare cells with KRAS mutations pre-exist at low levels in tumours with ostensibly wild-type KRAS genes. Although this hypothesis would seem readily testable, there is no evidence in pre-clinical models to support it, nor is there data from patients. To test this hypothesis, we determined whether mutant KRAS DNA could be detected in the circulation of 28 patients receiving monotherapy with panitumumab, a therapeutic anti-EGFR antibody. We found that 9 out of 24 (38%) patients whose tumours were initially KRAS wild type developed detectable mutations in KRAS in their sera, three of which developed multiple different KRAS mutations. The appearance of these mutations was very consistent, generally occurring between 5 and 6months following treatment. Mathematical modelling indicated that the mutations were present in expanded subclones before the initiation of panitumumab treatment. These results suggest that the emergence of KRAS mutations is a mediator of acquired resistance to EGFR blockade and that these mutations can be detected in a non-invasive manner. They explain why solid tumours develop resistance to targeted therapies in a highly reproducible fashion. AU - Diaz Jr, Luis AU - Williams, Richard AU - Wu, Jian AU - Kinde, Isaac AU - Hecht, Joel AU - Berlin, Jordan AU - Allen, Benjamin AU - Božić, Ivana AU - Reiter, Johannes AU - Nowak, Martin AU - Kinzler, Kenneth AU - Oliner, Kelly AU - Vogelstein, Bert ID - 3157 IS - 7404 JF - Nature TI - The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers VL - 486 ER - TY - JOUR AB - Many scenarios in the living world, where individual organisms compete for winning positions (or resources), have properties of auctions. Here we study the evolution of bids in biological auctions. For each auction, n individuals are drawn at random from a population of size N. Each individual makes a bid which entails a cost. The winner obtains a benefit of a certain value. Costs and benefits are translated into reproductive success (fitness). Therefore, successful bidding strategies spread in the population. We compare two types of auctions. In “biological all-pay auctions”, the costs are the bid for every participating individual. In “biological second price all-pay auctions”, the cost for everyone other than the winner is the bid, but the cost for the winner is the second highest bid. Second price all-pay auctions are generalizations of the “war of attrition” introduced by Maynard Smith. We study evolutionary dynamics in both types of auctions. We calculate pairwise invasion plots and evolutionarily stable distributions over the continuous strategy space. We find that the average bid in second price all-pay auctions is higher than in all-pay auctions, but the average cost for the winner is similar in both auctions. In both cases, the average bid is a declining function of the number of participants, n. The more individuals participate in an auction the smaller is the chance of winning, and thus expensive bids must be avoided. AU - Chatterjee, Krishnendu AU - Reiter, Johannes AU - Nowak, Martin ID - 3260 IS - 1 JF - Theoretical Population Biology TI - Evolutionary dynamics of biological auctions VL - 81 ER - TY - JOUR AB - CA3 pyramidal neurons are important for memory formation and pattern completion in the hippocampal network. It is generally thought that proximal synapses from the mossy fibers activate these neurons most efficiently, whereas distal inputs from the perforant path have a weaker modulatory influence. We used confocally targeted patch-clamp recording from dendrites and axons to map the activation of rat CA3 pyramidal neurons at the subcellular level. Our results reveal two distinct dendritic domains. In the proximal domain, action potentials initiated in the axon backpropagate actively with large amplitude and fast time course. In the distal domain, Na+ channel–mediated dendritic spikes are efficiently initiated by waveforms mimicking synaptic events. CA3 pyramidal neuron dendrites showed a high Na+-to-K+ conductance density ratio, providing ideal conditions for active backpropagation and dendritic spike initiation. Dendritic spikes may enhance the computational power of CA3 pyramidal neurons in the hippocampal network. AU - Kim, Sooyun AU - Guzmán, José AU - Hu, Hua AU - Jonas, Peter M ID - 3258 IS - 4 JF - Nature Neuroscience SN - 1546-1726 TI - Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons VL - 15 ER - TY - THES AB - CA3 pyramidal neurons are important for memory formation and pattern completion in the hippocampal network. These neurons receive multiple excitatory inputs from numerous sources. Therefore, the rules of spatiotemporal integration of multiple synaptic inputs and propagation of action potentials are important to understand how CA3 neurons contribute to higher brain functions at cellular level. By using confocally targeted patch-clamp recording techniques, we investigated the biophysical properties of rat CA3 pyramidal neuron dendrites. We found two distinct dendritic domains critical for action potential initiation and propagation: In the proximal domain, action potentials initiated in the axon backpropagate actively with large amplitude and fast time course. In the distal domain, Na+-channel mediated dendritic spikes are efficiently evoked by local dendritic depolarization or waveforms mimicking synaptic events. These findings can be explained by a high Na+-to-K+ conductance density ratio of CA3 pyramidal neuron dendrites. The results challenge the prevailing view that proximal mossy fiber inputs activate CA3 pyramidal neurons more efficiently than distal perforant inputs by showing that the distal synapses trigger a different form of activity represented by dendritic spikes. The high probability of dendritic spike initiation in the distal area may enhance the computational power of CA3 pyramidal neurons in the hippocampal network. AU - Kim, Sooyun ID - 2964 SN - 2663-337X TI - Active properties of hippocampal CA3 pyramidal neuron dendrites ER - TY - JOUR AB - Visualizing and analyzing shape changes at various scales, ranging from single molecules to whole organisms, are essential for understanding complex morphogenetic processes, such as early embryonic development. Embryo morphogenesis relies on the interplay between different tissues, the properties of which are again determined by the interaction between their constituent cells. Cell interactions, on the other hand, are controlled by various molecules, such as signaling and adhesion molecules, which in order to exert their functions need to be spatiotemporally organized within and between the interacting cells. In this review, we will focus on the role of cell adhesion functioning at different scales to organize cell, tissue and embryo morphogenesis. We will specifically ask how the subcellular distribution of adhesion molecules controls the formation of cell-cell contacts, how cell-cell contacts determine tissue shape, and how tissue interactions regulate embryo morphogenesis. AU - Barone, Vanessa AU - Heisenberg, Carl-Philipp J ID - 3246 IS - 1 JF - Current Opinion in Cell Biology TI - Cell adhesion in embryo morphogenesis VL - 24 ER - TY - JOUR AB - The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations. AU - Ibarra, Christian A. AU - Feng, Xiaoqi AU - Schoft, Vera K. AU - Hsieh, Tzung-Fu AU - Uzawa, Rie AU - Rodrigues, Jessica A. AU - Zemach, Assaf AU - Chumak, Nina AU - Machlicova, Adriana AU - Nishimura, Toshiro AU - Rojas, Denisse AU - Fischer, Robert L. AU - Tamaru, Hisashi AU - Zilberman, Daniel ID - 12198 IS - 6100 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes VL - 337 ER - TY - JOUR AB - First we note that the best polynomial approximation to vertical bar x vertical bar on the set, which consists of an interval on the positive half-axis and a point on the negative half-axis, can be given by means of the classical Chebyshev polynomials. Then we explore the cases when a solution of the related problem on two intervals can be given in elementary functions. AU - Pausinger, Florian ID - 6588 IS - 1 JF - Journal of Mathematical Physics, Analysis, Geometry SN - 1812-9471 TI - Elementary solutions of the Bernstein problem on two intervals VL - 8 ER - TY - CONF AB - We introduce the idea of using an explicit triangle mesh to track the air/fluid interface in a smoothed particle hydrodynamics (SPH) simulator. Once an initial surface mesh is created, this mesh is carried forward in time using nearby particle velocities to advect the mesh vertices. The mesh connectivity remains mostly unchanged across time-steps; it is only modified locally for topology change events or for the improvement of triangle quality. In order to ensure that the surface mesh does not diverge from the underlying particle simulation, we periodically project the mesh surface onto an implicit surface defined by the physics simulation. The mesh surface gives us several advantages over previous SPH surface tracking techniques. We demonstrate a new method for surface tension calculations that clearly outperforms the state of the art in SPH surface tension for computer graphics. We also demonstrate a method for tracking detailed surface information (like colors) that is less susceptible to numerical diffusion than competing techniques. Finally, our temporally-coherent surface mesh allows us to simulate high-resolution surface wave dynamics without being limited by the particle resolution of the SPH simulation. AU - Yu, Jihun AU - Wojtan, Christopher J AU - Turk, Greg AU - Yap, Chee ID - 3123 IS - 2 SN - 0167-7055 T2 - Computer Graphics Forum TI - Explicit mesh surfaces for particle based fluids VL - 31 ER - TY - JOUR AB - Bibliothekare haben die Aufgabe, sich mit neuen Medienformen auseinanderzusetzen. AU - Danowski, Patrick ID - 3244 IS - 4 JF - BuB - Forum Bibliothek und Information SN - 1869 -1137 TI - Die Zeit des Abwartens ist vorbei! VL - 64 ER - TY - JOUR AB - Wie wandelt sich das Berufsbild in Wissenschaftlichen Bibliotheken? Patrick Danowski gibt seine Einschätzung ab. AU - Danowski, Patrick ID - 3243 IS - 1 JF - Büchereiperspektiven SN - 1607-7172 TI - Zwischen Technologie und Information VL - 2012 ER - TY - CONF AU - Kroemer, Oliver AU - Lampert, Christoph AU - Peters, Jan ID - 2915 TI - Multi-modal learning for dynamic tactile sensing ER - TY - JOUR AU - Edelsbrunner, Herbert AU - Strelkova, Nataliya ID - 2912 IS - 6 JF - Russian Mathematical Surveys TI - On the configuration space for the shortest networks VL - 67 ER - TY - CONF AB - When searching for characteristic subpatterns in potentially noisy graph data, it appears self-evident that having multiple observations would be better than having just one. However, it turns out that the inconsistencies introduced when different graph instances have different edge sets pose a serious challenge. In this work we address this challenge for the problem of finding maximum weighted cliques. We introduce the concept of most persistent soft-clique. This is subset of vertices, that 1) is almost fully or at least densely connected, 2) occurs in all or almost all graph instances, and 3) has the maximum weight. We present a measure of clique-ness, that essentially counts the number of edge missing to make a subset of vertices into a clique. With this measure, we show that the problem of finding the most persistent soft-clique problem can be cast either as: a) a max-min two person game optimization problem, or b) a min-min soft margin optimization problem. Both formulations lead to the same solution when using a partial Lagrangian method to solve the optimization problems. By experiments on synthetic data and on real social network data, we show that the proposed method is able to reliably find soft cliques in graph data, even if that is distorted by random noise or unreliable observations. AU - Quadrianto, Novi AU - Lampert, Christoph AU - Chen, Chao ID - 3127 T2 - Proceedings of the 29th International Conference on Machine Learning TI - The most persistent soft-clique in a set of sampled graphs ER - TY - JOUR AB - Generalized van der Corput sequences are onedimensional, infinite sequences in the unit interval. They are generated from permutations in integer base b and are the building blocks of the multi-dimensional Halton sequences. Motivated by recent progress of Atanassov on the uniform distribution behavior of Halton sequences, we study, among others, permutations of the form P(i) = ai (mod b) for coprime integers a and b. We show that multipliers a that either divide b - 1 or b + 1 generate van der Corput sequences with weak distribution properties. We give explicit lower bounds for the asymptotic distribution behavior of these sequences and relate them to sequences generated from the identity permutation in smaller bases, which are, due to Faure, the weakest distributed generalized van der Corput sequences. AU - Pausinger, Florian ID - 2904 IS - 3 JF - Journal de Theorie des Nombres des Bordeaux SN - 1246-7405 TI - Weak multipliers for generalized van der Corput sequences VL - 24 ER - TY - JOUR AB - We present an algorithm for simplifying linear cartographic objects and results obtained with a computer program implementing this algorithm. AU - Edelsbrunner, Herbert AU - Musin, Oleg AU - Ukhalov, Alexey AU - Yakimova, Olga AU - Alexeev, Vladislav AU - Bogaevskaya, Victoriya AU - Gorohov, Andrey AU - Preobrazhenskaya, Margarita ID - 2902 IS - 6 JF - Modeling and Analysis of Information Systems TI - Fractal and computational geometry for generalizing cartographic objects VL - 19 ER - TY - JOUR AB - We perform numerical simulations to study self-assembly of nanoparticles mediated by an elastic planar surface. We show how the nontrivial elastic response to deformations of these surfaces leads to anisotropic interactions between the particles resulting in aggregates having different geometrical features. The morphology of the patterns can be controlled by the mechanical properties of the surface and the strength of the particle adhesion. We use simple scaling arguments to understand the formation of the different structures, and we show how the adhering particles can cause the underlying elastic substrate to wrinkle if two of its opposite edges are clamped. Finally, we discuss the implications of our results and suggest how elastic surfaces could be used in nanofabrication. AU - Šarić, Anđela AU - Cacciuto, Angelo ID - 10389 IS - 18 JF - Soft Matter KW - condensed matter physics KW - general chemistry SN - 1744-683X TI - Soft elastic surfaces as a platform for particle self-assembly VL - 7 ER - TY - JOUR AB - We present experimentally derived potential curves 1?and spin-orbit interaction functions for the strongly perturbed AΣu+ 3?and bΠu states of the cesium dimer. The results are based on data from several sources. Laser-induced fluorescence Fourier transform spectroscopy (LIF FTS) was used some time ago in the Laboratoire Aimé Cotton primarily to study the XΣg+ state. More recent work at Tsinghua University provides information from moderate 3?resolution spectroscopy on the lowest levels of the bΠ0u± state as well as additional high-resolution data. From Innsbruck University, we have precision data obtained with cold Cs2 molecules. Recent data from Temple University was obtained using the optical-optical double resonance polarization spectroscopy technique, and finally, a group at the University of Latvia has added additional LIF FTS data. In the Hamiltonian matrix, we have used analytic potentials (the expanded Morse oscillator form) with both finite-difference (FD) coupled-channel and discrete variable representation (DVR) calculations of the term values. Fitted diagonal and off-diagonal spin-orbit functions are obtained and compared with ab initio results from Temple and Moscow State universities. AU - Bai, Jianmei AU - Ahmed, Ergin AU - Beser, Bediha AU - Guan, Yafei AU - Kotochigova, Svetlana AU - Lyyra, Marjatta AU - Ashman, Seth AU - Wolfe, Christopher AU - Huennekens, John AU - Xie, Feng AU - Li, Dan AU - Li, Li AU - Tamanis, Maris AU - Ferber, Ruvin AU - Drozdova, Anastasia AU - Pazyuk, Elena AU - Stolyarov, Andrey AU - Danzl, Johann G AU - Nägerl, Hanns AU - Bouloufa, Nadia AU - Dulieu, Olivier AU - Amiot, Claude AU - Salami, Houssam AU - Bergeman, Thomas ID - 1050 IS - 3 JF - Physical Review A - Atomic, Molecular, and Optical Physics TI - Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2 VL - 83 ER - TY - JOUR AB - We produce an ultracold and dense sample of rovibronic ground state Cs 2 molecules close to the regime of quantum degeneracy, in a single hyperfine level, in the presence of an optical lattice. The molecules are individually trapped, in the motional ground state of an optical lattice well, with a lifetime of 8 s. For preparation, we start with a zero-temperature atomic Mott-insulator state with optimized double-site occupancy and efficiently associate weakly-bound dimer molecules on a Feshbach resonance. Despite extremely weak Franck-Condon wavefunction overlap, the molecules are subsequently transferred with >50% efficiency to the rovibronic ground state by a stimulated four-photon process. Our results present a crucial step towards the generation of Bose-Einstein condensates of ground-state molecules and, when suitably generalized to polar heteronuclear molecules such as RbCs, the realization of dipolar many-body quantum-gas phases in periodic potentials. AU - Nägerl, Hanns AU - Mark, Manfred AU - Haller, Elmar AU - Gustavsson, Mattias AU - Hart, Russell AU - Danzl, Johann G ID - 1048 IS - 1 JF - Journal of Physics: Conference Series TI - Ultracold and dense samples of ground-state molecules in lattice potentials VL - 264 ER - TY - JOUR AB - The present paper aims at finding optimal parameters for trapping of Cs 2 molecules in optical lattices, with the perspective of creating a quantum degenerate gas of ground-state molecules. We have calculated dynamic polarizabilities of Cs 2 molecules subject to an oscillating electric field, using accurate potential curves and electronic transition dipole moments. We show that for some particular wavelengths of the optical lattice, called "magic wavelengths", the polarizability of the ground-state molecules is equal to the one of a Feshbach molecule. As the creation of the sample of ground-state molecules relies on an adiabatic population transfer from weakly-bound molecules created on a Feshbach resonance, such a coincidence ensures that both the initial and final states are favorably trapped by the lattice light, allowing optimized transfer in agreement with the experimental observation. AU - Vexiau, Romain AU - Bouloufa, Nadia AU - Aymar, Mireille AU - Danzl, Johann G AU - Mark, Manfred AU - Nägerl, Hanns AU - Dulieu, Olivier ID - 1052 IS - 1-2 JF - European Physical Journal D TI - Optimal trapping wavelengths of Cs 2 molecules in an optical lattice VL - 65 ER - TY - JOUR AB - We demonstrate the temporal Talbot effect for trapped matter waves using ultracold atoms in an optical lattice. We investigate the phase evolution of an array of essentially non-interacting matter waves and observe matter-wave collapse and revival in the form of a Talbot interference pattern. By using long expansion times, we image momentum space with sub-recoil resolution, allowing us to observe fractional Talbot fringes up to tenth order. AU - Mark, Manfred AU - Haller, Elmar AU - Danzl, Johann G AU - Lauber, Katharina AU - Gustavsson, Mattias AU - Nägerl, Hanns ID - 1051 JF - New Journal of Physics TI - Demonstration of the temporal matter-wave Talbot effect for trapped matter waves VL - 13 ER - TY - JOUR AB - We perform precision measurements on a Mott-insulator quantum state of ultracold atoms with tunable interactions. We probe the dependence of the superfluid-to-Mott-insulator transition on the interaction strength and explore the limits of the standard Bose-Hubbard model description. By tuning the on-site interaction energies to values comparable to the interband separation, we are able to quantitatively measure number-dependent shifts in the excitation spectrum caused by effective multibody interactions. AU - Mark, Manfred AU - Haller, Elmar AU - Lauber, Katharina AU - Danzl, Johann G AU - Daley, Andrew AU - Nägerl, Hanns ID - 1053 IS - 17 JF - Physical Review Letters TI - Precision measurements on a tunable Mott insulator of ultracold atoms VL - 107 ER - TY - JOUR AB - We investigate local three-body correlations for bosonic particles in three dimensions and one dimension as a function of the interaction strength. The three-body correlation function g(3) is determined by measuring the three-body recombination rate in an ultracold gas of Cs atoms. In three dimensions, we measure the dependence of g(3) on the gas parameter in a BEC, finding good agreement with the theoretical prediction accounting for beyond-mean-field effects. In one dimension, we observe a reduction of g( 3) by several orders of magnitude upon increasing interactions from the weakly interacting BEC to the strongly interacting Tonks-Girardeau regime, in good agreement with predictions from the Lieb-Liniger model for all strengths of interaction. AU - Haller, Elmar AU - Rabie, Mahmoud AU - Mark, Manfred AU - Danzl, Johann G AU - Hart, Russell AU - Lauber, Katharina AU - Pupillo, Guido AU - Nägerl, Hanns ID - 1054 IS - 23 JF - Physical Review Letters TI - Three-body correlation functions and recombination rates for bosons in three dimensions and one dimension VL - 107 ER - TY - JOUR AB - Nuclear pore complexes (NPCs) assemble at the end of mitosis during nuclear envelope (NE) reformation and into an intact NE as cells progress through interphase. Although recent studies have shown that NPC formation occurs by two different molecular mechanisms at two distinct cell cycle stages, little is known about the molecular players that mediate the fusion of the outer and inner nuclear membranes to form pores. In this paper, we provide evidence that the transmembrane nucleoporin (Nup), POM121, but not the Nup107–160 complex, is present at new pore assembly sites at a time that coincides with inner nuclear membrane (INM) and outer nuclear membrane (ONM) fusion. Overexpression of POM121 resulted in juxtaposition of the INM and ONM. Additionally, Sun1, an INM protein that is known to interact with the cytoskeleton, was specifically required for interphase assembly and localized with POM121 at forming pores. We propose a model in which POM121 and Sun1 interact transiently to promote early steps of interphase NPC assembly. AU - Talamas, Jessica A. AU - HETZER, Martin W ID - 11094 IS - 1 JF - Journal of Cell Biology KW - Cell Biology SN - 0021-9525 TI - POM121 and Sun1 play a role in early steps of interphase NPC assembly VL - 194 ER - TY - JOUR AB - As the gatekeepers of the eukaryotic cell nucleus, nuclear pore complexes (NPCs) mediate all molecular trafficking between the nucleoplasm and the cytoplasm. In recent years, transport-independent functions of NPC components, nucleoporins, have been identified including roles in chromatin organization and gene regulation. Here, we summarize our current view of the NPC as a dynamic hub for the integration of chromatin regulation and nuclear trafficking and discuss the functional interplay between nucleoporins and the nuclear genome. AU - Liang, Yun AU - HETZER, Martin W ID - 11096 IS - 1 JF - Current Opinion in Cell Biology KW - Cell Biology SN - 0955-0674 TI - Functional interactions between nucleoporins and chromatin VL - 23 ER - TY - JOUR AU - HETZER, Martin W AU - Cavalli, Giacomo ID - 11095 IS - 3 JF - Current Opinion in Cell Biology KW - Cell Biology SN - 0955-0674 TI - Editorial overview VL - 23 ER - TY - JOUR AB - Eukaryotic cell function depends on the physical separation of nucleoplasmic and cytoplasmic components by the nuclear envelope (NE). Molecular communication between the two compartments involves active, signal-mediated trafficking, a function that is exclusively performed by nuclear pore complexes (NPCs). The individual NPC components and the mechanisms that are involved in nuclear trafficking are well documented and have become textbook knowledge. However, in addition to their roles as nuclear gatekeepers, NPC components-nucleoporins-have been shown to have critical roles in chromatin organization and gene regulation. These findings have sparked new enthusiasm to study the roles of this multiprotein complex in nuclear organization and explore novel functions that in some cases appear to go beyond a role in transport. Here, we discuss our present view of NPC biogenesis, which is tightly linked to proper cell cycle progression and cell differentiation. In addition, we summarize new data suggesting that NPCs represent dynamic hubs for the integration of gene regulation and nuclear transport processes. AU - Capelson, M. AU - Doucet, C. AU - HETZER, Martin W ID - 11100 JF - Cold Spring Harbor Symposia on Quantitative Biology KW - Genetics KW - Molecular Biology KW - Biochemistry SN - 0091-7451 TI - Nuclear pore complexes: Guardians of the nuclear genome VL - 75 ER - TY - JOUR AB - Particle beams are important tools for probing atomic and molecular interactions. Here we demonstrate that particle beams also offer a unique opportunity to investigate interactions in macroscopic systems, such as granular media. Motivated by recent experiments on streams of grains that exhibit liquid-like breakup into droplets, we use molecular dynamics simulations to investigate the evolution of a dense stream of macroscopic spheres accelerating out of an opening at the bottom of a reservoir. We show how nanoscale details associated with energy dissipation during collisions modify the stream\'s macroscopic behavior. We find that inelastic collisions collimate the stream, while the presence of short-range attractive interactions drives structure formation. Parameterizing the collision dynamics by the coefficient of restitution (i.e., the ratio of relative velocities before and after impact) and the strength of the cohesive interaction, we map out a spectrum of behaviors that ranges from gaslike jets in which all grains drift apart to liquid-like streams that break into large droplets containing hundreds of grains. We also find a new, intermediate regime in which small aggregates form by capture from the gas phase, similar to what can be observed in molecular beams. Our results show that nearly all aspects of stream behavior are closely related to the velocity gradient associated with vertical free fall. Led by this observation, we propose a simple energy balance model to explain the droplet formation process. The qualitative as well as many quantitative features of the simulations and the model compare well with available experimental data and provide a first quantitative measure of the role of attractions in freely cooling granular streams. AU - Waitukaitis, Scott R AU - Grütjen, Helge AU - Royer, John AU - Jaeger, Heinrich ID - 112 IS - 5 JF - Physical Review E TI - Droplet and cluster formation in freely falling granular streams VL - 83 ER - TY - JOUR AB - Given only the URL of a Web page, can we identify its topic? We study this problem in detail by exploring a large number of different feature sets and algorithms on several datasets. We also show that the inherent overlap between topics and the sparsity of the information in URLs makes this a very challenging problem. Web page classification without a page’s content is desirable when the content is not available at all, when a classification is needed before obtaining the content, or when classification speed is of utmost importance. For our experiments we used five different corpora comprising a total of about 3 million (URL, classification) pairs. We evaluated several techniques for feature generation and classification algorithms. The individual binary classifiers were then combined via boosting into metabinary classifiers. We achieve typical F-measure values between 80 and 85, and a typical precision of around 86. The precision can be pushed further over 90 while maintaining a typical level of recall between 30 and 40. AU - Baykan, Eda AU - Henzinger, Monika H AU - Marian, Ludmila AU - Weber, Ingmar ID - 11673 IS - 3 JF - ACM Transactions on the Web KW - Topic classification KW - URL KW - ODP SN - 1559-1131 TI - A comprehensive study of features and algorithms for URL-based topic classification VL - 5 ER - TY - JOUR AB - We study a novel load balancing problem that arises in web search engines. The problem is a combination of an offline assignment problem, where files need to be (copied and) assigned to machines, and an online load balancing problem, where requests ask for specific files and need to be assigned to a corresponding machine, whose load is increased by this. We present simple deterministic algorithms for this problem and exhibit an interesting trade-off between the available space to make file copies and the obtainable makespan. We also give non-trivial lower bounds for a large class of deterministic algorithms and present a randomized algorithm that beats these bounds with high probability. AU - Dütting, Paul AU - Henzinger, Monika H AU - Weber, Ingmar ID - 11760 IS - 4 JF - Information Processing Letters SN - 0020-0190 TI - Offline file assignments for online load balancing VL - 111 ER - TY - CONF AB - The design of truthful auctions that approximate the optimal expected revenue is a central problem in algorithmic mechanism design. 30 years after Myerson’s characterization of Bayesian optimal auctions in single-parameter domains [8], characterizing but also providing efficient mechanisms for multi-parameter domains still remains a very important unsolved problem. Our work improves upon recent results in this area, introducing new techniques for tackling the problem, while also combining and extending recently introduced tools. In particular we give the first approximation algorithms for Bayesian auctions with multiple heterogeneous items when bidders have additive valuations, budget constraints and general matroid feasibility constraints. AU - Henzinger, Monika H AU - Vidali, Angelina ID - 11796 SN - 1611-3349 T2 - 19th Annual European Symposium on Algorithms TI - Multi-parameter mechanism design under budget and matroid constraints VL - 6942 ER - TY - CONF AB - Auctions are widely used on the Web. Applications range from internet advertising to platforms such as eBay. In most of these applications the auctions in use are single/multi-item auctions with unit demand. The main drawback of standard mechanisms for this type of auctions, such as VCG and GSP, is the limited expressiveness that they offer to the bidders. The General Auction Mechanism (GAM) of [1] is taking a first step towards addressing the problem of limited expressiveness by computing a bidder optimal, envy free outcome for linear utility functions with identical slopes and a single discontinuity per bidder-item pair. We show that in many practical situations this does not suffice to adequately model the preferences of the bidders, and we overcome this problem by presenting the first mechanism for piece-wise linear utility functions with non-identical slopes and multiple discontinuities. Our mechanism runs in polynomial time. Like GAM it is incentive compatible for inputs that fulfill a certain non-degeneracy requirement, but our requirement is more general than the requirement of GAM. For discontinuous utility functions that are non-degenerate as well as for continuous utility functions the outcome of our mechanism is a competitive equilibrium. We also show how our mechanism can be used to compute approximately bidder optimal, envy free outcomes for a general class of continuous utility functions via piece-wise linear approximation. Finally, we prove hardness results for even more expressive settings. AU - Dütting, Paul AU - Henzinger, Monika H AU - Weber, Ingmar ID - 11864 SN - 978-145030632-4 T2 - Proceedings of the 20th international conference on World wide web TI - An expressive mechanism for auctions on the web ER - TY - JOUR AB - Temperature data from three Automatic Weather Stations and twelve Temperature Loggers are used to investigate the spatiotemporal variability of temperature over a glacier, its main atmospheric controls, the suitability of extrapolation techniques and their effect on melt modeling. We use data collected on Juncal Norte Glacier, central Chile, during one ablation season. We examine temporal and spatial variability in lapse rates (LRs), together with alternative statistical interpolation methods. The main control over the glacier thermal regime is the development of a katabatic boundary layer (KBL). Katabatic wind occurs at night and in the morning and is eroded in the afternoon. LRs reveal strong diurnal variability, with steeper LRs during the day when the katabatic wind weakens and shallower LRs during the night and morning. We suggest that temporally variable LRs should be used to account for the observed change. They tend to be steeper than equivalent constant LRs, and therefore result in a reduction in simulated melt compared to use of constant LRs when extrapolating from lower to higher elevations. In addition to the temporal variability, the temperature-elevation relationship varies also in space. Differences are evident between local LRs and including such variability in melt modeling affects melt simulations. Extrapolation methods based on the spatial variability of the observations after removal of the elevation trend, such as Inverse Distance Weighting or Kriging, do not seem necessary for simulations of gridded temperature data over a glacier. AU - Petersen, L. AU - Pellicciotti, Francesca ID - 12651 IS - D23 JF - Journal of Geophysical Research: Atmospheres KW - Paleontology KW - Space and Planetary Science KW - Earth and Planetary Sciences (miscellaneous) KW - Atmospheric Science KW - Earth-Surface Processes KW - Geochemistry and Petrology KW - Soil Science KW - Water Science and Technology KW - Ecology KW - Aquatic Science KW - Forestry KW - Oceanography KW - Geophysics SN - 0148-0227 TI - Spatial and temporal variability of air temperature on a melting glacier: Atmospheric controls, extrapolation methods and their effect on melt modeling, Juncal Norte Glacier, Chile VL - 116 ER - TY - JOUR AB - Physically based hydrological models describe natural processes more accurately than conceptual models but require extensive data sets to produce accurate results. To identify the value of different data sets for improving the performance of the distributed hydrological model TOPKAPI we combine a multivariable validation technique with Monte Carlo simulations. The study is carried out in the snow and ice-dominated Rhonegletscher basin, as these types of mountainous basins are generally the most critical with respect to data availability and sensitivity to climate fluctuations. Each observational data set is used individually and in combination with the other data sets to determine a subset of best parameter combinations out of 10,000 Monte Carlos runs performed with randomly generated parameter sets. We validate model results against discharge, glacier mass balance, and satellite snow cover images for a 14 year time period (1994–2007). While the use of all data sets combined provides the best overall model performance (defined by the concurrent best agreement of simulated discharge, snow cover and mass balance with their respective measurements), the use of one or two variables for constraining the model results in poorer performance. Using only one data set for constraining the model glacier mass balance proved to be the most efficient observation leading to the best overall model performance. Our main result is that a combination of discharge and satellite snow cover images is best for improving model performance, since the volumetric information of discharge data and the spatial information of snow cover images are complementary. AU - Finger, David AU - Pellicciotti, Francesca AU - Konz, Markus AU - Rimkus, Stefan AU - Burlando, Paolo ID - 12649 IS - 7 JF - Water Resources Research SN - 0043-1397 TI - The value of glacier mass balance, satellite snow cover images, and hourly discharge for improving the performance of a physically based distributed hydrological model VL - 47 ER - TY - JOUR AB - We explore the robustness and transferability of parameterizations of cloud radiative forcing used in glacier melt models at two sites in the Swiss Alps. We also look at the rationale behind some of the most commonly used approaches, and explore the relationship between cloud transmittance and several standard meteorological variables. The 2 m air-temperature diurnal range is the best predictor of variations in cloud transmittance. However, linear and exponential parameterizations can only explain 30–50% of the observed variance in computed cloud transmittance factors. We examine the impact of modelled cloud transmittance factors on both solar radiation and ablation rates computed with an enhanced temperature-index model. The melt model performance decreases when modelled radiation is used, the reduction being due to an underestimation of incoming solar radiation on clear-sky days. The model works well under overcast conditions. We also seek alternatives to the use of in situ ground data. However, outputs from an atmospheric model (2.2 km horizontal resolution) do not seem to provide an alternative to the parameterizations of cloud radiative forcing based on observations of air temperature at glacier automatic weather stations. Conversely, the correct definition of overcast conditions is important. AU - Pellicciotti, Francesca AU - Raschle, Thomas AU - Huerlimann, Thomas AU - Carenzo, Marco AU - Burlando, Paolo ID - 12652 IS - 202 JF - Journal of Glaciology SN - 0022-1430 TI - Transmission of solar radiation through clouds on melting glaciers: A comparison of parameterizations and their impact on melt modelling VL - 57 ER - TY - CHAP AB - Streamflow is a hydrological variable measured at a defined river cross-section; it spatially integrates the runoff generating processes in the contributing watershed, including precipitation and air temperature. Trends in streamflow are progressive changes in the time series of streamflow that can be detected with statistical methods and their statistical significance can be assessed. Mountainous regions are particularly vulnerable to streamflow change because of their high specific runoff and the sensitivity to the distribution of precipitation and air temperature, and the processes of snow accumulation and melt. AU - Molnar, Peter AU - Burlando, Paolo AU - Pellicciotti, Francesca ED - Singh, Vijay ED - Singh, Pratap ED - Haritashya, Umesh ID - 12650 SN - 1388-4360 T2 - Encyclopedia of Snow, Ice and Glaciers TI - Streamflow Trends in Mountainous Regions ER - TY - JOUR AB - Recent experiments have shown that motion detection in Drosophila starts with splitting the visual input into two parallel channels encoding brightness increments (ON) or decrements (OFF). This suggests the existence of either two (ON-ON, OFF-OFF) or four (for all pairwise interactions) separate motion detectors. To decide between these possibilities, we stimulated flies using sequences of ON and OFF brightness pulses while recording from motion-sensitive tangential cells. We found direction-selective responses to sequences of same sign (ON-ON, OFF-OFF), but not of opposite sign (ON-OFF, OFF-ON), refuting the existence of four separate detectors. Based on further measurements, we propose a model that reproduces a variety of additional experimental data sets, including ones that were previously interpreted as support for four separate detectors. Our experiments and the derived model mark an important step in guiding further dissection of the fly motion detection circuit. AU - Eichner, Hubert AU - Maximilian Jösch AU - Schnell, Bettina AU - Reiff, Dierk F AU - Borst, Alexander ID - 1299 IS - 6 JF - Neuron TI - Internal structure of the fly elementary motion detector VL - 70 ER - TY - JOUR AB - We propose a general conjecture for the mixed Hodge polynomial of the generic character varieties of representations of the fundamental group of a Riemann surface of genus g to GLn(C) with fixed generic semisimple conjugacy classes at k punctures. This conjecture generalizes the Cauchy identity for Macdonald polynomials and is a common generalization of two formulas that we prove in this paper. The first is a formula for the E-polynomial of these character varieties which we obtain using the character table of GLn(Fq). We use this formula to compute the Euler characteristic of character varieties. The second formula gives the Poincaré polynomial of certain associated quiver varieties which we obtain using the character table of gln(Fq). In the last main result we prove that the Poincaré polynomials of the quiver varieties equal certain multiplicities in the tensor product of irreducible characters of GLn(Fq). As a consequence we find a curious connection between Kac-Moody algebras associated with comet-shaped, and typically wild, quivers and the representation theory of GLn(Fq). AU - Tamas Hausel AU - Letellier, Emmanuel AU - Rodríguez Villegas, Fernando ID - 1467 IS - 2 JF - Duke Mathematical Journal TI - Arithmetic harmonic analysis on character and quiver varieties VL - 160 ER - TY - JOUR AB - The emergence of differences in the arrangement of cells is the first step towards the establishment of many organs. Understanding this process is limited by the lack of systematic characterization of epithelial organisation. Here we apply network theory at the scale of individual cells to uncover patterns in cell-to-cell contacts that govern epithelial organisation. We provide an objective characterisation of epithelia using network representation, where cells are nodes and cell contacts are links. The features of individual cells, together with attributes of the cellular network, produce a defining signature that distinguishes epithelia from different organs, species, developmental stages and genetic conditions. The approach permits characterization, quantification and classification of normal and perturbed epithelia, and establishes a framework for understanding molecular mechanisms that underpin the architecture of complex tissues. AU - Escudero, Luis M AU - Costa, Luciano AU - Anna Kicheva AU - Briscoe, James AU - Freeman, Matthew AU - Babu, Madan M ID - 1723 IS - 1 JF - Nature Communications TI - Epithelial organisation revealed by a network of cellular contacts VL - 2 ER - TY - JOUR AB - Morphogens, such as Decapentaplegic (Dpp) in the fly imaginal discs, form graded concentration profiles that control patterning and growth of developing organs. In the imaginal discs, proliferative growth is homogeneous in space, posing the conundrum of how morphogen concentration gradients could control position-independent growth. To understand the mechanism of proliferation control by the Dpp gradient, we quantified Dpp concentration and signaling levels during wing disc growth. Both Dpp concentration and signaling gradients scale with tissue size during development. On average, cells divide when Dpp signaling levels have increased by 50%. Our observations are consistent with a growth control mechanism based on temporal changes of cellular morphogen signaling levels. For a scaling gradient, this mechanism generates position-independent growth rates. AU - Wartlick, Ortrud AU - Mumcu, Peer AU - Anna Kicheva AU - Bittig, Thomas AU - Seum, Carole AU - Jülicher, Frank AU - González-Gaitán, Marcos A ID - 1724 IS - 6021 JF - Science TI - Dynamics of Dpp signaling and proliferation control VL - 331 ER - TY - JOUR AB - We report on a technique enabling electrical control of the contact silicidation process in silicon nanowire devices. Undoped silicon nanowires were contacted by pairs of nickel electrodes and each contact was selectively silicided by means of the Joule effect. By a realtime monitoring of the nanowire electrical resistance during the contact silicidation process we were able to fabricate nickel-silicide/silicon/nickel- silicide devices with controlled silicon channel length down to 8 nm. AU - Mongillo, Massimo AU - Spathis, Panayotis AU - Katsaros, Georgios AU - Gentile, Pascal AU - Sanquer, Marc AU - De Franceschi, Silvano ID - 1754 IS - 9 JF - ACS Nano TI - Joule-assisted silicidation for short-channel silicon nanowire devices VL - 5 ER - TY - JOUR AB - Spin-selective tunneling of holes in SiGe nanocrystals contacted by normal-metal leads is reported. The spin selectivity arises from an interplay of the orbital effect of the magnetic field with the strong spin-orbit interaction present in the valence band of the semiconductor. We demonstrate both experimentally and theoretically that spin-selective tunneling in semiconductor nanostructures can be achieved without the use of ferromagnetic contacts. The reported effect, which relies on mixing the light and heavy holes, should be observable in a broad class of quantum-dot systems formed in semiconductors with a degenerate valence band. AU - Georgios Katsaros AU - Golovach, Vitaly N AU - Spathis, Panayotis N AU - Ares, Natalia AU - Stoffel, Mathieu AU - Fournel, Frank AU - Schmidt, Oliver G AU - Glazman, Leonid I AU - De Franceschi, Silvano ID - 1755 IS - 24 JF - Physical Review Letters TI - Observation of spin-selective tunneling in sige nanocrystals VL - 107 ER - TY - CONF AB - Superconducting circuits have been successfully established as systems to prepare and investigate microwave light fields at the quantum level. In contrast to optical experiments where light is detected using photon counters, microwaves are usually measured with well developed linear amplifiers. This makes measurements of correlation functions - one of the important tools in optics - harder to achieve because they traditionally rely on photon counters and beam splitters. Here, we demonstrate a system where we can prepare on demand single microwave photons in a cavity and detect them at the two outputs of the cavity using linear amplifiers. Together with efficient data processing, this allows us to measure different observables of the cavity photons, including the first-order correlation function. Using these techniques we demonstrate cooling of a thermal background field in the cavity. AU - Bozyigit, Deniz AU - Lang, C AU - Steffen, L. Kraig AU - Johannes Fink AU - Eichler, Christopher AU - Baur, Matthias P AU - Bianchetti, R AU - Leek, Peter J AU - Filipp, Stefan AU - Wallraff, Andreas AU - Da Silva, Marcus P AU - Blais, Alexandre ID - 1776 IS - 1 TI - Correlation measurements of individual microwave photons emitted from a symmetric cavity VL - 264 ER - TY - JOUR AB - A wide range of experiments studying microwave photons localized in superconducting cavities have made important contributions to our understanding of the quantum properties of radiation. Propagating microwave photons, however, have so far been studied much less intensely. Here we present measurements in which we reconstruct the quantum state of itinerant single photon Fock states and their superposition with the vacuum by analyzing moments of the measured amplitude distribution up to fourth order. Using linear amplifiers and quadrature amplitude detectors, we have developed efficient methods to separate the detected single photon signal from the noise added by the amplifier. From our measurement data we have also reconstructed the corresponding Wigner function. AU - Eichler, Christopher AU - Bozyigit, Deniz AU - Lang, C AU - Steffen, L. AU - Fink, Johannes M AU - Wallraff, Andreas ID - 1777 IS - 22 JF - Physical Review Letters TI - Experimental state tomography of itinerant single microwave photons VL - 106 ER - TY - JOUR AB - Creating a train of single photons and monitoring its propagation and interaction is challenging in most physical systems, as photons generally interact very weakly with other systems. However, when confining microwave frequency photons in a transmission line resonator, effective photon-photon interactions can be mediated by qubits embedded in the resonator. Here, we observe the phenomenon of photon blockade through second-order correlation function measurements. The experiments clearly demonstrate antibunching in a continuously pumped source of single microwave photons measured by using microwave beam splitters, linear amplifiers, and quadrature amplitude detectors. We also investigate resonance fluorescence and Rayleigh scattering in Mollow-triplet-like spectra. AU - Lang, C AU - Bozyigit, Deniz AU - Eichler, Christopher AU - Steffen, L. Kraig AU - Johannes Fink AU - Abdumalikov, Abdufarrukh A AU - Baur, Matthias P AU - Filipp, Stefan AU - Da Silva, Marcus P AU - Blais, Alexandre AU - Wallraff, Andreas ID - 1778 IS - 24 JF - Physical Review Letters TI - Observation of resonant photon blockade at microwave frequencies using correlation function measurements VL - 106 ER - TY - JOUR AB - At optical frequencies the radiation produced by a source, such as a laser, a black body or a single-photon emitter, is frequently characterized by analysing the temporal correlations of emitted photons using single-photon counters. At microwave frequencies, however, there are no efficient single-photon counters yet. Instead, well-developed linear amplifiers allow for efficient measurement of the amplitude of an electromagnetic field. Here, we demonstrate first- and second-order correlation function measurements of a pulsed microwave-frequency single-photon source integrated on the same chip with a 50/50 beam splitter followed by linear amplifiers and quadrature amplitude detectors. We clearly observe single-photon coherence in first-order and photon antibunching in second-order correlation function measurements of the propagating fields. AU - Bozyigit, Deniz AU - Lang, C AU - Steffen, L. Kraig AU - Johannes Fink AU - Eichler, Christopher AU - Baur, Matthias P AU - Bianchetti, R AU - Leek, Peter J AU - Filipp, Stefan AU - Da Silva, Marcus P AU - Blais, Alexandre AU - Wallraff, Andreas ID - 1775 IS - 2 JF - Nature Physics TI - Antibunching of microwave-frequency photons observed in correlation measurements using linear detectors VL - 7 ER - TY - JOUR AB - Microwave cavities with high quality factors enable coherent coupling of distant quantum systems. Virtual photons lead to a transverse interaction between qubits when they are nonresonant with the cavity but resonant with each other. We experimentally investigate the inverse scaling of the interqubit coupling with the detuning from a cavity mode and its proportionality to the qubit-cavity interaction strength. We demonstrate that the enhanced coupling at higher frequencies is mediated by multiple higher-harmonic cavity modes. Moreover, we observe dark states of the coupled qubit-qubit system and analyze their relation to the symmetry of the applied driving field at different frequencies. AU - Filipp, Stefan AU - Göppl, M AU - Johannes Fink AU - Baur, Matthias P AU - Bianchetti, R AU - Steffen, L. Kraig AU - Wallraff, Andreas ID - 1781 IS - 6 JF - Physical Review A - Atomic, Molecular, and Optical Physics TI - Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics VL - 83 ER - TY - JOUR AB - Continuous variable entanglement between two modes of a radiation field is usually studied at optical frequencies. Here we demonstrate experiments that show the entanglement between microwave photons of different energy in a broadband squeezed beam. We use a Josephson parametric amplifier to generate the two-mode correlated state and detect all four quadrature components simultaneously in a two-channel heterodyne setup using amplitude detectors. Analyzing two-dimensional phase space histograms for all possible pairs of quadratures allows us to determine the full covariance matrix, which is in good agreement with the one expected for a two-mode squeezed state. AU - Eichler, Christopher AU - Bozyigit, Deniz AU - Lang, C AU - Baur, Matthias P AU - Steffen, L. Kraig AU - Johannes Fink AU - Filipp, Stefan AU - Wallraff, Andreas ID - 1780 IS - 11 JF - Physical Review Letters TI - Observation of two-mode squeezing in the microwave frequency domain VL - 107 ER - TY - JOUR AB - Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus, often supported by protein activity-dependent inactivation. Adaptive response is thought to be related to various cellular functions such as homeostasis and enlargement of dynamic range by background compensation. Here we study the quantitative relation between adaptive response and background compensation within a modeling framework. We show that any particular type of adaptive response is neither sufficient nor necessary for adaptive enlargement of dynamic range. In particular a precise adaptive response, where system activity is maintained at a constant level at steady state, does not ensure a large dynamic range neither in input signal nor in system output. A general mechanism for input dynamic range enlargement can come about from the activity-dependent modulation of protein responsiveness by multiple biochemical modification, regardless of the type of adaptive response it induces. Therefore hierarchical biochemical processes such as methylation and phosphorylation are natural candidates to induce this property in signaling systems. AU - Tamar Friedlander AU - Brenner, Naama ID - 1815 IS - 2 JF - Mathematical Biosciences and Engineering TI - Adaptive response and enlargement of dynamic range VL - 8 ER - TY - JOUR AB - The Levene model is the simplest mathematical model to describe the evolution of gene frequencies in spatially subdivided populations. It provides insight into how locally varying selection promotes a population’s genetic diversity. Despite its simplicity, interesting problems have remained unsolved even in the diallelic case. In this paper we answer an open problem by establishing that for two alleles at one locus and J demes, up to 2J−1 polymorphic equilibria may coexist. We first present a proof for the case of stable monomorphisms and then show that the result also holds for protected alleles. These findings allow us to prove that any odd number (up to 2J−1) of equilibria is possible, before we extend the proof to even numbers. We conclude with some numerical results and show that for J>2, the proportion of parameter space affording this maximum is extremely small. AU - Sebastian Novak ID - 1863 IS - 3 JF - Theoretical Population Biology TI - The number of equilibria in the diallelic Levene model with multiple demes VL - 79 ER - TY - JOUR AB - Modern α-proteobacteria are thought to be closely related to the ancient symbiont of eukaryotes, an ancestor of mitochondria. Respiratory complex I from α-proteobacteria and mitochondria is well conserved at the level of the 14 "core" subunits, consistent with that notion. Mitochondrial complex I contains the core subunits, present in all species, and up to 31 "supernumerary" subunits, generally thought to have originated only within eukaryotic lineages. However, the full protein composition of an α-proteobacterial complex I has not been established previously. Here, we report the first purification and characterization of complex I from the α-proteobacterium Paracoccus denitrificans. Single particle electron microscopy shows that the complex has a well defined L-shape. Unexpectedly, in addition to the 14 core subunits, the enzyme also contains homologues of three supernumerary mitochondrial subunits as follows: B17.2, AQDQ/18, and 13 kDa (bovine nomenclature). This finding suggests that evolution of complex I via addition of supernumerary or "accessory" subunits started before the original endosymbiotic event that led to the creation of the eukaryotic cell. It also provides further confirmation that α-proteobacteria are the closest extant relatives of mitochondria. AU - Yip, Chui Y AU - Harbour, Michael E AU - Jayawardena, Kamburapola G AU - Fearnley, Ian M AU - Leonid Sazanov ID - 1975 IS - 7 JF - Journal of Biological Chemistry TI - Evolution of respiratory complex I "Supernumerary" subunits are present in the α-proteobacterial enzyme VL - 286 ER - TY - JOUR AB - Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases. The L-shaped enzyme consists of hydrophilic and membrane domains. Previously, we determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 Ã. resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-like subunits L, M and N is novel, with two inverted structural repeats of five transmembrane helices arranged, unusually, face-to-back. Each repeat includes a discontinuous transmembrane helix and forms half of a channel across the membrane. A network of conserved polar residues connects the two half-channels, completing the proton translocation pathway. Unexpectedly, lysines rather than carboxylate residues act as the main elements of the proton pump in these subunits. The fourth probable proton-translocation channel is at the interface of subunits N, K, J and A. The structure indicates that proton translocation in complex I, uniquely, involves coordinated conformational changes in six symmetrical structural elements. AU - Efremov, Rouslan G AU - Leonid Sazanov ID - 1973 IS - 7361 JF - Nature TI - Structure of the membrane domain of respiratory complex i VL - 476 ER - TY - JOUR AB - Complex I is the first enzyme of the respiratory chain and plays a central role in cellular energy production. It has been implicated in many human neurodegenerative diseases, as well as in ageing. One of the biggest membrane protein complexes, it is an L-shaped assembly consisting of hydrophilic and membrane domains. Previously, we have determined structures of the hydrophilic domain in several redox states. Last year was marked by fascinating breakthroughs in the understanding of the complete structure. We described the architecture of the membrane domain and of the entire bacterial complex I. X-ray analysis of the larger mitochondrial enzyme has also been published. The core subunits of the bacterial and mitochondrial enzymes have remarkably similar structures. The proposed mechanism of coupling between electron transfer and proton translocation involves long-range conformational changes, coordinated in part by a long α-helix, akin to the coupling rod of a steam engine. AU - Efremov, Rouslan G AU - Leonid Sazanov ID - 1974 IS - 4 JF - Current Opinion in Structural Biology TI - Respiratory complex I: 'steam engine' of the cell? VL - 21 ER - TY - JOUR AB - In Escherichia coli, the pole-to-pole oscillation of the Min proteins directs septum formation to midcell, which is required for symmetric cell division. In vitro, protein waves emerge from the self-organization of MinD, a membrane-binding ATPase, and its activator MinE. For wave propagation, the proteins need to cycle through states of collective membrane binding and unbinding. Although MinD presumably undergoes cooperative membrane attachment, it is unclear how synchronous detachment is coordinated. We used confocal and single-molecule microscopy to elucidate the order of events during Min wave propagation. We propose that protein detachment at the rear of the wave, and the formation of the E-ring, are accomplished by two complementary processes: first, local accumulation of MinE due to rapid rebinding, leading to dynamic instability; and second, a structural change induced by membrane-interaction of MinE in an equimolar MinD-MinE (MinDE) complex, which supports the robustness of pattern formation. AU - Martin Loose AU - Fischer-Friedrich, Elisabeth AU - Herold, Christoph AU - Kruse, Karsten AU - Schwille, Petra ID - 1985 IS - 5 JF - Nature Structural and Molecular Biology TI - Min protein patterns emerge from rapid rebinding and membrane interaction of MinE VL - 18 ER - TY - JOUR AB - One of the most fundamental features of biological systems is probably their ability to self-organize in space and time on different scales. Despite many elaborate theoretical models of how molecular self-organization can come about, only a few experimental systems of biological origin have so far been rigorously described, due mostly to their inherent complexity. The most promising strategy of modern biophysics is thus to identify minimal biological systems showing self-organized emergent behavior. One of the best-understood examples of protein self-organization, which has recently been successfully reconstituted in vitro, is represented by the oscillations of the Min proteins in Escherichia coli. In this review, we summarize the current understanding of the mechanism of Min protein self-organization in vivo and in vitro. We discuss the potential of the Min oscillations to sense the geometry of the cell and suggest that spontaneous protein waves could be a general means of intracellular organization. We hypothesize that cooperative membrane binding and unbinding, e.g., as an energy-dependent switch, may act as an important regulatory mechanism for protein oscillations and pattern formation in the cell. AU - Martin Loose AU - Kruse, Karsten AU - Schwille, Petra ID - 1986 IS - 1 JF - Annual Review of Biophysics TI - Protein self-organization: Lessons from the min system VL - 40 ER - TY - JOUR AB - Many species have morphologically and genetically differentiated sex chromosomes, such as the XY pair of mammals. Y chromosomes are often highly degenerated and carry few functional genes, so that XY males have only one copy of most Xlinked genes (whereas females have two). As a result, chromosome-wide mechanisms of dosage compensation, such as the mammalian X-inactivation, often evolve to reestablish expression balance. A similar phenomenon is expected in femaleheterogametic species, where ZW females should suffer from imbalances due to W-chromosome degeneration. However, no global dosage compensation mechanisms have been detected in the two independent ZW systems that have been studied systematically (birds and silkworm), leading to the suggestion that lack of global dosage compensation may be a general feature of female-heterogametic species. However, analyses of other independently evolved ZW systems are required to test if this is the case. In this study, we use published genomic and expression data to test for the presence of global dosage compensation in Schistosoma mansoni, a trematode parasite that causes schistosomiasis in humans. We find that Z-linked expression is reduced relative to autosomal expression in females but not males, consistent with incomplete or localized dosage compensation. This gives further support to the theory that female-heterogametic species may not require global mechanisms of dosage compensation. AU - Vicoso, Beatriz AU - Bachtrog, Doris ID - 2072 IS - 1 JF - Genome Biology and Evolution TI - Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite VL - 3 ER - TY - JOUR AB - We present a new technique for passive and markerless facial performance capture based on anchor frames. Our method starts with high resolution per-frame geometry acquisition using state-of-theart stereo reconstruction, and proceeds to establish a single triangle mesh that is propagated through the entire performance. Leveraging the fact that facial performances often contain repetitive subsequences, we identify anchor frames as those which contain similar facial expressions to a manually chosen reference expression. Anchor frames are automatically computed over one or even multiple performances. We introduce a robust image-space tracking method that computes pixel matches directly from the reference frame to all anchor frames, and thereby to the remaining frames in the sequence via sequential matching. This allows us to propagate one reconstructed frame to an entire sequence in parallel, in contrast to previous sequential methods. Our anchored reconstruction approach also limits tracker drift and robustly handles occlusions and motion blur. The parallel tracking and mesh propagation offer low computation times. Our technique will even automatically match anchor frames across different sequences captured on different occasions, propagating a single mesh to all performances. AU - Beeler, Thabo AU - Hahn, Fabian AU - Bradley, Derek J AU - Bernd Bickel AU - Beardsley, Paul A AU - Gotsman, Craig AU - Sumner, Robert W AU - Groß, Markus S ID - 2099 IS - 4 JF - ACM Transactions on Graphics TI - High-quality passive facial performance capture using anchor frames VL - 30 ER - TY - CHAP AB - This chapter presents a method for real-time animation of highly detailed facial expressions based on sparse motion captures data and a limited set of static example poses. The method for real-time animation of highly detailed facial expressions decomposes geometry into large-scale motion and fine-scale details, such as expression wrinkles. Both large- and fine-scale deformation algorithms run entirely on the GPU, and our implementation based on CUDA achieves an overall performance of about 30 fps. The face conveys the most relevant visual characteristics of human identity and expression. Hence, realistic facial animations or interactions with virtual avatars are important for storytelling and gameplay. However, current approaches are either computationally expensive, require very specialized capture hardware, or are extremely labor intensive. At runtime, given an arbitrary facial expression, the algorithm computes the skin strain from the relative distance between marker points and derives fine-scale corrections for the largescale deformation. During gameplay only the sparse set of marker-point positions is transmitted to the GPU. The face animation is entirely computed on the GPU where the resulting mesh can directly be used as input for the rendering stages. This data can be easily obtained by traditional capture hardware. The proposed in-game algorithm is fast. It also is easy to implement and maps well onto programmable GPUs. AU - Bernd Bickel AU - Lang, Manuel ID - 2098 T2 - GPU Computing Gems Emerald Edition TI - From sparse mocap to highly detailed facial animation ER - TY - CONF AB - Acquiring panoramic images using stitching takes a lot of time and moving objects may cause ghosting. It is also difficult to obtain a full spherical panorama, because the downward picture cannot be captured while the camera is mounted on the tripod. AU - Pfeil, Jonas AU - Hildebrand, Kristian AU - Gremzow, Carsten AU - Bernd Bickel AU - Alexa, Marc ID - 2100 TI - Throwable panoramic ball camera ER - TY - CHAP AB - Let P be the Ornstein-Uhlenbeck semigroup associated with the stochastic Cauchy problem dU(t)=AU(t)dt+dWH(t), where A is the generator of a C 0-semigroup S on a Banach space E, H is a Hilbert subspace of E, and W H is an H-cylindrical Brownian motion. Assuming that S restricts to a C 0-semigroup on H, we obtain L p -bounds for D H P(t). We show that if P is analytic, then the invariance assumption is fulfilled. As an application we determine the L p -domain of the generator of P explicitly in the case where S restricts to a C 0-semigroup on H which is similar to an analytic contraction semigroup. The results are applied to the 1D stochastic heat equation driven by additive space-time white noise. AU - Jan Maas AU - Van Neerven, Jan ID - 2116 T2 - Parabolic Problems TI - Gradient estimates and domain identification for analytic Ornstein-Uhlenbeck operators VL - 80 ER - TY - JOUR AB - We study, in L1(R̃n; γ) with respect to the gaussian measure, non- tangential maximal functions and conical square functions associ- ated with the Ornstein-Uhlenbeck operator by developing a set of techniques which allow us, to some extent, to compensate for the non-doubling character of the gaussian measure. The main result asserts that conical square functions can be controlled in L1-norm by non-tangential maximal functions. Along the way we prove a change of aperture result for the latter. This complements recent results on gaussian Hardy spaces due to Mauceri and Meda. AU - Jan Maas AU - van Neerven, Jan M AU - Portal, Pierre ID - 2122 IS - 2 JF - Publicacions Matemàtiques TI - Conical square functions and non-tangential maximal functions with respect to the Gaussian measure VL - 55 ER - TY - JOUR AB - We prove a Trotter product formula for gradient flows in metric spaces. This result is applied to establish convergence in the L 2-Wasserstein metric of the splitting method for some Fokker-Planck equations and porous medium type equations perturbed by a potential. AU - Clément, Philippe AU - Maas, Jan ID - 2123 IS - 2 JF - Journal of Evolution Equations TI - A Trotter product formula for gradient flows in metric spaces VL - 11 ER - TY - JOUR AB - Let K be an irreducible and reversible Markov kernel on a finite set X. We construct a metric W on the set of probability measures on X and show that with respect to this metric, the law of the continuous time Markov chain evolves as the gradient flow of the entropy. This result is a discrete counterpart of the Wasserstein gradient flow interpretation of the heat flow in Rn by Jordan, Kinderlehrer and Otto (1998). The metric W is similar to, but different from, the L2-Wasserstein metric, and is defined via a discrete variant of the Benamou–Brenier formula. AU - Jan Maas ID - 2126 IS - 8 JF - Journal of Functional Analysis TI - Gradient flows of the entropy for finite Markov chains VL - 261 ER - TY - GEN AB - A (diatomic) shape resonance is a metastable state of a pair of colliding atoms quasi-bound by the centrifugal barrier imposed by the angular momentum involved in the collision. The temporary trapping of the atoms' scattering wavefunction corresponds to an enhanced atom pair density at low interatomic separations. This leads to larger overlap of the wavefunctions involved in a molecule formation process such as photoassociation, rendering the process more efficient. However, for an ensemble of atoms, the atom pair density will only be enhanced if the energy of the resonance comes close to the temperature of the atomic ensemble. Herein we explore the possibility of controlling the energy of a shape resonance by shifting it toward the temperature of atoms confined in a trap. The shifts are imparted by the interaction of non-resonant light with the anisotropic polarizability of the atom pair, which affects both the centrifugal barrier and the pair's rotational and vibrational levels. We find that at laser intensities of up to 5×109 W/cm2 the pair density is increased by one order of magnitude for 87Rb atoms at 100μK and by two orders of magnitude for 88Sr atoms at 20μK. AU - Ağanoğlu, Ruzin AU - Mikhail Lemeshko AU - Friedrich, Břetislav AU - González-Férez, Rosario AU - Koch, Christiane P ID - 2138 T2 - Unknown TI - Controlling a diatomic shape resonance with non-resonant light ER - TY - JOUR AB - We made use of supersymmetric (SUSY) quantum mechanics to find the condition under which the Stark effect problem for a polar and polarizable closed-shell diatomic molecule subjected to collinear electrostatic and nonresonant radiative fields becomes exactly solvable. The condition Δω = ω2/4(m+1)2 connects values of the dimensionless parameters ω and Δω that characterize the strengths of the permanent and induced dipole interactions of the molecule with the respective fields. The exact solutions are obtained for the \J̃ = m, m; ω, Δω) family of 'stretched' states. The field-free and strong-field limits of the combined-fields problem were found to exhibit supersymmetry and shape invariance, which is indeed the reason why they are analytically solvable. By making use of the analytic form of the \J̃ = m,m; ω, Δω) wavefunctions, we obtained simple formulae for the expectation values of the space-fixed electric dipole moment, the alignment cosine and the angular momentum squared, and derived a 'sum rule' that combines the above expectation values into a formula for the eigenenergy. The analytic expressions for the characteristics of the strongly oriented and aligned states provide direct access to the values of the interaction parameters required for creating such states in the laboratory. AU - Mikhail Lemeshko AU - Mustafa, Mustafa K AU - Kais, Sabre AU - Friedrich, Břetislav ID - 2200 JF - New Journal of Physics TI - Supersymmetry identifies molecular Stark states whose eigenproperties can be obtained analytically VL - 13 ER - TY - JOUR AB - By invoking supersymmetry, we found a condition under which the Stark-effect problem for a polar and polarizable molecule subject to nonresonant electric fields becomes exactly solvable for the family of stretched states. The analytic expressions for the wave function and eigenenergy and other expectation values allow one to readily reverse-engineer the problem of finding the values of the interaction parameters required for creating quantum states with preordained characteristics. The method also allows the construction of families of isospectral potentials, realizable with combined fields. AU - Mikhail Lemeshko AU - Mustafa, Mustafa K AU - Kais, Sabre AU - Friedrich, Břetislav ID - 2199 IS - 4 JF - Physical Review A - Atomic, Molecular, and Optical Physics TI - Supersymmetric factorization yields exact solutions to the molecular Stark-effect problem for "stretched" states VL - 83 ER -